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Large-Scale, Wavelet-Based Analysis of Lysosomal Trajectories and Co-Movements of Lysosomes with Nanoparticle Cargos. Cells 2022; 11:cells11020270. [PMID: 35053385 PMCID: PMC8774281 DOI: 10.3390/cells11020270] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 02/01/2023] Open
Abstract
Lysosomes—that is, acidic organelles known for degradation/recycling—move through the cytoplasm alternating between bursts of active transport and short, diffusive motions or even pauses. While their mobility is essential for lysosomes’ fusogenic and non-fusogenic interactions with target organelles, their movements have not been characterized in adequate detail. Here, large-scale statistical analysis of lysosomal movement trajectories reveals that lysosome trajectories in all examined cell types—both cancer and noncancerous ones—are superdiffusive and characterized by heavy-tailed distributions of run and flight lengths. Consideration of Akaike weights for various potential models (lognormal, power law, truncated power law, stretched exponential, and exponential) indicates that the experimental data are best described by the lognormal distribution, which, in turn, can be related to one of the space-search strategies particularly effective when “thorough” search needs to balance search for rare target(s) (organelles). In addition, automated, wavelet-based analysis allows for co-tracking the motions of lysosomes and the cargos they carry—particularly the nanoparticle aggregates known to cause selective lysosome disruption in cancerous cells. The methods we describe here could help study nanoparticle assemblies, viruses, and other objects transported inside various vesicle types, as well as coordinated movements of organelles/particles in the cytoplasm. Custom-written code that includes integrated workflow for our analyses is made available for academic use.
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2
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Gunning CE, Ferrari MJ, Erhardt EB, Wearing HJ. Evidence of cryptic incidence in childhood diseases. Proc Biol Sci 2018; 284:rspb.2017.1268. [PMID: 28855364 DOI: 10.1098/rspb.2017.1268] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/19/2017] [Indexed: 02/06/2023] Open
Abstract
Persistence and extinction are key processes in infectious disease dynamics that, owing to incomplete reporting, are seldom directly observable. For fully immunizing diseases, reporting probabilities can be readily estimated from demographic records and case reports. Yet reporting probabilities are not sufficient to unambiguously reconstruct disease incidence from case reports. Here, we focus on disease presence (i.e. marginal probability of non-zero incidence), which provides an upper bound on the marginal probability of disease extinction. We examine measles and pertussis in pre-vaccine era United States (US) cities, and describe a conserved scaling relationship between population size, reporting probability and observed presence (i.e. non-zero case reports). We use this relationship to estimate disease presence given perfect reporting, and define cryptic presence as the difference between estimated and observed presence. We estimate that, in early twentieth century US cities, pertussis presence was higher than measles presence across a range of population sizes, and that cryptic presence was common in small cities with imperfect reporting. While the methods employed here are specific to fully immunizing diseases, our results suggest that cryptic incidence deserves careful attention, particularly in diseases with low case counts, poor reporting and longer infectious periods.
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Affiliation(s)
| | - Matthew J Ferrari
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Erik B Erhardt
- Department of Mathematics and Statistics, University of New Mexico, Albuquerque, NM, USA
| | - Helen J Wearing
- Department of Biology, University of New Mexico, Albuquerque, NM, USA.,Department of Mathematics and Statistics, University of New Mexico, Albuquerque, NM, USA
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3
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Dallas TA, Krkošek M, Drake JM. Experimental evidence of a pathogen invasion threshold. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171975. [PMID: 29410876 PMCID: PMC5792953 DOI: 10.1098/rsos.171975] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 12/11/2017] [Indexed: 05/15/2023]
Abstract
Host density thresholds to pathogen invasion separate regions of parameter space corresponding to endemic and disease-free states. The host density threshold is a central concept in theoretical epidemiology and a common target of human and wildlife disease control programmes, but there is mixed evidence supporting the existence of thresholds, especially in wildlife populations or for pathogens with complex transmission modes (e.g. environmental transmission). Here, we demonstrate the existence of a host density threshold for an environmentally transmitted pathogen by combining an epidemiological model with a microcosm experiment. Experimental epidemics consisted of replicate populations of naive crustacean zooplankton (Daphnia dentifera) hosts across a range of host densities (20-640 hosts l-1) that were exposed to an environmentally transmitted fungal pathogen (Metschnikowia bicuspidata). Epidemiological model simulations, parametrized independently of the experiment, qualitatively predicted experimental pathogen invasion thresholds. Variability in parameter estimates did not strongly influence outcomes, though systematic changes to key parameters have the potential to shift pathogen invasion thresholds. In summary, we provide one of the first clear experimental demonstrations of pathogen invasion thresholds in a replicated experimental system, and provide evidence that such thresholds may be predictable using independently constructed epidemiological models.
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Affiliation(s)
- Tad A. Dallas
- Department of Environmental Science and Policy, University of California, Davis, CA, USA
- Odum School of Ecology, University of Georgia, Athens, GA, USA
| | - Martin Krkošek
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - John M. Drake
- Odum School of Ecology, University of Georgia, Athens, GA, USA
- Center for the Ecology of Infectious Disease, University of Georgia, Athens, GA, USA
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4
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Brownwright TK, Dodson ZM, van Panhuis WG. Spatial clustering of measles vaccination coverage among children in sub-Saharan Africa. BMC Public Health 2017; 17:957. [PMID: 29246217 PMCID: PMC5732449 DOI: 10.1186/s12889-017-4961-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 11/29/2017] [Indexed: 11/18/2022] Open
Abstract
Background During the past two decades, vaccination programs have greatly reduced global morbidity and mortality due to measles, but recently this progress has stalled. Even in countries that report high vaccination coverage rates, transmission has continued, particularly in spatially clustered subpopulations with low vaccination coverage. Methods We examined the spatial heterogeneity of measles vaccination coverage among children aged 12–23 months in ten Sub-Saharan African countries. We used the Anselin Local Moran’s I to estimate clustering of vaccination coverage based on data from Demographic and Health Surveys conducted between 2008 and 2013. We also examined the role of sociodemographic factors to explain clustering of low vaccination. Results We detected 477 spatial clusters with low vaccination coverage, many of which were located in countries with relatively high nationwide vaccination coverage rates such as Zambia and Malawi. We also found clusters in border areas with transient populations. Clustering of low vaccination coverage was related to low health education and limited access to healthcare. Conclusions Systematically monitoring clustered populations with low vaccination coverage can inform supplemental immunization activities and strengthen elimination programs. Metrics of spatial heterogeneity should be used routinely to determine the success of immunization programs and the risk of disease persistence.
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Affiliation(s)
- Tenley K Brownwright
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, 130 DeSoto Street, 715 Parran Hall, Pittsburgh, PA, 15261, USA
| | - Zan M Dodson
- Department of Health Policy and Management, University of Pittsburgh Graduate School of Public Health, 130 DeSoto Street, 702 Parran Hall, Pittsburgh, PA, 15261, USA
| | - Willem G van Panhuis
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, 130 DeSoto Street, 715 Parran Hall, Pittsburgh, PA, 15261, USA.
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Bourhy H, Nakouné E, Hall M, Nouvellet P, Lepelletier A, Talbi C, Watier L, Holmes EC, Cauchemez S, Lemey P, Donnelly CA, Rambaut A. Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting. PLoS Pathog 2016; 12:e1005525. [PMID: 27058957 PMCID: PMC4825935 DOI: 10.1371/journal.ppat.1005525] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 03/03/2016] [Indexed: 11/24/2022] Open
Abstract
The development of novel approaches that combine epidemiological and genomic data provides new opportunities to reveal the spatiotemporal dynamics of infectious diseases and determine the processes responsible for their spread and maintenance. Taking advantage of detailed epidemiological time series and viral sequence data from more than 20 years reported by the National Reference Centre for Rabies of Bangui, the capital city of Central African Republic, we used a combination of mathematical modeling and phylogenetic analysis to determine the spatiotemporal dynamics of rabies in domestic dogs as well as the frequency of extinction and introduction events in an African city. We show that although dog rabies virus (RABV) appears to be endemic in Bangui, its epidemiology is in fact shaped by the regular extinction of local chains of transmission coupled with the introduction of new lineages, generating successive waves of spread. Notably, the effective reproduction number during each wave was rarely above the critical value of 1, such that rabies is not self-sustaining in Bangui. In turn, this suggests that rabies at local geographic scales is driven by human-mediated dispersal of RABV among sparsely connected peri-urban and rural areas as opposed to dispersion in a relatively large homogenous urban dog population. This combined epidemiological and genomic approach enables development of a comprehensive framework for understanding disease persistence and informing control measures, indicating that control measures are probably best targeted towards areas neighbouring the city that appear as the source of frequent incursions seeding outbreaks in Bangui.
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Affiliation(s)
- Hervé Bourhy
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | | | - Matthew Hall
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Pierre Nouvellet
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Anthony Lepelletier
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Chiraz Talbi
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Laurence Watier
- INSERM, UMR 1181 and Institut Pasteur, B2PHI, Paris, France
- Faculté de Médecine Paris Ile de France-Ouest, Université de Versailles–Saint-Quentin, Versailles, France
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases & Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, Sydney, Australia
| | - Simon Cauchemez
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Paris, France
| | | | - Christl A. Donnelly
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
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6
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Fricke GM, Letendre KA, Moses ME, Cannon JL. Persistence and Adaptation in Immunity: T Cells Balance the Extent and Thoroughness of Search. PLoS Comput Biol 2016; 12:e1004818. [PMID: 26990103 PMCID: PMC4798282 DOI: 10.1371/journal.pcbi.1004818] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/17/2016] [Indexed: 11/19/2022] Open
Abstract
Effective search strategies have evolved in many biological systems, including the immune system. T cells are key effectors of the immune response, required for clearance of pathogenic infection. T cell activation requires that T cells encounter antigen-bearing dendritic cells within lymph nodes, thus, T cell search patterns within lymph nodes may be a crucial determinant of how quickly a T cell immune response can be initiated. Previous work suggests that T cell motion in the lymph node is similar to a Brownian random walk, however, no detailed analysis has definitively shown whether T cell movement is consistent with Brownian motion. Here, we provide a precise description of T cell motility in lymph nodes and a computational model that demonstrates how motility impacts T cell search efficiency. We find that both Brownian and Lévy walks fail to capture the complexity of T cell motion. Instead, T cell movement is better described as a correlated random walk with a heavy-tailed distribution of step lengths. Using computer simulations, we identify three distinct factors that contribute to increasing T cell search efficiency: 1) a lognormal distribution of step lengths, 2) motion that is directionally persistent over short time scales, and 3) heterogeneity in movement patterns. Furthermore, we show that T cells move differently in specific frequently visited locations that we call "hotspots" within lymph nodes, suggesting that T cells change their movement in response to the lymph node environment. Our results show that like foraging animals, T cells adapt to environmental cues, suggesting that adaption is a fundamental feature of biological search.
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Affiliation(s)
- G. Matthew Fricke
- Department of Computer Science, The University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Kenneth A. Letendre
- Department of Biology, The University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Melanie E. Moses
- Department of Computer Science, The University of New Mexico, Albuquerque, New Mexico, United States of America
- Department of Biology, The University of New Mexico, Albuquerque, New Mexico, United States of America
- External Faculty, Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Judy L. Cannon
- Department of Molecular Genetics and Microbiology, The University of New Mexico School of Medicine, Albuquerque, New Mexico, United States of America
- Department of Pathology, The University of New Mexico School of Medicine, Albuquerque, New Mexico, United States of America
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Gunning CE, Erhardt E, Wearing HJ. Conserved patterns of incomplete reporting in pre-vaccine era childhood diseases. Proc Biol Sci 2015; 281:20140886. [PMID: 25232131 DOI: 10.1098/rspb.2014.0886] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Incomplete observation is an important yet often neglected feature of observational ecological timeseries. In particular, observational case report timeseries of childhood diseases have played an important role in the formulation of mechanistic dynamical models of populations and metapopulations. Yet to our knowledge, no comprehensive study of childhood disease reporting probabilities (commonly referred to as reporting rates) has been conducted to date. Here, we provide a detailed analysis of measles and whooping cough reporting probabilities in pre-vaccine United States cities and states, as well as measles in cities of England and Wales. Overall, we find the variability between locations and diseases greatly exceeds that between methods or time periods. We demonstrate a strong relationship within location between diseases and within disease between geographical areas. In addition, we find that demographic covariates such as ethnic composition and school attendance explain a non-trivial proportion of reporting probability variation. Overall, our findings show that disease reporting is both variable and non-random and that completeness of reporting is influenced by disease identity, geography and socioeconomic factors. We suggest that variations in incomplete observation can be accounted for and that doing so can reveal ecologically important features that are otherwise obscured.
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Affiliation(s)
| | - Erik Erhardt
- Department of Mathematics and Statistics, University of New Mexico, Albuquerque, NM, USA
| | - Helen J Wearing
- Department of Biology, University of New Mexico, Albuquerque, NM, USA Department of Mathematics and Statistics, University of New Mexico, Albuquerque, NM, USA
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Assembling evidence for identifying reservoirs of infection. Trends Ecol Evol 2014; 29:270-9. [PMID: 24726345 PMCID: PMC4007595 DOI: 10.1016/j.tree.2014.03.002] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 03/03/2014] [Accepted: 03/10/2014] [Indexed: 12/25/2022]
Abstract
We review the problem of identifying reservoirs of infection for multihost pathogens and provide an overview of current approaches and future directions. We provide a conceptual framework for classifying patterns of incidence and prevalence. We review current methods that allow us to characterise the components of reservoir-target systems. Ecological theory offers promising new ways to prioritise populations when designing interventions. We propose using interventions as quasi-experiments embedded in adaptive management frameworks. Integration of data and analysis provides powerful new opportunities for studying multihost systems.
Many pathogens persist in multihost systems, making the identification of infection reservoirs crucial for devising effective interventions. Here, we present a conceptual framework for classifying patterns of incidence and prevalence, and review recent scientific advances that allow us to study and manage reservoirs simultaneously. We argue that interventions can have a crucial role in enriching our mechanistic understanding of how reservoirs function and should be embedded as quasi-experimental studies in adaptive management frameworks. Single approaches to the study of reservoirs are unlikely to generate conclusive insights whereas the formal integration of data and methodologies, involving interventions, pathogen genetics, and contemporary surveillance techniques, promises to open up new opportunities to advance understanding of complex multihost systems.
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Tack AJM, Laine AL. Ecological and evolutionary implications of spatial heterogeneity during the off-season for a wild plant pathogen. THE NEW PHYTOLOGIST 2014; 202:297-308. [PMID: 24372358 PMCID: PMC4285854 DOI: 10.1111/nph.12646] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 11/04/2013] [Indexed: 05/20/2023]
Abstract
While recent studies have elucidated many of the factors driving parasite dynamics during the growing season, the ecological and evolutionary dynamics during the off-season (i.e. the period between growing seasons) remain largely unexplored. We combined large-scale surveys and detailed experiments to investigate the overwintering success of the specialist plant pathogen Podosphaera plantaginis on its patchily distributed host plant Plantago lanceolata in the Åland Islands. Twelve years of epidemiological data establish the off-season as a crucial stage in pathogen metapopulation dynamics, with c. 40% of the populations going extinct during the off-season. At the end of the growing season, we observed environmentally mediated variation in the production of resting structures, with major consequences for spring infection at spatial scales ranging from single individuals to populations within a metapopulation. Reciprocal transplant experiments further demonstrated that pathogen population of origin and overwintering site jointly shaped infection intensity in spring, with a weak signal of parasite adaptation to the local off-season environment. We conclude that environmentally mediated changes in the distribution and evolution of parasites during the off-season are crucial for our understanding of host-parasite dynamics, with applied implications for combating parasites and diseases in agriculture, wildlife and human disease systems.
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Affiliation(s)
- Ayco J M Tack
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, PO Box 65 (Viikinkaari 1), FI-00014, Helsinki, Finland
| | - Anna-Liisa Laine
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, PO Box 65 (Viikinkaari 1), FI-00014, Helsinki, Finland
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