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  • Oxford University Press  (79)
  • 2020-2023
  • 2015-2019  (79)
  • 1950-1954
  • 1
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    A metallicity recipe for rocky planets (2015)
    Oxford University Press
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    Publication Date: 2015-08-27
    Description: Planets with sizes between those of Earth and Neptune divide into two populations: purely rocky bodies whose atmospheres contribute negligibly to their sizes, and larger gas-enveloped planets possessing voluminous and optically thick atmospheres. We show that whether a planet forms rocky or gas-enveloped depends on the solid surface density of its parent disc. Assembly times for rocky cores are sensitive to disc solid surface density. Lower surface densities spawn smaller planetary embryos; to assemble a core of given mass, smaller embryos require more mergers between bodies farther apart and therefore exponentially longer formation times. Gas accretion simulations yield a rule of thumb that a rocky core must be at least 2M before it can acquire a volumetrically significant atmosphere from its parent nebula. In discs of low solid surface density, cores of such mass appear only after the gas disc has dissipated, and so remain purely rocky. Higher surface density discs breed massive cores more quickly, within the gas disc lifetime, and so produce gas-enveloped planets. We test model predictions against observations, using planet radius as an observational proxy for gas-to-rock content and host star metallicity as a proxy for disc solid surface density. Theory can explain the observation that metal-rich stars host predominantly gas-enveloped planets.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 2
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    Bioreactors and in situ product recovery techniques for acetone-butanol-ethanol fermentation (2016)
    Oxford University Press
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    Publication Date: 2016-06-02
    Description: The microbial fermentation process is one of the sustainable and environment-friendly ways to produce 1-butanol and other bio-based chemicals. The success of the fermentation process greatly relies on the choice of bioreactors and the separation methods. In this review, the history and the performance of bioreactors for the acetone–butanol–ethanol (ABE) fermentation is discussed. The subject is then focused on in situ product recovery (ISPR) techniques, particularly for the integrated extraction-gas stripping. The usefulness of this promising hybrid ISPR device is acknowledged by its incorporation with batch, fed-batch and continuous processes to improve the performance of ABE fermentation.
    Keywords: Biotechnology & Synthetic Biology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Latent transforming growth factor binding protein 4 regulates transforming growth factor beta receptor stability (2015)
    Oxford University Press
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    Publication Date: 2015-06-23
    Description: Mutations in the gene for the latent transforming growth factor beta binding protein 4 ( LTBP4 ) cause autosomal recessive cutis laxa type 1C. To understand the molecular disease mechanisms of this disease, we investigated the impact of LTBP4 loss on transforming growth factor beta (TGFβ) signaling. Despite elevated extracellular TGFβ activity, downstream signaling molecules of the TGFβ pathway, including pSMAD2 and pERK, were down-regulated in LTBP4 mutant human dermal fibroblasts. In addition, TGFβ receptors 1 and 2 (TGFBR1 and TGFBR2) were reduced at the protein but not at the ribonucleic acid level. Treatment with exogenous TGFβ1 led to an initially rapid increase in SMAD2 phosphorylation followed by a sustained depression of phosphorylation and receptor abundance. In mutant cells TGFBR1 was co-localized with lysosomes. Treatment with a TGFBR1 kinase inhibitor, endocytosis inhibitors or a lysosome inhibitor, normalized the levels of TGFBR1 and TGFBR2. Co-immunoprecipitation demonstrated a molecular interaction between LTBP4 and TGFBR2. Knockdown of LTBP4 reduced TGFβ receptor abundance and signaling in normal cells and supplementation of recombinant LTBP4 enhanced these measures in mutant cells. In a mouse model of Ltbp4 deficiency, reduced TGFβ signaling and receptor levels were normalized upon TGFBR1 kinase inhibitor treatment. Our results show that LTBP4 interacts with TGFBR2 and stabilizes TGFβ receptors by preventing their endocytosis and lysosomal degradation in a ligand-dependent and receptor kinase activity-dependent manner. These findings identify LTBP4 as a key molecule required for the stability of the TGFβ receptor complex, and a new mechanism by which the extracellular matrix regulates cytokine receptor signaling.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 4
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    Searching for T dwarfs in the {rho} Oph dark cloud L 1688 (2015)
    Oxford University Press
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    Publication Date: 2015-02-07
    Description: We present a list of T dwarf candidates in the dark cloud L 1688 in the  Oph star-forming region. These candidates are selected with infrared colours sensitive to T dwarf characteristics of methane absorptions and of cool atmospheres. The 1.6-μm methane feature is diagnosed by on–off imaging using an H -band and an intermediate-band methane filter, calibrated to a set of known brown dwarfs of M, L, and T types in the field. Another methane feature at 3.3 μm is traced with the Spitzer /Infrared Array Camera (IRAC) [3.6] – [4.5] colour. For cool atmospheres, the H  – [4.5] and K  – [4.5] colours are utilized. With an additional criterion of mid-infrared brightness to eliminate extragalactic interlopers, a total of 28 T dwarf candidates have been identified. A comprehensive assessment was conducted to estimate the level of contamination of our sample by young stellar variability, by extragalactic sources sharing the same colour behaviour, or by foreground T dwarfs. Though extragalactic sources may contribute up to about half of the false positives, our candidates show close spatial association with the dark cloud, rather than randomly distributed as a background population would have been. Furthermore, even though our candidates are not selected a priori by a colour–magnitude relation, they mostly follow the 1 Myr isochrones, ascertaining their youth. Our selection methodology provides guidance to search for T dwarfs in other star-forming regions. Our candidate list, when comparing with those in the literature, which often rely on a single criterion on cool temperature or methane, is more conservative but should be more secure for follow-up spectroscopic confirmation of a T dwarf sample at the early evolutionary stage.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam (2015)
    Oxford University Press
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    Publication Date: 2015-09-16
    Description: Transport systems comprise roughly 10% of all proteins in a cell, playing critical roles in many processes. Improving and expanding their classification is an important goal that can affect studies ranging from comparative genomics to potential drug target searches. It is not surprising that different classification systems for transport proteins have arisen, be it within a specialized database, focused on this functional class of proteins, or as part of a broader classification system for all proteins. Two such databases are the Transporter Classification Database (TCDB) and the Protein family (Pfam) database. As part of a long-term endeavor to improve consistency between the two classification systems, we have compared transporter annotations in the two databases to understand the rationale for differences and to improve both systems. Differences sometimes reflect the fact that one database has a particular transporter family while the other does not. Differing family definitions and hierarchical organizations were reconciled, resulting in recognition of 69 Pfam ‘Domains of Unknown Function’, which proved to be transport protein families to be renamed using TCDB annotations. Of over 400 potential new Pfam families identified from TCDB, 10% have already been added to Pfam, and TCDB has created 60 new entries based on Pfam data. This work, for the first time, reveals the benefits of comprehensive database comparisons and explains the differences between Pfam and TCDB.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 6
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    Regulation of mammalian transcription and splicing by Nuclear RNAi (2016)
    Oxford University Press
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    Publication Date: 2016-01-30
    Description: RNA interference (RNAi) is well known as a mechanism for controlling mammalian mRNA translation in the cytoplasm, but what would be the consequences if it also functions in cell nuclei? Although RNAi has also been found in nuclei of plants, yeast, and other organisms, there has been relatively little progress towards understanding the potential involvement of mammalian RNAi factors in nuclear processes including transcription and splicing. This review summarizes evidence for mammalian RNAi factors in cell nuclei and mechanisms that might contribute to the control of gene expression. When RNAi factors bind small RNAs, they form ribonucleoprotein complexes that can be selective for target sequences within different classes of nuclear RNA substrates. The versatility of nuclear RNAi may supply a previously underappreciated layer of regulation to transcription, splicing, and other nuclear processes.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-20
    Description: Analysis of RNA-seq data often detects numerous ‘non-co-linear’ (NCL) transcripts, which comprised sequence segments that are topologically inconsistent with their corresponding DNA sequences in the reference genome. However, detection of NCL transcripts involves two major challenges: removal of false positives arising from alignment artifacts and discrimination between different types of NCL transcripts ( trans -spliced, circular or fusion transcripts). Here, we developed a new NCL-transcript-detecting method (‘NCLscan’), which utilized a stepwise alignment strategy to almost completely eliminate false calls (〉98% precision) without sacrificing true positives, enabling NCLscan outperform 18 other publicly-available tools (including fusion- and circular-RNA-detecting tools) in terms of sensitivity and precision, regardless of the generation strategy of simulated dataset, type of intragenic or intergenic NCL event, read depth of coverage, read length or expression level of NCL transcript. With the high accuracy, NCLscan was applied to distinguishing between trans -spliced, circular and fusion transcripts on the basis of poly(A)- and nonpoly(A)-selected RNA-seq data. We showed that circular RNAs were expressed more ubiquitously, more abundantly and less cell type-specifically than trans -spliced and fusion transcripts. Our study thus describes a robust pipeline for the discovery of NCL transcripts, and sheds light on the fundamental biology of these non-canonical RNA events in human transcriptome.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    DTIE, a novel core promoter element that directs start site selection in TATA-less genes (2016)
    Oxford University Press
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    Publication Date: 2016-02-20
    Description: The transcription start site (TSS) determines the length and composition of the 5' UTR and therefore can have a profound effect on translation. Yet, little is known about the mechanism underlying start site selection, particularly from promoters lacking conventional core elements such as TATA-box and Initiator. Here we report a novel mechanism of start site selection in the TATA- and Initiator-less promoter of miR-22, through a strictly localized downstream element termed DTIE and an upstream distal element. Changing the distance between them reduced promoter strength, altered TSS selection and diminished Pol II recruitment. Biochemical assays suggest that DTIE does not serve as a docking site for TFIID, the major core promoter-binding factor. TFIID is recruited to the promoter through DTIE but is dispensable for TSS selection. We determined DTIE consensus and found it to be remarkably prevalent, present at the same TSS downstream location in 20.8% of human promoters, the vast majority of which are TATA-less. Analysis of DTIE in the tumor suppressor p53 confirmed a similar function. Our findings reveal a novel mechanism of transcription initiation from TATA-less promoters.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Expression of a pathogenic mutation of SOD1 sensitizes aprataxin-deficient cells and mice to oxidative stress and triggers hallmarks of premature ageing (2015)
    Oxford University Press
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    Publication Date: 2015-01-13
    Description: Aprataxin (APTX) deficiency causes progressive cerebellar degeneration, ataxia and oculomotor apraxia in man. Cell free assays and crystal structure studies demonstrate a role for APTX in resolving 5'-adenylated nucleic acid breaks, however, APTX function in vertebrates remains unclear due to the lack of an appropriate model system. Here, we generated a murine model in which a pathogenic mutant of superoxide dismutase 1 (SOD1 G93A ) is expressed in an Aptx –/– mouse strain. We report a delayed population doubling and accelerated senescence in Aptx –/– primary mouse fibroblasts, which is not due to detectable telomere instability or cell cycle deregulation but is associated with a reduction in transcription recovery following oxidative stress. Expression of SOD1 G93A uncovers a survival defect ex vivo in cultured cells and in vivo in tissues lacking Aptx. The surviving neurons feature numerous and deep nuclear envelope invaginations, a hallmark of cellular stress. Furthermore, they possess an elevated number of high-density nuclear regions and a concomitant increase in histone H3 K9 trimethylation, hallmarks of silenced chromatin. Finally, the accelerated cellular senescence was also observed at the organismal level as shown by down-regulation of insulin-like growth factor 1 (IGF-1), a hallmark of premature ageing. Together, this study demonstrates a protective role of Aptx in vivo and suggests that its loss results in progressive accumulation of DNA breaks in the nervous system, triggering hallmarks of premature ageing, systemically.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 10
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    Separate universe simulations (2015)
    Oxford University Press
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    Publication Date: 2015-01-02
    Description: The large-scale statistics of observables such as the galaxy density are chiefly determined by their dependence on the local coarse-grained matter density. This dependence can be measured directly and efficiently in N -body simulations by using the fact that a uniform density perturbation with respect to some fiducial background cosmology is equivalent to modifying the background and including curvature, i.e. by simulating a ‘separate universe’. We derive this mapping to fully non-linear order, and provide a step-by-step description of how to perform and analyse the separate universe simulations. This technique can be applied to a wide range of observables. As an example, we calculate the response of the non-linear matter power spectrum to long-wavelength density perturbations, which corresponds to the angle-averaged squeezed limit of the matter bispectrum and higher n -point functions. Using only a modest simulation volume, we obtain simulation results for the bispectrum and trispectrum with per cent-level precision over a wide range of scales.
    Print ISSN: 1745-3925
    Electronic ISSN: 1745-3933
    Topics: Physics
    Published by Oxford University Press
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