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  • PANGAEA  (41)
  • American Association for the Advancement of Science (AAAS)
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  • 1
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    Evolution of a highly active and enantiospecific metalloenzyme from short peptides (2018)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2018
    Description: 〈p〉Primordial sequence signatures in modern proteins imply ancestral origins tracing back to simple peptides. Although short peptides seldom adopt unique folds, metal ions might have templated their assembly into higher-order structures in early evolution and imparted useful chemical reactivity. Recapitulating such a biogenetic scenario, we have combined design and laboratory evolution to transform a zinc-binding peptide into a globular enzyme capable of accelerating ester cleavage with exacting enantiospecificity and high catalytic efficiency (〈i〉k〈/i〉〈sub〉cat〈/sub〉/〈i〉K〈/i〉〈sub〉M〈/sub〉 ~ 10〈sup〉6〈/sup〉 M〈sup〉–1〈/sup〉 s〈sup〉–1〈/sup〉). The simultaneous optimization of structure and function in a naïve peptide scaffold not only illustrates a plausible enzyme evolutionary pathway from the distant past to the present but also proffers exciting future opportunities for enzyme design and engineering.〈/p〉
    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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  • 2
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    Differentiation of embryonic stem cell lines generated from adult somatic cells by nuclear transfer (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-04-28
    Description: Embryonic stem (ES) cells are fully pluripotent in that they can differentiate into all cell types, including gametes. We have derived 35 ES cell lines via nuclear transfer (ntES cell lines) from adult mouse somatic cells of inbred, hybrid, and mutant strains. ntES cells contributed to an extensive variety of cell types, including dopaminergic and serotonergic neurons in vitro and germ cells in vivo. Cloning by transfer of ntES cell nuclei could result in normal development of fertile adults. These studies demonstrate the full pluripotency of ntES cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wakayama, T -- Tabar, V -- Rodriguez, I -- Perry, A C -- Studer, L -- Mombaerts, P -- New York, N.Y. -- Science. 2001 Apr 27;292(5517):740-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Rockefeller University, New York, NY 10021, USA. teru@advancedcell.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11326103" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Blastocyst/*cytology ; *Cell Differentiation ; Cell Line ; Cell Lineage ; Chimera ; Cloning, Organism ; Crosses, Genetic ; Dopamine/metabolism ; Embryo Transfer ; Female ; Germ Cells/*cytology ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Inbred DBA ; Mice, Inbred ICR ; Mice, Nude ; Neurons/*cytology ; *Nuclear Transfer Techniques ; Serotonin/metabolism ; Stem Cells/*cytology
    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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  • 3
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    Evolution of a highly active and enantiospecific metalloenzyme from short peptides (2018)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2018-12-14
    Description: Primordial sequence signatures in modern proteins imply ancestral origins tracing back to simple peptides. Although short peptides seldom adopt unique folds, metal ions might have templated their assembly into higher-order structures in early evolution and imparted useful chemical reactivity. Recapitulating such a biogenetic scenario, we have combined design and laboratory evolution to transform a zinc-binding peptide into a globular enzyme capable of accelerating ester cleavage with exacting enantiospecificity and high catalytic efficiency ( k cat / K M ~ 10 6 M –1 s –1 ). The simultaneous optimization of structure and function in a naïve peptide scaffold not only illustrates a plausible enzyme evolutionary pathway from the distant past to the present but also proffers exciting future opportunities for enzyme design and engineering.
    Keywords: Biochemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Fluorous synthesis: a fluorous-phase strategy for improving separation efficiency in organic synthesis (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-02-07
    Description: Recovery and purification difficulties can limit the yield and utility of otherwise successful organic synthesis strategies. A "fluorous synthesis" approach is outlined in which organic molecules are rendered soluble in fluorocarbon solvents by attachment of a suitable fluorocarbon group. Fluorocarbon solvents are usually immiscible in organic solutions, and fluorous molecules partition out of an organic phase and into a fluorous phase in a standard liquid-liquid extraction. Simple yet substantive separations of organic reaction mixtures are achieved without resorting to chromatography. Because fluorous synthesis combines in many respects the favorable purification features of solid-phase synthesis with the favorable reaction, identification, and analysis features of traditional organic synthesis, it should prove valuable in the automated synthesis of libraries of individual pure organic compounds.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Studer, A -- Hadida, S -- Ferritto, R -- Kim, S Y -- Jeger, P -- Wipf, P -- Curran, D P -- New York, N.Y. -- Science. 1997 Feb 7;275(5301):823-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9012347" target="_blank"〉PubMed〈/a〉
    Keywords: Benzamides/*chemical synthesis/chemistry ; Benzoates/*chemical synthesis/chemistry ; Chemistry, Organic/*methods ; Cyclohexylamines/*chemical synthesis/chemistry ; Fluorocarbons/*chemistry ; Nitriles/chemistry ; Pyrimidinones/*chemical synthesis/chemistry ; Solubility ; Solvents
    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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  • 5
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    Parthenogenetic stem cells in nonhuman primates (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-02-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cibelli, Jose B -- Grant, Kathleen A -- Chapman, Karen B -- Cunniff, Kerrianne -- Worst, Travis -- Green, Heather L -- Walker, Stephen J -- Gutin, Philip H -- Vilner, Lucy -- Tabar, Viviane -- Dominko, Tanja -- Kane, Jeff -- Wettstein, Peter J -- Lanza, Robert P -- Studer, Lorenz -- Vrana, Kent E -- West, Michael D -- P50-AA11997/AA/NIAAA NIH HHS/ -- T32-AA07565/AA/NIAAA NIH HHS/ -- New York, N.Y. -- Science. 2002 Feb 1;295(5556):819.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Advanced Cell Technology, One Innovation Drive, Worcester, MA 01605, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11823632" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Astrocytes/cytology ; Blastocyst/*cytology/physiology ; Cell Culture Techniques ; Cell Differentiation ; Cell Division ; Cell Line ; Cell Separation ; Cloning, Organism ; Dopamine/metabolism ; Embryo, Mammalian/*cytology ; Karyotyping ; *Macaca fascicularis ; Mice ; Mice, SCID ; Neurons/cytology ; *Parthenogenesis ; Serotonin/metabolism ; Stem Cells/*cytology/physiology ; Teratoma/pathology
    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
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    Role of a conserved retinoic acid response element in rhombomere restriction of Hoxb-1 (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-09-16
    Description: After activation in mesoderm and neuroectoderm, expression of the Hoxb-1 gene is progressively restricted to rhombomere (r) 4 in the hindbrain. Analysis of the chick and mouse Hoxb-1 genes identified positive and negative regulatory regions that cooperate to mediate segment-restricted expression during rhombomere formation. An enhancer generates expression extending into r3 and r5, and a repressor limits this domain to r4. The repressor contains a conserved retinoic acid response element, point mutations in which allow expression to spread into adjacent rhombomeres. Retinoids and their nuclear receptors may therefore participate in sharpening segment-restricted expression of Hoxb-1 during rhombomere boundary formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Studer, M -- Popperl, H -- Marshall, H -- Kuroiwa, A -- Krumlauf, R -- New York, N.Y. -- Science. 1994 Sep 16;265(5179):1728-32.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lab of Developmental Neurobiology, National Institute for Medical Research, Mill Hill, London, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7916164" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Chick Embryo ; Enhancer Elements, Genetic ; Gene Expression Regulation ; *Genes, Homeobox ; Mice ; Mice, Transgenic ; Molecular Sequence Data ; Neural Crest/metabolism ; Oligonucleotides/metabolism ; Point Mutation ; Receptors, Cytoplasmic and Nuclear/metabolism ; Receptors, Retinoic Acid/metabolism ; *Regulatory Sequences, Nucleic Acid ; Retinoid X Receptors ; Rhombencephalon/*embryology/metabolism ; *Transcription Factors ; Tretinoin/*pharmacology
    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
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    Geniculocortical input drives genetic distinctions between primary and higher-order visual areas (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-06-08
    Description: Studies of area patterning of the neocortex have focused on primary areas, concluding that the primary visual area, V1, is specified by transcription factors (TFs) expressed by progenitors. Mechanisms that determine higher-order visual areas (V(HO)) and distinguish them from V1 are unknown. We demonstrated a requirement for thalamocortical axon (TCA) input by genetically deleting geniculocortical TCAs and showed that they drive differentiation of patterned gene expression that distinguishes V1 and V(HO). Our findings suggest a multistage process for area patterning: TFs expressed by progenitors specify an occipital visual cortical field that differentiates into V1 and V(HO); this latter phase requires geniculocortical TCA input to the nascent V1 that determines genetic distinctions between V1 and V(HO) for all layers and ultimately determines their area-specific functional properties.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3851411/" 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/PMC3851411/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chou, Shen-Ju -- Babot, Zoila -- Leingartner, Axel -- Studer, Michele -- Nakagawa, Yasushi -- O'Leary, Dennis D M -- MH086147/MH/NIMH NIH HHS/ -- R01 MH086147/MH/NIMH NIH HHS/ -- R01 NS031558/NS/NINDS NIH HHS/ -- R01 NS31558/NS/NINDS NIH HHS/ -- R37 NS031558/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2013 Jun 7;340(6137):1239-42. doi: 10.1126/science.1232806.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23744949" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Axons/*physiology ; Gene Deletion ; Gene Expression Regulation ; Genetic Markers ; Mice ; Mice, Knockout ; Neocortex/*physiology ; Neural Stem Cells/metabolism ; Thalamus/*physiology ; Transcription Factors/biosynthesis ; Visual Cortex/*physiology ; Visual Fields/*genetics
    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
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    [Report] Evolution of protein phosphorylation across 18 fungal species (2016)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2016-10-14
    Description: Living organisms have evolved protein phosphorylation, a rapid and versatile mechanism that drives signaling and regulates protein function. We report the phosphoproteomes of 18 fungal species and a phylogenetic-based approach to study phosphosite evolution. We observe rapid divergence, with only a small fraction of phosphosites conserved over hundreds of millions of years. Relative to recently acquired phosphosites, ancient sites are enriched at protein interfaces and are more likely to be functionally important, as we show for sites on H2A1 and eIF4E. We also observe a change in phosphorylation motif frequencies and kinase activities that coincides with the whole-genome duplication event. Our results provide an evolutionary history for phosphosites and suggest that rapid evolution of phosphorylation can contribute strongly to phenotypic diversity. Authors: Romain A. Studer, Ricard A. Rodriguez-Mias, Kelsey M. Haas, Joanne I. Hsu, Cristina Viéitez, Carme Solé, Danielle L. Swaney, Lindsay B. Stanford, Ivan Liachko, René Böttcher, Maitreya J. Dunham, Eulàlia de Nadal, Francesc Posas, Pedro Beltrao, Judit Villén
    Keywords: PROTEIN EVOLUTION
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Foraminifera-bound nitrogen isotope data from eastern equatorial Pacific cores ME-24 and ME-27 back to the last ice age (2020)
    PANGAEA
    Details
    Publication Date: 2023-10-05
    Description: Previous paleoceanographic applications of the N isotopes in the eastern equatorial Pacific have used the N isotopic composition of the bulk sediment, which can be biased by diagenetic alteration or foreign N input. To avoid these biases, we measured foraminifera shell-bound d15N (FB-d15N) on the two species Neogloboquadrina dutertrei and Neogloboquadrina incompta in two sediment cores extending back to the last ice age. The datafile contains FB-d15N data measured on the two sediment cores ME0005-24JC (0°1.3' N, 86°27.8' W, 2941m) and ME0005-27JC (1°51.2' S, 82°47.2'W, 2203m) from the eastern equatorial Pacific, as well as updated age models for the two sediment cores. Moreover, it contains estimated changes in Pacific oxygen concentration from the LGM to the Holocene. The age models for both sediment cores have been updated by Dubois et al. (2014) and are based on (1) radiocarbon ages measured on the planktonic foraminifera N. dutertrei by accelerator mass spectrometry, (2) correlation of benthic foraminifera oxygen isotopes to the LR04 stack and (3) the identification of the Los Chocoyos Ash Layer in the sediment cores. In core ME0005-27JC, three additional 14C dates on N. dutertrei from Mekik (2014) were included. All radiocarbon ages were calibrated with Calib 7.1. and the marine calibration curve MARINE13, assuming a reservoir age of 467 years as given in Dubois et al. (2014). Ages were linearly interpolated between the stratigraphic tie points. Foraminifera-bound d15N (FB-d15N) was measured with the “persulfate-denitrifier” technique (Ren et al., 2009; Straub et al., 2013). In short, ~3-5 mg of foraminifera (N. dutertrei and N. incompta from the 300-600µm size fraction) were picked, cut open with a scalpel and underwent a chemical cleaning. The organic N bound within the calcite was then released by dissolution with HCl and converted to nitrate in a basic potassium persulfate solution. The nitrate concentration of the solution was determined by chemiluminescence, and an aliquot of the nitrate solution equivalent to 5nmol of N was converted to nitrous oxide (N2O) by denitrifying bacteria. The N isotopic composition of the N2O was measured with a custom continuous-flow system for N2O extraction and purification on-line to a Thermo MAT253 stable isotope mass spectrometer and referenced to air N2 using the international nitrate standards IAEA-N3 and USGS-34. The FB-d15N data were then corrected for the contribution of the oxidation procedural blank with an in-house aminocaproic acid standard of known isotopic composition. Changes in Pacific oxygen concentration from the LGM to the Holocene were calculated based on solubility changes as well as CYCLOPS box model results of Hain et al., (2010). Changes in oxygen saturation result from changes in temperature and salinity; changes in oxygen utilization result from a glacial shoaling of the Atlantic Meridional Overturning Circulation, enhanced nutrient consumption due to Subantarctic iron fertilization, reduced Antarctic surface-to-deep exchange and more complete Antarctic nutrient consumption. Oxygen utilization is calculated using O2:Pregenerated of -170:1 (Anderson and Sarmiento, 1994).
    Keywords: Eastern Equatorial Pacific; Foraminifera-bound nitrogen isotopes; Holocene; Last Glacial; suboxia; water column denitrification
    Type: Dataset
    Format: application/zip, 4 datasets
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  • 10
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    Age model and sedimentation rates of sediment core PS75/072-4 (2015)
    PANGAEA
    Details
    Publication Date: 2023-10-05
    Keywords: Age, comment; Age model; ANT-XXVI/2; AWI_Paleo; DEPTH, sediment/rock; Gravity corer (Kiel type); Paleoenvironmental Reconstructions from Marine Sediments @ AWI; Polarstern; PS75/072-4; PS75 BIPOMAC; Sedimentation rate; SL; South Pacific Ocean
    Type: Dataset
    Format: text/tab-separated-values, 72 data points
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