scholarly journals Evolutionary divergence of locomotion in two related vertebrate species

2021 ◽  
Author(s):  
Gokul Rajan ◽  
Julie Lafaye ◽  
Martin Carbo-Tano ◽  
Karine Duroure ◽  
Giulia Faini ◽  
...  
Keyword(s):  
Larval Fish ◽  
Beat Frequency ◽  
Brain Anatomy ◽  
Evolutionary Divergence ◽  
Environmental Constraints ◽  
Swimming Pattern ◽  
Powerful Approach ◽  
Motor Region ◽  
Swim Bladder Inflation ◽  
High Degree

AbstractLocomotion exists in diverse forms in nature and is adapted to the environmental constraints of each species1. However, little is known about how closely related species with similar neuronal circuitry can evolve different navigational strategies to explore their environments. We established a powerful approach in comparative neuroethology to investigate evolution of neuronal circuits in vertebrates by comparing divergent swimming pattern of two closely related larval fish species, Danionella translucida (DT) and Danio rerio or zebrafish (ZF)2,3. During swimming, we demonstrate that DT utilizes lower half tail-beat frequency and amplitude to generate a slower and continuous swimming pattern when compared to the burst-and-glide swimming pattern in ZF. We found a high degree of conservation in the brain anatomy between the two species. However, we revealed that the activity of a higher motor region, referred here as the Mesencephalic Locomotion Maintenance Neurons (MLMN) correlates with the duration of swim events and differs strikingly between DT and ZF. Using holographic stimulation, we show that the activation of the MLMN is sufficient to increase the frequency and duration of swim events in ZF. Moreover, we propose two characteristics, availability of dissolved oxygen and timing of swim bladder inflation, which drive the observed differences in the swim pattern. Our findings uncover the neuronal circuit substrate underlying the evolutionary divergence of navigational strategies and how they are adapted to their respective environmental constraints.

scholarly journals Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sajjad Asaf ◽  
Abdul Latif Khan ◽  
Muhammad Numan ◽  
Ahmed Al-Harrasi
Keyword(s):  
Chloroplast Genome ◽  
Related Species ◽  
Evolutionary Genetics ◽  
Single Copy ◽  
Avicennia Marina ◽  
Pairwise Distance ◽  
Trna Genes ◽  
Evolutionary Divergence ◽  
Mangrove Tree ◽  
High Degree

AbstractAvicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its comparison with related species in family Acanthaceae. Detailed next-generation sequencing and analysis showed a complete chloroplast genome of 150,279 bp, comprising 38.6% GC. Genome architecture is quadripartite revealing large single copy (82,522 bp), small single copy (17,523 bp), and pair of inverted repeats (25,117 bp). Furthermore, the genome contains 132 different genes, including 87 protein-coding genes, 8 rRNA, 37 tRNA genes, and 126 simple sequence repeats (122 mononucleotide, 2 dinucleotides, and 2 trinucleotides). Interestingly, about 25 forward, 15 reversed and 14 palindromic repeats were also found in the A. marina. High degree synteny was observed in the pairwise alignment with related genomes. The chloroplast genome comparative assessment showed a high degree of sequence similarity in coding regions and varying divergence in the intergenic spacers among ten Acanthaceae species. The pairwise distance showed that A. marina exhibited the highest divergence (0.084) with Justicia flava and showed lowest divergence with Aphelandra knappiae (0.059). Current genomic datasets are a valuable resource for investigating the population and evolutionary genetics of family Acanthaceae members’ specifically A. marina and related species.

scholarly journals Marine Prasinovirus Genomes Show Low Evolutionary Divergence and Acquisition of Protein Metabolism Genes by Horizontal Gene Transfer

2010 ◽  
Vol 84 (24) ◽  
pp. 12555-12563 ◽  
Author(s):  
Hervé Moreau ◽  
Gwenael Piganeau ◽  
Yves Desdevises ◽  
Richard Cooke ◽  
Evelyne Derelle ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Viral Evolution ◽  
Genome Comparison ◽  
Evolutionary Divergence ◽  
Gene Repertoire ◽  
Whole Genomes ◽  
Complete Sequences ◽  
Virus Genomes ◽  
High Degree ◽  
Ostreococcus Lucimarinus

ABSTRACT Although marine picophytoplankton are at the base of the global food chain, accounting for half of the planetary primary production, they are outnumbered 10 to 1 and are largely controlled by hugely diverse populations of viruses. Eukaryotic microalgae form a ubiquitous and particularly dynamic fraction of such plankton, with environmental clone libraries from coastal regions sometimes being dominated by one or more of the three genera Bathycoccus, Micromonas, and Ostreococcus (class Prasinophyceae). The complete sequences of two double-stranded (dsDNA) Bathycoccus, one dsDNA Micromonas, and one new dsDNA Ostreococcus virus genomes are described. Genome comparison of these giant viruses revealed a high degree of conservation, both for orthologous genes and for synteny, except for one 36-kb inversion in the Ostreococcus lucimarinus virus and two very large predicted proteins in Bathycoccus prasinos viruses. These viruses encode a gene repertoire of certain amino acid biosynthesis pathways never previously observed in viruses that are likely to have been acquired from lateral gene transfer from their host or from bacteria. Pairwise comparisons of whole genomes using all coding sequences with homologous counterparts, either between viruses or between their corresponding hosts, revealed that the evolutionary divergences between viruses are lower than those between their hosts, suggesting either multiple recent host transfers or lower viral evolution rates.

scholarly journals Hydrodynamic and electrophoretic properties of Trastuzumab/HER2 complexes. Experiments and modeling.

2018 ◽  
Author(s):  
Javier Ramos ◽  
Juan Francisco Vega ◽  
Victor Cruz ◽  
Eduardo Sanchez-Sanchez ◽  
Javier Cortes ◽  
...  
Keyword(s):  
Monoclonal Antibody ◽  
General Interest ◽  
Breast Cancers ◽  
Biophysical Properties ◽  
Net Charge ◽  
Her2 Protein ◽  
Electrostatic Properties ◽  
Powerful Approach ◽  
High Degree

The combination of hydrodynamic and electrophoretic experiments and computer simulations is indeed a powerful approach to study the interaction between proteins. In this work, we present hydrodynamic and electrophoretic experiments in aqueous solution along with molecular dynamics and hydrodynamic modeling to monitor and compute biophysical properties of the interactions between the extracellular domain of the HER2 protein (eHER2) and the monoclonal antibody trastuzumab (TZM). The importance of this system relies on the fact that the overexpression of HER2 protein is related with the poor prognosis breast cancers (HER2++ positives) being the TZM a monoclonal antibody for the treatment of this cancer. We have found and characterize two different complexes between the TZM and eHER2 proteins (1:1 and 1:2 TZM:eHER2 complexes). The conformational features of these complexes regulate their hydrodynamic and electrostatic properties. Thus, the results indicate a high degree of molecular flexibility in the systems, that ultimately leads to higher values of the intrinsic viscosity and as well as lower values of diffusion coefficient than those expected for simple globular proteins. A highly asymmetric charge distribution is detected for the monovalent complex (1:1 complex), which has strong implications in correlations between the experimental electrophoretic mobility and the modeled net charge. In order to understand the dynamics of these systems and the role of the specific domains involved, it is essential to find biophysical correlations between dynamics, macroscopic transport and electrostatic properties. The results should be of general interest for researchers working in this area.

scholarly journals How body torque and Strouhal number change with swimming speed and developmental stage in larval zebrafish

2015 ◽  
Vol 12 (110) ◽  
pp. 20150479 ◽  
Author(s):  
Johan L. van Leeuwen ◽  
Cees J. Voesenek ◽  
Ulrike K. Müller
Keyword(s):  
Strouhal Number ◽  
Swimming Speed ◽  
Inverse Dynamics ◽  
Larval Fish ◽  
Beat Frequency ◽  
Relative Effect ◽  
Viscous Drag ◽  
Propulsive Efficiency ◽  
Viscous Forces ◽  
Larval Zebrafish

Small undulatory swimmers such as larval zebrafish experience both inertial and viscous forces, the relative importance of which is indicated by the Reynolds number ( Re ). Re is proportional to swimming speed ( v swim ) and body length; faster swimming reduces the relative effect of viscous forces. Compared with adults, larval fish experience relatively high (mainly viscous) drag during cyclic swimming. To enhance thrust to an equally high level, they must employ a high product of tail-beat frequency and (peak-to-peak) amplitude fA tail , resulting in a relatively high fA tail / v swim ratio (Strouhal number, St), and implying relatively high lateral momentum shedding and low propulsive efficiency. Using kinematic and inverse-dynamics analyses, we studied cyclic swimming of larval zebrafish aged 2–5 days post-fertilization (dpf). Larvae at 4–5 dpf reach higher f (95 Hz) and A tail (2.4 mm) than at 2 dpf (80 Hz, 1.8 mm), increasing swimming speed and Re , indicating increasing muscle powers. As Re increases (60 → 1400), St (2.5 → 0.72) decreases nonlinearly towards values of large swimmers (0.2–0.6), indicating increased propulsive efficiency with v swim and age. Swimming at high St is associated with high-amplitude body torques and rotations. Low propulsive efficiencies and large yawing amplitudes are unavoidable physical constraints for small undulatory swimmers.

Interspecific comparison of the transformer gene of Drosophila reveals an unusually high degree of evolutionary divergence.

Genetics ◽  
1992 ◽  
Vol 131 (1) ◽  
pp. 113-128 ◽  
Author(s):  
M T O'Neil ◽  
J M Belote
Keyword(s):  
Alternative Splicing ◽  
Drosophila Virilis ◽  
Evolutionary Divergence ◽  
Sequence Comparisons ◽  
Specific Expression ◽  
Cis Acting ◽  
Conserved Sequence ◽  
Homologous Genes ◽  
Specific Alternative ◽  
High Degree

Abstract The transformer (tra) gene of Drosophila melanogaster occupies an intermediate position in the regulatory pathway controlling all aspects of somatic sexual differentiation. The female-specific expression of this gene's function is regulated by the Sex lethal (Sxl) gene, through a mechanism involving sex-specific alternative splicing of tra pre-mRNA. The tra gene encodes a protein that is thought to act in conjunction with the transformer-2 (tra-2) gene product to control the sex-specific processing of doublesex (dsx) pre-mRNA. The bifunctional dsx gene carries out opposite functions in the two sexes, repressing female differentiation in males and repressing male differentiation in females. Here we report the results from an evolutionary approach to investigate tra regulation and function, by isolating the tra-homologous genes from selected Drosophila species, and then using the interspecific DNA sequence comparisons to help identify regions of functional significance. The tra-homologous genes from two Sophophoran subgenus species, Drosophila simulans and Drosophila erecta, and two Drosophila subgenus species, Drosophila hydei and Drosophila virilis, were cloned, sequenced and compared to the D. melanogaster tra gene. This comparison reveals an unusually high degree of evolutionary divergence among the tra coding sequences. These studies also highlight a highly conserved sequence within intron one that probably defines a cis-acting regulator of the sex-specific alternative splicing event.

Genetic relationships between Native Sheep breeds in Nigeria based on microsatellite DNA polymorphisms

2004 ◽  
Vol 34 ◽  
pp. 27-39 ◽  
Author(s):  
Adebambo Olufunmilayo ◽  
J.L. Williams ◽  
Sara Blott ◽  
B. Urquhart
Keyword(s):  
Microsatellite Dna ◽  
Genetic Relationships ◽  
Genetic Distances ◽  
West African ◽  
Dna Polymorphisms ◽  
Evolutionary Divergence ◽  
West African Dwarf ◽  
Sheep Breeds ◽  
Breed Improvement ◽  
High Degree

SummaryThe genetic relationship among Nigeria's breeds of sheep and their crosses was studied using microsatellite DNA polymorphisms. DNA samples extracted from four Nigeria's breeds of sheep (West African Dwarf, the Balami, Uda and Yankassa) and their crosses were analysed using 30 Bovine microsatellite markers for diversity studies. Twenty of the markers were amplified by the sheep genome. Nineteen of the loci were polymorphic and were used to calculate genetic distances (Ds) between the breeds based on allele frequencies of the microsatellite. The phylogenetic relationships between the breeds were similarly estimated.With the total number of loci studied, 285 alleles were generated and a high degree of heterozygosity was recorded (0.57 to 0.72). A relatively high degree of reliability could be placed on the tree topology with the relationship between breeds displaying a closer relationship between the Yankassa and Uda (Ds 0.356). The genetic distance was 0.432, 0.534 and 0.665 between the West African Dwarf (WAD) and the Yankassa, Uda and Balami respectively which also indicated a closer relationship between the Yankassa and the WAD compared to the essentially Northern breeds (Uda and Balami). This further confirms the evolutionary divergence of the breeds which makes them distinct entities.The data suggests that microsatellite DNA markers are very useful tools for studying the genetic relationships among these sheep breeds. The highly polymorphic alleles could similarly be exploited in breed improvement and development.

scholarly journals Comparative development of simple and compound leaves in the genus Cecropia

Botany ◽  
2017 ◽  
Vol 95 (2) ◽  
pp. 185-193 ◽  
Author(s):  
Michael S. Ogden ◽  
Christian R. Lacroix
Keyword(s):  
Shoot Apex ◽  
Leaf Shape ◽  
Leaf Primordium ◽  
Developmental Pathways ◽  
Signalling Pathways ◽  
Evolutionary Divergence ◽  
Molecular Processes ◽  
Closely Related Species ◽  
Nonsignificant Difference ◽  
High Degree

Plants develop leaves that range from simple to compound in shape. The evolutionary divergence of simple and compound leaves has spurred research into identifying the cellular and molecular processes involved in determining leaf shape. The roles of various genes and signalling pathways have been characterized in specifying leaf shape; however, few studies have investigated leaf primordium structure and shoot apex organization throughout the development of both simple and compound leaves. Using Cecropia obtusa Trécul and Cecropia sciadophylla Martius, two putatively closely related species bearing simple palmate and palmately-compound leaves, respectively, we compared the morphogenesis of leaves of both species at the shoot apex. Analysis of shoot apices using scanning electron microscopy yielded a nonsignificant difference in leaf primordium divergence angles and plastochron ratios, suggesting that divergence of the two leaf types occurred independently of primordium organization and growth rate at the shoot apex. Qualitative analysis of primordium initiation and morphogenesis revealed that both species share highly homologous development, as primordium structure and lobe/leaflet initiation sites are complementary in both leaf types. Our observations suggest a high degree of conserved ontogeny in the developmental pathways underlying the morphogenesis of simple palmate and palmately-compound leaves in these two species.

scholarly journals GENETIC RELATIONSHIPS BETWEEN NATIVE SHEEP BREEDS IN NIGERIA BASED ON MICROSATELLITE DNA POLYMORPHISMS.

2021 ◽  
Vol 27 ◽  
pp. 1-8
Author(s):  
O. ADEBAMBO ◽  
J. I. WILLAMS ◽  
S. BLOTT ◽  
B. URQUHART
Keyword(s):  
Genetic Relationship ◽  
Microsatellite Dna ◽  
Genetic Relationships ◽  
Genetic Distances ◽  
Dna Polymorphisms ◽  
Evolutionary Divergence ◽  
Microsatellite Dna Markers ◽  
Diversity Studies ◽  
High Degree ◽  
The Relationship

Genetic relationship among Nigeria's breeds of sheeps and crosses was studied using microsatellite DNA polymorphisms. DNA samples extracted from four Nigeria's breeds of sheeps (West African Dwarf,the balami, Uda and yankassa) and crosses were analysed using 30 microsatellite markers for diversity studies. Twenty of the makers were by the sheeps genome . Nineteen of the loci were polymorphic and were used to calculate genetic distances (Ds) between the based on allelefrequences of microsatellite. The phylogenetic relatioship between the breeds were similarly estimated. With the total number of loci studied, 285 alleles were generated and a high decree of heterozysity was recorded, (0.57 to 0.72), a relative high degree of relaibility could be placed on the tree topology with the relationship between breeds potraying a closer relationship between the yankassa and Uda (Ds 0.356). The genetic distance (Ds) was 0.432, 0.534 and 0.665 between the African Dwarf and the Yankassa, Uda and Balami respectively also indictating a closer relatioship between the Yankassa, and the WAD compared to the basically Northern breeds (Uda and Balami). This further confirms the evolutionary divergence of the breeds which makes them distint entitles. The data suggests that microsatellite DNA markers are useful tools for studying the genetic relationship among these sheeps breeds. The high polymorphic alleles could thus be exploited in breeds improvement and development.

Application of Chiral Isocyanides in Multicomponent Reactions

2020 ◽  
Vol 24 (2) ◽  
pp. 162-183 ◽  
Author(s):  
Vaezeh Fathi Vavsari ◽  
Pegah Shakeri ◽  
Saeed Balalaie
Keyword(s):  
Organic Synthesis ◽  
Multicomponent Reactions ◽  
Structural Diversity ◽  
Building Blocks ◽  
Willingness To Participate ◽  
Metal Centers ◽  
Wide Range ◽  
Powerful Approach ◽  
One Step ◽  
High Degree

As one of the most important building blocks in organic synthesis, isocyanides come in for a wide range of transformations owing mostly to their unusual terminal carbon center adsorbed electrophiles, reacted with nucleophiles, get involved in radical reactions and coordinated with metal centers. The distinctive feature of isocyanide is its ready willingness to participate in multicomponent reactions (MCRs). MCRs represent a great tool in organic synthesis for the construction of new lead structures in a single procedure introducing both structural diversity and molecular complexity in only one step. Isocyanide-based multicomponent reactions (IMCRs) have become a powerful approach for the synthesis of complex molecules providing high degree of atom and bond economy under very mild reaction conditions. The use of enantiomerically pure isocyanides can, in principle, bring about two advantages: (i) the possibility to obtain a stereochemically diverse adduct, controlling the absolute configuration of the starting isocyanide; and (ii) the possibility to induce diastereoselection in the multicomponent reaction. The most commonly-used IMCRs are the Ugi and Passerini reactions. Many published reviews have focused on the Ugi and Passerini reactions from different viewpoints, but this review describes advances in the application of chiral isocyanides in MCRs. The rationale for applying such diversity generating chemistries is also discussed.

scholarly journals Hydrodynamic and Electrophoretic Properties of Trastuzumab/HER2 Extracellular Domain Complexes as Revealed by Experimental Techniques and Computational Simulations

2019 ◽  
Vol 20 (5) ◽  
pp. 1076
Author(s):  
Javier Ramos ◽  
Juan Francisco Vega ◽  
Victor Cruz ◽  
Eduardo Sanchez-Sanchez ◽  
Javier Cortes ◽  
...  
Keyword(s):  
Monoclonal Antibody ◽  
Extracellular Domain ◽  
General Interest ◽  
Breast Cancers ◽  
Net Charge ◽  
Her2 Protein ◽  
Electrostatic Properties ◽  
Powerful Approach ◽  
High Degree

The combination of hydrodynamic and electrophoretic experiments and computer simulations is a powerful approach to study the interaction between proteins. In this work, we present hydrodynamic and electrophoretic experiments in an aqueous solution along with molecular dynamics and hydrodynamic modeling to monitor and compute biophysical properties of the interactions between the extracellular domain of the HER2 protein (eHER2) and the monoclonal antibody trastuzumab (TZM). The importance of this system relies on the fact that the overexpression of HER2 protein is related with the poor prognosis breast cancers (HER2++ positives), while the TZM is a monoclonal antibody for the treatment of this cancer. We have found and characterized two different complexes between the TZM and eHER2 proteins (1:1 and 1:2 TZM:eHER2 complexes). The conformational features of these complexes regulate their hydrodynamic and electrostatic properties. Thus, the results indicate a high degree of molecular flexibility in the systems that ultimately leads to higher values of the intrinsic viscosity, as well as lower values of diffusion coefficient than those expected for simple globular proteins. A highly asymmetric charge distribution is detected for the monovalent complex (1:1 complex), which has strong implications in correlations between the experimental electrophoretic mobility and the modeled net charge. In order to understand the dynamics of these systems and the role of the specific domains involved, it is essential to find biophysical correlations between dynamics, macroscopic transport and electrostatic properties. The results should be of general interest for researchers working in this area.

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