scholarly journals Adaptive evolution of nontransitive fitness in yeast

2019 ◽  
Author(s):  
Sean W. Buskirk ◽  
Alecia B. Rokes ◽  
Gregory I. Lang
Keyword(s):  
Adaptive Evolution ◽  
Initial Conditions ◽  
Nuclear Genome ◽  
Selective Advantage ◽  
Viral Genomes ◽  
Adaptive Mutations ◽  
Extant Species ◽  
Evolutionary Success ◽  
Intracellular Virus

AbstractNontransitivity – commonly illustrated by the rock-paper-scissors game – is well documented among extant species as a contributor to biodiversity. However, it is unclear if nontransitive interactions also arise by way of genealogical succession, and if so, through what mechanisms. Here we identify a nontransitive evolutionary sequence in the context of yeast experimental evolution in which a 1,000-generation evolved clone outcompetes a recent ancestor but loses in direct competition with a distant ancestor. We show that nontransitivity arises due to the combined forces of adaptation in the yeast nuclear genome and the stepwise deterioration of an intracellular virus. We show that, given the initial conditions of the experiment, this outcome likely to arise: nearly half of all populations experience multilevel selection, fixing adaptive mutations in both the nuclear and viral genomes. In contrast to conventional views of virus-host coevolution, we find no evidence that viral mutations (including loss of the virus) increase the fitness of the host. Instead, the evolutionary success of evolved viral variants results from their selective advantage over viral competitors within the context of individual cells. Our results provide the first mechanistic case-study of the adaptive evolution of nontransitivity, in which a series of adaptive replacements produce organisms that are less fit when compared to a distant genealogical ancestor.

scholarly journals Adaptive evolution of nontransitive fitness in yeast

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Sean W Buskirk ◽  
Alecia B Rokes ◽  
Gregory I Lang
Keyword(s):  
Adaptive Evolution ◽  
Nuclear Genome ◽  
Multilevel Selection ◽  
Host Cells ◽  
Viral Genomes ◽  
Adaptive Mutations ◽  
Common Misconception ◽  
Evolution Experiment ◽  
Intracellular Virus

A common misconception is that evolution is a linear 'march of progress', where each organism along a line of descent is more fit than all those that came before it. Rejecting this misconception implies that evolution is nontransitive: a series of adaptive events will, on occasion, produce organisms that are less fit compared to a distant ancestor. Here we identify a nontransitive evolutionary sequence in a 1,000-generation yeast evolution experiment. We show that nontransitivity arises due to adaptation in the yeast nuclear genome combined with the stepwise deterioration of an intracellular virus, which provides an advantage over viral competitors within host cells. Extending our analysis, we find that nearly half of our ~140 populations experience multilevel selection, fixing adaptive mutations in both the nuclear and viral genomes. Our results provide a mechanistic case-study for the adaptive evolution of nontransitivity due to multilevel selection in a 1,000-generation host/virus evolution experiment.

scholarly journals Extended and Unscented Kalman Filtering Applied to a Flexible-Joint Robot with Jerk Estimation

2010 ◽  
Vol 2010 ◽  
pp. 1-14 ◽  
Author(s):  
Mohammad Ali Badamchizadeh ◽  
Iraj Hassanzadeh ◽  
Mehdi Abedinpour Fallah
Keyword(s):  
Initial Conditions ◽  
Covariance Matrices ◽  
Flexible Joints ◽  
Velocity Measurements ◽  
Lagrange Equations ◽  
Robust Nonlinear Control ◽  
Flexible Joint ◽  
Flexible Joint Robots ◽  
Simulation Results

Robust nonlinear control of flexible-joint robots requires that the link position, velocity, acceleration, and jerk be available. In this paper, we derive the dynamic model of a nonlinear flexible-joint robot based on the governing Euler-Lagrange equations and propose extended and unscented Kalman filters to estimate the link acceleration and jerk from position and velocity measurements. Both observers are designed for the same model and run with the same covariance matrices under the same initial conditions. A five-bar linkage robot with revolute flexible joints is considered as a case study. Simulation results verify the effectiveness of the proposed filters.

scholarly journals Simultaneous Parameters Identifiability and Estimation of anE. coliMetabolic Network Model

2015 ◽  
Vol 2015 ◽  
pp. 1-21 ◽  
Author(s):  
Kese Pontes Freitas Alberton ◽  
André Luís Alberton ◽  
Jimena Andrea Di Maggio ◽  
Vanina Gisela Estrada ◽  
María Soledad Díaz ◽  
...  
Keyword(s):  
Experimental Data ◽  
Escherichia Coli ◽  
Metabolic Networks ◽  
Initial Conditions ◽  
Model Fit ◽  
Real Problem ◽  
Kinetic Rates ◽  
K 12 ◽  
Procedure Model

This work proposes a procedure for simultaneous parameters identifiability and estimation in metabolic networks in order to overcome difficulties associated with lack of experimental data and large number of parameters, a common scenario in the modeling of such systems. As case study, the complex real problem of parameters identifiability of theEscherichia coliK-12 W3110 dynamic model was investigated, composed by 18 differential ordinary equations and 35 kinetic rates, containing 125 parameters. With the procedure, model fit was improved for most of the measured metabolites, achieving 58 parameters estimated, including 5 unknown initial conditions. The results indicate that simultaneous parameters identifiability and estimation approach in metabolic networks is appealing, since model fit to the most of measured metabolites was possible even when important measures of intracellular metabolites and good initial estimates of parameters are not available.

scholarly journals Development of dynamic system response curve method for estimating initial conditions of conceptual hydrological models

2018 ◽  
Vol 20 (6) ◽  
pp. 1387-1400
Author(s):  
Yiqun Sun ◽  
Weimin Bao ◽  
Peng Jiang ◽  
Xuying Wang ◽  
Chengmin He ◽  
...  
Keyword(s):  
Dynamic System ◽  
Response Curve ◽  
Initial Conditions ◽  
Model Performance ◽  
System Response ◽  
Hydrological Models ◽  
Flood Prediction ◽  
Ill Posed ◽  
Value Decomposition

Abstract The dynamic system response curve (DSRC) has its origin in correcting model variables of hydrologic models to improve the accuracy of flood prediction. The DSRC method can lead to unstable performance since the least squares (LS) method, employed by DSRC to estimate the errors, often breaks down for ill-posed problems. A previous study has shown that under certain assumptions the DSRC method can be regarded as a specific form of the numerical solution of the Fredholm equation of the first kind, which is a typical ill-posed problem. This paper introduces the truncated singular value decomposition (TSVD) to propose an improved version of the DSRC method (TSVD-DSRC). The proposed method is extended to correct the initial conditions of a conceptual hydrological model. The usefulness of the proposed method is first demonstrated via a synthetic case study where both the perturbed initial conditions, the true initial conditions, and the corrected initial conditions are precisely known. Then the proposed method is used in two real basins. The results measured by two different criteria clearly demonstrate that correcting the initial conditions of hydrological models has significantly improved the model performance. Similar good results are obtained for the real case study.

scholarly journals Computational Design of Sensitized Combustion Chemistry Experiments

2021 ◽  
Vol 7 ◽  
Author(s):  
Cody Ising ◽  
Pedro Rodriguez ◽  
Daniel Lopez ◽  
Jeffrey Santner
Keyword(s):  
Shock Tube ◽  
Initial Conditions ◽  
Computational Design ◽  
Reaction Rates ◽  
Oxidation Reactions ◽  
Combustion Chemistry ◽  
Experimental Conditions ◽  
As Species ◽  
User Friendly

In combustion chemistry experiments, reaction rates are often extracted from complex experiments using detailed models. To aid in this process, experiments are performed such that measurable quantities, such as species concentrations, flame speed, and ignition delay, are sensitive to reaction rates of interest. In this work, a systematic method for determining such sensitized experimental conditions is demonstrated. An open-source python script was created using the Cantera module to simulate thousands of 0D and hundreds of 1D combustion chemistry experiments in parallel across a broad, user-defined range of mixture conditions. The results of the simulation are post-processed to normalize and compare sensitivity values among reactions and across initial conditions for time-varying and steady-state simulations, in order to determine the “most useful” experimental conditions. This software can be utilized by researchers as a fast, user-friendly screening tool to determine the thermodynamic and mixture parameters for an experimental campaign. We demonstrate this software through two case studies comparing results of the 0D script against a shock tube experiment and results of the 1D script against a spherical flame experiment. In the shock tube case study we present mixture conditions compared to those used in the literature to study H + O2 (+M)→HO2(+M). In the flame case study, we present mixture conditions compared to those in the literature to study formyl radical (HCO) decomposition and oxidation reactions. The systematically determined experimental conditions identified in the present work are similar to the conditions chosen in the literature.

scholarly journals SEJARAH, KENDALA DAN HAMBATAN INVESTASI SEKTOR RIIL TERHADAP PERKEMBANGAN EKONOMI MASYARAKAT PESISIR (Studi Kasus Pabrik Pengolahan Ikan)

2013 ◽  
Vol 1 (2) ◽  
Author(s):  
Eddy Mantjoro
Keyword(s):  
Scientific Explanation ◽  
Initial Conditions ◽  
Fishing Effort ◽  
Small Scale ◽  
Processing Plant ◽  
Fish Processing ◽  
Case Study Method ◽  
Processing Industry ◽  
North Sulawesi

Abstract Goals to be achieved through this research are as follows: (1) the scientific explanation about the initial conditions of fishing effort in the area of ​​research in this area is South Minahasa; (2) To obtain information on the historical development of the fish processing industry in North Sulawesi and Minahasa south in particular; (3) To be informed of the obstacles and challenges faced by the fisheries sector investors, especially fish processing timber. This research focuses on one unit of the fish processing industry wooden fish processing plant, and then in the case study method is relevant. The case study method is expected that researchers can examine more detailed and focused on problems experienced by fish processing company. As a consequence the results can not be generalized as like which would otherwise require science. Unless some case studies on the same topic on other companies and the result is the same, the efforts generalizations can be made. However the results of the case study can paint a picture on the history, constraints and barriers to investment that occur in similar industries and other industries. The initial condition of fisheries business investment in South Minahasa in 1995 was still dominated by small-scale businesses, which is limited to household livelihoods of fishermen. How governance is still very traditional in terms of business objectives just to meet daily food needs. Wooden fish processing technology already existed and developed since the year 700 BC in Japan. In Indonesia, especially in North Sulawesi started introduced in 1927 by a Japanese man named Hara Ko. The new investment started in 1971 until now. Investment in fish processing faces many obstacles and challenges, namely (1) the limited market share, (2) Legal certainty is not guaranteed, (3) Investors from outside the region and abroad to invest by holding on minimal information about the culture and traditions of local communities (4 ) morale of local residents very traditional if not arguably worse. (5) The investment policy is supported by the local government level only at the Regent while Assiten level, down to the village more displays of terror and intimidation to investors. Keywords: fish factory, investment, history, constraints, obstacles Abstrak Tujuan yang ingin dicapai melalui penelitian ini ialah sebagai berikut: (1) Penjelasan ilmiah tentang kondisi awal usaha perikanan di wilayah penelitian dalam hal ini Daerah Minahasa Selatan. (2) Memperoleh informasi tentang sejarah perkembangan industri pengolahan ikan di Sulawesi Utara dan Minahasa selatan khususnya. (3) Mendapatkan informasi mengenai kendala dan tantangan yang dihadapi oleh investor bidang perikanan khususnya pengolahan ikan kayu. Penelitian ini berfokus pada satu unit industri pengolahan ikan yakni pabrik pengolahan ikan kayu, maka metode studi kasus di pandang relevan. Metode studi kasus diharapkan peneliti dapat mengkaji lebih rinci dan fokus pada masalah yang dialami oleh perusahan pengolahan ikan. Sebagai konsekwensinya hasil penelitian tidak dapat digeneralisir sebagai layaknya yang di syaratkan oleh ilmu pengetahuan. Kecuali beberapa studi kasus dengan topik yang sama pada perusahan lain dan hasilnya sama maka upaya generalisasi dapat dilakukan. Walau demikian hasil studi kasus dapat melukiskan gambaran mengenai sejarah, kendala dan hambatan investasi yang terjadi pada industri sejenis dan industri lainnya. Kondisi awal usaha perikanan di wilayah Minahasa selatan pada tahun 1995 ketika investasi pabrik pengolahan ikan kayu di mulai masih didominasi oleh usaha skala kecil, yaitu sebatas mata pencaharian rumah tangga nelayan. Cara kelola pun masih sangat tradisional dalam pengertian tujuan usaha hanya untuk memenuhi kebutuhan makanan harian. Teknologi pengolahan ikan kayu sudah ada dan berkembang sejak tahun 700 sebelum masehi di Jepang. Di Indonesia khususnya di Sulawesi Utara mulai di perkenalkan pada tahun 1927 oleh orang Jepang bernama Hara Ko. Investasi baru dimulai pada tahun 1971 hingga sekarang. Investasi bidang pengolahan ikan menghadapi banyak kendala dan tantangan, yaitu (1) keterbatasan pangsa pasar, (2) Kepastian hukum tidak terjamin, (3) Investor dari luar daerah dan luar negeri berinvestasi dengan berpegang pada informasi minim mengenai budaya dan tradisi masyarakat lokal (4) moral kerja penduduk lokal amat tradisional jika tidak boleh dikatakan buruk.(5) Kebijakan investasi ditunjang oleh pemerintah daerah hanya pada level Bupati sedangkan level assiten, ke bawah sampai kelurahan lebih banyak menampilkan teror dan intimidasi kepada investor. Kata Kunci : pabrik ikan, investasi, sejarah, kendala, hambatan

scholarly journals Extending the Coding Potential of Viral Genomes with Overlapping Antisense ORFs: A Case for the De Novo Creation of the Gene Encoding the Antisense Protein ASP of HIV-1

Viruses ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 146
Author(s):  
Angelo Pavesi ◽  
Fabio Romerio
Keyword(s):  
De Novo ◽  
Point Mutations ◽  
Selective Advantage ◽  
Genomic Region ◽  
Fine Tuning ◽  
Sequence Evolution ◽  
Viral Genomes ◽  
Stop Codons ◽  
Hiv 1

Gene overprinting occurs when point mutations within a genomic region with an existing coding sequence create a new one in another reading frame. This process is quite frequent in viral genomes either to maximize the amount of information that they encode or in response to strong selective pressure. The most frequent scenario involves two different reading frames in the same DNA strand (sense overlap). Much less frequent are cases of overlapping genes that are encoded on opposite DNA strands (antisense overlap). One such example is the antisense ORF, asp in the minus strand of the HIV-1 genome overlapping the env gene. The asp gene is highly conserved in pandemic HIV-1 strains of group M, and it is absent in non-pandemic HIV-1 groups, HIV-2, and lentiviruses infecting non-human primates, suggesting that the ~190-amino acid protein that is expressed from this gene (ASP) may play a role in virus spread. While the function of ASP in the virus life cycle remains to be elucidated, mounting evidence from several research groups indicates that ASP is expressed in vivo. There are two alternative hypotheses that could be envisioned to explain the origin of the asp ORF. On one hand, asp may have originally been present in the ancestor of contemporary lentiviruses, and subsequently lost in all descendants except for most HIV-1 strains of group M due to selective advantage. Alternatively, the asp ORF may have originated very recently with the emergence of group M HIV-1 strains from SIVcpz. Here, we used a combination of computational and statistical approaches to study the genomic region of env in primate lentiviruses to shed light on the origin, structure, and sequence evolution of the asp ORF. The results emerging from our studies support the hypothesis of a recent de novo addition of the antisense ORF to the HIV-1 genome through a process that entailed progressive removal of existing internal stop codons from SIV strains to HIV-1 strains of group M, and fine tuning of the codon sequence in env that reduced the chances of new stop codons occurring in asp. Altogether, the study supports the notion that the HIV-1 asp gene encodes an accessory protein, providing a selective advantage to the virus.

scholarly journals On the comparability of knowledge transfer activities – a case study at the German Baltic Sea Coast focusing regional climate services

2017 ◽  
Vol 14 ◽  
pp. 145-151 ◽  
Author(s):  
Insa Meinke
Keyword(s):  
Knowledge Transfer ◽  
Baltic Sea ◽  
Initial Conditions ◽  
Regional Climate ◽  
Potential Usefulness ◽  
Climate Services ◽  
Transfer Activity ◽  
Spatial Coverage ◽  
Sea Coast

Abstract. In this article the comparability of knowledge transfer activities is discussed by accounting for external impacts. It is shown that factors which are neither part of the knowledge transfer activity nor part of the participating institution may have significant impact on the potential usefulness of knowledge transfer activities. Differences in the potential usefulness are leading to different initial conditions of the knowledge transfer activities. This needs to be taken into account when comparing different knowledge transfer activities, e.g., in program evaluations. This study is focusing on regional climate services at the German Baltic Sea coast. It is based on two surveys and experiences with two identical web tools applied on two regions with different spatial coverage. The results show that comparability among science based knowledge transfer activities is strongly limited through several external impacts. The potential usefulness and thus the initial condition of a particular knowledge transfer activity strongly depends on (1) the perceived priority of the focused topic, (2) the used information channels, (3) the conformity between the research agenda of service providing institutions and information demands in the public, as well as (4) on the spatial coverage of a service. It is suggested to account for the described external impacts for evaluations of knowledge transfer activities. The results show that the comparability of knowledge transfer activities is limited and challenge the adequacy of quantitative measures in this context. Moreover, as shown in this case study, in particular regional climate services should be individually evaluated on a long term perspective, by potential user groups and/or by its real users. It is further suggested that evaluation criteria should be co-developed with these stakeholder groups.

Managing to Facilitate Cross-Sectoral Inter-Organizational Collaborations

2020 ◽  
Vol 10 (2) ◽  
pp. 13-41
Author(s):  
Yuki Kawabata
Keyword(s):  
Medical Technology ◽  
Initial Conditions ◽  
The Self ◽  
Management Theory ◽  
Self Organization ◽  
Comprehensive Management ◽  
Technology Industry ◽  
German States ◽  
Organization Process

The promotion of new and competitive industries through cross-sectoral inter-organizational collaborations are tackled in many regions globally. This study explores the management of facilitating collaboration with consideration of the planned approach to change based on change management theory. The “initial conditions,” “field,” and “emerging interaction toward the collaborations” are clarified as key elements for management through intervention. It is considered how these interventions are implemented on these elements. A conceptual model for considering comprehensive management of the self-organization process toward collaboration is proposed. In the case study, experiences of the medical technology industry of three German states are examined. The activities of cluster organizations of these states, which provide services to facilitate cross-sectoral collaborations, are scrutinized. The results of the case study are comparatively analyzed, and the modified conceptual framework is depicted by reflecting the findings of the study. The implications are then discussed.

A Fuzzy Nonlinear Modeling of a McPherson Suspension System

2005 ◽  
Author(s):  
Ali Tavassoli ◽  
Hamed Jafarian ◽  
Mohammad Eghtesad
Keyword(s):  
Dynamical Systems ◽  
Initial Conditions ◽  
Nonlinear Modeling ◽  
Fuzzy Model ◽  
Domain Of Attraction ◽  
Suspension System ◽  
Reliable Model ◽  
Sugeno Model ◽  
Takagi Sugeno

The Takagi-Sugeno fuzzy model (TSfm) is a universal approximation of continuous real functions that are defined in a closed and bounded subset of Rn. This strong property of the TSfm can find several applications in modeling of dynamical systems that are described by differential equations. In this paper, we consider Takagi-Sugeno fuzzy model for a McPherson suspension system. One advantage of TSfm is its wide domain of attraction in compare with the other methods. To apply TSf modeling, one must precisely choose the nonlinear terms of the system governing equations. For each nonlinear term, there should be selected some linear subsystems that together represent the equivalent of the original nonlinear suspension system. This equivalence, for our case study, is illustrated by simulation results for various road disturbances and initial conditions which show the Takagi-Sugeno model can give a realistic and reliable model for dynamical systems.

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