scholarly journals The evolution of developmental patterning under genetic duplication constraints

2007 ◽  
Vol 5 (19) ◽  
pp. 237-245 ◽  
Author(s):  
Miguel A Fuentes ◽  
David C Krakauer
Keyword(s):  
Gene Duplication ◽  
Phenotypic Variability ◽  
Three Dimensional ◽  
Evolutionary Process ◽  
Evolutionary Model ◽  
Dimensional System ◽  
Genetic Robustness ◽  
Complex Adaptive ◽  
Duplication Events ◽  
The Stability

Of considerable interest are the evolutionary and developmental origins of complex, adaptive structures and the mechanisms that stabilize these structures. We consider the relationship between the evolutionary process of gene duplication and deletion and the stability of morphogenetic patterns produced by interacting activators and inhibitors. We compare the relative stability of patterns with a single activator and inhibitor (two-dimensional system) against a ‘redundant’ system with two activators or two inhibitors (three-dimensional system). We find that duplication events can both expand and contract the space of patterns. We study developmental robustness in terms of stochastic escape times from this space, also known as a ‘canalization potential’. We embed the output of pattern formation into an explicit evolutionary model of gene duplication, gene loss and variation in the steepness of the canalization potential. We find that under all constant conditions, the system evolves towards a preference for steep potentials associated with low phenotypic variability and longer lifespans. This preference leads to an overall decrease in the density of redundant genotypes as developmental robustness neutralizes the advantages of genetic robustness.

scholarly journals Phylotranscriptomic analyses reveal asymmetrical gene duplication dynamics and signatures of ancient polyploidy in mints

2019 ◽  
Author(s):  
Grant T Godden ◽  
Taliesin J Kinser ◽  
Pamela S Soltis ◽  
Douglas E Soltis
Keyword(s):  
Gene Duplication ◽  
Large Scale ◽  
Plant Traits ◽  
Divergence Time ◽  
Evolutionary Process ◽  
Driver Gene ◽  
Important Species ◽  
Plant Groups ◽  
Duplication Events ◽  
Gene Duplicates

Abstract Ancient duplication events and retained gene duplicates have contributed to the evolution of many novel plant traits and, consequently, to the diversity and complexity within and across plant lineages. While mounting evidence highlights the importance of whole-genome duplication (WGD; polyploidy) and its key role as an evolutionary driver, gene duplication dynamics and mechanisms, both of which are fundamental to our understanding of evolutionary process and patterns of plant diversity, remain poorly characterized in many clades. We use newly available transcriptomic data and a robust phylogeny to investigate the prevalence, occurrence, and timing of gene duplications in Lamiaceae (mints), a species-rich and chemically diverse clade with many ecologically, economically, and culturally important species. We also infer putative WGDs—an extreme mechanism of gene duplication—using large-scale data sets from synonymous divergence (KS), phylotranscriptomic, and divergence time analyses. We find evidence for widespread but asymmetrical levels of gene duplication and ancient polyploidy in Lamiaceae that correlate with species richness, including pronounced levels of gene duplication and putative ancient WGDs (7–18 events) within the large subclade Nepetoideae and up to 10 additional WGD events in other subclades. Our results help disentangle WGD-derived gene duplicates from those produced by other mechanisms and illustrate the non-uniformity of duplication dynamics in mints, setting the stage for future investigations that explore their impacts on trait diversity and species diversification. Our results also provide a practical context for evaluating the benefits and limitations of transcriptome-based approaches to inferring WGD, and we offer recommendations for researchers interested in investigating ancient WGDs in other plant groups.

Crystal structure, hydrogen bonds and thermal transformations of superprotonic conductor Cs6(SO4)3(H3PO4)4

2021 ◽  
Vol 77 (2) ◽  
Author(s):  
Irina Makarova ◽  
Elena Selezneva ◽  
Laura Canadillas-Delgado ◽  
Estelle Mossou ◽  
Aleksander Vasiliev ◽  
...  
Keyword(s):  
Chemical Composition ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Three Dimensional ◽  
Dimensional System ◽  
Polarization Microscopy ◽  
Cubic Symmetry ◽  
Temperature Changes ◽  
Minimum Potential ◽  
The Stability

Crystals of Cs6(SO4)3(H3PO4)4 belong to the family of alkali metal acid salts that show a high protonic conductivity at relatively low temperatures. Such properties make superprotonic crystals an excellent choice for the study of the influence of the hydrogen subsystem on the physicochemical properties and promising materials for energy-efficient technologies. Single crystals of Cs6(SO4)3(H3PO4)4 were studied by neutron diffraction methods, optical polarization microscopy, scanning electron microscopy and energy-dispersive X-ray spectroscopy. Neutron diffraction studies made it possible to determine the positions of all the atoms with high accuracy, including the H atom on a hydrogen bond characterized by a single-minimum potential, to confirm the chemical composition of the Cs6(SO4)3(H3PO4)4 crystals and their cubic symmetry in low- and high-temperature phases, and to draw conclusions about the three-dimensional system of hydrogen bonds, which is fundamentally different in comparison with other superprotonic compounds. Based on the experimental data obtained, crystal transformations with temperature changes are reported, and the stability of the chemical composition is shown.

PERIODIC ORBITS OF THE LORENZ SYSTEM THROUGH PERTURBATION THEORY

2001 ◽  
Vol 11 (10) ◽  
pp. 2559-2566 ◽  
Author(s):  
J. PALACIÁN ◽  
P. YANGUAS
Keyword(s):  
Periodic Orbits ◽  
Lorenz System ◽  
Linear Part ◽  
Three Dimensional ◽  
Invariant Sets ◽  
Dimensional System ◽  
The Matrix ◽  
Lie Transformations ◽  
The Lorenz System ◽  
The Stability

Different transformations are applied to the Lorenz system with the aim of reducing the initial three-dimensional system into others of dimension two. The symmetries of the linear part of the system are determined by calculating the matrices which commute with the matrix associated to the linear part. These symmetries are extended to the whole system up to an adequate order by using Lie transformations. After the reduction, we formulate the resulting systems using the invariants associated to each reduction. At this step, we calculate for each reduced system the equilibria and their stability. They are in correspondence with the periodic orbits and invariant sets of the initial system, the stability being the same.

scholarly journals Tidal Conversion and Dissipation at Steep Topography in a Channel Poleward of the Critical Latitude

2019 ◽  
Vol 49 (5) ◽  
pp. 1269-1291 ◽  
Author(s):  
Kenneth G. Hughes ◽  
Jody M. Klymak
Keyword(s):  
Three Dimensional ◽  
Tidal Energy ◽  
Kelvin Waves ◽  
Internal Tides ◽  
The Arctic ◽  
Energy Budgets ◽  
Dimensional System ◽  
Deep Layers ◽  
The Stability ◽  
Critical Latitude

Abstract In high-latitude fjords and channels in the Canadian Arctic Archipelago, walls support radiating internal tides as Kelvin waves. Such waves allow for significant barotropic to baroclinic tidal energy conversion, which is otherwise small or negligible when poleward of the critical latitude. This fundamentally three-dimensional system of a subinertial channel is investigated with a suite of numerical simulations in rectangular channels of varying width featuring idealized, isolated ridges. Even in channels as wide as 5 times the internal Rossby radius, tidal conversion can remain as high as predicted by an equivalent two-dimensional, nonrotating system. Curves of tidal conversion as a function of channel width, however, do not vary monotonically. Instead, they display peaks and nulls owing to interference between the Kelvin waves along the wall and similar waves that propagate along the ridge flanks, the wavelengths of which can be estimated from linear theory to guide prediction. Because the wavelengths are comparable to width scales of Arctic channels and fjords, the interference will play a first-order role in tidal energy budgets and may consequently influence the stability of glaciers, the ventilation of deep layers, the locations of sediment deposition, and the fate of freshwater exiting the Arctic Ocean.

Microevolution of the VQ gene family in six species of Fragaria

Genome ◽  
2018 ◽  
Vol 61 (1) ◽  
pp. 49-57 ◽  
Author(s):  
Yan Zhong ◽  
Cong Guo ◽  
Jinjin Chu ◽  
Hui Liu ◽  
Zong-Ming Cheng
Keyword(s):  
Gene Duplication ◽  
Stress Responses ◽  
Plant Stress ◽  
Evolutionary Process ◽  
Purifying Selection ◽  
Plant Stress Responses ◽  
Duplication Events ◽  
Motif Composition ◽  
Important Basis ◽  
Evolutionary Fate

VQ motif-containing proteins play crucial roles in plant growth, development, and stress responses. However, no information of VQ motif-containing proteins has been studied at the microevolutionary level in species of Fragaria. In this study, a total of 19, 21, 23, 23, 23, and 25 genes containing the VQ motif were identified from the genomes of F. nipponica, F. iinumae, F. orientalis, F. vesca, F. nubicola, and F. x ananassa, respectively. We classified the VQ genes into 15 clades with grapevine VQ genes, which indicated that at least 15 ancient VQ genes existed before the divergence of the six studied species of Fragaria. Phylogenetic analysis indicated that 28 gene duplication events have occurred in the evolutionary process of the six species of Fragaria. Structural analysis showed that most of the VQ genes have no introns and that VQ proteins in each clade have a similar motif composition. The majority of gene pairs had Ka/Ks ratios less than 1, which illustrated that most of the VQ genes underwent purifying selection in the six species of Fragaria. Four types of cis-elements in promoters of VQ genes were detected, which is an important basis for further studies about plant stress responses. Furthermore, the expression analysis of FvVQ genes indicated that these genes are expressed differentially in the examined organs and tissues. The identification of VQ genes and the analysis of VQ gene duplication and polyploidization events in the six species of Fragaria provide important information on the evolutionary fate of VQ genes during the divergence of the six species of Fragaria.

scholarly journals Evolution and Structural Variations of Chloroplast tRNAs in Gymnosperms

2020 ◽  
Author(s):  
Yu-he Zhao ◽  
Tong Zhou ◽  
Ting-Ting Zhang ◽  
Peng-Bin Dong ◽  
Min-Feng Fang ◽  
...  
Keyword(s):  
Structural Changes ◽  
Evolutionary Process ◽  
Minimum Free Energy ◽  
Trna Genes ◽  
Structural Variations ◽  
Transfer Rnas ◽  
Molecular Sequence ◽  
The North ◽  
Duplication Events ◽  
The Stability

Abstract Background: Transfer RNAs can participate in a variety of vital life activities. The gymnosperms with important ecological and economic values were the dominant and constructive species in the forest ecosystems in the North hemisphere. However, evolution and structural changes of chloroplast tRNA in gymnosperms remain largely unclear.Results: In this study, the nucleotide evolution, phylogenetic relationships and structural variations of 1,779 chloroplast tRNAs in gymnosperms were determined. The number and types of tRNA genes contained in the chloroplast genome of different gymnosperms were not much different, the average amount of tRNA contained was 33, and the occurrence frequency of various types of tRNA in gymnosperms was generally consistent. Nearly half of the anti-codons were absent. Molecular sequence variation analysis revealed the conservative secondary structure of tRNA. About a quarter of the tRNA genes were found to contain precoded 3’ CCA tails. A few tRNAs underwent novel structural changes that were closely related to their minimum free energy, these structural changes affected the stability of tRNA. Phylogenetic analysis showed that tRNAs have evolved from multiple common ancestors and tRNALeu was the most primitive type of tRNA. The transition rate of chloroplast tRNAs was higher than the transversion rate in gymnosperms. The tRNAs continuously have experienced more loss than duplication events during the evolutionary process. Conclusions: These findings provided novel insights into the molecular evolution and biological characteristics of the chloroplast tRNA in gymnosperms.

scholarly journals Evolution and structural variations in chloroplast tRNAs in gymnosperms

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yu-He Zhao ◽  
Tong Zhou ◽  
Jiu-Xia Wang ◽  
Yan Li ◽  
Min-Feng Fang ◽  
...  
Keyword(s):  
Structural Changes ◽  
Economic Value ◽  
Evolutionary Process ◽  
Minimum Free Energy ◽  
Trna Genes ◽  
Structural Variations ◽  
Molecular Sequence ◽  
Chloroplast Genomes ◽  
Duplication Events ◽  
The Stability

Abstract Background Chloroplast transfer RNAs (tRNAs) can participate in various vital processes. Gymnosperms have important ecological and economic value, and they are the dominant species in forest ecosystems in the Northern Hemisphere. However, the evolution and structural changes in chloroplast tRNAs in gymnosperms remain largely unclear. Results In this study, we determined the nucleotide evolution, phylogenetic relationships, and structural variations in 1779 chloroplast tRNAs in gymnosperms. The numbers and types of tRNA genes present in the chloroplast genomes of different gymnosperms did not differ greatly, where the average number of tRNAs was 33 and the frequencies of occurrence for various types of tRNAs were generally consistent. Nearly half of the anticodons were absent. Molecular sequence variation analysis identified the conserved secondary structures of tRNAs. About a quarter of the tRNA genes were found to contain precoded 3′ CCA tails. A few tRNAs have undergone novel structural changes that are closely related to their minimum free energy, and these structural changes affect the stability of the tRNAs. Phylogenetic analysis showed that tRNAs have evolved from multiple common ancestors. The transition rate was higher than the transversion rate in gymnosperm chloroplast tRNAs. More loss events than duplication events have occurred in gymnosperm chloroplast tRNAs during their evolutionary process. Conclusions These findings provide novel insights into the molecular evolution and biological characteristics of chloroplast tRNAs in gymnosperms.

A Liquid Metal Flow Between Two Coaxial Cylinders System

2019 ◽  
Vol 11 (1) ◽  
pp. 79-86
Author(s):  
Abdelkrim Merah ◽  
Ridha Kelaiaia ◽  
Faiza Mokhtari
Keyword(s):  
Couette Flow ◽  
Metal Flow ◽  
Three Dimensional ◽  
Liquid Sodium ◽  
Taylor Vortex ◽  
Turbulent Regime ◽  
Coaxial Cylinders ◽  
Concentric Cylinders ◽  
Ideal Tool ◽  
The Stability

Abstract The Taylor-Couette flow between two rotating coaxial cylinders remains an ideal tool for understanding the mechanism of the transition from laminar to turbulent regime in rotating flow for the scientific community. We present for different Taylor numbers a set of three-dimensional numerical investigations of the stability and transition from Couette flow to Taylor vortex regime of a viscous incompressible fluid (liquid sodium) between two concentric cylinders with the inner one rotating and the outer one at rest. We seek the onset of the first instability and we compare the obtained results for different velocity rates. We calculate the corresponding Taylor number in order to show its effect on flow patterns and pressure field.

Handheld Laser Scanner Research

2019 ◽  
Vol 952 (10) ◽  
pp. 47-54
Author(s):  
A.V. Komissarov ◽  
A.V. Remizov ◽  
M.M. Shlyakhova ◽  
K.K. Yambaev
Keyword(s):  
Point Cloud ◽  
Three Dimensional ◽  
Laser Scanner ◽  
Test Site ◽  
Optical Systems ◽  
Advantages And Disadvantages ◽  
Site Survey ◽  
Laser Scanners ◽  
Three Dimensional Models ◽  
The Stability

The authors consider hand-held laser scanners, as a new photogrammetric tool for obtaining three-dimensional models of objects. The principle of their work and the newest optical systems based on various sensors measuring the depth of space are described in detail. The method of simultaneous navigation and mapping (SLAM) used for combining single scans into point cloud is outlined. The formulated tasks and methods for performing studies of the DotProduct (USA) hand-held laser scanner DPI?8X based on a test site survey are presented. The accuracy requirements for determining the coordinates of polygon points are given. The essence of the performed experimental research of the DPI?8X scanner is described, including scanning of a test object at various scanner distances, shooting a test polygon from various scanner positions and building point cloud, repeatedly shooting the same area of the polygon to check the stability of the scanner. The data on the assessment of accuracy and analysis of research results are given. Fields of applying hand-held laser scanners, their advantages and disadvantages are identified.

scholarly journals Gum Tragacanth (GT): A Versatile Biocompatible Material beyond Borders

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1510 ◽  
Author(s):  
Mohammad Ehsan Taghavizadeh Yazdi ◽  
Simin Nazarnezhad ◽  
Seyed Hadi Mousavi ◽  
Mohammad Sadegh Amiri ◽  
Majid Darroudi ◽  
...  
Keyword(s):  
Tissue Engineering ◽  
Food Packaging ◽  
Three Dimensional ◽  
Great Promise ◽  
Anionic Polymer ◽  
Gum Tragacanth ◽  
New Horizons ◽  
Tissue Healing ◽  
The Stability ◽  
Therapeutic Substance

The use of naturally occurring materials in biomedicine has been increasingly attracting the researchers’ interest and, in this regard, gum tragacanth (GT) is recently showing great promise as a therapeutic substance in tissue engineering and regenerative medicine. As a polysaccharide, GT can be easily extracted from the stems and branches of various species of Astragalus. This anionic polymer is known to be a biodegradable, non-allergenic, non-toxic, and non-carcinogenic material. The stability against microbial, heat and acid degradation has made GT an attractive material not only in industrial settings (e.g., food packaging) but also in biomedical approaches (e.g., drug delivery). Over time, GT has been shown to be a useful reagent in the formation and stabilization of metal nanoparticles in the context of green chemistry. With the advent of tissue engineering, GT has also been utilized for the fabrication of three-dimensional (3D) scaffolds applied for both hard and soft tissue healing strategies. However, more research is needed for defining GT applicability in the future of biomedical engineering. On this object, the present review aims to provide a state-of-the-art overview of GT in biomedicine and tries to open new horizons in the field based on its inherent characteristics.

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