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  • 1
    Publication Date: 2016-03-23
    Description: Escherichia coli strain MRE600 was originally identified for its low RNase I activity and has therefore been widely adopted by the biomedical research community as a preferred source for the expression and purification of transfer RNAs and ribosomes. Despite its widespread use, surprisingly little information about its genome or genetic content exists. Here, we present the first de novo assembly and description of the MRE600 genome and epigenome. To provide context to these studies of MRE600, we include comparative analyses with E. coli K-12 MG1655 (K12). Pacific Biosciences Single Molecule, Real-Time sequencing reads were assembled into one large chromosome (4.83 Mb) and three smaller plasmids (89.1, 56.9, and 7.1 kb). Interestingly, the 7.1-kb plasmid possesses genes encoding a colicin E1 protein and its associated immunity protein. The MRE600 genome has a G + C content of 50.8% and contains a total of 5,181 genes, including 4,913 protein-encoding genes and 268 RNA genes. We identified 41,469 modified DNA bases (0.83% of total) and found that MRE600 lacks the gene for type I methyltransferase, EcoKI. Phylogenetic, taxonomic, and genetic analyses demonstrate that MRE600 is a divergent E. coli strain that displays features of the closely related genus, Shigella . Nevertheless, comparative analyses between MRE600 and E. coli K12 show that these two strains exhibit nearly identical ribosomal proteins, ribosomal RNAs, and highly homologous tRNA species. Substantiating prior suggestions that MRE600 lacks RNase I activity, the RNase I-encoding gene, rna , contains a single premature stop codon early in its open-reading frame.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 2
    Publication Date: 2015-12-25
    Description: We present the first results from the KMOS ( K -band Multi-Object Spectrograph) AGN (active galactic nuclei) Survey at High redshift (KASH z ), a VLT/KMOS integral-field spectroscopic (IFS) survey of z 0.6 AGN. We present galaxy-integrated spectra of 89 X-ray AGN ( L 2–10 keV = 10 42 –10 45  erg s –1 ), for which we observed [O iii ] ( z 1.1–1.7) or Hα emission ( z 0.6–1.1). The targets have X-ray luminosities representative of the parent AGN population and we explore the emission-line luminosities as a function of X-ray luminosity. For the [O iii ] targets, 50 per cent have ionized gas velocities indicative of gas that is dominated by outflows and/or highly turbulent material (i.e. overall line widths 600 km s –1 ). The most luminous half (i.e. L X 〉 6 x 10 43  erg s –1 ) have a 2 times higher incidence of such velocities. On the basis of our results, we find no evidence that X-ray obscured AGN are more likely to host extreme kinematics than unobscured AGN. Our KASH z sample has a distribution of gas velocities that is consistent with a luminosity-matched sample of z 〈 0.4 AGN. This implies little evolution in the prevalence of ionized outflows, for a fixed AGN luminosity, despite an order-of-magnitude decrease in average star formation rates over this redshift range. Furthermore, we compare our Hα targets to a redshift-matched sample of star-forming galaxies and despite a similar distribution of Hα luminosities and likely star formation rates, we find extreme ionized gas velocities are up to 10 times more prevalent in the AGN-host galaxies. Our results reveal a high prevalence of extreme ionized gas velocities in high-luminosity X-ray AGN and imply that the most powerful ionized outflows in high-redshift galaxies are driven by AGN activity.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 3
    Publication Date: 2015-03-20
    Description: Functional defects of the mitochondrial translation machinery, as a result of mutations in nuclear-encoded genes, have been associated with combined oxidative phosphorylation (OXPHOS) deficiencies. We report siblings with congenital sensorineural deafness and lactic acidemia in association with combined respiratory chain (RC) deficiencies of complexes I, III and IV observed in fibroblasts and liver. One of the siblings had a more severe phenotype showing progressive hepatic and renal failure. Whole-exome sequencing revealed a homozygous mutation in the gene encoding mitochondrial ribosomal protein S7 ( MRPS7 ), a c.550A〉G transition that encodes a substitution of valine for a highly conserved methionine (p.Met184Val) in both affected siblings. MRPS7 is a 12S ribosomal RNA-binding subunit of the small mitochondrial ribosomal subunit, and is required for the assembly of the small ribosomal subunit. Pulse labeling of mitochondrial protein synthesis products revealed impaired mitochondrial protein synthesis in patient fibroblasts. Exogenous expression of wild-type MRPS7 in patient fibroblasts rescued complexes I and IV activities, demonstrating the deleterious effect of the mutation on RC function. Moreover, reduced 12S rRNA transcript levels observed in the patient's fibroblasts were also restored to normal levels by exogenous expression of wild-type MRPS7. Our data demonstrate the pathogenicity of the identified MRPS7 mutation as a novel cause of mitochondrial RC dysfunction, congenital sensorineural deafness and progressive hepatic and renal failure.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 4
    Publication Date: 2014-09-17
    Description: Barcoded vectors are promising tools for investigating clonal diversity and dynamics in hematopoietic gene therapy. Analysis of clones marked with barcoded vectors requires accurate identification of potentially large numbers of individually rare barcodes, when the exact number, sequence identity and abundance are unknown. This is an inherently challenging application, and the feasibility of using contemporary next-generation sequencing technologies is unresolved. To explore this potential application empirically, without prior assumptions, we sequenced barcode libraries of known complexity. Libraries containing 1, 10 and 100 Sanger-sequenced barcodes were sequenced using an Illumina platform, with a 100-barcode library also sequenced using a SOLiD platform. Libraries containing 1 and 10 barcodes were distinguished from false barcodes generated by sequencing error by a several log-fold difference in abundance. In 100-barcode libraries, however, expected and false barcodes overlapped and could not be resolved by bioinformatic filtering and clustering strategies. In independent sequencing runs multiple false-positive barcodes appeared to be represented at higher abundance than known barcodes, despite their confirmed absence from the original library. Such errors, which potentially impact barcoding studies in an application-dependent manner, are consistent with the existence of both stochastic and systematic error, the mechanism of which is yet to be fully resolved.
    Keywords: Massively Parallel (Deep) Sequencing
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 5
    Publication Date: 2001-03-07
    Description: Chondrules in the metal-rich meteorites Hammadah al Hamra 237 and QUE 94411 have recorded highly energetic thermal events that resulted in complete vaporization of a dusty region of the solar nebula (dust/gas ratio of about 10 to 50 times solar). These chondrules formed under oxidizing conditions before condensation of iron-nickel metal, at temperatures greater than or equal to 1500 K, and were isolated from the cooling gas before condensation of moderately volatile elements such as manganese, sodium, potassium, and sulfur. This astrophysical environment is fundamentally different from conventional models for chondrule formation by localized, brief, repetitive heating events that resulted in incomplete melting of solid precursors initially residing at ambient temperatures below approximately 650 K.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krot, A N -- Meibom, A -- Russell, S S -- Alexander, C M -- Jeffries, T E -- Keil, K -- New York, N.Y. -- Science. 2001 Mar 2;291(5509):1776-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hawai'i Institute of Geophysics and Planetology (HIGP), School of Ocean and Earth Science and Technology (SOEST), University of Hawai'i at Manoa, Honolulu, HI 96822, USA. sasha@pgd.hawaii.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11230691" target="_blank"〉PubMed〈/a〉
    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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  • 6
    Publication Date: 2006-12-16
    Description: The Stardust spacecraft collected thousands of particles from comet 81P/Wild 2 and returned them to Earth for laboratory study. The preliminary examination of these samples shows that the nonvolatile portion of the comet is an unequilibrated assortment of materials that have both presolar and solar system origin. The comet contains an abundance of silicate grains that are much larger than predictions of interstellar grain models, and many of these are high-temperature minerals that appear to have formed in the inner regions of the solar nebula. Their presence in a comet proves that the formation of the solar system included mixing on the grandest scales.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brownlee, Don -- Tsou, Peter -- Aleon, Jerome -- Alexander, Conel M O'd -- Araki, Tohru -- Bajt, Sasa -- Baratta, Giuseppe A -- Bastien, Ron -- Bland, Phil -- Bleuet, Pierre -- Borg, Janet -- Bradley, John P -- Brearley, Adrian -- Brenker, F -- Brennan, Sean -- Bridges, John C -- Browning, Nigel D -- Brucato, John R -- Bullock, E -- Burchell, Mark J -- Busemann, Henner -- Butterworth, Anna -- Chaussidon, Marc -- Cheuvront, Allan -- Chi, Miaofang -- Cintala, Mark J -- Clark, B C -- Clemett, Simon J -- Cody, George -- Colangeli, Luigi -- Cooper, George -- Cordier, Patrick -- Daghlian, C -- Dai, Zurong -- D'Hendecourt, Louis -- Djouadi, Zahia -- Dominguez, Gerardo -- Duxbury, Tom -- Dworkin, Jason P -- Ebel, Denton S -- Economou, Thanasis E -- Fakra, Sirine -- Fairey, Sam A J -- Fallon, Stewart -- Ferrini, Gianluca -- Ferroir, T -- Fleckenstein, Holger -- Floss, Christine -- Flynn, George -- Franchi, Ian A -- Fries, Marc -- Gainsforth, Z -- Gallien, J-P -- Genge, Matt -- Gilles, Mary K -- Gillet, Philipe -- Gilmour, Jamie -- Glavin, Daniel P -- Gounelle, Matthieu -- Grady, Monica M -- Graham, Giles A -- Grant, P G -- Green, Simon F -- Grossemy, Faustine -- Grossman, Lawrence -- Grossman, Jeffrey N -- Guan, Yunbin -- Hagiya, Kenji -- Harvey, Ralph -- Heck, Philipp -- Herzog, Gregory F -- Hoppe, Peter -- Horz, Friedrich -- Huth, Joachim -- Hutcheon, Ian D -- Ignatyev, Konstantin -- Ishii, Hope -- Ito, Motoo -- Jacob, Damien -- Jacobsen, Chris -- Jacobsen, Stein -- Jones, Steven -- Joswiak, David -- Jurewicz, Amy -- Kearsley, Anton T -- Keller, Lindsay P -- Khodja, H -- Kilcoyne, A L David -- Kissel, Jochen -- Krot, Alexander -- Langenhorst, Falko -- Lanzirotti, Antonio -- Le, Loan -- Leshin, Laurie A -- Leitner, J -- Lemelle, L -- Leroux, Hugues -- Liu, Ming-Chang -- Luening, K -- Lyon, Ian -- Macpherson, Glen -- Marcus, Matthew A -- Marhas, Kuljeet -- Marty, Bernard -- Matrajt, Graciela -- McKeegan, Kevin -- Meibom, Anders -- Mennella, Vito -- Messenger, Keiko -- Messenger, Scott -- Mikouchi, Takashi -- Mostefaoui, Smail -- Nakamura, Tomoki -- Nakano, T -- Newville, M -- Nittler, Larry R -- Ohnishi, Ichiro -- Ohsumi, Kazumasa -- Okudaira, Kyoko -- Papanastassiou, Dimitri A -- Palma, Russ -- Palumbo, Maria E -- Pepin, Robert O -- Perkins, David -- Perronnet, Murielle -- Pianetta, P -- Rao, William -- Rietmeijer, Frans J M -- Robert, Francois -- Rost, D -- Rotundi, Alessandra -- Ryan, Robert -- Sandford, Scott A -- Schwandt, Craig S -- See, Thomas H -- Schlutter, Dennis -- Sheffield-Parker, J -- Simionovici, Alexandre -- Simon, Steven -- Sitnitsky, I -- Snead, Christopher J -- Spencer, Maegan K -- Stadermann, Frank J -- Steele, Andrew -- Stephan, Thomas -- Stroud, Rhonda -- Susini, Jean -- Sutton, S R -- Suzuki, Y -- Taheri, Mitra -- Taylor, Susan -- Teslich, Nick -- Tomeoka, Kazu -- Tomioka, Naotaka -- Toppani, Alice -- Trigo-Rodriguez, Josep M -- Troadec, David -- Tsuchiyama, Akira -- Tuzzolino, Anthony J -- Tyliszczak, Tolek -- Uesugi, K -- Velbel, Michael -- Vellenga, Joe -- Vicenzi, E -- Vincze, L -- Warren, Jack -- Weber, Iris -- Weisberg, Mike -- Westphal, Andrew J -- Wirick, Sue -- Wooden, Diane -- Wopenka, Brigitte -- Wozniakiewicz, Penelope -- Wright, Ian -- Yabuta, Hikaru -- Yano, Hajime -- Young, Edward D -- Zare, Richard N -- Zega, Thomas -- Ziegler, Karen -- Zimmerman, Laurent -- Zinner, Ernst -- Zolensky, Michael -- New York, N.Y. -- Science. 2006 Dec 15;314(5806):1711-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Astronomy, University of Washington, Seattle, WA 98195, USA. brownlee@astro.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17170289" target="_blank"〉PubMed〈/a〉
    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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  • 7
    Publication Date: 2006-05-06
    Description: Organic matter in extraterrestrial materials has isotopic anomalies in hydrogen and nitrogen that suggest an origin in the presolar molecular cloud or perhaps in the protoplanetary disk. Interplanetary dust particles are generally regarded as the most primitive solar system matter available, in part because until recently they exhibited the most extreme isotope anomalies. However, we show that hydrogen and nitrogen isotopic compositions in carbonaceous chondrite organic matter reach and even exceed those found in interplanetary dust particles. Hence, both meteorites (originating from the asteroid belt) and interplanetary dust particles (possibly from comets) preserve primitive organics that were a component of the original building blocks of the solar system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Busemann, Henner -- Young, Andrea F -- Alexander, Conel M O'd -- Hoppe, Peter -- Mukhopadhyay, Sujoy -- Nittler, Larry R -- New York, N.Y. -- Science. 2006 May 5;312(5774):727-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Terrestrial Magnetism, Carnegie Institution of Washington, 5241 Broad Branch Road, NW, Washington, DC 20015, USA. busemann@dtm.ciw.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16675696" target="_blank"〉PubMed〈/a〉
    Keywords: *Cosmic Dust ; Deuterium/*analysis ; Evolution, Planetary ; *Meteoroids ; Nitrogen Isotopes/*analysis ; Organic Chemicals/*analysis ; *Solar System ; Temperature
    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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  • 8
    Publication Date: 2006-12-16
    Description: Organics found in comet 81P/Wild 2 samples show a heterogeneous and unequilibrated distribution in abundance and composition. Some organics are similar, but not identical, to those in interplanetary dust particles and carbonaceous meteorites. A class of aromatic-poor organic material is also present. The organics are rich in oxygen and nitrogen compared with meteoritic organics. Aromatic compounds are present, but the samples tend to be relatively poorer in aromatics than are meteorites and interplanetary dust particles. The presence of deuterium and nitrogen-15 excesses suggest that some organics have an interstellar/protostellar heritage. Although the variable extent of modification of these materials by impact capture is not yet fully constrained, a diverse suite of organic compounds is present and identifiable within the returned samples.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sandford, Scott A -- Aleon, Jerome -- Alexander, Conel M O'd -- Araki, Tohru -- Bajt, Sasa -- Baratta, Giuseppe A -- Borg, Janet -- Bradley, John P -- Brownlee, Donald E -- Brucato, John R -- Burchell, Mark J -- Busemann, Henner -- Butterworth, Anna -- Clemett, Simon J -- Cody, George -- Colangeli, Luigi -- Cooper, George -- D'Hendecourt, Louis -- Djouadi, Zahia -- Dworkin, Jason P -- Ferrini, Gianluca -- Fleckenstein, Holger -- Flynn, George J -- Franchi, Ian A -- Fries, Marc -- Gilles, Mary K -- Glavin, Daniel P -- Gounelle, Matthieu -- Grossemy, Faustine -- Jacobsen, Chris -- Keller, Lindsay P -- Kilcoyne, A L David -- Leitner, Jan -- Matrajt, Graciela -- Meibom, Anders -- Mennella, Vito -- Mostefaoui, Smail -- Nittler, Larry R -- Palumbo, Maria E -- Papanastassiou, Dimitri A -- Robert, Francois -- Rotundi, Alessandra -- Snead, Christopher J -- Spencer, Maegan K -- Stadermann, Frank J -- Steele, Andrew -- Stephan, Thomas -- Tsou, Peter -- Tyliszczak, Tolek -- Westphal, Andrew J -- Wirick, Sue -- Wopenka, Brigitte -- Yabuta, Hikaru -- Zare, Richard N -- Zolensky, Michael E -- New York, N.Y. -- Science. 2006 Dec 15;314(5806):1720-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Astrophysics Branch, NASA-Ames Research Center, Moffett Field, CA 94035, USA. ssandford@mail.arc.nasa.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17170291" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon/analysis ; Cosmic Dust/analysis ; Deuterium/analysis ; *Meteoroids ; Nitrogen/analysis ; Nitrogen Isotopes/analysis ; Organic Chemicals/*analysis ; Oxygen/analysis ; Polycyclic Hydrocarbons, Aromatic/analysis ; Spacecraft
    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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  • 9
    Publication Date: 2011-06-11
    Description: The complex suite of organic materials in carbonaceous chondrite meteorites probably originally formed in the interstellar medium and/or the solar protoplanetary disk, but was subsequently modified in the meteorites' asteroidal parent bodies. The mechanisms of formation and modification are still very poorly understood. We carried out a systematic study of variations in the mineralogy, petrology, and soluble and insoluble organic matter in distinct fragments of the Tagish Lake meteorite. The variations correlate with indicators of parent body aqueous alteration. At least some molecules of prebiotic importance formed during the alteration.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Herd, Christopher D K -- Blinova, Alexandra -- Simkus, Danielle N -- Huang, Yongsong -- Tarozo, Rafael -- Alexander, Conel M O'D -- Gyngard, Frank -- Nittler, Larry R -- Cody, George D -- Fogel, Marilyn L -- Kebukawa, Yoko -- Kilcoyne, A L David -- Hilts, Robert W -- Slater, Greg F -- Glavin, Daniel P -- Dworkin, Jason P -- Callahan, Michael P -- Elsila, Jamie E -- De Gregorio, Bradley T -- Stroud, Rhonda M -- New York, N.Y. -- Science. 2011 Jun 10;332(6035):1304-7. doi: 10.1126/science.1203290.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta T6G 2E3, Canada. herd@ualberta.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21659601" target="_blank"〉PubMed〈/a〉
    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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  • 10
    Publication Date: 2012-07-17
    Description: Determining the source(s) of hydrogen, carbon, and nitrogen accreted by Earth is important for understanding the origins of water and life and for constraining dynamical processes that operated during planet formation. Chondritic meteorites are asteroidal fragments that retain records of the first few million years of solar system history. The deuterium/hydrogen (D/H) values of water in carbonaceous chondrites are distinct from those in comets and Saturn's moon Enceladus, implying that they formed in a different region of the solar system, contrary to predictions of recent dynamical models. The D/H values of water in carbonaceous chondrites also argue against an influx of water ice from the outer solar system, which has been invoked to explain the nonsolar oxygen isotopic composition of the inner solar system. The bulk hydrogen and nitrogen isotopic compositions of CI chondrites suggest that they were the principal source of Earth's volatiles.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alexander, C M O'D -- Bowden, R -- Fogel, M L -- Howard, K T -- Herd, C D K -- Nittler, L R -- New York, N.Y. -- Science. 2012 Aug 10;337(6095):721-3. doi: 10.1126/science.1223474. Epub 2012 Jul 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Terrestrial Magnetism, Carnegie Institution of Washington, 5241 Broad Branch Road, NW, Washington, DC 20015, USA. alexander@dtm.ciw.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22798405" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon/*analysis ; Carbon Isotopes/analysis ; Deuterium/analysis ; *Earth (Planet) ; Evolution, Planetary ; Hydrogen/*analysis ; Ice ; *Minor Planets ; Nitrogen/*analysis ; Nitrogen Isotopes/analysis ; Oxygen Isotopes/analysis ; *Planets ; Water
    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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