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King MR, Ruff KM, Lin AZ, Pant A, Farag M, Lalmansingh JM, Wu T, Fossat MJ, Ouyang W, Lew MD, Lundberg E, Vahey MD, Pappu RV. Macromolecular condensation organizes nucleolar sub-phases to set up a pH gradient. Cell 2024; 187:1889-1906.e24. [PMID: 38503281 DOI: 10.1016/j.cell.2024.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 01/02/2024] [Accepted: 02/22/2024] [Indexed: 03/21/2024]
Abstract
Nucleoli are multicomponent condensates defined by coexisting sub-phases. We identified distinct intrinsically disordered regions (IDRs), including acidic (D/E) tracts and K-blocks interspersed by E-rich regions, as defining features of nucleolar proteins. We show that the localization preferences of nucleolar proteins are determined by their IDRs and the types of RNA or DNA binding domains they encompass. In vitro reconstitutions and studies in cells showed how condensation, which combines binding and complex coacervation of nucleolar components, contributes to nucleolar organization. D/E tracts of nucleolar proteins contribute to lowering the pH of co-condensates formed with nucleolar RNAs in vitro. In cells, this sets up a pH gradient between nucleoli and the nucleoplasm. By contrast, juxta-nucleolar bodies, which have different macromolecular compositions, featuring protein IDRs with very different charge profiles, have pH values that are equivalent to or higher than the nucleoplasm. Our findings show that distinct compositional specificities generate distinct physicochemical properties for condensates.
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Affiliation(s)
- Matthew R King
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Kiersten M Ruff
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrew Z Lin
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Avnika Pant
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Mina Farag
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Jared M Lalmansingh
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Tingting Wu
- Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Department of Electrical and Systems Engineering, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Martin J Fossat
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Wei Ouyang
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA; Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Matthew D Lew
- Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Department of Electrical and Systems Engineering, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Emma Lundberg
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA; Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Michael D Vahey
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA; Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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Hassani MA, Cui Z, LaReau J, Huntley RB, Steven B, Zeng Q. Inter-species interactions between two bacterial flower commensals and a floral pathogen reduce disease incidence and alter pathogen activity. mBio 2024; 15:e0021324. [PMID: 38376185 PMCID: PMC10936193 DOI: 10.1128/mbio.00213-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Flowers are colonized by a diverse community of microorganisms that can alter plant health and interact with floral pathogens. Erwinia amylovora is a flower-inhabiting bacterium and a pathogen that infects different plant species, including Malus × domestica (apple). Previously, we showed that the co-inoculation of two bacterial strains, members of the genera Pseudomonas and Pantoea, isolated from apple flowers, reduced disease incidence caused by this floral pathogen. Here, we decipher the ecological interactions between the two flower-associated bacteria and E. amylovora in field experimentation and in vitro co-cultures. The two flower commensal strains did not competitively exclude E. amylovora from the stigma habitat, as both bacteria and the pathogen co-existed on the stigma of apple flowers and in vitro. This suggests that plant protection might be mediated by other mechanisms than competitive niche exclusion. Using a synthetic stigma exudation medium, ternary co-culture of the bacterial strains led to a substantial alteration of gene expression in both the pathogen and the two microbiota members. Importantly, the gene expression profiles for the ternary co-culture were not just additive from binary co-cultures, suggesting that some functions only emerged in multipartite co-culture. Additionally, the ternary co-culture of the strains resulted in a stronger acidification of the growth milieu than mono- or binary co-cultures, pointing to another emergent property of co-inoculation. Our study emphasizes the critical role of emergent properties mediated by inter-species interactions within the plant holobiont and their potential impact on plant health and pathogen behavior. IMPORTANCE Fire blight, caused by Erwinia amylovora, is one of the most important plant diseases of pome fruits. Previous work largely suggested plant microbiota commensals suppressed disease by antagonizing pathogen growth. However, inter-species interactions of multiple flower commensals and their influence on pathogen activity and behavior have not been well studied. Here, we show that co-inoculating two bacterial strains that naturally colonize the apple flowers reduces disease incidence. We further demonstrate that the interactions between these two microbiota commensals and the floral pathogen led to the emergence of new gene expression patterns and a strong alteration of the external pH, factors that may modify the pathogen's behavior. Our findings emphasize the critical role of emergent properties mediated by inter-species interactions between plant microbiota and plant pathogens and their impact on plant health.
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Affiliation(s)
- M. Amine Hassani
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Zhouqi Cui
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Jacquelyn LaReau
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Regan B. Huntley
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Blaire Steven
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Quan Zeng
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
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Nakata S, Takezawa M. Hierarchical structures emerge from the cultural transmission: an iterated learning experiment using a non-linguistic task. Front Artif Intell 2023; 6:1221329. [PMID: 38188591 PMCID: PMC10770839 DOI: 10.3389/frai.2023.1221329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Human language is characterized by complex structural features, such as the hierarchical combination of words to form sentences. Although other animals use communication systems, empirical evidence of hierarchical structures is rare. Computational studies of language evolution have suggested that cultural transmission plays a key role in the emergence of structural features in human languages, including hierarchy. While the previous study demonstrated the emergence of hierarchical structures in non-linguistic systems, we argue that their laboratory study may have overestimated the role of cultural transmission because of a lack of appropriate controls and analyses. To directly test the effect of cultural transmission, we conducted an experiment with no cultural transmission as a control (individual condition) in addition to replicating the previous transmission experiment (transmission condition). Our study has added a quantitative analysis of the hierarchical depth. We found that sequences became more structured as the number of generations increased; however, those produced under the transmission condition were more structured than those under the individual condition. These findings suggest that cultural transmission plays an important role in the emergence of hierarchical structures, which cannot be explained by increased learnability alone. The emergence of complex structural properties in human culture, such as language, technology, and music, may have resulted from information transmission processes between different individuals. In conclusion, this study provides evidence of the crucial role of cultural transmission in the emergence of hierarchical structures in non-linguistic communication systems. Our results contribute to the ongoing debate on the origins of human language and the emergence of complex cultural artifacts. The results of this study have implications for the study of cultural evolution and the role of transmission in shaping the emergence of structural features across diverse domains.
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Affiliation(s)
- Seiya Nakata
- Department of Behavioral Science, Graduate School of Humanities and Human Sciences, Hokkaido University, Sapporo, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, Japan
| | - Masanori Takezawa
- Department of Behavioral Science, Graduate School of Humanities and Human Sciences, Hokkaido University, Sapporo, Japan
- Center for Experimental Research in Social Sciences, Hokkaido University, Sapporo, Japan
- Center for Human Nature, Artificial Intelligence and Neuroscience, Hokkaido University, Sapporo, Japan
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Spillmann L, Hsu LC, Wang W, Chen CC, Yeh CI, Tseng CH. Gestalt neurons and emergent properties in visual perception: A novel concept for the transformation from local to global processing. J Vis 2023; 23:4. [PMID: 38091030 PMCID: PMC10746863 DOI: 10.1167/jov.23.14.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/06/2023] [Indexed: 12/18/2023] Open
Abstract
Gestalten in visual perception are defined by emergent properties of the whole, which cannot be predicted from the sum of its parts; rather, they arise by virtue of inherent principles, the Laws of Seeing. This review attempts to assign neurophysiological correlates to select emergent properties in motion and contour perception and proposes parallels to the processing of local versus global attributes by classical versus contextual receptive fields. The aim is to identify Gestalt neurons in the visual system to account for the Laws of Seeing in causal terms and to explain "Why do things look as they do" (Koffka, 1935, p. 76).
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Affiliation(s)
- Lothar Spillmann
- Department of Neurology, University of Freiburg, Freiburg, Germany
| | | | - Wei Wang
- Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, China
| | - Chien-Chung Chen
- Department of Psychology, National Taiwan University, Taipei, Taiwan
| | - Chun-I Yeh
- Department of Psychology, National Taiwan University, Taipei, Taiwan
| | - Chia-Huei Tseng
- Research Institute of Electrical Communication, Interdisciplinary ICT Research Center for Cyber and Real Spaces, Tohoku University, Sendai, Japan
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Abstract
Spatial partitioning of chemical processes is an important attribute of many biological systems, the effect of which is reflected in the high efficiency of enzymes found within otherwise chaotic cellular environments. Barriers, often provided through the formation of compartments or phase segregation, gate the access of macromolecules and small molecules within the cell and provide an added level of metabolic control. Taking inspiration from nature, we have designed virus-like particles (VLPs) as nanoreactor compartments that sequester enzyme catalysts and have used these as building blocks to construct 3D protein macromolecular framework (PMF) materials, which are structurally characterized using small-angle X-ray scattering (SAXS). The highly charged PMFs form a separate phase in suspension, and by tuning the ionic strength, we show positively charged molecules preferentially partition into the PMF, while negatively charged molecules are excluded. This molecular partitioning was exploited to tune the catalytic activity of enzymes enclosed within the individual particles in the PMF, the results of which showed that positively charged substrates had turnover rates that were 8500× faster than their negatively charged counterparts. Moreover, the catalytic PMF led to cooperative behavior resulting in charge dependent trends opposite to those observed with individual P22 nanoreactor particles.
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Affiliation(s)
- Ekaterina Selivanovitch
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Masaki Uchida
- Department of Chemistry and Biochemistry, California State University Fresno, Fresno, California 93740, Unites States
| | - Byeongdu Lee
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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Wang Z, Shi G, Shang M, Zhang Y. The Stock Market Model with Delayed Information Impact from a Socioeconomic View. Entropy (Basel) 2021; 23:e23070893. [PMID: 34356434 PMCID: PMC8304283 DOI: 10.3390/e23070893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/09/2021] [Accepted: 07/10/2021] [Indexed: 01/23/2023]
Abstract
Finding the critical factor and possible "Newton's laws" in financial markets has been an important issue. However, with the development of information and communication technologies, financial models are becoming more realistic but complex, contradicting the objective law "Greatest truths are the simplest." Therefore, this paper presents an evolutionary model independent of micro features and attempts to discover the most critical factor. In the model, information is the only critical factor, and stock price is the emergence of collective behavior. The statistical properties of the model are significantly similar to the real market. It also explains the correlations of stocks within an industry, which provides a new idea for studying critical factors and core structures in the financial markets.
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Affiliation(s)
- Zhiting Wang
- Physics and Photoelectricity School, South China University of Technology, Guangzhou 510640, China;
| | - Guiyuan Shi
- International Academic Center of Complex Systems, Beijing Normal University at Zhuhai, Zhuhai 519087, China;
| | - Mingsheng Shang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China;
| | - Yuxia Zhang
- Physics and Photoelectricity School, South China University of Technology, Guangzhou 510640, China;
- Correspondence:
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Bouain N, Krouk G, Lacombe B, Rouached H. Getting to the Root of Plant Mineral Nutrition: Combinatorial Nutrient Stresses Reveal Emergent Properties. Trends Plant Sci 2019; 24:542-552. [PMID: 31006547 DOI: 10.1016/j.tplants.2019.03.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 05/02/2023]
Abstract
In nature, plants have to handle daily fluctuations in light and temperature. In addition, plants face biotic and abiotic stresses that often come in various combinations. For instance, the availability of various nutrients in soil is heterogeneous, resulting in combined nutrient stress. Recent studies reveal that plant responses to multiple nutrient stresses are not the summation of the plant responses to each individual stress. Here, we present and discuss the interactions between phosphate, nitrogen, and zinc to illustrate the effect of macro- and micronutrient interactions on plant growth and ion homeostasis. Solving the mystery of these interactions will pave the way to the development of strategies to improve crop productivity.
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Affiliation(s)
- Nadia Bouain
- BPMP, Univ Montpellier, INRA, CNRS, SupAgro, Montpellier, France
| | - Gabriel Krouk
- BPMP, Univ Montpellier, INRA, CNRS, SupAgro, Montpellier, France
| | - Benoit Lacombe
- BPMP, Univ Montpellier, INRA, CNRS, SupAgro, Montpellier, France
| | - Hatem Rouached
- BPMP, Univ Montpellier, INRA, CNRS, SupAgro, Montpellier, France.
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Carlson RP, Beck AE, Phalak P, Fields MW, Gedeon T, Hanley L, Harcombe WR, Henson MA, Heys JJ. Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia. Biochem Soc Trans 2018; 46:269-84. [PMID: 29472366 DOI: 10.1042/BST20170242] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/21/2017] [Accepted: 01/01/2018] [Indexed: 01/24/2023]
Abstract
Resource scarcity is a common stress in nature and has a major impact on microbial physiology. This review highlights microbial acclimations to resource scarcity, focusing on resource investment strategies for chemoheterotrophs from the molecular level to the pathway level. Competitive resource allocation strategies often lead to a phenotype known as overflow metabolism; the resulting overflow byproducts can stabilize cooperative interactions in microbial communities and can lead to cross-feeding consortia. These consortia can exhibit emergent properties such as enhanced resource usage and biomass productivity. The literature distilled here draws parallels between in silico and laboratory studies and ties them together with ecological theories to better understand microbial stress responses and mutualistic consortia functioning.
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Abstract
Improved therapy of brain disorders can be achieved by focusing on neuronal networks, utilizing combined pharmacological and stimulation paradigms guided by neuroimaging. Neuronal networks that mediate normal brain functions, such as hearing, interact with other networks, which is important but commonly neglected. Network interaction changes often underlie brain disorders, including epilepsy. "Conditional multireceptive" (CMR) brain areas (e.g., brainstem reticular formation and amygdala) are critical in mediating neuroplastic changes that facilitate network interactions. CMR neurons receive multiple inputs but exhibit extensive response variability due to milieu and behavioral state changes and are exquisitely sensitive to agents that increase or inhibit GABA-mediated inhibition. Enhanced CMR neuronal responsiveness leads to expression of emergent properties--nonlinear events--resulting from network self-organization. Determining brain disorder mechanisms requires animals that model behaviors and neuroanatomical substrates of human disorders identified by neuroimaging. However, not all sites activated during network operation are requisite for that operation. Other active sites are ancillary, because their blockade does not alter network function. Requisite network sites exhibit emergent properties that are critical targets for pharmacological and stimulation therapies. Improved treatment of brain disorders should involve combined pharmacological and stimulation therapies, guided by neuroimaging, to correct network malfunctions by targeting specific network neurons.
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Affiliation(s)
- Carl L Faingold
- Departments of Pharmacology and Neurology, Division of Neurosurgery, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Hal Blumenfeld
- Departmens of Neurology, Neurobiology, and Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
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Vanneste S, De Ridder D. The auditory and non-auditory brain areas involved in tinnitus. An emergent property of multiple parallel overlapping subnetworks. Front Syst Neurosci 2012; 6:31. [PMID: 22586375 PMCID: PMC3347475 DOI: 10.3389/fnsys.2012.00031] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 04/13/2012] [Indexed: 11/23/2022] Open
Abstract
Tinnitus is the perception of a sound in the absence of an external sound source. It is characterized by sensory components such as the perceived loudness, the lateralization, the tinnitus type (pure tone, noise-like) and associated emotional components, such as distress and mood changes. Source localization of quantitative electroencephalography (qEEG) data demonstrate the involvement of auditory brain areas as well as several non-auditory brain areas such as the anterior cingulate cortex (dorsal and subgenual), auditory cortex (primary and secondary), dorsal lateral prefrontal cortex, insula, supplementary motor area, orbitofrontal cortex (including the inferior frontal gyrus), parahippocampus, posterior cingulate cortex and the precuneus, in different aspects of tinnitus. Explaining these non-auditory brain areas as constituents of separable subnetworks, each reflecting a specific aspect of the tinnitus percept increases the explanatory power of the non-auditory brain areas involvement in tinnitus. Thus, the unified percept of tinnitus can be considered an emergent property of multiple parallel dynamically changing and partially overlapping subnetworks, each with a specific spontaneous oscillatory pattern and functional connectivity signature.
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Affiliation(s)
- Sven Vanneste
- Brain, TRI and Department of Neurosurgery, University Hospital Antwerp Antwerp, Belgium
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