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43 results on '"Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE)"'

1. Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe

Author: Claire, Guinat, Cecilia, Valenzuela Agüí, Timothy G, Vaughan, Jérémie, Scire, Anne, Pohlmann, Christoph, Staubach, Jacqueline, King, Edyta, Świętoń, Ádám, Dán, Lenka, Černíková, Mariette F, Ducatez, Tanja, Stadler, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Friedrich-Loeffler-Institut (FLI), National Veterinary Research Institute [Pulawy, Pologne] (NVRI), Institute for Veterinary Medical Research [Budapest] (AOTI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), State Veterinary Institute Prague, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 842621., European Project: 777657,H2020-EU.1.3.3. - Stimulating innovation by means of cross-fertilisation of knowledge,777657,MSCA-RISE(2018), and Université de Toulouse (UT)-Université de Toulouse (UT)
Subjects: [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, highly pathogenic avian influenza, virus transmission and evolution, phylodynamics, domestic-wildlife interface
Abstract: In winter 2016-7, Europe was severely hit by an unprecedented epidemic of highly pathogenic avian influenza viruses (HPAIVs), causing a significant impact on animal health, wildlife conservation, and livestock economic sustainability. By applying phylodynamic tools to virus sequences collected during the epidemic, we investigated when the first infections occurred, how many infections were unreported, which factors influenced virus spread, and how many spillover events occurred. HPAIV was likely introduced into poultry farms during the autumn, in line with the timing of wild birds' migration. In Germany, Hungary, and Poland, the epidemic was dominated by farm-to-farm transmission, showing that understanding of how farms are connected would greatly help control efforts. In the Czech Republic, the epidemic was dominated by wild bird-to-farm transmission, implying that more sustainable prevention strategies should be developed to reduce HPAIV exposure from wild birds. Inferred transmission parameters will be useful to parameterize predictive models of HPAIV spread. None of the predictors related to live poultry trade, poultry census, and geographic proximity were identified as supportive predictors of HPAIV spread between farms across borders. These results are crucial to better understand HPAIV transmission dynamics at the domestic-wildlife interface with the view to reduce the impact of future epidemics., Virus Evolution, 8 (2), ISSN:2057-1577
Published: 2023

2. Tuning of cytokine signaling through imbalanced abundances of receptors and kinases

Author: Léa Sta, Guillaume Voisinne, Jesse Cotari, Michael F. Adamer, Carmen Molina-París, Grégoire Altan-Bonnet, School of Mathematics [Leeds], University of Leeds, Centre d’Immunologie de Marseille Luminy (CIML - INSERM U631 - CNRS UMR 6102), Université de la Méditerranée - Aix-Marseille 2-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Immunebridge, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), National Cancer Institute [Bethesda] (NCI-NIH), and National Institutes of Health [Bethesda] (NIH)
Subjects: [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Abstract: Cells use surface receptors to detect extra-cellular ligands (e.g., growth factors or cytokines) and engender signaling cascades. We explore the effect of cell-to-cell variability in receptor subunit copy number for cells responding to γc cytokines (e.g., IL-2, IL-7 and IL-15). We find that primary T cells expressing higher levels of the common γc receptor chain have weaker responses to IL-7, both in terms of lowered STAT5 phosphorylation amplitude and higher EC50. A mathematical model that accounts for abundance imbalance (e.g., insufficient expression of JAK kinases compared to the number of receptors, or γc competition for other receptor subunit chains) predicts the formation of non-signalling complexes, consistent with the observed cellular behaviour. This type of built-in limit on signaling responses illustrates how phenotypic heterogeneity generates biological functional diversity.Significance StatementCells rely on cytokines to coordinate their activation, differentiation, proliferation and survival. In particular, γc cytokines (interleukins IL-2, 4, 7, 9, 15, and 21) regulate the fate of leukocytes. The signaling cascade induced by these cytokines is relatively simple, and involves the phosphorylation of receptor-associated Janus-like kinases (JAK). Here, we explore the cell-to-cell variability of cytokine responses in primary mouse T cells, and find a paradoxical and quantitative imprint of receptor expression levels and other signaling components. For instance, high abundance of the common γc chain reduces cytokine responses (both in terms of signaling amplitudes and characteristic cytokine concentrations triggering 50% of the response). We develop mathematical models to quantify how limited abundances of signaling components (e.g., JAK or other cytokine receptor subunit chains) may explain our experimental observations. We conclude by generalizing this observation of cell-to-cell signaling variability to other ligand-receptor-kinase systems.
Published: 2022

3. Inferring within‐flock transmission dynamics of highly pathogenic avian influenza H5N8 virus in France, 2020

Author: Simon Gubbins, Debapriyo Chakraborty, Jean-Luc Guérin, Hugo Gruson, Billy Bauzile, Claire Guinat, Timothée Vergne, Mathieu Andraud, Mattias Delpont, Mathilde Paul, Benjamin Roche, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The Pirbright Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Sorbonne Université (SU), Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Facultad de Medicina Veterinaria y Zootecnia, Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), The authors would like to thank the French Ministry of Agriculture and the veterinary services of the Landes department for their support inimplementing this study. The work was carried out within the frame work of the 'Chaire de Biosécurité aviaire' at the 'École Nationale Vétérinaire de Toulouse', which is funded by the French Ministry of Agriculture. CG has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 842621.SG was funded by the Biotechnology and Biological Sciences Research Council (grant codes: BB/E/I/00007036andBB/E/I/00007037)., European Project: 0842621(2009), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute for Animal Health, the Pirbright Institute, Université de Lausanne (UNIL), and Universidad Nacional Autónoma de México (UNAM)
Subjects: Veterinary medicine, Avian flu, Beta, Duck, Interference, Mechanistic model, Mortality, R0, Spread, duck, 040301 veterinary sciences, [SDV]Life Sciences [q-bio], 030231 tropical medicine, spread, Biology, medicine.disease_cause, Disease Outbreaks, 0403 veterinary science, 03 medical and health sciences, 0302 clinical medicine, medicine, Credible interval, Animals, avian flu, Influenza A Virus, H5N8 Subtype, Poultry Diseases, inference, General Veterinary, General Immunology and Microbiology, mechanistic model, business.industry, Transmission (medicine), Outbreak, Bayes Theorem, 04 agricultural and veterinary sciences, General Medicine, Poultry farming, mortality, Influenza A virus subtype H5N1, 3. Good health, Ducks, Infectious disease (medical specialty), Influenza in Birds, beta, France, Flock, business, Epidemic model
Abstract: Following the emergence of highly pathogenic avian influenza (H5N8) in France in early December 2020, we used duck mortality data from the index farm to investigate within-flock transmission dynamics. A stochastic epidemic model was fitted to the daily mortality data and model parameters were estimated using an approximate Bayesian computation sequential Monte Carlo (ABC-SMC) algorithm. The model predicted that the first bird in the flock was infected 5 days (95% credible interval, CI: 3–6) prior to the day of suspicion and that the transmission rate was 4.1 new infections per day (95% CI: 2.8–5.8). On average, ducks became infectious 4.1 h (95% CI: 0.7–9.1) after infection and remained infectious for 4.3 days (95% CI: 2.8–5.7). The model also predicted that 34% (50% prediction interval: 8%–76%) of birds would already be infectious by the day of suspicion, emphasizing the substantial latent threat this virus could pose to other poultry farms and to neighbouring wild birds. This study illustrates how mechanistic models can help provide rapid relevant insights that contribute to the management of infectious disease outbreaks of farmed animals. These methods can be applied to future outbreaks and the resulting parameter estimates made available to veterinary services within a few hours. ISSN:1865-1674 ISSN:1865-1682
Published: 2021

4. Quantification and characterisation of commensal wild birds and their interactions with domestic ducks on a free-range farm in southwest France

Author: Chloé Le Gall-Ladevèze, Claire Guinat, Pierre Fievet, Benjamin Vollot, Jean-Luc Guérin, Julien Cappelle, Guillaume Le Loc’h, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Conservatoire d'Espaces Naturels de Provence-Alpes-Côte d'Azur (CEN PACA ), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), This study was performed in the framework of the 'Chaire de Biosecurite Aviaire', hosted by the National Veterinary College of Toulouse (ENVT) and funded by the Direction Generale de l'Alimentation, Ministere de l'Agriculture et de l'Alimentation, France. This work was financially supported by the FEDER/Region Occitanie Recherche et Societes 2018-AI-TRACK. CG is funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 842621., and European Project: 777657,H2020-EU.1.3.3. - Stimulating innovation by means of cross-fertilisation of knowledge,777657,MSCA-RISE(2018)
Subjects: Farms, [SDV]Life Sciences [q-bio], animal diseases, Analyse de réseau, Animals, Wild, L73 - Maladies des animaux, Poultry, Birds, Passer domesticus, Animals, Canard, Élevage en liberté, Poultry Diseases, Moineau, Multidisciplinary, Passer montanus, Distribution spatiale, Oiseau, Ducks, Influenza in Birds, commensal, Élevage de volailles
Abstract: The role of commensal birds in the epidemiology of pathogens in poultry farms remains unclear. Our study aimed to identify potential key species for interactions with domestic ducks on one free-range duck farm in southwest France. Methods combined direct individual observations on duck outdoor foraging areas, network analysis, and general linear mixed models of abundances. Results showed a wide diversity of wild bird species visiting foraging areas, heavily dominated in frequency by White wagtails (Motacilla alba) and Sparrows (Passer domesticus and Passer montanus). These also were the only species seen entering duck premises or perching on drinkers in the presence of ducks. Moreover, White wagtails were the species most frequently observed on the ground and in close proximity to ducks. Network analysis suggested the role of White wagtails and Sparrows in linking ducks to other wild birds on the farm. The abundance of White wagtails was positively associated with open vegetation, with the presence of ducks and particularly in the afternoon, while the abundance of Sparrows was positively associated only with the fall-winter season. By precisely characterising interactions, the study was able to identify few wild bird species which should be prioritized in infectious investigations at the interface with poultry., Scientific Reports, 12, ISSN:2045-2322
Published: 2022

5. Phylodynamic analysis of the highly pathogenic avian influenza H5N8 epidemic in France, 2016–2017

Author: Debapriyo Chakraborty, Claire Guinat, Nicola F. Müller, Francois‐Xavier Briand, Mathieu Andraud, Axelle Scoizec, Sophie Lebouquin, Eric Niqueux, Audrey Schmitz, Beatrice Grasland, Jean‐Luc Guerin, Mathilde C. Paul, Timothée Vergne, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Fred Hutchinson Cancer Research Centre, Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), FEDER/Région Occitanie Recherche et Sociétés 2018-AI-TRACK, PREDYT project (Fonds de la Recherche pour l'Influenza Aviaire 2019), the Direction Generale de l'Alimentation, Ministère de l'Agriculture et de l'Alimentation, France, the Swiss National Science Foundation, and European Project: 730997,EUROCHAMP2020(2020)
Subjects: virus evolution, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, General Veterinary, General Immunology and Microbiology, modelling infectious disease dynamics, virus molecular epidemiology, animal diseases, viruses, General Medicine, Poultry, Disease Outbreaks, emerging infectious diseases, outbreak analytics, reconstruction of viral transmission, Ducks, Influenza in Birds, Animals, Influenza A Virus, H5N8 Subtype, France, Poultry Diseases
Abstract: In 2016-2017, France experienced a devastating epidemic of highly pathogenic avian influenza (HPAI) H5N8, with more than 400 outbreaks reported in poultry farms. We analyzed the spatiotemporal dynamics of the epidemic using a structured-coalescent-based phylodynamic approach that combined viral genomic data (n = 196; one viral genome per farm) and epidemiological data. In the process, we estimated viral migration rates between departements (French administrative regions) and the temporal dynamics of the effective viral population size (Ne) in each departement. Viral migration rates quantify viral spread between departements and Ne is a population genetic measure of the epidemic size and, in turn, is indicative of the within-departement transmission intensity. We extended the phylodynamic analysis with a generalized linear model to assess the impact of multiple factors-including large-scale preventive culling and live-duck movement bans-on viral migration rates and Ne. We showed that the large-scale culling of ducks that was initiated on 4 January 2017 significantly reduced the viral spread between departements. No relationship was found between the viral spread and duck movements between departements. The within-departement transmission intensity was found to be weakly associated with the intensity of duck movements within departements. Together, these results indicated that the virus spread in short distances, either between adjacent departements or within departements. Results also suggested that the restrictions on duck transport within departements might not have stopped the viral spread completely. Overall, we demonstrated the usefulness of phylodynamics in characterizing the dynamics of a HPAI epidemic and assessing control measures. This method can be adapted to investigate other epidemics of fast-evolving livestock pathogens., Transboundary and Emerging Diseases, 69 (5), ISSN:1865-1674, ISSN:1865-1682
Published: 2022
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6. How do spike collisions affect spike sorting performance?

Author: Alessio Paolo Buccino, Samuel Garcia, Pierre Yger, Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Institut de la Vision, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Garcia, Samuel
Subjects: Neurons, Spatial density, Computer science, General Neuroscience, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Models, Neurological, [SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Action Potentials, Signal Processing, Computer-Assisted, General Medicine, Neural activity, benchmark, Spike sorting, spike sorting, Benchmark (computing), Spike (software development), overlapping spikes, Biological system, spike collision, Algorithms
Abstract: Recently, a new generation of devices have been developed to record neural activity simultaneously from hundreds of electrodes with a very high spatial density, both forin vitroandin vivoapplications. While these advances enable to record from many more cells, they also challenge the already complicated process of spike sorting (i.e., extracting isolated single-neuron activity from extracellular signals). In this work, we used synthetic ground-truth recordings with controlled levels of correlations among neurons to quantitatively benchmark the performance of state-of-the-art spike sorters focusing specifically on spike collisions. Our results show that while modern template-matching-based algorithms are more accurate than density-based approaches, all methods, to some extent, failed to detect synchronous spike events of neurons with similar extracellular signals. Interestingly, the performance of the sorters is not largely affected by the spiking activity in the recordings, with respect to average firing rates and spike-train correlation levels. Since the performances of all modern spike sorting algorithms can be affected as function of the activity of the recorded neurons, scientific claims on correlations and synchrony should be carefully assessed based on the analysis provided in this paper.
Published: 2021

7. Quantifying Age-dependent Extinction from Species Phylogenies

Author: Tanja Stadler, Amaury Lambert, Helen K. Alexander, Institute for Integrative Biology [Zürich] (IBZ), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Probabilités et Modèles Aléatoires (LPMA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), and Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: 0106 biological sciences, 0301 basic medicine, diversification, Maximum likelihood, [SDV]Life Sciences [q-bio], maximum likelihood estimation, Biology, Macroevolution, Extinction, Biological, 010603 evolutionary biology, 01 natural sciences, Models, Biological, Time, Birds, 03 medical and health sciences, Phylogenetics, Genetic algorithm, Genetics, coalescent point process, Animals, Computer Simulation, diversification macroevolution, Clade, Ecology, Evolution, Behavior and Systematics, Solanaceae, Phylogeny, macroevolution, Likelihood Functions, Extinction, Phylogenetic tree, Estimation theory, Ecology, Classification, Biological Evolution, phylogenetics, [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], 030104 developmental biology, Evolutionary biology, Aves, Regular Articles
Abstract: Several ecological factors that could play into species extinction are expected to correlate with species age, i.e., time elapsed since the species arose by speciation. To date, however, statistical tools to incorporate species age into likelihood-based phylogenetic inference have been lacking. We present here a computational framework to quantify age-dependent extinction through maximum likelihood parameter estimation based on phylogenetic trees, assuming species lifetimes are gamma distributed. Testing on simulated trees shows that neglecting age dependence can lead to biased estimates of key macroevolutionary parameters. We then apply this method to two real data sets, namely a complete phylogeny of birds (class Aves) and a clade of self-compatible and -incompatible nightshades (Solanaceae), gaining initial insights into the extent to which age-dependent extinction may help explain macroevolutionary patterns. Our methods have been added to the R package TreePar., Systematic Biology, 65 (1), ISSN:1063-5157, ISSN:1076-836X
Published: 2021

8. What can phylodynamics bring to animal health research?

Author: Mathilde Paul, Mariette F. Ducatez, Claire Guinat, Tanja Stadler, Arthur Kocher, Debapryio Chakraborty, Timothée Vergne, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 842621., European Project: 0842621(2009), Université de Lausanne (UNIL), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0301 basic medicine, medicine.medical_specialty, Livestock, Policy making, [SDV]Life Sciences [q-bio], 030106 microbiology, Animals, Wild, wildlife and livestock populations, Communicable Diseases, molecular epidemiology, 03 medical and health sciences, medicine, population dynamics, Animals, Disease management (health), Epidemics, Ecology, Evolution, Behavior and Systematics, Animal health, Transmission (medicine), Public health, Genetic data, phylodynamics, Data science, pathogen evolution and transmission, 030104 developmental biology, Geography, Viral phylodynamics
Abstract: Trends in Ecology & Evolution, 36 (9), ISSN:0169-5347, ISSN:1872-8383
Published: 2021

9. Optimized Protocol for Subcutaneous Implantation of Encapsulated Cells Device and Evaluation of Biocompatibility

Author: Emilie Audouard, Lisa Rousselot, Marc Folcher, Nathalie Cartier, Françoise Piguet, Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), and Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)
Subjects: 0301 basic medicine, Histology, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Biocompatibility, Biomedical Engineering, Bioengineering, encapsulated cell, 03 medical and health sciences, 0302 clinical medicine, biocompatibility, vascularization, On demand, Methods, Medicine, Protocol (object-oriented programming), business.industry, Bioengineering and Biotechnology, fibrotic capsule, 3. Good health, 030104 developmental biology, Drug delivery, Subcutaneous implantation, device implantation, business, 030217 neurology & neurosurgery, TP248.13-248.65, Biomedical engineering, Biotechnology
Abstract: Improving a drug delivery system is critical to treat central nervous system disorders. Here we studied an innovative approach based on implantation of a wireless-powered cell-based device in mice. This device, coupling biologic material and electronics, is the first of its kind. The advantage of this technology is its ability to control the secretion of a therapeutic molecule and to switch the classical permanent delivery to activation on demand. In diseases with relapsing-remitting phases such as multiple sclerosis, such activation could be selectively achieved in relapsing phases. However, the safety (tolerance to biomaterials and surgical procedure) of such a clinical device needs to be verified. Therefore, the development of tools to assess the biocompatibility of the system in animal models is an essential step. We present the development of this new therapeutic approach, the challenges we encountered during the different steps of its development (such as cell loading in the chamber, surgery protocol for subcutaneous implantation of the device) and the tools we used to evaluate cell viability and biocompatibility of the device., Frontiers in Bioengineering and Biotechnology, 9, ISSN:2296-4185
Published: 2021

10. Extracellular LGALS3BP regulates neural progenitor position and relates to human cortical complexity

Author: Zhisong He, Matteo Lenge, Laure Coquand, Pierpaolo D' Andrea, Stephan A. Sieber, Adam C. O’Neill, Davide Mei, Silvia Cappello, Christina Kyrousi, Rossella Di Giaimo, Stephen P. Robertson, Alexandre D Baffet, Isabel Y. Buchsbaum, Andrea Forero Echeverry, Guimiot Fabien, Cristiana Cruceanu, Pavel Kielkowski, Agnieska Brazovskaja, Elisabeth B. Binder, Barbara Treutlein, Renzo Guerrini, Alexander Belka, Shahryar Khattak, Frances Elmslie, Max Planck Institute of Psychiatry, Max-Planck-Gesellschaft, National and Kapodistrian University of Athens (NKUA), University of Otago [Dunedin, Nouvelle-Zélande], Max Planck Institute for Evolutionary Anthropology [Leipzig], Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Center for Integrated Protein Science (CIPSM), Technical University of Munich (TUM)-Helmholtz-Zentrum München (HZM)-Ludwig Maximilian University of Munich [Germany] (LMU München), Ludwig-Maximilians-Universität München (LMU), Optimisation thérapeutique en Neuropsychopharmacologie (OPTeN (UMR_S_1144 / U1144)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Institut Curie [Paris], University of Naples Federico II, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Technische Universität Dresden = Dresden University of Technology (TU Dresden), Royal College of Surgeons in Ireland (RCSI), Hôpital Robert Debré, University of London [London], Kyrousi, Christina, O'Neill, Adam C, Brazovskaja, Agnieska, He, Zhisong, Kielkowski, Pavel, Coquand, Laure, Di Giaimo, Rossella, D' Andrea, Pierpaolo, Belka, Alexander, Forero Echeverry, Andrea, Mei, Davide, Lenge, Matteo, Cruceanu, Cristiana, Buchsbaum, Isabel Y, Khattak, Shahryar, Fabien, Guimiot, Binder, Elisabeth, Elmslie, France, Guerrini, Renzo, Baffet, Alexandre D, Sieber, Stephan A, Treutlein, Barbara, Robertson, Stephen P, Cappello, Silvia, and Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM)-Helmholtz-Zentrum München (HZM)-Ludwig Maximilian University of Munich [Germany] (LMU München)
Subjects: [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, General Physics and Astronomy, Neocortex, Induced Pluripotent Stem Cell, Extracellular matrix, Mice, 0302 clinical medicine, Lateral Ventricle, Lateral Ventricles, Neural Stem Cell, Gyrification, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Cerebral Cortex, 0303 health sciences, Multidisciplinary, Neurodevelopmental disorders, Cell Differentiation, Human brain, Cell biology, ddc, Corticogenesis, medicine.anatomical_structure, Models, Animal, Female, Neuroglia, Human, Extracellular Vesicle, Science, Induced Pluripotent Stem Cells, Subventricular zone, Biology, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Extracellular Vesicles, Antigens, Neoplasm, Extracellular, medicine, Biomarkers, Tumor, Animals, Humans, Progenitor cell, 030304 developmental biology, Progenitor, Neural stem cells, Development of the nervous system, Neurological disorders, Animal, General Chemistry, Mice, Inbred C57BL, 030217 neurology & neurosurgery
Abstract: Basal progenitors (BPs), including intermediate progenitors and basal radial glia, are generated from apical radial glia and are enriched in gyrencephalic species like humans, contributing to neuronal expansion. Shortly after generation, BPs delaminate towards the subventricular zone, where they further proliferate before differentiation. Gene expression alterations involved in BP delamination and function in humans are poorly understood. Here, we study the role of LGALS3BP, so far known as a cancer biomarker, which is a secreted protein enriched in human neural progenitors (NPCs). We show that individuals with LGALS3BP de novo variants exhibit altered local gyrification, sulcal depth, surface area and thickness in their cortex. Additionally, using cerebral organoids, human fetal tissues and mice, we show that LGALS3BP regulates the position of NPCs. Single-cell RNA-sequencing and proteomics reveal that LGALS3BP-mediated mechanisms involve the extracellular matrix in NPCs’ anchoring and migration within the human brain. We propose that its temporal expression influences NPCs’ delamination, corticogenesis and gyrification extrinsically., Nature Communications, 12, ISSN:2041-1723
Published: 2021

11. Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean

Author: Royo-Llonch, Marta, Sánchez, Pablo, Ruiz-González, Clara, Salazar, Guillem, Pedrós-Alió, Carlos, Sebastián, Marta, Labadie, Karine, Paoli, Lucas, M. Ibarbalz, Federico, Zinger, Lucie, Churcheward, Benjamin, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Cochrane, Guy, de Vargas, Colomban, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stéphane, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Setmmann, Lars, Sullivan, Matthew B., Chaffron, Samuel, Eveillard, Damien, Karsenti, Eric, Sunagawa, Shinichi, Wincker, Patrick, Karp-Boss, Lee, Bowler, Chris, Acinas, Silvia G., Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Centre National de la Recherche Scientifique (France), European Commission, European Molecular Biology Laboratory, Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Universidad de Granada = University of Granada (UGR), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institute of Microbiology and Swiss Institute of Bioinformatics, Institut de biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numérique de Nantes (LS2N), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ), Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche pour le Développement (IRD [France-Nord])-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili, European Molecular Biology Laboratory [Heidelberg] (EMBL), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), University of Maine, ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), and European Project: 862923,AtlantECO
Subjects: Microbiology (medical), Environmental change, SURFACE, Mesopelagic zone, education, Immunology, DIVERSITY, PROTEIN, ECOLOGY, Applied Microbiology and Biotechnology, Microbiology, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Marine ecosystem, GENE-EXPRESSION, Science & Technology, biology, KINGDOMS, Ecology, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Cell Biology, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], READ ALIGNMENT, Polar circle, Arctic, Habitat, Metagenomics, SEA-ICE, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, COMMUNITIES, Life Sciences & Biomedicine, Archaea, BIOGEOGRAPHY, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: 14 pages, 6 figures, additional information https://doi.org/10.1038/s41564-021-00979-9.-- Data availability: Accession numbers for the data used and generated in this study can be found in Supplementary Table 12, which includes the Arctic MAGs Catalogue and their functional annotation (European Bioinformatics Institute BioStudies ID: S-BSST451) and the co-assembly of metagenomic samples used to generate the metagenomic bins (European Nucleotide Archive PRJEB41575). Accession numbers for the metagenomic and metatranscriptomic samples used in the fragment recruitment analyses can be found in Supplementary Table 13. Publicly available datasets used in this study include the following: CheckM v.1.0.11 (https://github.com/Ecogenomics/CheckM/releases/tag/v1.1.0), GTDB release 89 (https://data.gtdb.ecogenomic.org/releases/release89/), SILVA 132 (https://www.arb-silva.de/documentation/release-132/), KEGG release 89.1 (https://www.genome.jp/kegg/docs/relnote.html) and Pfam database release 31.0 (http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam31.0/). Source data are provided with this paper, The role of the Arctic Ocean ecosystem in climate regulation may depend on the responses of marine microorganisms to environmental change. We applied genome-resolved metagenomics to 41 Arctic seawater samples, collected at various depths in different seasons during the Tara Oceans Polar Circle expedition, to evaluate the ecology, metabolic potential and activity of resident bacteria and archaea. We assembled 530 metagenome-assembled genomes (MAGs) to form the Arctic MAGs catalogue comprising 526 species. A total of 441 MAGs belonged to species that have not previously been reported and 299 genomes showed an exclusively polar distribution. Most Arctic MAGs have large genomes and the potential for fast generation times, both of which may enable adaptation to a copiotrophic lifestyle in nutrient-rich waters. We identified 38 habitat generalists and 111 specialists in the Arctic Ocean. We also found a general prevalence of 14 mixotrophs, while chemolithoautotrophs were mostly present in the mesopelagic layer during spring and autumn. We revealed 62 MAGs classified as key Arctic species, found only in the Arctic Ocean, showing the highest gene expression values and predicted to have habitat-specific traits. The Artic MAGs catalogue will inform our understanding of polar microorganisms that drive global biogeochemical cycles, This work acknowledges the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S). We thank the commitment of the following sponsors and research funding agencies: the Spanish Ministry of Economy and Competitiveness (project MAGGY, grant no. CTM2017-87736-R and Polar EcoGen PID2020-116489RB-I00), Horizon 2020-Research and Innovation Framework Programme (Atlantic ECOsystems assessment, forecasting & sustainability, grant no. H2020-BG-2019-2), Centre National de la Recherche Scientifique (in particular Groupement de Recherche GDR3280 and the Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE), European Molecular Biology Laboratory, Genoscope/Commissariat à l’Énergie Atomique et aux Énergies Alternatives, the French Ministry of Research and the French Government’s ‘Investissements d’Avenir’ programmes OCEANOMICS (project no. ANR-11-BTBR-0008), FRANCE GENOMIQUE (project no. ANR-10-INBS-09-08), MEMO LIFE (project no. ANR-10-LABX-54), Paris Sciences et Lettres University (project no. ANR-11-IDEX-0001-02), Eidgenössische Technische Hochschule Zürich and Helmut Horten Foundation, the Swiss National Foundation (project no. 205321_184955), MEXT/JSPS/KAKENHI (project nos. 16H06429, 16K21723, 16H06437 and 18H02279)
Published: 2021
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12. A skyline birth-death process for inferring the population size from a reconstructed tree with occurrences

Author: Tanja Stadler, Gabriel Aguirre-Fernández, Joëlle Barido-Sottani, Antoine Zwaans, Jérémy Andréoletti, Rachel C. M. Warnock, Marc Manceau, Ankit Gupta, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), GeoZentrum Nordbayern, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Paleontological Institute and Museum, University of Zurich, Department of Ecology, Evolution and Organismal Biology, and Iowa State University (ISU)
Subjects: 0106 biological sciences, Population, Inference, Macroevolution, Bayesian inference, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, education, RevBayes, 030304 developmental biology, skyline birth-death process, 0303 health sciences, education.field_of_study, macroevolution, Phylogenetic tree, Population size, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Birth–death process, phylogenetics, Geography, Evolutionary biology, Molecular phylogenetics, epidemiology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, fossils, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology
Abstract: Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model parameters, and more recently, population size through time for clades of interest, based on molecular sequence data. In the fields of epidemiology and macroevolution these models can be used to estimate, respectively, the past number of infected individuals (prevalence) or the past number of species (paleodiversity) through time. Recent years have seen the development of “total-evidence” analyses, which combine molecular and morphological data from extant and past sampled individuals in a unified Bayesian inference framework. Even sampled individuals characterized only by their sampling time, i.e. lacking morphological and molecular data, which we calloccurrences, provide invaluable information to reconstruct past population sizes.Here, we present new methodological developments around the Fossilized Birth-Death Process enabling us to (i) efficiently incorporate occurrence data while remaining computationally tractable and scalable; (ii) consider piecewise-constant birth, death and sampling rates; and (iii) reconstruct past population sizes, with or without knowledge of the underlying tree. We implement our method in the RevBayes software environment, enabling its use along with a large set of models of molecular and morphological evolution, and validate the inference workflow using simulations under a wide range of conditions.We finally illustrate our new implementation using two empirical datasets stemming from the fields of epidemiology and macroevolution. In epidemiology, we apply our model to the Covid-19 outbreak on the Diamond Princess ship. We infer the total prevalence throughout the outbreak, by taking into account jointly the case count record (occurrences) along with viral sequences for a fraction of infected individuals. In macroevolution, we present an empirical case study of cetaceans. We infer the diversity trajectory using molecular and morphological data from extant taxa, morphological data from fossils, as well as numerous fossil occurrences. Our case studies highlight that the advances we present allow us to further bridge the gap between between epidemiology and pathogen genomics, as well as paleontology and molecular phylogenetics.
Published: 2020

13. Disentangling the mechanisms shaping the surface ocean microbiota

Author: Caterina R. Giner, Mireia Mestre, Guillem Salazar, Marta Sebastián, Silvia G. Acinas, Josep M. Gasol, Pedro C. Junger, Ina M. Deutschmann, Colomban de Vargas, Ramon Massana, Laura Rubinat-Ripoll, Clara Ruiz-González, Ramiro Logares, Anders K. Krabberød, Thomas Schmidt, Carlos M. Duarte, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), University of Oslo (UiO), Universidade Federal de São Carlos [São Carlos] (UFSCar), University of British Columbia (UBC), European Molecular Biology Laboratory (EMBL), Adaptation et diversité en milieu marin (AD2M), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Universidad de Concepción [Chile], Universidad Austral de Chile, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), University of Las Palmas de Gran Canaria (ULPGC), King Abdullah University of Science and Technology (KAUST), Edith Cowan University (ECU), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO)-Planning and Transport Research Centre (PATREC), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Ministerio de Economía y Competitividad (España), European Commission, Fundação de Amparo à Pesquisa do Estado de São Paulo, Comisión Nacional de Investigación Científica y Tecnológica (Chile), Research Council of Norway, and Agencia Estatal de Investigación (España)
Subjects: Ocean, 0106 biological sciences, Microbiology (medical), Drift, Oceans and Seas, [SDV]Life Sciences [q-bio], Biogeography, Context (language use), Biology, Plankton, Microbiota, Picoeukaryotes, Prokaryotes, Community structure, Ecological processes, Selection, Dispersal, 010603 evolutionary biology, 01 natural sciences, Microbiology, lcsh:Microbial ecology, 03 medical and health sciences, RNA, Ribosomal, 16S, RNA, Ribosomal, 18S, 14. Life underwater, 030304 developmental biology, Abiotic component, Spatial Analysis, 0303 health sciences, Bacteria, Ecology, 010604 marine biology & hydrobiology, Research, fungi, Temperature, Eukaryota, Global change, 15. Life on land, Archaea, Phylogeography, 13. Climate action, Spatial ecology, lcsh:QR100-130, Biological dispersal, Water Microbiology
Abstract: 17 pages, 4 figures, supplementary information https://doi.org/10.1186/s40168-020-00827-8.-- DNA sequences and metadata from the Malaspina expedition are publicly available at the European Nucleotide Archive (http://www.ebi.ac.uk/ena; accession numbers PRJEB23913 [18S rRNA genes] & PRJEB25224 [16S rRNA genes]). The data used from TARA Oceans is publicly available through Pangaea (https://doi.org/10.1594/PANGAEA.873275) as well as in (http://ocean-microbiome.embl.de/companion.html) [34, 56]. The code for generating OTU-99% tables is available in: https://doi.org/10.5281/zenodo.259579. R-Scripts for calculating the β-Nearest Taxon Index and the Raup-Crick metric are available in https://github.com/stegen/Stegen_etal_ISME_2013. The code for calculating the TINA and PINA indices is available in https://github.com/defleury/Schmidt_et_al_2016_community_similarity, while the code for calculating MIC is available at http://www.exploredata.net. All used R packages as well as other software are cited in ‘Methods’ section, Background: The ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have large-scale consequences. Yet, the underlying ecological mechanisms structuring it are unclear. Here, we investigate how fundamental ecological mechanisms (selection, dispersal and ecological drift) shape the smallest members of the tropical and subtropical surface-ocean microbiota: prokaryotes and minute eukaryotes (picoeukaryotes). Furthermore, we investigate the agents exerting abiotic selection on this assemblage as well as the spatial patterns emerging from the action of ecological mechanisms. To explore this, we analysed the composition of surface-ocean prokaryotic and picoeukaryotic communities using DNA-sequence data (16S- and 18S-rRNA genes) collected during the circumglobal expeditions Malaspina-2010 and TARA-Oceans. Results: We found that the two main components of the tropical and subtropical surface-ocean microbiota, prokaryotes and picoeukaryotes, appear to be structured by different ecological mechanisms. Picoeukaryotic communities were predominantly structured by dispersal-limitation, while prokaryotic counterparts appeared to be shaped by the combined action of dispersal-limitation, selection and drift. Temperature-driven selection appeared as a major factor, out of a few selected factors, influencing species co-occurrence networks in prokaryotes but not in picoeukaryotes, indicating that association patterns may contribute to understand ocean microbiota structure and response to selection. Other measured abiotic variables seemed to have limited selective effects on community structure in the tropical and subtropical ocean. Picoeukaryotes displayed a higher spatial differentiation between communities and a higher distance decay when compared to prokaryotes, consistent with a scenario of higher dispersal limitation in the former after considering environmental heterogeneity. Lastly, random dynamics or drift seemed to have a more important role in structuring prokaryotic communities than picoeukaryotic counterparts. Conclusions: The differential action of ecological mechanisms seems to cause contrasting biogeography, in the tropical and subtropical ocean, among the smallest surface plankton, prokaryotes and picoeukaryotes. This suggests that the idiosyncrasy of the main constituents of the ocean microbiota should be considered in order to understand its current and future configuration, which is especially relevant in a context of global change, where the reaction of surface ocean plankton to temperature increase is still unclear, RL was supported by a Ramón y Cajal fellowship (RYC-2013-12554, MINECO, Spain). IMD was supported by an ITN-SINGEK fellowship (ESR2-EU-H2020-MSCA-ITN-2015, Grant Agreement 675752 [ESR2] to RL), PCJ by Fundação de Amparo à Pesquisa do Estado de São Paulo—FAPESP (PhD grant 2017/26786-1) and CR-González by a Juan de la Cierva (IJCI-2015-23505, MINECO, Spain) fellowship. MM was partially supported by CONICYT (FONDAP-IDEAL 15150003), Chile. This work was supported by the projects Malaspina 2010 Expedition (CSD2008-00077, MINECO, Spain to CMD), INTERACTOMICS (CTM2015-69936-P, MINECO, Spain to RL), REMEI (CTM2015-70340-P, MINECO, Spain to JMG) and MicroEcoSystems (240904, RCN, Norway to RL), With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)
Published: 2020

14. Advances in fast multiphoton microscopy using light-sheet illumination

Author: Antoine Boniface, Elodie Chaudan, Emmanuel Beaurepaire, Júlia Ferrer Ortas, Guy Malkinson, Ali Yasin Sonay, Thierry Gacoin, Vincent Maioli, Lamiae Abdeladim, Willy Supatto, Pierre Mahou, Periklis Pantazis, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de physique de la matière condensée (LPMC), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), and Imperial College London
Subjects: Multimodal imaging, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], 0303 health sciences, Materials science, business.industry, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], [SDV]Life Sciences [q-bio], Second-harmonic generation, Fluorescence, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, Optics, Multiphoton fluorescence microscope, Light propagation, Light sheet fluorescence microscopy, Microscopy, [SPI.OPTI]Engineering Sciences [physics]/Optics / Photonic, business, ComputingMilieux_MISCELLANEOUS, 030217 neurology & neurosurgery, Preclinical imaging, 030304 developmental biology
Abstract: We report on recent advances in multiphoton light-sheet microscopy to perform fast multimodal imaging combining fluorescence with second-harmonic generation and to mitigate photodamage during in vivo imaging of embryos.
Published: 2020

15. Fast

Author: Periklis Pantazis, Pierre Mahou, Guy Malkinson, Willy Supatto, Elodie Chaudan, Ali Yasin Sonay, Thierry Gacoin, Emmanuel Beaurepaire, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de physique de la matière condensée (LPMC), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Bioengineering, Imperial College London, and Supatto, Willy
Subjects: Fluorescence-lifetime imaging microscopy, Technology, Microscope, [SPI.OPTI] Engineering Sciences [physics]/Optics / Photonic, Metrics & More Article Recommendations nanocrystal, 02 engineering and technology, 01 natural sciences, law.invention, nanocrystal, law, Microscopy, single-plane illumination microscopy, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], [PHYS.PHYS.PHYS-BIO-PH] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Physics, nanoparticle, OPTICAL-PROPERTIES, nonlinear microscopy, 021001 nanoscience & nanotechnology, Polarization (waves), Atomic and Molecular Physics, and Optics, Electronic, Optical and Magnetic Materials, Numerical aperture, 0906 Electrical and Electronic Engineering, Physics, Condensed Matter, Physical Sciences, Science & Technology - Other Topics, KTIOPO4, 0210 nano-technology, Preclinical imaging, Biotechnology, [PHYS.PHYS.PHYS-OPTICS] Physics [physics]/Physics [physics]/Optics [physics.optics], Materials science, DEEP, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Materials Science, 0205 Optical Physics, second-harmonic generation, zebrafish, Materials Science, Multidisciplinary, NM, Article, Physics, Applied, 010309 optics, Optics, 0103 physical sciences, SCATTERING, 2ND-HARMONIC GENERATION, Electrical and Electronic Engineering, Nanoscience & Nanotechnology, 0206 Quantum Physics, Science & Technology, business.industry, Second-harmonic generation, COLLAGEN, NANOCRYSTALS, Light sheet fluorescence microscopy, [SPI.OPTI]Engineering Sciences [physics]/Optics / Photonic, ORIENTATION, business
Abstract: Two-photon light-sheet microscopy (2P-SPIM) provides a unique combination of advantages for fast and deep fluorescence imaging in live tissues. Detecting coherent signals such as second-harmonic generation (SHG) in 2P-SPIM in addition to fluorescence would open further imaging opportunities. However, light-sheet microscopy involves an orthogonal configuration of illumination and detection that questions the ability to detect coherent signals. Indeed, coherent scattering from micron-sized structures occurs predominantly along the illumination beam. By contrast, point-like sources such as SHG nanocrystals can efficiently scatter light in multiple directions and be detected using the orthogonal geometry of a light-sheet microscope. This study investigates the suitability of SHG light-sheet microscopy (SHG-SPIM) for fast imaging of SHG nanoprobes. Parameters that govern the detection efficiency of KTiOPO4 and BaTiO3 nanocrystals using SHG-SPIM are investigated theoretically and experimentally. The effects of incident polarization, detection numerical aperture, nanocrystal rotational motion, and second-order susceptibility tensor symmetries on the detectability of SHG nanoprobes in this specific geometry are clarified. Guidelines for optimizing SHG-SPIM imaging are established, enabling fast in vivo light-sheet imaging combining SHG and two-photon excited fluorescence. Finally, microangiography was achieved in live zebrafish embryos by SHG imaging at up to 180 frames per second and single-particle tracking of SHG nanoprobes in the blood flow., ACS Photonics, 7 (4), ISSN:2330-4022
Published: 2019

16. Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila

Author: Anne Xuéreb, Quentin Szabo, Maria Ninova, Filippo Ciabrelli, Giacomo Cavalli, Alexei A. Aravin, Simon Fellous, Boyan B. Bonev, Christophe Klopp, Renato Paro, Federico Comoglio, Frédéric Bantignies, Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), California Institute of Technology (CALTECH), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), University of Basel (Unibas), This study benefited from the CNRS human and technical resources allocated to the ECOTRONS Research Infrastructure as well as from the state allocation 'Investissement d'Avenir' AnaEE-France ANR-11-INBS-0001. F. Ciabrelli was supported by the Fondation pour la Recherche Medicale (FRM). F.B. was supported by CNRS. F. Comoglio was supported by ETH Zurich. B.B. was supported by the Sir Henry Wellcome Postdoctoral Fellowship (WT100136MA). The research of R.P. was supported by the FP7 European Network of Excellence EpiGeneSys, the Swiss National Science Foundation and ETH Zurich. M.N. and A.A. were supported by NIH R01 grant GM097363. Research in the laboratory of G.C. was supported by grants from the European Research Council (ERC-2008-AdG no. 232947), the CNRS, the FP7 European Network of Excellence EpiGeneSys, the European Union's Horizon 2020 Research and Innovation Programme under grant agreement 676556 (MuG), the Agence Nationale de la Recherche, the Fondation pour la Recherche Medicale, the INSERM, the French National Cancer Institute (INCa) and the Laboratory of Excellence EpiGenMed., ANR-11-INBS-0001,ANAEE-FR,ANAEE-Services(2011), ANR-10-LABX-0012,EpiGenMed,From Genome and Epigenome to Molecular Medicine: turning new paradigms in biology into the therapeutic strategies of tomorrow(2010), European Project: 257082,EC:FP7:HEALTH,FP7-HEALTH-2010-two-stage,EPIGENESYS(2010), European Project: 232947,EC:FP7:ERC,ERC-2008-AdG,FLYINGPOLYCOMB(2009), European Project: 676556,H2020,H2020-EINFRA-2015-1,MuG(2015), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: Male, 0301 basic medicine, 1.1 Normal biological development and functioning, [SDE.MCG]Environmental Sciences/Global Changes, Genetically Modified, Biology, Medical and Health Sciences, Fluorescence, Article, Epigenesis, Genetic, Animals, Genetically Modified, Histones, Paramutation, 03 medical and health sciences, Histone H3, Genetic, Genetics, Animals, Drosophila Proteins, Developmental, Expressivity (genetics), Epigenetics, In Situ Hybridization, In Situ Hybridization, Fluorescence, ComputingMilieux_MISCELLANEOUS, Epigenesis, Regulation of gene expression, [SDV.GEN]Life Sciences [q-bio]/Genetics, Lysine, fungi, Inheritance (genetic algorithm), Gene Expression Regulation, Developmental, Histone-Lysine N-Methyltransferase, Biological Sciences, Chromatin, Gene regulation, Drosophila melanogaster, 030104 developmental biology, Gene Expression Regulation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Developmental Biology
Abstract: International audience; Transgenerational epigenetic inheritance (TEI) describes the transmission of alternative functional states through multiple generations in the presence of the same genomic DNA sequence. Very little is known about the principles and the molecular mechanisms governing this type of inheritance. Here, by transiently enhancing 3D chromatin interactions, we established stable and isogenic Drosophila epilines that carry alternative epialleles, as defined by differential levels of Polycomb-dependent trimethylation of histone H3 Lys27 (forming H3K27me3). After being established, epialleles can be dominantly transmitted to naive flies and can induce paramutation. Importantly, epilines can be reset to a naive state by disruption of chromatin interactions. Finally, we found that environmental changes modulate the expressivity of the epialleles, and we extended our paradigm to naturally occurring phenotypes. Our work sheds light on how nuclear organization and Polycomb group (PcG) proteins contribute to epigenetically inheritable phenotypic variability.
Published: 2017

17. Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen

Author: Barney S. Graham, Jean-François Eléouët, Patricia Corthésy, Bruno E. Correia, Pablo Gainza, Che Yang, Fabian Sesterhenn, Marie Galloux, Marie-Anne Rameix-Welti, Sabrina Vollers, Stéphane Rosset, Delphyne Descamps, Jaume Bonet, Sabine Riffault, Man Chen, Simon Friedensohn, Sai T. Reddy, Lucia Csepregi, Institute of Bioengineering [Lausanne, Suisse], Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute of Bioinformatics (SIB), Swiss Institute of Bioinformatics, Molecular Immunology and Virology (VIM-UR892), Institut National de la Recherche Agronomique (INRA), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Viral Pathogenesis Laboratory [Bethesda, MD, États-Unis], Vaccine Research Center [Bethesda, MD, États-Unis], National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH)-National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), Infection et inflammation chronique (2I), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Laboratoire de Microbiologie [Boulogne-Billancourt], Hôpital Ambroise Paré, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), FS was supported by the Swiss initiative for systems biology (SystemsX.ch). BEC was supported by the European Research Council (Starting grant - 716058) and the Swiss National Science Foundation (Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, 310030_163139)., Bodescot, Myriam, Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Infection et inflammation (2I), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital Ambroise Paré [AP-HP], and Université de Lausanne (UNIL)
Subjects: 0301 basic medicine, RNA viruses, rsv antibody, Immunogen, Physiology, Gene Expression, Antibody Response, hiv, dependent enhancement, Antibodies, Viral, Pathology and Laboratory Medicine, Biochemistry, Epitope, Epitopes, Mice, Immunologic Adjuvants, 0302 clinical medicine, Immunogenicity, Vaccine, Immune Physiology, Medicine and Health Sciences, Public and Occupational Health, Biology (General), Cloning, Molecular, Enzyme-Linked Immunoassays, Neutralizing antibody, Immune Response, 0303 health sciences, hemagglutinin-stem, Mice, Inbred BALB C, Immune System Proteins, biology, General Neuroscience, Immunogenicity, respiratory syncytial virus, fusion-glycoprotein vaccine, structural basis, dengue virus, infection, cells, Vaccination and Immunization, 3. Good health, Respiratory Syncytial Viruses, Vaccination, Medical Microbiology, Viral Pathogens, Viruses, [SDV.IMM]Life Sciences [q-bio]/Immunology, Computer-Aided Design, Female, Antibody, Pathogens, General Agricultural and Biological Sciences, medicine.drug, Research Article, Palivizumab, Subdominant, [SDV.IMM] Life Sciences [q-bio]/Immunology, QH301-705.5, Recombinant Fusion Proteins, Genetic Vectors, Immunology, Receptors, Antigen, B-Cell, Immunodominance, Antibodies, Monoclonal, Humanized, Research and Analysis Methods, Microbiology, General Biochemistry, Genetics and Molecular Biology, Antibodies, 03 medical and health sciences, Antigen, Vaccine Development, medicine, Escherichia coli, Respiratory Syncytial Virus Vaccines, Animals, Antigens, Immunoassays, Microbial Pathogens, 030304 developmental biology, General Immunology and Microbiology, Organisms, Biology and Life Sciences, Proteins, Virology, Antibodies, Neutralizing, 030104 developmental biology, Structural Homology, Protein, Paramyxoviruses, biology.protein, Immunologic Techniques, Nanoparticles, Immunization, Respiratory Syncytial Virus, Preventive Medicine, Viral Fusion Proteins, 030217 neurology & neurosurgery
Abstract: Throughout the last several decades, vaccination has been key to prevent and eradicate infectious diseases. However, many pathogens (e.g., respiratory syncytial virus [RSV], influenza, dengue, and others) have resisted vaccine development efforts, largely because of the failure to induce potent antibody responses targeting conserved epitopes. Deep profiling of human B cells often reveals potent neutralizing antibodies that emerge from natural infection, but these specificities are generally subdominant (i.e., are present in low titers). A major challenge for next-generation vaccines is to overcome established immunodominance hierarchies and focus antibody responses on crucial neutralization epitopes. Here, we show that a computationally designed epitope-focused immunogen presenting a single RSV neutralization epitope elicits superior epitope-specific responses compared to the viral fusion protein. In addition, the epitope-focused immunogen efficiently boosts antibodies targeting the palivizumab epitope, resulting in enhanced neutralization. Overall, we show that epitope-focused immunogens can boost subdominant neutralizing antibody responses in vivo and reshape established antibody hierarchies., A computationally designed epitope-focused immunogen presenting a single neutralization epitope from Respiratory Syncytial Virus elicits superior epitope-specific responses compared to the viral fusion protein. Furthermore, epitope-focused immunogens can reshape established antibody hierarchies., Author summary Vaccines are one of the most valuable instruments to prevent and control infectious diseases. Their primary correlate of protection is the level of induction of neutralizing antibodies that target critical antigenic sites and thereby block infection. Natural infections with pathogens such as the respiratory syncytial virus (RSV) or influenza induce a broad repertoire of antibodies that target multiple epitopes. Among those, functional antibodies with key specificities are often subdominant (present in low titers). Thus, a central goal for vaccine development is to focus antibody responses on such neutralization epitopes. Here, we show that a computationally designed, epitope-focused immunogen mimicking an important RSV neutralization epitope (site II) can focus antibodies onto this well-defined epitope. In a scenario of preexisting immunity, in which site II–specific antibodies were subdominant, the epitope-focused immunogen selectively boosted site II–specific antibodies, resulting in an increased viral neutralization through this epitope. We propose that rationally designed immunogens spotlighting defined epitopes have a unique potential to focus antibody responses on functionally conserved sites in cases of preexisting immunity. Our results have broad implications for vaccine design as a strategy to steer preexisting antibody responses away from immunodominant, variable epitopes and toward subdominant epitopes that confer broad and potent neutralization.
Published: 2019
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18. Earlier initiation of antiretroviral treatment coincides with an initial control of the HIV-1 sub-subtype F1 outbreak among men-having-sex-with-men in Flanders, Belgium

Author: Lore Vinken, Katrien Fransen, Lize Cuypers, Ivailo Alexiev, Claudia Balotta, Laurent Debaisieux, Carole Seguin-Devaux, Sergio García Ribas, Perpétua Gomes, Francesca Incardona, Rolf Kaiser, Jean Ruelle, Murat Sayan, Simona Paraschiv, Roger Paredes, Martine Peeters, Anders Sönnerborg, Ellen Vancutsem, Anne-Mieke Vandamme, Sigi Van den Wijngaert, Marc Van Ranst, Chris Verhofstede, Tanja Stadler, Philippe Lemey, Kristel Van Laethem, Rega Institute for Medical Research [Leuven, België], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Department of Biomedical Sciences [Antwerp], Institute of Tropical Medicine [Antwerp] (ITM), National Center of Infectious and Parasitic Diseases [Sofia, Bulgarie] (NCIPD), Luxembourg Institute of Health (LIH), University Hospital of Cologne [Cologne], Kocaeli University [Turkey], Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Institut de Recherche pour le Développement (IRD [France-Sud]), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), UCL - SSS/IREC/MBLG - Pôle de Microbiologie médicale, UCL - (SLuc) Service de microbiologie, Global Health and Tropical Medicine (GHTM), TB, HIV and opportunistic diseases and pathogens (THOP), Microbiology and Infection Control, Clinical Biology, Department of Bio-engineering Sciences, Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), and Université de Lausanne = University of Lausanne (UNIL)
Subjects: lcsh:QR1-502, DIVERSITY, Social Sciences, Sub-subtype F1, Hylodynamics+, THERAPY, lcsh:Microbiology, Belgium, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Epidemiology, Medicine and Health Sciences, Clade, Original Research, 0303 health sciences, Transmission (medicine), phylodynamics, Phylodynamics, 3. Good health, PREVALENCE, sub-subtype F1, Microbiologie et protistologie [entomologie,phytoparasitolog.], BLOOD-DONORS, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, treatment as prevention, Men-having-sex-with-men, Life Sciences & Biomedicine, Microbiologie et protistologie [parasitologie hum. et anim.], Microbiology (medical), medicine.medical_specialty, Biology, Microbiology, 03 medical and health sciences, Acquired immunodeficiency syndrome (AIDS), SDG 3 - Good Health and Well-being, EPIDEMIC, medicine, 030304 developmental biology, DRUG-RESISTANCE, Science & Technology, NORTHWEST SPAIN, Molecular epidemiology, 030306 microbiology, MUTATIONS, STRAINS, NON-B, Outbreak, Treatment as prevention, men-having-sex-with-men, medicine.disease, Viral phylodynamics, HIV-1, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Microbiologie et protistologie [bacteriol.virolog.mycolog.], Demography
Abstract: Human immunodeficiency virus type 1 (HIV-1) non-B subtype infections occurred in Belgium since the 1980s, mainly amongst migrants and heterosexuals, whereas subtype B predominated in men-having-sex-with-men (MSM). In the last decade, the diagnosis of F1 sub-subtype in particular has increased substantially, which prompted us to perform a detailed reconstruction of its epidemiological history. To this purpose, the Belgian AIDS Reference Laboratories collected HIV-1 pol sequences from all sub-subtype F1-infected patients for whom genotypic drug resistance testing was requested as part of routine clinical follow-up. This data was complemented with HIV-1 pol sequences from countries with a high burden of F1 infections or a potential role in the global origin of sub-subtype F1. The molecular epidemiology of the Belgian subtype F1 epidemic was investigated using Bayesian phylogenetic inference and transmission dynamics were characterized based on birth-death models. F1 sequences were retained from 297 patients diagnosed and linked to care in Belgium between 1988 and 2015. Phylogenetic inference indicated that among the 297 Belgian F1 sequences, 191 belonged to a monophyletic group that mainly contained sequences from people likely infected in Belgium (OR 26.67, 95% CI 9.59–74.15), diagnosed in Flanders (OR 7.28, 95% CI 4.23–12.53), diagnosed at a recent stage of infection (OR 7.19, 95% CI 2.88-17.95) or declared to be MSM (OR 34.8, 95% CI 16.0–75.6). Together with a Spanish clade, this Belgian clade was embedded in the genetic diversity of Brazilian subtype F1 strains and most probably emerged after one or only a few migration events from Brazil to the European continent before 2002. The origin of the Belgian outbreak was dated back to 2002 (95% higher posterior density 2000–2004) and birth-death models suggested that its extensive growth had been controlled (R e < 1) by 2012, coinciding with a time period where delay in antiretroviral treatment initiation substantially declined. In conclusion, phylogenetic reconstruction of the Belgian HIV-1 sub-subtype F1 epidemic illustrates the introduction and substantial dissemination of viral strains in a geographically restricted risk group that was most likely controlled by effective treatment as prevention., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2019

19. Image Correlation Spectroscopy with Second Harmonic Generating Nanoparticles in Suspension and in Cells

Author: Luigi Bonacina, Mathias Urbain, Yannick Mugnier, Ali Yasin Sonay, Hannelore Bové, Eli Slenders, Pieter Vanden Berghe, Periklis Pantazis, Martin vandeVen, Marcel Ameloot, Hasselt University (UHasselt), Laboratoire SYstèmes et Matériaux pour la MEcatronique (SYMME), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Group of Applied Physics [Geneva] (GAP), University of Geneva [Switzerland], Translational Research Center for Gastrointestinal Disorders, Technologie campus Gent - KU Leuven (KU Leuven), Laboratory for Fluorescence Dynamics [Irvine], University of California [Irvine] (UCI), and University of California-University of California
Subjects: DYNAMICS, 0301 basic medicine, Technology, Nonlinear optics, Niobium, Analytical chemistry, Nanoparticle, 02 engineering and technology, Physics, Atomic, Molecular & Chemical, [SPI]Engineering Sciences [physics], General Materials Science, Diffusion (business), Suspension (vehicle), ComputingMilieux_MISCELLANEOUS, Chemistry, Physical, Physics, Temperature, MICROSCOPY, Oxides, 021001 nanoscience & nanotechnology, DIFFUSION, TIME, FLUORESCENCE CORRELATION SPECTROSCOPY, Chemistry, Second Harmonic Generation Microscopy, Physical Sciences, Harmonic, Science & Technology - Other Topics, 0210 nano-technology, Two-dimensional nuclear magnetic resonance spectroscopy, Digital image correlation, Materials science, Cells, Materials Science, Materials Science, Multidisciplinary, SHG NANOPROBES, ddc:500.2, AUTOCORRELATION, 03 medical and health sciences, Humans, Nanoscience & Nanotechnology, Physical and Theoretical Chemistry, Spectroscopy, Science & Technology, Harmonic generation, Spectrum Analysis, Correlation spectroscopy, Water, Photobleaching, MODEL, NANOCRYSTALS, 030104 developmental biology, A549 Cells, FLUCTUATION CORRELATION SPECTROSCOPY, [SPI.OPTI]Engineering Sciences [physics]/Optics / Photonic, Nanoparticles
Abstract: The absence of photobleaching, blinking, and saturation combined with a high contrast provides unique advantages of higher-harmonic generating nanoparticles over fluorescent probes, allowing for prolonged correlation spectroscopy studies. We apply the coherent intensity fluctuation model to study the mobility of second harmonic generating nanoparticles. A concise protocol is presented for quantifying the diffusion coefficient from a single spectroscopy measurement without the need for separate point-spread-function calibrations. The technique's applicability is illustrated on nominally 56 nm LiNbO3 nanoparticles. We perform label-free raster image correlation spectroscopy imaging in aqueous suspension and spatiotemporal image correlation spectroscopy in A549 human lung carcinoma cells. In good agreement with the expected theoretical result, the measured diffusion coefficient in water at room temperature is (7.5 +/- 0.3) mu m(2)/s. The diffusion coefficient in the cells is more than 10(3) times lower and heterogeneous, with an average of (3.7 +/- 1.5) X 10(-3) mu m(2)/s. This research was supported by the Research Foundation Flanders (Fonds Wetenschappelijk Onderzoek, project G092915FWO) and by the Interuniversity Attraction Poles Program (IAP FS2 P7/05, Functional Supramolecular Systems) initiated by the Belgian Science Policy Office. The authors are grateful to Prof. Dr. J. D'Haen for the SEM image, to Dr. N. Smisdom for fruitful discussions, and to Dr. R. Paesen and Dr. N. Smisdom for the design of the polarization unit. Research in P.P.'s laboratory was supported by the Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
Published: 2018

20. Vaccination of dogs in an African city interrupts rabies transmission and reduces human exposure

Author: Daugla Doumagoum Moto, Abdallah Traoré, Idriss O. Alfaroukh, Jakob Zinsstag, Germain Rives, Kebkiba Bidjeh, Seraphin Madjaninan, Anthony Lepelletier, Hervé Bourhy, Lauriane Kergoat, Rolande Mindekem, Jan Hattendorf, Assandi Oussiguere, Julie Tessier, Tanja Stadler, Yvonne Muthiani, Mirjam Laager, Laurent Dacheux, Monique Léchenne, Mahamat Ouagal, Nakul Chitnis, Swiss Tropical and Public Health Institute [Basel], University of Basel (Unibas), Centre de Support en Santé Internationale [N'Djamena, Tchad] (CSSI), Institut de Recherche en Elevage pour le Developpement [N'Djamena, Tchad] (IRED), Laboratoire Central Vétérinaire [Bamako, Mali], Centre Collaborateur de l'OMS pour la Rage - Dynamique des lyssavirus et adaptation à l'hôte (CC-OMS), Institut Pasteur [Paris], Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Funding for this study was provided by the Chadian government, the UBS Optimus Foundation (to M. Lechenne and R.M.) and the Swiss Federal Food Safety and Veterinary Office (to M. Lechenne), the European Union Seventh Framework Programme PREDEMICS (grant 278433), the European Research Council under the Seventh Framework Programme of the European Commission (PhyPD, grant agreement number 335529, to T.S.), the Wolfermann-Nägeli Foundation (to M. Lechenne), the Emilia Guggenheim Schnurr Foundation, and the Swiss National Science Foundation (grant 310030_160067/1, to M. Laager), European Project: 278433,EC:FP7:HEALTH,FP7-HEALTH-2011-two-stage,PREDEMICS(2011), European Project: 335529,EC:FP7:ERC,ERC-2013-StG,PHYPD(2014), Institut Pasteur [Paris] (IP), and Université de Lausanne = University of Lausanne (UNIL)
Subjects: 0301 basic medicine, Basic Reproduction Number, law.invention, MESH: Dogs, 0302 clinical medicine, law, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Animals, MESH: Incidence, MESH: Phylogeny, Phylogeny, Incidence (epidemiology), Incidence, Vaccination, MESH: Chad, MESH: Rabies Vaccines, General Medicine, 3. Good health, Transmission (mechanics), MESH: Stochastic Processes, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Chad, Rabies, 030231 tropical medicine, Models, Biological, 03 medical and health sciences, Dogs, MESH: Rabies, MESH: Computer Simulation, Vaccination of dogs, medicine, MESH: Cities, Animals, Humans, Computer Simulation, Cities, Rabies transmission, Stochastic Processes, MESH: Humans, business.industry, MESH: Models, Biological, MESH: Vaccination, medicine.disease, 030104 developmental biology, Vaccination Campaigns, Rabies Vaccines, MESH: Basic Reproduction Number, Human exposure, business, Demography
Abstract: International audience; Despite the existence of effective rabies vaccines for dogs, dog-transmitted human rabies persists and has reemerged in Africa. Two consecutive dog vaccination campaigns took place in Chad in 2012 and 2013 (coverage of 71% in both years) in the capital city of N’Djaména, as previously published. We developed a deterministic model of dog-human rabies transmission fitted to weekly incidence data of rabid dogs and exposed human cases in N’Djaména. Our analysis showed that the effective reproductive number, that is, the number of new dogs infected by a rabid dog, fell to below one through November 2014. The modeled incidence of human rabies exposure fell to less than one person per million people per year. A phylodynamic estimation of the effective reproductive number from 29 canine rabies virus genetic sequences of the viral N-protein confirmed the results of the deterministic transmission model, implying that rabies transmission between dogs was interrupted for 9 months. However, new dog rabies cases appeared earlier than the transmission and phylodynamic models predicted. This may have been due to the continuous movement of rabies-exposed dogs into N’Djaména from outside the city. Our results show that canine rabies transmission to humans can be interrupted in an African city with currently available dog rabies vaccines, provided that the vaccination area includes larger adjacent regions, and local communities are informed and engaged.
Published: 2017

21. Stability analysis of uncertain sampled-data systems with incremental delay using looped-functionals

Author: Alexandre Seuret, Corentin Briat, Équipe Méthodes et Algorithmes en Commande (LAAS-MAC), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), ANR-12-BS03-0005,LimICoS,Synthèse et analyse des systèmes avec informations limitées(2012), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), and Université de Toulouse (UT)
Subjects: looped-functionals, 0209 industrial biotechnology, impulsive systems, Stability (learning theory), 02 engineering and technology, [SPI.AUTO]Engineering Sciences [physics]/Automatic, incremental delay, Stability conditions, 020901 industrial engineering & automation, Control and Systems Engineering, Control theory, Asynchronous communication, 0202 electrical engineering, electronic engineering, information engineering, 020201 artificial intelligence & image processing, Sampled-data systems, Affine transformation, LMI, Electrical and Electronic Engineering, Constant (mathematics), Mathematics, Sampled data systems
Abstract: International audience; The robust stability analysis of asynchronous and uncertain sampled-data systems with constant incremental input delay is addressed in the looped-functional framework. These functionals have been shown to be suitable for the analysis of impulsive systems as they allow one to express discrete-time stability conditions in an affine way, enabling then the consideration of uncertain and time-varying systems. The stability conditions are obtained by first reformulating the sampled-data system as an impulsive system, and by then considering a tailored looped-functional along with Wirtinger's inequality, a recently introduced inequality that has been shown to be less conservative than Jensen's inequality. Several examples are given for illustration.
Published: 2015

22. Simulations of Seismic Wave Propagation on Mars

Author: Ebru Bozdag, Martin van Driel, Amir Khan, Carene Larmat, Y. Ruan, Mark A. Wieczorek, Domenico Giardini, Bruce Banerdt, Philippe Lognonné, Nathan Metthez, Kuangdai Leng, Attilio Rivoldini, Jeroen Tromp, Department of Geosciences [Princeton], Princeton University, Géoazur (GEOAZUR 7329), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Institute of Geophysics [ETH Zürich], Department of Earth Sciences [Swiss Federal Institute of Technology - ETH Zürich] (D-ERDW), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), University of Oxford, Joseph Louis LAGRANGE (LAGRANGE), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Royal Observatory of Belgium [Brussels] (ROB), Institut de Physique du Globe de Paris (IPGP), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS), Computational Science and Engineering Laboratory (CSE Lab), Département de géophysique spatiale et planétaire (DGSP (UMR_7096)), Université Paris Diderot - Paris 7 (UPD7)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS), Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), University of Oxford [Oxford], Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-IPG PARIS-Institut national des sciences de l'Univers (INSU - CNRS), IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), California Institute of Technology (CALTECH)-NASA, Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Department of Earth Sciences [ETH Zürich] (D-ERDW), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich)-Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Royal Observatory of Belgium [Brussels], and Université Paris Diderot - Paris 7 (UPD7)-IPG PARIS-Centre National de la Recherche Scientifique (CNRS)
Subjects: Body waves, Computational seismology, Crust, Numerical methods, Surface waves, 010504 meteorology & atmospheric sciences, Wave propagation, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Astronomy and Astrophysics, Mars Exploration Program, Geophysics, Solver, 010502 geochemistry & geophysics, 01 natural sciences, Planetary science, [SDU.STU.PL]Sciences of the Universe [physics]/Earth Sciences/Planetology, 13. Climate action, Space and Planetary Science, Surface wave, Planet, Seismogram, Geology, 0105 earth and related environmental sciences
Abstract: International audience; We present global and regional synthetic seismograms computed for 1D and 3D Mars models based on the spectral-element method. For global simulations, we implemented a radially-symmetric Mars model with a 110 km thick crust (Sohl and Spohn in J. Geophys. Res., Planets 102(E1):1613–1635, 1997). For this 1D model, we successfully benchmarked the 3D seismic wave propagation solver SPECFEM3D_GLOBE (Komatitsch and Tromp in Geophys. J. Int. 149(2):390–412, 2002a; 150(1):303–318, 2002b) against the 2D axisymmetric wave propagation solver AxiSEM (Nissen-Meyer et al. in Solid Earth 5(1):425–445, 2014) at periods down to 10 s. We also present higher-resolution body-wave simulations with AxiSEM down to 1 s in a model with a more complex 1D crust, revealing wave propagation effects that would have been difficult to interpret based on ray theory. For 3D global simulations based on SPECFEM3D_GLOBE, we superimposed 3D crustal thickness variations capturing the distinct crustal dichotomy between Mars’ northern and southern hemispheres, as well as topography, ellipticity, gravity, and rotation. The global simulations clearly indicate that the 3D crust speeds up body waves compared to the reference 1D model, whereas it significantly changes surface waveforms and their dispersive character depending on its thickness. We also perform regional simulations with the solver SES3D (Fichtner et al. Geophys. J. Int. 179:1703–1725, 2009) based on 3D crustal models derived from surface composition, thereby addressing the effects of various distinct crustal features down to 2 s. The regional simulations confirm the strong effects of crustal variations on waveforms. We conclude that the numerical tools are ready for examining more scenarios, including various other seismic models and sources.
Published: 2017

23. Inflammasome Regulates Hematopoiesis through Cleavage of the Master Erythroid Transcription Factor GATA1

Author: Sylwia D. Tyrkalska, Irene Pardo-Sánchez, Francisco J. Martínez-Navarro, Nouraiz Ahmed, Ana B. Pérez-Oliva, Francisco J. Martínez-Morcillo, Avik Choudhuri, Victoriano Mulero, Francisca Alcaraz-Pérez, Christophe Lachaud, Leonard I. Zon, Lola Rodríguez-Ruiz, Marlies P. Rossmann, Azucena López-Muñoz, Timm Schroeder, María L. Cayuela, Sergio Candel, Diana García-Moreno, IMIB-Arrixaca [Murcia, Spain], Universidad de Murcia, Hospital Clínico Universitario Virgen de la Arrixaca = University Hospital Virgen de la Arrixaca [Murcia], Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Harvard University, Division of Hematology-Oncology [Boston, MA, USA] (Boston Children’s Hospital), Harvard Medical School [Boston] (HMS), Dana-Farber Cancer Institute [Boston], This work was supported by the Spanish Ministry of Science, Innovation and Universities (grants BIO2014-52655-R and BIO2017-84702-R to VM and PI13/0234 to MLC, PhD fellowship to FJMM and Juan de 383 la Cierva postdoctoral contract to FAP), all co-funded with Fondos Europeos de Desarrollo Regional/European Regional Development Funds), Fundación Séneca-Murcia (grant 19400/PI/14 to MLC), the University of Murcia (postdoctoral contracts to ABPO and DGM, and PhD fellowship to FJMM), SNF grant 179490 to TS, and the European 7th Framework Initial Training Network FishForPharma (PhD fellowship to SDT, PITG-GA-2011-289209)., European Project: 289209,EC:FP7:PEOPLE,FP7-PEOPLE-2011-ITN,FISHFORPHARMA(2012), Hospital Clínico Universitario Virgen de la Arrixaca [Murcia, Spain], Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Aix Marseille Université (AMU), Harvard University [Cambridge], lachaud, christophe, and Training Network on Zebrafish Infection Models for Pharmaceutical Screens - FISHFORPHARMA - - EC:FP7:PEOPLE2012-01-01 - 2015-12-31 - 289209 - VALID
Subjects: Male, 0301 basic medicine, Myeloid, Neutrophils, Inflammasomes, [SDV]Life Sciences [q-bio], [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Animals, Genetically Modified, Fish Diseases, Mice, 0302 clinical medicine, hemic and lymphatic diseases, Immunology and Allergy, GATA1 Transcription Factor, Zebrafish, biology, Caspase 1, Gene Expression Regulation, Developmental, Cell Differentiation, GATA1, Inflammasome, anemia, Cell biology, [SDV] Life Sciences [q-bio], Haematopoiesis, Infectious Diseases, medicine.anatomical_structure, Caspase-1, 030220 oncology & carcinogenesis, Erythropoiesis, Myelopoiesis, medicine.drug, Immunology, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Article, 03 medical and health sciences, Erythroid Cells, inflammasome, NLR Family, Pyrin Domain-Containing 3 Protein, medicine, Animals, Humans, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, mouse, Inflammation, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Zebrafish Proteins, zebrafish, biology.organism_classification, Immunity, Innate, neutrophilic inflammation, Hematopoiesis, Mice, Inbred C57BL, 030104 developmental biology, Proteolysis, K562 Cells
Abstract: International audience; Chronic inflammatory diseases are associated with altered hematopoiesis that could result in neutrophilia and anemia. Here we report that genetic or chemical manipulation of different inflammasome components altered the differentiation of hematopoietic stem and progenitor cells (HSPC) in zebrafish. Although the inflammasome was dispensable for the emergence of HSPC, it was intrinsically required for their myeloid differentiation. In addition, Gata1 transcript and protein amounts increased in inflammasome-deficient larvae, enforcing erythropoiesis and inhibiting myelopoiesis. This mechanism is evolutionarily conserved, since pharmacological inhibition of the inflammasome altered erythroid differentiation of human erythroleukemic K562 cells. In addition, caspase-1 inhibition rapidly upregulated GATA1 protein in mouse HSPC promoting their erythroid differentiation. Importantly, pharmacological inhibition of the inflammasome rescued zebrafish disease models of neutrophilic inflammation and anemia. These results indicate that the inflammasome plays a major role in the pathogenesis of neutrophilia and anemia of chronic diseases and reveal druggable targets for therapeutic interventions.
Published: 2019

24. Reconstructing dynamic molecular states from single-cell time series

Author: Anders S. Hansen, Lirong Huang, Loïc Paulevé, Michael Unger, Heinz Koeppl, Christoph Zechner, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Bioinformatique (LRI) (BioInfo - LRI), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Institute of Biochemistry (IBC), Department of Chemistry and Chemical Biology, Harvard University [Cambridge], Bioinspired Communication Systems Lab, and Technische Universität Darmstadt (TU Darmstadt)
Subjects: 0301 basic medicine, Theoretical computer science, Computer science, In silico, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Biomedical Engineering, Biophysics, Markov process, Bioengineering, Optimal filtering, Saccharomyces cerevisiae, moment dynamics, Models, Biological, 01 natural sciences, Biochemistry, continuous-time Markov chains, Biomaterials, 03 medical and health sciences, symbols.namesake, chemical master equation, Gene Expression Regulation, Fungal, 0103 physical sciences, Master equation, [INFO.INFO-SY]Computer Science [cs]/Systems and Control [cs.SY], RNA, Messenger, Promoter Regions, Genetic, 010304 chemical physics, Series (mathematics), Markov chain, Quantitative Biology::Molecular Networks, Time evolution, RNA, Fungal, State (functional analysis), Markov Chains, Moment (mathematics), 030104 developmental biology, symbols, gene expression, Life Sciences–Mathematics interface, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Algorithm, Biotechnology
Abstract: The notion of state for a system is prevalent in the quantitative sciences and refers to the minimal system summary sufficient to describe the time evolution of the system in a self-consistent manner. This is a prerequisite for a principled understanding of the inner workings of a system. Owing to the complexity of intracellular processes, experimental techniques that can retrieve a sufficient summary are beyond our reach. For the case of stochastic biomolecular reaction networks, we show how to convert the partial state information accessible by experimental techniques into a full system state using mathematical analysis together with a computational model. This is intimately related to the notion of conditional Markov processes and we introduce the posterior master equation and derive novel approximations to the corresponding infinite-dimensional posterior moment dynamics. We exemplify this state reconstruction approach using both in silico data and single-cell data from two gene expression systems in Saccharomyces cerevisiae , where we reconstruct the dynamic promoter and mRNA states from noisy protein abundance measurements.
Published: 2016

25. Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism

Author: Claus Hultschig, Patrick Veiga, Edda Klipp, Michael Hecker, Annette Hansen, Etienne Dervyn, Elena Bidnenko, Philippe Noirot, Bernd Hessling, Emma L. Denham, Markus Uhr, Susanne Pohl, Ludovic Le Chat, Joerg Martin Buescher, Benno Schwikowski, Hanne Østergaard Jarmer, Jan Muntel, Bernd Rinn, Pierre Nicolas, Jan Maarten van Dijl, Roelco J. Kleijn, Simon Rasmussen, Colin R. Harwood, Samuel Drulhe, Liza Felicori, Jörg Stelling, Sean Walsh, Kevin M. Devine, Frank Rügheimer, Nathalie Pigeonneau, Dörte Becher, Mark J. Fogg, Peter J. Lewis, Eric Botella, Geoff Doherty, Philippe Bessières, Ulrike Mäder, Marc Schaffer, Sjouke Piersma, Stéphane Aymerich, Anthony J. Wilkinson, Anne Goelzer, Julian Schnidder, F. Molina, Wolfram Liebermeister, Uwe Sauer, Sabine Peres, Sebastian Hubner, Matthieu Jules, François Lecointe, Aurélie Leduc, Institute of Molecular Systems Biology [Zurich], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Theoretical Biophysics [Berlin], Humboldt Universität zu Berlin, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Institut für Mikrobiologie - Institute for Microbiology, Universität Greifswald - University of Greifswald, Smurfit Institute of Genetics, Trinity College Dublin, Unité Mathématique, Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), Department of Medical Microbiology, University of Groningen [Groningen], Biologie systémique - Systems Biology, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), School of Environmental and Life Sciences, Newcastle University [Newcastle], Sysdiag CNRS Bio-Rad UMR 3145, Cap Delta/Parc Euromédecine, Centre National de la Recherche Scientifique (CNRS), York Structural Biology Laboratory, Department of Chemistry, University of York [York, UK], Centre for Bacterial Cell Biology, Institute of Cell and Molecular Biosciences, Center for Information Sciences and Databases - Department of Biosystems Science and Engineering, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark [Lyngby] (DTU), Centre for Bacterial Cell Biology, Institute, of Cell and Molecular Biosciences, University of Northumbria at Newcastle [United Kingdom], Institute Molecular Systems Biology, Center for Information Sciences and Databases, Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Humboldt-Universität zu Berlin, Departement Erdwissenschaften [ETH Zürich] (D-ERDW), Humboldt University Of Berlin, Genes and Behavior Department [Göttingen], Max Planck Institute for Biophysical Chemistry (MPI-BPC), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Ernst-Moritz-Arndt-Universität Greifswald, Interfaculty Institute for Genetics and Functional Genomics, Biosynthèse des Signaux Peptidiques [IBPS] (IBPS-BIOSIPE), Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University Medical Center Groningen, Partenaires INRAE, Biologie Systémique, Institut Pasteur [Paris] (IP), Unité Mathématique Informatique et Génome (MIG), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sysdiag-Modélisation et Ingénierie des Systèmes Complexes Biologiques pour le Diagnostic (SysDiag ), BIO-RAD-Centre National de la Recherche Scientifique (CNRS), This work was funded through the European Commission 7th Framework project BaSys Bio (LSHG-CT-2006-037469), coordinated by P. Noirot, the Department of Education, Science and Training (CG110055),and the National Health and Medical Research Council (455646), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Faculteit Medische Wetenschappen/UMCG, Microbes in Health and Disease (MHD), and Translational Immunology Groningen (TRIGR)
Subjects: carbon metabolism, Transcription, Genetic, Operon, [SDV]Life Sciences [q-bio], Gene regulatory network, Malates, Bacillus subtilis, Transcriptional regulation, Gene Regulatory Networks, bacteria, Promoter Regions, Genetic, bacterie, 0303 health sciences, Multidisciplinary, TRANSCRIPTIONAL REGULATION, regulation, Adaptation, Physiological, Biochemistry, ESCHERICHIA-COLI, Data Interpretation, Statistical, Metabolome, Algorithms, Metabolic Networks and Pathways, Computational biology, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Models, Biological, 03 medical and health sciences, Metabolomics, Bacterial Proteins, SYSTEMS, metabolisme du carbone, Computer Simulation, YEAST, RECONSTRUCTION, Reorganization, Gene, 030304 developmental biology, COMPLEXITY, 030306 microbiology, BIOLOGIE, Gene Expression Regulation, Bacterial, BIOLOGIE MOLECULAIRE, biology.organism_classification, Glucose, Adaptation, STARVATION, Genome, Bacterial, Transcription Factors
Abstract: Outside In Acquisition and analysis of large data sets promises to move us toward a greater understanding of the mechanisms by which biological systems are dynamically regulated to respond to external cues. Now, two papers explore the responses of a bacterium to changing nutritional conditions (see the Perspective by Chalancon et al. ). Nicolas et al. (p. 1103 ) measured transcriptional regulation for more than 100 different conditions. Greater amounts of antisense RNA were generated than expected and appeared to be produced by alternative RNA polymerase targeting subunits called sigma factors. One transition, from malate to glucose as the primary nutrient, was studied in more detail by Buescher et al. (p. 1099 ) who monitored RNA abundance, promoter activity in live cells, protein abundance, and absolute concentrations of intracellular and extracellular metabolites. In this case, the bacteria responded rapidly and largely without transcriptional changes to life on malate, but only slowly adapted to use glucose, a shift that required changes in nearly half the transcription network. These data offer an initial understanding of why certain regulatory strategies may be favored during evolution of dynamic control systems.
Published: 2012

26. How Diverse Retinal Functions Arise from Feedback at the First Visual Synapse

Author: Antonia Drinnenberg, Rava Azeredo da Silveira, Josephine Jüttner, Felix Franke, Andreas Hierlemann, Péter Hantz, Rei K. Morikawa, Daniel Hillier, Botond Roska, Friedrich Miescher Institute for Biomedical Research (FMI), Novartis Research Foundation, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Laboratoire de Physique Statistique de l'ENS (LPS), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Princeton Neuroscience Institute [Princeton]
Subjects: Retinal Ganglion Cells, 0301 basic medicine, Retinal Bipolar Cells, Cell type, Interneuron, [SDV]Life Sciences [q-bio], Models, Neurological, Retinal Horizontal Cells, Biology, Feedback, Synapse, Mice, 03 medical and health sciences, chemistry.chemical_compound, Interneurons, medicine, Animals, Vision, Ocular, Retina, General Neuroscience, Retinal, Ganglion, Brain region, 030104 developmental biology, medicine.anatomical_structure, chemistry, Mouse Retina, Synapses, Calcium, Neuroscience, Photoreceptor Cells, Vertebrate
Abstract: International audience; Many brain regions contain local interneurons of distinct types. How does an interneuron type contribute to the input-output transformations of a given brain region? We addressed this question in the mouse retina by chemogenetically perturbing horizontal cells, an interneuron type providing feedback at the first visual synapse, while monitoring the light-driven spiking activity in thousands of ganglion cells, the retinal output neurons. We uncovered six reversible perturbation-induced effects in the response dynamics and response range of ganglion cells. The effects were enhancing or suppressive, occurred in different response epochs, and depended on the ganglion cell type. A computational model of the retinal circuitry reproduced all perturbation-induced effects and led us to assign specific functions to horizontal cells with respect to different ganglion cell types. Our combined experimental and theoretical work reveals how a single interneuron type can differentially shape the dynamical properties of distinct output channels of a brain region.
Published: 2018

27. Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis

Author: Francis Repoila, Philippe Bouloc, Caroline Lacoux, Erik Aurell, Pascale Serror, Sean Kennedy, Nicolas Innocenti, Françoise Wessner, Aymeric Fouquier d'Hérouël, Rémy A. Bonnin, Monica Golumbeanu, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Royal Inst Technol, Dept Computat Biol, Albanova University Center, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Luxembourg Centre for Systems Biomedicine, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), INRA US1367 MetaGenoPolis, Signalisation et Réseaux de Régulations Bactériens (SRRB), Département Biologie des Génomes (DBG), Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Information and Computer Science, Aalto University, MICrobiologie de l'ALImentation au Service de la Santé humaine ( MICALIS ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Department of Biosystems Science and Engineering ( ETH-Z ), Swiss Federal Institute of Technology in Zürich ( ETH Zürich ), Institut de génétique et microbiologie [Orsay] ( IGM ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Signalisation et Réseaux de Régulations Bactériens ( SRRB ), Département Biologie des Génomes ( DBG ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Royal Institute of Technology [Stockholm] (KTH ), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Swiss Institute of Bioinformatics [Genève] (SIB), Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg [Luxembourg], MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), This research was supported by the Swedish Science Council through grant 621-2012-2982 (E.A.), and by the Academy of Finland through Finland Distinguished Professor Programme and the Center of Excellence COIN (E.A.), and grant ANR-12-BSV6-0008 (ReadRNA) from the Agence Nationale pour la Recherche., We thank the eBIO computing platform of Orsay, particularly C. Drevet and C. Toffano-Nioche, for hosting the 'ppRNome browser.' We thank Ingemar Ernberg at Karolinska Institutet for his hospitality by providing laboratory space and equipment for A.F.d'H., and V. Cantoni for the suggestion to use edge detection algorithms. We are grateful to the 'CPE team,' A. Gruss, and D. Halpern for comments and discussions, and to S. Gaubert, L. Girbal, T. Esquerré, and M. Cocaign-Bousquet for communicating results prior to publication. Many thanks to our colleagues, P. Palcy, V. Bourgogne, N. Eberlin, and P. Régent for invaluable administrative, IT, and equipment-related support., ANR-12-BSV6-0008,ReadRNA,Les transcriptomes bactériens primaires et maturés pour décrypter les réseaux de régulation(2012), Department of Applied Physics, Department of Computer Science, and Aalto-yliopisto
Subjects: MESH: RNA, Bacterial/genetics, [SDV]Life Sciences [q-bio], Nucleic Acid Denaturation, medicine.disease_cause, MESH: Genome, Bacterial, Quantitative Biology - Quantitative Methods, MESH: Sequence Tagged Sites, Methods, Enterococcus faecalis, RNA Processing, Post-Transcriptional, Promoter Regions, Genetic, Quantitative Methods (q-bio.QM), Sequence Tagged Sites, 0303 health sciences, MESH: Gene Expression Regulation, Bacterial, ta214, Transcription start, biology, Chromosome Mapping, Bacterial RNA, MESH: Chromosome Mapping/methods, RNA, Bacterial, processed RNA, MESH: Transcription Initiation Site, Transcription Initiation Site, MESH: RNA Processing, Post-Transcriptional, MESH: 5' Untranslated Regions/genetics, ta221, Computational biology, MESH: Nucleic Acid Denaturation, Bioinformatik och systembiologi, Microbiology, 03 medical and health sciences, Gene mapping, RNA degradation, primary RNA, medicine, Genetics, Quantitative Biology - Genomics, Genetik, Molecular Biology, Escherichia coli, ta218, 030304 developmental biology, Genomics (q-bio.GN), promoter, ta114, Bioinformatics and Systems Biology, [ SDV ] Life Sciences [q-bio], Sequence Analysis, RNA, 030306 microbiology, MESH: Enterococcus faecalis/genetics, MESH: Transcriptome, RNA, Promoter, Biomolecules (q-bio.BM), Gene Expression Regulation, Bacterial, biology.organism_classification, MESH: Sequence Analysis, RNA/methods, Mikrobiologi, Quantitative Biology - Biomolecules, MESH: Promoter Regions, Genetic/genetics, FOS: Biological sciences, 5' Untranslated Regions, Transcriptome, Genome, Bacterial, Bacteria
Abstract: Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first snapshot of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from processed 5′ RNA ends. We also validated our approach by confirming known features in Escherichia coli. We mapped 559 transcription start sites (TSSs) and 352 processing sites (PSSs) in E. faecalis. A blind motif search retrieved canonical features of SigA- and SigN-dependent promoters preceding transcription start sites mapped. We discovered 85 novel putative regulatory RNAs, small- and antisense RNAs, and 72 transcriptional antisense organizations. Presented data constitute a significant insight into bacterial RNA landscapes and a step toward the inference of regulatory processes at transcriptional and post-transcriptional levels in a comprehensive manner.
Published: 2015

28. Development of High-Speed Image Acquisition Systems for Spray Characterization Based on Single-Droplet Experiments

Author: Sofija Vulgarakis Minov, Jan Pieters, Frédéric Cointault, David Nuyttens, Jürgen Vangeyte, Research Institute for Agricultural, Fisheries and Food (ILVO), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Institute for Agricultural and Fisheries Research (ILVO), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Department of Biosystems Science and Engineering ( ETH-Z ), Swiss Federal Institute of Technology in Zürich ( ETH Zürich ), and Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich)
Subjects: Spray characteristics, Engineering, Droplet generator, Image quality, [SDV]Life Sciences [q-bio], Biomedical Engineering, Soil Science, Image processing, Field of view, [ SPI.SIGNAL ] Engineering Sciences [physics]/Signal and Image processing, Backlight, law.invention, Optics, law, Diffuser (optics), Zoom lens, [ SDV ] Life Sciences [q-bio], business.industry, Droplet characteristics, Forestry, 15. Life on land, 6. Clean water, Lens (optics), business, Agronomy and Crop Science, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, Food Science
Abstract: Stream temperature is one of the most influential parameters impacting the survival, growth rates, distribution, and migration patterns of many aquatic organisms. Distributed stream temperature models are crucial for providing insights into variations of stream temperature for regions and time periods for which observed data do not exist. This study uses a relatively new stream temperature model incorporated into a modified version of the Soil and Water Assessment Tool (SWAT) in order to simulate stream temperatures at five sites on the Calapooia River within the Calapooia basin in northwest Oregon. The Nondominated Sorting Genetic Algorithm II (NSGA-II) is used to calibrate flow at a single outlet and stream temperatures at five sites. Few studies have calibrated this stream temperature model for different basins, and this is the first demonstration of an automatic, subbasin-level calibration for stream temperature at multiple sites. The subbasin calibration is shown to better match the observed data than the original SWAT temperature model as well as the modified temperature model calibrated basinwide. In addition to providing improved stream temperature simulations for the Calapooia River, the subbasin-level automatic calibration technique extends the applicability of the model, especially for complex basins with large spatial variability of topography, land use, and soil type.
Published: 2015

29. Stability analysis of asynchronous sampled-data systems with discrete-time constant input delay

Author: Corentin Briat, Frédéric Gouaisbaut, Alexandre Seuret, Laboratoire d'analyse et d'architecture des systèmes (LAAS), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Équipe Méthodes et Algorithmes en Commande (LAAS-MAC), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), ANR-12-BS03-0005,LimICoS,Synthèse et analyse des systèmes avec informations limitées(2012), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, and Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1)
Subjects: 0209 industrial biotechnology, Sampled-data Systems, 020208 electrical & electronic engineering, 02 engineering and technology, Stability (probability), [SPI.AUTO]Engineering Sciences [physics]/Automatic, 020901 industrial engineering & automation, Looped functionals, Discrete time and continuous time, Sampling (signal processing), Asynchronous communication, Aperiodic graph, Control theory, Control system, 0202 electrical engineering, electronic engineering, information engineering, LMI, Time Delay Systems, Constant (mathematics), Mathematics
Abstract: International audience; Aperiodic sampled-data systems controlled by a delayed state-feedback controller arise naturally in networked control systems. We propose a novel way to analyze the stability of sampled-data systems with discrete-time constant input delay by, first, reformulating the system into an aperiodic discrete-time system with constant delay and by, then, considering a mixture of a discrete-time Lyapunov-Krasovskii functional and a looped-functional in order to account for the presence of the delay and the sampling aperiodicity, respectively. Stability criteria, expressed as linear matrix inequalities, are derived for both certain and uncertain (time-varying) systems. An example is given for illustration.
Published: 2014

30. Bridging the gaps in systems biology

Author: Stefan Hohmann, Natasa Przulj, Edda Klipp, Marija Cvijovic, Andrea Pagnani, Joerg Stelling, Mats Jirstrand, Hans-Michael Kaltenbach, Jens Nielsen, Joachim Almquist, Jonas Hagmar, Judith A. H. Wodke, Andreas Raue, Frank Tobin, Sven Nelander, Marcus Krantz, Pedro Mendes, Riccardo Zecchina, Szymon Stoma, Chalmers University of Technology [Göteborg], Fraunhofer-Chalmers Center [Gothenburg] (FCC), Chalmers University of Technology [Göteborg]-Fraunhofer (Fraunhofer-Gesellschaft), University of Gothenburg (GU), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Theoretical Biophysics [Berlin], Humboldt University Of Berlin, Manchester Institute of Biotechnology, University of Manchester [Manchester], Uppsala University, Systems Biology, Department of Applied Science and Technology [Politecnico di Torino] (DISAT), Politecnico di Torino = Polytechnic of Turin (Polito), Imperial College London, University of Freiburg [Freiburg], Computational systems biology and optimization (Lifeware), Inria Paris-Rocquencourt, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Tobin Consulting, European Project: 223137,EC:FP7:HEALTH,FP7-HEALTH-2007-B,FUTURESYSBIO(2008), Humboldt-Universität zu Berlin, and Publica
Subjects: Systems biology, Modeling, Sensitivity analysis, Model merging, Model standards, Biomedical Research, Computational biology, Biology, Models, Biological, Bridging (programming), 03 medical and health sciences, 0302 clinical medicine, Genetics, Humans, Complex systems biology, Molecular Biology, 030304 developmental biology, 0303 health sciences, Mathematical model, Modelling biological systems, General Medicine, Reference Standards, Data science, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 030217 neurology & neurosurgery, Biological network
Abstract: International audience; Systems biology aims at creating mathematical models, i.e., computational reconstructions of biological systems and processes that will result in a new level of understanding-the elucidation of the basic and presumably conserved "design" and "engineering" principles of biomolecular systems. Thus, systems biology will move biology from a phenomenological to a predictive science. Mathematical modeling of biological networks and processes has already greatly improved our understanding of many cellular processes. However, given the massive amount of qualitative and quantitative data currently produced and number of burning questions in health care and biotechnology needed to be solved is still in its early phases. The field requires novel approaches for abstraction, for modeling bioprocesses that follow different biochemical and biophysical rules, and for combining different modules into larger models that still allow realistic simulation with the computational power available today. We have identified and discussed currently most prominent problems in systems biology: (1) how to bridge different scales of modeling abstraction, (2) how to bridge the gap between topological and mechanistic modeling, and (3) how to bridge the wet and dry laboratory gap. The future success of systems biology largely depends on bridging the recognized gaps.
Published: 2014

31. Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs

Author: Dario Speziale, Sabrina Rodriguez, Andrew D. Courtney, Benoît Robert, Sandrine Floriot, Christophe Klopp, Jing Liu, Dagmar Iber, Philipp Germann, Javier Lopez-Rios, Christian Beisel, Yves Gallard, Amandine Duchesne, Sarah Barbey, Magdalena Müller-Gerbl, Denis Duboule, Carol Wicking, Robert Ivanek, Guillaume Andrey, Rolf Zeller, Kevin A. Peterson, Erkan Ünal, Andrew P. McMahon, Developmental Genetics, Department Biomedicine, University of Basel (Unibas), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), School of Life Sciences, Federal Institute of Technology Lausann, Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California (USC), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Domaine expérimental animal du Pin (SEA), Institut National de la Recherche Agronomique (INRA), Institute of Anatomy, Department Biomedicine, Institute for Molecular Bioscience, University of Queensland [Brisbane], Unité de Biométrie et Intelligence Artificielle (UBIA), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Swiss Institute of Bioinformatics, Génétique Moléculaire de la Morphogénèse, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Department of Genetics and Evolution, Université de Genève (UNIGE), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Domaine Expérimental du Pin (DEP), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), Université de Lausanne (UNIL), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: Male, Patched Receptors, Extremities/anatomy & histology/embryology, Mesenchyme, [SDV]Life Sciences [q-bio], Cell Surface/genetics/metabolism, Transgenic, Limb Buds/anatomy & histology/embryology, Mice, 03 medical and health sciences, Limb bud, 0302 clinical medicine, ddc:590, Nucleic Acid/genetics, Receptors, Gene expression, medicine, Animals, Hedgehog Proteins/metabolism, Limb development, Sonic hedgehog, Body Patterning, 030304 developmental biology, Regulation of gene expression, Mesoderm/metabolism, 0303 health sciences, Multidisciplinary, biology, Anatomy, Biological Evolution, Cell biology, Patched-1 Receptor, body regions, Developmental/genetics, medicine.anatomical_structure, Gene Expression Regulation, PTCH1, biology.protein, Evolutionary developmental biology, Cattle, Female, Regulatory Sequences, 030217 neurology & neurosurgery
Abstract: Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-Access; The large spectrum of limb morphologies reflects the wide evolutionary diversification of the basic pentadactyl pattern in tetrapods. In even-toed ungulates (artiodactyls, including cattle), limbs are adapted for running as a consequence of progressive reduction of their distal skeleton to symmetrical and elongated middle digits with hoofed phalanges. Here we analyse bovine embryos to establish that polarized gene expression is progressively lost during limb development in comparison to the mouse. Notably, the transcriptional upregulation of the Ptch1 gene, which encodes a Sonic hedgehog (SHH) receptor, is disrupted specifically in the bovine limb bud mesenchyme. This is due to evolutionary alteration of a Ptch1 cis-regulatory module, which no longer responds to graded SHH signalling during bovine handplate development. Our study provides a molecular explanation for the loss of digit asymmetry in bovine limb buds and suggests that modifications affecting the Ptch1 cis-regulatory landscape have contributed to evolutionary diversification of artiodactyl limbs.
Published: 2014

32. Advances in whole-embryo imaging: a quantitative transition is underway

Author: Periklis Pantazis, Willy Supatto, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Laboratoire d'optique et biosciences (LOB), and École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0303 health sciences, Embryo, Nonmammalian, Computer science, Green Fluorescent Proteins, Embryonic Development, Cell Biology, Data science, Cell biology, Molecular Imaging, 03 medical and health sciences, 0302 clinical medicine, Drosophila melanogaster, Microscopy, Fluorescence, Multiphoton, Spectrometry, Fluorescence, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, Genes, Reporter, Molecular Probes, Image Processing, Computer-Assisted, Animals, Caenorhabditis elegans, Molecular Biology, 030217 neurology & neurosurgery, Zebrafish, 030304 developmental biology
Abstract: International audience; With the advent of imaging probes and live microscopy, developmental biologists have markedly extended our understanding of the molecular and cellular details of embryonic development. To fully comprehend the complex mechanistic framework that forms the developing organism, quantitative studies with high fidelity in space and time are now required. We discuss how integrating established, newly introduced and future imaging tools with quantitative analysis will ensure that imaging can fulfil its promise to elucidate how new life begins.
Published: 2014

33. Automated processing of zebrafish imaging data: a survey

Author: Nadine Peyriéras, Maria J. Ledesma-Carbayo, Wolfgang Driever, Bernhard X. Kausler, Karol Mikula, Periklis Pantazis, Pierre Geurts, Raphaël Marée, Rainer Stotzka, Thomas Dickmeis, Fred A. Hamprecht, Andres Santos, Olaf Ronneberger, Uwe Strähle, Ralf Mikut, Karlsruhe Institute of Technology (KIT), BIOSS Centre for Biological Signalling Studies, University of Freiburg [Freiburg], Department of Electrical Engineering and Computer Science (Institut Montefiore), Université de Liège, Heidelberg Collaboratory for Image Processing (HCI), Universität Heidelberg [Heidelberg], Biomedical Image Technologies, Biomedical Research Center (CIBER-BBN), Universidad Politécnica de Madrid (UPM), Department of Mathematics (STUBA), Slovak University of Technology in Bratislava, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Neurobiologie et Développement (N&eD), Centre National de la Recherche Scientifique (CNRS), Institut des Systèmes Complexes - Paris Ile-de-France (ISC-PIF), École normale supérieure - Cachan (ENS Cachan)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris-Sud - Paris 11 (UP11)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-École polytechnique (X), Institut de Neurobiologie Alfred Fessard (INAF), Universität Heidelberg [Heidelberg] = Heidelberg University, École normale supérieure - Cachan (ENS Cachan)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris-Sud - Paris 11 (UP11)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École polytechnique (X)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS), Fonds Européen de Développement Régional - FEDER [sponsor], Région wallonne: Direction générale opérationnelle de l'Economie, de l'Emploi & de la Recherche (DGO6) [sponsor], and Giga-Systems Biology and Chemical Biology [research center]
Subjects: animal structures, Image processing, Review, Terabyte, computer.software_genre, Bioinformatics, 03 medical and health sciences, 0302 clinical medicine, Software, Image Processing, Computer-Assisted, Animals, Preprocessor, Zebrafish, 030304 developmental biology, 0303 health sciences, Telecomunicaciones, biology, business.industry, Biochemistry, biophysics & molecular biology [Life sciences], Biochimie, biophysique & biologie moléculaire [Sciences du vivant], Brain atlas, Modular design, biology.organism_classification, 13. Climate action, Data quality, Animal Science and Zoology, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Electrónica, Data mining, business, computer, 030217 neurology & neurosurgery, Developmental Biology
Abstract: International audience; Abstract Due to the relative transparency of its embryos and larvae, the zebrafish is an ideal model organism for bioimaging approaches in vertebrates. Novel microscope technologies allow the imaging of developmental processes in unprecedented detail, and they enable the use of complex image-based read-outs for high-throughput/high-content screening. Such applications can easily generate Terabytes of image data, the handling and analysis of which becomes a major bottleneck in extracting the targeted information. Here, we describe the current state of the art in computational image analysis in the zebrafish system. We discuss the challenges encountered when handling high-content image data, especially with regard to data quality, annotation, and storage. We survey methods for preprocessing image data for further analysis, and describe selected examples of automated image analysis, including the tracking of cells during embryogenesis, heartbeat detection, identification of dead embryos, recognition of tissues and anatomical landmarks, and quantification of behavioral patterns of adult fish. We review recent examples for applications using such methods, such as the comprehensive analysis of cell lineages during early development, the generation of a three-dimensional brain atlas of zebrafish larvae, and high-throughput drug screens based on movement patterns. Finally, we identify future challenges for the zebrafish image analysis community, notably those concerning the compatibility of algorithms and data formats for the assembly of modular analysis pipelines.
Published: 2013

34. Affine characterizations of minimum and mode-dependent dwell-times for uncertain linear switched systems

Author: Alexandre Seuret, Corentin Briat, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Networked Controlled Systems (NECS), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Département Automatique (GIPSA-DA), Grenoble Images Parole Signal Automatique (GIPSA-lab), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Stendhal - Grenoble 3-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Stendhal - Grenoble 3-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Grenoble Images Parole Signal Automatique (GIPSA-lab), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Stendhal - Grenoble 3-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Stendhal - Grenoble 3-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS), Équipe Méthodes et Algorithmes en Commande (LAAS-MAC), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), and Université de Toulouse (UT)
Subjects: Lyapunov function, 0209 industrial biotechnology, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Structure (category theory), 02 engineering and technology, Systems and Control (eess.SY), Dynamical Systems (math.DS), [MATH.MATH-CA]Mathematics [math]/Classical Analysis and ODEs [math.CA], Type (model theory), symbols.namesake, 020901 industrial engineering & automation, Control theory, Computer Science::Systems and Control, Stability theory, 0202 electrical engineering, electronic engineering, information engineering, Classical Analysis and ODEs (math.CA), FOS: Mathematics, FOS: Electrical engineering, electronic engineering, information engineering, Mathematics - Dynamical Systems, Electrical and Electronic Engineering, Mathematics - Optimization and Control, Mathematics, Mode (statistics), Computer Science Applications, Range (mathematics), Stability conditions, Mathematics - Classical Analysis and ODEs, Control and Systems Engineering, Optimization and Control (math.OC), symbols, Computer Science - Systems and Control, 020201 artificial intelligence & image processing, Affine transformation, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC]
Abstract: An alternative approach for minimum and mode-dependent dwell-time characterization for switched systems is derived. The proposed technique is related to Lyapunov looped-functionals, a new type of functionals leading to stability conditions affine in the system matrices, unlike standard results for minimum dwell-time. These conditions are expressed as infinite-dimensional LMIs which can be solved using recent polynomial optimization techniques such as sum-of-squares. The specific structure of the conditions is finally utilized in order to derive dwell-time stability results for uncertain switched systems. Several examples illustrate the efficiency of the approach., Comment: 7 pages, 1 figure, To appear in IEEE Transactions on Automatic Control
Published: 2013

35. Transcriptional regulation is insufficient to explain substrate‐induced flux changes in Bacillus subtilis

Author: Hannes Link, Stéphane Aymerich, Roelco J. Kleijn, Victor Chubukov, Markus Uhr, Uwe Sauer, Matthieu Jules, Jörg Stelling, Ludovic Le Chat, Institute of Molecular System Biology, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, European Commission projects BaSysBio [LSHG-CT-2006-037469, FP7-244093], German Research Foundation (DFG), and Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich)
Subjects: Central carbon metabolism, Metabolic flux, Transcriptional regulation, Transcription, Genetic, [SDV]Life Sciences [q-bio], Allosteric regulation, Bacillus subtilis, central carbon metabolism, Biology, Article, General Biochemistry, Genetics and Molecular Biology, régulation de la transcription, 03 medical and health sciences, Metabolomics, transcriptional regulation, RNA, Messenger, flux métabolique, 030304 developmental biology, chemistry.chemical_classification, Regulation of gene expression, Carbon Isotopes, 0303 health sciences, General Immunology and Microbiology, 030306 microbiology, Applied Mathematics, Gene Expression Regulation, Bacterial, Metabolism, metabolic flux, biology.organism_classification, Citric acid cycle, Kinetics, Enzyme, Computational Theory and Mathematics, chemistry, Biochemistry, métabolisme du carbone, General Agricultural and Biological Sciences, Metabolic Networks and Pathways, Information Systems
Abstract: One of the key ways in which microbes are thought to regulate their metabolism is by modulating the availability of enzymes through transcriptional regulation. However, the limited success of efforts to manipulate metabolic fluxes by rewiring the transcriptional network has cast doubt on the idea that transcript abundance controls metabolic fluxes. In this study, we investigate control of metabolic flux in the model bacterium Bacillus subtilis by quantifying fluxes, transcripts, and metabolites in eight metabolic states enforced by different environmental conditions. We find that most enzymes whose flux switches between on and off states, such as those involved in substrate uptake, exhibit large corresponding transcriptional changes. However, for the majority of enzymes in central metabolism, enzyme concentrations were insufficient to explain the observed fluxes—only for a number of reactions in the tricarboxylic acid cycle were enzyme changes approximately proportional to flux changes. Surprisingly, substrate changes revealed by metabolomics were also insufficient to explain observed fluxes, leaving a large role for allosteric regulation and enzyme modification in the control of metabolic fluxes., Molecular Systems Biology, 9 (1), ISSN:1744-4292
Published: 2013

36. A looped-functional approach for robust stability analysis of linear impulsive systems

Author: Corentin Briat, Alexandre Seuret, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Networked Controlled Systems (NECS), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Département Automatique (GIPSA-DA), Grenoble Images Parole Signal Automatique (GIPSA-lab), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Stendhal - Grenoble 3-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Stendhal - Grenoble 3-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Grenoble Images Parole Signal Automatique (GIPSA-lab), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Stendhal - Grenoble 3-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Stendhal - Grenoble 3-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées
Subjects: Lyapunov function, 0209 industrial biotechnology, Class (set theory), General Computer Science, Computer science, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Stability (learning theory), Uncertain systems, Functional approach, Systems and Control (eess.SY), Dynamical Systems (math.DS), 02 engineering and technology, Impulsive systems, [MATH.MATH-CA]Mathematics [math]/Classical Analysis and ODEs [math.CA], symbols.namesake, 020901 industrial engineering & automation, Classical Analysis and ODEs (math.CA), FOS: Mathematics, FOS: Electrical engineering, electronic engineering, information engineering, 0202 electrical engineering, electronic engineering, information engineering, Applied mathematics, Electrical and Electronic Engineering, Mathematics - Dynamical Systems, Mathematics - Optimization and Control, LMIs, Mechanical Engineering, Exponential function, Optimization and Control (math.OC), Control and Systems Engineering, Mathematics - Classical Analysis and ODEs, symbols, Computer Science - Systems and Control, 020201 artificial intelligence & image processing, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], Looped-functionals
Abstract: A new functional-based approach is developed for the stability analysis of linear impulsive systems. The new method, which introduces looped-functionals, considers non-monotonic Lyapunov functions and leads to LMIs conditions devoid of exponential terms. This allows one to easily formulate dwell-times results, for both certain and uncertain systems. It is also shown that this approach may be applied to a wider class of impulsive systems than existing methods. Some examples, notably on sampled-data systems, illustrate the efficiency of the approach., 13 pages, 2 figures, Accepted at Systems & Control Letters
Published: 2012

37. Dynamics of Klebsiella pneumoniae OmpA transmembrane domain: The four extracellular loops display restricted motion behavior in micelles and in lipid bilayers

Author: Patrick D. Bosshart, Alain Milon, Valérie Réat, Olivier Saurel, Marie Renault, Andreas Engel, Iordan Iordanov, Institut de pharmacologie et de biologie structurale (IPBS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), and Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)
Subjects: Sucrose, Magnetic Resonance Spectroscopy, Protein reconstitution, Detergents, Lipid Bilayers, Molecular Sequence Data, Biophysics, Spin–lattice relaxation, Protein dynamics, Biology, 010402 general chemistry, 01 natural sciences, Biochemistry, Solid-state NMR, Protein Structure, Secondary, Serine, 03 medical and health sciences, Protein structure, Microscopy, Electron, Transmission, Extracellular, Electron microscopy, Centrifugation, Density Gradient, Escherichia coli, Amino Acid Sequence, Lipid bilayer, Outer membrane protein A, Peptide sequence, Micelles, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Cell Biology, 0104 chemical sciences, Protein Structure, Tertiary, Transmembrane domain, Klebsiella pneumoniae, Bacterial Outer Membrane Proteins
Abstract: The transmembrane domain of Klebsiella pneumoniae OmpA (KpOmpA) possesses four long extracellular loops that exhibit substantial sequence variability throughout OmpA homologs in Enterobacteria, in comparison with the highly conserved membrane-embedded β-barrel core. These loops are responsible for the immunological properties of the protein, including cellular and humoral recognition. In addition to key features revealed by structural elucidation of the KpOmpA transmembrane domain in detergent micelles, studies of protein dynamics provide insight into its function and/or mechanism of action. We have investigated the dynamics of KpOmpA in a lipid bilayer, using magic angle spinning solid-state NMR. The dynamics of the β-barrel and loop regions were probed by the spin–lattice relaxation times of the Cα and Cβ atoms of the serine and threonine residues, and by cross-polarization dynamics. The β-barrel core of the protein is rigid; the C-terminal halves of two of the four extracellular loops (L1 and L3), which are particularly long in KpOmpA, are highly mobile. The other two loops (L2 and L4), which are very similar to their homologs in Escherichia coli OmpA, and the N-terminal halves of L1 and L3 exhibit more restricted motions. We suggest a correlation between the sequence variability and the dynamics of certain loop regions, which accounts for their respective contributions to the structural and immunological properties of the protein.
Published: 2012

38. Adsorption of Arsenic on Polyaluminum Granulate

Author: Ralf Kägi, Jérôme Rose, Perrine Chaurand, Jasmin Mertens, Gerhard Furrer, Bernhard Wehrli, Michael Plötze, Institute of Biogeochemistry and Pollutant Dynamics [ETH Zürich] (IBP), Department of Environmental Systems Science [ETH Zürich] (D-USYS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich)-Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Swiss Federal Institute for Environmental Science and Technology [Dübendorf] (EAWAG), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), and Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)
Subjects: Arsenites, chemistry.chemical_element, Mineralogy, 02 engineering and technology, 010501 environmental sciences, 01 natural sciences, Water Purification, chemistry.chemical_compound, symbols.namesake, Adsorption, Specific surface area, Environmental Chemistry, Freundlich equation, Aluminum Compounds, Groundwater, Arsenic, 0105 earth and related environmental sciences, Arsenite, [SDE.IE]Environmental Sciences/Environmental Engineering, Arsenate, Water, Langmuir adsorption model, Sorption, General Chemistry, 021001 nanoscience & nanotechnology, 6. Clean water, Nanostructures, chemistry, symbols, Arsenates, Calcium, 0210 nano-technology, Porosity, Water Pollutants, Chemical, Nuclear chemistry
Abstract: International audience; The kinetics and efficiencies of arsenite and arsenate removal from water were evaluated using poly-aluminum granulates (PAG) with high content of aluminum nanoclusters. PAG was characterized to be meso- and macroporous, with a specific surface area of 35 +/- 1 m(2) g(-1). Adsorption experiments were conducted at pH 7.5 in deionized water and synthetic water with composition of As-contaminated groundwater in the Pannonian Basin. As(III) and As(V) sorption was best described by the Freundlich and Langmuir isotherm, respectively, with a maximum As(V) uptake capacity of similar to 200 mu mol g(-1) in synthetic water. While As(III) removal reached equilibrium within 40 h, As(V) was removed almost entirely within 20 h. Micro X-ray fluorescence and electron microscopy revealed that As(III) was distributed uniformly within the grain, whereas As(V) diffused up to 81 pm into PAG. The results imply that As(V) is adsorbed 3 times faster while being transported 105 times slower than As(III) in Al hydroxide materials.
Published: 2012

39. Polyaluminum chloride with high Al30 content as removal agent for arsenic-contaminated well water

Author: Armand Masion, Gerhard Furrer, Jasmin Mertens, Barbara Casentini, Rosemarie Pöthig, Bernhard Wehrli, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), and Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Flocculation, Al nanocluster, Environmental Engineering, Magnetic Resonance Spectroscopy, Water Wells, Inorganic chemistry, chemistry.chemical_element, Al-13, Portable water purification, Aluminum Hydroxide, [object Object], 010501 environmental sciences, 010402 general chemistry, 01 natural sciences, Nanoclusters, Arsenic, Water Purification, Aggregation, Water treatment, Point of zero charge, Water pollution, Waste Management and Disposal, 0105 earth and related environmental sciences, Water Science and Technology, Civil and Structural Engineering, Chemistry, Ecological Modeling, Coagulation-flocculation-sedimentation, Water Pollution, Titrimetry, Reproducibility of Results, Hydrogen-Ion Concentration, Silicon Dioxide, Pollution, 6. Clean water, 0104 chemical sciences, Solutions, Kinetics, [SDE]Environmental Sciences, Hydroxyquinolines, Titration, Acids, Water Pollutants, Chemical, Aluminum
Abstract: International audience; Polyaluminum chloride (PACl) is a well-established coagulant in water treatment with high removal efficiency for arsenic. A high content of Al-30 nanoclusters in PACl improves the removal efficiency over broader dosage and pH range. In this study we tested PACl with 75% Al-30 nanoclusters (PACl(Al30)) for the treatment of arsenic-contaminated well water by laboratory batch experiments and field application in the geothermal area of Chalkidiki, Greece, and in the Pannonian Basin, Romania. The treatment efficiency was studied as a function of dosage and the nanoclusters' protonation degree. Acid-base titration revealed increasing deprotonation of PACl(Al30) from pH 4.7 to the point of zero charge at pH 6.7. The most efficient removal of As(III) and As(V) coincided with optimal aggregation of the Al nanoclusters at pH 7-8, a common pH range for groundwater. The application of PACl(Al30) with an Al-tot concentration of 1-5 mM in laboratory batch experiments successfully lowered dissolved As(V) concentrations from 20 to 230 mu g/L to less than 5 mu g/L. Field tests confirmed laboratory results, and showed that the WHO threshold value of 10 mu g/L was only slightly exceeded (10.8 mu g/L) at initial concentrations as high as 2300 mu g/L As(V). However, As(III) removal was less efficient (
Published: 2011

40. The NoRC complex mediates the heterochromatin formation and stability of silent rRNA genes and centromeric repeats

Author: Raffaella Santoro, Martin Fussenegger, Claudio Guetg, Danièle Hernandez-Verdun, Michael O. Hottiger, Philipp S. Lienemann, Ingrid Grummt, Valentina Sirri, Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Institute of Veterinary Biochemistry and Molecular Biology, Universität Zürich [Zürich] = University of Zurich (UZH), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Division of Molecular Biology of the Cell, German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), University of Zürich [Zürich] (UZH), University of Zurich, and Santoro, R
Subjects: Genome instability, Heterochromatin, Chromosomal Proteins, Non-Histone, 610 Medicine & health, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, DNA, Ribosomal, General Biochemistry, Genetics and Molecular Biology, Article, Genomic Instability, 03 medical and health sciences, Mice, 0302 clinical medicine, 1300 General Biochemistry, Genetics and Molecular Biology, Transcription (biology), 2400 General Immunology and Microbiology, 1312 Molecular Biology, Gene silencing, Constitutive heterochromatin, Animals, Gene Silencing, 10026 Clinic for Obstetrics, Molecular Biology, Gene, 030304 developmental biology, Cell Proliferation, Genetics, 0303 health sciences, General Immunology and Microbiology, General Neuroscience, 2800 General Neuroscience, Genes, rRNA, Ribosomal RNA, 10226 Department of Molecular Mechanisms of Disease, 030220 oncology & carcinogenesis, NIH 3T3 Cells, 570 Life sciences, biology, NoRC complex
Abstract: International audience; Maintenance of specific heterochromatic domains is crucial for genome stability. In eukaryotic cells, a fraction of the tandem-repeated ribosomal RNA (rRNA) genes is organized in the heterochromatic structures. The principal determinant of rDNA silencing is the nucleolar remodelling complex, NoRC, that consists of TIP5 (TTF-1-interacting protein-5) and the ATPase SNF2h. Here we showed that TIP5 not only mediates the establishment of rDNA silencing but also the formation of perinucleolar heterochromatin that contains centric and pericentric repeats. Our data indicated that the TIP5-mediated heterochromatin is indispensable for stability of silent rRNA genes and of major and minor satellite repeats. Moreover, depletion of TIP5 impairs rDNA silencing, upregulates rDNA transcription levels and induces cell transformation. These findings point to a role of TIP5 in protecting genome stability and suggest that it can play a role in the cellular transformation process.
Published: 2010

41. Probing the reproducibility of leaf growth and molecular phenotypes: a comparison of three arabidopsis accessions cultivated in ten laboratories

Author: Juliette Fabre, Bernd Rinn, Josip Perkovic, Christian Meyer, Jesper T. Gronlund, Lothar Willmitzer, Christine Granier, Sean T. May, Michael W. Bevan, Vicky Buchanan-Wollaston, Gerrit T.S. Beemster, Catherine Massonnet, Camila Caldana, Gaëlle Messerli, José Luis Micol, Lars Hennig, Wilhelm Gruissem, Fabio Fiorani, Pierre Hilson, Matthew A. Hannah, Denis Vile, Sean Walsh, Silvia Rubio-Díaz, Rhonda C. Meyer, Emma Wigmore, Detlef Weigel, Jan Lisec, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Department of Plant Systems Biology, Flanders Institute for Biotechnology, Department of Plant Biotechnology and Genetics, Ghent University [Belgium] (UGENT), Department of Biology, Plant Biotechnology, Warwick Horticulture Research International, University of Warwick [Coventry], Max Planck Institute for Developmental Biology, Plant Sciences, School of Biosciences, University of Nottingham, UK (UON), Cell and Developmental Biology Department, John Innes Centre [Norwich], Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, División de Genética and Instituto de Bioingeniería, Universidad Miguel Hernández [Elche] (UMH), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Department of Plant Biotechnology and Bioinformatics, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Universiteit Gent = Ghent University [Belgium] (UGENT), and Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)
Subjects: 0106 biological sciences, feuille, Genotype, Physiology, croissance végétale, méthode de mesure, Arabidopsis, Plant Science, Computational biology, Plants genetics, 01 natural sciences, Transcriptome, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Species Specificity, RELATION GENOTYPE x ENVIRONNEMENT, métabolite, Génétique des plantes, Genetics, Transcriptome Profiles, Arabidopsis thaliana, RNA, Messenger, Biology, 030304 developmental biology, Blue light, 0303 health sciences, SIGNATURE METABOLIQUE, biology, Gene Expression Profiling, fungi, Reproducibility of Results, food and beverages, biology.organism_classification, Phenotype, environnement, Systems Biology, Molecular Biology, and Gene Regulation, Gene expression profiling, Plant Leaves, phénotype, transcriptome, 010606 plant biology & botany
Abstract: L'article original est publié par The American Society of Plant Biologists; A major goal of the life sciences is to understand how molecular processes control phenotypes. Because understanding biological systems relies on the work of multiple laboratories, biologists implicitly assume that organisms with the same genotype will display similar phenotypes when grown in comparable conditions. We investigated to what extent this holds true for leaf growth variables and metabolite and transcriptome profiles of three Arabidopsis (Arabidopsis thaliana) genotypes grown in 10 laboratories using a standardized and detailed protocol. A core group of four laboratories generated similar leaf growth phenotypes, demonstrating that standardization is possible. But some laboratories presented significant differences in some leaf growth variables, sometimes changing the genotype ranking. Metabolite profiles derived from the same leaf displayed a strong genotype x environment (laboratory) component. Genotypes could be separated on the basis of their metabolic signature, but only when the analysis was limited to samples derived from one laboratory. Transcriptome data revealed considerable plant-to-plant variation, but the standardization ensured that interlaboratory variation was not considerably larger than intralaboratory variation. The different impacts of the standardization on phenotypes and molecular profiles could result from differences of temporal scale between processes involved at these organizational levels. Our findings underscore the challenge of describing, monitoring, and precisely controlling environmental conditions but also demonstrate that dedicated efforts can result in reproducible data across multiple laboratories. Finally, our comparative analysis revealed that small variations in growing conditions (light quality principally) and handling of plants can account for significant differences in phenotypes and molecular profiles obtained in independent laboratories.
Published: 2010

42. Discussion on: 'Time-delay model-based control of the glucose-insulin system, by means of a state observer'

Author: Olivier Sename, Corentin Briat, Sename, Olivier, GIPSA - Systèmes linéaires et robustesse (GIPSA-SLR), Département Automatique (GIPSA-DA), Grenoble Images Parole Signal Automatique (GIPSA-lab), Université Stendhal - Grenoble 3-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Stendhal - Grenoble 3-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Grenoble Images Parole Signal Automatique (GIPSA-lab), Université Stendhal - Grenoble 3-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Stendhal - Grenoble 3-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), and Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)
Subjects: 0209 industrial biotechnology, education.field_of_study, Computer science, Population, General Engineering, 02 engineering and technology, Model based control, [SPI.AUTO]Engineering Sciences [physics]/Automatic, 020901 industrial engineering & automation, [SPI.AUTO] Engineering Sciences [physics]/Automatic, Population evolution, Transmission (telecommunications), Control theory, 0202 electrical engineering, electronic engineering, information engineering, 020201 artificial intelligence & image processing, State observer, education
Abstract: International audience; Time-delay systems are ubiquitous in nature and engineering. Delays account for transmission, diffusion and migration phenomena as well as maturation and aging in physical, biological, ecological, epidemiological and population systems. Lotka-Volterra models describing prey-predator models or Pearl-Verhulst equations for population dynamics are instances of deterministic models aiming to describe population evolution. These models do not account for aging/maturation of the population and this is the reason why refinement of the models have been proposed.

43. HOL-TestGen Version 1.8 USER GUIDE

Author: Achim Brucker, Lukas Brügger, Abderrahmane Feliachi, Chantal Keller, Matthias Krieger, Delphine Longuet, Yakoub Nemouchi, Frédéric Tuong, Burkhart Wolff, Institute of Information Security [ETH Zürich], Department of Computer Science [ETH Zürich] (D-INFK), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Laboratoire de Recherche en Informatique (LRI), CentraleSupélec-Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11), Centre National de la Recherche Scientifique (CNRS), CentraleSupélec, Université Paris-Saclay, IRT SystemX (IRT SystemX), Univeristé Paris-Saclay, and LRI - CNRS, University Paris-Sud
Subjects: [SCCO.COMP]Cognitive science/Computer science

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