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  • 1
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    Hepaticites iporangae Ricardi-Branco, Faria, Jasper, and Guerra-Sommer, 2011 from the early Permian of the Parana Basin, Brazil, is not a liverwort but a tracheophyte (2016)
    Paleontological Society
    Details
    Publication Date: 2016-09-22
    Description: From new and more complete material, which includes frond fragments with casts of tracheid remains of the rachis, it can be demonstrated that the putative liverwort Hepaticites iporangae Ricardi-Branco, Faria, Jasper, and Guerra-Sommer, 2011, from the early Permian Rio Bonito Formation (Sakmarian) of the Paraná Basin, Brazil, is not a bryophyte but a tracheophyte. The new material was collected from the same locality and layer as the type material, in the Quitéria outcrop in the municipality of Encruzilhada do Sul, state of Rio Grande do Sul, Brazil. From the morphology of the deeply dissected pinnatifid pinnules with narrow laminar lobes, the taxon is provisionally reassigned to the genus Rhodeopteridium . Thus we propose the new combination ‘ Rhodeopteridium ’ iporangae new combination for this taxon. This new systematic interpretation contributes to our understanding of early liverworts (by removing Hepaticites iporangae as a possible taxon thereof) and clarifies an issue of diversity of the flora of the early Permian Rio Bonito Formation resulting from the original misidentification.
    Print ISSN: 0022-3360
    Electronic ISSN: 1937-2337
    Topics: Geosciences
    Published by Paleontological Society
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  • 2
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    Evasive mimicry: too beetle, or not too beetle? (2019)
    Wiley
    In: Ecology
    Details
    Publication Date: 2019
    Description: Ecology, EarlyView.
    Print ISSN: 0012-9658
    Electronic ISSN: 1939-9170
    Topics: Biology
    Published by Wiley on behalf of The Ecological Society of America (ESA).
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  • 3
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    BCCTBbp: the Breast Cancer Campaign Tissue Bank bioinformatics portal (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-16
    Description: BCCTBbp ( http://bioinformatics.breastcancertissue bank.org ) was initially developed as the data-mining portal of the Breast Cancer Campaign Tissue Bank (BCCTB), a vital resource of breast cancer tissue for researchers to support and promote cutting-edge research. BCCTBbp is dedicated to maximising research on patient tissues by initially storing genomics, methylomics, transcriptomics, proteomics and microRNA data that has been mined from the literature and linking to pathways and mechanisms involved in breast cancer. Currently, the portal holds 146 datasets comprising over 227 795 expression/genomic measurements from various breast tissues (e.g. normal, malignant or benign lesions), cell lines and body fluids. BCCTBbp can be used to build on breast cancer knowledge and maximise the value of existing research. By recording a large number of annotations on samples and studies, and linking to other databases, such as NCBI, Ensembl and Reactome, a wide variety of different investigations can be carried out. Additionally, BCCTBbp has a dedicated analytical layer allowing researchers to further analyse stored datasets. A future important role for BCCTBbp is to make available all data generated on BCCTB tissues thus building a valuable resource of information on the tissues in BCCTB that will save repetition of experiments and expand scientific knowledge.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Materials, Vol. 11, Pages 1427: Design of a Scaffold Parameter Selection System with Additive Manufacturing for a Biomedical Cell Culture (2018)
    MDPI Publishing
    In: Materials
    Details
    Publication Date: 2018-08-15
    Description: Materials, Vol. 11, Pages 1427: Design of a Scaffold Parameter Selection System with Additive Manufacturing for a Biomedical Cell Culture Materials doi: 10.3390/ma11081427 Authors: Marc Rabionet Emma Polonio Antonio J. Guerra Jessica Martin Teresa Puig Joaquim Ciurana Open-source 3D printers mean objects can be quickly and efficiently produced. However, design and fabrication parameters need to be optimized to set up the correct printing procedure; a procedure in which the characteristics of the printing materials selected for use can also influence the process. This work focuses on optimizing the printing process of the open-source 3D extruder machine RepRap, which is used to manufacture poly(ε-caprolactone) (PCL) scaffolds for cell culture applications. PCL is a biocompatible polymer that is free of toxic dye and has been used to fabricate scaffolds, i.e., solid structures suitable for 3D cancer cell cultures. Scaffold cell culture has been described as enhancing cancer stem cell (CSC) populations related to tumor chemoresistance and/or their recurrence after chemotherapy. A RepRap BCN3D+ printer and 3 mm PCL wire were used to fabricate circular scaffolds. Design and fabrication parameters were first determined with SolidWorks and Slic3r software and subsequently optimized following a novel sequential flowchart. In the flowchart described here, the parameters were gradually optimized step by step, by taking several measurable variables of the resulting scaffolds into consideration to guarantee high-quality printing. Three deposition angles (45°, 60° and 90°) were fabricated and tested. MCF-7 breast carcinoma cells and NIH/3T3 murine fibroblasts were used to assess scaffold adequacy for 3D cell cultures. The 60° scaffolds were found to be suitable for the purpose. Therefore, PCL scaffolds fabricated via the flowchart optimization with a RepRap 3D printer could be used for 3D cell cultures and may boost CSCs to study new therapeutic treatments for this malignant population. Moreover, the flowchart defined here could represent a standard procedure for non-engineers (i.e., mainly physicians) when manufacturing new culture systems is required.
    Electronic ISSN: 1996-1944
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by MDPI Publishing
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  • 5
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    TRIM5 is an innate immune sensor for the retrovirus capsid lattice (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-04-23
    Description: TRIM5 is a RING domain-E3 ubiquitin ligase that restricts infection by human immunodeficiency virus (HIV)-1 and other retroviruses immediately following virus invasion of the target cell cytoplasm. Antiviral potency correlates with TRIM5 avidity for the retrovirion capsid lattice and several reports indicate that TRIM5 has a role in signal transduction, but the precise mechanism of restriction is unknown. Here we demonstrate that TRIM5 promotes innate immune signalling and that this activity is amplified by retroviral infection and interaction with the capsid lattice. Acting with the heterodimeric, ubiquitin-conjugating enzyme UBC13-UEV1A (also known as UBE2N-UBE2V1), TRIM5 catalyses the synthesis of unattached K63-linked ubiquitin chains that activate the TAK1 (also known as MAP3K7) kinase complex and stimulate AP-1 and NFkappaB signalling. Interaction with the HIV-1 capsid lattice greatly enhances the UBC13-UEV1A-dependent E3 activity of TRIM5 and challenge with retroviruses induces the transcription of AP-1 and NF-kappaB-dependent factors with a magnitude that tracks with TRIM5 avidity for the invading capsid. Finally, TAK1 and UBC13-UEV1A contribute to capsid-specific restriction by TRIM5. Thus, the retroviral restriction factor TRIM5 has two additional activities that are linked to restriction: it constitutively promotes innate immune signalling and it acts as a pattern recognition receptor specific for the retrovirus capsid lattice.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3081621/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3081621/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pertel, Thomas -- Hausmann, Stephane -- Morger, Damien -- Zuger, Sara -- Guerra, Jessica -- Lascano, Josefina -- Reinhard, Christian -- Santoni, Federico A -- Uchil, Pradeep D -- Chatel, Laurence -- Bisiaux, Aurelie -- Albert, Matthew L -- Strambio-De-Castillia, Caterina -- Mothes, Walther -- Pizzato, Massimo -- Grutter, Markus G -- Luban, Jeremy -- R01 AI059159/AI/NIAID NIH HHS/ -- R01 AI059159-06/AI/NIAID NIH HHS/ -- R01AI59159/AI/NIAID NIH HHS/ -- R21 AI087467/AI/NIAID NIH HHS/ -- R21AI087467/AI/NIAID NIH HHS/ -- England -- Nature. 2011 Apr 21;472(7343):361-5. doi: 10.1038/nature09976.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Molecular Medicine, University of Geneva, Geneva CH-1211, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21512573" target="_blank"〉PubMed〈/a〉
    Keywords: Capsid/*chemistry/*immunology ; Carrier Proteins/genetics/*immunology/*metabolism ; Cell Line ; Enzyme Activation ; HEK293 Cells ; HIV-1/chemistry/immunology ; Humans ; Immunity, Innate/*immunology ; Lipopolysaccharides/immunology/pharmacology ; MAP Kinase Kinase Kinases/metabolism ; NF-kappa B/metabolism ; Protein Binding ; Receptors, Pattern Recognition/immunology/metabolism ; Retroviridae/chemistry/*immunology ; Signal Transduction/drug effects/immunology ; Transcription Factor AP-1/metabolism ; Transcription Factors/metabolism ; Ubiquitin/metabolism ; Ubiquitin-Conjugating Enzymes/metabolism ; Ubiquitin-Protein Ligases/genetics/immunology/metabolism
    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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  • 6
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    Genes, Vol. 8, Pages 349: The Potential of Zebrafish as a Model Organism for Improving the Translation of Genetic Anticancer Nanomedicines (2017)
    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Details
    Publication Date: 2017-11-29
    Description: Genes, Vol. 8, Pages 349: The Potential of Zebrafish as a Model Organism for Improving the Translation of Genetic Anticancer Nanomedicines Genes doi: 10.3390/genes8120349 Authors: C. Gutiérrez-Lovera A.J. Vázquez-Ríos J. Guerra-Varela L. Sánchez M. de la Fuente In the last few decades, the field of nanomedicine applied to cancer has revolutionized cancer treatment: several nanoformulations have already reached the market and are routinely being used in the clinical practice. In the case of genetic nanomedicines, i.e., designed to deliver gene therapies to cancer cells for therapeutic purposes, advances have been less impressive. This is because of the many barriers that limit the access of the therapeutic nucleic acids to their target site, and the lack of models that would allow for an improvement in the understanding of how nanocarriers can be tailored to overcome them. Zebrafish has important advantages as a model species for the study of anticancer therapies, and have a lot to offer regarding the rational development of efficient delivery of genetic nanomedicines, and hence increasing the chances of their successful translation. This review aims to provide an overview of the recent advances in the development of genetic anticancer nanomedicines, and of the zebrafish models that stand as promising tools to shed light on their mechanisms of action and overall potential in oncology.
    Electronic ISSN: 2073-4425
    Topics: Biology
    Published by Molecular Diversity Preservation International (MDPI)
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  • 7
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    Energetics of Zinc-Mediated Interactions in the Allosteric Pathways of Metal Sensor Proteins (2012)
    American Chemical Society (ACS)
    Details
    Publication Date: 2012-12-27
    Description: Journal of the American Chemical Society DOI: 10.1021/ja309170g
    Print ISSN: 0002-7863
    Electronic ISSN: 1520-5126
    Topics: Chemistry and Pharmacology
    Published by American Chemical Society (ACS)
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  • 8
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    Ca2+ and PI(4,5)P2 binding modes of C2 domains [Biochemistry] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-12-18
    Description: Proteins containing C2 domains are the sensors for Ca2+ and PI(4,5)P2 in a myriad of secretory pathways. Here, the use of a free-mounting system has enabled us to capture an intermediate state of Ca2+ binding to the C2A domain of rabphilin 3A that suggests a different mechanism of ion interaction....
    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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  • 9
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    Extending Deep Meta-Modelling for Practical Model-Driven Engineering (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-27
    Description: Meta-modelling is one of the pillars of model-driven engineering (MDE), where it is used for language engineering and domain modelling. Even though the current trend is the use of two-level meta-modelling frameworks, several researchers have pointed out limitations of this scheme for some scenarios and suggested a meta-modelling approach with an arbitrary number of meta-levels in order to obtain more flexible and simpler system descriptions. Unfortunately, such multi-level meta-modelling systems are still in their infancy, lacking, for example, integration with model manipulation languages, a characterization of different possibilities for instantiation and inheritance and primitives for interconnecting multi-level languages in a flexible way. In the paper, we propose a number of extensions to multi-level (also called deep ) meta-modelling, on the basis of the needs raised by its use for practical MDE. In particular, we discuss on the issues related to code generation from deep languages, the benefits of allowing inheritance at every meta-level and patterns and techniques for a fine-grain control of the meta-level of elements. Finally, we provide primitives to control the impedance mismatch when connecting models at different meta-levels.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 10
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    Materials, Vol. 11, Pages 1679: 3D-Printed PCL/PLA Composite Stents: Towards a New Solution to Cardiovascular Problems (2018)
    MDPI Publishing
    In: Materials
    Details
    Publication Date: 2018-09-12
    Description: Materials, Vol. 11, Pages 1679: 3D-Printed PCL/PLA Composite Stents: Towards a New Solution to Cardiovascular Problems Materials doi: 10.3390/ma11091679 Authors: Antonio J. Guerra Paula Cano Marc Rabionet Teresa Puig Joaquim Ciurana Biodegradable stents (BRS) offer enormous potential but first they must meet five specific requirements: (i) their manufacturing process must be precise; (ii) degradation should have minimal toxicity; (iii) the rate of degradation should match the recovery rate of vascular tissue; (iv) ideally, they should induce rapid endothelialization to restore the functions of vascular tissue, but at the same time reduce the risk of restenosis; and (v) their mechanical behavior should comply with medical requirements, namely, the flexibility required to facilitate placement but also sufficient radial rigidity to support the vessel. Although the first three requirements have been comprehensively studied, the last two have been overlooked. One possible way of addressing these issues would be to fabricate composite stents using materials that have different mechanical, biological, or medical properties, for instance, Polylactide Acid (PLA) or Polycaprolactone (PCL). However, fashioning such stents using the traditional stent manufacturing process known as laser cutting would be impossible. Our work, therefore, aims to produce PCL/PLA composite stents using a novel 3D tubular printer based on Fused Deposition Modelling (FDM). The cell geometry (shape and area) and the materials (PCL and PLA) of the stents were analyzed and correlated with 3T3 cell proliferation, degradation rates, dynamic mechanical and radial expansion tests to determine the best parameters for a stent that will satisfy the five strict BRS requirements. Results proved that the 3D-printing process was highly suitable for producing composite stents (approximately 85–95% accuracy). Both PCL and PLA demonstrated their biocompatibility with PCL stents presenting an average cell proliferation of 12.46% and PLA 8.28% after only 3 days. Furthermore, the PCL/PLA composite stents demonstrated their potential in degradation, dynamic mechanical and expansion tests. Moreover, and regardless of the order of the layers, the composite stents showed (virtually) medium levels of degradation rates and mechanical modulus. Radially, they exhibited the virtues of PCL in the expansion step (elasticity) and those of PLA in the recoil step (rigidity). Results have clearly demonstrated that composite PCL/PLA stents are a highly promising solution to fulfilling the rigorous BRS requirements.
    Electronic ISSN: 1996-1944
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by MDPI Publishing
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