| 1. |
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| 2. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
- Huang, Zi-Gang, et al.
(författare)
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Role of collective influence in promoting cooperation
- 2008
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Ingår i: Europhysics letters. - Les Ulis : European Physical Society. - 0295-5075 .- 1286-4854. ; 84:5, s. 50008-
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Tidskriftsartikel (refereegranskat)abstract
- The collective influence on the individuals' behavior have attracted much attention, and interesting phenomena such as social facilitation and social loafing have been studied. In this paper, we consider how the collective influence affects the evolution of cooperation in a structured population of individuals who nourish and benefit from public goods in groups. Individuals are supposed to distribute endowments to different groups to nourish the corresponding public goods. The collective influence is indicated by a tunable parameter α, with larger α corresponding to the players' higher preference to contribute more to the larger groups, which is similar to the social-facilitation effect in the real world, whereas, with smaller α corresponding to individuals' contrary preference, i.e., the social-loafing effect. Interestingly, we find that the heterogeneity of public-goods setting favors cooperation. Furthermore, the system where social loafing occurs performs better than that with social facilitation, in the case of heterogeneous formation.
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| 5. |
- Rong, Zhi-Hai, et al.
(författare)
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Emergence of cooperation through coevolving time scale in spatial prisoner's dilemma
- 2010
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - : American Physical Society. - 1063-651X .- 1095-3787. ; 82:2, s. 026101-
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Tidskriftsartikel (refereegranskat)abstract
- We study evolutionary prisoner’s dilemma game by considering adaptive strategy-selection time scale among individuals according to a “win-slower, lose-faster” rule: if an individual successfully resists the invasion of an opponent, she is prone to hold her strategy for longer time through decreasing her strategy-selection time scale; otherwise, she increases the time scale because of losing. We find that the greater the losers increase their strategy-selection time scales, the better for cooperation. Interestingly, optimal cooperation can be induced by proper adaptive rate in the strategy-selection time scale. Our results may have potential implications in the design of consensus protocol in multiagent systems.
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| 6. |
- Feng, Cun-Feng, et al.
(författare)
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Effects of average degree of network on an order-disorder transition in opinion dynamics
- 2010
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Ingår i: Chinese Physics B. - : IOPScience. - 1674-1056. ; 19:6, s. 060203-
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Tidskriftsartikel (refereegranskat)abstract
- We have investigated the influence of the average degree (k) of network on the location of an order-disorder transition in opinion dynamics. For this purpose, a variant of majority rule (VMR) model is applied to Watts–Strogatz (WS) small-world networks and Barabási–Albert (BA) scale-free networks which may describe some non-trivial properties of social systems. Using Monte Carlo simulations, we find that the order–disorder transition point of the VMR model is greatly affected by the average degree (k) of the networks; a larger value of (k) results in a more ordered state of the system. Comparing WS networks with BA networks, we find WS networks have better orderliness than BA networks when the average degree (k) is small. With the increase of (k), BA networks have a more ordered state. By implementing finite-size scaling analysis, we also obtain critical exponents β/ν, γ/ν and 1/ν for several values of average degree (k). Our results may be helpful to understand structural effects on order–disorder phase transition in the context of the majority rule model.
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| 7. |
- Guan, Jian-Yue, et al.
(författare)
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Cooperation influenced by the correlation degree of two-layered complex networks in evolutionary prisoner's dilemma games
- 2010
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Ingår i: Chinese Physics B. - : Institute of Physics (IOP). - 1674-1056. ; 19:2
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Tidskriftsartikel (refereegranskat)abstract
- An evolutionary prisoner's dilemma game is investigated on two-layered complex networks respectively representing interaction and learning networks in one and two dimensions. A parameter q is introduced to denote the correlation degree between the two-layered networks. Using Monte Carlo simulations we studied the effects of the correlation degree on cooperative behaviour and found that the cooperator density nontrivially changes with q for different payoff parameter values depending on the detailed strategy updating and network dimension. An explanation for the obtained results is provided.
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| 8. |
- Holme, Petter, 1973-, et al.
(författare)
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Multiscaling in an YX model of networks
- 2009
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1063-651X .- 1095-3787. ; 80, s. 036120-
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Tidskriftsartikel (refereegranskat)abstract
- Weinvestigate a Hamiltonian model of networks. The model is amirror formulation of the XY model (hence the name)—instead ofletting the XY spins vary, keeping the coupling topology static,we keep the spins conserved and sample different underlying networks.Our numerical simulations show complex scaling behaviors with various exponentsas the system grows and temperature approaches zero, but nofinite-temperature universal critical behavior. The ground-state and low-order excitations forsparse, finite graphs are a fragmented set of isolated networkclusters. Configurations of higher energy are typically more connected. Theconnected networks of lowest energy are stretched out giving thenetwork large average distances. For the finite sizes we investigate,there are three regions—a low-energy regime of fragmented networks, anintermediate regime of stretched-out networks, and a high-energy regime ofcompact, disordered topologies. Scaling up the system size, the bordersbetween these regimes approach zero temperature algebraically, but different network-structuralquantities approach their T=0 values with different exponents. We arguethis is a, perhaps rare, example of a statistical-physics modelwhere finite sizes show a more interesting behavior than thethermodynamic limit.
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| 9. |
- Lee, Sungmin, et al.
(författare)
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Cooperation, structure, and hierarchy in multiadaptive games
- 2011
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - Melville, N. Y. : American Physical Society. - 1539-3755 .- 1550-2376. ; 84:6, s. 61148-
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Tidskriftsartikel (refereegranskat)abstract
- Game-theoretical models where the rules of the game and the interaction structure both coevolve with the game dynamics-multiadaptive games-capture very flexible situations where cooperation among selfish agents can emerge. In this work, we will discuss a multiadaptive model presented in a recent Letter [Phys. Rev. Lett. 106, 028702 (2011)] as well as generalizations of it. The model captures a nonequilibrium situation where social unrest increases the incentive to cooperate and, simultaneously, agents are partly free to influence with whom they interact. First, we investigate the details of how feedback from the behavior of agents determines the emergence of cooperation and hierarchical contact structures. We also study the stability of the system to different types of noise, and find that different regions of parameter space show very different response. Some types of noise can destroy an all-cooperator (C) state. If, on the other hand, hubs are stable, then so is the all-C state. Finally, we investigate the dependence of the ratio between the time scales of strategy updates and the evolution of the interaction structure. We find that a comparatively fast strategy dynamics is a prerequisite for the emergence of cooperation.
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| 10. |
- Lee, Sungmin, et al.
(författare)
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Emergent hierarchical structures in multiadaptive games
- 2011
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Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 106:2, s. 028702-4
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Tidskriftsartikel (refereegranskat)abstract
- We investigate a game-theoretic model of a social system where both the rules of the game and the interaction structure are shaped by the behavior of the agents. We call this type of model, with several types of feedback couplings from the behavior of the agents to their environment, a multiadaptive game. Our model has a complex behavior with several regimes of different dynamic behavior accompanied by different network topological properties. Some of these regimes are characterized by heterogeneous, hierarchical interaction networks, where cooperation and network topology coemerge from the dynamics.
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