scholarly journals Universal constraints on selection strength in lineage trees

2020 ◽  
Author(s):  
Arthur Genthon ◽  
David Lacoste
Keyword(s):  
Natural Selection ◽  
Upper Bound ◽  
Fitness Landscape ◽  
Time Lapse ◽  
Jensen Inequality ◽  
Phenotypic Trait ◽  
Stochastic Thermodynamics ◽  
Growing Cell ◽  
The Difference ◽  
Lineage Trees

We obtain general inequalities constraining the difference between the average of an arbitrary function of a phenotypic trait, which includes the fitness landscape of the trait itself, in the presence or in the absence of natural selection. These inequalities imply bounds on the strength of selection, which can be measured from the statistics of traits or divisions along lineages. The upper bound is related to recent generalizations of linear response relations in Stochastic Thermodynamics, and is reminiscent of the fundamental theorem of Natural selection of R. Fisher and of its generalization by Price. The lower bound follows from recent improvements on Jensen inequality and is typically less tight than the upper bound. We illustrate our results using numerical simulations of growing cell colonies and with experimental data of time-lapse microscopy experiments of bacteria cell colonies.

scholarly journals Fluctuation relations and fitness landscapes of growing cell populations

2020 ◽  
Author(s):  
Arthur Genthon ◽  
David Lacoste
Keyword(s):  
Fitness Landscape ◽  
Size Control ◽  
Phenotypic Trait ◽  
Symmetry Relation ◽  
General Symmetry ◽  
Fluctuation Relations ◽  
Growing Cell ◽  
Fluctuation Relation ◽  
The Mean ◽  
Size Controlled

AbstractWe construct a pathwise formulation of a growing population of cells, based on two different samplings of lineages within the population, namely the forward and backward samplings. We show that a general symmetry relation, called fluctuation relation relates these two samplings, independently of the model used to generate divisions and growth in the cell population. Known models of cell size control are studied with a formalism based on path integrals or on operators. We investigate some consequences of this fluctuation relation, which constrains the distributions of the number of cell divisions and leads to inequalities between the mean number of divisions and the doubling time of the population. We finally study the concept of fitness landscape, which quantifies the correlations between a phenotypic trait of interest and the number of divisions. We obtain explicit results when the trait is the age or the size, for age and size-controlled models.

Elastic inverse scattering for fluid variation with time-lapse seismic data

Geophysics ◽  
2015 ◽  
Vol 80 (2) ◽  
pp. WA61-WA67 ◽  
Author(s):  
Zhaoyun Zong ◽  
Xingyao Yin ◽  
Guochen Wu ◽  
Zhiping Wu
Keyword(s):  
Shear Modulus ◽  
Inverse Scattering ◽  
Seismic Data ◽  
Scattering Theory ◽  
Time Lapse ◽  
Monitoring Data ◽  
Prestack Inversion ◽  
Fluid Factor ◽  
Reference Medium ◽  
The Difference

Elastic inverse-scattering theory has been extended for fluid discrimination using the time-lapse seismic data. The fluid factor, shear modulus, and density are used to parameterize the reference medium and the monitoring medium, and the fluid factor works as the hydrocarbon indicator. The baseline medium is, in the conception of elastic scattering theory, the reference medium, and the monitoring medium is corresponding to the perturbed medium. The difference in the earth properties between the monitoring medium and the baseline medium is taken as the variation in the properties between the reference medium and perturbed medium. The baseline and monitoring data correspond to the background wavefields and measured full fields, respectively. And the variation between the baseline data and monitoring data is taken as the scattered wavefields. Under the above hypothesis, we derived a linearized and qualitative approximation of the reflectivity variation in terms of the changes of fluid factor, shear modulus, and density with the perturbation theory. Incorporating the effect of the wavelet into the reflectivity approximation as the forward solver, we determined a practical prestack inversion approach in a Bayesian scheme to estimate the fluid factor, shear modulus, and density changes directly with the time-lapse seismic data. We evaluated the examples revealing that the proposed approach rendered the estimation of the fluid factor, shear modulus, and density changes stably, even with moderate noise.

scholarly journals Refinements of the Lower Bounds of the Jensen Functional

2011 ◽  
Vol 2011 ◽  
pp. 1-13 ◽  
Author(s):  
Iva Franjić ◽  
Sadia Khalid ◽  
Josip Pečarić
Keyword(s):  
Lower Bounds ◽  
Jensen Inequality ◽  
Left Hand ◽  
Right Hand ◽  
Special Cases ◽  
Jensen Functional ◽  
The Difference ◽  
The Right

The lower bounds of the functional defined as the difference of the right-hand and the left-hand side of the Jensen inequality are studied. Refinements of some previously known results are given by applying results from the theory of majorization. Furthermore, some interesting special cases are considered.

The tradeoff between fit perceptions across recruitment stages by new job seekers

2017 ◽  
Vol 29 (10) ◽  
pp. 2610-2628 ◽  
Author(s):  
Chih-Lun (Alan) Yen
Keyword(s):  
Empirical Support ◽  
Time Lapse ◽  
Job Choice ◽  
Job Seekers ◽  
Recruitment Process ◽  
Content Type ◽  
Face To Face ◽  
Tourism Management ◽  
The Difference ◽  
Recruitment Stages

Purpose The purpose of this study is to explore the tradeoff between person-job (PJ) fit and person-organization (PO) fit by new job seekers across different recruitment stages and the influence on their job choice decisions. Design/methodology/approach A time-lapse research design was adopted with data from a survey over a two-year period of college students majoring in hospitality and tourism management at different recruitment stages (i.e. generating applications, maintaining applicant status and making a job choice). Findings The results suggest that PJ fit has a stronger influence on job choice decisions than PO fit, and both fit perceptions are consistent across recruitment stages. However, the difference between the two fit perceptions may be affected by direct interactions with recruiters at career fairs and interviews. Practical implications When recruiters start interacting with job seekers during the initial stage of the recruitment process, the recruiters are more likely to receive a favorable job choice decision from these potential applicants. Additionally, recruiters should create a positive perception of hiring companies and jobs through career fairs or other face-to-face communications to keep job seekers interested and maintain their applicant status throughout the recruitment stages. Originality/value This paper explores important factors that influence job seekers’ job choice decisions throughout the recruitment process with three main stages, which provides a more holistic overview of the transition of job seekers’ fit perceptions of the job and the organization. It also provides empirical support for current understanding of recruitment issues in the hospitality industry.

scholarly journals Intrinsic linking and knotting in tournaments

2019 ◽  
Vol 28 (12) ◽  
pp. 1950076
Author(s):  
Thomas Fleming ◽  
Joel Foisy
Keyword(s):  
Directed Graph ◽  
Upper Bound ◽  
Directed Edge ◽  
Undirected Graphs ◽  
Oriented Cycle ◽  
Minimum Number ◽  
The Difference

A directed graph [Formula: see text] is intrinsically linked if every embedding of that graph contains a nonsplit link [Formula: see text], where each component of [Formula: see text] is a consistently oriented cycle in [Formula: see text]. A tournament is a directed graph where each pair of vertices is connected by exactly one directed edge. We consider intrinsic linking and knotting in tournaments, and study the minimum number of vertices required for a tournament to have various intrinsic linking or knotting properties. We produce the following bounds: intrinsically linked ([Formula: see text]), intrinsically knotted ([Formula: see text]), intrinsically 3-linked ([Formula: see text]), intrinsically 4-linked ([Formula: see text]), intrinsically 5-linked ([Formula: see text]), intrinsically [Formula: see text]-linked ([Formula: see text]), intrinsically linked with knotted components ([Formula: see text]), and the disjoint linking property ([Formula: see text]). We also introduce the consistency gap, which measures the difference in the order of a graph required for intrinsic [Formula: see text]-linking in tournaments versus undirected graphs. We conjecture the consistency gap to be nondecreasing in [Formula: see text], and provide an upper bound at each [Formula: see text].

scholarly journals On L h , k -Labeling Index of Inverse Graphs Associated with Finite Cyclic Groups

2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
K. Mageshwaran ◽  
G. Kalaimurugan ◽  
Bussakorn Hammachukiattikul ◽  
Vediyappan Govindan ◽  
Ismail Naci Cangul
Keyword(s):  
Cyclic Group ◽  
Upper Bound ◽  
Labeling Index ◽  
Positive Difference ◽  
Cyclic Groups ◽  
Finite Cyclic Group ◽  
Minimum Number ◽  
The Difference ◽  
Radio Labeling

An L h , k -labeling of a graph G = V , E is a function f : V ⟶ 0 , ∞ such that the positive difference between labels of the neighbouring vertices is at least h and the positive difference between the vertices separated by a distance 2 is at least k . The difference between the highest and lowest assigned values is the index of an L h , k -labeling. The minimum number for which the graph admits an L h , k -labeling is called the required possible index of L h , k -labeling of G , and it is denoted by λ k h G . In this paper, we obtain an upper bound for the index of the L h , k -labeling for an inverse graph associated with a finite cyclic group, and we also establish the fact that the upper bound is sharp. Finally, we investigate a relation between L h , k -labeling with radio labeling of an inverse graph associated with a finite cyclic group.

scholarly journals The Evolution of Mass Cell Suicide in Bacterial Warfare

2020 ◽  
Author(s):  
Elisa T. Granato ◽  
Kevin R. Foster
Keyword(s):  
Escherichia Coli ◽  
Natural Selection ◽  
Reproductive Potential ◽  
Time Lapse ◽  
List Type ◽  
E Coli ◽  
Toxin Exposure ◽  
Small Benefit ◽  
Will Self ◽  
Cell Suicide

SUMMARYBehaviours that reliably cause the death of an actor are typically strongly disfavoured by natural selection, and yet many bacteria undergo cell lysis to release anti-competitor toxins [1–4]. This behaviour is most easily explained if only a few cells die to release toxins and help their clonemates, but the number of cells that actually lyse during bacterial warfare is unknown. The challenge is that one cannot distinguish cells that have undergone programmed suicide from those that were simply killed by a competitor’s toxin. We developed a two-colour fluorescence reporter assay in Escherichia coli to overcome this problem. Surprisingly, this revealed conditions where nearly all cells undergo programmed lysis. Adding a DNA-damaging toxin (DNase colicin) to a focal strain causes it to engage in mass cell suicide where around 85% of cells lyse to release their own toxin. Time-lapse 3D confocal microscopy revealed that self-lysis occurs at even higher frequencies (~94%) at the interface between competing colonies. We sought to understand how such high levels of cell suicide could be favoured by natural selection. Exposing E. coli that do not perform lysis to the DNase colicin revealed that mass lysis only occurs when cells are going to die anyway from toxin exposure. From an evolutionary perspective, this renders the behaviour cost-free as these cells have zero reproductive potential. This explains how mass cell suicide can evolve, as any small benefit to surviving clonemates can lead to the strategy being favoured by natural selection. Our findings have strong parallels to the suicidal attacks of social insects [5–8], which are also performed by individuals with low reproductive potential, suggesting convergent evolution in these very different organisms.HIGHLIGHTSA novel assay can detect Escherichia coli undergoing cell suicide to release toxinsWe quantified the frequency of suicidal self-lysis during competitionsUnder some conditions, nearly all cells will self-lyse to release toxinsSelf-lysis makes evolutionary sense as cells will die anyway from competitors’ toxins

scholarly journals Evolution of gene regulatory networks by means of selection and random genetic drift

2018 ◽  
Author(s):  
Antonios Kioukis ◽  
Pavlos Pavlidis
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Genetic Drift ◽  
Regulatory Networks ◽  
Fitness Landscape ◽  
Random Genetic Drift ◽  
Maturation Period ◽  
Evolutionary Forces ◽  
Gene Regulatory

The evolution of a population by means of genetic drift and natural selection operating on a gene regulatory network (GRN) of an individual has not been scrutinized in depth. Thus, the relative importance of various evolutionary forces and processes on shaping genetic variability in GRNs is understudied. Furthermore, it is not known if existing tools that identify recent and strong positive selection from genomic sequences, in simple models of evolution, can detect recent positive selection when it operates on GRNs. Here, we propose a simulation framework, called EvoNET, that simulates forward-in-time the evolution of GRNs in a population. Since the population size is finite, random genetic drift is explicitly applied. The fitness of a mutation is not constant, but we evaluate the fitness of each individual by measuring its genetic distance from an optimal genotype. Mutations and recombination may take place from generation to generation, modifying the genotypic composition of the population. Each individual goes through a maturation period, where its GRN reaches equilibrium. At the next step, individuals compete to produce the next generation. As time progresses, the beneficial genotypes push the population higher in the fitness landscape. We examine properties of the GRN evolution such as robustness against the deleterious effect of mutations and the role of genetic drift. We confirm classical results from Andreas Wagner’s work that GRNs show robustness against mutations and we provide new results regarding the interplay between random genetic drift and natural selection.

scholarly journals Research Advance: Extending chemical perturbations of the Ubiquitin fitness landscape in a classroom setting

2017 ◽  
Author(s):  
David Mavor ◽  
Kyle A. Barlow ◽  
Daniel Asarnow ◽  
Yuliya Birman ◽  
Derek Britain ◽  
...  
Keyword(s):  
Fitness Landscape ◽  
Nickel Chloride ◽  
Cobalt Acetate ◽  
Laboratory Culture ◽  
Culture Conditions ◽  
Sequence Conservation ◽  
Classroom Setting ◽  
Evolutionary Time ◽  
The Difference ◽  
Chemical Conditions

AbstractAlthough the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it is highly tolerant to mutation during selection experiments performed in the laboratory. We have proposed that this discrepancy results from the difference between fitness under laboratory culture conditions and the selective pressures in changing environments over evolutionary time scales. Building on our previous work (Mavor et al 2016), we used deep mutational scanning to determine how twelve new chemicals (3-Amino-1,2,4-triazole, 5-fluorocytosine, Amphotericin B, CaCl2, Cerulenin, Cobalt Acetate, Menadione, Nickel Chloride, p-fluorophenylalanine, Rapamycin, Tamoxifen, and Tunicamycin) reveal novel mutational sensitivities of ubiquitin residues. We found sensitization of Lys63 in eight new conditions. In total, our experiments have uncovered a sensitizing condition for every position in Ub except Ser57 and Gln62. By determining the Ubiquitin fitness landscape under different chemical constraints, our work helps to resolve the inconsistencies between deep mutational scanning experiments and sequence conservation over evolutionary timescales.Builds onMavor D, Barlow KA, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate R, Green EM, Hulce KR, Ji W, Kenner LR, Mensa B, Morinishi LS, Moss SM, Mravic M, Muir RK, Niekamp S, Nnadi CI, Palovcak E, Poss EM, Ross TD, Salcedo E, See S, Subramaniam M, Wong AW, Li J, Thorn KS, Conchúir SÓ, Roscoe BP, Chow ED, DeRisi JL, Kortemme T, Bolon DN, Fraser JS. Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting. eLife. 2016.Impact StatementWe organized a project-based course that used deep mutational scanning in multiple chemical conditions to resolve the inconsistencies between tolerance to mutations in laboratory conditions and sequence conservation over evolutionary timescales.

Revisiting Hull's Evolutionary Model of Science

2021 ◽  
Vol 13 (2) ◽  
pp. 145-152
Author(s):  
Mohammad Mahdi Hatef ◽  
Keyword(s):  
Natural Selection ◽  
Selection Process ◽  
Biological Evolution ◽  
Evolutionary Model ◽  
Scientific Change ◽  
Evolutionary Models ◽  
Natural Evolution ◽  
The Difference

Evolutionary models for scientific change are generally based on an analogy between scientific changes and biological evolution. Some dissimilarity cases, however, challenge this analogy. An issue discussed in this essay is that despite natural evolution, which is currently considered to be non-globally progressive, science is a phenomenon that we understand as globally progressive. David Hull's solution to this disanalogy is to trace the difference back to their environments, in which processes of natural selection and conceptual selection occur. I will provide two arguments against this solution, showing that Hull's formulation of natural selection prohibits him from removing the environment from the selection process. Then I point to a related tension in his theory, between realism and externalism in science, and give some suggestions to solve these tensions.

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