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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Sukackaite, Rasa; Cornacchia, Daniela; Jensen, Malene Ringkjøbing; Mas, Philippe J.; +7 Authors

    AbstractRif1 is a conserved protein that plays essential roles in orchestrating DNA replication timing, controlling nuclear architecture, telomere length and DNA repair. However, the relationship between these different roles, as well as the molecular basis of Rif1 function is still unclear. The association of Rif1 with insoluble nuclear lamina has thus far hampered exhaustive characterization of the associated protein complexes. We devised a protocol that overcomes this problem, and were thus able to discover a number of novel Rif1 interactors, involved in chromatin metabolism and phosphorylation. Among them, we focus here on PP1. Data from different systems have suggested that Rif1-PP1 interaction is conserved and has important biological roles. Using mutagenesis, NMR, isothermal calorimetry and surface plasmon resonance we demonstrate that Rif1 is a high-affinity PP1 adaptor, able to out-compete the well-established PP1-inhibitor I2 in vitro. Our conclusions have important implications for understanding Rif1 diverse roles and the relationship between the biological processes controlled by Rif1.

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    Scientific Reports
    Article . 2017
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    Scientific Reports
    Article . 2017 . Peer-reviewed
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      Scientific Reports
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      Scientific Reports
      Article . 2017 . Peer-reviewed
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    Sustainability Working Group meeting report

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    Authors: Marquevielle, Julien; Robert, Coralie; Lagrabette, Olivier; Wahid, Mona; +4 Authors

    International audience; KRAS is one of the most mutated oncogenes and still considered an undruggable target. An alternative strategy would consist in targeting its gene rather than the protein, specifically the formation of G-quadruplexes (G4) in its promoter. G4 are secondary structures implicated in biological processes, which can be formed among G-rich DNA (or RNA) sequences. Here we have studied the major conforma-tions of the commonly known KRAS 32R, or simply 32R, a 32 residue sequence within the KRAS Nucle-ase Hypersensitive Element (NHE) region. We have determined the structure of the two major stable con-formers that 32R can adopt and which display slow equilibrium (>ms) with each other. By using different biophysical methods, we found that the nucleotides G9, G25, G28 and G32 are particularly implicated in the exchange between these two conformations. We also showed that a triad at the 3 end further stabilizes one of the G4 conformations, while the second conformer remains more flexible and less stable.

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    HAL-Inserm
    Other literature type . 2020
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    Authors: Pereira, Filipa;

    Submitted by sdum uminho (rcaap@sdum.uminho.pt) on 2020-07-03T17:04:49Z No. of bitstreams: 1 EOSC Synergy Landscape Analysis Portugal - Final.pdf: 1576516 bytes, checksum: bf3d92a85001af6cdae1a74459d49b9e (MD5) Made available in DSpace on 2020-07-03T17:04:49Z (GMT). No. of bitstreams: 1 EOSC Synergy Landscape Analysis Portugal - Final.pdf: 1576516 bytes, checksum: bf3d92a85001af6cdae1a74459d49b9e (MD5) Previous issue date: 2020-05-29 info:eu-repo/semantics/publishedVersion

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ LAReferencia - Red F...arrow_drop_down
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    Repositório Comum
    Report . 2020
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      Repositório Comum
      Report . 2020
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    Authors: Kateřina Peterková; Ivo Durník; Radek Marek; Janez Plavec; +1 Authors

    Abstract Several sequences forming G-quadruplex are highly conserved in regulatory regions of genomes of different organisms and affect various biological processes like gene expression. Diverse G-quadruplex properties can be modulated via their interaction with small polyaromatic molecules such as pyrene. To investigate how pyrene interacts with G-rich DNAs, we incorporated deoxyuridine nucleotide(s) with a covalently attached pyrene moiety (Upy) into a model system that forms parallel G-quadruplex structures. We individually substituted terminal positions and positions in the pentaloop of the c-kit2 sequence originating from the KIT proto-oncogene with Upy and performed a detailed NMR structural study accompanied with molecular dynamic simulations. Our results showed that incorporation into the pentaloop leads to structural polymorphism and in some cases also thermal destabilization. In contrast, terminal positions were found to cause a substantial thermodynamic stabilization while preserving topology of the parent c-kit2 G-quadruplex. Thermodynamic stabilization results from π–π stacking between the polyaromatic core of the pyrene moiety and guanine nucleotides of outer G-quartets. Thanks to the prevalent overall conformation, our structures mimic the G-quadruplex found in human KIT proto-oncogene and could potentially have antiproliferative effects on cancer cells. Graphical Abstract Graphical AbstractDifferent stacking modes of pyrene at 5′ and 3′-ends of the c-ki2 G-quadruplex.

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    Nucleic Acids Research
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      Nucleic Acids Research
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    Authors: Jacopo Sforzi; Giuseppe Ferrauto; Silvio Aime; Simonetta Geninatti Crich;

    The development of an innovative and easy way to run assays for the quantitative detection of DNA present in biological fluids (i.e., blood, urine, and saliva) is of great interest for early diagnosis (e.g., tumors) and personalized medicine. Herein, a new quantitative assay based on the use of highly sensitive carboxyfluorescein-loaded liposomes as signal amplification systems is reported. The method has been tested for the detection of low amounts of DNA sequences. The reported proof of concept exploits a target DNA molecule as a linker between two complementary oligonucleotides. One oligonucleotide is biotinylated at its 3′ end and binds to streptavidin-coupled magnetic beads, whereas the other one is conjugated to a cholesterol molecule incorporated in the phospholipidic bilayer of the fluorescent liposomes. In the presence of the target fragment, the correct formation of a construct takes place as witnessed by a strong fluorescence signal, amplified by dissolving lipidic nanoparticles with Triton X-100. The system is able to detect specific nucleotide sequences with a very low detection threshold of target DNA (tens of picomolar). The assay allows the detection of both single- and double-stranded DNA. Studies performed in human blood serum show the correct assembling of the probe but with a reduction of limit of detection (up to ∼1 nM). This liposome signal amplification strategy could be used not only for the detection of DNA but also for other nucleic acids (mRNA; microRNA) that are difficult to be quantified by currently available protocols.

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    ACS Omega
    Other literature type . Article . 2020 . Peer-reviewed
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    ACS Omega
    Article . 2019
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      ACS Omega
      Other literature type . Article . 2020 . Peer-reviewed
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      ACS Omega
      Article
      License: acs-specific: authorchoice/editors choice usage agreement
      Data sources: UnpayWall
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      ACS Omega
      Article . 2019
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    Authors: Stian Soiland-Reyes; Carole Goble; Raquel Villodres Toledo; Romina Royo; +1 Authors

    Presented at the FAIR-IMPACT kick-off meeting. Introduces the EOSC4Cancer projects and potential synergies with FAIR-IMPACT work.

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    Authors: Hermjakob, Henning; Kleemola, Mari; Moilanen, Katja; Sansone, Susanna-Assunta; +8 Authors

    BY-COVID Work Package 3 is focused on services for the discovery and integration of COVID-19 data by delivering a flexible, tiered metadata discovery system across different domains, metadata standards, and maturity/robustness levels of data sources. This will enable the linking of FAIR data and metadata on SARS-CoV-2 and COVID-19, on other related viruses and diseases, and on socio-economic consequences, across research fields, from omics, clinical, and epidemiological research, to social sciences and humanities. In a series of work package meetings and a workshop, with participation from all other work packages, we have surveyed community metadata standards used by (potential) BY-COVID-19 portal resources (4.1), defined a flexible, three-tiered approach to metadata indexing in the COVID-19 portal (section 4.2), derived common metadata attributes for record level discovery (4.3) and established a workflow with FAIRsharing for resource level metadata capture and exchange (4.4). This work establishes the basis for the further development of the COVID-19 Portal metadata discovery and provides a path for integration of metadata from multi-domain partners in BY-COVID, as well as our ISIDORe sibling project, and relevant external resources. To ensure smooth integration of partner-provided metadata, we will run a technical workshop open to all partners, discussing workflows, metadata attributes and formats, and support tools. Contributor: Morris Swertz (UMCG/BBMRI)

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    Authors: Atherton, Christopher John; Barton, Thomas; Basney, Jim; Broeder, Daan; +36 Authors

    The authors also acknowledge the support and collaboration of many other colleagues in their respective institutes, research communities and IT Infrastructures, together with the funding received by these from many different sources. These include but are not limited to the following: (i) The Worldwide LHC Computing Grid (WLCG) project is a global collaboration of more than 170 computing centres in 43 countries, linking up national and international grid infrastructures. Funding is acknowledged from many national funding bodies and we acknowledge the support of several operational infrastructures including EGI, OSG and NDGF/NeIC. (ii) EGI acknowledges the funding and support received from the European Commission and the many National Grid Initiatives and other members. EOSC-hub receives funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 777536. (iii) The work leading to these results has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. 730941 (AARC2). (iv) Work on the development of ESGF's identity management system has been supported by The UK Natural Environment Research Council and funding from the European Union's Seventh Framework Programme for research, technological development and demonstration through projects IS-ENES (grant agreement no 228203) and IS-ENES2 (grant agreement no 312979). (v) Ludek Matyska and Michal Prochazka acknowledge funding from the RI ELIXIR CZ project funded by MEYS Czech Republic No. LM2015047. (vi) Scott Koranda acknowledges support provided by the United States National Science Foundation under Grant No. PHY-1700765. (vii) GÉANT Association on behalf of the GN4 Phase 2 project (GN4-2).The research leading to these results has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. 731122(GN4-2). (viii) ELIXIR acknowledges support from Research Infrastructure programme of Horizon 2020 grant No 676559 EXCELERATE. (ix) CORBEL life science cluster acknowledges support from Horizon 2020 research and innovation programme under grant agreement No 654248. (x) Mirjam van Daalen acknowledges that the research leading to this result has been supported by the project CALIPSOplus under the Grant Agreement 730872 from the EU Framework Programme for Research and Innovation HORIZON 2020. (xi) EISCAT is an international association supported by research organisations in China (CRIRP), Finland (SA), Japan (NIPR), Norway (NFR), Sweden (VR), and the United Kingdom (NERC). This white-paper expresses common requirements of Research Communities seeking to leverage Identity Federation for Authentication and Authorisation. Recommendations are made to Stakeholders to guide the future evolution of Federated Identity Management in a direction that better satisfies research use cases. The authors represent research communities, Research Services, Infrastructures, Identity Federations and Interfederations, with a joint motivation to ease collaboration for distributed researchers. The content has been edited collaboratively by the Federated Identity Management for Research (FIM4R) Community, with input sought at conferences and meetings in Europe, Asia and North America.

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    https://doi.org/10.5445/ir/100...
    Other literature type . 2018
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    https://zenodo.org/record/1307...
    Article . 2018
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    KITopen
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      https://doi.org/10.5445/ir/100...
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      https://zenodo.org/record/1307...
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    Authors: Sumera, Perveen; Naeem, Rashid; Xiao-Feng, Tang; Tadayuki, Imanaka; +1 Authors

    Anthranilate phosphoribosyltransferase (TrpD) is involved in tryptophan biosynthesis, catalyzing the transfer of a phosphoribosyl group to anthranilate, leading to the generation of phosphoribosyl anthranilate. TrpD belongs to the phosphoribosyltransferase (PRT) superfamily and is the only member of the structural class IV. X‐ray structures of TrpD from seven species have been solved to date. Here, functional and structural characterization of a recombinant TrpD from hyperthermophilic archaeon Thermococcus kodakarensis KOD1 (TkTrpD) was carried out. Contrary to previously characterized Mg2+‐dependent TrpD enzymes, TkTrpD was found to have a unique divalent cation dependency characterized by maximum activity in the presence of Zn2+ (1580 μmol·min−1·mg−1, the highest reported for any TrpD) followed by Ca2+ (948 μmol·min−1·mg−1) and Mg2+ (711 μmol·min−1·mg−1). TkTrpD displayed an unusually low thermostability compared to other previously characterized proteins from T. kodakarensis KOD1. The crystal structure of TkTrpD was determined in free form and in the presence of Zn2+ to 1.9 and 2.4 Å resolutions, respectively. TkTrpD structure displayed the typical PRT fold similar to other class IV PRTs, with a small N‐terminal α‐helical domain and a larger C‐terminal α/β domain. Electron densities for Zn2+ were identified at the expected zinc‐binding motif, DE(217–218), of the enzyme in each subunit of the dimer. Two additional Zn2+ were found at a new dimer interface formed in the presence of Zn2+. A fifth Zn2+ was found bound to Glu118 at crystal lattice contacts and a sixth one was ligated with Glu235. Based on the TkTrpD–Zn2+ structure, it is suggested that the formation of a new dimer may be responsible for the higher enzyme activity of TkTrpD in the presence of Zn2+ ions.

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    Authors: Mohammad Mubinur Rahman; Martina Andberg; Anu Koivula; Juha Rouvinen; +1 Authors

    AbstractThe Ilv/ED dehydratase protein family includes dihydroxy acid-, gluconate-, 6-phosphogluconate- and pentonate dehydratases. The members of this family are involved in various biosynthetic and carbohydrate metabolic pathways. Here, we describe the first crystal structure of D-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) at 2.7 Å resolution and compare it with other available enzyme structures from the IlvD/EDD protein family. The quaternary structure of CcXyDHT is a tetramer, and each monomer is composed of two domains in which the N-terminal domain forms a binding site for a [2Fe-2S] cluster and a Mg2+ ion. The active site is located at the monomer-monomer interface and contains residues from both the N-terminal recognition helix and the C-terminus of the dimeric counterpart. The active site also contains a conserved Ser490, which probably acts as a base in catalysis. Importantly, the cysteines that participate in the binding and formation of the [2Fe-2S] cluster are not all conserved within the Ilv/ED dehydratase family, which suggests that some members of the IlvD/EDD family may bind different types of [Fe-S] clusters.

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    Scientific Reports
    Article . 2018 . Peer-reviewed
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    Authors: Swertz, Morris; Kelpin, Fleur; van Enckevort, David; Lappalainen, Ilkka; +6 Authors

    The mission of CORBEL is to facilitate joint operation of research infrastructures of Europe and to provide access to bioscientific resources in a standardised fashion. Task 3 in Work Package 6 addresses the secure data management and compute needs of service providers dealing with data that needs to be access controlled, for example human identifiable data such as genome sequences and related personal meta-data, and dealing with users acting in different roles. As first deliverable we here report on models and pilot designs for sustainable scalable cloud-based provision of data and compute across infrastructures, providing guidance to BMS infrastructure development. Therefore we have first surveyed use cases and needs of BMS infrastructures and their users. Subsequently we surveyed existing models for the provisioning of data access and compute. Finally, we have shortlisted a series of pilot designs to inform next steps in the joint development across BMS infrastructures and e-infrastructure providers, in particular within deliverable 6.5 of CORBEL but also in ongoing projects EXCELERATE, EGI-engage, BBMRI-ERIC ADOPT, etc. 

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    Optimisation of cytokine/chemokine multiplex platform analysis as innovative assays to evaluate innate immune responses in vitro directly using blood samples

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    Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled "An intrinsically disordered protein user community proposal for ELIXIR" held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders.

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    Authors: Paradžik, Tina; Ivić, Nives; Filić, Želimira; Manjasetty, Babbu A.; +3 Authors

    The linear chromosome of Streptomyces coelicolor contains two paralogous ssb genes, ssbA and ssbB. Following mutational analysis, we concluded that ssbA is essential, whereas ssbB plays a key role in chromosome segregation during sporulation. In the ssbB mutant, ~30% of spores lacked DNA. The two ssb genes were expressed differently ; in minimal medium, gene expression was prolonged for both genes and significantly upregulated for ssbB. The ssbA gene is transcribed as part of a polycistronic mRNA from two initiation sites, 163 bp and 75 bp upstream of the rpsF translational start codon. The ssbB gene is transcribed as a monocistronic mRNA, from an unusual promoter region, 73 bp upstream of the AUG codon. Distinctive DNA-binding affinities of single-stranded DNA-binding proteins monitored by tryptophan fluorescent quenching and electrophoretic mobility shift were observed. The crystal structure of SsbB at 1.7A° resolution revealed a common OB-fold, lack of the clamp-like structure conserved in SsbA and previously unpublished S-S bridges between the A/B and C/D subunits. This is the first report of the determination of paralogous singlestranded DNA-binding protein structures from the same organism. Phylogenetic analysis revealed frequent duplication of ssb genes in Actinobacteria, whereas their strong retention suggests that they are involved in important cellular functions.

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    Nucleic Acids Research
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      Nucleic Acids Research
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    Authors: Tim Schulte; Jonas Lofling; Cecilia Mikaelsson; Alexey Kikhney; +7 Authors

    Streptococcus pneumoniaeis a major human pathogen, and a leading cause of disease and death worldwide. Pneumococcal invasive disease is triggered by initial asymptomatic colonization of the human upper respiratory tract. The pneumococcal serine-rich repeat protein (PsrP) is a lung-specific virulence factor whose functional binding region (BR) binds to keratin-10 (KRT10) and promotes pneumococcal biofilm formation through self-oligomerization. We present the crystal structure of the KRT10-binding domain of PsrP (BR187–385) determined to 2.0 Å resolution. BR187–385adopts a novel variant of the DEv-IgG fold, typical for microbial surface components recognizing adhesive matrix molecules adhesins, despite very low sequence identity. An extended β-sheet on one side of the compressed, two-sided barrel presents a basic groove that possibly binds to the acidic helical rod domain of KRT10. Our study also demonstrates the importance of the other side of the barrel, formed by extensive well-ordered loops and stabilized by short β-strands, for interaction with KRT10.

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    Open Biology
    Other literature type . Article . 2014 . Peer-reviewed
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