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  • 1
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    Strategy for combinatorial genome engineering [Microbiology] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-06-27
    Description: We describe a directed genome-engineering approach that combines genome-wide methods for mapping genes to traits [Warner JR, Reeder PJ, Karimpour-Fard A, Woodruff LBA, Gill RT (2010) Nat Biotechnol 28:856–862] with strategies for rapidly creating combinatorial ribosomal binding site (RBS) mutation libraries containing billions of targeted modifications [Wang HH, et al. (2009) Nature 460:894–898]. This approach should prove broadly applicable to various efforts focused on improving production of fuels, chemicals, and pharmaceuticals, among other products. We used barcoded promoter mutation libraries to map the effect of increased or decreased expression of nearly every gene in Escherichia coli onto growth in several model environments (cellulosic hydrolysate, low pH, and high acetate). Based on these data, we created and evaluated RBS mutant libraries (containing greater than 100,000,000 targeted mutations), targeting the genes identified to most affect growth. On laboratory timescales, we successfully identified a broad range of mutations (〉25 growth-enhancing mutations confirmed), which improved growth rate 10–200% for several different conditions. Although successful, our efforts to identify superior combinations of growth-enhancing genes emphasized the importance of epistatic interactions among the targeted genes (synergistic, antagonistic) for taking full advantage of this approach to directed genome engineering.
    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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  • 2
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    Renewable acrylonitrile production (2017)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2017-12-08
    Description: Acrylonitrile (ACN) is a petroleum-derived compound used in resins, polymers, acrylics, and carbon fiber. We present a process for renewable ACN production using 3-hydroxypropionic acid (3-HP), which can be produced microbially from sugars. The process achieves ACN molar yields exceeding 90% from ethyl 3-hydroxypropanoate (ethyl 3-HP) via dehydration and nitrilation with ammonia over an inexpensive titanium dioxide solid acid catalyst. We further describe an integrated process modeled at scale that is based on this chemistry and achieves near-quantitative ACN yields (98 ± 2%) from ethyl acrylate. This endothermic approach eliminates runaway reaction hazards and achieves higher yields than the standard propylene ammoxidation process. Avoidance of hydrogen cyanide as a by-product also improves process safety and mitigates product handling requirements.
    Keywords: Chemistry, Engineering
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Spatial distribution of low-energy plasma around comet 67P/CG from Rosetta measurements (2015)
    Wiley
    Details
    Publication Date: 2015-05-20
    Description: We use measurements from the Rosetta plasma consortium (RPC) Langmuir probe (LAP) and mutual impedance probe (MIP) to study the spatial distribution of low-energy plasma in the near-nucleus coma of comet 67P/Churyumov-Gerasimenko. The spatial distribution is highly structured with the highest density in the summer hemisphere and above the region connecting the two main lobes of the comet, i.e. the neck region. There is a clear correlation with the neutral density and the plasma to neutral density ratio is found to be ~ 1 - 2 ⋅ 10 − 6 , at a cometocentric distance of 10 km and at 3.1 AU from the sun. A clear 6.2 h modulation of the plasma is seen as the neck is exposed twice per rotation. The electron density of the collisonless plasma within 260 km from the nucleus falls of with radial distance as ~ 1/ r . The spatial structure indicates that local ionization of neutral gas is the dominant source of low-energy plasma around the comet.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 4
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    Detection of Productively Rearranged TcR-α V–J Sequences in TCGA Exome Files: Implications for Tumor Immunoscoring and Recovery of Antitumor T-cells (2016)
    Libertas Academica
    Details
    Publication Date: 2016-02-26
    Description: Tumor immunoscoring is rapidly becoming a universal parameter of prognosis, and T-cells isolated from tumor masses are used for ex vivo amplification and readministration to patients to facilitate an antitumor immune response. We recently exploited the cancer genome atlas (TCGA) RNASeq data to assess T-cell receptor (TcR) expression and, in particular, discovered strong correlations between major histocompatibility class II (MHCII) and TcR-α constant region expression levels. In this article, we describe the results of searching TCGA exome files for TcR-α V-regions, followed by searching the V-region datasets for TcR-α-J regions. Both primary and metastatic breast cancer sample files contained recombined TcR-α V–J regions, ranging in read counts from 16–39, at the higher level. Among four such V–J rearrangements, three were productive rearrangements. Rearranged TcR-α V–J regions were also detected in TCGA–bladder cancer, –lung cancer, and –ovarian cancer datasets, as well as exome files representing bladder cancer, in Moffitt Cancer Center patients. These results suggest that a direct search of commonly available, conventional exome files for rearranged TcR segments could play a role in more sophisticated immunoscoring or in identifying particular T-cell clones and TcRs directed against tumor antigens.
    Electronic ISSN: 1176-9351
    Topics: Computer Science , Medicine
    Published by Libertas Academica
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  • 5
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    Pulse of atmospheric oxygen during the late Cambrian [Geology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-03-09
    Description: A rise in atmospheric O2 has been linked to the Cambrian explosion of life. For the plankton and animal radiation that began some 40 million yr later and continued through much of the Ordovician (Great Ordovician Biodiversification Event), the search for an environmental trigger(s) has remained elusive. Here we present a carbon and sulfur isotope mass balance model for the latest Cambrian time interval spanning the globally recognized Steptoean Positive Carbon Isotope Excursion (SPICE) that indicates a major increase in atmospheric O2. We estimate that this organic carbon and pyrite burial event added approximately 19 × 1018 moles of O2 to the atmosphere (i.e., equal to change from an initial starting point for O2 between 10–18% to a peak of 20–28% O2) beginning at approximately 500 million years. We further report on new paired carbon isotope results from carbonate and organic matter through the SPICE in North America, Australia, and China that reveal an approximately 2‰ increase in biological fractionation, also consistent with a major increase in atmospheric O2. The SPICE is followed by an increase in plankton diversity that may relate to changes in macro- and micronutrient abundances in increasingly oxic marine environments, representing a critical initial step in the trophic chain. Ecologically diverse plankton groups could provide new food sources for an animal biota expanding into progressively more ventilated marine habitats during the Ordovician, ultimately establishing complex ecosystems that are a hallmark of the Great Ordovician Biodiversification Event.
    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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    An experimental limit on the charge of antihydrogen (2014)
    Springer Nature
    Details
    Publication Date: 2014-06-05
    Description: Article Fundamental theories do not predict a difference between the properties of matter and antimatter, but experimental tests of this are still in their infancy. To this end, this study analyses the effects of electric fields on antihydrogen atoms in the ALPHA trap to place a bound on the charge of antihydrogen. Nature Communications doi: 10.1038/ncomms4955 Authors: C. Amole, M. D. Ashkezari, M. Baquero-Ruiz, W. Bertsche, E. Butler, A. Capra, C. L. Cesar, M. Charlton, S. Eriksson, J. Fajans, T. Friesen, M. C. Fujiwara, D. R. Gill, A. Gutierrez, J. S. Hangst, W. N. Hardy, M. E. Hayden, C. A. Isaac, S. Jonsell, L. Kurchaninov, A. Little, N. Madsen, J. T. K. McKenna, S. Menary, S. C. Napoli, P. Nolan, K. Olchanski, A. Olin, A. Povilus, P. Pusa, C.Ø. Rasmussen, F. Robicheaux, E. Sarid, D. M. Silveira, C. So, T. D. Tharp, R. I. Thompson, D. P. van der Werf, Z. Vendeiro, J. S. Wurtele, A. I. Zhmoginov, A. E. Charman
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 7
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    Global transposon mutagenesis and a minimal Mycoplasma genome (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-12-11
    Description: Mycoplasma genitalium with 517 genes has the smallest gene complement of any independently replicating cell so far identified. Global transposon mutagenesis was used to identify nonessential genes in an effort to learn whether the naturally occurring gene complement is a true minimal genome under laboratory growth conditions. The positions of 2209 transposon insertions in the completely sequenced genomes of M. genitalium and its close relative M. pneumoniae were determined by sequencing across the junction of the transposon and the genomic DNA. These junctions defined 1354 distinct sites of insertion that were not lethal. The analysis suggests that 265 to 350 of the 480 protein-coding genes of M. genitalium are essential under laboratory growth conditions, including about 100 genes of unknown function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hutchison, C A -- Peterson, S N -- Gill, S R -- Cline, R T -- White, O -- Fraser, C M -- Smith, H O -- Venter, J C -- New York, N.Y. -- Science. 1999 Dec 10;286(5447):2165-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10591650" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/genetics/metabolism ; Amino Acyl-tRNA Synthetases/genetics ; Bacterial Proteins/genetics ; Chromosome Mapping ; DNA Polymerase III/genetics/metabolism ; DNA Replication/genetics ; *DNA Transposable Elements ; *Genes, Essential ; *Genome, Bacterial ; Glycolysis/genetics ; Lipoproteins/genetics ; *Mutagenesis, Insertional ; Mycoplasma/*genetics/metabolism ; Mycoplasma pneumoniae/genetics/metabolism ; Ribosomal Proteins/genetics ; Transcription, Genetic
    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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  • 8
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    Trapped antihydrogen (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-11-19
    Description: Antimatter was first predicted in 1931, by Dirac. Work with high-energy antiparticles is now commonplace, and anti-electrons are used regularly in the medical technique of positron emission tomography scanning. Antihydrogen, the bound state of an antiproton and a positron, has been produced at low energies at CERN (the European Organization for Nuclear Research) since 2002. Antihydrogen is of interest for use in a precision test of nature's fundamental symmetries. The charge conjugation/parity/time reversal (CPT) theorem, a crucial part of the foundation of the standard model of elementary particles and interactions, demands that hydrogen and antihydrogen have the same spectrum. Given the current experimental precision of measurements on the hydrogen atom (about two parts in 10(14) for the frequency of the 1s-to-2s transition), subjecting antihydrogen to rigorous spectroscopic examination would constitute a compelling, model-independent test of CPT. Antihydrogen could also be used to study the gravitational behaviour of antimatter. However, so far experiments have produced antihydrogen that is not confined, precluding detailed study of its structure. Here we demonstrate trapping of antihydrogen atoms. From the interaction of about 10(7) antiprotons and 7 x 10(8) positrons, we observed 38 annihilation events consistent with the controlled release of trapped antihydrogen from our magnetic trap; the measured background is 1.4 +/- 1.4 events. This result opens the door to precision measurements on anti-atoms, which can soon be subjected to the same techniques as developed for hydrogen.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Andresen, G B -- Ashkezari, M D -- Baquero-Ruiz, M -- Bertsche, W -- Bowe, P D -- Butler, E -- Cesar, C L -- Chapman, S -- Charlton, M -- Deller, A -- Eriksson, S -- Fajans, J -- Friesen, T -- Fujiwara, M C -- Gill, D R -- Gutierrez, A -- Hangst, J S -- Hardy, W N -- Hayden, M E -- Humphries, A J -- Hydomako, R -- Jenkins, M J -- Jonsell, S -- Jorgensen, L V -- Kurchaninov, L -- Madsen, N -- Menary, S -- Nolan, P -- Olchanski, K -- Olin, A -- Povilus, A -- Pusa, P -- Robicheaux, F -- Sarid, E -- el Nasr, S Seif -- Silveira, D M -- So, C -- Storey, J W -- Thompson, R I -- van der Werf, D P -- Wurtele, J S -- Yamazaki, Y -- England -- Nature. 2010 Dec 2;468(7324):673-6. doi: 10.1038/nature09610. Epub 2010 Nov 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21085118" 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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  • 9
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    Choline acetyltransferase-expressing T cells are required to control chronic viral infection (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉Although widely studied as a neurotransmitter, T cell–derived acetylcholine (ACh) has recently been reported to play an important role in regulating immunity. However, the role of lymphocyte-derived ACh in viral infection is unknown. Here, we show that the enzyme choline acetyltransferase (ChAT), which catalyzes the rate-limiting step of ACh production, is robustly induced in both CD4〈sup〉+〈/sup〉 and CD8〈sup〉+〈/sup〉 T cells during lymphocytic choriomeningitis virus (LCMV) infection in an IL-21–dependent manner. Deletion of 〈i〉Chat〈/i〉 within the T cell compartment in mice ablated vasodilation in response to infection, impaired the migration of antiviral T cells into infected tissues, and ultimately compromised the control of chronic LCMV clone 13 infection. Our results reveal a genetic proof of function for ChAT in T cells during viral infection and identify a pathway of T cell migration that sustains antiviral immunity.〈/p〉
    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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  • 10
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    Genetic analysis of a high-level vancomycin-resistant isolate of Staphylococcus aureus (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-04
    Description: Vancomycin is usually reserved for treatment of serious infections, including those caused by multidrug-resistant Staphylococcus aureus. A clinical isolate of S. aureus with high-level resistance to vancomycin (minimal inhibitory concentration = 1024 microg/ml) was isolated in June 2002. This isolate harbored a 57.9-kilobase multiresistance conjugative plasmid within which Tn1546 (vanA) was integrated. Additional elements on the plasmid encoded resistance to trimethoprim (dfrA), beta-lactams (blaZ), aminoglycosides (aacA-aphD), and disinfectants (qacC). Genetic analyses suggest that the long-anticipated transfer of vancomycin resistance to a methicillin-resistant S. aureus occurred in vivo by interspecies transfer of Tn1546 from a co-isolate of Enterococcus faecalis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weigel, Linda M -- Clewell, Don B -- Gill, Steven R -- Clark, Nancye C -- McDougal, Linda K -- Flannagan, Susan E -- Kolonay, James F -- Shetty, Jyoti -- Killgore, George E -- Tenover, Fred C -- N01-AI-95359/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2003 Nov 28;302(5650):1569-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA. lweigel@cdc.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14645850" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Carbon-Oxygen Ligases/*genetics ; Conjugation, Genetic ; *DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/genetics ; Enterococcus faecalis/drug effects/*genetics/isolation & purification ; Genes, Bacterial ; Humans ; Methicillin Resistance/genetics ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Plasmids ; *R Factors ; Recombination, Genetic ; Renal Dialysis ; Staphylococcus aureus/*drug effects/*genetics/isolation & purification ; Vancomycin/pharmacology ; Vancomycin Resistance/*genetics
    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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