Physical biology最新文献

{"title":"Network topology enables efficient response to environment in Physarum polycephalum","authors":"Siyu Chen, K. Alim","doi":"10.1101/2022.11.09.515897","DOIUrl":"https://doi.org/10.1101/2022.11.09.515897","url":null,"abstract":"The network-shaped body plan distinguishes the unicellular slime mould Physarum polycephalum in body architecture from other unicellular organisms. Yet, network-shaped body plans dominate branches of multi-cellular life such as in fungi. What survival advantage does a network structure provide when facing a dynamic environment with adverse conditions? Here, we probe how network topology impacts P. polycephalum’s avoidance response to an adverse blue light. We stimulate either an elongated, I-shaped amoeboid or a Y-shaped networked specimen and subsequently quantify the evacuation process of the light-exposed body part. The result shows that Y-shaped specimen complete the avoidance retraction in a comparable time frame, even slightly faster than I-shaped organisms, yet, at a lower almost negligible increase in migration velocity. Contraction amplitude driving mass motion is further only locally increased in Y-shaped specimen compared to I-shaped—providing further evidence that Y-shaped’s avoidance reaction is energetically more efficient than in I-shaped amoeboid organisms. The difference in the retraction behaviour suggests that the complexity of network topology provides a key advantage when encountering adverse environments. Our findings could lead to a better understanding of the transition from unicellular to multicellularity.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49500103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Collective response to local perturbations: how to evade threats without losing coherence.","authors":"Emanuele Loffredo,&nbsp;Davide Venturelli,&nbsp;Irene Giardina","doi":"10.1088/1478-3975/acc5cc","DOIUrl":"https://doi.org/10.1088/1478-3975/acc5cc","url":null,"abstract":"<p><p>Living groups move in complex environments and are constantly subject to external stimuli, predatory attacks and disturbances. An efficient response to such perturbations is vital to maintain the group's coherence and cohesion. Perturbations are often local, i.e. they are initially perceived only by few individuals in the group, but can elicit a global response. This is the case of starling flocks, that can turn very quickly to evade predators. In this paper, we investigate the conditions under which a global change of direction can occur upon local perturbations. Using minimal models of self-propelled particles, we show that a collective directional response occurs on timescales that grow with the system size and it is, therefore, a finite-size effect. The larger the group is, the longer it will take to turn. We also show that global coherent turns can only take place if i) the mechanism for information propagation is efficient enough to transmit the local reaction undamped through the whole group; and if ii) motility is not too strong, to avoid that the perturbed individual leaves the group before the turn is complete. No compliance with such conditions results in the group's fragmentation or in a non-efficient response.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9408711","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computer simulation reveals the effect of severing enzymes on dynamic and stabilized microtubules.","authors":"Aritra Sen,&nbsp;Ambarish Kunwar","doi":"10.1088/1478-3975/acc301","DOIUrl":"https://doi.org/10.1088/1478-3975/acc301","url":null,"abstract":"<p><p>Microtubule (MT) severing enzymes Katanin and Spastin cut the MT into smaller fragments and are being studied extensively using<i>in-vitro</i>experiments due to their crucial role in different cancers and neurodevelopmental disorders. It has been reported that the severing enzymes are either involved in increasing or decreasing the tubulin mass. Currently, there are a few analytical and computational models for MT amplification and severing. However, these models do not capture the action of MT severing explicitly, as these are based on partial differential equations in one dimension. On the other hand, a few discrete lattice-based models were used earlier to understand the activity of severing enzymes only on stabilized MTs. Hence, in this study, discrete lattice-based Monte Carlo models that included MT dynamics and severing enzyme activity have been developed to understand the effect of severing enzymes on tubulin mass, MT number, and MT length. It was found that the action of severing enzyme reduces average MT length while increasing their number; however, the total tubulin mass can decrease or increase depending on the concentration of GMPCPP (Guanylyl-(<i>α</i>,<i>β</i>)-methylene-diphosphonate)-which is a slowly hydrolyzable analogue of GTP (Guanosine triphosphate). Further, relative tubulin mass also depends on the detachment ratio of GTP/GMPCPP and Guanosine diphosphate tubulin dimers and the binding energies of tubulin dimers covered by the severing enzyme.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9408683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid prediction of lab-grown tissue properties using deep learning","authors":"Allison E. Andrews, H. Dickinson, J. Hague","doi":"10.48550/arXiv.2303.18017","DOIUrl":"https://doi.org/10.48550/arXiv.2303.18017","url":null,"abstract":"The interactions between cells and the extracellular matrix are vital for the self-organisation of tissues. In this paper we present proof-of-concept to use machine learning tools to predict the role of this mechanobiology in the self-organisation of cell-laden hydrogels grown in tethered moulds. We develop a process for the automated generation of mould designs with and without key symmetries. We create a large training set with $N=6400$ cases by running detailed biophysical simulations of cell-matrix interactions using the contractile network dipole orientation (CONDOR) model for the self-organisation of cellular hydrogels within these moulds. These are used to train an implementation of the texttt{pix2pix} deep learning model, with an additional $100$ cases that were unseen in the training of the neural network for review and testing of the trained model. Comparison between the predictions of the machine learning technique and the reserved predictions from the biophysical algorithm show that the machine learning algorithm makes excellent predictions. The machine learning algorithm is significantly faster than the biophysical method, opening the possibility of very high throughput rational design of moulds for pharmaceutical testing, regenerative medicine and fundamental studies of biology. Future extensions for scaffolds and 3D bioprinting will open additional applications.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44964745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transfer function approach to understanding periodic forcing of signal transduction networks.","authors":"Nguyen H N Tran,&nbsp;Andrew H A Clayton","doi":"10.1088/1478-3975/acc300","DOIUrl":"https://doi.org/10.1088/1478-3975/acc300","url":null,"abstract":"<p><p>Signal transduction networks are responsible for transferring biochemical signals from the extracellular to the intracellular environment. Understanding the dynamics of these networks helps understand their biological processes. Signals are often delivered in pulses and oscillations. Therefore, understanding the dynamics of these networks under pulsatile and periodic stimuli is useful. One tool to do this is the transfer function. This tutorial outlines the basic theory behind the transfer function approach and walks through some examples of simple signal transduction networks.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9408685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sociogenesis in unbounded space: modelling self-organised cohesive collective motion.","authors":"Zohar Neu, Luca Giuggioli","doi":"10.1088/1478-3975/acc4ff","DOIUrl":"10.1088/1478-3975/acc4ff","url":null,"abstract":"<p><p>Maintaining cohesion between randomly moving agents in unbounded space is an essential functionality for many real-world applications requiring distributed multi-agent systems. We develop a bio-inspired collective movement model in 1D unbounded space to ensure such functionality. Using an internal agent belief to estimate the mesoscopic state of the system, agent motion is coupled to a dynamically self-generated social ranking variable. This coupling between social information and individual movement is exploited to induce spatial self-sorting and produces an adaptive, group-relative coordinate system that stabilises random motion in unbounded space. We investigate the state-space of the model in terms of its key control parameters and find two separate regimes for the system to attain dynamical cohesive states, including a Partial Sensing regime in which the system self-selects nearest-neighbour distances so as to ensure a near-constant mean number of sensed neighbours. Overall, our approach constitutes a novel theoretical development in models of collective movement, as it considers agents who make decisions based on internal representations of their social environment that explicitly take into account spatial variation in a dynamic internal variable.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7616385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9401011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimal metabolic strategies for microbial growth in stationary random environments.","authors":"Anna Paola Muntoni,&nbsp;Andrea De Martino","doi":"10.1088/1478-3975/acc1bc","DOIUrl":"https://doi.org/10.1088/1478-3975/acc1bc","url":null,"abstract":"<p><p>In order to grow in any given environment, bacteria need to collect information about the medium composition and implement suitable growth strategies by adjusting their regulatory and metabolic degrees of freedom. In the standard sense, optimal strategy selection is achieved when bacteria grow at the fastest rate possible in that medium. While this view of optimality is well suited for cells that have perfect knowledge about their surroundings (e.g. nutrient levels), things are more involved in uncertain or fluctuating conditions, especially when changes occur over timescales comparable to (or faster than) those required to organize a response. Information theory however provides recipes for how cells can choose the optimal growth strategy under uncertainty about the stress levels they will face. Here we analyse the theoretically optimal scenarios for a coarse-grained, experiment-inspired model of bacterial metabolism for growth in a medium described by the (static) probability density of a single variable (the 'stress level'). We show that heterogeneity in growth rates consistently emerges as the optimal response when the environment is sufficiently complex and/or when perfect adjustment of metabolic degrees of freedom is not possible (e.g. due to limited resources). In addition, outcomes close to those achievable with unlimited resources are often attained effectively with a modest amount of fine tuning. In other terms, heterogeneous population structures in complex media may be rather robust with respect to the resources available to probe the environment and adjust reaction rates.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9464265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stochasticity may generate coherent motion in bird flocks.","authors":"Andy M Reynolds","doi":"10.1088/1478-3975/acbad7","DOIUrl":"https://doi.org/10.1088/1478-3975/acbad7","url":null,"abstract":"<p><p>Murmurations along with other forms of flocking have come to epitomize collective animal movements. Most studies into these stunning aerial displays have aimed to understand how coherent motion may emerge from simple behavioral rules and behavioral correlations. These studies may now need revision because recently it has been shown that flocking birds, like swarming insects, behave on the average as if they are trapped in elastic potential wells. Here I show, somewhat paradoxically, how coherent motion can be generated by variations in the intensity of multiplicative noise which causes the shape of a potential well to change, thereby shifting the positions and strengths of centres of attraction. Each bird, irrespective of its position in the flock will respond in a similar way to such changes, giving the impression that the flock behaves as one, and typically resulting in scale-free correlations. I thereby show how correlations can be an emergent property of noisy, confining potential wells. I also show how such wells can lead to high density borders, a characteristic of flocks, and I show how they can account for the complex patterns of collective escape patterns of starling flocks under predation. I suggest swarming and flocking do not constitute two distinctly different kinds of collective behavior but rather that insects are residing in relatively stable potential wells whilst birds are residing in unstable potential wells. It is shown how, dependent upon individual perceptual capabilities, bird flocks can be poised at criticality.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9079811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Swarm formation as backward diffusion.","authors":"Andy M Reynolds,&nbsp;Nicholas T Ouellette","doi":"10.1088/1478-3975/acb986","DOIUrl":"https://doi.org/10.1088/1478-3975/acb986","url":null,"abstract":"<p><p>Considerable progress has been made in understanding insect swarms-forms of collective animal behaviour that unlike bird flocks, fish schools and animal herds do not possess global order. Nonetheless, little is known about swarm formation. Here we posit a mechanism for the formation of insect swarms that is consistent with recent empirical observations reported by (Patel and Ouellette 2022). It correctly predicts new features of swarm formation that have not been reported on previously. Our simple analytically tractable model shows how harmonic potential wells, a characteristic feature of swarming, and so swarm cohesion, arise from diffusion and local fission-fusion dynamics and how, in accord with observations, these wells deepen over time. The overall form of these potential wells is predicted to depend on the number and spatial distribution of all individuals, making them manifestly a collective phenomenon. Finally, swarms are predicted to 'cool' (that is, condense) as they form.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9079803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correlation between speed and turning naturally arises for sparsely sampled cell movements.","authors":"Vitaly V Ganusov, Viktor S Zenkov, Barun Majumder","doi":"10.1088/1478-3975/acb18c","DOIUrl":"10.1088/1478-3975/acb18c","url":null,"abstract":"<p><p>Mechanisms regulating cell movement are not fully understood. One feature of cell movement that determines how far cells displace from an initial position is persistence, the ability to perform movements in a direction similar to the previous movement direction. Persistence is thus determined by turning angles (TA) between two sequential displacements and can be characterized by an average TA or persistence time. Recent studies documenting T cell movement in zebrafish found that a cell's average speed and average TA are negatively correlated, suggesting a fundamental cell-intrinsic program whereby cells with a lower TA (and larger persistence time) are intrinsically faster (or faster cells turn less). In this paper we confirm the existence of the correlation between turning and speed for six different datasets on 3D movement of CD8 T cells in murine lymph nodes or liver. Interestingly, the negative correlation between TA and speed was observed in experiments in which liver-localized CD8 T cells rapidly displace due to floating with the blood flow, suggesting that other mechanisms besides cell-intrinsic program may be at play. By simulating correlated random walks using two different frameworks (one based on the von Mises-Fisher (vMF) distribution and another based on the Ornstein-Uhlenbeck (OU) process) we show that the negative correlation between speed and turning naturally arises when cell trajectories are sub-sampled, i.e. when the frequency of sampling is lower than frequency at which cells typically make movements. This effect is strongest when the sampling frequency is of the order of magnitude of the inverse of persistence time of cells and when cells vary in persistence time. The effect arises in part due to the sensitivity of estimated cell speeds to the frequency of imaging whereby less frequent imaging results in slower speeds. Interestingly, by using estimated persistence times for cells in two of our datasets and simulating cell movements using the OU process, we could partially reproduce the experimentally observed correlation between TA and speed without a cell-intrinsic program linking the two processes. Our results thus suggest that sub-sampling may contribute to (and perhaps fully explains) the observed correlation between speed and turning at least for some cell trajectory data and emphasize the role of sampling frequency in the inference of critical cellular parameters of cell motility such as speeds.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9918869/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9078931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}