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  • Oxford University Press  (55)
  • American Association for the Advancement of Science (AAAS)  (15)
  • 1
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    Sub-single-exciton lasing using charged quantum dots coupled to a distributed feedback cavity (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉Colloidal semiconductor quantum dots (QDs) are attractive materials for realizing highly flexible, solution-processable optical gain media, but they are difficult to use in lasing because of complications associated with extremely short optical-gain lifetimes limited by nonradiative Auger recombination. By combining compositional grading of the QD’s interior for hindering Auger decay with postsynthetic charging for suppressing parasitic ground-state absorption, we can reduce the lasing threshold to values below the single-exciton-per-dot limit. As a favorable departure from traditional multi-exciton–based lasing schemes, our approach should facilitate the development of solution-processable lasing devices and thereby help to extend the reach of lasing technologies into areas not accessible with traditional, epitaxially grown semiconductor materials.〈/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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  • 2
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    Arc-continent collisions in the tropics set Earths climate state (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉 On multi-million-year timescales, Earth has experienced warm ice-free and cold glacial climates, but it is unknown if transitions between these background climate states were the result of changes in CO〈sub〉2〈/sub〉 sources or sinks. Low-latitude arc-continent collisions are hypothesized to drive cooling by uplifting and eroding mafic and ultramafic rocks in the warm, wet tropics, thereby increasing Earth’s potential to sequester carbon through chemical weathering. To better constrain global weatherability through time, the paleogeographic position of all major Phanerozoic arc-continent collisions was reconstructed and compared to the latitudinal distribution of ice-sheets. This analysis reveals a strong correlation between the extent of glaciation and arc-continent collisions in the tropics. Earth’s climate state is set primarily by global weatherability, which changes with the latitudinal distribution of arc-continent collisions.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Increased expression of genes involved in uptake and degradation of murein tripeptide under nitrogen starvation in Escherichia coli (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-17
    Description: Peptidoglycan (also known as murein) is an important envelope component of bacteria, and its turnover usually takes place at considerable levels during normal growth. Amino sugars and murein tripeptide resulting from murein degradation are used for resynthesis of peptidoglycan or as self-generated nutrients or energy sources for cell growth. PgrR (regulator of peptide glycan recycling; formerly YcjZ) was recently identified as a repressor of several genes participating in uptake and degradation of murein tripeptide. In this study, we identified the ycjG gene involved in murein tripeptide degradation as a new direct target of PgrR. The expression of PgrR-regulated genes including ycjY , mppA , mpaA and ycjG was repressed in the presence of a good nitrogen source, but their expression increased under poor nitrogen conditions. Under nitrogen starvation, the pgrR mutant cells exhibited faster growth than wild-type cells, implying that derepression of genes under the control of PgrR may help cells overcome nitrogen limitation. Therefore, these results suggest that nitrogen starvation induces derepression of PgrR-controlled genes involved in uptake and degradation of murein tripeptide, and this may stimulate the utilization of murein tripeptide as a nitrogen source.
    Keywords: Physiology & Biochemistry
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    The EMBL-EBI bioinformatics web and programmatic tools framework (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-02
    Description: Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services ( https://www.ebi.ac.uk/Tools/sss/ ) such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools ( https://www.ebi.ac.uk/Tools/msa/ ) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools ( https://www.ebi.ac.uk/Tools/pfa/ ) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically through Web Services interfaces ( https://www.ebi.ac.uk/Tools/webservices/ ) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search ( https://www.ebi.ac.uk/ebisearch/ ) and the dbfetch retrieval service ( https://www.ebi.ac.uk/Tools/dbfetch/ ) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, InterProScan 5 and PfamScan, new categories such as RNA analysis tools ( https://www.ebi.ac.uk/Tools/rna/ ), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-02
    Description: The European Bioinformatics Institute (EMBL-EBI— https://www.ebi.ac.uk ) provides free and unrestricted access to data across all major areas of biology and biomedicine. Searching and extracting knowledge across these domains requires a fast and scalable solution that addresses the requirements of domain experts as well as casual users. We present the EBI Search engine, referred to here as ‘EBI Search’, an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities. API integration provides access to analytical tools, allowing users to further investigate the results of their search. The interconnectivity that exists between data resources at EMBL-EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types including sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromolecular structures, together with relevant life science literature.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Facing growth in the European Nucleotide Archive (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-20
    Description: The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/ ) collects, maintains and presents comprehensive nucleic acid sequence and related information as part of the permanent public scientific record. Here, we provide brief updates on ENA content developments and major service enhancements in 2012 and describe in more detail two important areas of development and policy that are driven by ongoing growth in sequencing technologies. First, we describe the ENA data warehouse, a resource for which we provide a programmatic entry point to integrated content across the breadth of ENA. Second, we detail our plans for the deployment of CRAM data compression technology in ENA.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Exploiting enzyme specificities in digestions of chondroitin sulfates A and C: Production of well-defined hexasaccharides (2012)
    Oxford University Press
    Details
    Publication Date: 2012-04-26
    Description: Interactions between proteins and glycosaminoglycans (GAGs) of the extracellular matrix are important to the regulation of cellular processes including growth, differentiation and migration. Understanding these processes can benefit greatly from the study of protein–GAG interactions using GAG oligosaccharides of well-defined structure. Materials for such studies have, however, been difficult to obtain because of challenges in synthetic approaches and the extreme structural heterogeneity in GAG polymers. Here, it is demonstrated that diversity in structures of oligosaccharides derived by limited enzymatic digestion of materials from natural sources can be greatly curtailed by a proper selection of combinations of source materials and digestive enzymes, a process aided by an improved understanding of the specificities of certain commercial preparations of hydrolases and lyases. Separation of well-defined oligosaccharides can then be accomplished by size-exclusion chromatography followed by strong anion-exchange chromatography. We focus here on two types of chondroitin sulfate (CS) as starting material (CS-A, and CS-C) and the use of three digestive enzymes with varying specificities (testicular hyaluronidase and bacterial chondroitinases ABC and C). Analysis using nuclear magnetic resonance and mass spectrometry focuses on isolated CS disaccharides and hexasaccharides. In all, 15 CS hexasaccharides have been isolated and characterized. These serve as useful contributions to growing libraries of well-defined GAG oligosaccharides that can be used in further biophysical assays.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 8
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    Crystal structure of a heterodimer of editosome interaction proteins in complex with two copies of a cross-reacting nanobody (2012)
    Oxford University Press
    Details
    Publication Date: 2012-02-28
    Description: The parasite Trypanosoma brucei , the causative agent of sleeping sickness across sub-Saharan Africa, depends on a remarkable U-insertion/deletion RNA editing process in its mitochondrion. A approximately 20 S multi-protein complex, called the editosome, is an essential machinery for editing pre-mRNA molecules encoding the majority of mitochondrial proteins. Editosomes contain a common core of twelve proteins where six OB-fold interaction proteins, called A1–A6, play a crucial role. Here, we report the structure of two single-strand nucleic acid-binding OB-folds from interaction proteins A3 and A6 that surprisingly, form a heterodimer. Crystal growth required the assistance of an anti-A3 nanobody as a crystallization chaperone. Unexpectedly, this anti-A3 nanobody binds to both A3 OB and A6, despite only ~40% amino acid sequence identity between the OB-folds of A3 and A6. The A3 OB -A6 heterodimer buries 35% more surface area than the A6 homodimer. This is attributed mainly to the presence of a conserved Pro-rich loop in A3 OB . The implications of the A3 OB –A6 heterodimer, and of a dimer of heterodimers observed in the crystals, for the architecture of the editosome are profound, resulting in a proposal of a ‘five OB-fold center’ in the core of the editosome.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    High-resolution, reconfigurable printing of liquid metals with three-dimensional structures (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉We report an unconventional approach for high-resolution, reconfigurable 3D printing using liquid metals for stretchable, 3D integrations. A minimum line width of 1.9 μm can be reliably formed using direct printing, and printed patterns can be reconfigured into diverse 3D structures with maintaining pristine resolutions. This reconfiguration can be performed multiple times, and it also generates a thin oxide interface that can be effective in preventing the spontaneous penetration of gallium atoms into different metal layers while preserving electrical properties under ambient conditions. Moreover, these free-standing features can be encapsulated with stretchable, conformal passivations. We demonstrate applications in the form of a reconfigurable antenna, which is tunable by changing geometeries, and reversibly movable interconnections used as mechanical switches. The free-standing 3D structure of electrodes is also advantageous for minimizing the number and space between interconnections, which is important for achieving higher integrations, as demonstrated in an array of microLEDs.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    The regulatory B cell-mediated peripheral tolerance maintained by mast cell IL-5 suppresses oxazolone-induced contact hypersensitivity (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉The function of regulatory immune cells in peripheral tissues is crucial to the onset and severity of various diseases. Interleukin-10 (IL-10)–producing regulatory B (IL-10〈sup〉+〈/sup〉 B〈sub〉reg〈/sub〉) cells are known to suppress various inflammatory diseases. However, evidence for the mechanism by which IL-10〈sup〉+〈/sup〉 B〈sub〉reg〈/sub〉 cells are generated and maintained is still very limited. Here, we found that IL-10〈sup〉+〈/sup〉 B〈sub〉reg〈/sub〉 cells suppress the activation of IL-13–producing type 2 innate lymphoid cells (IL-13〈sup〉+〈/sup〉 ILC2s) in an IL-10–dependent manner in mice with oxazolone-induced severe contact hypersensitivity (CHS). Mast cell (MC) IL-5 was important for maintaining the population of IL-10〈sup〉+〈/sup〉 B〈sub〉reg〈/sub〉 cells in peripheral lymphoid tissues. Overall, these results uncover a previously unknown mechanism of MCs as a type of immunoregulatory cell and elucidate the cross-talk among MCs, IL-10〈sup〉+〈/sup〉 B〈sub〉reg〈/sub〉 cells, and IL-13〈sup〉+〈/sup〉 ILC2s in CHS.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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