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Melaugh G, Hutchison J, Kragh KN, Irie Y, Roberts A, Bjarnsholt T, Diggle SP, Gordon VD, Allen RJ. Shaping the Growth Behaviour of Biofilms Initiated from Bacterial Aggregates. PLoS One 2016; 11:e0149683. [PMID: 26934187 PMCID: PMC4774936 DOI: 10.1371/journal.pone.0149683] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/03/2016] [Indexed: 01/26/2023] Open
Abstract
Bacterial biofilms are usually assumed to originate from individual cells deposited on a surface. However, many biofilm-forming bacteria tend to aggregate in the planktonic phase so that it is possible that many natural and infectious biofilms originate wholly or partially from pre-formed cell aggregates. Here, we use agent-based computer simulations to investigate the role of pre-formed aggregates in biofilm development. Focusing on the initial shape the aggregate forms on the surface, we find that the degree of spreading of an aggregate on a surface can play an important role in determining its eventual fate during biofilm development. Specifically, initially spread aggregates perform better when competition with surrounding unaggregated bacterial cells is low, while initially rounded aggregates perform better when competition with surrounding unaggregated cells is high. These contrasting outcomes are governed by a trade-off between aggregate surface area and height. Our results provide new insight into biofilm formation and development, and reveal new factors that may be at play in the social evolution of biofilm communities.
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Affiliation(s)
- Gavin Melaugh
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, United Kingdom
- * E-mail:
| | - Jaime Hutchison
- Center for Nonlinear Dynamics and Department of Physics, The University of Texas at Austin, Austin, Texas 78712-1199, United States of America
| | - Kasper Nørskov Kragh
- Department of International Health, Immunology and Microbiology, Faculty Of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Yasuhiko Irie
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Aled Roberts
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Thomas Bjarnsholt
- Department of International Health, Immunology and Microbiology, Faculty Of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Department for Clinical Microbiology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Stephen P. Diggle
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Vernita D. Gordon
- Center for Nonlinear Dynamics and Department of Physics, The University of Texas at Austin, Austin, Texas 78712-1199, United States of America
| | - Rosalind J. Allen
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, United Kingdom
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Zárybnická M, Riegert J, Brejšková L, Šindelář J, Kouba M, Hanel J, Popelková A, Menclová P, Tomášek V, Šťastný K. Factors Affecting Growth of Tengmalm's Owl (Aegolius funereus) Nestlings: Prey Abundance, Sex and Hatching Order. PLoS One 2015; 10:e0138177. [PMID: 26444564 PMCID: PMC4596578 DOI: 10.1371/journal.pone.0138177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/27/2015] [Indexed: 11/19/2022] Open
Abstract
In altricial birds, energy supply during growth is a major predictor of the physical condition and survival prospects of fledglings. A number of experimental studies have shown that nestling body mass and wing length can vary with particular extrinsic factors, but between-year observational data on this topic are scarce. Based on a seven-year observational study in a central European Tengmalm's owl population we examine the effect of year, brood size, hatching order, and sex on nestling body mass and wing length, as well as the effect of prey abundance on parameters of growth curve. We found that nestling body mass varied among years, and parameters of growth curve, i.e. growth rate and inflection point in particular, increased with increasing abundance of the owl's main prey (Apodemus mice, Microtus voles), and pooled prey abundance (Apodemus mice, Microtus voles, and Sorex shrews). Furthermore, nestling body mass varied with hatching order and between sexes being larger for females and for the first-hatched brood mates. Brood size had no effect on nestling body mass. Simultaneously, we found no effect of year, brood size, hatching order, or sex on the wing length of nestlings. Our findings suggest that in this temperate owl population, nestling body mass is more sensitive to prey abundance than is wing length. The latter is probably more limited by the physiology of the species.
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Affiliation(s)
- Markéta Zárybnická
- Department of Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
- * E-mail:
| | - Jan Riegert
- Department of Zoology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | - Lucie Brejšková
- Department of Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jiří Šindelář
- Department of Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Marek Kouba
- Department of Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jan Hanel
- Department of Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Alena Popelková
- Department of Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Petra Menclová
- Department of Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Václav Tomášek
- Department of Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Karel Šťastný
- Department of Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
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Affiliation(s)
- Anthony L Komaroff
- Harvard Medical School, Brigham & Women's Hospital, Boston, Massachusetts
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Yuasa K, Yotsumoto Y. Opposite Distortions in Interval Timing Perception for Visual and Auditory Stimuli with Temporal Modulations. PLoS One 2015; 10:e0135646. [PMID: 26292285 PMCID: PMC4546296 DOI: 10.1371/journal.pone.0135646] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/23/2015] [Indexed: 12/27/2022] Open
Abstract
When an object is presented visually and moves or flickers, the perception of its duration tends to be overestimated. Such an overestimation is called time dilation. Perceived time can also be distorted when a stimulus is presented aurally as an auditory flutter, but the mechanisms and their relationship to visual processing remains unclear. In the present study, we measured interval timing perception while modulating the temporal characteristics of visual and auditory stimuli, and investigated whether the interval times of visually and aurally presented objects shared a common mechanism. In these experiments, participants compared the durations of flickering or fluttering stimuli to standard stimuli, which were presented continuously. Perceived durations for auditory flutters were underestimated, while perceived durations of visual flickers were overestimated. When auditory flutters and visual flickers were presented simultaneously, these distortion effects were cancelled out. When auditory flutters were presented with a constantly presented visual stimulus, the interval timing perception of the visual stimulus was affected by the auditory flutters. These results indicate that interval timing perception is governed by independent mechanisms for visual and auditory processing, and that there are some interactions between the two processing systems.
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Affiliation(s)
- Kenichi Yuasa
- Department of Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuko Yotsumoto
- Department of Life Sciences, The University of Tokyo, Tokyo, Japan
- * E-mail:
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Liu Z, Li X, Wang Z, Sun Q. Contrasting Strategies of Alfalfa Stem Elongation in Response to Fall Dormancy in Early Growth Stage: The Tradeoff between Internode Length and Internode Number. PLoS One 2015; 10:e0135934. [PMID: 26281014 PMCID: PMC4539217 DOI: 10.1371/journal.pone.0135934] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 07/29/2015] [Indexed: 11/18/2022] Open
Abstract
Fall dormancy (FD) in alfalfa (Medicago sativa L.) can be described using 11 FD ratings, is widely used as an important indicator of stress resistance, productive performance and spring growth. However, the contrasting growth strategies in internode length and internode number in alfalfa cultivars with different FD rating are poorly understood. Here, a growth chamber study was conducted to investigate the effect of FD on plant height, aboveground biomass, internode length, and internode number in alfalfa individuals in the early growth stages. In order to simulate the alfalfa growth environment in the early stage, 11 alfalfa cultivars with FD ratings from one to 11 were chosen and seeded at the greenhouse, and then were transplanted into an artificial growth chamber. The experimental design was a randomized complete block in a split-plot arrangement with three replicates. Plant height, above-ground biomass, internode length, and internode number were measured in early growth stage in all individuals. Our findings showed that plant height and the aboveground biomass of alfalfa did not significantly differ among 11 different FD rated cultivars. Also, internode length and internode number positively affected plant height and the aboveground biomass of alfalfa individuals and the average internode length significantly increased with increasing FD rating. However, internode number tended to sharply decline when the FD rating increased. Moreover, there were no correlations, slightly negative correlations, and strongly negative correlations between internode length and internode number in alfalfa individuals among the three scales, including within-FD ratings, within-FD categories and inter-FD ratings, respectively. Therefore, our results highlighted that contrasting growth strategies in stem elongation were adopted by alfalfa with different FD ratings in the early growth stage. Alfalfa cultivars with a high FD rating have longer internodes, whereas more dormant alfalfa cultivars have a larger number of internodes. There were tradeoffs between internode length and internode number in response to FD in alfalfa, which reflected certain scale-dependence.
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Affiliation(s)
- Zhiying Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, P.R. China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Xiliang Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, P.R. China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Zongli Wang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, P.R. China
- Animal husbandry department of Ministry of Agriculture, Beijing, P.R. China
| | - Qizhong Sun
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, P.R. China
- * E-mail:
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Laiz-Carrión R, Gerard T, Uriarte A, Malca E, Quintanilla JM, Muhling BA, Alemany F, Privoznik SL, Shiroza A, Lamkin JT, García A. Trophic ecology of Atlantic Bluefin Tuna (Thunnus thynnus) [corrected] larvae from the Gulf of Mexico and NW Mediterranean spawning grounds: A Comparative Stable Isotope Study. PLoS One 2015. [PMID: 26225849 PMCID: PMC4520599 DOI: 10.1371/journal.pone.0133406] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The present study uses stable isotopes of nitrogen and carbon (δ15Nandδ13C) as trophic indicators for Atlantic bluefin tuna larvae (BFT) (6–10 mm standard length) in the highly contrasting environmental conditions of the Gulf of Mexico (GOM) and the Balearic Sea (MED). These regions are differentiated by their temperature regime and relative productivity, with the GOM being significantly warmer and more productive. MED BFT larvae showed the highest δ15N signatures, implying an elevated trophic position above the underlying microzooplankton baseline. Ontogenetic dietary shifts were observed in the BFT larvae from the GOM and MED which indicates early life trophodynamics differences between these spawning habitats. Significant trophic differences between the GOM and MED larvae were observed in relation to δ15N signatures in favour of the MED larvae, which may have important implications in their growth during their early life stages.These low δ15N levels in the zooplankton from the GOM may be an indication of a shifting isotopic baseline in pelagic food webs due to diatrophic inputs by cyanobacteria. Lack of enrichment for δ15N in BFT larvae compared to zooplankton implies an alternative grazing pathway from the traditional food chain of phytoplankton—zooplankton—larval fish. Results provide insight for a comparative characterization of the trophic pathways variability of the two main spawning grounds for BFT larvae.
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Affiliation(s)
- Raúl Laiz-Carrión
- Instituto Español de Oceanografía—Centro Oceanográfico de Málaga (COM-IEO), Fuengirola, Spain
- * E-mail:
| | - Trika Gerard
- Southeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration (NOAA), Miami, Florida, United States of America
- South Florida Campus- University of Phoenix, Miramar, Florida, United States of America
| | - Amaya Uriarte
- Instituto Español de Oceanografía—Centro Oceanográfico de Málaga (COM-IEO), Fuengirola, Spain
| | - Estrella Malca
- South Florida Campus- University of Phoenix, Miramar, Florida, United States of America
- Cooperative Institute for Marine and Atmospheric Studies (CIMAS), University of Miami, Miami, Florida, United States of America
| | - José María Quintanilla
- Instituto Español de Oceanografía—Centro Oceanográfico de Málaga (COM-IEO), Fuengirola, Spain
| | - Barbara A. Muhling
- Princeton University Program in Atmospheric and Oceanic Science, Forrestal Campus/Sayre Hall, Princeton, New Jersey, United States of America
- NOAA Geophysical Fluid Dynamics Laboratory, 201 Forrestal Road, Princeton, New Jersey, United States of America
| | - Francisco Alemany
- Instituto Español de Oceanografía Centro Oceanográfico de Baleares (COB-IEO), Palma de Mallorca, Balearic Islands, Spain
| | - Sarah L. Privoznik
- South Florida Campus- University of Phoenix, Miramar, Florida, United States of America
- Cooperative Institute for Marine and Atmospheric Studies (CIMAS), University of Miami, Miami, Florida, United States of America
| | - Akihiro Shiroza
- South Florida Campus- University of Phoenix, Miramar, Florida, United States of America
- Cooperative Institute for Marine and Atmospheric Studies (CIMAS), University of Miami, Miami, Florida, United States of America
| | - John T. Lamkin
- Southeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration (NOAA), Miami, Florida, United States of America
| | - Alberto García
- Instituto Español de Oceanografía—Centro Oceanográfico de Málaga (COM-IEO), Fuengirola, Spain
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Walsh JC, Angstmann CN, Duggin IG, Curmi PMG. Molecular Interactions of the Min Protein System Reproduce Spatiotemporal Patterning in Growing and Dividing Escherichia coli Cells. PLoS One 2015; 10:e0128148. [PMID: 26018614 PMCID: PMC4446092 DOI: 10.1371/journal.pone.0128148] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/22/2015] [Indexed: 11/24/2022] Open
Abstract
Oscillations of the Min protein system are involved in the correct midcell placement of the divisome during Escherichia coli cell division. Based on molecular interactions of the Min system, we formulated a mathematical model that reproduces Min patterning during cell growth and division. Specifically, the increase in the residence time of MinD attached to the membrane as its own concentration increases, is accounted for by dimerisation of membrane-bound MinD and its interaction with MinE. Simulation of this system generates unparalleled correlation between the waveshape of experimental and theoretical MinD distributions, suggesting that the dominant interactions of the physical system have been successfully incorporated into the model. For cells where MinD is fully-labelled with GFP, the model reproduces the stationary localization of MinD-GFP for short cells, followed by oscillations from pole to pole in larger cells, and the transition to the symmetric distribution during cell filamentation. Cells containing a secondary, GFP-labelled MinD display a contrasting pattern. The model is able to account for these differences, including temporary midcell localization just prior to division, by increasing the rate constant controlling MinD ATPase and heterotetramer dissociation. For both experimental conditions, the model can explain how cell division results in an equal distribution of MinD and MinE in the two daughter cells, and accounts for the temperature dependence of the period of Min oscillations. Thus, we show that while other interactions may be present, they are not needed to reproduce the main characteristics of the Min system in vivo.
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Affiliation(s)
- James C. Walsh
- School of Physics, University of New South Wales, Sydney NSW 2052, Australia
- The ithree institute, University of Technology, Sydney NSW 2007, Australia
| | | | - Iain G. Duggin
- The ithree institute, University of Technology, Sydney NSW 2007, Australia
| | - Paul M. G. Curmi
- School of Physics, University of New South Wales, Sydney NSW 2052, Australia
- * E-mail:
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Wright DS, Pierotti MER, Rundle HD, McKinnon JS. Conspicuous female ornamentation and tests of male mate preference in threespine sticklebacks (Gasterosteus aculeatus). PLoS One 2015; 10:e0120723. [PMID: 25806520 PMCID: PMC4373685 DOI: 10.1371/journal.pone.0120723] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 01/26/2015] [Indexed: 11/19/2022] Open
Abstract
Sexual selection drives the evolution of exaggerated male ornaments in many animal species. Female ornamentation is now acknowledged also to be common but is generally less well understood. One example is the recently documented red female throat coloration in some threespine stickleback (Gasterosteus aculeatus) populations. Although female sticklebacks often exhibit a preference for red male throat coloration, the possibility of sexual selection on female coloration has been little studied. Using sequential and simultaneous mate choice trials, we examined male mate preferences for female throat color, as well as pelvic spine color and standard length, using wild-captured threespine sticklebacks from the Little Campbell River, British Columbia. In a multivariate analysis, we found no evidence for a population-level mate preference in males, suggesting the absence of directional sexual selection on these traits arising from male mate choice. Significant variation was detected among males in their preference functions, but this appeared to arise from differences in their mean responsiveness across mating trials and not from variation in the strength (i.e., slope) of their preference, suggesting the absence of individual-level preferences as well. When presented with conspecific intruder males, male response decreased as intruder red throat coloration increased, suggesting that males can discriminate color and other aspects of phenotype in our experiment and that males may use these traits in intrasexual interactions. The results presented here are the first to explicitly address male preference for female throat color in threespine sticklebacks.
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Affiliation(s)
- Daniel Shane Wright
- Department of Biology and Center for Biodiversity, East Carolina University, Greenville, North Carolina, United States of America
- * E-mail:
| | - Michele E. R. Pierotti
- Department of Biology and Center for Biodiversity, East Carolina University, Greenville, North Carolina, United States of America
| | - Howard D. Rundle
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Jeffrey S. McKinnon
- Department of Biology and Center for Biodiversity, East Carolina University, Greenville, North Carolina, United States of America
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Abstract
The liver plays a vital role in glucose homeostasis, the synthesis of bile acids and the detoxification of foreign substances. Liver culture systems are widely used to test adverse effects of drugs and environmental toxicants. The two most prevalent liver culture systems are hepatocyte monolayers (HMs) and collagen sandwiches (CS). Despite their wide use, comprehensive transcriptional programs and interaction networks in these culture systems have not been systematically investigated. We integrated an existing temporal transcriptional dataset for HM and CS cultures of rat hepatocytes with a functional interaction network of rat genes. We aimed to exploit the functional interactions to identify statistically significant linkages between perturbed biological processes. To this end, we developed a novel approach to compute Contextual Biological Process Linkage Networks (CBPLNs). CBPLNs revealed numerous meaningful connections between different biological processes and gene sets, which we were successful in interpreting within the context of liver metabolism. Multiple phenomena captured by CBPLNs at the process level such as regulation, downstream effects, and feedback loops have well described counterparts at the gene and protein level. CBPLNs reveal high-level linkages between pathways and processes, making the identification of important biological trends more tractable than through interactions between individual genes and molecules alone. Our approach may provide a new route to explore, analyze, and understand cellular responses to internal and external cues within the context of the intricate networks of molecular interactions that control cellular behavior.
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Affiliation(s)
- Christopher D. Lasher
- Genetics, Bioinformatics, and Computational Biology PhD Program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Padmavathy Rajagopalan
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- ICTAS Center for Systems Biology of Engineered Tissues, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - T. M. Murali
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- ICTAS Center for Systems Biology of Engineered Tissues, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- * E-mail:
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