scholarly journals It takes extremes to be robust

2018 ◽  
Author(s):  
Felipe Bastos Rocha ◽  
Maria Dulcetti Vibranovski ◽  
Louis Bernard Klaczko
Keyword(s):  
Gene Activity ◽  
Experimental Results ◽  
Regulatory Sequences ◽  
Multiple Traits ◽  
Large Dataset ◽  
Elementary Model ◽  
Developmental System ◽  
Elementary System ◽  
Phenotypic Robustness ◽  
Phenotypic Responses

SummaryPhenotypic robustness is a central property of life, manifested in the ability of organisms to endure perturbing conditions throughout their development and often yield rather constant phenotypes. Fundamental questions on robustness (canalization) remain to be answered (see [1]). Do alleles that confer robustness against one perturbation also confer robustness to others? Is the robustness observed in multiple traits/taxa achieved through shared or specific mechanisms? Here, we describe an elementary model of trait development that yields phenotypic robustness without dedicated systems of developmental or transcriptional buffering. Robustness emerges when extremely low or high levels of gene activity lead to either depletion or saturation of the developmental system. We use this model to show that experimental results associating robustness to apparently redundant cis-regulatory sequences (from [2]) probably reflect a similar elementary system of saturation/depletion. We then analyze a large dataset of phenotypic responses of diverse traits of animals, plants and bacteria (from [3]) and show that the amount of response is mostly determined by the distance to the phenotypic extremes. Moreover, the most robust genotypes are often those that yield either extremely low or high phenotypes. Our results help reframing the concepts of canalization and plasticity, suggesting that phenotypic responses are mainly the result of variation in the very systems controlling each trait, rather than being attributable to either “plasticity genes” or “canalization genes”. Furthermore, they provide a hint on the causes of the genomic ubiquity of apparently redundant cis-regulatory sequences [4,5].

scholarly journals Plasticity across levels: relating epigenomic, transcriptomic, and phenotypic responses to osmotic stress in a halotolerant microalga

2021 ◽  
Author(s):  
Christelle Leung ◽  
Daphne Grulois ◽  
Luis-Miguel Chevin
Keyword(s):  
Gene Expression ◽  
Phenotypic Plasticity ◽  
Osmotic Stress ◽  
Model Organism ◽  
Methylation Pattern ◽  
Marginal Effect ◽  
Environment Interaction ◽  
Multiple Traits ◽  
Genotype Effect ◽  
Phenotypic Responses

Phenotypic plasticity, the ability of a given genotype to produce alternative phenotypes in response to its environment of development, is an important mechanism for coping with variable environments. While the mechanisms underlying phenotypic plasticity are diverse, their relative contributions need to be investigated quantitatively to better understand the evolvability of plasticity across biological levels. This requires relating plastic responses of the epigenome, transcriptome, and organismal phenotype, and how they vary with the genotype. Here we carried out this approach for responses to osmotic stress in Dunaliella salina, a green microalga that is a model organism for salinity tolerance. We compared two strains that show markedly different demographic responses to osmotic stress, and showed that these phenotypic responses involve strain- and environment-specific variation in gene expression levels, but a relative low - but significant - effect of strain x environment interaction. We also found an important genotype effect on the genome-wide methylation pattern, but little contribution from environmental conditions to the latter. However, we did detect a significant marginal effect of epigenetic variation on gene expression, beyond the influence of genetic differences on epigenetic state, and we showed that hypomethylated regions are correlated with higher gene expression. Our results indicate that epigenetic mechanisms are either not involved in the rapid plastic response to environmental change in this species, or involve only few changes in trans that are sufficient to trigger concerted changes in the expression of many genes, and phenotypic responses by multiple traits.

scholarly journals Zbrowse: an interactive GWAS results browser

2015 ◽  
Author(s):  
Greg R Ziegler ◽  
Ryan H Hartsock ◽  
Ivan Baxter
Keyword(s):  
Candidate Gene ◽  
High Throughput ◽  
Experimental Results ◽  
Easy Access ◽  
Analysis Software ◽  
Multiple Traits ◽  
Desktop Computer ◽  
Web Browser ◽  
Specific Effects ◽  
High Throughput Phenotyping

The growing number of genotyped populations, the advent of high-throughput phenotyping techniques and the development of GWAS analysis software has rapidly accelerated the number of GWAS experimental results. Candidate gene discovery from these results files is often tedious, involving many manual steps searching for genes in windows around a significant SNP. This problem rapidly becomes more complex when an analyst wishes to compare multiple GWAS studies for pleiotropic or environment specific effects. To this end, we have developed a fast and intuitive interactive browser for the viewing of GWAS results with a focus on an ability to compare results across multiple traits or experiments. The software can easily be run on a desktop computer with software that bioinformaticians are likely already familiar with. Additionally, the software can be hosted or embedded on a server for easy access by anyone with a modern web browser.

BigFeel—A Distributed Processing Environment for the Integration of Sentiment Analysis Methods

2019 ◽  
Vol 62 (11) ◽  
pp. 1671-1683 ◽  
Author(s):  
Roger Santos Ferreira ◽  
Denilson Alves Pereira
Keyword(s):  
Sentiment Analysis ◽  
Distributed Processing ◽  
Source Code ◽  
Experimental Results ◽  
Apache Spark ◽  
Large Dataset ◽  
Native Form ◽  
Experimental Assessment ◽  
Processing Methods ◽  
Computer Cluster

Abstract Sentiment analysis has been the main focus of plenty of research efforts, particularly justified by its commercial significance, both for consumers and businesses. Thus, many methods have been proposed so far, and the most prominent have been compared in terms of effectiveness. Nonetheless, the literature is deficient when it comes to assessing the efficiency of these methods for processing large volumes of data. In this study, we performed an experimental assessment of the efficiency of 22 methods in total, whose implementations were available. We also proposed and assessed an environment for distributed processing methods for sentiment analysis, using the Apache Spark platform, named BigFeel. In this environment, the existing methods, outlined to run in a non-distributed way, can be adapted, without altering their source code, to run in a distributed manner. The experimental results reveal that (i) few methods are efficient in their native form, (ii) the methods improve their efficiency after having been integrated into BigFeel, (iii) some of them, which were unfeasible to process a large dataset, became viable when deployed in a computer cluster and (iv) some methods can only handle small datasets, even in a distributed manner.

scholarly journals Zbrowse: an interactive GWAS results browser

2015 ◽  
Author(s):  
Greg R Ziegler ◽  
Ryan H Hartsock ◽  
Ivan Baxter
Keyword(s):  
Candidate Gene ◽  
High Throughput ◽  
Experimental Results ◽  
Easy Access ◽  
Analysis Software ◽  
Multiple Traits ◽  
Desktop Computer ◽  
Web Browser ◽  
Specific Effects ◽  
High Throughput Phenotyping

The growing number of genotyped populations, the advent of high-throughput phenotyping techniques and the development of GWAS analysis software has rapidly accelerated the number of GWAS experimental results. Candidate gene discovery from these results files is often tedious, involving many manual steps searching for genes in windows around a significant SNP. This problem rapidly becomes more complex when an analyst wishes to compare multiple GWAS studies for pleiotropic or environment specific effects. To this end, we have developed a fast and intuitive interactive browser for the viewing of GWAS results with a focus on an ability to compare results across multiple traits or experiments. The software can easily be run on a desktop computer with software that bioinformaticians are likely already familiar with. Additionally, the software can be hosted or embedded on a server for easy access by anyone with a modern web browser.

Diagnostics of Gold Laser Plasmas

1988 ◽  
Vol 102 ◽  
pp. 357-360
Author(s):  
J.C. Gauthier ◽  
J.P. Geindre ◽  
P. Monier ◽  
C. Chenais-Popovics ◽  
N. Tragin ◽  
...  
Keyword(s):  
Experimental Results ◽  
Pure Gold ◽  
Electronic Temperature ◽  
X Ray ◽  
Laser Plasmas ◽  
Collisional Radiative Model ◽  
Radiative Model

AbstractIn order to achieve a nickel-like X ray laser scheme we need a tool to determine the parameters which characterise the high-Z plasma. The aim of this work is to study gold laser plasmas and to compare experimental results to a collisional-radiative model which describes nickel-like ions. The electronic temperature and density are measured by the emission of an aluminium tracer. They are compared to the predictions of the nickel-like model for pure gold. The results show that the density and temperature can be estimated in a pure gold plasma.

Introduction

1978 ◽  
Vol 36 (3) ◽  
pp. 543-544
Author(s):  
W. Bernard
Keyword(s):  
Molecular Weight ◽  
Electron Microscope ◽  
Nucleic Acid ◽  
Gene Mapping ◽  
Molecular Genetics ◽  
Cell Biology ◽  
Gene Activity ◽  
Close Connection ◽  
Basic Information ◽  
Simple Systems

In comparison to many other fields of ultrastructural research in Cell Biology, the successful exploration of genes and gene activity with the electron microscope in higher organisms is a late conquest. Nucleic acid molecules of Prokaryotes could be successfully visualized already since the early sixties, thanks to the Kleinschmidt spreading technique - and much basic information was obtained concerning the shape, length, molecular weight of viral, mitochondrial and chloroplast nucleic acid. Later, additonal methods revealed denaturation profiles, distinction between single and double strandedness and the use of heteroduplexes-led to gene mapping of relatively simple systems carried out in close connection with other methods of molecular genetics.

Observation of Phase Contrast Images in STEM and CTEM Modes by Using 100 kV Field Emission Electron Gun

1974 ◽  
Vol 32 ◽  
pp. 390-391
Author(s):  
Y. Harada ◽  
T. Goto ◽  
H. Koike ◽  
T. Someya
Keyword(s):  
Field Emission ◽  
Phase Contrast ◽  
Image Formation ◽  
Fresnel Diffraction ◽  
Experimental Results ◽  
Electron Gun ◽  
Scanning Microscopy ◽  
Emission Electron ◽  
Lattice Images

Since phase contrasts of STEM images, that is, Fresnel diffraction fringes or lattice images, manifest themselves in field emission scanning microscopy, the mechanism for image formation in the STEM mode has been investigated and compared with that in CTEM mode, resulting in the theory of reciprocity. It reveals that contrast in STEM images exhibits the same properties as contrast in CTEM images. However, it appears that the validity of the reciprocity theory, especially on the details of phase contrast, has not yet been fully proven by the experiments. In this work, we shall investigate the phase contrast images obtained in both the STEM and CTEM modes of a field emission microscope (100kV), and evaluate the validity of the reciprocity theory by comparing the experimental results.

A new dissociation mode for dislocations in silicon

1978 ◽  
Vol 36 (1) ◽  
pp. 346-347
Author(s):  
A. Ourmazd ◽  
G.R. Booker ◽  
C.J. Humphreys
Keyword(s):  
Detailed Examination ◽  
Experimental Results ◽  
Dislocation Network ◽  
Weak Beam ◽  
Phosphorus Doped

A (111) phosphorus-doped Si specimen, thinned to give a TEM foil of thickness ∼ 150nm, contained a dislocation network lying on the (111) plane. The dislocation lines were along the three <211> directions and their total Burgers vectors,ḇt, were of the type , each dislocation being of edge character. TEM examination under proper weak-beam conditions seemed initially to show the standard contrast behaviour for such dislocations, indicating some dislocation segments were undissociated (contrast A), while other segments were dissociated to give two Shockley partials separated by approximately 6nm (contrast B) . A more detailed examination, however, revealed that some segments exhibited a third and anomalous contrast behaviour (contrast C), interpreted here as being due to a new dissociation not previously reported. Experimental results obtained for a dislocation along [211] with for the six <220> type reflections using (g,5g) weak-beam conditions are summarised in the table below, together with the relevant values.

Multislice calculations of RHEED patterns from vicinal Si (001)

1993 ◽  
Vol 51 ◽  
pp. 1000-1001
Author(s):  
Scott Lordi
Keyword(s):  
Misorientation Angle ◽  
Incident Angle ◽  
Incident Beam ◽  
Experimental Results ◽  
Bragg Condition ◽  
Vicinal Surfaces ◽  
Kinematic Theory ◽  
Step Edges

Vicinal Si (001) surfaces are interesting because they are good substrates for the growth of III-V semiconductors. Spots in RHEED patterns from vicinal surfaces are split due to scattering from ordered step arrays and this splitting can be used to determine the misorientation angle, using kinematic arguments. Kinematic theory is generally regarded to be inadequate for the calculation of RHEED intensities; however, only a few dynamical RHEED simulations have been attempted for vicinal surfaces. The multislice formulation of Cowley and Moodie with a recently developed edge patching method was used to calculate RHEED patterns from vicinal Si (001) surfaces. The calculated patterns are qualitatively similar to published experimental results and the positions of the split spots quantitatively agree with kinematic calculations.RHEED patterns were calculated for unreconstructed (bulk terminated) Si (001) surfaces misoriented towards [110] ,with an energy of 15 keV, at an incident angle of 36.63 mrad ([004] bragg condition), and a beam azimuth of [110] (perpendicular to the step edges) and the incident beam pointed down the step staircase.

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