Journal articles on the topic 'Multi-organisms interactions'
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1
Sun, Xuelong, Cheng Hu, Tian Liu, Shigang Yue, Jigen Peng, and Qinbing Fu. "Translating Virtual Prey-Predator Interaction to Real-World Robotic Environments: Enabling Multimodal Sensing and Evolutionary Dynamics." Biomimetics 8, no. 8 (December 1, 2023): 580. http://dx.doi.org/10.3390/biomimetics8080580.
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Prey-predator interactions play a pivotal role in elucidating the evolution and adaptation of various organism’s traits. Numerous approaches have been employed to study the dynamics of prey-predator interaction systems, with agent-based methodologies gaining popularity. However, existing agent-based models are limited in their ability to handle multi-modal interactions, which are believed to be crucial for understanding living organisms. Conversely, prevailing prey-predator integration studies often rely on mathematical models and computer simulations, neglecting real-world constraints and noise. These elusive attributes, challenging to model, can lead to emergent behaviors and embodied intelligence. To bridge these gaps, our study designs and implements a prey-predator interaction scenario that incorporates visual and olfactory sensory cues not only in computer simulations but also in a real multi-robot system. Observed emergent spatial-temporal dynamics demonstrate successful transitioning of investigating prey-predator interactions from virtual simulations to the tangible world. It highlights the potential of multi-robotics approaches for studying prey-predator interactions and lays the groundwork for future investigations involving multi-modal sensory processing while considering real-world constraints.
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Henriques, Gil J. B., Simon van Vliet, and Michael Doebeli. "Multilevel selection favors fragmentation modes that maintain cooperative interactions in multispecies communities." PLOS Computational Biology 17, no. 9 (September 13, 2021): e1008896. http://dx.doi.org/10.1371/journal.pcbi.1008896.
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Reproduction is one of the requirements for evolution and a defining feature of life. Yet, across the tree of life, organisms reproduce in many different ways. Groups of cells (e.g., multicellular organisms, colonial microbes, or multispecies biofilms) divide by releasing propagules that can be single-celled or multicellular. What conditions determine the number and size of reproductive propagules? In multicellular organisms, existing theory suggests that single-cell propagules prevent the accumulation of deleterious mutations (e.g., cheaters). However, groups of cells, such as biofilms, sometimes contain multiple metabolically interdependent species. This creates a reproductive dilemma: small daughter groups, which prevent the accumulation of cheaters, are also unlikely to contain the species diversity that is required for ecological success. Here, we developed an individual-based, multilevel selection model to investigate how such multi-species groups can resolve this dilemma. By tracking the dynamics of groups of cells that reproduce by fragmenting into smaller groups, we identified fragmentation modes that can maintain cooperative interactions. We systematically varied the fragmentation mode and calculated the maximum mutation rate that communities can withstand before being driven to extinction by the accumulation of cheaters. We find that for groups consisting of a single species, the optimal fragmentation mode consists of releasing single-cell propagules. For multi-species groups we find various optimal strategies. With migration between groups, single-cell propagules are favored. Without migration, larger propagules sizes are optimal; in this case, group-size dependent fissioning rates can prevent the accumulation of cheaters. Our work shows that multi-species groups can evolve reproductive strategies that allow them to maintain cooperative interactions.
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Leggett, Helen C., Sam P. Brown, and Sarah E. Reece. "War and peace: social interactions in infections." Philosophical Transactions of the Royal Society B: Biological Sciences 369, no. 1642 (May 19, 2014): 20130365. http://dx.doi.org/10.1098/rstb.2013.0365.
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One of the most striking facts about parasites and microbial pathogens that has emerged in the fields of social evolution and disease ecology in the past few decades is that these simple organisms have complex social lives, indulging in a variety of cooperative, communicative and coordinated behaviours. These organisms have provided elegant experimental tests of the importance of relatedness, kin discrimination, cooperation and competition, in driving the evolution of social strategies. Here, we briefly review the social behaviours of parasites and microbial pathogens, including their contributions to virulence, and outline how inclusive fitness theory has helped to explain their evolution. We then take a mechanistically inspired ‘bottom-up’ approach, discussing how key aspects of the ways in which parasites and pathogens exploit hosts, namely public goods, mobile elements, phenotypic plasticity, spatial structure and multi-species interactions, contribute to the emergent properties of virulence and transmission. We argue that unravelling the complexities of within-host ecology is interesting in its own right, and also needs to be better incorporated into theoretical evolution studies if social behaviours are to be understood and used to control the spread and severity of infectious diseases.
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Golombek, Diego A., Ivana L. Bussi, and Patricia V. Agostino. "Minutes, days and years: molecular interactions among different scales of biological timing." Philosophical Transactions of the Royal Society B: Biological Sciences 369, no. 1637 (March 5, 2014): 20120465. http://dx.doi.org/10.1098/rstb.2012.0465.
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Biological clocks are genetically encoded oscillators that allow organisms to keep track of their environment. Among them, the circadian system is a highly conserved timing structure that regulates several physiological, metabolic and behavioural functions with periods close to 24 h. Time is also crucial for everyday activities that involve conscious time estimation. Timing behaviour in the second-to-minutes range, known as interval timing, involves the interaction of cortico-striatal circuits. In this review, we summarize current findings on the neurobiological basis of the circadian system, both at the genetic and behavioural level, and also focus on its interactions with interval timing and seasonal rhythms, in order to construct a multi-level biological clock.
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Kaitaniemi, Pekka, Annette Scheiner, Tero Klemola, and Kai Ruohomäki. "Multi-objective optimization shapes ecological variation." Proceedings of the Royal Society B: Biological Sciences 279, no. 1729 (August 17, 2011): 820–25. http://dx.doi.org/10.1098/rspb.2011.1371.
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Ecological systems contain a huge amount of quantitative variation between and within species and locations, which makes it difficult to obtain unambiguous verification of theoretical predictions. Ordinary experiments consider just a few explanatory factors and are prone to providing oversimplified answers because they ignore the complexity of the factors that underlie variation. We used multi-objective optimization (MO) for a mechanistic analysis of the potential ecological and evolutionary causes and consequences of variation in the life-history traits of a species of moth. Optimal life-history solutions were sought for environmental conditions where different life stages of the moth were subject to predation and other known fitness-reducing factors in a manner that was dependent on the duration of these life stages and on variable mortality rates. We found that multi-objective optimal solutions to these conditions that the moths regularly experience explained most of the life-history variation within this species. Our results demonstrate that variation can have a causal interpretation even for organisms under steady conditions. The results suggest that weather and species interactions can act as underlying causes of variation, and MO acts as a corresponding adaptive mechanism that maintains variation in the traits of organisms.
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Cairns, Johannes, Matti Jalasvuori, Ville Ojala, Michael Brockhurst, and Teppo Hiltunen. "Conjugation is necessary for a bacterial plasmid to survive under protozoan predation." Biology Letters 12, no. 2 (February 2016): 20150953. http://dx.doi.org/10.1098/rsbl.2015.0953.
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Horizontal gene transfer by conjugative plasmids plays a critical role in the evolution of antibiotic resistance. Interactions between bacteria and other organisms can affect the persistence and spread of conjugative plasmids. Here we show that protozoan predation increased the persistence and spread of the antibiotic resistance plasmid RP4 in populations of the opportunist bacterial pathogen Serratia marcescens . A conjugation-defective mutant plasmid was unable to survive under predation, suggesting that conjugative transfer is required for plasmid persistence under the realistic condition of predation. These results indicate that multi-trophic interactions can affect the maintenance of conjugative plasmids with implications for bacterial evolution and the spread of antibiotic resistance genes.
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Prayogo, Doddy, Min-Yuan Cheng, Yu-Wei Wu, A. A. N. Perwira Redi, Vincent F. Yu, Satria Fadil Persada, and Reny Nadlifatin. "A Novel Hybrid Metaheuristic Algorithm for Optimization of Construction Management Site Layout Planning." Algorithms 13, no. 5 (May 6, 2020): 117. http://dx.doi.org/10.3390/a13050117.
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Symbiotic organisms search (SOS) is a promising metaheuristic algorithm that has been studied recently by numerous researchers due to its capability to solve various hard and complex optimization problems. SOS is a powerful optimization technique that mimics the simulation of the typical symbiotic interactions among organisms in an ecosystem. This study presents a new SOS-based hybrid algorithm for solving the challenging construction site layout planning (CSLP) discrete problems. A new algorithm called the hybrid symbiotic organisms search with local operators (HSOS-LO) represents a combination of the canonical SOS and several local search mechanisms aimed at increasing the searching capability in discrete-based solution space. In this study, three CSLP problems that consist of single and multi-floor facility layout problems are tested, and the obtained results were compared with other widely used metaheuristic algorithms. The results indicate the robust performance of the HSOS-LO algorithm in handling discrete-based CSLP problems.
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Araújo, Cristiano V. M., Abdelmourhit Laissaoui, Daniel C. V. R. Silva, Eloisa Ramos-Rodríguez, Enrique González-Ortegón, Evaldo L. G. Espíndola, Francisco Baldó, et al. "Not Only Toxic but Repellent: What Can Organisms’ Responses Tell Us about Contamination and What Are the Ecological Consequences When They Flee from an Environment?" Toxics 8, no. 4 (December 12, 2020): 118. http://dx.doi.org/10.3390/toxics8040118.
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The ability of aquatic organisms to sense the surrounding environment chemically and interpret such signals correctly is crucial for their ecological niche and survival. Although it is an oversimplification of the ecological interactions, we could consider that a significant part of the decisions taken by organisms are, to some extent, chemically driven. Accordingly, chemical contamination might interfere in the way organisms behave and interact with the environment. Just as any environmental factor, contamination can make a habitat less attractive or even unsuitable to accommodate life, conditioning to some degree the decision of organisms to stay in, or move from, an ecosystem. If we consider that contamination is not always spatially homogeneous and that many organisms can avoid it, the ability of contaminants to repel organisms should also be of concern. Thus, in this critical review, we have discussed the dual role of contamination: toxicity (disruption of the physiological and behavioral homeostasis) vs. repellency (contamination-driven changes in spatial distribution/habitat selection). The discussion is centered on methodologies (forced exposure against non-forced multi-compartmented exposure systems) and conceptual improvements (individual stress due to the toxic effects caused by a continuous exposure against contamination-driven spatial distribution). Finally, we propose an approach in which Stress and Landscape Ecology could be integrated with each other to improve our understanding of the threat contaminants represent to aquatic ecosystems.
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Jordan, J. Scott. "Wild agency: nested intentionalities in cognitive neuroscience and archaeology." Philosophical Transactions of the Royal Society B: Biological Sciences 363, no. 1499 (February 21, 2008): 1981–91. http://dx.doi.org/10.1098/rstb.2008.0009.
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The present paper addresses the tensions between internalist and radical-interactionist approaches to cognitive neuroscience, and the conflicting conclusions these positions lead to as regards the issue of whether archaeological artefacts constitute ‘results’ or ‘components’ of cognition. Wild systems theory (WST) and the notion of wild agency are presented as a potential resolution. Specifically, WST conceptualizes organisms (i.e. wild agents) as open, multi-scale self-sustaining systems. It is thus able to address the causal properties of wild systems in a manner that is consistent with radical-interactionist concerns regarding multi-scale contingent interactions. Furthermore, by conceptualizing wild agents as self-sustaining embodiments of the persistent, multi-scale contexts that afforded their emergence and in which they sustain themselves, WST is able to address the semantic properties of wild agents in a way that acknowledges the internalist concerns regarding meaningful (i.e. semantic) internal states (i.e. causal content ). In conclusion, WST agrees with radical interactionism and asserts that archaeological artefacts constitute components of cognition. In addition, given its ability to resolve tensions between the internalist and the radical interactionist approaches to cognition, WST is presented as potentially integrative for cognitive science in general.
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Carvalho, Sylvestre, Henrique Mota, and Marcelo Martins. "Landscapes of Biochemical Warfare: Spatial Self-Organization Woven from Allelopathic Interactions." Life 13, no. 2 (February 13, 2023): 512. http://dx.doi.org/10.3390/life13020512.
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Evidence shows that diversity and spatial distributions of biological communities are largely driven by the race of living organisms in their adaptation to chemicals synthesized by their neighbors. In this report, the emergence of mathematical models on pure spatial self-organization induced by biochemical suppression (allelopathy) and competition between species were investigated through numerical analysis. For both random and patched initial spatial distributions of species, we demonstrate that warfare survivors are self-organized on the landscape in Turing-like patterns driven by diffusive instabilities of allelochemicals. These patterns are simple; either all species coexist at low diffusion rates or are massively extinct, except for a few at high diffusivities, but they are complex and biodiversity-sustained at intermediate diffusion rates. “Defensive alliances” and ecotones seem to be basic mechanisms that sustain great biodiversity in our hybrid cellular automata model. Moreover, species coexistence and extinction exhibit multi-stationarity.
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Escobedo, R., V. Lecheval, V. Papaspyros, F. Bonnet, F. Mondada, C. Sire, and G. Theraulaz. "A data-driven method for reconstructing and modelling social interactions in moving animal groups." Philosophical Transactions of the Royal Society B: Biological Sciences 375, no. 1807 (July 27, 2020): 20190380. http://dx.doi.org/10.1098/rstb.2019.0380.
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Group-living organisms that collectively migrate range from cells and bacteria to human crowds, and include swarms of insects, schools of fish, and flocks of birds or ungulates. Unveiling the behavioural and cognitive mechanisms by which these groups coordinate their movements is a challenging task. These mechanisms take place at the individual scale and can be described as a combination of interactions between individuals and interactions between these individuals and the physical obstacles in the environment. Thanks to the development of novel tracking techniques that provide large and accurate datasets, the main characteristics of individual and collective behavioural patterns can be quantified with an unprecedented level of precision. However, in a large number of studies, social interactions are usually described by force map methods that only have a limited capacity of explanation and prediction, being rarely suitable for a direct implementation in a concise and explicit mathematical model. Here, we present a general method to extract the interactions between individuals that are involved in the coordination of collective movements in groups of organisms. We then apply this method to characterize social interactions in two species of shoaling fish, the rummy-nose tetra ( Hemigrammus rhodostomus ) and the zebrafish ( Danio rerio ), which both present a burst-and-coast motion. From the detailed quantitative description of individual-level interactions, it is thus possible to develop a quantitative model of the emergent dynamics observed at the group level, whose predictions can be checked against experimental results. This method can be applied to a wide range of biological and social systems. This article is part of the theme issue ‘Multi-scale analysis and modelling of collective migration in biological systems’.
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Manzalini, Antonio, and Bruno Galeazzi. "Explaining Homeopathy with Quantum Electrodynamics." Homeopathy 108, no. 03 (March 22, 2019): 169–76. http://dx.doi.org/10.1055/s-0039-1681037.
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Background Every living organism is an open system operating far from thermodynamic equilibrium and exchanging energy, matter and information with an external environment. These exchanges are performed through non-linear interactions of billions of different biological components, at different levels, from the quantum to the macro-dimensional. The concept of quantum coherence is an inherent property of living cells, used for long-range interactions such as synchronization of cell division processes. There is support from recent advances in quantum biology, which demonstrate that coherence, as a state of order of matter coupled with electromagnetic (EM) fields, is one of the key quantum phenomena supporting life dynamics. Coherent phenomena are well explained by quantum field theory (QFT), a well-established theoretical framework in quantum physics. Water is essential for life, being the medium used by living organisms to carry out various biochemical reactions and playing a fundamental role in coherent phenomena. Methods Quantum electrodynamics (QED), which is the relativistic QFT of electrodynamics, deals with the interactions between EM fields and matter. QED provides theoretical models and experimental frameworks for the emergence and dynamics of coherent structures, even in living organisms. This article provides a model of multi-level coherence for living organisms in which fractal phase oscillations of water are able to link and regulate a biochemical reaction. A mathematical approach, based on the eigenfunctions of Laplace operator in hyper-structures, is explored as a valuable framework to simulate and explain the oneness dynamics of multi-level coherence in life. The preparation process of a homeopathic medicine is analyzed according to QED principles, thus providing a scientific explanation for the theoretical model of “information transfer” from the substance to the water solution. A subsequent step explores the action of a homeopathic medicine in a living organism according to QED principles and the phase-space attractor's dynamics. Results According to the developed model, all levels of a living organism—organelles, cells, tissues, organs, organ systems, whole organism—are characterized by their own specific wave functions, whose phases are perfectly orchestrated in a multi-level coherence oneness. When this multi-level coherence is broken, a disease emerges. An example shows how a homeopathic medicine can bring back a patient from a disease state to a healthy one. In particular, by adopting QED, it is argued that in the preparation of homeopathic medicines, the progressive dilution/succussion processes create the conditions for the emergence of coherence domains (CDs) in the aqueous solution. Those domains code the original substance information (in terms of phase oscillations) and therefore they can transfer said information (by phase resonance) to the multi-level coherent structures of the living organism. Conclusions We encourage that QED principles and explanations become embodied in the fundamental teachings of the homeopathic method, thus providing the homeopath with a firm grounding in the practice of rational medicine. Systematic efforts in this direction should include multiple disciplines, such as quantum physics, quantum biology, conventional and homeopathic medicine and psychology.
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Vöcking, Oliver, Aide Macias-Muñoz, Stuart J. Jaeger, and Todd H. Oakley. "Deep Diversity: Extensive Variation in the Components of Complex Visual Systems across Animals." Cells 11, no. 24 (December 8, 2022): 3966. http://dx.doi.org/10.3390/cells11243966.
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Understanding the molecular underpinnings of the evolution of complex (multi-part) systems is a fundamental topic in biology. One unanswered question is to what the extent do similar or different genes and regulatory interactions underlie similar complex systems across species? Animal eyes and phototransduction (light detection) are outstanding systems to investigate this question because some of the genetics underlying these traits are well characterized in model organisms. However, comparative studies using non-model organisms are also necessary to understand the diversity and evolution of these traits. Here, we compare the characteristics of photoreceptor cells, opsins, and phototransduction cascades in diverse taxa, with a particular focus on cnidarians. In contrast to the common theme of deep homology, whereby similar traits develop mainly using homologous genes, comparisons of visual systems, especially in non-model organisms, are beginning to highlight a “deep diversity” of underlying components, illustrating how variation can underlie similar complex systems across taxa. Although using candidate genes from model organisms across diversity was a good starting point to understand the evolution of complex systems, unbiased genome-wide comparisons and subsequent functional validation will be necessary to uncover unique genes that comprise the complex systems of non-model groups to better understand biodiversity and its evolution.
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Tang, Zhidong, Weiliang Fan, Qiming Li, Dehe Wang, Miaomiao Wen, Junhao Wang, Xingqiao Li, and Yu Zhou. "MVIP: multi-omics portal of viral infection." Nucleic Acids Research 50, no. D1 (October 30, 2021): D817—D827. http://dx.doi.org/10.1093/nar/gkab958.
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Abstract Virus infections are huge threats to living organisms and cause many diseases, such as COVID-19 caused by SARS-CoV-2, which has led to millions of deaths. To develop effective strategies to control viral infection, we need to understand its molecular events in host cells. Virus related functional genomic datasets are growing rapidly, however, an integrative platform for systematically investigating host responses to viruses is missing. Here, we developed a user-friendly multi-omics portal of viral infection named as MVIP (https://mvip.whu.edu.cn/). We manually collected available high-throughput sequencing data under viral infection, and unified their detailed metadata including virus, host species, infection time, assay, and target, etc. We processed multi-layered omics data of more than 4900 viral infected samples from 77 viruses and 33 host species with standard pipelines, including RNA-seq, ChIP-seq, and CLIP-seq, etc. In addition, we integrated these genome-wide signals into customized genome browsers, and developed multiple dynamic charts to exhibit the information, such as time-course dynamic and differential gene expression profiles, alternative splicing changes and enriched GO/KEGG terms. Furthermore, we implemented several tools for efficiently mining the virus-host interactions by virus, host and genes. MVIP would help users to retrieve large-scale functional information and promote the understanding of virus-host interactions.
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Härri, Simone A., Jochen Krauss, and Christine B. Müller. "Fungal endosymbionts of plants reduce lifespan of an aphid secondary parasitoid and influence host selection." Proceedings of the Royal Society B: Biological Sciences 275, no. 1651 (August 5, 2008): 2627–32. http://dx.doi.org/10.1098/rspb.2008.0594.
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Complex biotic interactions shape ecological communities of plants, herbivores and their natural enemies. In studies of multi-trophic interactions, the presence of small, invisible micro-organisms associated with plants and those of a fourth above-ground trophic level have often been neglected. Incorporating these neglected factors improves our understanding of the processes within a multi-trophic network. Here, we ask whether the presence of a fungal endosymbiont, which alters plant quality by producing herbivore-toxic substances, trickles up the food chain and affects the performance and host-selection behaviour of aphid secondary parasitoids. We simultaneously offered hosts from endophyte-free and endophyte-infected environments to secondary parasitoids. Older and more experienced parasitoid females discriminated against hosts from the endophyte-infected environment. Developing in lower quality hosts from the endophyte-infected environment reduced the lifespan of secondary parasitoids. This indicates that aphid secondary parasitoids can perceive the disadvantage for their developing offspring in parasitoids from the endophyte environment and can learn to discriminate against them. In the field, this discrimination ability may shift the success of primary parasitoids to endophyte-infected plants, which co-occur with endophyte-free plants. Ultimately, the control of aphids depends on complex interactions between primary and secondary parasitoids and their relative sensitivity to endophytic fungi.
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Bush, Andrew M., and Philip M. Novack-Gottshall. "Modelling the ecological–functional diversification of marine Metazoa on geological time scales." Biology Letters 8, no. 1 (August 3, 2011): 151–55. http://dx.doi.org/10.1098/rsbl.2011.0641.
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The ecological traits and functional capabilities of marine animals have changed significantly since their origin in the late Precambrian. These changes can be analysed quantitatively using multi-dimensional parameter spaces in which the ecological lifestyles of species are represented by particular combinations of parameter values. Here, we present models that describe the filling of this multi-dimensional ‘ecospace’ by ecological lifestyles during metazoan diversification. These models reflect varying assumptions about the processes that drove ecological diversification; they contrast diffusive expansion with driven expansion and niche conservatism with niche partitioning. Some models highlight the importance of interactions among organisms (ecosystem engineering and predator–prey escalation) in promoting new lifestyles or eliminating existing ones. These models reflect processes that were not mutually exclusive; rigorous analyses will continue to reveal their applicability to episodes in metazoan history.
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Bartlett, Lewis J., Tim Newbold, Drew W. Purves, Derek P. Tittensor, and Michael B. J. Harfoot. "Synergistic impacts of habitat loss and fragmentation on model ecosystems." Proceedings of the Royal Society B: Biological Sciences 283, no. 1839 (September 28, 2016): 20161027. http://dx.doi.org/10.1098/rspb.2016.1027.
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Habitat loss and fragmentation are major threats to biodiversity, yet separating their effects is challenging. We use a multi-trophic, trait-based, and spatially explicit general ecosystem model to examine the independent and synergistic effects of these processes on ecosystem structure. We manipulated habitat by removing plant biomass in varying spatial extents, intensities, and configurations. We found that emergent synergistic interactions of loss and fragmentation are major determinants of ecosystem response, including population declines and trophic pyramid shifts. Furthermore, trait-mediated interactions, such as a disproportionate sensitivity of large-sized organisms to fragmentation, produce significant effects in shaping responses. We also show that top-down regulation mitigates the effects of land use on plant biomass loss, suggesting that models lacking these interactions—including most carbon stock models—may not adequately capture land-use change impacts. Our results have important implications for understanding ecosystem responses to environmental change, and assessing the impacts of habitat fragmentation.
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Backhaus, Thomas. "Medicines, shaken and stirred: a critical review on the ecotoxicology of pharmaceutical mixtures." Philosophical Transactions of the Royal Society B: Biological Sciences 369, no. 1656 (November 19, 2014): 20130585. http://dx.doi.org/10.1098/rstb.2013.0585.
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Analytical monitoring surveys routinely confirm that organisms in the environment are exposed to complex multi-component pharmaceutical mixtures. We are hence tasked with the challenge to take this into consideration when investigating the ecotoxicology of pharmaceuticals. This review first provides a brief overview of the fundamental approaches for mixture toxicity assessment, which is then followed by a critical review on the empirical evidence that is currently at hand on the ecotoxicology of pharmaceutical mixtures. It is concluded that, while the classical concepts of concentration addition and independent action (response addition) provide a robust scientific footing, several knowledge gaps remain. This includes, in particular, the need for more and better empirical data on the effects of pharmaceutical mixtures on soil organisms as well as marine flora and fauna, and exploring the quantitative consequences of toxicokinetic, toxicodynamic and ecological interactions. Increased focus should be put on investigating the ecotoxicology of pharmaceutical mixtures in environmentally realistic settings.
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Cloninger, C. Robert, and Igor Zwir. "What is the natural measurement unit of temperament: single traits or profiles?" Philosophical Transactions of the Royal Society B: Biological Sciences 373, no. 1744 (February 26, 2018): 20170163. http://dx.doi.org/10.1098/rstb.2017.0163.
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There is fundamental doubt about whether the natural unit of measurement for temperament and personality corresponds to single traits or to multi-trait profiles that describe the functioning of a whole person. Biogenetic researchers of temperament usually assume they need to focus on individual traits that differ between individuals. Recent research indicates that a shift of emphasis to understand processes within the individual is crucial for identifying the natural building blocks of temperament. Evolution and development operate on adaptation of whole organisms or persons, not on individual traits or categories. Adaptive functioning generally depends on feedback among many variable processes in ways that are characteristic of complex adaptive systems, not machines with separate parts. Advanced methods of unsupervised machine learning can now be applied to genome-wide association studies and brain imaging in order to uncover the genotypic–phenotypic architecture of traits like temperament, which are strongly influenced by complex interactions, such as genetic epistasis, pleiotropy and gene–environment interactions. We have found that the heritability of temperament can be nearly fully explained by a large number of genetic variants that are unique for multi-trait profiles, not single traits. The implications of this finding for research design and precision medicine are discussed. This article is part of the theme issue ‘Diverse perspectives on diversity: multi-disciplinary approaches to taxonomies of individual differences'.
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Tsata, Vasiliki, and Dimitris Beis. "In Full Force. Mechanotransduction and Morphogenesis during Homeostasis and Tissue Regeneration." Journal of Cardiovascular Development and Disease 7, no. 4 (October 1, 2020): 40. http://dx.doi.org/10.3390/jcdd7040040.
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The interactions of form and function have been the focus of numerous studies in the context of development and more recently regeneration. Our understanding on how cells, tissues and organs sense and interpret external cues, such as mechanical forces, is becoming deeper as novel techniques in imaging are applied and the relevant signaling pathways emerge. These cellular responses can be found from bacteria to all multicellular organisms such as plants and animals. In this review, we focus on hemodynamic flow and endothelial shear stress during cardiovascular development and regeneration, where the interactions of morphogenesis and proper function are more prominent. In addition, we address the recent literature on the role of extracellular matrix and fibrotic response during tissue repair and regeneration. Finally, we refer to examples where the integration of multi-disciplinary approaches to understand the biomechanics of cellular responses could be utilized in novel medical applications.
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Srinivasan, N., G. Agarwal, R. M. Bhaskara, R. Gadkari, O. Krishnadev, B. Lakshmi, S. Mahajan, et al. "Influence of Genomic and Other Biological Data Sets in the Understanding of Protein Structures, Functions and Interactions." International Journal of Knowledge Discovery in Bioinformatics 2, no. 1 (January 2011): 24–44. http://dx.doi.org/10.4018/jkdb.2011010102.
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In the post-genomic era, biological databases are growing at a tremendous rate. Despite rapid accumulation of biological information, functions and other biological properties of many putative gene products of various organisms remain either unknown or obscure. This paper examines how strategic integration of large biological databases and combinations of various biological information helps address some of the fundamental questions on protein structure, function and interactions. New developments in function recognition by remote homology detection and strategic use of sequence databases aid recognition of functions of newly discovered proteins. Knowledge of 3-D structures and combined use of sequences and 3-D structures of homologous protein domains expands the ability of remote homology detection enormously. The authors also demonstrate how combined consideration of functions of individual domains of multi-domain proteins helps in recognizing gross biological attributes. This paper also discusses a few cases of combining disparate biological datasets or combination of disparate biological information in obtaining new insights about protein-protein interactions across a host and a pathogen. Finally, the authors discuss how combinations of low resolution structural data, obtained using cryoEM studies, of gigantic multi-component assemblies, and atomic level 3-D structures of the components is effective in inferring finer features in the assembly.
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Bolanos-Garcia, Victor M., Qian Wu, Takashi Ochi, Dimitri Y. Chirgadze, Bancinyane Lynn Sibanda, and Tom L. Blundell. "Spatial and temporal organization of multi-protein assemblies: achieving sensitive control in information-rich cell-regulatory systems." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 370, no. 1969 (June 28, 2012): 3023–39. http://dx.doi.org/10.1098/rsta.2011.0268.
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The regulation of cellular processes in living organisms requires signalling systems that have a high signal-to-noise ratio. This is usually achieved by transient, multi-protein complexes that assemble cooperatively. Even in the crowded environment of the cell, such assemblies are unlikely to form by chance, thereby providing a sensitive regulation of cellular processes. Furthermore, selectivity and sensitivity may be achieved by the requirement for concerted folding and binding of previously unfolded components. We illustrate these features by focusing on two essential signalling pathways of eukaryotic cells: first, the monitoring and repair of DNA damage by non-homologous end joining, and second, the mitotic spindle assembly checkpoint, which detects and corrects defective attachments of chromosomes to the kinetochore. We show that multi-protein assemblies moderate the full range of functional complexity and diversity in the two signalling systems. Deciphering the nature of the interactions is central to understanding the mechanisms that control the flow of information in cell signalling and regulation.
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Coventry, Brendon J., Martin Ashdown, Maciej Henneberg, and Paul C. W. Davies. "The Immune System and Responses to Cancer: Coordinated Evolution." F1000Research 4 (August 12, 2015): 552. http://dx.doi.org/10.12688/f1000research.6718.1.
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This review explores the evolutionary interaction and co-development between immune system and somatic evolution. Over immense durations, continuous interactions between microbes, aberrant somatic cells, including malignant cells, and the immune system have successively shaped the evolutionary development of the immune system, somatic cells and microorganisms through continuous adaptive symbiotic processes of progressive immunological and somatic change providing what we observe today. The immune system is powerful enough to remove cancer and induce long-term cures. Our knowledge of how this occurs is just emerging. It is less clear why the immune system would detect cancer cells, when it is usually focused on combatting infection. Here we show the connections between immunity, infection and cancer, by searching back in time hundreds of millions of years and more to when multi-cellular organisms first began, and the immune system eventually evolved into the truly brilliant and efficient protective mechanism, the importance of which we are just beginning to now understand. What we do know is that comprehending these points will likely lead to more effective cancer therapies.
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Szolnoki, Attila, Mauro Mobilia, Luo-Luo Jiang, Bartosz Szczesny, Alastair M. Rucklidge, and Matjaž Perc. "Cyclic dominance in evolutionary games: a review." Journal of The Royal Society Interface 11, no. 100 (November 6, 2014): 20140735. http://dx.doi.org/10.1098/rsif.2014.0735.
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Rock is wrapped by paper, paper is cut by scissors and scissors are crushed by rock. This simple game is popular among children and adults to decide on trivial disputes that have no obvious winner, but cyclic dominance is also at the heart of predator–prey interactions, the mating strategy of side-blotched lizards, the overgrowth of marine sessile organisms and competition in microbial populations. Cyclical interactions also emerge spontaneously in evolutionary games entailing volunteering, reward, punishment, and in fact are common when the competing strategies are three or more, regardless of the particularities of the game. Here, we review recent advances on the rock–paper–scissors (RPS) and related evolutionary games, focusing, in particular, on pattern formation, the impact of mobility and the spontaneous emergence of cyclic dominance. We also review mean-field and zero-dimensional RPS models and the application of the complex Ginzburg–Landau equation, and we highlight the importance and usefulness of statistical physics for the successful study of large-scale ecological systems. Directions for future research, related, for example, to dynamical effects of coevolutionary rules and invasion reversals owing to multi-point interactions, are also outlined.
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Kuru-Schors, Merve, Monika Haemmerle, and Tony Gutschner. "The Cohesin Complex and Its Interplay with Non-Coding RNAs." Non-Coding RNA 7, no. 4 (October 22, 2021): 67. http://dx.doi.org/10.3390/ncrna7040067.
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The cohesin complex is a multi-subunit protein complex initially discovered for its role in sister chromatid cohesion. However, cohesin also has several other functions and plays important roles in transcriptional regulation, DNA double strand break repair, and chromosome architecture thereby influencing gene expression and development in organisms from yeast to man. While most of these functions rely on protein–protein interactions, post-translational protein, as well as DNA modifications, non-coding RNAs are emerging as additional players that facilitate and modulate the function or expression of cohesin and its individual components. This review provides a condensed overview about the architecture as well as the function of the cohesin complex and highlights its multifaceted interplay with both short and long non-coding RNAs.
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Mikkilineni, Rao. "Architectural Resiliency in Distributed Computing." International Journal of Grid and High Performance Computing 4, no. 4 (October 2012): 37–51. http://dx.doi.org/10.4018/jghpc.2012100103.
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Cellular organisms have evolved to manage themselves and their interactions with their surroundings with a high degree of resiliency, efficiency and scalability. Signaling and collaboration of autonomous distributed computing elements accomplishing a common goal with optimal resource utilization are the differentiating characteristics that contribute to the computing model of cellular organisms. By introducing signaling and self-management abstractions in an autonomic computing element called Distributed Intelligent Managed Element (DIME), the authors improve the architectural resiliency, efficiency, and scaling in distributed computing systems. Described are two implementations of DIME network architecture to demonstrate auto-scaling, self-repair, dynamic performance optimization, and end to end distributed transaction management. By virtualizing a process (by converting it into a DIME) in the Linux operating system and also building a new native operating system called Parallax OS optimized for Intel-multi-core processors, which converts each core into a DIME, implications of the DIME computing model to future cloud computing services and datacenter infrastructure management practices and discuss the relationship of the DIME computing model to current discussions on Turing machines, Gödel’s theorems and a call for no less than a Kuhnian paradigm shift by some computer scientists.
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Terrell, Kristofer, Suyun Choi, and Sangyong Choi. "Calcium’s Role and Signaling in Aging Muscle, Cellular Senescence, and Mineral Interactions." International Journal of Molecular Sciences 24, no. 23 (December 1, 2023): 17034. http://dx.doi.org/10.3390/ijms242317034.
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Calcium research, since its pivotal discovery in the early 1800s through the heating of limestone, has led to the identification of its multi-functional roles. These include its functions as a reducing agent in chemical processes, structural properties in shells and bones, and significant role in cells relating to this review: cellular signaling. Calcium signaling involves the movement of calcium ions within or between cells, which can affect the electrochemical gradients between intra- and extracellular membranes, ligand binding, enzyme activity, and other mechanisms that determine cell fate. Calcium signaling in muscle, as elucidated by the sliding filament model, plays a significant role in muscle contraction. However, as organisms age, alterations occur within muscle tissue. These changes include sarcopenia, loss of neuromuscular junctions, and changes in mineral concentration, all of which have implications for calcium’s role. Additionally, a field of study that has gained recent attention, cellular senescence, is associated with aging and disturbed calcium homeostasis, and is thought to affect sarcopenia progression. Changes seen in calcium upon aging may also be influenced by its crosstalk with other minerals such as iron and zinc. This review investigates the role of calcium signaling in aging muscle and cellular senescence. We also aim to elucidate the interactions among calcium, iron, and zinc across various cells and conditions, ultimately deepening our understanding of calcium signaling in muscle aging.
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Iyer, Swami, and Timothy Killingback. "Evolution of Cooperation in Social Dilemmas with Assortative Interactions." Games 11, no. 4 (September 23, 2020): 41. http://dx.doi.org/10.3390/g11040041.
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Cooperation in social dilemmas plays a pivotal role in the formation of systems at all levels of complexity, from replicating molecules to multi-cellular organisms to human and animal societies. In spite of its ubiquity, the origin and stability of cooperation pose an evolutionary conundrum, since cooperation, though beneficial to others, is costly to the individual cooperator. Thus natural selection would be expected to favor selfish behavior in which individuals reap the benefits of cooperation without bearing the costs of cooperating themselves. Many proximate mechanisms have been proposed to account for the origin and maintenance of cooperation, including kin selection, direct reciprocity, indirect reciprocity, and evolution in structured populations. Despite the apparent diversity of these approaches they all share a unified underlying logic: namely, each mechanism results in assortative interactions in which individuals using the same strategy interact with a higher probability than they would at random. Here we study the evolution of cooperation in both discrete strategy and continuous strategy social dilemmas with assortative interactions. For the sake of tractability, assortativity is modeled by an individual interacting with another of the same type with probability r and interacting with a random individual in the population with probability 1−r, where r is a parameter that characterizes the degree of assortativity in the system. For discrete strategy social dilemmas we use both a generalization of replicator dynamics and individual-based simulations to elucidate the donation, snowdrift, and sculling games with assortative interactions, and determine the analogs of Hamilton’s rule, which govern the evolution of cooperation in these games. For continuous strategy social dilemmas we employ both a generalization of deterministic adaptive dynamics and individual-based simulations to study the donation, snowdrift, and tragedy of the commons games, and determine the effect of assortativity on the emergence and stability of cooperation.
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Bereczki, Allan, Jessica Dipold, Anderson Z. Freitas, and Niklaus U. Wetter. "Sub-10 nm Nanoparticle Detection Using Multi-Technique-Based Micro-Raman Spectroscopy." Polymers 15, no. 24 (December 8, 2023): 4644. http://dx.doi.org/10.3390/polym15244644.
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Microplastic pollution is a growing public concern as these particles are ubiquitous in various environments and can fragment into smaller nanoplastics. Another environmental concern arises from widely used engineered nanoparticles. Despite the increasing abundance of these nano-sized pollutants and the possibility of interactions with organisms at the sub cellular level, with many risks still being unknown, there are only a few publications on this topic due to the lack of reliable techniques for nanoparticle characterization. We propose a multi-technique approach for the characterization of nanoparticles down to the 10 nm level using standard micro-Raman spectroscopy combined with standard atomic force microscopy. We successfully obtained single-particle spectra from 25 nm sized polystyrene and 9 nm sized TiO2 nanoparticles with corresponding mass limits of detection of 8.6 ag (attogram) and 1.6 ag, respectively, thus demonstrating the possibility of achieving an unambiguous Raman signal from a single, small nanoparticle with a resolution comparable to more complex and time-consuming technologies such as Tip-Enhanced Raman Spectroscopy and Photo-Induced Force Microscopy.
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Martinez, David Lopez, Yugo Tsuchiya, and Ivan Gout. "Coenzyme A biosynthetic machinery in mammalian cells." Biochemical Society Transactions 42, no. 4 (August 1, 2014): 1112–17. http://dx.doi.org/10.1042/bst20140124.
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CoA (coenzyme A) is an essential cofactor in all living organisms. CoA and its thioester derivatives [acetyl-CoA, malonyl-CoA, HMG-CoA (3-hydroxy-3-methylglutaryl-CoA) etc.] participate in diverse anabolic and catabolic pathways, allosteric regulatory interactions and the regulation of gene expression. The biosynthesis of CoA requires pantothenic acid, cysteine and ATP, and involves five enzymatic steps that are highly conserved from prokaryotes to eukaryotes. The intracellular levels of CoA and its derivatives change in response to extracellular stimuli, stresses and metabolites, and in human pathologies, such as cancer, metabolic disorders and neurodegeneration. In the present mini-review, we describe the current understanding of the CoA biosynthetic pathway, provide a detailed overview on expression and subcellular localization of enzymes implicated in CoA biosynthesis, their regulation and the potential to form multi-enzyme complexes for efficient and highly co-ordinated biosynthetic process.
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Abusrewil, Sumaya, Jason L. Brown, Christopher Delaney, Mark C. Butcher, Mohammed Tiba, J. Alun Scott, Gordon Ramage, and William McLean. "Chitosan Enhances the Anti-Biofilm Activity of Biodentine against an Interkingdom Biofilm Model." Antibiotics 10, no. 11 (October 29, 2021): 1317. http://dx.doi.org/10.3390/antibiotics10111317.
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Endodontic infection is a biofilm disease that is difficult to irradicate with current treatment protocols, and as such, persistent micro-organisms may lead to ongoing or recurrent disease. The potential for the use of enhanced filling materials to modify biofilm regrowth is a promising strategy. This current study aimed to evaluate the anti-biofilm efficacy of calcium silicate cements modified with chitosan. The development of mono-species and multi-species biofilms on ProRoot MTA, Biodentine and bovine dentine discs were explored using quantitative microbiology analysis. The effect on regrowth of biofilms was assessed following the addition of chitosan to each cement. In comparison to a dentine substrate, both materials did not show the ability to inhibit biofilm regrowth. Biodentine incorporated with chitosan displayed a dose-dependent reduction in multi-species biofilm regrowth, unlike MTA. Notably, interkingdom biofilms were shown to enhance bacterial tolerance in the presence of chitosan. This study demonstrates the potential to enhance the antimicrobial properties of Biodentine. The findings highlight the need for appropriate model systems when exploring antimicrobial properties of materials in vitro so that interspecies and interkingdom interactions that modify tolerance are not overlooked while still supporting the development of innovative materials.
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Kang, Le. "Overview: biotic signalling for smart pest management." Philosophical Transactions of the Royal Society B: Biological Sciences 374, no. 1767 (January 14, 2019): 20180306. http://dx.doi.org/10.1098/rstb.2018.0306.
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Biotic signalling refers to species or phylogenetic-clade-specific signals that elicit adaptive and acceptable responses within and among organisms. It is not only the molecular basis of the ecological relationships among different species, such as parasitism, symbiosis and predation, but also serves as ideal targets that can be used to manipulate these ecological relationships. This concept was proposed by a group of scientists from the Chinese Academy of Sciences (CAS) and actively pursued in a five-year research project in 2014 funded by the CAS ($40 million), entitled ‘Decoding biotic interactions and mechanism for target management of agricultural pests'. The multi-disciplinary project aimed at a systematic investigation of the intra-species and inter-species and interactions via biotic signalling, with the ultimate goal being the development of novel methods to manage the pest insects and diseases. We hereby propose a topic ‘Biotic signalling sheds light on smart pest control’ as a theme issue for the Philosophical Transactions of the Royal Society B . It contains a total of 18 reviews and research articles under the topic of signalling manipulation for pest management. Unravelling these complex interactions among plants, microbial pathogens and insects holds promise for developing novel strategies to protect crop plants without compromising agricultural productivity and environmental health. This article is part of the theme issue ‘Biotic signalling sheds light on smart pest management’.
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Bourgeois, Bérenger, Sabrina Gaba, Christine Plumejeaud, and Vincent Bretagnolle. "Weed diversity is driven by complex interplay between multi-scale dispersal and local filtering." Proceedings of the Royal Society B: Biological Sciences 287, no. 1930 (July 8, 2020): 20201118. http://dx.doi.org/10.1098/rspb.2020.1118.
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Arable weeds are key organisms for biodiversity maintenance and ecosystem service provision in agroecosystems. Disentangling the drivers of weed diversity is critical to counteract the global decline of farmland biodiversity. Even if distinct scale-dependent processes were alternatively proposed, no general framework unifying the multi-scale drivers of weed dynamics has yet emerged. Here, we investigate the joint effects of field- and landscape-scale processes on weed assemblages in 444 arable fields. First, field margins sheltered greater weed diversity than field core, evidencing their role as biodiversity refugia. Second, community similarity between field core and margin decreased with the distance to margin, highlighting a major role of local dispersal. Third, weed diversity at field margins increased with organic field cover in the landscape, pointing out massive regional dispersal. Fourth, while both local and landscape dispersal explained up to 41% of field core weed diversity, crop type strongly modulated their strength, depicting an intense filtering effect by agricultural management. This study sheds new light on the complex multi-scale interactions shaping weed diversity, field margins playing a key role by strengthening regional dispersal and sustaining local dispersal. Land-sharing strategies improving habitat heterogeneity both locally and regionally should largely promote agroecosystem multifunctionality and sustainability.
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Ding, Siyu Serena, Leah S. Muhle, André E. X. Brown, Linus J. Schumacher, and Robert G. Endres. "Comparison of solitary and collective foraging strategies of Caenorhabditis elegans in patchy food distributions." Philosophical Transactions of the Royal Society B: Biological Sciences 375, no. 1807 (July 27, 2020): 20190382. http://dx.doi.org/10.1098/rstb.2019.0382.
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Collective foraging has been shown to benefit organisms in environments where food is patchily distributed, but whether this is true in the case where organisms do not rely on long-range communications to coordinate their collective behaviour has been understudied. To address this question, we use the tractable laboratory model organism Caenorhabditis elegans , where a social strain ( npr-1 mutant) and a solitary strain (N2) are available for direct comparison of foraging strategies. We first developed an on-lattice minimal model for comparing collective and solitary foraging strategies, finding that social agents benefit from feeding faster and more efficiently simply owing to group formation. Our laboratory foraging experiments with npr-1 and N2 worm populations, however, show an advantage for solitary N2 in all food distribution environments that we tested. We incorporated additional strain-specific behavioural parameters of npr-1 and N2 worms into our model and computationally identified N2's higher feeding rate to be the key factor underlying its advantage, without which it is possible to recapitulate the advantage of collective foraging in patchy environments. Our work highlights the theoretical advantage of collective foraging owing to group formation alone without long-range interactions and the valuable role of modelling to guide experiments. This article is part of the theme issue ‘Multi-scale analysis and modelling of collective migration in biological systems'.
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Baltadakis, A., J. Casserly, L. Falconer, M. Sprague, and TC Telfer. "European lobsters utilise Atlantic salmon wastes in coastal integrated multi-trophic aquaculture systems." Aquaculture Environment Interactions 12 (November 5, 2020): 485–94. http://dx.doi.org/10.3354/aei00378.
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In this study, we investigated if juvenile European lobsters Homarus gammarus would eat waste from Atlantic salmon Salmo salar cages in a coastal integrated multi-trophic aquaculture (IMTA) setup and if there were any impacts on growth. Trophic interactions between salmon and lobsters were assessed using δ15N and δ13C stable isotope analysis and fatty acid profiling from fish feed as indicators of nutrient flow. Analysis revealed that lobsters directly utilised particulate waste from salmon production, as levels of indicator fatty acids from salmon feed were significantly higher in lobster tissues near the fish cages compared to the control site. Route of uptake may have been direct consumption of waste feed or faecal material or indirectly through fouling organisms. Stable isotope analysis did not indicate nutrient transfer to lobsters, suggesting that the duration of the study and/or the amount of waste consumed was not sufficient for stable isotope analysis. Lobsters grew significantly over the trial period at both sites, but there was no significant difference in lobster growth between the sites. Our results show a trophic relationship between salmon and lobsters within this IMTA system, with no apparent advantage or disadvantage to growth.
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Pulido, Hannier, Kerry E. Mauck, Consuelo M. De Moraes, and Mark C. Mescher. "Combined effects of mutualistic rhizobacteria counteract virus-induced suppression of indirect plant defences in soya bean." Proceedings of the Royal Society B: Biological Sciences 286, no. 1903 (May 22, 2019): 20190211. http://dx.doi.org/10.1098/rspb.2019.0211.
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It is increasingly clear that microbial plant symbionts can influence interactions between their plant hosts and other organisms. However, such effects remain poorly understood, particularly under ecologically realistic conditions where plants simultaneously interact with diverse mutualists and antagonists. Here, we examine how the effects of a plant virus on indirect plant defences against its insect vector are influenced by co-occurrence of other microbial plant symbionts. Using a multi-factorial design, we manipulated colonization of soya bean using three different microbes: a pathogenic plant virus (bean pod mottle virus (BPMV)), a nodule-forming beneficial rhizobacterium ( Bradyrhizobium japonicum ) and a plant growth-promoting rhizobacterium ( Delftia acidovorans ). We then assessed recruitment of parasitoids ( Pediobious foveolatus (Eulophidae)) and parasitism rates following feeding by the BPMV vector Epilachna varivestis (Coccinellidae). BPMV infection suppressed parasitoid recruitment, prolonged parasitoid foraging time and reduced parasitism rates in semi-natural foraging assays. However, simultaneous colonization of BPMV-infected hosts by both rhizobacteria restored parasitoid recruitment and rates of parasitism to levels similar to uninfected controls. Co-colonization by the two rhizobacteria also enhanced parasitoid recruitment in the absence of BPMV infection. These results illustrate the potential of plant-associated microbes to influence indirect plant defences, with implications for disease transmission and herbivory, but also highlight the potential complexity of such interactions.
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Schär, Sämi, Rodney Eastwood, Kimberly G. Arnaldi, Gerard Talavera, Zofia A. Kaliszewska, John H. Boyle, Marianne Espeland, David R. Nash, Roger Vila, and Naomi E. Pierce. "Ecological specialization is associated with genetic structure in the ant-associated butterfly family Lycaenidae." Proceedings of the Royal Society B: Biological Sciences 285, no. 1886 (September 12, 2018): 20181158. http://dx.doi.org/10.1098/rspb.2018.1158.
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The role of specialization in diversification can be explored along two geological axes in the butterfly family Lycaenidae. In addition to variation in host-plant specialization normally exhibited by butterflies, the caterpillars of most Lycaenidae have symbioses with ants ranging from no interactions through to obligate and specific associations, increasing niche dimensionality in ant-associated taxa. Based on mitochondrial sequences from 8282 specimens from 967 species and 249 genera, we show that the degree of ecological specialization of lycaenid species is positively correlated with genetic divergence, haplotype diversity and an increase in isolation by distance. Nucleotide substitution rate is higher in carnivorous than phytophagous lycaenids. The effects documented here for both micro- and macroevolutionary processes could result from increased spatial segregation as a consequence of reduced connectivity in specialists, niche-based divergence or a combination of both. They could also provide an explanation for the extraordinary diversity of the Lycaenidae and, more generally, for diversity in groups of organisms with similar multi-dimensional ecological specialization.
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Burnham, Rianna, and David Duffus. "Implication of Altered Acoustic Active Space for Cetacean Species That Result from Soundscape Changes and Noise Additions." Acoustics 5, no. 2 (April 28, 2023): 444–61. http://dx.doi.org/10.3390/acoustics5020026.
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Organisms use multi-modal, scale-dependent, sensory information to decipher their surroundings. This can include, for example, recognizing the presence of con- or heterospecifics, including a predatory threat, the presence and abundance of prey, or navigational cues to travel between breeding or feeding areas. Here we advocate for the use of the concept of active space to understand the extent to which an individual might be sending and receiving habitat information, describing this as the active component of their niche space. We present the use of active space as a means to understand ecological interactions, giving focus to those species whose active space is acoustically defined, in particular, cetacean species. We show how the application of estimates of active space, and changes in extent, can help better understand the potential disturbance effects of changes in the soundscape, and be a useful metric to estimate possible adverse effects even when stress responses, or behavioral or calling modifications are not obvious.
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Giles, Rachel K., and Bonnie M. Hamilton. "Freshwater systems in the Anthropocene: why we need to evaluate microplastics in the context of multiple stressors." F1000Research 13 (March 8, 2024): 163. http://dx.doi.org/10.12688/f1000research.145488.1.
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Microplastics are a diverse contaminant with complex physical and chemical properties. While microplastics have varying effects, most studies to date have focused on evaluating microplastics as a single stressor under stable environmental conditions. In reality, organisms are exposed to more than microplastics, and thus, it will be increasingly important to evaluate the effects of microplastics in the context of multiple anthropogenic stressors. Here, we highlight the need to assess the physical and chemical effects of microplastics, as well as their interactions with other anthropogenic stressors, at multiple levels of biological organization (i.e., sub-organismal, individual, population, community, ecosystem). We also outline research priorities and recommendations that will facilitate ecotoxicological assessments to better encompass the multidimensionality of microplastics as environmental conditions continue to change. By taking a multi-stressor ecotoxicological approach, we can work toward a better understanding of microplastic and other stressor effects at multiple levels of biological organization to help inform robust, evidenced-based policy and management decisions.
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Miller-Rushing, Abraham J., Toke Thomas Høye, David W. Inouye, and Eric Post. "The effects of phenological mismatches on demography." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1555 (October 12, 2010): 3177–86. http://dx.doi.org/10.1098/rstb.2010.0148.
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Climate change is altering the phenology of species across the world, but what are the consequences of these phenological changes for the demography and population dynamics of species? Time-sensitive relationships, such as migration, breeding and predation, may be disrupted or altered, which may in turn alter the rates of reproduction and survival, leading some populations to decline and others to increase in abundance. However, finding evidence for disrupted relationships, or lack thereof, and their demographic effects, is difficult because the necessary detailed observational data are rare. Moreover, we do not know how sensitive species will generally be to phenological mismatches when they occur. Existing long-term studies provide preliminary data for analysing the phenology and demography of species in several locations. In many instances, though, observational protocols may need to be optimized to characterize timing-based multi-trophic interactions. As a basis for future research, we outline some of the key questions and approaches to improving our understanding of the relationships among phenology, demography and climate in a multi-trophic context. There are many challenges associated with this line of research, not the least of which is the need for detailed, long-term data on many organisms in a single system. However, we identify key questions that can be addressed with data that already exist and propose approaches that could guide future research.
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Zhang, Weiwen, Feng Li, and Lei Nie. "Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies." Microbiology 156, no. 2 (February 1, 2010): 287–301. http://dx.doi.org/10.1099/mic.0.034793-0.
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Recent advances in various ‘omics’ technologies enable quantitative monitoring of the abundance of various biological molecules in a high-throughput manner, and thus allow determination of their variation between different biological states on a genomic scale. Several popular ‘omics’ platforms that have been used in microbial systems biology include transcriptomics, which measures mRNA transcript levels; proteomics, which quantifies protein abundance; metabolomics, which determines abundance of small cellular metabolites; interactomics, which resolves the whole set of molecular interactions in cells; and fluxomics, which establishes dynamic changes of molecules within a cell over time. However, no single ‘omics’ analysis can fully unravel the complexities of fundamental microbial biology. Therefore, integration of multiple layers of information, the multi-‘omics’ approach, is required to acquire a precise picture of living micro-organisms. In spite of this being a challenging task, some attempts have been made recently to integrate heterogeneous ‘omics’ datasets in various microbial systems and the results have demonstrated that the multi-‘omics’ approach is a powerful tool for understanding the functional principles and dynamics of total cellular systems. This article reviews some basic concepts of various experimental ‘omics’ approaches, recent application of the integrated ‘omics’ for exploring metabolic and regulatory mechanisms in microbes, and advances in computational and statistical methodologies associated with integrated ‘omics’ analyses. Online databases and bioinformatic infrastructure available for integrated ‘omics’ analyses are also briefly discussed.
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Devi, Varadharajan Subhadra, Dr Ushanandhini, Kuppusamy AsokKumar, Muthuswamy UmaMaheswari, Andichettiar Thirumalaisamy Sivashanmugham, and Puliyath Jagannath. "Synergistic Antibacterial Activity of Cassia auriculata L. Flowers and Ofloxacin." Bangladesh Journal of Microbiology 28, no. 2 (September 5, 2012): 92–94. http://dx.doi.org/10.3329/bjm.v28i2.11824.
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A cost effective antimicrobial agent for multi drug resistant organisms, based on the synergistic activity of ofloxacin with ethanolic extract of flowers of Cassia auriculata was determined. The Minimum Inhibition Concentration (MIC) of ethanolic extract using 3 different Gram-positive bacteria, such as Staphylococcus aureus NCIM 2127 and Bacillus subtilis NCIM 2010, and Gram-negative bacteria Escherichia coli NCIM 2118 was found to be around 1024 to 2048 mg/ml. The synergistic activity varied using checkerboard synergy technique. The results of the conducted experiments showed in vitro interactions between antimicrobial agents and plant extract were additive against the strains tested, it also showed synergistic effects between combination of antibiotics and plant extracts with significant reduction in the MICs of the test antibiotics against these strains. It showed maximum synergistic activity against Gram-negative species. The higher synergistic rate was attained against E. coli NCIM 2118, and lowest synergistic shows against S. aureus NCIM 2127. DOI: http://dx.doi.org/10.3329/bjm.v28i2.11824 Bangladesh J Microbiol, Volume 28, Number 2, December 2011, pp 92-94
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Das, Rina, Gyati S. Asthana, Krishan A. Suri, Dinesh Mehta, and Abhay Asthana. "Recent Developments in Azole Compounds as Antitubercular Agent." Mini-Reviews in Organic Chemistry 16, no. 3 (January 25, 2019): 290–306. http://dx.doi.org/10.2174/1570193x15666180622144414.
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Tuberculosis (TB) is a global health disaster and is a wide-reaching hitch. The improper use of antibiotics in chemotherapy of TB patients led to the current problem of tuberculosis therapy which gives rise to Multi-Drug Resistant (MDR) strains. Nitrogen heterocycles including azole compounds are an important class of therapeutic agent with electron-rich property. Azole-based derivatives easily bind with the enzymes and receptors in organisms through noncovalent interactions, thereby possessing various applications in medicinal chemistry. Research on azoles derivatives have been expansively carried out and have become one of the extremely active area in recent years and the progress is quite rapid. A genuine attempt to review chemistry of azoles and to describe various azole-based compounds synthesized in the last two decades having promising antitubercular potential is described in the present article. It is hopeful that azole compounds may continue to serve as an important direction for the exploitation of azole-based antitubercular drugs with better curative effect, lower toxicity, less side effects, especially fewer resistances and so on.
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Ferreira, Ana, Pedro Neves, and Raffaella Gozzelino. "Multilevel Impacts of Iron in the Brain: The Cross Talk between Neurophysiological Mechanisms, Cognition, and Social Behavior." Pharmaceuticals 12, no. 3 (August 29, 2019): 126. http://dx.doi.org/10.3390/ph12030126.
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Iron is a critical element for most organisms, which plays a fundamental role in the great majority of physiological processes. So much so, that disruption of iron homeostasis has severe multi-organ impacts with the brain being particularly sensitive to such modifications. More specifically, disruption of iron homeostasis in the brain can affect neurophysiological mechanisms, cognition, and social behavior, which eventually contributes to the development of a diverse set of neuro-pathologies. This article starts by exploring the mechanisms of iron action in the brain and follows with a discussion on cognitive and behavioral implications of iron deficiency and overload and how these are framed by the social context. Subsequently, we scrutinize the implications of the disruption of iron homeostasis for the onset and progression of psychosocial disorders. Lastly, we discuss the links between biological, psychological, and social dimensions and outline potential avenues of research. The study of these interactions could ultimately contribute to a broader understanding of how individuals think and act under physiological and pathophysiological conditions.
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Li, Hong-Dong, Tianjian Bai, Erin Sandford, Margit Burmeister, and Yuanfang Guan. "BaiHui: cross-species brain-specific network built with hundreds of hand-curated datasets." Bioinformatics 35, no. 14 (December 5, 2018): 2486–88. http://dx.doi.org/10.1093/bioinformatics/bty1001.
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Abstract Motivation Functional gene networks, representing how likely two genes work in the same biological process, are important models for studying gene interactions in complex tissues. However, a limitation of the current network-building scheme is the lack of leveraging evidence from multiple model organisms as well as the lack of expert curation and quality control of the input genomic data. Results Here, we present BaiHui, a brain-specific functional gene network built by probabilistically integrating expertly-hand-curated (by reading original publications) heterogeneous and multi-species genomic data in human, mouse and rat brains. To facilitate the use of this network, we deployed a web server through which users can query their genes of interest, visualize the network, gain functional insight from enrichment analysis and download network data. We also illustrated how this network could be used to generate testable hypotheses on disease gene prioritization of brain disorders. Availability and implementation BaiHui is freely available at: http://guanlab.ccmb.med.umich.edu/BaiHui/. Supplementary information Supplementary data are available at Bioinformatics online.
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Dillon, Lucy, Nicholas J. Dimonaco, and Christopher J. Creevey. "Accessory genes define species-specific routes to antibiotic resistance." Life Science Alliance 7, no. 4 (January 16, 2024): e202302420. http://dx.doi.org/10.26508/lsa.202302420.
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A deeper understanding of the relationship between the antimicrobial resistance (AMR) gene carriage and phenotype is necessary to develop effective response strategies against this global burden. AMR phenotype is often a result of multi-gene interactions; therefore, we need approaches that go beyond current simple AMR gene identification tools. Machine-learning (ML) methods may meet this challenge and allow the development of rapid computational approaches for AMR phenotype classification. To examine this, we applied multiple ML techniques to 16,950 bacterial genomes across 28 genera, with corresponding MICs for 23 antibiotics with the aim of training models to accurately determine the AMR phenotype from sequenced genomes. This resulted in a >1.5-fold increase in AMR phenotype prediction accuracy over AMR gene identification alone. Furthermore, we revealed 528 unique (often species-specific) genomic routes to antibiotic resistance, including genes not previously linked to the AMR phenotype. Our study demonstrates the utility of ML in predicting AMR phenotypes across diverse clinically relevant organisms and antibiotics. This research proposes a rapid computational method to support laboratory-based identification of the AMR phenotype in pathogens.
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Sudar, D., D. Callahan, B. Parvin, D. Knowles, C. Ortiz de Solorzano, and M. H. Barcellos Hoff. "Design of a Microscopy System for Quantitative Spatial and Temporal Analysis of Multicellular Interactions." Microscopy and Microanalysis 7, S2 (August 2001): 32–33. http://dx.doi.org/10.1017/s1431927600026234.
Full textAbstract:
The challenge of the post-genomic era is functional genomics, i.e. understanding how the genome is expressed to produce myriad cell phenotypes. A phenotype is the result of selective expression of the genome in response to the microenvironment. to use genomic information to understand the biology of complex organisms, the biological responses and signaling pathways in cells need to be studied in context, i.e. within the proper tissue structure. Nonetheless, most current biology is conducted using cells cultured in monolayers on traditional tissue culture plastic. These non-physiological models impede the ability to predict in vivo responses from model systems. The same cells cultured in 2-dimensions (i.e. monolayers) vs. 3-dimensions (e.g. multicellular tumor spheroids) differ in their responses to external stimuli such as ionizing radiation, viral infection, cytotoxic drugs, and chemotherapeutic agents. Our laboratory has led the way in promoting and developing 3-dimensional cell culture models that more accurately reflect in vivo biology, beginning with the establishment 15 years ago of physiologically functional reconstituted mammary acini in culture.Quantitation of spatial and temporal concurrent behavior of multiple markers in these 3-dimensional cell cultures is hampered by the currently routine mode of sequential image acquisition, measurement and analysis of specific targets. This precludes the detailed analysis of multi-dimensional, time sequence responses and fails to relate features in novel and meaningful ways that will further our understanding of basic biology. Thus new methodology was needed for high-throughput, dynamic evaluations of large numbers of live multicellular specimens. Rather than using confocal microscopy methods, which interfere with live cell systems due to photo-damage, optical sectioning of the 3-dimensional structures is achieved with structured light illumination using the Wilson grating in an implementation described by Lanni.
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Zhang, Xiaoyong, Wenbing Hu, Jing Li, Lei Tao, and Yen Wei. "A comparative study of cellular uptake and cytotoxicity of multi-walled carbon nanotubes, graphene oxide, and nanodiamond." Toxicology Research 1, no. 1 (May 11, 2012): 62–68. http://dx.doi.org/10.1039/c2tx20006f.
Full textAbstract:
Abstract Investigations of the interactions between carbon nanomaterials (CNMs) and living organisms and their subsequent biological responses are of fundamental significance for toxicity assessment and further biomedical applications. In this work, the cellular uptake and cytotoxicity of multi-walled carbon nanotubes (MWCNTs), graphene oxide (GO) and nanodiamond (ND) were examined and compared. We demonstrated that all of the CNMs were readily internalized by HeLa cells through nonspecific cellular uptake. Their cell uptake ratios showed significant differences in the following order: ND > MWCNTs > GO. A series of biological assays were used to evaluate the cytotoxicity of CNMs. It was found that CNMs showed dose- and time-dependent cytotoxicity to HeLa cells. However, cytotoxicity of CNMs was not associated with their cell uptake ratios. Among them, ND exhibited the highest cell uptake ratio and the least cytotoxicity. To the best of our knowledge, this is the first study which has quantitatively determined and compared the cell uptake ratios and cytotoxicities of MWCNTs, GO and ND. And we expect that these results described here could provide useful information for the development of new strategies to design efficient drug delivery nanocarriers and therapeutic systems as well as deep insights into the mechanism of CNMs' cytotoxicity.
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Coventry, Brendon J., and Maciej Henneberg. "The Immune System and Responses to Cancer: Coordinated Evolution." F1000Research 4 (January 27, 2021): 552. http://dx.doi.org/10.12688/f1000research.6718.3.
Full textAbstract:
This review explores the incessant evolutionary interaction and co-development between immune system evolution and somatic evolution, to put it into context with the short, over 60-year, detailed human study of this extraordinary protective system. Over millions of years, the evolutionary development of the immune system in most species has been continuously shaped by environmental interactions between microbes, and aberrant somatic cells, including malignant cells. Not only has evolution occurred in somatic cells to adapt to environmental pressures for survival purposes, but the immune system and its function has been successively shaped by those same evolving somatic cells and microorganisms through continuous adaptive symbiotic processes of progressive simultaneous immunological and somatic change to provide what we observe today. Indeed, the immune system as an environmental influence has also shaped somatic and microbial evolution. Although the immune system is tuned to primarily controlling microbiological challenges for combatting infection, it can also remove damaged and aberrant cells, including cancer cells to induce long-term cures. Our knowledge of how this occurs is just emerging. Here we consider the connections between immunity, infection and cancer, by searching back in time hundreds of millions of years to when multi-cellular organisms first began. We are gradually appreciating that the immune system has evolved into a truly brilliant and efficient protective mechanism, the importance of which we are just beginning to now comprehend. Understanding these aspects will likely lead to more effective cancer and other therapies.
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Coventry, Brendon J., Martin Ashdown, and Maciej Henneberg. "The Immune System and Responses to Cancer: Coordinated Evolution." F1000Research 4 (November 6, 2020): 552. http://dx.doi.org/10.12688/f1000research.6718.2.
Full textAbstract:
This review explores the incessant evolutionary interaction and co-development between immune system evolution and somatic evolution, to put it into context with the short, over 60-year, detailed human study of this extraordinary protective system. Over millions of years, the evolutionary development of the immune system in most species has been continuously shaped by environmental interactions between microbes, and aberrant somatic cells, including malignant cells. Not only has evolution occurred in somatic cells to adapt to environmental pressures for survival purposes, but the immune system and its function has been successively shaped by those same evolving somatic cells and microorganisms through continuous adaptive symbiotic processes of progressive simultaneous immunological and somatic change to provide what we observe today. Indeed, the immune system as an environmental influence has also shaped somatic and microbial evolution. Although the immune system is tuned to primarily controlling microbiological challenges for combatting infection, it can also remove damaged and aberrant cells, including cancer cells to induce long-term cures. Our knowledge of how this occurs is just emerging. Here we consider the connections between immunity, infection and cancer, by searching back in time hundreds of millions of years to when multi-cellular organisms first began. We are gradually appreciating that the immune system has evolved into a truly brilliant and efficient protective mechanism, the importance of which we are just beginning to now comprehend. Understanding these aspects will likely lead to more effective cancer and other therapies.