Hasil untuk "q-bio.SC"

Luca Quaroni

Hydrogen cations, or protons, provide the medium by which energy is stored and converted in biological systems. Such pre-eminence relies on the interplay between interfacial and bulk chemical transformations, according to mechanisms that are shared by organisms in all phyla of life. The present work provides an introduction to the fundamental aspects of biological energy management by focusing on the relationship between vectorial proton flows and the geometry of energy producing organelles in eukaryotes. The leading models of proton-mediated energy conversion, the delocalised proton (or chemiosmotic) model and the localised proton model, are presented in a complementary perspective. While the delocalised model provides a description that relies on equilibrium thermodynamics, the localised model addresses dynamic processes that are better described using out-of-equilibrium thermodynamics. The work reviews the salient aspects of such mechanisms, traces the development of our present understanding, and highlights areas that are open to future developments.

Juraj Szavits-Nossan, Ramon Grima

Stochastic models of gene expression are typically formulated using the chemical master equation, which can be solved exactly or approximately using a repertoire of analytical methods. Here, we provide a tutorial review of an alternative approach based on queueing theory that has rarely been used in the literature of gene expression. We discuss the interpretation of six types of infinite server queues from the angle of stochastic single-cell biology and provide analytical expressions for the stationary and non-stationary distributions and/or moments of mRNA/protein numbers, and bounds on the Fano factor. This approach may enable the solution of complex models which have hitherto evaded analytical solution.

Mario Josupeit, Joachim Krug

Motivated by recent experiments on an antibiotic resistance gene, we investigate genetic interactions between synonymous mutations in the framework of exclusion models of translation. We show that the range of possible interactions is markedly different depending on whether translation efficiency is assumed to be proportional to ribosome current or ribosome speed. In the first case every mutational effect has a definite sign that is independent of genetic background, whereas in the second case the effect-sign can vary depending on the presence of other mutations. The latter result is demonstrated using configurations of multiple translational bottlenecks induced by slow codons.

Ina Humpert, Danila Di Meo, Andreas W. Püschel et al.

The processes that determine the establishment of the complex morphology of neurons during development are still poorly understood. We present experiments that use live imaging to examine the role of vesicle transport and propose a lattice-based model that shows symmetry breaking features similar to a neuron during its polarization. In a otherwise symmetric situation our model predicts that a difference in neurite length increases the growth potential of the longer neurite indicating that vesicle transport can be regarded as a major factor in neurite growth.

Pascal S. Rogalla, Timothy J. Rudge, Luca Ciandrini

The number of ribosomes in a cell is considered as limiting, and gene expression is thus largely determined by their cellular concentration. In this work we develop a toy model to study the trade-off between the ribosomal supply and the demand of the translation machinery, dictated by the composition of the transcript pool. Our equilibrium framework is useful to highlight qualitative behaviours and new means of gene expression regulation determined by the fine balance of this trade-off. We also speculate on the possible impact of these mechanisms on cellular physiology.

William Bialek, Thomas Gregor, Gašper Tkačik

There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but interacting sites are embedded in a liquid droplet of proteins which condenses out of the surrounding solution. We argue that droplet-mediated interactions can account for crucial features of gene regulation only if the droplet is poised at a non-generic point in its phase diagram. We explore a minimal model that embodies this idea, show that this model has a natural mechanism for self-tuning, and suggest direct experimental tests.

Sean M. Murray, Martin Howard

We review the key role played by mathematical modelling in elucidating two centre-finding patterning systems in E. coli: midcell division positioning by the MinCDE system and DNA partitioning by the ParABS system. We focus particularly on how, despite much experimental effort, these systems were simply too complex to unravel by experiments alone, and instead required key injections of quantitative, mathematical thinking. We conclude the review by analysing the frequency of modelling approaches in microbiology over time. We find that while such methods are increasing in popularity, they are still probably heavily under-utilised for optimal progress on complex biological questions.

R. Agarwal

Kelath Murali Manoj, Daniel Andrew Gideon, Vivian David Jacob

Thermogenesis by uncoupling protein (UCP) has traditionally been explained as the dissipation of proton gradient across the inner mitochondrial membrane into heat. Herein, we propose that UCPs, aided by the large pore and positively charged amino acids of suspended loops, enable protonation and transport of DROS. Thus, UCP facilitates DROS-reactions amongst themselves, forming water and liberating heat around the inner mitochondrial membrane. Thereby, the simple murburn scheme for biothermogenesis integrates structural information of UCP with its attributed physiological function.

Maria P. Kochugaeva, Alexey A. Shvets, Anatoly B. Kolomeisky

All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of investigating dynamics of protein-DNA interactions, which govern all major biological processes. It is based on a first-passage analysis of biochemical and biophysical transitions, and it provides a fully analytic description of the processes. Our approach is explained for the case of a single protein searching for a specific binding site on DNA. In addition, the application of the method to investigations of the effect of DNA sequence heterogeneity, and the role multiple targets and traps in the protein search dynamics are discussed.

L. Collot, V. Lefèvre-Seguin, M. Brune et al.

K. Folkers, P. Langsjoen, R. Willis et al.

K. Enqvist, J. McDonald

We show that Q-balls naturally exist in the Minimal Supersymmetric Standard Model (MSSM) with soft SUSY breaking terms of the minimal N = 1 SUGRA type. These are associated with the F-and D-flat directions of the scalar potential once radiative corrections are taken into account. We consider two distinct cases, corresponding to the "HuL" (slepton) direction with L-balls and the "u(c)d(c)d(c)" and "u(c)u(c)d(c)e(c)" (squark) directions with B-balls. The L-ball always has a small charge, typically of the order of 1000, whilst the B-ball can have an arbitrarily large charge, which, when created cosmologically by the collapse of an unstable Affleck-Dine condensate, is likely to be greater than 10(14). The B-balls typically decay at temperatures less than that of the electroweak phase transition, leading to a novel version of Affleck-Dine baryogenesis, in which the B asymmetry comes from Q-ball decay rather than condensate decay. This mechanism can work even in the presence of additional L violating interactions or B-L conservation, which would rule out conventional Affleck-Dine baryogenesis.

Gao-De Li

This paper proposes that eukaryotic cells, under severe genotoxic stress, can commit genoautotomy (genome 'self-injury') that involves cutting and releasing single-stranded DNA (ssDNA) fragments from double-stranded DNA and leaving ssDNA gaps in the genome. The ssDNA gaps could be easily and precisely repaired later. The released ssDNA fragments may play some role in the regulation of cell cycle progression. Taken together, genoautotomy causes limited nonlethal DNA damage, but prevents the whole genome from lethal damage, and thus should be deemed as a eukaryotic cellular defence response to genotoxic stress.

Anjana Badrinarayanan, Mark C. Leake

The SMC complex, MukBEF, is important for chromosome organization and segregation in Escherichia coli. Fluorescently tagged MukBEF forms distinct spots (or 'foci') in the cell, where it is thought to carry out most of its chromosome associated activities. This chapter outlines the technique of Fluorescence Recovery After Photobleaching (FRAP) as a method to study the properties of YFP-tagged MukB in fluorescent foci. This method can provide important insight into the dynamics of MukB on DNA and be used to study its biochemical properties in vivo.

M. El-Tawil, S. N. Huseen

Emmanouil Angelakis, D. Raoult

David S. Weiss, Vahid Sandoghdar, J. Hare et al.

C. Castellano, M. A. Muñoz, R. Pastor-Satorras

We introduce a nonlinear variant of the voter model, the q-voter model, in which q neighbors (with possible repetition) are consulted for a voter to change opinion. If the q neighbors agree, the voter takes their opinion; if they do not have a unanimous opinion, still a voter can flip its state with probability epsilon . We solve the model on a fully connected network (i.e., in mean field) and compute the exit probability as well as the average time to reach consensus by employing the backward Fokker-Planck formalism and scaling arguments. We analyze the results in the perspective of a recently proposed Langevin equation aimed at describing generic phase transitions in systems with two ( Z2-symmetric) absorbing states. In particular, by deriving explicitly the coefficients of such a Langevin equation as a function of the microscopic flipping probabilities, we find that in mean field the q-voter model exhibits a disordered phase for high epsilon and an ordered one for low epsilon with three possible ways to go from one to the other: (i) a unique (generalized-voter-like) transition, (ii) a series of two consecutive transitions, one (Ising-like) in which the Z2 symmetry is broken and a separate one (in the directed-percolation class) in which the system falls into an absorbing state, and (iii) a series of two transitions, including an intermediate regime in which the final state depends on initial conditions. This third (so far unexplored) scenario, in which a type of ordering dynamics emerges, is rationalized and found to be specific of mean field, i.e., fluctuations are explicitly shown to wash it out in spatially extended systems.

S. Ramlo, I. Newman

In volume 32 of this journal, Paul Stenner suggests that Stephenson was resistant to Q methodology being placed within other theoretical frameworks. Yet in this same piece, Stenner states that it is time for Q methodology to be brought into a greater dialogue with contemporary social theory and research practice. This article seeks to demonstrate how Qfits into the contemporaryresearch practice ofmixed methods and argues that this perspective is not in conflict with Stephenson's positiQns on Q as a methodology. Further, our position reflects recent calls for the developmentofnew techniques and procedures to be used in mixed-methods research. Those making the call will find interest in what Q has to offer the social and behavioral sciences now, 75 years after it emerged in Stephenson's 1935 letter to Nature, and even though the term mixed-methodsresearch has only emerged in last couple of decades. Q methodology is shown to fit well methodologically into the mixed-methods continuum as described by prominent mixed-methods scholars, which further supports a position that Q represents a mixed research methodology.