Distribution of fitness effects of mutations obtained from a simple genetic regulatory network model.

Abstract:

:Beneficial and deleterious mutations change an organism's fitness but the distribution of these mutational effects on fitness are unknown. Several experimental, theoretical, and computational studies have explored this question but are limited because of experimental restrictions, or disconnect with physiology. Here we attempt to characterize the distribution of fitness effects (DFE) due to mutations in a cellular regulatory motif. We use a simple mathematical model to describe the dynamics of gene expression in the lactose utilization network, and use a cost-benefit framework to link the model output to fitness. We simulate mutations by changing model parameters and computing altered fitness to obtain the DFE. We find beneficial mutations distributed exponentially, but distribution of deleterious mutations seems far more complex. In addition, we find neither the starting fitness, nor the exact location on the fitness landscape, affecting these distributions qualitatively. Lastly, we quantify epistasis in our model and find that the distribution of epistatic effects remains qualitatively conserved across different locations on the fitness landscape. Overall, we present a first attempt at exploring the specific statistical features of the fitness landscape associated with a system, by using the specific mathematical model associated with it.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Brajesh RG,Dutta D,Saini S

doi

10.1038/s41598-019-46401-7

subject

Has Abstract

pub_date

2019-07-08 00:00:00

pages

9842

issue

1

issn

2045-2322

pii

10.1038/s41598-019-46401-7

journal_volume

9

pub_type

杂志文章
  • Extensive genetic diversity of Rickettsiales bacteria in multiple mosquito species.

    abstract::Rickettsiales are important zoonotic pathogens, causing severe disease in humans globally. Although mosquitoes are an important vector for diverse pathogens, with the exception of members of the genus Wolbachia little is known about their role in the transmission of Rickettsiales. Herein, Rickettsiales were identified...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep38770

    authors: Guo WP,Tian JH,Lin XD,Ni XB,Chen XP,Liao Y,Yang SY,Dumler JS,Holmes EC,Zhang YZ

    更新日期:2016-12-09 00:00:00

  • Sequence analysis of pooled bacterial samples enables identification of strain variation in group A streptococcus.

    abstract::Knowledge of the genomic variation among different strains of a pathogenic microbial species can help in selecting optimal candidates for diagnostic assays and vaccine development. Pooled sequencing (Pool-seq) is a cost effective approach for population level genetic studies that require large numbers of samples such ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep45771

    authors: Weldatsadik RG,Wang J,Puhakainen K,Jiao H,Jalava J,Räisänen K,Datta N,Skoog T,Vuopio J,Jokiranta TS,Kere J

    更新日期:2017-03-31 00:00:00

  • Semi-quantized Spin Pumping and Spin-Orbit Torques in Topological Dirac Semimetals.

    abstract::We study the time-development processes of spin and charge transport phenomena in a topological Dirac semimetal attached to a ferromagnetic insulator with a precessing magnetization. Compared to conventional normal metals, topological Dirac semimetals manifest a large inverse spin Hall effect when a spin current is pu...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-55802-7

    authors: Misawa T,Nomura K

    更新日期:2019-12-23 00:00:00

  • Low-frequency ultrasound-induced VEGF suppression and synergy with dendritic cell-mediated anti-tumor immunity in murine prostate cancer cells in vitro.

    abstract::High tumor vascular endothelial growth factor (VEGF) levels are associated with poor treatment outcomes in prostate cancer (PCa), and immune deficiency in the PCa microenvironment, especially suppression of dendritic cell (DC) proliferation, has been confirmed. In this study, we (1) investigated whether VEGF participa...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-06242-8

    authors: Zhang W,Shou WD,Xu YJ,Bai WK,Hu B

    更新日期:2017-07-18 00:00:00

  • The FGFR4-388arg Variant Promotes Lung Cancer Progression by N-Cadherin Induction.

    abstract::The FGFR4-388Arg variant has been related to poor prognosis in several types of cancer, including lung cancer. The mechanism underlying this association has not been addressed in detail in patients with this pathology. Here, we report that this FGFR4 variant induces MAPK and STAT3 activation and causes pro-oncogenic e...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-20570-3

    authors: Quintanal-Villalonga Á,Ojeda-Márquez L,Marrugal Á,Yagüe P,Ponce-Aix S,Salinas A,Carnero A,Ferrer I,Molina-Pinelo S,Paz-Ares L

    更新日期:2018-02-05 00:00:00

  • Tumor-derived exosomes regulate expression of immune function-related genes in human T cell subsets.

    abstract::Tumor cell-derived exosomes (TEX) suppress functions of immune cells. Here, changes in the gene profiles of primary human T lymphocytes exposed in vitro to exosomes were evaluated. CD4(+) Tconv, CD8(+) T or CD4(+) CD39(+) Treg were isolated from normal donors' peripheral blood and co-incubated with TEX or exosomes iso...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep20254

    authors: Muller L,Mitsuhashi M,Simms P,Gooding WE,Whiteside TL

    更新日期:2016-02-04 00:00:00

  • Landscape of the spliced leader trans-splicing mechanism in Schistosoma mansoni.

    abstract::Spliced leader dependent trans-splicing (SLTS) has been described as an important RNA regulatory process that occurs in different organisms, including the trematode Schistosoma mansoni. We identified more than seven thousand putative SLTS sites in the parasite, comprising genes with a wide spectrum of functional class...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-22093-3

    authors: Boroni M,Sammeth M,Gava SG,Jorge NAN,Macedo AM,Machado CR,Mourão MM,Franco GR

    更新日期:2018-03-01 00:00:00

  • The efficacy and safety of docetaxel plus thalidomide vs. docetaxel alone in patients with androgen-independent prostate cancer: a systematic review.

    abstract::The aim of this systematic review was taken to investigate the efficacy and safety of docetaxel plus thalidomide vs. docetaxel alone for treating androgen-independent prostate cancer (AIPC). Data were collected from different databases independently by three researchers according to the pre-defined inclusion and exclu...

    journal_title:Scientific reports

    pub_type: 杂志文章,meta分析,评审

    doi:10.1038/srep04818

    authors: Chen L,Qiu X,Wang R,Xie X

    更新日期:2014-04-28 00:00:00

  • Dual dynamics of mitochondrial permeability transition pore opening.

    abstract::Mitochondria play an essential role in bioenergetics and cellular Ca[Formula: see text] handling. The mitochondrial permeability transition pore (mPTP) is a non-specific channel located in the inner mitochondrial membrane. Long-lasting openings of the pore allow the rapid passage of ions and large molecules, which can...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-60177-1

    authors: Wacquier B,Combettes L,Dupont G

    更新日期:2020-03-03 00:00:00

  • Immunization with DNA prime-subunit protein boost strategy based on influenza H9N2 virus conserved matrix protein M1 and its epitope screening.

    abstract::Developing an effective universal influenza vaccine against influenza virus with highly conserved antigenic epitopes could induce a broad-spectrum immune response to prevent infection. The soluble protein M1 that can induce the M1 specific immune response was first confirmed in our previous study. In this study, we ch...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-60783-z

    authors: Liu F,Wang X,Zheng M,Xiong F,Liu X,Zhou L,Tan W,Chen Z

    更新日期:2020-03-05 00:00:00

  • Comparison of Alterations in miRNA Expression in Matched Tissue and Blood Samples during Spinal Cord Glioma Progression.

    abstract::Abnormal expression of microRNAs (miRNAs) contributes to glioma initiation. However, the expression of miRNAs in tumour tissue or blood of spinal cord glioma (SCG) patients, particularly in high-grade spinal gliomas (Grade IV) known as glioblastoma (GBM), remains largely unknown. In this study we aimed to determine di...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-42364-x

    authors: An T,Fan T,Zhang XQ,Liu YF,Huang J,Liang C,Lv BH,Wang YQ,Zhao XG,Liu JX,Fu YH,Jiang GJ

    更新日期:2019-06-24 00:00:00

  • Neonatal thrombocytopenia: Thrombin generation in presence of reduced platelet counts and effects of rFVIIa in cord blood.

    abstract::Healthy neonates exhibit a well-functioning haemostatic system despite peculiarities regarding composition of clotting factors and inhibitors as well as impaired platelet aggregation. Thrombocytopenia and severe bleeding events are feared in sick infants. Recombinant factor VIIa (rFVIIa) is a haemostatic agent used as...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-44199-y

    authors: Haidl H,Pohl S,Leschnik B,Gallistl S,Muntean W,Schlagenhauf A

    更新日期:2019-05-29 00:00:00

  • High inhaled oxygen concentration quadruples exhaled CO in healthy volunteers monitored by a highly sensitive laser spectrometer.

    abstract::Carbon monoxide (CO) monitoring in human breath is the focus of many investigations as CO could possibly be used as a marker of various diseases. Detecting CO in human breath remains a challenge because low concentrations (

    journal_title:Scientific reports

    pub_type: 临床试验,杂志文章

    doi:10.1038/s41598-019-48789-8

    authors: Brenckmann V,Ventrillard I,Romanini D,Jaulin K,Calabrèse P,Briot R

    更新日期:2019-08-22 00:00:00

  • Highly functionalized β-lactams and 2-ketopiperazines as TRPM8 antagonists with antiallodynic activity.

    abstract::The cool sensor transient receptor potential melastatin channel 8 (TRPM8) is highly expressed in trigeminal and dorsal root ganglia, playing a key role in cold hypersensitivity associated to different peripheral neuropathies. Moreover, these channels are aberrantly expressed in different cancers, and seem to participa...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-70691-x

    authors: Bonache MÁ,Martín-Escura C,de la Torre Martínez R,Medina A,González-Rodríguez S,Francesch A,Cuevas C,Roa AM,Fernández-Ballester G,Ferrer-Montiel A,Fernández-Carvajal A,González-Muñiz R

    更新日期:2020-08-25 00:00:00

  • Tai Chi Chuan and Baduanjin practice modulates functional connectivity of the cognitive control network in older adults.

    abstract::Cognitive impairment is one of the most common problem saffecting older adults. In this study, we investigated whether Tai Chi Chuan and Baduanjin practice can modulate mental control functionand the resting state functional connectivity (rsFC) of the cognitive control network in older adults. Participants in the two ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep41581

    authors: Tao J,Chen X,Egorova N,Liu J,Xue X,Wang Q,Zheng G,Li M,Hong W,Sun S,Chen L,Kong J

    更新日期:2017-02-07 00:00:00

  • Flower induction, microscope-aided cross-pollination, and seed production in the duckweed Lemna gibba with discovery of a male-sterile clone.

    abstract::Duckweed species have a great potential to develop into fast-growing crops for water remediation and bioenergy production. Seed production and utilization of hybrid vigour are essential steps in this process. However, even in the extensively-studied duckweed species, Lemna gibba, flower primordia were often aborted pr...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-03240-8

    authors: Fu L,Huang M,Han B,Sun X,Sree KS,Appenroth KJ,Zhang J

    更新日期:2017-06-08 00:00:00

  • The impact of tumor location and multifocality on prognosis for patients with upper tract urothelial carcinoma: a meta-analysis.

    abstract::There is lack of consensus regarding the prognostic significance of primary tumor location of upper tract urothelial carcinoma(UTUC). We performed a meta-analysis to evaluate the impact of primary tumor location on prognosis in patients with UTUC who had undergone radical nephroureterectomy(RNU). We included eligible ...

    journal_title:Scientific reports

    pub_type: 杂志文章,meta分析

    doi:10.1038/srep06361

    authors: Wu Y,Dong Q,Liu L,Han P,Wei Q

    更新日期:2014-09-15 00:00:00

  • Overcoming challenges in human saliva gene expression measurements.

    abstract::Saliva, as a non-invasive and easily accessible biofluid, has been shown to contain RNA biomarkers for prediction and diagnosis of several diseases. However, systematic analysis done by our group identified two problematic issues not coherently described before: (1) most of the isolated RNA originates from the oral mi...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-67825-6

    authors: Ostheim P,Tichý A,Sirak I,Davidkova M,Stastna MM,Kultova G,Paunesku T,Woloschak G,Majewski M,Port M,Abend M

    更新日期:2020-07-07 00:00:00

  • Chimeras and complex cluster states in arrays of spin-torque oscillators.

    abstract::We consider synchronization properties of arrays of spin-torque nano-oscillators coupled via an RC load. We show that while the fully synchronized state of identical oscillators may be locally stable in some parameter range, this synchrony is not globally attracting. Instead, regimes of different levels of composition...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-04918-9

    authors: Zaks M,Pikovsky A

    更新日期:2017-07-05 00:00:00

  • Crystal structure of the BoNT/A2 receptor-binding domain in complex with the luminal domain of its neuronal receptor SV2C.

    abstract::A detailed molecular understanding of botulinum neurotoxin (BoNT)/host-cell-receptor interactions is fundamental both for developing strategies against botulism and for generating improved BoNT variants for medical applications. The X-ray crystal structure of the receptor-binding domain (HC) of BoNT/A1 in complex with...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep43588

    authors: Benoit RM,Schärer MA,Wieser MM,Li X,Frey D,Kammerer RA

    更新日期:2017-03-02 00:00:00

  • Orchid Bsister gene PeMADS28 displays conserved function in ovule integument development.

    abstract::The ovules and egg cells are well developed to be fertilized at anthesis in many flowering plants. However, ovule development is triggered by pollination in most orchids. In this study, we characterized the function of a Bsister gene, named PeMADS28, isolated from Phalaenopsis equestris, the genome-sequenced orchid. S...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-79877-9

    authors: Shen CY,Chen YY,Liu KW,Lu HC,Chang SB,Hsiao YY,Yang F,Zhu G,Zou SQ,Huang LQ,Liu ZJ,Tsai WC

    更新日期:2021-01-13 00:00:00

  • Experimental immunological demyelination enhances regeneration in autograft-repaired long peripheral nerve gaps.

    abstract::Peripheral nerve long gap defects are a clinical challenge in the regeneration field. Despite the wide variety of surgical techniques and therapies, autografting is the "gold standard" for peripheral nerve gap reconstruction. The pathological process of Wallerian degeneration from the time of acute injury to efficient...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep39828

    authors: Ge J,Zhu S,Yang Y,Liu Z,Hu X,Huang L,Quan X,Wang M,Huang J,Li Y,Luo Z

    更新日期:2016-12-23 00:00:00

  • Hydrogen storage and stability properties of Pd-Pt solid-solution nanoparticles revealed via atomic and electronic structure.

    abstract::Bimetallic Pd1-x Pt x solid-solution nanoparticles (NPs) display charging/discharging of hydrogen gas, which has relevance for fuel cell technologies; however, the constituent elements are immiscible in the bulk phase. We examined these material systems using high-energy synchrotron X-ray diffraction, X-ray absorption...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-14494-7

    authors: Kumara LSR,Sakata O,Kobayashi H,Song C,Kohara S,Ina T,Yoshimoto T,Yoshioka S,Matsumura S,Kitagawa H

    更新日期:2017-11-06 00:00:00

  • Site-specific Isopeptide Bridge Tethering of Chimeric gp41 N-terminal Heptad Repeat Helical Trimers for the Treatment of HIV-1 Infection.

    abstract::Peptides derived from the N-terminal heptad repeat (NHR) of HIV-1 gp41 can be potent inhibitors against viral entry when presented in a nonaggregating trimeric coiled-coil conformation via the introduction of exogenous trimerization motifs and intermolecular disulfide bonds. We recently discovered that crosslinking is...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep32161

    authors: Wang C,Li X,Yu F,Lu L,Jiang X,Xu X,Wang H,Lai W,Zhang T,Zhang Z,Ye L,Jiang S,Liu K

    更新日期:2016-08-26 00:00:00

  • Electronic system with memristive synapses for pattern recognition.

    abstract::Memristive synapses, the most promising passive devices for synaptic interconnections in artificial neural networks, are the driving force behind recent research on hardware neural networks. Despite significant efforts to utilize memristive synapses, progress to date has only shown the possibility of building a neural...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep10123

    authors: Park S,Chu M,Kim J,Noh J,Jeon M,Hun Lee B,Hwang H,Lee B,Lee BG

    更新日期:2015-05-05 00:00:00

  • Shape Tailored Magnetic Nanorings for Intracellular Hyperthermia Cancer Therapy.

    abstract:ABSTARCT:This work explores a new class of vortex/magnetite/iron oxide nanoparticles designed for magnetic hyperthermia applications. These nanoparticles, named Vortex Iron oxide Particles (VIPs), are an alternative to the traditional Superparamagnetic Iron Oxide Nanoparticles (SPIONs), since VIPs present superior heat...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-14633-0

    authors: Dias CSB,Hanchuk TDM,Wender H,Shigeyosi WT,Kobarg J,Rossi AL,Tanaka MN,Cardoso MB,Garcia F

    更新日期:2017-11-01 00:00:00

  • Neural Activities Underlying the Feedback Express Salience Prediction Errors for Appetitive and Aversive Stimuli.

    abstract::Feedback information is essential for us to adapt appropriately to the environment. The feedback-related negativity (FRN), a frontocentral negative deflection after the delivery of feedback, has been found to be larger for outcomes that are worse than expected, and it reflects a reward prediction error derived from th...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep34032

    authors: Gu Y,Hu X,Pan W,Yang C,Wang L,Li Y,Chen A

    更新日期:2016-10-03 00:00:00

  • Combinatorial metabolic engineering of Pseudomonas putida KT2440 for efficient mineralization of 1,2,3-trichloropropane.

    abstract::An industrial waste, 1,2,3-trichloropropane (TCP), is toxic and extremely recalcitrant to biodegradation. To date, no natural TCP degraders able to mineralize TCP aerobically have been isolated. In this work, we engineered a biosafety Pseudomonas putida strain KT2440 for aerobic mineralization of TCP by implantation o...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-07435-x

    authors: Gong T,Xu X,Che Y,Liu R,Gao W,Zhao F,Yu H,Liang J,Xu P,Song C,Yang C

    更新日期:2017-08-01 00:00:00

  • Composition and temperature dependence of self-diffusion in Si1-x Ge x alloys.

    abstract::The knowledge of diffusion processes in semiconducting alloys is very important both technologically and from a theoretical point of view. Here we show that, self-diffusion in Si1-x Ge x alloys as a function of temperature and Ge concentration can be described by the cBΩ thermodynamic model. This model connects the ac...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-01301-6

    authors: Saltas V,Chroneos A,Vallianatos F

    更新日期:2017-05-02 00:00:00

  • Windscapes and olfactory foraging in a large carnivore.

    abstract::The theoretical optimal olfactory search strategy is to move cross-wind. Empirical evidence supporting wind-associated directionality among carnivores, however, is sparse. We examined satellite-linked telemetry movement data of adult female polar bears (Ursus maritimus) from Hudson Bay, Canada, in relation to modelled...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep46332

    authors: Togunov RR,Derocher AE,Lunn NJ

    更新日期:2017-04-12 00:00:00