1
|
Bello-Madruga R, Valle J, Jiménez MÁ, Torrent M, Montero-Alejo V, Andreu D. The C-Terminus of Panusin, a Lobster β-Defensin, Is Crucial for Optimal Antimicrobial Activity and Serum Stability. Pharmaceutics 2023; 15:1777. [PMID: 37376223 DOI: 10.3390/pharmaceutics15061777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
β-defensins are one of the most abundant and studied families of antimicrobial peptides (AMPs). Because of their selective toxicity to bacterial membranes and a broad spectrum of microbicidal action, β-defensins are regarded as potential therapeutic agents. This work focuses on a β-defensin-like AMP from the spiny lobster Panulirus argus (hereafter referred to as panusin or PaD). This AMP is structurally related to mammalian defensins via the presence of an αβ domain stabilized by disulfide bonds. Previous studies of PaD suggest that its C-terminus (Ct_PaD) contains the main structural determinants of antibacterial activity. To confirm this hypothesis, we made synthetic versions of PaD and Ct_PaD to determine the influence of the C-terminus on antimicrobial activity, cytotoxicity, proteolytic stability, and 3D structure. After successful solid-phase synthesis and folding, antibacterial assays of both peptides showed truncated Ct_PaD to be more active than native PaD, confirming the role of the C-terminus in activity and suggesting that cationic residues in that region enhance binding to negatively charged membranes. On the other hand, neither PaD nor Ct_PaD were hemolytic or cytotoxic in human cells. Proteolysis in human serum was also studied, showing high (>24 h) t1/2 values for PaD and lower but still considerable for Ct_PaD, indicating that the missing native disulfide bond in Ct_PaD alters protease resistance, albeit not decisively. NMR-2D experiments in water agree with the results obtained by circular dichroism (CD), where in SDS micelles, CD showed both peptides adopting an increasingly ordered structure in a hydrophobic environment, in tune with their ability to perturb bacterial membrane systems. In conclusion, while the β-defensin features of PaD are confirmed as advantageous in terms of antimicrobial activity, toxicity, and protease stability, the results of the present work suggest that these same features are preserved, even enhanced, in the structurally simpler Ct_PaD, which must therefore be viewed as a valuable lead for the development of novel anti-infectives.
Collapse
Affiliation(s)
- Roberto Bello-Madruga
- Barcelona Biomedical Research Park, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- Department of Biochemistry and Molecular Biology, Center for Pharmaceutical Research and Development, (CIDEM), La Habana 10400, Cuba
| | - Javier Valle
- Barcelona Biomedical Research Park, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - M Ángeles Jiménez
- Instituto de Química Física Blas Cabrera-CSIC, Serrano 119, 28006 Madrid, Spain
| | - Marc Torrent
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Vivian Montero-Alejo
- Department of Biochemistry and Molecular Biology, Center for Pharmaceutical Research and Development, (CIDEM), La Habana 10400, Cuba
| | - David Andreu
- Barcelona Biomedical Research Park, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| |
Collapse
|
2
|
Sandín D, Valle J, Morata J, Andreu D, Torrent M. Antimicrobial Peptides Can Generate Tolerance by Lag and Interfere with Antimicrobial Therapy. Pharmaceutics 2022; 14:pharmaceutics14102169. [PMID: 36297604 PMCID: PMC9611985 DOI: 10.3390/pharmaceutics14102169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial peptides (AMPs) are widely distributed molecules secreted mostly by cells of the innate immune system to prevent bacterial proliferation at the site of infection. As with classic antibiotics, continued treatment with AMPs can create resistance in bacteria. However, whether AMPs can generate tolerance as an intermediate stage towards resistance is not known. Here, we show that the treatment of Escherichia coli with different AMPs induces tolerance by lag, particularly for those peptides that have internal targets. This tolerance can be detected as different morphological and physiological changes, which depend on the type of peptide molecule the bacterium has been exposed to. In addition, we show that AMP tolerance can also affect antibiotic treatment. The genomic sequencing of AMP-tolerant strains shows that different mutations alter membrane composition, DNA replication, and translation. Some of these mutations have also been observed in antibiotic-resistant strains, suggesting that AMP tolerance could be a relevant step in the development of antibiotic resistance. Monitoring AMP tolerance is relevant vis-á-vis the eventual therapeutic use of AMPs and because cross-tolerance might favor the emergence of resistance against conventional antibiotic treatments.
Collapse
Affiliation(s)
- Daniel Sandín
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Cerdanyola del Vallés 08193, Spain
| | - Javier Valle
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona 08003, Spain
| | - Jordi Morata
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain
| | - David Andreu
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona 08003, Spain
- Correspondence: (D.A.); (M.T.)
| | - Marc Torrent
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Cerdanyola del Vallés 08193, Spain
- Correspondence: (D.A.); (M.T.)
| |
Collapse
|
3
|
Carrera-Aubesart A, Defaus S, Pérez-Peinado C, Sandín D, Torrent M, Jiménez MÁ, Andreu D. Examining Topoisomers of a Snake-Venom-Derived Peptide for Improved Antimicrobial and Antitumoral Properties. Biomedicines 2022; 10:biomedicines10092110. [PMID: 36140211 PMCID: PMC9495681 DOI: 10.3390/biomedicines10092110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/30/2022] Open
Abstract
Ctn[15-34], the C-terminal section of crotalicidin (Ctn), a cathelicidin from a South American pit viper, is an antimicrobial and antitumoral peptide with remarkably longer stability in human serum than the parent Ctn. In this work, a set of topoisomers of both Ctn and Ctn[15-34], including the retro, enantio, and retroenantio versions, were synthesized and tested to investigate the structural requirements for activity. All topoisomers were as active as the cognate sequences against Gram-negative bacteria and tumor cells while slightly more toxic towards normal cells. More importantly, the enhanced serum stability of the D-amino-acid-containing versions suggests that such topoisomers must be preferentially considered as future antimicrobial and anticancer peptide leads.
Collapse
Affiliation(s)
- Adam Carrera-Aubesart
- Proteomics and Protein Chemistry Unit, Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain
| | - Sira Defaus
- Proteomics and Protein Chemistry Unit, Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain
- Correspondence: (S.D.); (D.A.)
| | - Clara Pérez-Peinado
- Proteomics and Protein Chemistry Unit, Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain
| | - Daniel Sandín
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marc Torrent
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Maria Ángeles Jiménez
- Institute of Physical Chemistry “Rocasolano” (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - David Andreu
- Proteomics and Protein Chemistry Unit, Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain
- Correspondence: (S.D.); (D.A.)
| |
Collapse
|
4
|
Abengózar MÁ, Fernández-Reyes M, Salazar VA, Torrent M, de la Torre BG, Andreu D, Boix E, Rivas L. Essential Role of Enzymatic Activity in the Leishmanicidal Mechanism of the Eosinophil Cationic Protein (RNase 3). ACS Infect Dis 2022; 8:1207-1217. [PMID: 35731709 PMCID: PMC9274760 DOI: 10.1021/acsinfecdis.1c00537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The recruitment of
eosinophils into Leishmania lesions is frequently
associated with a favorable evolution. A feasible
effector for this process is eosinophil cationic protein (ECP, RNase
3), one of the main human eosinophil granule proteins, endowed with
a broad spectrum of antimicrobial activity, including parasites. ECP
was active on Leishmania promastigotes and axenic
amastigotes (LC50’s = 3 and 16 μM, respectively)
but, in contrast to the irreversible membrane damage caused on bacteria
and reproduced by its N-terminal peptides, it only
induced a mild and transient plasma membrane destabilization on Leishmania donovani promastigotes. To assess the
contribution of RNase activity to the overall leishmanicidal activity
of ECP, parasites were challenged in parallel with a single-mutant
version, ECP-H15A, devoid of RNase activity, that fully preserves
the conformation and liposome permeabilization ability. ECP-H15A showed
a similar uptake to ECP on promastigotes, but with higher LC50’s (>25 μM) for both parasite stages. ECP-treated
promastigotes
showed a degraded RNA pattern, absent in ECP-H15A-treated samples.
Moreover ECP, but not ECP-H15A, reduced more than 2-fold the parasite
burden of infected macrophages. Altogether, our results suggest that
ECP enters the Leishmania cytoplasm by an endocytic
pathway, ultimately leading to RNA degradation as a key contribution
to the leishmanicidal mechanism. Thus, ECP combines both membrane
destabilization and enzymatic activities to effect parasite killing.
Taken together, our data highlight the microbicidal versatility of
ECP as an innate immunity component and support the development of
cell-penetrating RNases as putative leishmanicidal agents.
Collapse
Affiliation(s)
- María Ángeles Abengózar
- Department of Structural and Chemical Biology, Consejo Superior de Investigaciones Científicas (CSIC), Centro de Investigaciones Biológicas Margarita Salas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - María Fernández-Reyes
- Department of Structural and Chemical Biology, Consejo Superior de Investigaciones Científicas (CSIC), Centro de Investigaciones Biológicas Margarita Salas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Vivian A Salazar
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Department of Biomedical Engineering, Universidad de los Andes, Cra. 1E No. 19a-40, Bogota, Colorado 111711, Colombia
| | - Marc Torrent
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Beatriz G de la Torre
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - David Andreu
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Luis Rivas
- Department of Structural and Chemical Biology, Consejo Superior de Investigaciones Científicas (CSIC), Centro de Investigaciones Biológicas Margarita Salas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| |
Collapse
|
5
|
Charraud JB, Geneste G, Torrent M, Maillet JB. Machine learning accelerated random structure searching: Application to yttrium superhydrides. J Chem Phys 2022; 156:204102. [DOI: 10.1063/5.0085173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The search for new superhydrides, promising materials for both hydrogen storage and high temperature superconductivity, made great progress, thanks to atomistic simulations and Crystal Structure Prediction (CSP) algorithms. When they are combined with Density Functional Theory (DFT), these methods are highly reliable and often match a great part of the experimental results. However, systems of increasing complexity (number of atoms and chemical species) become rapidly challenging as the number of minima to explore grows exponentially with the number of degrees of freedom in the simulation cell. An efficient sampling strategy preserving a sustainable computational cost then remains to be found. We propose such a strategy based on an active-learning process where machine learning potentials and DFT simulations are jointly used, opening the way to the discovery of complex structures. As a proof of concept, this method is applied to the exploration of tin crystal structures under various pressures. We showed that the α phase, not included in the learning process, is correctly retrieved, despite its singular nature of bonding. Moreover, all the expected phases are correctly predicted under pressure (20 and 100 GPa), suggesting the high transferability of our approach. The method has then been applied to the search of yttrium superhydrides (YH x) crystal structures under pressure. The YH6 structure of space group Im-3m is successfully retrieved. However, the exploration of more complex systems leads to the appearance of a large number of structures. The selection of the relevant ones to be included in the active learning process is performed through the analysis of atomic environments and the clustering algorithm. Finally, a metric involving a distance based on x-ray spectra is introduced, which guides the structural search toward experimentally relevant structures. The global process (active-learning and new selection methods) is finally considered to explore more complex and unknown YH x phases, unreachable by former CSP algorithms. New complex phases are found, demonstrating the ability of our approach to push back the exponential wall of complexity related to CSP.
Collapse
Affiliation(s)
| | - G. Geneste
- CEA-DAM, DIF, F-91297 Arpajon Cedex, France
- Université Paris-Saclay, CEA, LMCE, 91680, Bruyères-le-Châtel, France
| | - M. Torrent
- CEA-DAM, DIF, F-91297 Arpajon Cedex, France
- Université Paris-Saclay, CEA, LMCE, 91680, Bruyères-le-Châtel, France
| | - J.-B. Maillet
- CEA-DAM, DIF, F-91297 Arpajon Cedex, France
- Université Paris-Saclay, CEA, LMCE, 91680, Bruyères-le-Châtel, France
| |
Collapse
|
6
|
Sandín D, Valle J, Chaves-Arquero B, Prats-Ejarque G, Larrosa MN, González-López JJ, Jiménez MÁ, Boix E, Andreu D, Torrent M. Rationally Modified Antimicrobial Peptides from the N-Terminal Domain of Human RNase 3 Show Exceptional Serum Stability. J Med Chem 2021; 64:11472-11482. [PMID: 34342438 PMCID: PMC8483441 DOI: 10.1021/acs.jmedchem.1c00795] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Multidrug
resistance against conventional antibiotics poses an
important threat to human health. In this context, antimicrobial peptides
(AMPs) have been extensively studied for their antibacterial activity
and promising results have been shown so far. However, AMPs tend to
be rather vulnerable to protease degradation, which offsets their
therapeutic appeal. Here, we demonstrate how replacing functional
residues in the antimicrobial region of human RNase 3—also
named eosinophil cationic protein—by non-natural amino acids
increases stability in human serum. These changes were also shown
to reduce the hemolytic effect of the peptides in general terms, whereas
the antimicrobial activity was reasonably preserved. Digestion profiles enabled us to design new peptides
with superior stability and lower toxicity that could become relevant
candidates to reach clinical stages.
Collapse
Affiliation(s)
- Daniel Sandín
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Javier Valle
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona 08003, Spain
| | - Belén Chaves-Arquero
- Departamento de Química-Física Biológica, Instituto de Química Física Rocasolano (IQFR-CSIC), Serrano 119, Madrid 28006, Spain
| | - Guillem Prats-Ejarque
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - María Nieves Larrosa
- Servei de Microbiologia, Hospital Universitari Vall d'Hebron, Barcelona 08035, Spain.,Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Juan José González-López
- Servei de Microbiologia, Hospital Universitari Vall d'Hebron, Barcelona 08035, Spain.,Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - María Ángeles Jiménez
- Departamento de Química-Física Biológica, Instituto de Química Física Rocasolano (IQFR-CSIC), Serrano 119, Madrid 28006, Spain
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - David Andreu
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona 08003, Spain
| | - Marc Torrent
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| |
Collapse
|
7
|
Lu L, Wei R, Prats-Ejarque G, Goetz M, Wang G, Torrent M, Boix E. Human RNase3 immune modulation by catalytic-dependent and independent modes in a macrophage-cell line infection model. Cell Mol Life Sci 2021; 78:2963-2985. [PMID: 33226440 PMCID: PMC8004517 DOI: 10.1007/s00018-020-03695-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 09/21/2020] [Accepted: 10/31/2020] [Indexed: 02/06/2023]
Abstract
The human RNase3 is a member of the RNaseA superfamily involved in host immunity. RNase3 is expressed by leukocytes and shows broad-spectrum antimicrobial activity. Together with a direct antimicrobial action, RNase3 exhibits immunomodulatory properties. Here, we have analysed the transcriptome of macrophages exposed to the wild-type protein and a catalytic-defective mutant (RNase3-H15A). The analysis of differently expressed genes (DEGs) in treated THP1-derived macrophages highlighted a common pro-inflammatory "core-response" independent of the protein ribonucleolytic activity. Network analysis identified the epidermal growth factor receptor (EGFR) as the main central regulatory protein. Expression of selected DEGs and MAPK phosphorylation were inhibited by an anti-EGFR antibody. Structural analysis suggested that RNase3 activates the EGFR pathway by direct interaction with the receptor. Besides, we identified a subset of DEGs related to the protein ribonucleolytic activity, characteristic of virus infection response. Transcriptome analysis revealed an early pro-inflammatory response, not associated to the protein catalytic activity, followed by a late activation in a ribonucleolytic-dependent manner. Next, we demonstrated that overexpression of macrophage endogenous RNase3 protects the cells against infection by Mycobacterium aurum and the human respiratory syncytial virus. Comparison of cell infection profiles in the presence of Erlotinib, an EGFR inhibitor, revealed that the receptor activation is required for the antibacterial but not for the antiviral protein action. Moreover, the DEGs related and unrelated to the protein catalytic activity are associated to the immune response to bacterial and viral infection, respectively. We conclude that RNase3 modulates the macrophage defence against infection in both catalytic-dependent and independent manners.
Collapse
Affiliation(s)
- Lu Lu
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autonoma de Barcelona, Cerdanyola del Vallès, Spain
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - RanLei Wei
- Center of Precision Medicine and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, China
| | - Guillem Prats-Ejarque
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autonoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Maria Goetz
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autonoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Gang Wang
- Center of Precision Medicine and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, China
| | - Marc Torrent
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autonoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autonoma de Barcelona, Cerdanyola del Vallès, Spain.
| |
Collapse
|
8
|
Oliveira MJT, Papior N, Pouillon Y, Blum V, Artacho E, Caliste D, Corsetti F, de Gironcoli S, Elena AM, García A, García-Suárez VM, Genovese L, Huhn WP, Huhs G, Kokott S, Küçükbenli E, Larsen AH, Lazzaro A, Lebedeva IV, Li Y, López-Durán D, López-Tarifa P, Lüders M, Marques MAL, Minar J, Mohr S, Mostofi AA, O'Cais A, Payne MC, Ruh T, Smith DGA, Soler JM, Strubbe DA, Tancogne-Dejean N, Tildesley D, Torrent M, Yu VWZ. The CECAM electronic structure library and the modular software development paradigm. J Chem Phys 2020; 153:024117. [PMID: 32668924 DOI: 10.1063/5.0012901] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
First-principles electronic structure calculations are now accessible to a very large community of users across many disciplines, thanks to many successful software packages, some of which are described in this special issue. The traditional coding paradigm for such packages is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, essentially from the compiler up, possibly with the exception of linear-algebra and message-passing libraries. This model has endured and been quite successful for decades. The successful evolution of the electronic structure methodology itself, however, has resulted in an increasing complexity and an ever longer list of features expected within all software packages, which implies a growing amount of replication between different packages, not only in the initial coding but, more importantly, every time a code needs to be re-engineered to adapt to the evolution of computer hardware architecture. The Electronic Structure Library (ESL) was initiated by CECAM (the European Centre for Atomic and Molecular Calculations) to catalyze a paradigm shift away from the monolithic model and promote modularization, with the ambition to extract common tasks from electronic structure codes and redesign them as open-source libraries available to everybody. Such libraries include "heavy-duty" ones that have the potential for a high degree of parallelization and adaptation to novel hardware within them, thereby separating the sophisticated computer science aspects of performance optimization and re-engineering from the computational science done by, e.g., physicists and chemists when implementing new ideas. We envisage that this modular paradigm will improve overall coding efficiency and enable specialists (whether they be computer scientists or computational scientists) to use their skills more effectively and will lead to a more dynamic evolution of software in the community as well as lower barriers to entry for new developers. The model comes with new challenges, though. The building and compilation of a code based on many interdependent libraries (and their versions) is a much more complex task than that of a code delivered in a single self-contained package. Here, we describe the state of the ESL, the different libraries it now contains, the short- and mid-term plans for further libraries, and the way the new challenges are faced. The ESL is a community initiative into which several pre-existing codes and their developers have contributed with their software and efforts, from which several codes are already benefiting, and which remains open to the community.
Collapse
Affiliation(s)
- Micael J T Oliveira
- Max Planck Institute for the Structure and Dynamics of Matter, D-22761 Hamburg, Germany
| | - Nick Papior
- DTU Computing Center, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Yann Pouillon
- Departamento CITIMAC, Universidad de Cantabria, Santander, Spain
| | - Volker Blum
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | | | - Damien Caliste
- Department of Physics, IRIG, Univ. Grenoble Alpes and CEA, F-38000 Grenoble, France
| | - Fabiano Corsetti
- Departments of Materials and Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Alin M Elena
- Scientific Computing Department, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom
| | - Alberto García
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Bellaterra E-08193, Spain
| | | | - Luigi Genovese
- Department of Physics, IRIG, Univ. Grenoble Alpes and CEA, F-38000 Grenoble, France
| | - William P Huhn
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - Georg Huhs
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | | | - Emine Küçükbenli
- Scuola Internazionale Superiore di Studi Avanzati, 34136 Trieste, Italy
| | | | - Alfio Lazzaro
- Department of Chemistry, University of Zürich, CH-8057 Zürich, Switzerland
| | | | - Yingzhou Li
- Department of Mathematics, Duke University, Durham, North Carolina 27708-0320, USA
| | | | - Pablo López-Tarifa
- Centro de Física de Materiales, Centro Mixto CSIC-UPV/EHU, 20018 San Sebastián, Spain
| | - Martin Lüders
- Max Planck Institute for the Structure and Dynamics of Matter, D-22761 Hamburg, Germany
| | - Miguel A L Marques
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Jan Minar
- New Technologies Research Centre, University of West Bohemia, 301 00 Plzen, Czech Republic
| | - Stephan Mohr
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Arash A Mostofi
- Departments of Materials and Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Alan O'Cais
- Institute for Advanced Simulation (IAS), Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Mike C Payne
- Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Thomas Ruh
- Institute of Materials Chemistry, TU Wien, 1060 Vienna, Austria
| | - Daniel G A Smith
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - José M Soler
- Departamento e Instituto de Física de la Materia Condensada (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - David A Strubbe
- Department of Physics, University of California, Merced, California 95343, USA
| | | | - Dominic Tildesley
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | | | - Victor Wen-Zhe Yu
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| |
Collapse
|
9
|
Romero AH, Allan DC, Amadon B, Antonius G, Applencourt T, Baguet L, Bieder J, Bottin F, Bouchet J, Bousquet E, Bruneval F, Brunin G, Caliste D, Côté M, Denier J, Dreyer C, Ghosez P, Giantomassi M, Gillet Y, Gingras O, Hamann DR, Hautier G, Jollet F, Jomard G, Martin A, Miranda HPC, Naccarato F, Petretto G, Pike NA, Planes V, Prokhorenko S, Rangel T, Ricci F, Rignanese GM, Royo M, Stengel M, Torrent M, van Setten MJ, Van Troeye B, Verstraete MJ, Wiktor J, Zwanziger JW, Gonze X. ABINIT: Overview and focus on selected capabilities. J Chem Phys 2020; 152:124102. [DOI: 10.1063/1.5144261] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Aldo H. Romero
- Physics and Astronomy Department, West Virginia University, Morgantown, West Virginia 26506-6315, USA
| | - Douglas C. Allan
- Corning Incorporated, SP-FR-05, Sullivan Park, Corning, New York 14831, USA
| | | | - Gabriel Antonius
- Dépt. de Chimie, Biochimie et Physique, Institut de recherche sur l’hydrogène, U. du Québec à Trois-Rivières, C.P. 500, Trois-Rivières (Quebec) G9A 5H7, Canada
| | | | - Lucas Baguet
- CEA DAM-DIF, F-91297 Arpajon, France
- IMPMC, UMR 7590 of Sorbonne Université/CNRS/MNHN/IRD, Paris, France
| | - Jordan Bieder
- CEA DAM-DIF, F-91297 Arpajon, France
- Theoretical Materials Physics/Q-Mat/CESAM, Université de Liège (B5), B-4000 Liège, Belgium
| | | | | | - Eric Bousquet
- Theoretical Materials Physics/Q-Mat/CESAM, Université de Liège (B5), B-4000 Liège, Belgium
| | - Fabien Bruneval
- DEN, Service de Recherches de Métallurgie Physique, CEA, Université Paris-Saclay, F-91191 Gif-sur Yvette, France
| | - Guillaume Brunin
- Institute of Condensed Matter and Nanoscience, UCLouvain, B-1348 Louvain-la-Neuve, Belgium
| | - Damien Caliste
- IRIG-MEM, L-SIM, University Grenoble Alpes, CEA, F-38000 Grenoble, France
| | - Michel Côté
- Dépt. de Physique, U. de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal H3C 3J7, Canada
| | | | - Cyrus Dreyer
- Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854-8019, USA
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
- Center for Computational Quantum Physics, Flatiron Institute, 162 5th Avenue, New York, New York 10010, USA
| | - Philippe Ghosez
- Theoretical Materials Physics/Q-Mat/CESAM, Université de Liège (B5), B-4000 Liège, Belgium
| | - Matteo Giantomassi
- Institute of Condensed Matter and Nanoscience, UCLouvain, B-1348 Louvain-la-Neuve, Belgium
- European Theoretical Spectroscopy Facility,
| | - Yannick Gillet
- Institute of Condensed Matter and Nanoscience, UCLouvain, B-1348 Louvain-la-Neuve, Belgium
| | - Olivier Gingras
- Dépt. de Physique, U. de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal H3C 3J7, Canada
| | - Donald R. Hamann
- Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854-8019, USA
- Mat-Sim Research LLC, P.O. Box 742, Murray Hill, New Jersey 07974, USA
| | - Geoffroy Hautier
- Institute of Condensed Matter and Nanoscience, UCLouvain, B-1348 Louvain-la-Neuve, Belgium
| | | | - Gérald Jomard
- CEA, DEN, DEC, Cadarache, F-13108 Saint-Paul-Lez-Durance, France
| | - Alexandre Martin
- CEA DAM-DIF, F-91297 Arpajon, France
- Theoretical Materials Physics/Q-Mat/CESAM, Université de Liège (B5), B-4000 Liège, Belgium
| | - Henrique P. C. Miranda
- Institute of Condensed Matter and Nanoscience, UCLouvain, B-1348 Louvain-la-Neuve, Belgium
| | - Francesco Naccarato
- Institute of Condensed Matter and Nanoscience, UCLouvain, B-1348 Louvain-la-Neuve, Belgium
| | - Guido Petretto
- Institute of Condensed Matter and Nanoscience, UCLouvain, B-1348 Louvain-la-Neuve, Belgium
| | - Nicholas A. Pike
- European Theoretical Spectroscopy Facility,
- NanoMat/Q-Mat/CESAM, Université de Liège (B5), B-4000 Liège, Belgium
| | | | - Sergei Prokhorenko
- Theoretical Materials Physics/Q-Mat/CESAM, Université de Liège (B5), B-4000 Liège, Belgium
| | | | - Fabio Ricci
- Theoretical Materials Physics/Q-Mat/CESAM, Université de Liège (B5), B-4000 Liège, Belgium
| | - Gian-Marco Rignanese
- Institute of Condensed Matter and Nanoscience, UCLouvain, B-1348 Louvain-la-Neuve, Belgium
- European Theoretical Spectroscopy Facility,
| | - Miquel Royo
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Bellaterra, Spain
| | - Massimiliano Stengel
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Bellaterra, Spain
- ICREA - Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | | | - Michiel J. van Setten
- Institute of Condensed Matter and Nanoscience, UCLouvain, B-1348 Louvain-la-Neuve, Belgium
- European Theoretical Spectroscopy Facility,
- IMEC, Kapeldreef 75, B-3001 Leuven, Belgium
| | - Benoit Van Troeye
- Institute of Condensed Matter and Nanoscience, UCLouvain, B-1348 Louvain-la-Neuve, Belgium
- Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Matthieu J. Verstraete
- European Theoretical Spectroscopy Facility,
- NanoMat/Q-Mat/CESAM, Université de Liège (B5), B-4000 Liège, Belgium
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Julia Wiktor
- CEA, DEN, DEC, Cadarache, F-13108 Saint-Paul-Lez-Durance, France
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Josef W. Zwanziger
- Department of Chemistry, Dalhousie Univeristy, Halifax, Nova Scotia B3H 4R2, Canada
| | - Xavier Gonze
- Institute of Condensed Matter and Nanoscience, UCLouvain, B-1348 Louvain-la-Neuve, Belgium
- European Theoretical Spectroscopy Facility,
- Skolkovo Institute of Science and Technology, Moscow, Russia
| |
Collapse
|
10
|
Salazar VA, Arranz-Trullén J, Prats-Ejarque G, Torrent M, Andreu D, Pulido D, Boix E. Insight into the Antifungal Mechanism of Action of Human RNase N-terminus Derived Peptides. Int J Mol Sci 2019; 20:ijms20184558. [PMID: 31540052 PMCID: PMC6770517 DOI: 10.3390/ijms20184558] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 09/13/2019] [Indexed: 02/06/2023] Open
Abstract
Candida albicans is a polymorphic fungus responsible for mucosal and skin infections. Candida cells establish themselves into biofilm communities resistant to most currently available antifungal agents. An increase of severe infections ensuing in fungal septic shock in elderly or immunosuppressed patients, along with the emergence of drug-resistant strains, urge the need for the development of alternative antifungal agents. In the search for novel antifungal drugs our laboratory demonstrated that two human ribonucleases from the vertebrate-specific RNaseA superfamily, hRNase3 and hRNase7, display a high anticandidal activity. In a previous work, we proved that the N-terminal region of the RNases was sufficient to reproduce most of the parental protein bactericidal activity. Next, we explored their potency against a fungal pathogen. Here, we have tested the N-terminal derived peptides that correspond to the eight human canonical RNases (RN1-8) against planktonic cells and biofilms of C. albicans. RN3 and RN7 peptides displayed the most potent inhibitory effect with a mechanism of action characterized by cell-wall binding, membrane permeabilization and biofilm eradication activities. Both peptides are able to eradicate planktonic and sessile cells, and to alter their gene expression, reinforcing its role as a lead candidate to develop novel antifungal and antibiofilm therapies.
Collapse
Affiliation(s)
- Vivian A Salazar
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - Javier Arranz-Trullén
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - Guillem Prats-Ejarque
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - Marc Torrent
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - David Andreu
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - David Pulido
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| |
Collapse
|
11
|
Santos S, Voerman E, Amiano P, Barros H, Beilin LJ, Bergström A, Charles MA, Chatzi L, Chevrier C, Chrousos GP, Corpeleijn E, Costa O, Costet N, Crozier S, Devereux G, Doyon M, Eggesbø M, Fantini MP, Farchi S, Forastiere F, Georgiu V, Godfrey KM, Gori D, Grote V, Hanke W, Hertz-Picciotto I, Heude B, Hivert MF, Hryhorczuk D, Huang RC, Inskip H, Karvonen AM, Kenny LC, Koletzko B, Küpers LK, Lagström H, Lehmann I, Magnus P, Majewska R, Mäkelä J, Manios Y, McAuliffe FM, McDonald SW, Mehegan J, Melén E, Mommers M, Morgen CS, Moschonis G, Murray D, Ní Chaoimh C, Nohr EA, Nybo Andersen AM, Oken E, Oostvogels A, Pac A, Papadopoulou E, Pekkanen J, Pizzi C, Polanska K, Porta D, Richiardi L, Rifas-Shiman SL, Roeleveld N, Ronfani L, Santos AC, Standl M, Stigum H, Stoltenberg C, Thiering E, Thijs C, Torrent M, Tough SC, Trnovec T, Turner S, van Gelder M, van Rossem L, von Berg A, Vrijheid M, Vrijkotte T, West J, Wijga AH, Wright J, Zvinchuk O, Sørensen T, Lawlor DA, Gaillard R, Jaddoe V. Impact of maternal body mass index and gestational weight gain on pregnancy complications: an individual participant data meta-analysis of European, North American and Australian cohorts. BJOG 2019; 126:984-995. [PMID: 30786138 DOI: 10.1111/1471-0528.15661] [Citation(s) in RCA: 211] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2019] [Indexed: 01/06/2023]
Abstract
OBJECTIVE To assess the separate and combined associations of maternal pre-pregnancy body mass index (BMI) and gestational weight gain with the risks of pregnancy complications and their population impact. DESIGN Individual participant data meta-analysis of 39 cohorts. SETTING Europe, North America, and Oceania. POPULATION 265 270 births. METHODS Information on maternal pre-pregnancy BMI, gestational weight gain, and pregnancy complications was obtained. Multilevel binary logistic regression models were used. MAIN OUTCOME MEASURES Gestational hypertension, pre-eclampsia, gestational diabetes, preterm birth, small and large for gestational age at birth. RESULTS Higher maternal pre-pregnancy BMI and gestational weight gain were, across their full ranges, associated with higher risks of gestational hypertensive disorders, gestational diabetes, and large for gestational age at birth. Preterm birth risk was higher at lower and higher BMI and weight gain. Compared with normal weight mothers with medium gestational weight gain, obese mothers with high gestational weight gain had the highest risk of any pregnancy complication (odds ratio 2.51, 95% CI 2.31- 2.74). We estimated that 23.9% of any pregnancy complication was attributable to maternal overweight/obesity and 31.6% of large for gestational age infants was attributable to excessive gestational weight gain. CONCLUSIONS Maternal pre-pregnancy BMI and gestational weight gain are, across their full ranges, associated with risks of pregnancy complications. Obese mothers with high gestational weight gain are at the highest risk of pregnancy complications. Promoting a healthy pre-pregnancy BMI and gestational weight gain may reduce the burden of pregnancy complications and ultimately the risk of maternal and neonatal morbidity. TWEETABLE ABSTRACT Promoting a healthy body mass index and gestational weight gain might reduce the population burden of pregnancy complications.
Collapse
Affiliation(s)
- S Santos
- The Generation R Study Group, Erasmus MC, University Medical Center, Rotterdam, the Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - E Voerman
- The Generation R Study Group, Erasmus MC, University Medical Center, Rotterdam, the Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - P Amiano
- Public Health Division of Gipuzkoa, San Sebastián, Spain.,BioDonostia Research Institute, San Sebastián, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - H Barros
- EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal.,Department of Public Health and Forensic Sciences and Medical Education, Unit of Clinical Epidemiology, Predictive Medicine and Public Health, University of Porto Medical School, Porto, Portugal
| | - L J Beilin
- Medical School, Royal Perth Hospital Unit, The University of Western Australia, Perth, WA, Australia
| | - A Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - M-A Charles
- INSERM, UMR1153 Epidemiology and Biostatistics Sorbonne Paris Cité Center (CRESS), ORCHAD Team, Villejuif, France.,Paris Descartes University, Villejuif, France
| | - L Chatzi
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Faculty of Medicine, Department of Social Medicine, University of Crete, Heraklion, Greece.,Department of Genetics and Cell Biology, Maastricht University, Maastricht, the Netherlands
| | - C Chevrier
- Inserm UMR 1085, Irset - Research Institute for Environmental and Occupational Health, Rennes, France
| | - G P Chrousos
- First Department of Pediatrics, Athens University Medical School, 'Aghia Sophia' Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - E Corpeleijn
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - O Costa
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain
| | - N Costet
- Inserm UMR 1085, Irset - Research Institute for Environmental and Occupational Health, Rennes, France
| | - S Crozier
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - G Devereux
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - M Doyon
- Centre de Recherche du Centre Hospitalier de l'Universite de Sherbrooke, Sherbrooke, QC, Canada
| | - M Eggesbø
- Department of Exposure and Environmental Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
| | - M P Fantini
- The Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - S Farchi
- Department of Epidemiology, Lazio Regional Health Service, Rome, Italy
| | - F Forastiere
- Department of Epidemiology, Lazio Regional Health Service, Rome, Italy
| | - V Georgiu
- Faculty of Medicine, Department of Social Medicine, University of Crete, Heraklion, Greece
| | - K M Godfrey
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - D Gori
- The Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - V Grote
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilian-Universität Munich, Munich, Germany
| | - W Hanke
- Department of Environmental Epidemiology, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - I Hertz-Picciotto
- Department of Public Health Sciences, School of Medicine, University of California Davis, Davis, CA, USA
| | - B Heude
- INSERM, UMR1153 Epidemiology and Biostatistics Sorbonne Paris Cité Center (CRESS), ORCHAD Team, Villejuif, France.,Paris Descartes University, Villejuif, France
| | - M-F Hivert
- Centre de Recherche du Centre Hospitalier de l'Universite de Sherbrooke, Sherbrooke, QC, Canada.,Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA.,Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - D Hryhorczuk
- Center for Global Health, University of Illinois College of Medicine, Chicago, IL, USA
| | - R-C Huang
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - H Inskip
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - A M Karvonen
- Department of Health Security, National Institute for Health and Welfare, Kuopio, Finland
| | - L C Kenny
- Irish Centre for Fetal and Neonatal Translational Research, Cork University Maternity Hospital, University College Cork, Cork, Ireland.,Department of Obstetrics and Gynaecology, Cork University Maternity Hospital, Cork, Ireland
| | - B Koletzko
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilian-Universität Munich, Munich, Germany
| | - L K Küpers
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.,MRC Integrative Epidemiology Unit, Oakfield House, Oakfield Grove, University of Bristol, Bristol, UK.,Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK.,Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
| | - H Lagström
- Department of Public Health, University of Turku, Turku, Finland
| | - I Lehmann
- Department of Environmental Immunology/Core Facility Studies, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - P Magnus
- Division of Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - R Majewska
- Department of Epidemiology, Chair of Epidemiology and Preventive Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - J Mäkelä
- Turku Centre for Biotechnology, University of Turku and Abo Akademi University, Turku, Finland
| | - Y Manios
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - F M McAuliffe
- UCD Perinatal Research Centre, Obstetrics& Gynaecology, School of Medicine, National Maternity Hospital, University College Dublin, Dublin, Ireland
| | - S W McDonald
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - J Mehegan
- UCD Perinatal Research Centre, School of Public Health and Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - E Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Sach's Children Hospital, Stockholm, Sweden
| | - M Mommers
- Department of Epidemiology, Care and Public Health Research Institute, Maastricht University, Maastricht, the Netherlands
| | - C S Morgen
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark.,Department of Public Health, Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark
| | - G Moschonis
- Department of Rehabilitation, Nutrition and Sport, La Trobe University, Melbourne, Vic, Australia
| | - D Murray
- Irish Centre for Fetal and Neonatal Translational Research, Cork University Maternity Hospital, University College Cork, Cork, Ireland.,Paediatrics & Child Health, University College Cork, Cork, Ireland
| | - C Ní Chaoimh
- Irish Centre for Fetal and Neonatal Translational Research, Cork University Maternity Hospital, University College Cork, Cork, Ireland.,Cork Centre for Vitamin D and Nutrition Research, School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - E A Nohr
- Research Unit for Gynaecology and Obstetrics, Institute for Clinical Research, University of Southern Denmark, Odense, Denmark
| | - A-M Nybo Andersen
- Department of Public Health, Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark
| | - E Oken
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Ajjm Oostvogels
- Department of Public Health, Amsterdam Public Health Research Institute, Academic Medical Center, Amsterdam, the Netherlands
| | - A Pac
- Department of Epidemiology, Chair of Epidemiology and Preventive Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - E Papadopoulou
- Department of Environmental Exposures and Epidemiology, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - J Pekkanen
- Department of Health Security, National Institute for Health and Welfare, Kuopio, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland
| | - C Pizzi
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - K Polanska
- Department of Environmental Epidemiology, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - D Porta
- Department of Epidemiology, Lazio Regional Health Service, Rome, Italy
| | - L Richiardi
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - S L Rifas-Shiman
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - N Roeleveld
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - L Ronfani
- Institute for Maternal and Child Health - IRCCS 'Burlo Garofolo', Trieste, Italy
| | - A C Santos
- EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal.,Department of Public Health and Forensic Sciences and Medical Education, Unit of Clinical Epidemiology, Predictive Medicine and Public Health, University of Porto Medical School, Porto, Portugal
| | - M Standl
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - H Stigum
- Department of Non-communicable Diseases, Norwegian Institute of Public Health, Oslo, Norway
| | - C Stoltenberg
- Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - E Thiering
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - C Thijs
- Department of Epidemiology, Care and Public Health Research Institute, Maastricht University, Maastricht, the Netherlands
| | - M Torrent
- Ib-salut, Area de Salut de Menorca, Menorca, Spain
| | - S C Tough
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - T Trnovec
- Department of Environmental Medicine, Slovak Medical University, Bratislava, Slovak Republic
| | - S Turner
- Child Health, Royal Aberdeen Children's Hospital, Aberdeen, UK
| | - Mmhj van Gelder
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud REshape Innovation Center, Radboud University Medical Center, Nijmegen, the Netherlands
| | - L van Rossem
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - A von Berg
- Department of Pediatrics, Research Institute, Marien-Hospital Wesel, Wesel, Germany
| | - M Vrijheid
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,ISGlobal, Institute for Global Health, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Tgm Vrijkotte
- Department of Public Health, Amsterdam Public Health Research Institute, Academic Medical Center, Amsterdam, the Netherlands
| | - J West
- Bradford Institute for Health Research, Bradford Royal Infirmary, Bradford, UK
| | - A H Wijga
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - J Wright
- Bradford Institute for Health Research, Bradford Royal Infirmary, Bradford, UK
| | - O Zvinchuk
- Department of Medical and Social Problems of Family Health, Institute of Pediatrics, Obstetrics and Gynecology, Kyiv, Ukraine
| | - Tia Sørensen
- Department of Public Health, Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark.,Section of Metabolic Genetics, Faculty of Health and Medical Sciences, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - D A Lawlor
- MRC Integrative Epidemiology Unit, Oakfield House, Oakfield Grove, University of Bristol, Bristol, UK.,Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - R Gaillard
- The Generation R Study Group, Erasmus MC, University Medical Center, Rotterdam, the Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Vwv Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center, Rotterdam, the Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| |
Collapse
|
12
|
Dammak H, Brieuc F, Geneste G, Torrent M, Hayoun M. Isotope effect on hydrogen bond symmetrization in hydrogen and deuterium fluoride crystals by molecular dynamics simulation. Phys Chem Chem Phys 2019; 21:3211-3217. [PMID: 30681084 DOI: 10.1039/c8cp06949b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The isotope effect on the collective proton/deuteron transfer in hydrogen and deuterium fluoride crystals has been investigated at 100 K by ab initio quantum-thermal-bath path-integral molecular dynamics (QTB-PIMD) simulation. The deuterons within a planar zigzag chain of the orthorhombic structure simultaneously flip between covalent and hydrogen bonds due to the barrier crossing through tunnelling. The height of the corresponding static barrier normalized for one deuteron is 29.2 meV. In the HF crystal, all the protons are located at the center of the heavy-atom distance. This evidences the symmetrization of the H-bonds, and indicates that the proton zero-point energy is above the barrier top. The decrease of the heavy-atom distance due to quantum fluctuations in both HF and DF crystals corresponds to a large decrease and an increase of the hydrogen and covalent bond lengths, respectively. Upon deuteration, the increase of the heavy-atom distance (Ubbelohde effect) is in agreement with experimental data.
Collapse
Affiliation(s)
- Hichem Dammak
- Laboratoire Structures Propriétés et Modélisation des Solides, CentraleSupélec, CNRS, Université Paris-Saclay, F 91190 Gif-sur-Yvette, France.
| | | | | | | | | |
Collapse
|
13
|
Torrent M, Chalancon G, de Groot NS, Wuster A, Madan Babu M. Cells alter their tRNA abundance to selectively regulate protein synthesis during stress conditions. Sci Signal 2018; 11:11/546/eaat6409. [PMID: 30181241 PMCID: PMC6130803 DOI: 10.1126/scisignal.aat6409] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Decoding the information in mRNA during protein synthesis relies on tRNA adaptors, the abundance of which can affect the decoding rate and translation efficiency. To determine whether cells alter tRNA abundance to selectively regulate protein expression, we quantified changes in the abundance of individual tRNAs at different time points in response to diverse stress conditions in Saccharomyces cerevisiae. We found that the tRNA pool was dynamic and rearranged in a manner that facilitated selective translation of stress-related transcripts. Through genomic analysis of multiple data sets, stochastic simulations, and experiments with designed sequences of proteins with identical amino acids but altered codon usage, we showed that changes in tRNA abundance affected protein expression independently of factors such as mRNA abundance. We suggest that cells alter their tRNA abundance to selectively affect the translation rates of specific transcripts to increase the amounts of required proteins under diverse stress conditions.
Collapse
Affiliation(s)
- Marc Torrent
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK. .,Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Guilhem Chalancon
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Natalia S de Groot
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Arthur Wuster
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - M Madan Babu
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| |
Collapse
|
14
|
Pulido D, Rebollido-Rios R, Valle J, Andreu D, Boix E, Torrent M. Structural similarities in the CPC clip motif explain peptide-binding promiscuity between glycosaminoglycans and lipopolysaccharides. J R Soc Interface 2018; 14:rsif.2017.0423. [PMID: 29187635 DOI: 10.1098/rsif.2017.0423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/30/2017] [Indexed: 11/12/2022] Open
Abstract
Lipopolysaccharides (LPSs) and glycosaminoglycans (GAGs) are polymeric structures containing negatively charged disaccharide units that bind to specialized proteins and peptides in the human body and control fundamental processes such as inflammation and coagulation. Surprisingly, some proteins can bind both LPSs and GAGs with high affinity, suggesting that a cross-communication between these two pathways can occur. Here, we explore whether GAGs and LPSs can share common binding sites in proteins and what are the structural determinants of this binding. We found that the LPS-binding peptide YI12WF, derived from protein FhuA, can bind both heparin and E. coli LPS with high affinity. Most interestingly, mutations decreasing heparin binding in the peptide also reduce LPS affinity. We show that such mutations involve the CPC clip motif in the peptide, a small three-dimensional signature required for heparin binding. Overall, we conclude that negatively charged polysaccharide-containing polymers such as GAGs and LPSs can compete for similar binding sites in proteins, and that the CPC clip motif is essential to bind both ligands. Our results provide a structural framework to explain why these polymers can cross-interact with the same proteins and peptides and thus contribute to the regulation of apparently unrelated processes in the body.
Collapse
Affiliation(s)
- David Pulido
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, London SW7 2AZ, UK
| | - Rocío Rebollido-Rios
- Microbiology Service, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Javier Valle
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - David Andreu
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Marc Torrent
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain .,Microbiology Service, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| |
Collapse
|
15
|
Pulido D, Prats-Ejarque G, Villalba C, Albacar M, Moussaoui M, Andreu D, Volkmer R, Torrent M, Boix E. Positional scanning library applied to the human eosinophil cationic protein/RNase3 N-terminus reveals novel and potent anti-biofilm peptides. Eur J Med Chem 2018; 152:590-599. [DOI: 10.1016/j.ejmech.2018.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/20/2018] [Accepted: 05/07/2018] [Indexed: 01/14/2023]
|
16
|
Abstract
The dietary pattern of a population sample of males selected as a control group for a case-control study on bladder cancer carried out in four different regions of Spain is presented. Out of 807 population controls initially selected, 530 were interviewed, 465 males and 65 females. The method of selection of the study subjects and the diet assessment method are described. Our results confirm the Mediterranean pattern of the Spanish diet, with an important consumption of fresh fish, fruits and vegetables, and the use of vegetable oils, specially olive oil, for cooking and seasoning, accompanied with a high polyunsaturated/saturated ratio (0.7). The consumption of butter, cheese and other dairy products, on the other hand, is very low. Estimated total caloric intake is relatively low if compared with international figures, although questionnaire base assessment may seriously underestimate caloric intake, as it is the absolute amount of intake of lipids and carbohydrates. In relative terms, however, lipids provide the highest percentage of calories.
Collapse
Affiliation(s)
- C A González
- Unit of Epidemiology, Hospital de Mataró, Barcellona, Spain
| | | | | |
Collapse
|
17
|
Cabré A, Vrijheid M, Cardis E, Torrent M, Guxens M. Use of wireless communication devices and sleep quality and sleep problems in adolescents. Sleep Med 2017. [DOI: 10.1016/j.sleep.2017.11.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
18
|
Dorado B, Bieder J, Torrent M. Influence of point defects and impurities on the dynamical stability of δ-plutonium. J Phys Condens Matter 2017; 29:245402. [PMID: 28436383 DOI: 10.1088/1361-648x/aa6eb7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We use first-principles calculations to provide direct evidence of the effect of aluminum, gallium, iron and uranium on the dynamical stability of δ-plutonium. We first show that the δ phase is dynamically unstable at low temperature, as seen in experiments, and that this stability directly depends on the plutonium 5f orbital occupancies. Then, we demonstrate that both aluminum and gallium stabilize the δ phase, contrary to iron. As for uranium, which is created during self-irradiation and whose effect on plutonium has yet to be understood, we show that it leaves a few unstable vibrational modes and that higher concentrations lead to an almost complete stabilization. Finally, we provide an attempt at a consistent analysis of the experimental Pu-Ga phonon density of states. We show that the presence of gallium can reproduce only partially the experimental measurements, and we investigate how point defects, such as interstitials and vacancies, affect the calculated phonon density of states.
Collapse
Affiliation(s)
- B Dorado
- CEA, DAM, DIF, F-91297 Arpajon, France
| | | | | |
Collapse
|
19
|
Wiktor J, Jomard G, Torrent M, Bertolus M. First-principles calculations of momentum distributions of annihilating electron-positron pairs in defects in UO 2. J Phys Condens Matter 2017; 29:035503. [PMID: 27869643 DOI: 10.1088/1361-648x/29/3/035503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We performed first-principles calculations of the momentum distributions of annihilating electron-positron pairs in vacancies in uranium dioxide. Full atomic relaxation effects (due to both electronic and positronic forces) were taken into account and self-consistent two-component density functional theory schemes were used. We present one-dimensional momentum distributions (Doppler-broadened annihilation radiation line shapes) along with line-shape parameters S and W. We studied the effect of the charge state of the defect on the Doppler spectra. The effect of krypton incorporation in the vacancy was also considered and it was shown that it should be possible to observe the fission gas incorporation in defects in UO2 using positron annihilation spectroscopy. We suggest that the Doppler broadening measurements can be especially useful for studying impurities and dopants in UO2 and of mixed actinide oxides.
Collapse
Affiliation(s)
- Julia Wiktor
- CEA, DEN, DEC, Centre de Cadarache, 13108, Saint-Paul-lez-Durance, France
| | | | | | | |
Collapse
|
20
|
Bousquet J, Anto JM, Akdis M, Auffray C, Keil T, Momas I, Postma D, Valenta R, Wickman M, Cambon‐Thomsen A, Haahtela T, Lambrecht BN, Lodrup Carlsen KC, Koppelman GH, Sunyer J, Zuberbier T, Annesi‐Maesano I, Arno A, Bindslev‐Jensen C, De Carlo G, Forastiere F, Heinrich J, Kowalski ML, Maier D, Melén E, Palkonen S, Smit HA, Standl M, Wright J, Asarnoj A, Benet M, Ballardini N, Garcia‐Aymerich J, Gehring U, Guerra S, Hohman C, Kull I, Lupinek C, Pinart M, Skrindo I, Westman M, Smagghe D, Akdis C, Albang R, Anastasova V, Anderson N, Bachert C, Ballereau S, Ballester F, Basagana X, Bedbrook A, Bergstrom A, Berg A, Brunekreef B, Burte E, Carlsen KH, Chatzi L, Coquet JM, Curin M, Demoly P, Eller E, Fantini MP, Gerhard B, Hammad H, Hertzen L, Hovland V, Jacquemin B, Just J, Keller T, Kerkhof M, Kiss R, Kogevinas M, Koletzko S, Lau S, Lehmann I, Lemonnier N, McEachan R, Mäkelä M, Mestres J, Minina E, Mowinckel P, Nadif R, Nawijn M, Oddie S, Pellet J, Pin I, Porta D, Rancière F, Rial‐Sebbag A, Saeys Y, Schuijs MJ, Siroux V, Tischer CG, Torrent M, Varraso R, De Vocht J, Wenger K, Wieser S, Xu C. Paving the way of systems biology and precision medicine in allergic diseases: the MeDALL success story: Mechanisms of the Development of ALLergy; EU FP7-CP-IP; Project No: 261357; 2010-2015. Allergy 2016; 71:1513-1525. [PMID: 26970340 PMCID: PMC5248602 DOI: 10.1111/all.12880] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2016] [Indexed: 01/06/2023]
Abstract
MeDALL (Mechanisms of the Development of ALLergy; EU FP7-CP-IP; Project No: 261357; 2010-2015) has proposed an innovative approach to develop early indicators for the prediction, diagnosis, prevention and targets for therapy. MeDALL has linked epidemiological, clinical and basic research using a stepwise, large-scale and integrative approach: MeDALL data of precisely phenotyped children followed in 14 birth cohorts spread across Europe were combined with systems biology (omics, IgE measurement using microarrays) and environmental data. Multimorbidity in the same child is more common than expected by chance alone, suggesting that these diseases share causal mechanisms irrespective of IgE sensitization. IgE sensitization should be considered differently in monosensitized and polysensitized individuals. Allergic multimorbidities and IgE polysensitization are often associated with the persistence or severity of allergic diseases. Environmental exposures are relevant for the development of allergy-related diseases. To complement the population-based studies in children, MeDALL included mechanistic experimental animal studies and in vitro studies in humans. The integration of multimorbidities and polysensitization has resulted in a new classification framework of allergic diseases that could help to improve the understanding of genetic and epigenetic mechanisms of allergy as well as to better manage allergic diseases. Ethics and gender were considered. MeDALL has deployed translational activities within the EU agenda.
Collapse
Affiliation(s)
- J. Bousquet
- University Hospital Montpellier France
- MACVIA‐LR Contre les MAladies Chroniques pour un VIeillissement Actif en Languedoc‐Roussillon European Innovation Partnership on Active and Healthy Ageing Reference Site France
- INSERM VIMA: Ageing and Chronic Diseases, Epidemiological and Public Health Approaches UVSQ Université Versailles St‐Quentin‐en‐Yvelines Paris France
| | - J. M. Anto
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
- IMIM (Hospital del Mar Research Institute) Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
- Universitat Pompeu Fabra (UPF) Barcelona Spain
| | - M. Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | - C. Auffray
- European Institute for Systems Biology and Medicine CNRS‐ENS‐UCBL Université de Lyon Lyon France
| | - T. Keil
- Institute of Social Medicine, Epidemiology and Health Economics Charité–Universitätsmedizin Berlin Berlin Germany
- Institute for Clinical Epidemiology and Biometry University of Wuerzburg Wuerzburg Germany
| | - I. Momas
- Department of Public Health and Health Products Paris Descartes University‐Sorbonne Paris Cité Paris France
- Paris Municipal Department of Social Action, Childhood, and Health Paris France
| | - D.S. Postma
- Department of Pulmonary Medicine and Tuberculosis GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
| | - R. Valenta
- Division of Immunopathology Department of Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - M. Wickman
- Sachs’ Children and Youth Hospital, Södersjukhuset Stockholm and Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
| | - A. Cambon‐Thomsen
- UMR Inserm U1027 and Université de Toulouse III Paul Sabatier Toulouse France
| | - T. Haahtela
- Skin and Allergy Hospital Helsinki University Hospital Helsinki Finland
| | - B. N. Lambrecht
- VIB Inflammation Research Center Ghent University Ghent Belgium
| | - K. C. Lodrup Carlsen
- Department of Paediatrics Faculty of Medicine Institute of Clinical Medicine Oslo University Hospital University of Oslo Oslo Norway
| | - G. H. Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology Beatrix Children's Hospital GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
| | - J. Sunyer
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
- IMIM (Hospital del Mar Research Institute) Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
- Universitat Pompeu Fabra (UPF) Barcelona Spain
| | - T. Zuberbier
- Secretary General of the Global Allergy and Asthma European Network (GALEN) Allergy‐Centre‐Charité at the Department of Dermatology Charité–Universitätsmedizin Berlin Berlin Germany
| | | | - A. Arno
- Onmedic Networks Barcelona Spain
| | - C. Bindslev‐Jensen
- Department of Dermatology and Allergy Centre Odense University Hospital Odense Denmark
| | - G. De Carlo
- EFA European Federation of Allergy and Airways Diseases Patients’ Associations Brussels Belgium
| | - F. Forastiere
- Department of Epidemiology Regional Health Service Lazio Region Rome Italy
| | - J. Heinrich
- Institute of Epidemiology I German Research Centre for Environmental Health Helmholtz Zentrum München Neuherberg Germany
| | - M. L. Kowalski
- Department of Immunology, Rheumatology and Allergy Medical University of Lodz Lodz Poland
| | - D. Maier
- Biomax Informatics AG Munich Germany
| | - E. Melén
- Department of Pulmonary Medicine and Tuberculosis GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
- Stockholm County Council Centre for Occupational and Environmental Medicine Stockholm Sweden
| | - S. Palkonen
- EFA European Federation of Allergy and Airways Diseases Patients’ Associations Brussels Belgium
| | - H. A. Smit
- Julius Center of Health Sciences and Primary Care University Medical Center Utrecht University of Utrecht Utrecht the Netherlands
| | - M. Standl
- Institute of Epidemiology I German Research Centre for Environmental Health Helmholtz Zentrum München Neuherberg Germany
| | - J. Wright
- Bradford Institute for Health Research Bradford Royal Infirmary Bradford UK
| | - A. Asarnoj
- Clinical Immunology and Allergy Unit Department of Medicine Solna Karolinska Institutet Stockholm Sweden
- Astrid Lindgren Children's Hospital Department of Pediatric Pulmonology and Allergy Karolinska University Hospital Stockholm Sweden
| | - M. Benet
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
| | - N. Ballardini
- Sachs’ Children and Youth Hospital, Södersjukhuset Stockholm and Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
- St John's Institute of Dermatology King's College London London UK
| | - J. Garcia‐Aymerich
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
- IMIM (Hospital del Mar Research Institute) Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
- Universitat Pompeu Fabra (UPF) Barcelona Spain
| | - U. Gehring
- Institute for Risk Assessment Sciences Utrecht University Utrecht the Netherlands
| | - S. Guerra
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
| | - C. Hohman
- Institute of Social Medicine, Epidemiology and Health Economics Charité–Universitätsmedizin Berlin Germany
| | - I. Kull
- Sachs’ Children and Youth Hospital, Södersjukhuset Stockholm and Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
- Department of Clinical Science and Education, Södersjukhuset Karolinska InstitutetStockholm Sweden
| | - C. Lupinek
- Division of Immunopathology Department of Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - M. Pinart
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
| | - I. Skrindo
- Department of Paediatrics Faculty of Medicine Institute of Clinical Medicine Oslo University Hospital University of Oslo Oslo Norway
| | - M. Westman
- Department of Clinical Science, Intervention and Technology Karolinska Institutet Stockholm Sweden
- Department of ENT Diseases Karolinska University Hospital Stockholm Sweden
| | | | - C. Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | - R. Albang
- Biomax Informatics AG Munich Germany
| | - V. Anastasova
- UMR Inserm U1027 and Université de Toulouse III Paul Sabatier Toulouse France
| | - N. Anderson
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
| | - C. Bachert
- ENT Department Ghent University Hospital Gent Belgium
| | - S. Ballereau
- European Institute for Systems Biology and Medicine CNRS‐ENS‐UCBL Université de Lyon Lyon France
| | - F. Ballester
- Environment and Health Area Centre for Public Health Research (CSISP) CIBERESP Department of Nursing University of Valencia Valencia Spain
| | - X. Basagana
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
| | - A. Bedbrook
- MACVIA‐LR Contre les MAladies Chroniques pour un VIeillissement Actif en Languedoc‐Roussillon European Innovation Partnership on Active and Healthy Ageing Reference Site France
| | - A. Bergstrom
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
| | - A. Berg
- Research Institute Department of Pediatrics Marien‐Hospital Wesel Germany
| | - B. Brunekreef
- Julius Center of Health Sciences and Primary Care University Medical Center Utrecht University of Utrecht Utrecht the Netherlands
| | - E. Burte
- INSERM VIMA: Ageing and Chronic Diseases, Epidemiological and Public Health Approaches UVSQ Université Versailles St‐Quentin‐en‐Yvelines Paris France
| | - K. H. Carlsen
- Department of Paediatrics Oslo University Hospital University of Oslo Oslo Norway
| | - L. Chatzi
- Department of Social Medicine Faculty of Medicine University of Crete Heraklion Crete Greece
| | - J. M. Coquet
- VIB Inflammation Research Center Ghent University Ghent Belgium
| | - M. Curin
- Division of Immunopathology Department of Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - P. Demoly
- Department of Respiratory Diseases Montpellier University Hospital France
| | - E. Eller
- Department of Dermatology and Allergy Centre Odense University Hospital Odense Denmark
| | - M. P. Fantini
- Department of Medicine and Public Health Alma Mater Studiorum–University of Bologna Bologna Italy
| | | | - H. Hammad
- VIB Inflammation Research Center Ghent University Ghent Belgium
| | - L. Hertzen
- Skin and Allergy Hospital Helsinki University Hospital Helsinki Finland
| | - V. Hovland
- Department of Paediatrics Oslo University Hospital University of Oslo Oslo Norway
| | - B. Jacquemin
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
| | - J. Just
- Allergology Department Centre de l'Asthme et des Allergies Hôpital d'Enfants Armand‐Trousseau (APHP) Sorbonne Universités Institut Pierre Louis d'Epidémiologie et de Santé Publique Paris France
| | - T. Keller
- Institute of Social Medicine, Epidemiology and Health Economics Charité–Universitätsmedizin Berlin Germany
| | - M. Kerkhof
- Department of Pulmonary Medicine and Tuberculosis GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
| | - R. Kiss
- Division of Immunopathology Department of Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - M. Kogevinas
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
- IMIM (Hospital del Mar Research Institute) Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
- Universitat Pompeu Fabra (UPF) Barcelona Spain
| | - S. Koletzko
- Division of Paediatric Gastroenterology and Hepatology Ludwig Maximilians University of Munich Munich Germany
| | - S. Lau
- Department for Pediatric Pneumology and Immunology Charité Medical University Berlin Germany
| | - I. Lehmann
- Department of Environmental Immunology/Core Facility Studies Helmholtz Centre for Environmental Research, UFZ Leipzig Germany
| | - N. Lemonnier
- European Institute for Systems Biology and Medicine CNRS‐ENS‐UCBL Université de Lyon Lyon France
| | - R. McEachan
- Bradford Institute for Health Research Bradford Royal Infirmary Bradford UK
| | - M. Mäkelä
- Skin and Allergy Hospital Helsinki University Hospital Helsinki Finland
| | - J. Mestres
- Chemotargets SL and Chemogenomics Laboratory GRIB Unit IMIM‐Hospital del Mar and University Pompeu Fabra Barcelona Catalonia Spain
| | - E. Minina
- Biomax Informatics AG Munich Germany
| | - P. Mowinckel
- Department of Paediatrics Oslo University Hospital University of Oslo Oslo Norway
| | - R. Nadif
- INSERM VIMA: Ageing and Chronic Diseases, Epidemiological and Public Health Approaches UVSQ Université Versailles St‐Quentin‐en‐Yvelines Paris France
| | - M. Nawijn
- Department of Pediatric Pulmonology and Pediatric Allergology Beatrix Children's Hospital GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
| | - S. Oddie
- Bradford Institute for Health Research Bradford Royal Infirmary Bradford UK
| | - J. Pellet
- European Institute for Systems Biology and Medicine CNRS‐ENS‐UCBL Université de Lyon Lyon France
| | - I. Pin
- Département de Pédiatrie CHU de Grenoble Grenoble Cedex 9 France
| | - D. Porta
- Department of Epidemiology Regional Health Service Lazio Region Rome Italy
| | - F. Rancière
- Department of Public Health and Health Products Paris Descartes University‐Sorbonne Paris Cité Paris France
| | - A. Rial‐Sebbag
- UMR Inserm U1027 and Université de Toulouse III Paul Sabatier Toulouse France
| | - Y. Saeys
- VIB Inflammation Research Center Ghent University Ghent Belgium
| | - M. J. Schuijs
- VIB Inflammation Research Center Ghent University Ghent Belgium
| | | | - C. G. Tischer
- Institute of Epidemiology I German Research Centre for Environmental Health Helmholtz Zentrum München Neuherberg Germany
| | - M. Torrent
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
- ib‐salut Area de Salut de Menorca Spain
| | - R. Varraso
- INSERM VIMA: Ageing and Chronic Diseases, Epidemiological and Public Health Approaches UVSQ Université Versailles St‐Quentin‐en‐Yvelines Paris France
| | - J. De Vocht
- EFA European Federation of Allergy and Airways Diseases Patients’ Associations Brussels Belgium
| | - K. Wenger
- Biomax Informatics AG Munich Germany
| | - S. Wieser
- Division of Immunopathology Department of Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - C. Xu
- Department of Pulmonary Medicine and Tuberculosis GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
| |
Collapse
|
21
|
Pulido D, Garcia-Mayoral MF, Moussaoui M, Velázquez D, Torrent M, Bruix M, Boix E. Structural basis for endotoxin neutralization by the eosinophil cationic protein. FEBS J 2016; 283:4176-4191. [PMID: 27696685 DOI: 10.1111/febs.13915] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 09/07/2016] [Accepted: 09/29/2016] [Indexed: 12/13/2022]
Abstract
Acute infection by Gram-negative pathogens can induce an exacerbated immune response that leads to lethal septic shock syndrome. Bacterial lipopolysaccharide (LPS) is a major pathogen-associated molecular pattern molecule that can initiate massive and lethal immune system stimulation. Therefore, the development of new and effective LPS-neutralizing agents is a top priority. The eosinophil cationic protein (ECP) is an antimicrobial protein secreted in response to infection, with a remarkable affinity for LPS. In the present study, we demonstrate that ECP is able to neutralize bacterial LPS and inhibit tumor necrosis factor-α production in human macrophages. We also characterized ECP neutralizing activity using progressively truncated LPS mutants, and conclude that the polysaccharide moiety and lipid A portions are required for LPS-mediated neutralization. In addition, we mapped the structural determinants required for the ECP-LPS interaction by nuclear magnetic resonance. Our results show that ECP is able to neutralize LPS and therefore opens a new route for developing novel therapeutic agents based on the ECP structural scaffolding.
Collapse
Affiliation(s)
- David Pulido
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | | | - Mohammed Moussaoui
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Diego Velázquez
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Marc Torrent
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Marta Bruix
- Departamento de Química Biológica, Instituto de Química-Física Rocasolano, CSIC, Madrid, Spain
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| |
Collapse
|
22
|
Abstract
The pressure effects on three different AlOOH structures (α, γ, and δ phases) are systematically analyzed by density functional theory with different exchange and correlation energy functional approximations, namely two local, two generalized-gradient approximation (GGA), and two GGA for solids (GGAsol). Phase stability, compressibility and hydrogen bond evolution are studied in a range of pressures from 0 to 30 GPa. In general, the use of GGAsol functionals is mandatory in order to have the correct phase stability order, a good description of the hydrogen bonds, and a close agreement with the experimental lattice parameters at the various pressures. Pressure-induced hydrogen-bond symmetrization is found in γ and δ phases at high compression, while the hydrogen bonds in the α phase remain asymmetric. A detailed analysis of the uncertainties on the values of the bulk moduli and their pressure derivative at zero pressure deduced by fitting calculated or experimental (P,V) data is also presented.
Collapse
Affiliation(s)
- Andrés Cedillo
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, México DF, Mexico
| | | | | |
Collapse
|
23
|
Lejaeghere K, Bihlmayer G, Björkman T, Blaha P, Blügel S, Blum V, Caliste D, Castelli IE, Clark SJ, Dal Corso A, de Gironcoli S, Deutsch T, Dewhurst JK, Di Marco I, Draxl C, Dułak M, Eriksson O, Flores-Livas JA, Garrity KF, Genovese L, Giannozzi P, Giantomassi M, Goedecker S, Gonze X, Grånäs O, Gross EKU, Gulans A, Gygi F, Hamann DR, Hasnip PJ, Holzwarth NAW, Iuşan D, Jochym DB, Jollet F, Jones D, Kresse G, Koepernik K, Küçükbenli E, Kvashnin YO, Locht ILM, Lubeck S, Marsman M, Marzari N, Nitzsche U, Nordström L, Ozaki T, Paulatto L, Pickard CJ, Poelmans W, Probert MIJ, Refson K, Richter M, Rignanese GM, Saha S, Scheffler M, Schlipf M, Schwarz K, Sharma S, Tavazza F, Thunström P, Tkatchenko A, Torrent M, Vanderbilt D, van Setten MJ, Van Speybroeck V, Wills JM, Yates JR, Zhang GX, Cottenier S. Reproducibility in density functional theory calculations of solids. Science 2016; 351:aad3000. [PMID: 27013736 DOI: 10.1126/science.aad3000] [Citation(s) in RCA: 414] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 02/19/2016] [Indexed: 11/02/2022]
Abstract
The widespread popularity of density functional theory has given rise to an extensive range of dedicated codes for predicting molecular and crystalline properties. However, each code implements the formalism in a different way, raising questions about the reproducibility of such predictions. We report the results of a community-wide effort that compared 15 solid-state codes, using 40 different potentials or basis set types, to assess the quality of the Perdew-Burke-Ernzerhof equations of state for 71 elemental crystals. We conclude that predictions from recent codes and pseudopotentials agree very well, with pairwise differences that are comparable to those between different high-precision experiments. Older methods, however, have less precise agreement. Our benchmark provides a framework for users and developers to document the precision of new applications and methodological improvements.
Collapse
Affiliation(s)
- Kurt Lejaeghere
- Center for Molecular Modeling, Ghent University, Technologiepark 903, BE-9052 Zwijnaarde, Belgium
| | - Gustav Bihlmayer
- Peter Grünberg Institute and Institute for Advanced Simulation, Forschungszentrum Jülich and JARA (Jülich Aachen Research Alliance), D-52425 Jülich, Germany
| | - Torbjörn Björkman
- Department of Physics, Åbo Akademi, FI-20500 Turku, Finland. Centre of Excellence in Computational Nanoscience (COMP) and Department of Applied Physics, Aalto University School of Science, Post Office Box 11100, FI-00076 Aalto, Finland
| | - Peter Blaha
- Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9/165-TC, A-1060 Vienna, Austria
| | - Stefan Blügel
- Peter Grünberg Institute and Institute for Advanced Simulation, Forschungszentrum Jülich and JARA (Jülich Aachen Research Alliance), D-52425 Jülich, Germany
| | - Volker Blum
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Damien Caliste
- Université Grenoble Alpes, Institut Nanosciences et Cryogénie-Modeling and Material Exploration Department (INAC-MEM), Laboratoire de Simulation Atomistique (L_Sim), F-38042 Grenoble, France. Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), INAC-MEM, L_Sim, F-38054 Grenoble, France
| | - Ivano E Castelli
- Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Stewart J Clark
- Department of Physics, University of Durham, Durham DH1 3LE, UK
| | - Andrea Dal Corso
- International School for Advanced Studies (SISSA) and DEMOCRITOS, Consiglio Nazionale delle Ricerche-Istituto Officina dei Materiali (CNR-IOM), Via Bonomea 265, I-34136 Trieste, Italy
| | - Stefano de Gironcoli
- International School for Advanced Studies (SISSA) and DEMOCRITOS, Consiglio Nazionale delle Ricerche-Istituto Officina dei Materiali (CNR-IOM), Via Bonomea 265, I-34136 Trieste, Italy
| | - Thierry Deutsch
- Université Grenoble Alpes, Institut Nanosciences et Cryogénie-Modeling and Material Exploration Department (INAC-MEM), Laboratoire de Simulation Atomistique (L_Sim), F-38042 Grenoble, France. Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), INAC-MEM, L_Sim, F-38054 Grenoble, France
| | - John Kay Dewhurst
- Max-Planck-Institut für Mikrostrukturphysik, Weinberg 2, D-06120 Halle, Germany
| | - Igor Di Marco
- Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Post Office Box 516, SE-75120 Uppsala, Sweden
| | - Claudia Draxl
- Institut für Physik and Integrative Research Institute for the Sciences (IRIS)-Adlershof, Humboldt-Universität zu Berlin, Zum Großen Windkanal 6, D-12489 Berlin, Germany. Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Marcin Dułak
- Center for Atomic-Scale Materials Design, Department of Physics, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Olle Eriksson
- Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Post Office Box 516, SE-75120 Uppsala, Sweden
| | - José A Flores-Livas
- Max-Planck-Institut für Mikrostrukturphysik, Weinberg 2, D-06120 Halle, Germany
| | - Kevin F Garrity
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8553, Gaithersburg, MD 20899, USA
| | - Luigi Genovese
- Université Grenoble Alpes, Institut Nanosciences et Cryogénie-Modeling and Material Exploration Department (INAC-MEM), Laboratoire de Simulation Atomistique (L_Sim), F-38042 Grenoble, France. Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), INAC-MEM, L_Sim, F-38054 Grenoble, France
| | - Paolo Giannozzi
- Department of Mathematics, Computer Science, and Physics, University of Udine, Via delle Scienze 206, I-33100 Udine, Italy
| | - Matteo Giantomassi
- Institute of Condensed Matter and Nanosciences-Nanoscopic Physics (NAPS), Université Catholique de Louvain, Chemin des Étoiles 8, BE-1348 Louvain-la-Neuve, Belgium
| | - Stefan Goedecker
- Institut für Physik, Universität Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
| | - Xavier Gonze
- Institute of Condensed Matter and Nanosciences-Nanoscopic Physics (NAPS), Université Catholique de Louvain, Chemin des Étoiles 8, BE-1348 Louvain-la-Neuve, Belgium
| | - Oscar Grånäs
- Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Post Office Box 516, SE-75120 Uppsala, Sweden. School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - E K U Gross
- Max-Planck-Institut für Mikrostrukturphysik, Weinberg 2, D-06120 Halle, Germany
| | - Andris Gulans
- Institut für Physik and Integrative Research Institute for the Sciences (IRIS)-Adlershof, Humboldt-Universität zu Berlin, Zum Großen Windkanal 6, D-12489 Berlin, Germany. Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - François Gygi
- Department of Computer Science, University of California-Davis, Davis, CA 95616, USA
| | - D R Hamann
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854-8019, USA. Mat-Sim Research, Post Office Box 742, Murray Hill, NJ 07974, USA
| | - Phil J Hasnip
- Department of Physics, University of York, Heslington, York YO10 5DD, UK
| | - N A W Holzwarth
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Diana Iuşan
- Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Post Office Box 516, SE-75120 Uppsala, Sweden
| | - Dominik B Jochym
- Scientific Computing Department, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK
| | | | - Daniel Jones
- Department of Materials, University of Oxford, 16 Parks Road, Oxford OX1 3PH, UK
| | - Georg Kresse
- Faculty of Physics and Center for Computational Materials Science, University of Vienna, Sensengasse 8/12, A-1090 Vienna, Austria
| | - Klaus Koepernik
- Leibniz‑Institut für Festkörper- und Werkstoffforschung (IFW) Dresden, Post Office Box 270 116, D-01171 Dresden, Germany. Dresden Center for Computational Materials Science (DCMS), Technische Universität Dresden, D-01069 Dresden, Germany
| | - Emine Küçükbenli
- Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland. International School for Advanced Studies (SISSA) and DEMOCRITOS, Consiglio Nazionale delle Ricerche-Istituto Officina dei Materiali (CNR-IOM), Via Bonomea 265, I-34136 Trieste, Italy
| | - Yaroslav O Kvashnin
- Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Post Office Box 516, SE-75120 Uppsala, Sweden
| | - Inka L M Locht
- Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Post Office Box 516, SE-75120 Uppsala, Sweden. Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - Sven Lubeck
- Institut für Physik and Integrative Research Institute for the Sciences (IRIS)-Adlershof, Humboldt-Universität zu Berlin, Zum Großen Windkanal 6, D-12489 Berlin, Germany
| | - Martijn Marsman
- Faculty of Physics and Center for Computational Materials Science, University of Vienna, Sensengasse 8/12, A-1090 Vienna, Austria
| | - Nicola Marzari
- Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Ulrike Nitzsche
- Leibniz‑Institut für Festkörper- und Werkstoffforschung (IFW) Dresden, Post Office Box 270 116, D-01171 Dresden, Germany
| | - Lars Nordström
- Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Post Office Box 516, SE-75120 Uppsala, Sweden
| | - Taisuke Ozaki
- Institute for Solid State Physics, The University of Tokyo, Kashiwa 277-8581, Japan
| | - Lorenzo Paulatto
- Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie (IMPMC), Sorbonne Universités-Pierre and Marie Curie University Paris 06, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7590, Muséum National d'Histoire Naturelle, Institut de Recherche pour le Développement (IRD) Unité de Recherche 206, 4 Place Jussieu, F-75005 Paris, France
| | - Chris J Pickard
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS, UK
| | - Ward Poelmans
- Center for Molecular Modeling, Ghent University, Technologiepark 903, BE-9052 Zwijnaarde, Belgium. High Performance Computing Unit, Ghent University, Krijgslaan 281 S9, BE-9000 Ghent, Belgium
| | - Matt I J Probert
- Department of Physics, University of York, Heslington, York YO10 5DD, UK
| | - Keith Refson
- Department of Physics, Royal Holloway, University of London, Egham TW20 0EX, UK. ISIS Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK
| | - Manuel Richter
- Leibniz‑Institut für Festkörper- und Werkstoffforschung (IFW) Dresden, Post Office Box 270 116, D-01171 Dresden, Germany. Dresden Center for Computational Materials Science (DCMS), Technische Universität Dresden, D-01069 Dresden, Germany
| | - Gian-Marco Rignanese
- Institute of Condensed Matter and Nanosciences-Nanoscopic Physics (NAPS), Université Catholique de Louvain, Chemin des Étoiles 8, BE-1348 Louvain-la-Neuve, Belgium
| | - Santanu Saha
- Institut für Physik, Universität Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
| | - Matthias Scheffler
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany. Department of Chemistry and Biochemistry and Materials Department, University of California-Santa Barbara, Santa Barbara, CA 93106-5050, USA
| | - Martin Schlipf
- Department of Computer Science, University of California-Davis, Davis, CA 95616, USA
| | - Karlheinz Schwarz
- Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9/165-TC, A-1060 Vienna, Austria
| | - Sangeeta Sharma
- Max-Planck-Institut für Mikrostrukturphysik, Weinberg 2, D-06120 Halle, Germany
| | - Francesca Tavazza
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8553, Gaithersburg, MD 20899, USA
| | - Patrik Thunström
- Institute for Solid State Physics, Vienna University of Technology, A-1040 Vienna, Austria
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany. Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg
| | | | - David Vanderbilt
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854-8019, USA
| | - Michiel J van Setten
- Institute of Condensed Matter and Nanosciences-Nanoscopic Physics (NAPS), Université Catholique de Louvain, Chemin des Étoiles 8, BE-1348 Louvain-la-Neuve, Belgium
| | - Veronique Van Speybroeck
- Center for Molecular Modeling, Ghent University, Technologiepark 903, BE-9052 Zwijnaarde, Belgium
| | - John M Wills
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jonathan R Yates
- Department of Materials, University of Oxford, 16 Parks Road, Oxford OX1 3PH, UK
| | - Guo-Xu Zhang
- Institute of Theoretical and Simulational Chemistry, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, People's Republic of China
| | - Stefaan Cottenier
- Center for Molecular Modeling, Ghent University, Technologiepark 903, BE-9052 Zwijnaarde, Belgium. Department of Materials Science and Engineering, Ghent University, Technologiepark 903, BE-9052 Zwijnaarde, Belgium
| |
Collapse
|
24
|
Vardavas CI, Hohmann C, Patelarou E, Martinez D, Henderson AJ, Granell R, Sunyer J, Torrent M, Fantini MP, Gori D, Annesi-Maesano I, Slama R, Duijts L, de Jongste JC, Aurrekoetxea JJ, Basterrechea M, Morales E, Ballester F, Murcia M, Thijs C, Mommers M, Kuehni CE, Gaillard EA, Tischer C, Heinrich J, Pizzi C, Zugna D, Gehring U, Wijga A, Chatzi L, Vassilaki M, Bergström A, Eller E, Lau S, Keil T, Nieuwenhuijsen M, Kogevinas M. The independent role of prenatal and postnatal exposure to active and passive smoking on the development of early wheeze in children. Eur Respir J 2016; 48:115-24. [PMID: 26965294 DOI: 10.1183/13993003.01016-2015] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 01/27/2016] [Indexed: 11/05/2022]
Abstract
Maternal smoking during pregnancy increases childhood asthma risk, but health effects in children of nonsmoking mothers passively exposed to tobacco smoke during pregnancy are unclear. We examined the association of maternal passive smoking during pregnancy and wheeze in children aged ≤2 years.Individual data of 27 993 mother-child pairs from 15 European birth cohorts were combined in pooled analyses taking into consideration potential confounders.Children with maternal exposure to passive smoking during pregnancy and no other smoking exposure were more likely to develop wheeze up to the age of 2 years (OR 1.11, 95% CI 1.03-1.20) compared with unexposed children. Risk of wheeze was further increased by children's postnatal passive smoke exposure in addition to their mothers' passive exposure during pregnancy (OR 1.29, 95% CI 1.19-1.40) and highest in children with both sources of passive exposure and mothers who smoked actively during pregnancy (OR 1.73, 95% CI 1.59-1.88). Risk of wheeze associated with tobacco smoke exposure was higher in children with an allergic versus nonallergic family history.Maternal passive smoking exposure during pregnancy is an independent risk factor for wheeze in children up to the age of 2 years. Pregnant females should avoid active and passive exposure to tobacco smoke for the benefit of their children's health.
Collapse
Affiliation(s)
- C I Vardavas
- Dept of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Greece Center for Global Tobacco Control, Dept of Society, Human Development and Health, Harvard School of Public Health, Boston, MA, USA
| | - C Hohmann
- Institute of Social Medicine, Epidemiology and Health Economics, Charité Universitätsmedizin Berlin, Berlin, Germany University of Otago, Dunedin, New Zealand
| | - E Patelarou
- Dept of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Greece Florence Nightingale Faculty of Nursing and Midwifery, King's College London, London, UK
| | - D Martinez
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain Dept of Experimental and Health Sciences, University of Pompeu Fabra (UPF), Barcelona, Spain
| | - A J Henderson
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - R Granell
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - J Sunyer
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain Dept of Experimental and Health Sciences, University of Pompeu Fabra (UPF), Barcelona, Spain Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - M Torrent
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain IB-Salut, Area de Salut de Menorca, Spain
| | - M P Fantini
- Dept of Biomedical and Neuromotor Sciences, University of Bologna - Alma Mater Studiorum, Bologna, Italy
| | - D Gori
- Dept of Biomedical and Neuromotor Sciences, University of Bologna - Alma Mater Studiorum, Bologna, Italy
| | - I Annesi-Maesano
- Inserm, Epidemiology of Allergic and Respiratory diseases (EPAR) Dept, U1136, Medical School Saint-Antoine, Univ6, Sorbonne Universités Paris, Paris, France UPMC, EPAR UMR-S 707, Medical School Saint-Antoine, Univ6, Sorbonne Universités Paris, Paris, France
| | - R Slama
- Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, Inserm and Univ Grenoble Alpes Joint Research Centre (IAB, U823), Grenoble, France
| | - L Duijts
- The Generation R Study Group, Dept of Paediatrics, Division of Respiratory Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands Dept of Paediatrics, Division of Neonatology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands Dept of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - J C de Jongste
- The Generation R Study Group, Dept of Paediatrics, Division of Respiratory Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - J J Aurrekoetxea
- Faculty of Medicine, University of the Basque Country (UPV/EHU), San Sebastian, Spain BIODONOSTIA Health Research Institute, San Sebastian, Spain Subdirección de Salud Pública de Gipuzkoa; Departamento de Sanidad del Gobierno Vasco, San Sebastian, Spain
| | - M Basterrechea
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain BIODONOSTIA Health Research Institute, San Sebastian, Spain Subdirección de Salud Pública de Gipuzkoa; Departamento de Sanidad del Gobierno Vasco, San Sebastian, Spain
| | - E Morales
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain Virgen de la Arrixaca Universtiy Hospital, IMIB-Arrixaca Research Institute, Murcia, Spain
| | - F Ballester
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain FISABIO-Universitat de València-Universitat Jaume I Joint Research Unit of Epidemiology and Environmental Health, Valencia, Spain
| | - M Murcia
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain FISABIO-Universitat de València-Universitat Jaume I Joint Research Unit of Epidemiology and Environmental Health, Valencia, Spain
| | - C Thijs
- Dept of Epidemiology, CAPHRI School of Public Health and Primary Care, Maastricht University, Maastricht, The Netherlands
| | - M Mommers
- Dept of Epidemiology, CAPHRI School of Public Health and Primary Care, Maastricht University, Maastricht, The Netherlands
| | - C E Kuehni
- Paediatric Respiratory Epidemiology, Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - E A Gaillard
- Institute for Lung Health, Dept of Infection Immunity and Inflammation, NIHR Leicester Respiratory Biomedical Research Unit, University of Leicester, Leicester, UK
| | - C Tischer
- Institute of Epidemiology I, German Research Centre for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany
| | - J Heinrich
- Institute of Epidemiology I, German Research Centre for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany Institute and Outpatient Clinic for Occupational, Social, and Environmental Medicine, Ludwig Maximilians University Munich, München, Germany
| | - C Pizzi
- Cancer Epidemiology Unit, Dept of Medical Sciences, University of Turin, CPO Piedmont, Turin, Italy
| | - D Zugna
- Cancer Epidemiology Unit, Dept of Medical Sciences, University of Turin, CPO Piedmont, Turin, Italy
| | - U Gehring
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - A Wijga
- Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - L Chatzi
- Dept of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - M Vassilaki
- Dept of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - A Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - E Eller
- Dept of Dermatology and Allergy Centre, Odense University Hospital, Odense, Denmark
| | - S Lau
- Dept for Pediatric Pneumology and Immunology, Charité University Medical Centre, Berlin, Germany
| | - T Keil
- Institute of Social Medicine, Epidemiology and Health Economics, Charité Universitätsmedizin Berlin, Berlin, Germany Institute of Clinical Epidemiology and Biometry, University of Würzburg, Würzburg, Germany
| | - M Nieuwenhuijsen
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain Dept of Experimental and Health Sciences, University of Pompeu Fabra (UPF), Barcelona, Spain
| | - M Kogevinas
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain Dept of Experimental and Health Sciences, University of Pompeu Fabra (UPF), Barcelona, Spain Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| |
Collapse
|
25
|
Bousquet J, Anto JM, Wickman M, Keil T, Valenta R, Haahtela T, Lodrup Carlsen K, van Hage M, Akdis C, Bachert C, Akdis M, Auffray C, Annesi-Maesano I, Bindslev-Jensen C, Cambon-Thomsen A, Carlsen KH, Chatzi L, Forastiere F, Garcia-Aymerich J, Gehrig U, Guerra S, Heinrich J, Koppelman GH, Kowalski ML, Lambrecht B, Lupinek C, Maier D, Melén E, Momas I, Palkonen S, Pinart M, Postma D, Siroux V, Smit HA, Sunyer J, Wright J, Zuberbier T, Arshad SH, Nadif R, Thijs C, Andersson N, Asarnoj A, Ballardini N, Ballereau S, Bedbrook A, Benet M, Bergstrom A, Brunekreef B, Burte E, Calderon M, De Carlo G, Demoly P, Eller E, Fantini MP, Hammad H, Hohman C, Just J, Kerkhof M, Kogevinas M, Kull I, Lau S, Lemonnier N, Mommers M, Nawijn M, Neubauer A, Oddie S, Pellet J, Pin I, Porta D, Saes Y, Skrindo I, Tischer CG, Torrent M, von Hertzen L. Are allergic multimorbidities and IgE polysensitization associated with the persistence or re-occurrence of foetal type 2 signalling? The MeDALL hypothesis. Allergy 2015; 70:1062-78. [PMID: 25913421 DOI: 10.1111/all.12637] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2015] [Indexed: 12/22/2022]
Abstract
Allergic diseases [asthma, rhinitis and atopic dermatitis (AD)] are complex. They are associated with allergen-specific IgE and nonallergic mechanisms that may coexist in the same patient. In addition, these diseases tend to cluster and patients present concomitant or consecutive diseases (multimorbidity). IgE sensitization should be considered as a quantitative trait. Important clinical and immunological differences exist between mono- and polysensitized subjects. Multimorbidities of allergic diseases share common causal mechanisms that are only partly IgE-mediated. Persistence of allergic diseases over time is associated with multimorbidity and/or IgE polysensitization. The importance of the family history of allergy may decrease with age. This review puts forward the hypothesis that allergic multimorbidities and IgE polysensitization are associated and related to the persistence or re-occurrence of foetal type 2 signalling. Asthma, rhinitis and AD are manifestations of a common systemic immune imbalance (mesodermal origin) with specific patterns of remodelling (ectodermal or endodermal origin). This study proposes a new classification of IgE-mediated allergic diseases that allows the definition of novel phenotypes to (i) better understand genetic and epigenetic mechanisms, (ii) better stratify allergic preschool children for prognosis and (iii) propose novel strategies of treatment and prevention.
Collapse
Affiliation(s)
- J. Bousquet
- University Hospital; Montpellier France
- MACVIA-LR; Contre les MAladies Chroniques pour un VIeillissement Actif en Languedoc-Roussillon; European Innovation Partnership on Active and Healthy Ageing Reference Site; Paris France
- INSERM; VIMA: Ageing and Chronic Diseases Epidemiological and Public Health Approaches, U1168; Paris France
- UVSQ; UMR-S 1168; Université Versailles St-Quentin-en-Yvelines; Versailles France
| | - J. M. Anto
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- Hospital del Mar Research Institute (IMIM); Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP); Barcelona Spain
- Department of Experimental and Health Sciences; University of Pompeu Fabra (UPF); Barcelona Spain
| | - M. Wickman
- Sachs’ Children's Hospital; Stockholm Sweden
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | - T. Keil
- Institute of Social Medicine, Epidemiology and Health Economics; Charité - Universitätsmedizin Berlin; Berlin Germany
- Institute for Clinical Epidemiology and Biometry; University of Wuerzburg; Wuerzburg Germany
| | - R. Valenta
- Division of Immunopathology; Department of Pathophysiology and Allergy Research; Center for Pathophysiology, Infectiology and Immunology; Medical University of Vienna; Vienna Austria
| | - T. Haahtela
- Skin and Allergy Hospital; Helsinki University Hospital; Helsinki Finland
| | - K. Lodrup Carlsen
- Department of Paediatrics; Oslo University Hospital; Oslo Norway
- Faculty of Medicine; Institute of Clinical Medicine; University of Oslo; Oslo Norway
| | - M. van Hage
- Clinical Immunology and Allergy Unit; Department of Medicine Solna; Karolinska Institutet and University Hospital; Stockholm Sweden
| | - C. Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF); University of Zurich; Davos Switzerland
| | - C. Bachert
- ENT Department; Ghent University Hospital; Gent Belgium
| | - M. Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF); University of Zurich; Davos Switzerland
| | - C. Auffray
- European Institute for Systems Biology and Medicine; Lyon France
| | - I. Annesi-Maesano
- EPAR U707 INSERM; Paris France
- EPAR UMR-S UPMC; Paris VI; Paris France
| | - C. Bindslev-Jensen
- Department of Dermatology and Allergy Centre; Odense University Hospital; Odense Denmark
| | - A. Cambon-Thomsen
- UMR Inserm U1027; Université de Toulouse III Paul Sabatier; Toulouse France
| | - K. H. Carlsen
- Department of Paediatrics; Oslo University Hospital; Oslo Norway
- University of Oslo; Oslo Norway
| | - L. Chatzi
- Department of Social Medicine; Faculty of Medicine; University of Crete; Heraklion Crete Greece
| | - F. Forastiere
- Department of Epidemiology; Regional Health Service Lazio Region; Rome Italy
| | - J. Garcia-Aymerich
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- Hospital del Mar Research Institute (IMIM); Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP); Barcelona Spain
- Department of Experimental and Health Sciences; University of Pompeu Fabra (UPF); Barcelona Spain
| | - U. Gehrig
- Julius Center of Health Sciences and Primary Care; University Medical Center Utrecht; University of Utrecht; Utrecht the Netherlands
| | - S. Guerra
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
| | - J. Heinrich
- Institute of Epidemiology; German Research Centre for Environmental Health; Helmholtz Zentrum München; Neuherberg Germany
| | - G. H. Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology; GRIAC Research Institute; University Medical Center Groningen; Beatrix Children's Hospital; University of Groningen; Groningen the Netherlands
| | - M. L. Kowalski
- Department of Immunology, Rheumatology and Allergy; Medical University of Lodz; Lodz Poland
| | - B. Lambrecht
- VIB Inflammation Research Center; Ghent University; Ghent Belgium
| | - C. Lupinek
- Division of Immunopathology; Department of Pathophysiology and Allergy Research; Center for Pathophysiology, Infectiology and Immunology; Medical University of Vienna; Vienna Austria
| | | | - E. Melén
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | - I. Momas
- Department of Public Health and Biostatistics, EA 4064; Paris Descartes University; Paris France
- Paris Municipal Department of Social Action, Childhood, and Health; Paris France
| | - S. Palkonen
- EFA European Federation of Allergy and Airways Diseases Patients' Associations; Brussels Belgium
| | - M. Pinart
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
| | - D. Postma
- Department of Respiratory Medicine; GRIAC Research Institute; University Medical Center Groningen; Beatrix Children's Hospital; University of Groningen; Groningen the Netherlands
| | | | - H. A. Smit
- Julius Center of Health Sciences and Primary Care; University Medical Center Utrecht; University of Utrecht; Utrecht the Netherlands
| | - J. Sunyer
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- Hospital del Mar Research Institute (IMIM); Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP); Barcelona Spain
- Department of Experimental and Health Sciences; University of Pompeu Fabra (UPF); Barcelona Spain
| | - J. Wright
- Bradford Institute for Health Research; Bradford Royal Infirmary; Bradford UK
| | - T. Zuberbier
- Allergy-Centre-Charité at the Department of Dermatology; Charité - Universitätsmedizin Berlin; Berlin Germany
- Secretary General of the Global Allergy and Asthma European Network (GA2LEN); Berlin Germany
| | - S. H. Arshad
- David Hide Asthma and Allergy Research Centre; Isle of Wight UK
| | - R. Nadif
- INSERM; VIMA: Ageing and Chronic Diseases Epidemiological and Public Health Approaches, U1168; Paris France
- UVSQ; UMR-S 1168; Université Versailles St-Quentin-en-Yvelines; Versailles France
| | - C. Thijs
- Department of Epidemiology; CAPHRI School of Public Health and Primary Care; Maastricht University; Maastricht the Netherlands
| | - N. Andersson
- Sachs’ Children's Hospital; Stockholm Sweden
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | - A. Asarnoj
- Sachs’ Children's Hospital; Stockholm Sweden
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | - N. Ballardini
- Sachs’ Children's Hospital; Stockholm Sweden
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | - S. Ballereau
- European Institute for Systems Biology and Medicine; Lyon France
| | - A. Bedbrook
- MACVIA-LR; Contre les MAladies Chroniques pour un VIeillissement Actif en Languedoc-Roussillon; European Innovation Partnership on Active and Healthy Ageing Reference Site; Paris France
| | - M. Benet
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
| | - A. Bergstrom
- Sachs’ Children's Hospital; Stockholm Sweden
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | - B. Brunekreef
- Julius Center of Health Sciences and Primary Care; University Medical Center Utrecht; University of Utrecht; Utrecht the Netherlands
| | - E. Burte
- INSERM; VIMA: Ageing and Chronic Diseases Epidemiological and Public Health Approaches, U1168; Paris France
- UVSQ; UMR-S 1168; Université Versailles St-Quentin-en-Yvelines; Versailles France
| | - M. Calderon
- National Heart and Lung Institute; Imperial College London; Royal Brompton Hospital NHS; London UK
| | - G. De Carlo
- EFA European Federation of Allergy and Airways Diseases Patients' Associations; Brussels Belgium
| | - P. Demoly
- Department of Respiratory Diseases; Montpellier University Hospital; Montpellier France
| | - E. Eller
- Department of Dermatology and Allergy Centre; Odense University Hospital; Odense Denmark
| | - M. P. Fantini
- Department of Medicine and Public Health; Alma Mater Studiorum - University of Bologna; Bologna Italy
| | - H. Hammad
- VIB Inflammation Research Center; Ghent University; Ghent Belgium
| | - C. Hohman
- Institute of Social Medicine, Epidemiology and Health Economics; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - J. Just
- Allergology Department; Centre de l'Asthme et des Allergies; Hôpital d'Enfants Armand-Trousseau (APHP); Paris France
- Institut Pierre Louis d'Epidémiologie et de Santé Publique; Equipe EPAR; Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1136; Paris France
| | - M. Kerkhof
- Department of Respiratory Medicine; GRIAC Research Institute; University Medical Center Groningen; Beatrix Children's Hospital; University of Groningen; Groningen the Netherlands
| | - M. Kogevinas
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- Hospital del Mar Research Institute (IMIM); Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP); Barcelona Spain
- Department of Experimental and Health Sciences; University of Pompeu Fabra (UPF); Barcelona Spain
| | - I. Kull
- Sachs’ Children's Hospital; Stockholm Sweden
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | - S. Lau
- Department for Pediatric Pneumology and Immunology; Charité Medical University; Berlin Germany
| | - N. Lemonnier
- European Institute for Systems Biology and Medicine; Lyon France
| | - M. Mommers
- Department of Epidemiology; CAPHRI School of Public Health and Primary Care; Maastricht University; Maastricht the Netherlands
| | - M. Nawijn
- Department of Pediatric Pulmonology and Pediatric Allergology; GRIAC Research Institute; University Medical Center Groningen; Beatrix Children's Hospital; University of Groningen; Groningen the Netherlands
| | | | - S. Oddie
- Bradford Institute for Health Research; Bradford Royal Infirmary; Bradford UK
| | - J. Pellet
- European Institute for Systems Biology and Medicine; Lyon France
| | - I. Pin
- Département de pédiatrie; CHU de Grenoble; Grenoble Cedex 9 France
| | - D. Porta
- Department of Epidemiology; Regional Health Service Lazio Region; Rome Italy
| | - Y. Saes
- VIB Inflammation Research Center; Ghent University; Ghent Belgium
| | - I. Skrindo
- Department of Paediatrics; Oslo University Hospital; Oslo Norway
- Faculty of Medicine; Institute of Clinical Medicine; University of Oslo; Oslo Norway
| | - C. G. Tischer
- Institute of Epidemiology; German Research Centre for Environmental Health; Helmholtz Zentrum München; Neuherberg Germany
| | - M. Torrent
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- Area de Salut de Menorca, ib-salut; Illes Balears Spain
| | - L. von Hertzen
- Skin and Allergy Hospital; Helsinki University Hospital; Helsinki Finland
| |
Collapse
|
26
|
Casas L, Sunyer J, Tischer C, Gehring U, Wickman M, Garcia-Esteban R, Lehmann I, Kull I, Reich A, Lau S, Wijga A, Antó JM, Nawrot TS, Heinrich J, Keil T, Torrent M. Reply: To PMID 25858551. Allergy 2015; 70:1190-1191. [PMID: 26535423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- L Casas
- Centre for Environment and Health - Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Asselbergs IC, Eikenboom HC, Wartna JB, Koes BW, Casas L, Sunyer J, Tischer C, Gehring U, Wickman M, Garcia-Esteban R, Lehmann I, Kull I, Reich A, Lau S, Wijga A, Antó JM, Nawrot TS, Heinrich J, Keil T, Torrent M. Early-life house dust mite allergens, childhood mite sensitization, and respiratory outcomes. Allergy 2015; 70:1190-91. [DOI: 10.1111/all.12665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- I. C. Asselbergs
- Department of General Practice; Erasmus MC; University Medical Center Rotterdam; Rotterdam Netherlands
| | - H. C. Eikenboom
- Department of General Practice; Erasmus MC; University Medical Center Rotterdam; Rotterdam Netherlands
| | - J. B. Wartna
- Department of General Practice; Erasmus MC; University Medical Center Rotterdam; Rotterdam Netherlands
| | - B. W. Koes
- Department of General Practice; Erasmus MC; University Medical Center Rotterdam; Rotterdam Netherlands
| | - L. Casas
- Centre for Environment and Health - Department of Public Health and Primary Care; KU Leuven; Leuven Belgium
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- CIBER Epidemiologia y Salud Pública (CIBERESP); Barcelona Spain
| | - J. Sunyer
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- CIBER Epidemiologia y Salud Pública (CIBERESP); Barcelona Spain
- Hospital del Mar Medical Research Institute (IMIM); Barcelona Spain
- Universitat Pompeu Fabra (UPF); Barcelona Spain
| | - C. Tischer
- Helmholtz Zentrum München; German Research Centre for Environmental Health; Institute of Epidemiology I; Neuherberg Germany
| | - U. Gehring
- Division of Environmental Epidemiology; Institute for Risk Assessment Sciences; Utrecht University; Utrecht the Netherlands
| | - M. Wickman
- Department of Clinical Science and Education; Södersjukhuset; Karolinska Institutet; Stockholm Sweden
- Sach's Children's Hospital; Stockholm Sweden
| | - R. Garcia-Esteban
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- CIBER Epidemiologia y Salud Pública (CIBERESP); Barcelona Spain
- Hospital del Mar Medical Research Institute (IMIM); Barcelona Spain
| | - I. Lehmann
- Institute for environmental medicine; Karolinska Institutet; Stockholm Sweden
- Department of Environmental Immunology; FZ-Helmholtz Centre for Environmental Research Leipzig; Leipzig Germany
| | - I. Kull
- Department of Clinical Science and Education; Södersjukhuset; Karolinska Institutet; Stockholm Sweden
- Sach's Children's Hospital; Stockholm Sweden
| | - A. Reich
- Institute of Social Medicine, Epidemiology and Health Economics; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - S. Lau
- Klinik für Pädiatrie m. S. Pneumologie und Immunologie; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - A. Wijga
- Centre for Nutrition, Prevention and Health Services; National Institute for Public Health and the Environment (RIVM); Bilthoven the Netherlands
| | - J. M. Antó
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- CIBER Epidemiologia y Salud Pública (CIBERESP); Barcelona Spain
- Hospital del Mar Medical Research Institute (IMIM); Barcelona Spain
- Universitat Pompeu Fabra (UPF); Barcelona Spain
| | - T. S. Nawrot
- Centre for Environment and Health - Department of Public Health and Primary Care; KU Leuven; Leuven Belgium
- Centre for Environmental Sciences; Hasselt University; Hasselt Belgium
| | - J. Heinrich
- Helmholtz Zentrum München; German Research Centre for Environmental Health; Institute of Epidemiology I; Neuherberg Germany
- Comprehensive Pneumology Center Munich (CPC-M); German Center for Lung Research (DZL); Munich Germany
| | - T. Keil
- Institute of Social Medicine, Epidemiology and Health Economics; Charité - Universitätsmedizin Berlin; Berlin Germany
- Institute of Clinical Epidemiology and Biometry; University of Wuerzburg; Wuerzburg Germany
| | - M. Torrent
- Area de Salud de Menorca; IB-SALUT; Menorca Spain
| |
Collapse
|
28
|
Casas L, Sunyer J, Tischer C, Gehring U, Wickman M, Garcia-Esteban R, Lehmann I, Kull I, Reich A, Lau S, Wijga A, Antó JM, Nawrot TS, Heinrich J, Keil T, Torrent M. Early-life house dust mite allergens, childhood mite sensitization, and respiratory outcomes. Allergy 2015; 70:820-7. [PMID: 25858551 DOI: 10.1111/all.12626] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2015] [Indexed: 11/29/2022]
Abstract
BACKGROUND Exposure to indoor allergens during early life may play a role in the development of the immune system and inception of asthma. OBJECTIVE To describe the house dust mite (HDM) allergen concentrations in bedroom dust during early life and to evaluate its associations with HDM sensitization, wheezing, and asthma, from birth to school age, in 5 geographically spread European birth cohorts. METHODS We included 4334 children from INMA-Menorca (Spain), BAMSE (Sweden), LISAplus and MAS (Germany), and PIAMA-NHS (the Netherlands). Dust samples were collected from bedrooms during early life and analyzed for Dermatophagoides pteronyssinus (Der p1) and Dermatophagoides farinae (Der f1). HDM concentrations were divided into four categories. Sensitization was determined by specific IgE. Wheezing and asthma information up to 8/10 years was collected through questionnaires. We performed mixed-effects logistic regression models and expressed associations as odds ratios with 95% confidence intervals. RESULTS House dust mite concentrations varied across cohorts. Mean allergen concentrations were highest in INMA-Menorca (geometric mean (GM) Der p1 = 3.3 μg/g) and LISAplus (GM Der f1 = 2.1 μg/g) and lowest in BAMSE (GM Der p1 = 0.1 μg/g, Der f1 = 0.3 μg/g). Moderate and high HDM concentrations were significantly (P-values < 0.05) associated with 50-90% higher prevalence of HDM sensitization. No significant associations were observed with respiratory outcomes. CONCLUSION Our study based on geographically spread regions, a large sample size, and a wide range of allergen concentration shows that HDM allergen concentrations vary across regions and that exposure during early life plays a role in the development of allergic sensitization but not in the development of respiratory outcomes.
Collapse
Affiliation(s)
- L. Casas
- Department of Public Health and Primary Care; Centre for Environment and Health; KU Leuven; Leuven Belgium
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- CIBER Epidemiologia y Salud Pública (CIBERESP); Barcelona Spain
| | - J. Sunyer
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- CIBER Epidemiologia y Salud Pública (CIBERESP); Barcelona Spain
- Hospital del Mar Medical Research Institute (IMIM); Barcelona Spain
- Universitat Pompeu Fabra (UPF); Barcelona Spain
| | - C. Tischer
- Helmholtz Zentrum München; German Research Centre for Environmental Health; Institute of Epidemiology I; Neuherberg Germany
| | - U. Gehring
- Division of Environmental Epidemiology; Institute for Risk Assessment Sciences; Utrecht University; Utrecht The Netherlands
| | - M. Wickman
- Department of Clinical Science and Education; Södersjukhuset; Karolinska Institutet; Stockholm Sweden
- Sach's Children's Hospital; Stockholm Sweden
- Institute for Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | - R. Garcia-Esteban
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- CIBER Epidemiologia y Salud Pública (CIBERESP); Barcelona Spain
- Hospital del Mar Medical Research Institute (IMIM); Barcelona Spain
| | - I. Lehmann
- Department of Environmental Immunology; FZ-Helmholtz Centre for Environmental Research Leipzig; Leipzig Germany
| | - I. Kull
- Department of Clinical Science and Education; Södersjukhuset; Karolinska Institutet; Stockholm Sweden
- Sach's Children's Hospital; Stockholm Sweden
- Institute for Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | - A. Reich
- Institute of Social Medicine, Epidemiology and Health Economics; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - S. Lau
- Klinik für Pädiatrie m. S. Pneumologie und Immunologie; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - A. Wijga
- Centre for Nutrition, Prevention and Health Services; National Institute for Public Health and the Environment (RIVM); Bilthoven The Netherlands
| | - J. M. Antó
- Centre for Research in Environmental Epidemiology (CREAL); Barcelona Spain
- CIBER Epidemiologia y Salud Pública (CIBERESP); Barcelona Spain
- Hospital del Mar Medical Research Institute (IMIM); Barcelona Spain
- Universitat Pompeu Fabra (UPF); Barcelona Spain
| | - T. S. Nawrot
- Department of Public Health and Primary Care; Centre for Environment and Health; KU Leuven; Leuven Belgium
- Centre for Environmental Sciences; Hasselt University; Hasselt Belgium
| | - J. Heinrich
- Helmholtz Zentrum München; German Research Centre for Environmental Health; Institute of Epidemiology I; Neuherberg Germany
- Comprehensive Pneumology Center Munich (CPC-M); German Center for Lung Research (DZL); Munich Germany
| | - T. Keil
- Institute of Social Medicine, Epidemiology and Health Economics; Charité - Universitätsmedizin Berlin; Berlin Germany
- Institute of Clinical Epidemiology and Biometry; University of Wuerzburg; Wuerzburg Germany
| | - M. Torrent
- Area de Salud de Menorca; IB-SALUT; Menorca Spain
| |
Collapse
|
29
|
Abstract
Peptides are molecules of varying complexity, with different functions in the organism and with remarkable therapeutic interest. Predicting peptide activity by computational means can help us to understand their mechanism of action and deliver powerful drug-screening methodologies. In this chapter, we describe how to apply artificial neural networks to predict antimicrobial peptide activity.
Collapse
Affiliation(s)
- David Andreu
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003, Barcelona, Spain,
| | | |
Collapse
|
30
|
Abstract
In the assessment of lung cancer, computed tomography guides the use of bronchoscopy and establishes whether local treatment may be appropriate for the NSCLC or whether it is at an advanced stage. Percutaneous biopsy of a lesion suspected to be a metastasis can provide histological confirmation, allowing staging to be carried out at the same time. The initial presentation depends on the staging and histological type, ranging from an isolated nodule or mass to atelectasis or obstructive pneumonia, isolated lymph node disease or isolated pleural effusion to miliary metastasis in tumors showing EGFR mutation. Tumor (T) status depends on tumor size, distance from the carina, and invasion of the chest wall and mediastinal organs. PET-CT is superior to CT in identifying lymph node invasion (N2 for ipsilateral mediastinal disease and N3 for contralateral or supraclavicular disease). As a general rule, all contraindications for surgery should be confirmed via histological examination, with the exception of cerebral metastases.
Collapse
Affiliation(s)
- M-P Revel
- Radiology, Cochin Hospital, 27, rue du Fg St-Jacques, 75014 Paris, France.
| | - M-F Carette
- Radiology, Tenon Hospital, 4, rue de la Chine, 75970 Paris cedex 20, France
| | - M Torrent
- Radiology, La Forêt Polyclinic, 4, rue Lagorsse, 77300 Fontainebleau, France
| | - J Trédaniel
- Pneumology, Saint-Joseph Hospital, 1, avenue Claude-Vellefaux, 75010 Paris, France
| |
Collapse
|
31
|
Rösevall J, Rusu C, Talavera G, Carrabina J, Garcia J, Carenas C, Breuil F, Reixach E, Torrent M, Burkard S, Colitti W. A wireless sensor insole for collecting gait data. Stud Health Technol Inform 2014; 200:176-178. [PMID: 24851988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This paper presents the status of the EU project WIISEL - Wireless Insole for Independent and Safe Elderly Living, with the focus on sensors and wireless communications. Pressure and inertial sensors are embedded into insoles and a smartphone collects data utilizing Bluetooth Low Energy.
Collapse
Affiliation(s)
- John Rösevall
- Acreo Swedish ICT AB, Sensor Systems dept., Gothenburg, Sweden
| | - Cristina Rusu
- Acreo Swedish ICT AB, Sensor Systems dept., Gothenburg, Sweden
| | - Guillermo Talavera
- Universitat Autònoma de Barcelona- CAIAC- Wireless ULP, Barcelona, Spain
| | - Jordi Carrabina
- Universitat Autònoma de Barcelona- CAIAC- Wireless ULP, Barcelona, Spain
| | - Joan Garcia
- Universitat Autònoma de Barcelona- CAIAC- Wireless ULP, Barcelona, Spain
| | | | | | | | | | | | | |
Collapse
|
32
|
Pulido D, Moussaoui M, Nogués MV, Torrent M, Boix E. Towards the rational design of antimicrobial proteins. FEBS J 2013; 280:5841-52. [DOI: 10.1111/febs.12506] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 08/19/2013] [Accepted: 08/23/2013] [Indexed: 12/15/2022]
Affiliation(s)
- David Pulido
- Department of Biochemistry and Molecular Biology; Universitat Autònoma de Barcelona; Cerdanyola del Vallès Spain
| | - Mohammed Moussaoui
- Department of Biochemistry and Molecular Biology; Universitat Autònoma de Barcelona; Cerdanyola del Vallès Spain
| | - M. Victòria Nogués
- Department of Biochemistry and Molecular Biology; Universitat Autònoma de Barcelona; Cerdanyola del Vallès Spain
| | - Marc Torrent
- Department of Biochemistry and Molecular Biology; Universitat Autònoma de Barcelona; Cerdanyola del Vallès Spain
- Medical Research Council Laboratory of Molecular Biology; Francis Crick Avenue; Cambridge CB2 0QH UK
| | - Ester Boix
- Department of Biochemistry and Molecular Biology; Universitat Autònoma de Barcelona; Cerdanyola del Vallès Spain
| |
Collapse
|
33
|
Pulido D, Torrent M, Andreu D, Nogués MV, Boix E. Two human host defense ribonucleases against mycobacteria, the eosinophil cationic protein (RNase 3) and RNase 7. Antimicrob Agents Chemother 2013; 57:3797-805. [PMID: 23716047 PMCID: PMC3719706 DOI: 10.1128/aac.00428-13] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 05/20/2013] [Indexed: 01/21/2023] Open
Abstract
There is an urgent need to develop new agents against mycobacterial infections, such as tuberculosis and other respiratory tract or skin affections. In this study, we have tested two human antimicrobial RNases against mycobacteria. RNase 3, also called the eosinophil cationic protein, and RNase 7 are two small cationic proteins secreted by innate cells during host defense. Both proteins are induced upon infection displaying a wide range of antipathogen activities. In particular, they are released by leukocytes and epithelial cells, contributing to tissue protection. Here, the two RNases have been proven effective against Mycobacterium vaccae at a low micromolar level. High bactericidal activity correlated with their bacterial membrane depolarization and permeabilization activities. Further analysis on both protein-derived peptides identified for RNase 3 an N-terminus fragment that is even more active than the parental protein. Also, a potent bacterial agglutinating activity was unique to RNase 3 and its derived peptide. The particular biophysical properties of the RNase 3 active peptide are envisaged as a suitable reference for the development of novel antimycobacterial drugs. The results support the contribution of secreted RNases to the host immune response against mycobacteria.
Collapse
Affiliation(s)
- David Pulido
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Marc Torrent
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - David Andreu
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Spain
| | - M. Victoria Nogués
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| |
Collapse
|
34
|
Prescher S, Bourke AK, Koehler F, Martins A, Sereno Ferreira H, Boldt Sousa T, Castro RN, Santos A, Torrent M, Gomis S, Hospedales M, Nelson J. Ubiquitous ambient assisted living solution to promote safer independent living in older adults suffering from co-morbidity. Annu Int Conf IEEE Eng Med Biol Soc 2013; 2012:5118-21. [PMID: 23367080 DOI: 10.1109/embc.2012.6347145] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This paper describes the development, deployment and trial results from 9 volunteers using the eCAALYX system. The eCAALYX system is an ambient assisted living telemonitoring system aimed at older adults suffering with co-morbidity. Described is a raw account of the challenges that exist and results in bringing a Telemedicine system from laboratory to real-world implementation and results for usability, functionality and reliability.
Collapse
|
35
|
Casas L, Tischer C, Wouters IM, Valkonen M, Gehring U, Doekes G, Torrent M, Pekkanen J, Garcia-Esteban R, Hyvärinen A, Heinrich J, Sunyer J. Endotoxin, extracellular polysaccharides, and β(1-3)-glucan concentrations in dust and their determinants in four European birth cohorts: results from the HITEA project. Indoor Air 2013; 23:208-18. [PMID: 23176390 DOI: 10.1111/ina.12017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 11/12/2012] [Indexed: 05/15/2023]
Abstract
UNLABELLED Early-life exposure to microbial agents may play a protective role in asthma and allergies development. Geographical differences in the prevalence of these diseases exist, but the differences in early-life indoor microbial agent levels and their determinants have been hardly studied. We aimed to describe the early-life levels of endotoxin, extracellular polysaccharides (EPS), and β(1-3)-glucans in living room dust of four geographically spread European birth cohorts (LISA in Germany, PIAMA in the Netherlands, INMA in Spain, and LUKAS2 in Finland) and to assess their determinants. A total of 1572 dust samples from living rooms of participants were analyzed for endotoxin, Penicillium/Aspergillus EPS, and β(1-3)-glucans. Information on potential determinants was obtained through questionnaires. Concentrations of endotoxin, EPS, and β(1-3)-glucans were different across cohorts. Concentrations of endotoxin and EPS were respectively lower and higher in INMA than in other cohorts, while glucans were higher in LUKAS2. Season of sampling, dog ownership, dampness, and the number of people living at home were significantly associated with concentrations of at least one microbial agent, with heterogeneity of effect estimates of the determinants across cohorts. In conclusion, both early-life microbial exposure levels and exposure determinants differ across cohorts derived from diverse European countries. PRACTICAL IMPLICATIONS This study adds evidence of variability in the levels of indoor endotoxin, extracellular polysaccharide, and β(1-3)-glucans across four geographically spread European regions. Furthermore, we observed heterogeneity across regions in the effect of exposure determinants. We hypothesize that the variations observed in our study may play a role in the differences in asthma and allergies prevalences across countries.
Collapse
Affiliation(s)
- L Casas
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Boix E, Salazar VA, Torrent M, Pulido D, Nogués MV, Moussaoui M. Structural determinants of the eosinophil cationic protein antimicrobial activity. Biol Chem 2013; 393:801-15. [PMID: 22944682 DOI: 10.1515/hsz-2012-0160] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 04/17/2012] [Indexed: 11/15/2022]
Abstract
Antimicrobial RNases are small cationic proteins belonging to the vertebrate RNase A superfamily and endowed with a wide range of antipathogen activities. Vertebrate RNases, while sharing the active site architecture, are found to display a variety of noncatalytical biological properties, providing an excellent example of multitask proteins. The antibacterial activity of distant related RNases suggested that the family evolved from an ancestral host-defence function. The review provides a structural insight into antimicrobial RNases, taking as a reference the human RNase 3, also named eosinophil cationic protein (ECP). A particular high binding affinity against bacterial wall structures mediates the protein action. In particular, the interaction with the lipopolysaccharides at the Gram-negative outer membrane correlates with the protein antimicrobial and specific cell agglutinating activity. Although a direct mechanical action at the bacteria wall seems to be sufficient to trigger bacterial death, a potential intracellular target cannot be discarded. Indeed, the cationic clusters at the protein surface may serve both to interact with nucleic acids and cell surface heterosaccharides. Sequence determinants for ECP activity were screened by prediction tools, proteolysis and peptide synthesis. Docking results are complementing the structural analysis to delineate the protein anchoring sites for anionic targets of biological significance.
Collapse
Affiliation(s)
- Ester Boix
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Spain.
| | | | | | | | | | | |
Collapse
|
37
|
Torrent M, Pulido D, Rivas L, Andreu D. Antimicrobial peptide action on parasites. Curr Drug Targets 2012; 13:1138-47. [PMID: 22664071 DOI: 10.2174/138945012802002393] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 04/13/2012] [Accepted: 05/18/2012] [Indexed: 11/22/2022]
Abstract
Diseases caused by protozoan parasites can pose a severe thread to human health and are behind some serious neglected tropical diseases like malaria and leishmaniasis. Though several different drugs have been developed in order to eradicate these diseases, a successful candidate has not yet been discovered. Among the most active compounds tested, antimicrobial peptides (AMPs) are particularly appealing because of their wide spectrum of action. AMPs have been described to perturb protozoan homeostasis by disrupting the cellular membranes but also by interfering with key processes in the parasite metabolism. In this review we describe the diverse mechanisms of action of AMPs on protozoan targets and how they can be exploited to treat diseases. Moreover, we describe with detail the antimicrobial action of AMPs on two major parasitical infections: leishmaniasis and malaria. All the features reviewed here show that AMPs are promising drugs to target protozoan parasites and that further understanding of the mechanism of action of these compounds will lead to improved drugs that could be worth to test in a clinical phase.
Collapse
Affiliation(s)
- Marc Torrent
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Biosciences Faculty, 08193, Cerdanyola del Vallès, Spain
| | | | | | | |
Collapse
|
38
|
Torrent M, Nogués MV, Boix E. Discovering new in silico tools for antimicrobial peptide prediction. Curr Drug Targets 2012; 13:1148-57. [PMID: 22664076 DOI: 10.2174/138945012802002311] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 03/20/2012] [Accepted: 05/20/2012] [Indexed: 11/22/2022]
Abstract
Antimicrobial peptides (AMPs) are important effectors of the innate immune system and play a vital role in the prevention of infections. Due to the increased emergence of new antibiotic-resistant bacteria, new drugs are constantly under investigation. AMPs in particular are recognized as promising candidates because of their modularity and wide antimicrobial spectrum. However, the mechanisms of action of AMPs, as well as their structure-activity relationships, are not completely understood. AMPs display no conserved three-dimensional structure and poor sequence conservation, which hinders rational design. Several bioinformatics tools have been developed to generate new templates with appealing antimicrobial properties with the aim of finding highly active peptide compounds with low cytotoxicity. The current tools reviewed here allow for the prediction and design of new active peptides with reasonable accuracy. However, a reliable method to assess the antimicrobial activity of AMPs has not yet been developed. The standardization of procedures to experimentally evaluate the antimicrobial activity of AMPs, together with the constant growth of current well-established databases, may allow for the future development of new bioinformatics tools to accurately predict antimicrobial activity.
Collapse
Affiliation(s)
- Marc Torrent
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Spain.
| | | | | |
Collapse
|
39
|
Torrent M, Pulido D, Nogués MV, Boix E. Exploring new biological functions of amyloids: bacteria cell agglutination mediated by host protein aggregation. PLoS Pathog 2012; 8:e1003005. [PMID: 23133388 PMCID: PMC3486885 DOI: 10.1371/journal.ppat.1003005] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 09/17/2012] [Indexed: 01/02/2023] Open
Abstract
Antimicrobial proteins and peptides (AMPs) are important effectors of the innate immune system that play a vital role in the prevention of infections. Recent advances have highlighted the similarity between AMPs and amyloid proteins. Using the Eosinophil Cationic Protein as a model, we have rationalized the structure-activity relationships between amyloid aggregation and antimicrobial activity. Our results show how protein aggregation can induce bacteria agglutination and cell death. Using confocal and total internal reflection fluorescence microscopy we have tracked the formation in situ of protein amyloid-like aggregates at the bacteria surface and on membrane models. In both cases, fibrillar aggregates able to bind to amyloid diagnostic dyes were detected. Additionally, a single point mutation (Ile13 to Ala) can suppress the protein amyloid behavior, abolishing the agglutinating activity and impairing the antimicrobial action. The mutant is also defective in triggering both leakage and lipid vesicle aggregation. We conclude that ECP aggregation at the bacterial surface is essential for its cytotoxicity. Hence, we propose here a new prospective biological function for amyloid-like aggregates with potential biological relevance. Microbial infections are reported among the worst human diseases and cause millions of deaths per year over the world. Antibiotics are used to treat infections and have saved more lives than any other drug in human history. However, due to extended use, many strains are becoming refractive to common antibiotics. In this light, new promising compounds, like antimicrobial proteins and peptides (AMPs) are being investigated. Some AMPs also show agglutinating activity; this is the ability to clump bacteria after treatment. This feature is particularly appealing because agglutinating peptides could be used to keep bacteria to the infection focus, helping microbe clearance by host immune cells. In this study, we propose a novel mechanism to explain agglutinating activity at a molecular level using Eosinophil Cationic Protein. We show that the agglutinating mechanism is driven by the protein amyloid-like aggregation at the bacteria cell surface. Accordingly, elimination of the amyloid behavior abolishes both the agglutinating and the antimicrobial activities. This study provides a new concept on how Nature could exploit amyloid-like aggregates to fight bacterial infections. Moreover, these results could also add new insights in understanding the relation between infection and inflammation with dementia and amyloid-related diseases like Alzheimer.
Collapse
Affiliation(s)
- Marc Torrent
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
| | | | | | | |
Collapse
|
40
|
Geneste G, Torrent M, Bottin F, Loubeyre P. Strong isotope effect in phase II of dense solid hydrogen and deuterium. Phys Rev Lett 2012; 109:155303. [PMID: 23102325 DOI: 10.1103/physrevlett.109.155303] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Indexed: 06/01/2023]
Abstract
Quantum nuclear zero-point motions in solid H(2) and D(2) under pressure are investigated at 80 K up to 160 GPa by first-principles path-integral molecular dynamics calculations. Molecular orientations are well defined in phase II of D(2), while solid H(2) exhibits large and very asymmetric angular quantum fluctuations in this phase, with possible rotation in the (bc) plane, making it difficult to associate a well-identified single classical structure. The mechanism for the transition to phase III is also described. Existing structural data support this microscopic interpretation.
Collapse
|
41
|
Torrent M, Nogués MV, Andreu D, Boix E. The "CPC clip motif": a conserved structural signature for heparin-binding proteins. PLoS One 2012; 7:e42692. [PMID: 22880084 PMCID: PMC3412806 DOI: 10.1371/journal.pone.0042692] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/11/2012] [Indexed: 11/19/2022] Open
Abstract
Glycosaminoglycans (GAGs) are essential molecules that regulate diverse biological processes including cell adhesion, differentiation, signaling and growth, by interaction with a wide variety of proteins. However, despite the efforts committed to understand the molecular nature of the interactions in protein-GAG complexes, the answer to this question remains elusive.In the present study the interphases of 20 heparin-binding proteins have been analyzed searching for a conserved structural pattern. We have found that a structural motif encompassing one polar and two cationic residues (which has been named the CPC clip motif) is conserved among all the proteins deposited in the PDB. The distances between the α carbons and the side chain center of gravity of the residues composing this motif are also conserved. Furthermore, this pattern can be found in other proteins suggested to bind heparin for which no structural information is available. Hence we propose that the CPC clip motif, working like a staple, is a primary contributor to the attachment of heparin and other sulfated GAGs to heparin-binding proteins.
Collapse
Affiliation(s)
- Marc Torrent
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
| | | | | | | |
Collapse
|
42
|
Bourke AK, Torrent M, Parra X, Català A, Nelson J. Fall algorithm development using kinematic parameters measured from simulated falls performed in a quasi-realistic environment using accelerometry. Annu Int Conf IEEE Eng Med Biol Soc 2012; 2011:4449-52. [PMID: 22255326 DOI: 10.1109/iembs.2011.6091103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This study aims to determine the optimal temporal, angular and acceleration parameters and thresholds for an accelerometer based, chest-worn, fall detection algorithm. In total, 10 healthy male subjects performed 14 different fall types, 3 times by each. The falls were performed onto in a quasi-realistic environment consisting of mats of a minimum thickness. Optimum parameters for; t(falling): time-to-fall, θ(max): max-angle, t(θmax) : max-angle-time, t(RTStanding) : Return-to-standing-time and t(lying) : lying-time were determined using a data set consisting of a total of 420 falls.
Collapse
Affiliation(s)
- Alan K Bourke
- Department of Electronic and Computer Engineering, Faculty of Science and Engineering, University of Limerick, Ireland.
| | | | | | | | | |
Collapse
|
43
|
Pulido D, Nogués MV, Boix E, Torrent M. Lipopolysaccharide neutralization by antimicrobial peptides: a gambit in the innate host defense strategy. J Innate Immun 2012; 4:327-36. [PMID: 22441679 DOI: 10.1159/000336713] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 01/20/2012] [Indexed: 01/08/2023] Open
Abstract
Antimicrobial peptides (AMPs) are nowadays understood as broad multifunctional tools of the innate immune system to fight microbial infections. In addition to its direct antimicrobial action, AMPs can modulate the host immune response by promoting or restraining the recruitment of cells and chemicals to the infection focus. Binding of AMPs to lipopolysaccharide is a critical step for both their antimicrobial action and their immunomodulatory properties. On the one hand, removal of Gram-negative bacteria by AMPs can be an effective strategy to prevent a worsened inflammatory response that may lead to septic shock. On the other hand, by neutralizing circulating endotoxins, AMPs can successfully reduce nitric oxide and tumor necrosis factor-α production, hence preventing severe tissue damage. Furthermore, AMPs can also interfere with the Toll-like receptor 4 recognition system, suppressing cytokine production and contributing to modulate the inflammatory response. Here, we review the immune system strategies devised by AMPs to avoid an exacerbated inflammatory response and thus prevent a fatal end to the host.
Collapse
Affiliation(s)
- David Pulido
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | | | | | | |
Collapse
|
44
|
Torrent M, Di Tommaso P, Pulido D, Nogués MV, Notredame C, Boix E, Andreu D. AMPA: an automated web server for prediction of protein antimicrobial regions. Bioinformatics 2011; 28:130-1. [DOI: 10.1093/bioinformatics/btr604] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
|
45
|
Torrent M, Valle J, Nogués MV, Boix E, Andreu D. The generation of antimicrobial peptide activity: a trade-off between charge and aggregation? Angew Chem Int Ed Engl 2011; 50:10686-9. [PMID: 21928454 DOI: 10.1002/anie.201103589] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Indexed: 12/11/2022]
Affiliation(s)
- Marc Torrent
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | | | | | | |
Collapse
|
46
|
Torrent M, Valle J, Nogués MV, Boix E, Andreu D. The Generation of Antimicrobial Peptide Activity: A Trade-off between Charge and Aggregation? Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103589] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
47
|
Torrent M, Nogués MV, Boix E. Eosinophil cationic protein (ECP) can bind heparin and other glycosaminoglycans through its RNase active site. J Mol Recognit 2011; 24:90-100. [PMID: 20213669 DOI: 10.1002/jmr.1027] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The eosinophil cationic protein (ECP) is an eosinophil-secreted RNase involved in the immune host defense, with a cytotoxic activity against a wide range of pathogens. During inflammation and eosinophilia disorders, ECP is secreted to the inflammation area, where it would contribute to the immune response. ECP secretion causes also severe damage to the host own tissues. ECP presents a high affinity for heparin and this property might be crucial for its immunomodulating properties, antipathogen action, and its toxicity against eukaryotic cells. ECP, also known as human RNase 3, belongs to the mammalian RNase A superfamily and its RNase activity is required for some of its biological properties. We have now proven that ECP heparin binding affinity depends on its RNase catalytic site, as the enzymatic activity is blocked by heparin. We have applied molecular modeling to analyze ECP binding to heparin representative probes, and identified protein residues at the catalytic and substrate binding sites that could contribute to the interaction. ECP affinity for heparin and other negatively charged glycosaminoglycans (GAGs) can explain not only its binding to the eukaryote cells glycocalix but also the reported high affinity for the specific carbohydrates at bacteria cell wall, promoting its antimicrobial action.
Collapse
Affiliation(s)
- Marc Torrent
- Dpt. Bioquímica i Biologia Molecular, Fac. Biociències, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Spain
| | | | | |
Collapse
|
48
|
Torrent M, Pulido D, de la Torre BG, García-Mayoral MF, Nogués MV, Bruix M, Andreu D, Boix E. Refining the eosinophil cationic protein antibacterial pharmacophore by rational structure minimization. J Med Chem 2011; 54:5237-44. [PMID: 21696142 DOI: 10.1021/jm200701g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Sequence analysis of eosinophil cationic protein (ECP), a ribonuclease of broad antimicrobial activity, allowed identification of residues 1-45 as the antimicrobial domain. We have further dissected ECP(1-45) with a view to defining the minimal requirements for antimicrobial activity. Structure-based downsizing has focused on both α-helices of ECP(1-45) and yielded analogues with substantial potency against Gram-negative and -positive strains. Analogues ECP(8-36) and ECP(6-17)-Ahx-(23-36) (Ahx, 6-aminohexanoic acid) involve 36% and 40% size reduction relative to (1-45), respectively, and display a remarkably ECP-like antimicrobial profile. Both retain segments required for self-aggregation and lipolysaccharide binding, as well as the bacterial agglutination ability of parent ECP. Analogue (6-17)-Ahx-(23-36), in particular, is shown by NMR to preserve the helical traits of the native 8-16 (α1) and 33-36 (α2) regions and can be proposed as the minimal structure capable of reproducing the activity of the entire protein.
Collapse
Affiliation(s)
- Marc Torrent
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Spain
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Bousquet J, Anto J, Auffray C, Akdis M, Cambon-Thomsen A, Keil T, Haahtela T, Lambrecht BN, Postma DS, Sunyer J, Valenta R, Akdis CA, Annesi-Maesano I, Arno A, Bachert C, Ballester F, Basagana X, Baumgartner U, Bindslev-Jensen C, Brunekreef B, Carlsen KH, Chatzi L, Crameri R, Eveno E, Forastiere F, Garcia-Aymerich J, Guerra S, Hammad H, Heinrich J, Hirsch D, Jacquemin B, Kauffmann F, Kerkhof M, Kogevinas M, Koppelman GH, Kowalski ML, Lau S, Lodrup-Carlsen KC, Lopez-Botet M, Lotvall J, Lupinek C, Maier D, Makela MJ, Martinez FD, Mestres J, Momas I, Nawijn MC, Neubauer A, Oddie S, Palkonen S, Pin I, Pison C, Rancé F, Reitamo S, Rial-Sebbag E, Salapatas M, Siroux V, Smagghe D, Torrent M, Toskala E, van Cauwenberge P, van Oosterhout AJM, Varraso R, von Hertzen L, Wickman M, Wijmenga C, Worm M, Wright J, Zuberbier T. MeDALL (Mechanisms of the Development of ALLergy): an integrated approach from phenotypes to systems medicine. Allergy 2011; 66:596-604. [PMID: 21261657 DOI: 10.1111/j.1398-9995.2010.02534.x] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The origin of the epidemic of IgE-associated (allergic) diseases is unclear. MeDALL (Mechanisms of the Development of ALLergy), an FP7 European Union project (No. 264357), aims to generate novel knowledge on the mechanisms of initiation of allergy and to propose early diagnosis, prevention, and targets for therapy. A novel phenotype definition and an integrative translational approach are needed to understand how a network of molecular and environmental factors can lead to complex allergic diseases. A novel, stepwise, large-scale, and integrative approach will be led by a network of complementary experts in allergy, epidemiology, allergen biochemistry, immunology, molecular biology, epigenetics, functional genomics, bioinformatics, computational and systems biology. The following steps are proposed: (i) Identification of 'classical' and 'novel' phenotypes in existing birth cohorts; (ii) Building discovery of the relevant mechanisms in IgE-associated allergic diseases in existing longitudinal birth cohorts and Karelian children; (iii) Validation and redefinition of classical and novel phenotypes of IgE-associated allergic diseases; and (iv) Translational integration of systems biology outcomes into health care, including societal aspects. MeDALL will lead to: (i) A better understanding of allergic phenotypes, thus expanding current knowledge of the genomic and environmental determinants of allergic diseases in an integrative way; (ii) Novel diagnostic tools for the early diagnosis of allergy, targets for the development of novel treatment modalities, and prevention of allergic diseases; (iii) Improving the health of European citizens as well as increasing the competitiveness and boosting the innovative capacity of Europe, while addressing global health issues and ethical issues.
Collapse
Affiliation(s)
- J Bousquet
- University Hospital, Department of Respiratory Diseases, Hôpital Arnaud de Villeneuve, Montpellier, France.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Torrent M, Andreu D, Nogués VM, Boix E. Connecting peptide physicochemical and antimicrobial properties by a rational prediction model. PLoS One 2011; 6:e16968. [PMID: 21347392 PMCID: PMC3036733 DOI: 10.1371/journal.pone.0016968] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 01/19/2011] [Indexed: 11/18/2022] Open
Abstract
The increasing rate in antibiotic-resistant bacterial strains has become an imperative health issue. Thus, pharmaceutical industries have focussed their efforts to find new potent, non-toxic compounds to treat bacterial infections. Antimicrobial peptides (AMPs) are promising candidates in the fight against antibiotic-resistant pathogens due to their low toxicity, broad range of activity and unspecific mechanism of action. In this context, bioinformatics' strategies can inspire the design of new peptide leads with enhanced activity. Here, we describe an artificial neural network approach, based on the AMP's physicochemical characteristics, that is able not only to identify active peptides but also to assess its antimicrobial potency. The physicochemical properties considered are directly derived from the peptide sequence and comprise a complete set of parameters that accurately describe AMPs. Most interesting, the results obtained dovetail with a model for the AMP's mechanism of action that takes into account new concepts such as peptide aggregation. Moreover, this classification system displays high accuracy and is well correlated with the experimentally reported data. All together, these results suggest that the physicochemical properties of AMPs determine its action. In addition, we conclude that sequence derived parameters are enough to characterize antimicrobial peptides.
Collapse
Affiliation(s)
- Marc Torrent
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
| | | | | | | |
Collapse
|