Understanding the Role of Solvation Forces on the Preferential Attachment of Nanoparticles in Liquid

Abstract Domains are the structural, functional and evolutionary units of proteins. They combine to form multidomain proteins. The evolutionary history of this molecular combinatorics has been studied with phylogenomic methods. Here, we construct networks of domain organization and explore their evolution. These networks revealed two ancient waves of structural novelty arising from ancient ‘p-loop’ and ‘winged helix’ domains and a massive ‘big bang’ of domain organization. The evolutionary recruitment of domains was highly modular, hierarchical and ongoing. Domain rearrangements elicited non-random and scale-free network structure. Comparative analyses of preferential attachment, randomness and modularity of networks showed yin-and-yang complementary transition patterns along the evolutionary timeline. Remarkably, evolving networks highlighted a central evolutionary role of cofactor-supporting structures of non-ribosomal peptide synthesis (NRPS) pathways, likely crucial to the early development of the genetic code. Some highly modular domains featured dual response regulation in two-component signal transduction systems with DNA-binding activity linked to transcriptional regulation of responses to environmental change. Interestingly, hub domains across the evolving networks shared the historical role of DNA binding and editing, an ancient protein function in molecular evolution. Our investigation unfolds historical source-sink patterns of evolutionary recruitment that further our understanding of protein architectures and functions.

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Resilience and evolvability of protein-protein interaction networks

10.1101/2020.07.02.184325 ◽

2020 ◽

Author(s):

Brennan Klein ◽

Ludvig Holmér ◽

Keith M. Smith ◽

Mackenzie M. Johnson ◽

Anshuman Swain ◽

...

Keyword(s):

Gene Expression ◽

Protein Interaction ◽

Protein Interactions ◽

Preferential Attachment ◽

Network Resilience ◽

Biological Noise ◽

Ppi Network ◽

Protein Protein Interaction ◽

Ppi Networks

AbstractProtein-protein interaction (PPI) networks represent complex intra-cellular protein interactions, and the presence or absence of such interactions can lead to biological changes in an organism. Recent network-based approaches have shown that a phenotype’s PPI network’s resilience to environmental perturbations is related to its placement in the tree of life; though we still do not know how or why certain intra-cellular factors can bring about this resilience. One such factor is gene expression, which controls the simultaneous presence of proteins for allowed extant interactions and the possibility of novel associations. Here, we explore the influence of gene expression and network properties on a PPI network’s resilience, focusing especially on ribosomal proteins—vital molecular-complexes involved in protein synthesis, which have been extensively and reliably mapped in many species. Using publicly-available data of ribosomal PPIs for E. coli, S.cerevisae, and H. sapiens, we compute changes in network resilience as new nodes (proteins) are added to the networks under three node addition mechanisms—random, degree-based, and gene-expression-based attachments. By calculating the resilience of the resulting networks, we estimate the effectiveness of these node addition mechanisms. We demonstrate that adding nodes with gene-expression-based preferential attachment (as opposed to random or degree-based) preserves and can increase the original resilience of PPI network. This holds in all three species regardless of their distributions of gene expressions or their network community structure. These findings introduce a general notion of prospective resilience, which highlights the key role of network structures in understanding the evolvability of phenotypic traits.1Author SummaryProteins in organismal cells are present at different levels of concentration and interact with other proteins to provide specific functional roles. Accumulating lists of all of these interactions, complex networks of protein interactions become apparent. This allows us to begin asking whether there are network-level mechanisms at play guiding the evolution of biological systems. Here, using this network perspective, we address two important themes in evolutionary biology (i) How are biological systems able to successfully incorporate novelty? (ii) What is the evolutionary role of biological noise in evolutionary novelty? We consider novelty to be the introduction of a new protein, represented as a new “node”, into a network. We simulate incorporation of novel proteins into Protein-Protein Interaction (PPI) networks in different ways and analyse how the resilience of the PPI network alters. We find that novel interactions guided by gene expression (indicative of concentration levels of proteins) creates a more resilient network than either uniformly random interactions or interactions guided solely by the network structure (preferential attachment). Moreover, simulated biological noise in the gene expression increases network resilience. We suggest that biological noise induces novel structure in the PPI network which has the effect of making it more resilient.

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Force dependence of filopodia adhesion: involvement of myosin II and formins

10.1101/195420 ◽

2017 ◽

Cited By ~ 3

Author(s):

N. O. Alieva ◽

A. K. Efremov ◽

S. Hu ◽

D. Oh ◽

Z. Chen ◽

...

Keyword(s):

Optical Tweezers ◽

Actin Filaments ◽

Adhesion Force ◽

Preferential Attachment ◽

Cell Orientation ◽

Pulling Forces ◽

Membrane Protrusions ◽

Myosin Iia ◽

Pulling Force

AbstractFilopodia are dynamic membrane protrusions driven by polymerization of an actin filament core, mediated by formin molecules at the filopodia tips. Filopodia can adhere to the extracellular matrix and experience both external and cell generated pulling forces. The role of such forces in filopodia adhesion is however insufficiently understood. Here, we induced sustained growth of filopodia by applying pulling force to their tips via attached fibronectin-coated beads trapped by optical tweezers. Strikingly, pharmacological inhibition or knockdown of myosin IIA, which localized to the base of filopodia, resulted in weakening of filopodia adherence strength. Inhibition of formins, which caused detachment of actin filaments from formin molecules, produced similar effect. Thus, myosin IIA-generated centripetal force transmitted to the filopodia tips through interactions between formins and actin filaments are required for filopodia adhesion. Force-dependent adhesion led to preferential attachment of filopodia to rigid versus fluid substrates, which may underlie cell orientation and polarization.

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Networks, Proximities, and Interfirm Knowledge Exchanges

International Regional Science Review ◽

10.1177/0160017615576079 ◽

2015 ◽

Vol 40 (4) ◽

pp. 377-404 ◽

Cited By ~ 4

Author(s):

Stefano Usai ◽

Emanuela Marrocu ◽

Raffaele Paci

Keyword(s):

Strategic Alliances ◽

Preferential Attachment ◽

Full Range ◽

Economic Activities ◽

Positive Role ◽

Five Dimensions ◽

Social Proximity ◽

Relevant Effect ◽

Set Up

Building on previous literature that provides extensive evidence concerning flows of knowledge generated by interfirm agreements, in this article, we aim to analyze how the occurrence of such collaborations is driven by multidimensional proximity among participants and by their position within firms’ networks. More specifically, we assess how the likelihood that two firms set up a partnership is influenced by their bilateral geographical, technological, organizational, institutional, and social proximity and by their position within networks. Our analysis is based on agreements in the form of joint ventures or strategic alliances, announced over the period 2005–2012, in which at least one partner is localized in Italy. We consider the full range of economic activities, which allows us to offer a general scenario and to investigate specifically the role of technological relatedness across different sectors. The econometric analysis, based on the logistic framework for rare events, provided three noteworthy results. First, all five dimensions of proximity jointly exert a positive and relevant effect in determining the probability of interfirm knowledge exchanges, signaling that they complement each other rather than function as alternative channels. Second, the highest impact on probability is due to technological proximity, followed by organizational, geographical, and institutional proximities, while social proximity has a limited effect. Third, we find evidence concerning the positive role played by networks, through preferential attachment effects, in enhancing the probability of interfirm agreements.

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Role of dimensionality in preferential attachment growth in the Bianconi–Barabási model

Journal of Statistical Mechanics Theory and Experiment ◽

10.1088/1742-5468/aa8198 ◽

2017 ◽

Vol 2017 (9) ◽

pp. 093402 ◽

Cited By ~ 8

Author(s):

Thiago C Nunes ◽

Samurai Brito ◽

Luciano R da Silva ◽

Constantino Tsallis

Keyword(s):

Preferential Attachment

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Emergence of Power Laws in Online Communities: The Role of Social Mechanisms and Preferential Attachment

MIS Quarterly ◽

10.25300/misq/2014/38.3.08 ◽

2014 ◽

Vol 38 (3) ◽

pp. 795-808 ◽

Cited By ~ 41

Author(s):

Steven L. Johnson ◽

◽

Samer Faraj ◽

Srinivas Kudaravalli ◽

◽

...

Keyword(s):

Online Communities ◽

Preferential Attachment ◽

Power Laws ◽

Social Mechanisms

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The Role of Opinion Leaders in the Sustainable Development of Corporate-Led Consumer Advice Networks: Evidence from a Chinese Travel Content Community

Sustainability ◽

10.3390/su131911128 ◽

2021 ◽

Vol 13 (19) ◽

pp. 11128

Author(s):

Lianren Wu ◽

Jinjie Li ◽

Jiayin Qi ◽

Deli Kong ◽

Xu Li

Keyword(s):

Sustainable Development ◽

Online Community ◽

Corporate Strategy ◽

Preferential Attachment ◽

Network Evolution ◽

Opinion Leaders ◽

The Sustainable Development ◽

Advice Networks ◽

Community Marketing

Online community marketing and social media influencer marketing have aroused the interest of many researchers and practitioners around the world. Companies building online content communities to implement community marketing and influencer marketing has become a new corporate strategy, especially in the tourism and hotel industries in which experiential products are sold. However, based on the content community, maintaining the sustainable development of a consumer advice network composed of opinion leaders and consumers is a major challenge. This paper selects the travel content community of Qunar.com as the research object to study the role of opinion leaders in the sustainable development of corporate-led consumer advice networks (CANs). Empirical evidence based on network evolution data from 1356 “Hotel Sleep Testers” across 11 years shows that: (1) the creation and provision of information can obviously increase the probability of the relationship construction and increase the number of relationships, thus facilitating the formation of opinion leadership (OL); (2) active participation in interactions and withhigh-quality information brings greater effects; (3) the network structure variables, such as preferential attachment, structural equivalence, and similarity, can also better predict the probability of a potential relationship; and (4) reciprocity in consumer advice networks has no significant impact on the establishment of network relationships.

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