scholarly journals Mutation rate variability as a driving force in adaptive evolution

2018 ◽  
Author(s):  
Dalit Engelhardt ◽  
Eugene I. Shakhnovich

Mutation rate is a key determinant of the pace as well as outcome of evolution, and variability in this rate has been shown in different scenarios to play a key role in evolutionary adaptation and resistance evolution under stress. Here we investigate the dynamics of resistance fixation in a bacterial population with variable mutation rates and show that evolutionary outcomes are most sensitive to mutation rate variations when the population is subject to environmental and demographic conditions that suppress the evolutionary advantage of high-fitness subpopulations. By directly mapping a molecular-level biophysical fitness function to the system-level dynamics of the population we show that both low and very high, but not intermediate, levels of stress result in a disproportionate effect of hypermutation on resistance fixation and that traditional definitions of the selection coefficient are insufficient to account for this effect. We demonstrate how this behavior is directly tied to the extent of genetic hitchhiking in the system, the propagation of high-mutation rate cells through association with high-fitness mutations. Our results indicate a substantial role for mutation rate flexibility in the evolution of antibiotic resistance under conditions that present a weak advantage over wildtype to resistant cells.

2006 ◽  
Vol 969 ◽  
Author(s):  
Franck Murray ◽  
François LeCornec ◽  
Serge Bardy ◽  
Catherine Bunel ◽  
Jan Verhoeven ◽  
...  

AbstractThe very large development of home and domestic electronic appliances as well as portable device has led the microelectronics industry to evolve in two complimentary directions : “More Moore” with the continuous race towards extremely small dimensions hence the development of SoCs (System on Chip) and more recently a new direction that we could name “More than Moore” with the integration of devices that were laying outside the chips and here the creation of SiPs (System in Package).These two approaches are not in competition one with the other: the paper will show some examples of integrated nano systems that use several SoCs.The technology we have developed is called Silicon Based System in Package. The first products using this technology are now in volume production and used mainly in the field of wireless communications.This new technology relies on four pillars. Passive integration is the first. Very efficient and high quality factor capacitors and inductors have been integrated, allowing the creation of complete modules including active devices, filters and decoupling capacitors. High-density MOS capacitors with 1-1000 nF capacitance, and as high values as 25-250+ nF/mm2 specific capacitance have been fabricated in macroporous Si-wafers, containing over 1 billion macropores. Typically an ESR less than 100 mÙ and an ESL less than 25 pH were found for capacitors over 10 nF. This novel concept is an important step forward in improving the stability of power-amplifier modules by replacing conventional SMD technology.Whereas generations with capacitors density of up to 100 nF/mm2 will be using “conventional” materials and structures, the next steps in the roadmap will call for new 3D structures and materials such as high-k dielectrics.The second element is advanced packaging. New technologies, such as the assembly of Silicon chips onto other Silicon chips, also named “double flip chip” have been developed. This has been made possible thanks to the combination of the most advanced microbumping and die placement techniques. In addition to a tremendous reduction of size (up to a factor of 10 to 20) these techniques have also brought a better repeatability of system performance.The third element has been the development of design tools that allow a seamless system design for engineers used to IC design tools and flows. Our Design Environment allows co design of multiple technologies chips and their integration in a single system. This IC-like Design Environment has contributed a lot to the adoption of the technology.Testing is the fourth element and is one of the economical enablers of the technology. The key words are: “known good die”, RF test, system test? Some innovative RF probing and full on wafer subsystem test will be shown. Even though efficient test is not vital for the technical feasibility of this system integration, it becomes very quickly one of the most important enablers, especially when we deal with very high volumes of production. The conclusion of the paper will be an open door to the future. Some innovations like the integration of light or even energy storage inside our SiPs will be presented.


1990 ◽  
Vol 180 ◽  
Author(s):  
P. C. Cagle ◽  
W. G. Klemperer ◽  
C. A. Simmons

ABSTRACTSol-gel polymerization of [Si8O12](OCH3)8 in CH3CN under neutral conditions yields very high surface area (SBET > 900 m2/g) xerogels. This property is seen to result from the structure of the gel on the molecular level. According to N2 adsorption studies, model studies, and TEM studies, the large size and rigidity of the cubic [Si8O12] core structure leads to polymers whose rigidity inhibits extensive crosslinking of the type observed in orthosilicate derived xerogels.


1998 ◽  
Vol 09 (04) ◽  
pp. 555-571 ◽  
Author(s):  
F. Bagnoli ◽  
M. Bezzi

In this paper we consider a microscopic model of a simple ecosystem. The basic ingredients of this model are individuals, and both the phenotypic and genotypic levels are taken in account. The model is based on a long range cellular automaton (CA); introducing simple interactions between the individuals, we get some of the complex collective behaviors observed in a real ecosystem. Since our fitness function is smooth, the model does not exhibit the error threshold transition; on the other hand the size of total population is not kept constant, and the mutational meltdown transition is present. We study the effects of competition between genetically similar individuals and how it can lead to species formation. This speciation transition does not depend on the mutation rate. We present also an analytical approximation of the model.


F1000Research ◽  
2013 ◽  
Vol 2 ◽  
pp. 139
Author(s):  
Maxinder S Kanwal ◽  
Avinash S Ramesh ◽  
Lauren A Huang

The fields of molecular biology and neurobiology have advanced rapidly over the last two decades. These advances have resulted in the development of large proteomic and genetic databases that need to be searched for the prediction, early detection and treatment of neuropathologies and other genetic disorders. This need, in turn, has pushed the development of novel computational algorithms that are critical for searching genetic databases. One successful approach has been to use artificial intelligence and pattern recognition algorithms, such as neural networks and optimization algorithms (e.g. genetic algorithms). The focus of this paper is on optimizing the design of genetic algorithms by using an adaptive mutation rate based on the fitness function of passing generations. We propose a novel pseudo-derivative based mutation rate operator designed to allow a genetic algorithm to escape local optima and successfully continue to the global optimum. Once proven successful, this algorithm can be implemented to solve real problems in neurology and bioinformatics. As a first step towards this goal, we tested our algorithm on two 3-dimensional surfaces with multiple local optima, but only one global optimum, as well as on the N-queens problem, an applied problem in which the function that maps the curve is implicit. For all tests, the adaptive mutation rate allowed the genetic algorithm to find the global optimal solution, performing significantly better than other search methods, including genetic algorithms that implement fixed mutation rates.


Author(s):  
Michael Sheetz

AbstractThe contraction-relaxation cycle of the heart is one of the most robust mechanical systems in the body that adapts rapidly to the body’s needs by changing mechanical parameters. In many respects, we can consider the cardiac system as a complex machine and can use engineering approaches to describe its function. The classical physiology of the heart also focused on understanding function but the new molecular level tools in light microscopy and nanoengineering now enable a deeper understanding of the physiology. The field of mechanobiology has emerged with a focus on how mechanical activity alters biological systems at the molecular level and how those systems in turn control mechanical parameters. In the case of mechanical activity, there are clearly benefits of exercise for the heart, for cancer patients, and for aging but we do not understand the links at a molecular level. Why does regular exercise benefit the heart? We have some preliminary clues at a molecular level about the benefits of physical activity in the cases of cancer and aging; however, there is less known about how exercise affects cardiovascular performance. Unlike the omics approaches which generally link proteins to processes, a mechanobiological understanding of a process explains how forces and mechanical activity will regulate the process through modifications of protein activities. In other words, mechanical activity is an essential component of most biological systems that is transduced into biochemical changes in protein activity. Further, it follows logically that if a mechanical parameter of the cardiac system is typically controlled, then cellular mechanosensing systems must be able to directly or indirectly measure that parameter. The challenge is to understand how changes in activity of the heart are controlled in the short term and then how the system adapts to the integrated level of activity over the longer term. By way of introduction to molecular mechanobiology, I will present examples of mechanosensing from the molecular to the cellular scale and how they may be integrated at the cell and tissue levels. An important element of Mechanobiology at the system level is the physiological state of the cell: i.e., the cell in a senescent state, a cancer state, or a normal cell state (Sheetz 2019). The background for the mechanobiological approach is discussed in “The Cell as a Machine” (Sheetz and Yu, Cambridge Univ Press, 2018), which considers cell states and the molecular systems underlying the important cellular functions. A major challenge in mechanobiology is the understanding of the transduction of mechanical activity into changes in cell function. Of particular relevance here is the benefit of exercise to cardiac performance. This has been seen in many cases and there are a variety of factors that contribute. Further, exercise will benefit cancer patients and will reverse some of the adverse effects of aging. Exercise will cause increased cardiac activity that will be sensed by many mechanosensory systems from a molecular to a cellular level both in the heart and in the vasculature. At a molecular level in cardiac systems, proteins are able to measure stress and strain and to generate appropriate signals of the magnitude of stress and strain that can regulate the cellular contractility and other parameters. The protein sensors are generally passive systems that give a transient measure of local parameters such as the stress at cell-cell junctions during contraction and the strain of the sarcomeres during relaxation. Large stresses at the junctions can activate signaling systems that can reduce contractility or over time activate remodeling of the junctions to better support larger stresses. The proteins involved and their sensory mechanisms are not known currently; however, the mechanosensitive channel, Piezo1, has been implicated in the transduction process in the vasculature (Beech 2018). In the case of strain sensors, large stretches of titin during relaxation can unfold more titin domains that can send signals to the cell. Two different mechanisms of strain sensing are likely in titin. The titin kinase domain is activated by strain but the substrates of the kinase are not know in vivo (Linke 2018). In the backbone of titin are many Ig domains that unfold at different forces and unfolding could cause the binding of proteins that would then activate enzymatic pathways to alter the contractile cycle to give the proper level of strain (Ait-Mou et al. 2017; Granzier et al. 2014; Granzier et al. 2009). The cell-matrix adhesion protein, talin, has eleven cryptic binding sites for another adhesion protein, vinculin, that are revealed by the unfolding of domains in the talin molecule (Yao et al. 2016). Since some domains unfold at lower forces than others, small strains will preferentially unfold those domains, making the system an excellent sensor of the extent of stretch as expected for titin. Because there is an ordered array of many titin molecules, the sensing of strain can be very sensitive to small changes in sarcomere length. Needless to say, titin is only one part of the regulatory system that controls sarcomere length. As one goes more deeply into the working of the system, it is evident that many additional mechanosensory elements are involved in maintaining a functioning cardiac system.


2001 ◽  
Vol 268 (1471) ◽  
pp. 1001-1005 ◽  
Author(s):  
H. Sh. Weinberg ◽  
A. B. Korol ◽  
V. M. Kirzhner ◽  
A. Avivi ◽  
T. Fahima ◽  
...  

1987 ◽  
Vol 8 (12) ◽  
pp. 582-585 ◽  
Author(s):  
O.K. Kwon ◽  
B.W. Langley ◽  
R.F.W. Pease ◽  
M.R. Beasley
Keyword(s):  

2012 ◽  
Vol 110 (1) ◽  
pp. 222-227 ◽  
Author(s):  
S. Wielgoss ◽  
J. E. Barrick ◽  
O. Tenaillon ◽  
M. J. Wiser ◽  
W. J. Dittmar ◽  
...  

1933 ◽  
Vol 9 (3) ◽  
pp. 261-264 ◽  
Author(s):  
F. H. Peto

The recent discovery by Navashin (3), that the chromosomal mutation rate in Crepis was influenced by aging of the seed, has been corroborated by observations on the mutation rate of corn plants grown from seed of various ages.A very high chromosomal mutation rate in barley was induced by heat treatments of seed under various conditions of humidity. The most common type of aberration resulting from these treatments appeared to be fracture of the chromosomes either at the attachment constriction, the secondary constriction or the point of attachment of the trabants. The reattachment of fragments to other chromosomes was observed in two instances.Considerable importance is attached to the discovery that a large proportion of the mutant cells are eliminated during the growth of the plant. The principle that only the fittest survive seems equally true of cells as of individuals and groups of plants or animals.


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