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Journal articles on the topic 'Multi-organisms interactions'

Author: Grafiati

Published: 4 May 2024

Last updated: 31 July 2025

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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 (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 noi

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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 (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, somet

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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 (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 contribu

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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 (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,

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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 (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-hist

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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 (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 o

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Lyu, Yanfen, Ting Xiong, Shuaibo Shi, et al. "Prediction of the Trimer Protein Interface Residue Pair by CNN-GRU Model Based on Multi-Feature Map." Nanomaterials 15, no. 3 (2025): 188. https://doi.org/10.3390/nano15030188.

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Most life activities of organisms are realized through protein–protein interactions, and these interactions are mainly achieved through residue–residue contact between monomer proteins. Consequently, studying residue–residue contact at the protein interaction interface can contribute to a deeper understanding of the protein–protein interaction mechanism. In this paper, we focus on the research of the trimer protein interface residue pair. Firstly, we utilize the amino acid k-interval product factor descriptor () to integrate the positional information and physicochemical properties of amino ac

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Prayogo, Doddy, Min-Yuan Cheng, Yu-Wei Wu, et al. "A Novel Hybrid Metaheuristic Algorithm for Optimization of Construction Management Site Layout Planning." Algorithms 13, no. 5 (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 combinati

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Lan, Qiuhong, Zhongtuan Zheng, Zhen Tang, Xuehua Qiu, and Zhixiang Yin. "Protein-protein interaction prediction using bidirectional GRUs with explicit ensemble." PLOS One 20, no. 7 (2025): e0326960. https://doi.org/10.1371/journal.pone.0326960.

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Protein-protein interactions is essential for cellular processes in all organisms. The accurate in-silico identification of these interactions is a significant area of research in biology-related fields, which is crucial for protein function prediction and drug design. Protein sequence data serves as the primary source for computational protein prediction. However, existing models for predicting protein-protein interactions based on sequence information typically consider only a limited set of physicochemical properties of amino acids. Consequently, they fail to comprehensively characterize pr

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Araújo, Cristiano V. M., Abdelmourhit Laissaoui, Daniel C. V. R. Silva, 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 (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, condi

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Umidjon ugli, Sharipov Jasurbek, and Toshturdiyev Nurbek Nurali ugli. "GLOBAL CLIMATE CHANGE AND ITS EFFECTS ON LIVING ORGANISMS." International Journal of Economic Integration and Regional Competitiveness 1, no. 7 (2024): 9–14. https://doi.org/10.61796/ijeirc.v1i7.158.

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Global climate change, driven primarily by anthropogenic greenhouse gas emissions, represents a critical challenge with extensive implications for ecosystems and biodiversity. Rising global temperatures, altered precipitation patterns, and increased frequency of extreme weather events are influencing the habitat, distribution, and physiological processes of various organisms. Despite considerable research, there remains a limited understanding of how these climatic changes interact with other environmental stressors to affect different taxa and ecosystems. This study aims to elucidate the mult

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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 (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

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Escobedo, R., V. Lecheval, V. Papaspyros, et al. "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 (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 accur

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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 (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 t

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Manzalini, Antonio, and Bruno Galeazzi. "Explaining Homeopathy with Quantum Electrodynamics." Homeopathy 108, no. 03 (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

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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 (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 diffus

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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 (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 hos

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Kim, Ah-Young, Who-Seung Lee, and Yowhan Son. "The Interaction between Climate Change and Biodiversity Can Be Assessed from a Material Cycle Perspective." Diversity 16, no. 8 (2024): 506. http://dx.doi.org/10.3390/d16080506.

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This study focused on understanding biodiversity variability in response to climate change as an environmental stressor from a carbon cycle perspective. As the frequency and magnitude of environmental stresses are expected to increase due to rising carbon concentrations, these changes may affect the variability in biodiversity. However, several studies have argued that conventional methods for biodiversity assessment, primarily based on arithmetic indices utilized in national policies, are inadequate for accurately assessing these interactions among species, abiotic changes, and material cycli

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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 (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-medi

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Tang, Zhidong, Weiliang Fan, Qiming Li, et al. "MVIP: multi-omics portal of viral infection." Nucleic Acids Research 50, no. D1 (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

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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 (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 additi

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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 (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

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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 (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, wher

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Srinivasan, N., G. Agarwal, R. M. Bhaskara, 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 (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

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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 (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

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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 o

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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 (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 o

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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 (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 expressi

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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 (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 radi

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Geslain, Sandra Amandine Marie, Stéphane Hausmann, Johan Geiser, George Edward Allen, Diego Gonzalez, and Martina Valentini. "Critical functions and key interactions mediated by the RNase E scaffolding domain in Pseudomonas aeruginosa." PLOS Genetics 21, no. 3 (2025): e1011618. https://doi.org/10.1371/journal.pgen.1011618.

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The RNA degradosome is a bacterial multi-protein complex mediating mRNA processing and degradation. In Pseudomonadota, this complex assembles on the C-terminal domain (CTD) of RNase E through short linear motifs (SLiMs) that determine its composition and functionality. In the human pathogen Pseudomonas aeruginosa, the RNase E CTD exhibits limited similarity to that of model organisms, impeding our understanding of RNA metabolic processes in this bacterium. Our study systematically maps the interactions mediated by the P. aeruginosa RNase E CTD and highlights its critical role in transcript reg

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Mikkilineni, Rao. "Architectural Resiliency in Distributed Computing." International Journal of Grid and High Performance Computing 4, no. 4 (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, effi

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Saradha, Arumugam, S. Saravanan Dr., and Vasanth M. "DRUG DESIGN, TYPES AND ITS MODE OF ACTION IN BINDING TARGET PROTEIN WITH LIGAND." International Journal of Computational Research and Development 2, no. 1 (2017): 29–36. https://doi.org/10.5281/zenodo.290274.

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Bioinformatics has become emerging field and has been used in various areas of research. The principal goal of bioinformatics is to enhance the understanding of biological processes. This implicates the establishment and encroachment of databases, algorithms, computational and statistical techniques and theory to solve formal and practical problems originating from the management and analysis of biological data. Molecular interactions including protein-protein, enzyme-substrate, protein-nucleic acid, drug-protein and drug-nucleic acid play important roles in many essential biological processes

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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 (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.

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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 (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

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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 (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

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Iyer, Swami, and Timothy Killingback. "Evolution of Cooperation in Social Dilemmas with Assortative Interactions." Games 11, no. 4 (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

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Abusrewil, Sumaya, Jason L. Brown, Christopher Delaney, et al. "Chitosan Enhances the Anti-Biofilm Activity of Biodentine against an Interkingdom Biofilm Model." Antibiotics 10, no. 11 (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 regrow

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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 (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 inte

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Kulabas, Necla, Fahrettin Bugra Kilic, and Sevil Senkardes. "Investigations of Some Chlorocresol Hydrazones Against Tyrosinase Enzyme by Molecular Docking Method: In Silico Study." Pharmedicine Journal 2, no. 1 (2025): 16–23. https://doi.org/10.62482/pmj.23.

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Introduction: Tyrosinase, found in various organisms, including plants and mammals, and is responsible for pigmentation as well as the undesirable browning of fruits and vegetables, is a multi-copper enzyme involved in the synthesis of melanin in human. As it is known, melanin provides protection against harmful ultraviolet radiation, which can lead to serious conditions like skin cancers. However, excessive melanin accumulation could result in hyperpigmented spots, creating aesthetic concerns. Tyrosinase inhibitors could potentially lead to the development of novel skin-whitening agents, anti

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Rasuly, Mohammad Fahim, Sayed Hussain Mosawi, Sabihullah Nazir та Zameer Habibzada. "Integrating molecular docking and molecular dynamics simulation approaches for investigation of the affinity and interactions of the piperine with Class D β-Lactamase". Afghanistan Journal of Basic Medical Science 2, № 2 (2024): 29–41. http://dx.doi.org/10.62134/ajbms/v2.i2.khatamuni.4.

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Introduction: The study explores the potential of piperine, a natural compound with diverse medicinal effects, as a potential inhibitor targeting OXA-10 class D β-lactamase enzymes, as a potential solution to the drug resistance caused by β-lactamase-producing organisms, which contributes to millions of deaths and morbidity cases worldwide each year. Materials and Methods: Through the utilization of molecular approaches such as molecular docking and molecular dynamics simulation, this study investigated the binding sites and binding energy of class D β-lactamase in the presence of piperine. Th

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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 (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

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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 (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, findi

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Amin, Naweedullah, and Mohammad Arif Erfan. "Environmental Fate and Toxicity of Zinc Oxide Nanoparticles in Aquatic Ecosystems: A Comprehensive Review." Journal of Natural Science Review 3, no. 1 (2025): 104–25. https://doi.org/10.62810/jnsr.v3i1.103.

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Zinc oxide nanoparticles (ZnO NPs) are increasingly utilized in agriculture, electronics, and medicine, raising concerns about their environmental fate and toxicity in aquatic ecosystems. This study aims to review the fate, bioaccumulation, and toxicity of ZnO NPs in aquatic ecosystem. This review was conducted through a comprehensive analysis of peer-reviewed literature from databases such as Scopus, Web of Science, and PubMed. Finding indicates that ZnO NP fate in aquatic ecosystems is governed by key environmental factors, including pH, ionic strength, and DOM. ZnO NPs tend to aggregate in

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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 (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 pl

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Lyu, Cheng-An, Yao Shen, and Peijun Zhang. "Zooming in and out: Exploring RNA Viral Infections with Multiscale Microscopic Methods." Viruses 16, no. 9 (2024): 1504. http://dx.doi.org/10.3390/v16091504.

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RNA viruses, being submicroscopic organisms, have intriguing biological makeups and substantially impact human health. Microscopic methods have been utilized for studying RNA viruses at a variety of scales. In order of observation scale from large to small, fluorescence microscopy, cryo-soft X-ray tomography (cryo-SXT), serial cryo-focused ion beam/scanning electron microscopy (cryo-FIB/SEM) volume imaging, cryo-electron tomography (cryo-ET), and cryo-electron microscopy (cryo-EM) single-particle analysis (SPA) have been employed, enabling researchers to explore the intricate world of RNA viru

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Schär, Sämi, Rodney Eastwood, Kimberly G. Arnaldi, et al. "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 (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 genet

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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 (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 ecolog

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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 stres

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Banerjee, Ankita, Rojina Khatun, Sudeshna Sengupta, and Malavika Bhattacharya. "Decoding the Microbial World: An Introduction to Microbial Omics." International Journal of Current Microbiology and Applied Sciences 14, no. 4 (2025): 146–54. https://doi.org/10.20546/ijcmas.2025.1404.018.

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The microbial world is one of the most crucial parts of the ecosystem on Earth. It has a significant contribution to our human health along with several other organisms and the functioning of our environment. Genomics, transcriptomics, proteomics, metabolomics, and metagenomics are all included in the new discipline of microbial omics, which provides strong instruments to decipher the intricate relationships between microbial populations and their physiological functions. Recent advances in multi-omics and integrated omics techniques revolutionized our understanding of microbial diversity. The

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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 tis

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