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  • 1
    Series available for loan
    Series available for loan
    Use of an "automatic sulphur titrator" in rock and mineral analysis : determination of sulphur, total carbon, carbonate and ferrous iron (1972)
    Ottawa : Geological Survey of Canada
    Associated volumes
    Details Availability
    Call number: SR 90.0008(72-31)
    In: Paper
    Type of Medium: Series available for loan
    Pages: V, 22 S.
    Series Statement: Paper / Geological Survey of Canada 72-31
    Language: English
    Location: Lower compact magazine
    Branch Library: GFZ Library
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  • 2
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    The fossil record of insect color illuminated by maturation experiments (2013)
    Geological Society of America (GSA)
    In: Geology
    Details
    Publication Date: 2013-03-22
    Description: Structural coloration underpins communication strategies in many extant insects but its evolution is poorly understood. This stems, in part, from limited data on how color alters during fossilization. We resolve this by using elevated pressures and temperatures to simulate the effects of burial on structurally colored cuticles of modern beetles. Our experiments show that the color generated by multilayer reflectors changes due to alteration of the refractive index and periodicity of the cuticle layers. Three-dimensional photonic crystals are equally resistant to degradation and thus their absence in fossil insects is not a function of limited preservation potential but implies that these color-producing nanostructures evolved recently. Structural colors alter directly to black above a threshold temperature in experiments, identifying burial temperature as the primary control on their preservation in fossils. Color-producing nanostructures can, however, survive in experimentally treated and fossil cuticles that now are black. An extensive cryptic record is thus available in fossil insects to illuminate the evolution of structural color.
    Print ISSN: 0091-7613
    Electronic ISSN: 1943-2682
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 3
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    The long noncoding RNA ROCKI regulates inflammatory gene expression (2019)
    Springer Nature
    Details
    Publication Date: 2019
    Description: 〈sec〉〈st〉Synopsis〈/st〉〈p〉〈textbox textbox-type="graphic"〉〈p〉〈inline-fig〉〈/inline-fig〉〈/p〉〈/textbox〉〈/p〉 〈p〉Activation of Toll-like receptors (TLRs) induced expression changes in lncRNAs that regulate their neighboring genes involved in inflammation. A lncRNA named 〈i〉ROCKI〈/i〉 forms a ribonucleoprotein complex and controls inflammatory responses via chromatin modification.〈/p〉 〈p〉 〈l type="unord"〉〈li〉〈p〉More than 200 〈i〉cis〈/i〉-acting lncRNAs and protein-coding gene pairs were identified in TLR-stimulated macrophages.〈/p〉〈/li〉 〈li〉〈p〉〈i〉Lnc-MARCKS〈/i〉, also designated 〈i〉ROCKI〈/i〉, is a master regulator of inflammatory responses to TLR ligands.〈/p〉〈/li〉 〈li〉〈p〉〈i〉ROCKI〈/i〉 interacts with APEX1 and HDAC1 enzymes at the 〈i〉MARCKS〈/i〉 promoter.〈/p〉〈/li〉 〈li〉〈p〉〈i〉ROCKI〈/i〉 expression is significantly associated with inflammation- and infection-related disease phenotypes in humans.〈/p〉〈/li〉〈/l〉 〈/p〉〈/sec〉
    Print ISSN: 0261-4189
    Electronic ISSN: 1460-2075
    Topics: Biology , Medicine
    Published by Springer Nature on behalf of The European Molecular Biology Organization (EMBO).
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  • 4
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    SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations (2012)
    Oxford University Press
    Details
    Publication Date: 2012-11-11
    Description: Motivation: Cell growth and division affect the kinetics of internal cellular processes and the phenotype diversity of cell populations. Since the effects are complex, e.g. different cellular components are partitioned differently in cell division, to account for them in silico, one needs to simulate these processes in great detail. Results : We present SGNS2, a simulator of chemical reaction systems according to the Stochastic Simulation Algorithm with multi-delayed reactions within hierarchical, interlinked compartments which can be created, destroyed and divided at runtime. In division, molecules are randomly segregated into the daughter cells following a specified distribution corresponding to one of several partitioning schemes, applicable on a per-molecule-type basis. We exemplify its use with six models including a stochastic model of the disposal mechanism of unwanted protein aggregates in Escherichia coli , a model of phenotypic diversity in populations with different levels of synchrony, a model of a bacteriophage’s infection of a cell population and a model of prokaryotic gene expression at the nucleotide and codon levels. Availability : SGNS2, instructions and examples available at www.cs.tut.fi/~lloydpri/sgns2/ (open source under New BSD license). Contact : jason.lloyd-price@tut.fi Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 5
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    Spectral energy distributions of the BL Lac PKS 2155 - 304 from XMM-Newton (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-19
    Description: We have used all 20 archival XMM–Newton observations of PKS 2155 – 304 with simultaneous X-ray and UV/optical data to study its long-term flux and spectral variability. We find significant variations, in all bands, on time-scales of years with an rms amplitude of ~35–45 per cent, though the optical/UV variations are not correlated with those in the X-ray. We constructed spectral energy distributions (SEDs) that span more than three orders of magnitude in frequency and we first fitted them with a log-parabolic model; such models have been applied many times in the past for this, and other, blazars. These fits were poor, so we then examined combined power-law and log-parabolic fits that are improvements. These models indicate that the optical/UV and X-ray flux variations are mainly driven by model normalization variations, but the X-ray band flux is also affected by spectral variations, as parametrized with the model ‘curvature’ parameter, b . Overall, the energy at which the emitted power is maximum correlates positively with the total flux. As the spectrum shifts to higher frequencies, the spectral ‘curvature’ increases, in contrast to what is expected if a single log-parabolic model were an acceptable representation of the broad-band SEDs. Our results suggest that the optical/UV and X-ray emissions in this source may arise from different lepton populations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    Allosteric activation of ADAMTS13 by VWF [Biochemistry] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-12-31
    Description: The metalloprotease ADAMTS13 cleaves von Willebrand factor (VWF) within endovascular platelet aggregates, and ADAMTS13 deficiency causes fatal microvascular thrombosis. The proximal metalloprotease (M), disintegrin-like (D), thrombospondin-1 (T), Cys-rich (C), and spacer (S) domains of ADAMTS13 recognize a cryptic site in VWF that is exposed by tensile force. Another seven T...
    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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  • 7
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    ZBTB42 mutation defines a novel lethal congenital contracture syndrome (LCCS6) (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-21
    Description: Lethal congenital contracture syndrome (LCCS) is a lethal autosomal recessive form of arthrogryposis multiplex congenita (AMC). LCCS is genetically heterogeneous with mutations in five genes identified to date, all with a role in the innervation or contractile apparatus of skeletal muscles. In a consanguineous Saudi family with multiple stillbirths presenting with LCCS, we excluded linkage to all known LCCS loci and combined autozygome analysis and whole-exome sequencing to identify a novel homozygous variant in ZBTB42 , which had been shown to be enriched in skeletal muscles, especially at the neuromuscular junction. Knockdown experiments of zbtb42 in zebrafish consistently resulted in grossly abnormal skeletal muscle development and myofibrillar disorganization at the microscopic level. This severe muscular phenotype is successfully rescued with overexpression of the human wild-type ZBTB42 gene, but not with the mutant form of ZBTB42 that models the human missense change. Our data assign a novel muscular developmental phenotype to ZBTB42 in vertebrates and establish a new LCCS6 type caused by ZBTB42 mutation.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 8
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    Slow repair of lipid peroxidation-induced DNA damage at p53 mutation hotspots in human cells caused by low turnover of a DNA glycosylase (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-15
    Description: Repair of oxidative stress- and inflammation-induced DNA lesions by the base excision repair (BER) pathway prevents mutation, a form of genomic instability which is often observed in cancer as ‘mutation hotspots’. This suggests that some sequences have inherent mutability, possibly due to sequence-related differences in repair. This study has explored intrinsic mutability as a consequence of sequence-specific repair of lipid peroxidation-induced DNA adduct, 1, N 6 -ethenoadenine (A). For the first time, we observed significant delay in repair of A at mutation hotspots in the tumor suppressor gene p53 compared to non-hotspots in live human hepatocytes and endothelial cells using an in-cell real time PCR-based method. In-cell and in vitro mechanism studies revealed that this delay in repair was due to inefficient turnover of N -methylpurine-DNA glycosylase (MPG), which initiates BER of A. We determined that the product dissociation rate of MPG at the hotspot codons was 5–12-fold lower than the non-hotspots, suggesting a previously unknown mechanism for slower repair at mutation hotspots and implicating sequence-related variability of DNA repair efficiency to be responsible for mutation hotspot signatures.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Cooperative gene regulation by microRNA pairs and their identification using a computational workflow (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-04
    Description: MicroRNAs (miRNAs) are an integral part of gene regulation at the post-transcriptional level. Recently, it has been shown that pairs of miRNAs can repress the translation of a target mRNA in a cooperative manner, which leads to an enhanced effectiveness and specificity in target repression. However, it remains unclear which miRNA pairs can synergize and which genes are target of cooperative miRNA regulation. In this paper, we present a computational workflow for the prediction and analysis of cooperating miRNAs and their mutual target genes, which we refer to as RNA triplexes. The workflow integrates methods of miRNA target prediction; triplex structure analysis; molecular dynamics simulations and mathematical modeling for a reliable prediction of functional RNA triplexes and target repression efficiency. In a case study we analyzed the human genome and identified several thousand targets of cooperative gene regulation. Our results suggest that miRNA cooperativity is a frequent mechanism for an enhanced target repression by pairs of miRNAs facilitating distinctive and fine-tuned target gene expression patterns. Human RNA triplexes predicted and characterized in this study are organized in a web resource at www.sbi.uni-rostock.de/triplexrna/ .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    The long noncoding RNA ROCKI regulates inflammatory gene expression (2019)
    Springer Nature
    Details
    Publication Date: 2019
    Description: 〈p〉Long noncoding RNAs (lncRNAs) can regulate target gene expression by acting in 〈i〉cis〈/i〉 (locally) or in 〈i〉trans〈/i〉 (non-locally). Here, we performed genome-wide expression analysis of Toll-like receptor (TLR)-stimulated human macrophages to identify pairs of 〈i〉cis〈/i〉-acting lncRNAs and protein-coding genes involved in innate immunity. A total of 229 gene pairs were identified, many of which were commonly regulated by signaling through multiple TLRs and were involved in the cytokine responses to infection by group B 〈i〉Streptococcus〈/i〉. We focused on elucidating the function of one lncRNA, named 〈i〉lnc-MARCKS〈/i〉 or 〈i〉ROCKI〈/i〉 (Regulator of Cytokines and Inflammation), which was induced by multiple TLR stimuli and acted as a master regulator of inflammatory responses. 〈i〉ROCKI〈/i〉 interacted with APEX1 (apurinic/apyrimidinic endodeoxyribonuclease 1) to form a ribonucleoprotein complex at the 〈i〉MARCKS〈/i〉 promoter. In turn, 〈i〉ROCKI〈/i〉–APEX1 recruited the histone deacetylase HDAC1, which removed the H3K27ac modification from the promoter, thus reducing 〈i〉MARCKS〈/i〉 transcription and subsequent Ca〈sup〉2+〈/sup〉 signaling and inflammatory gene expression. Finally, genetic variants affecting 〈i〉ROCKI〈/i〉 expression were linked to a reduced risk of certain inflammatory and infectious disease in humans, including inflammatory bowel disease and tuberculosis. Collectively, these data highlight the importance of 〈i〉cis〈/i〉-acting lncRNAs in TLR signaling, innate immunity, and pathophysiological inflammation.〈/p〉
    Print ISSN: 0261-4189
    Electronic ISSN: 1460-2075
    Topics: Biology , Medicine
    Published by Springer Nature on behalf of The European Molecular Biology Organization (EMBO).
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