scholarly journals Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics

2018 ◽  
Vol 285 (1885) ◽  
pp. 20181524 ◽  
Author(s):  
Martin Schwentner ◽  
Stefan Richter ◽  
D. Christopher Rogers ◽  
Gonzalo Giribet
Keyword(s):  
Amino Acid ◽  
Analytical Methods ◽  
Special Focus ◽  
Evolutionary Models ◽  
Phylogenomic Analyses ◽  
New Generation ◽  
Analytical Approaches ◽  
Internal Relationships ◽  
Complete Matrix ◽  
Phylogenomic Study

Understanding the evolution of Tetraconata or Pancrustacea—the clade that includes crustaceans and insects—requires a well-resolved hypothesis regarding the relationships within and among its constituent taxa. Here, we assembled a taxon-rich phylogenomic dataset focusing on crustacean lineages based solely on genomes and new-generation Illumina-generated transcriptomes, including 89 representatives of Tetraconata. This constitutes, to our knowledge, the first phylogenomic study specifically addressing internal relationships of Malacostraca (with 26 species included) and Branchiopoda (36 species). Seven matrices comprising 81–684 orthogroups and 17 690–242 530 amino acid positions were assembled and analysed under five different analytical approaches. To maximize gene occupancy and to improve resolution, taxon-specific matrices were designed for Malacostraca and Branchiopoda. Key tetraconatan taxa (i.e. Oligostraca, Multicrustacea, Branchiopoda, Malacostraca, Thecostraca, Copepoda and Hexapoda) were monophyletic and well supported. Within Branchiopoda, Phyllopoda, Diplostraca, Cladoceromorpha and Cladocera were monophyletic. Within Malacostraca, the clades Eumalacostraca, Decapoda and Reptantia were well supported. Recovery of Caridoida or Peracarida was highly dependent on the analysis for the complete matrix, but it was consistently monophyletic in the malacostracan-specific matrices. From such examples, we demonstrate that taxon-specific matrices and particular evolutionary models and analytical methods, namely CAT-GTR and Dayhoff recoding, outperform other approaches in resolving certain recalcitrant nodes in phylogenomic analyses.

scholarly journals Phylogenetic Analysis: Basic Concepts and Its Use as a Tool for Virology and Molecular Epidemiology

2018 ◽  
Vol 44 (1) ◽  
pp. 20
Author(s):  
Eloiza Teles Caldart ◽  
Helena Mata ◽  
Cláudio Wageck Canal ◽  
Ana Paula Ravazzolo
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Molecular Epidemiology ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Evolutionary Process ◽  
Amino Acid Sequences ◽  
Evolutionary Models ◽  
Reconstruction Methods ◽  
Basic Concepts

Background: Phylogenetic analyses are an essential part in the exploratory assessment of nucleic acid and amino acid sequences. Particularly in virology, they are able to delineate the evolution and epidemiology of disease etiologic agents and/or the evolutionary path of their hosts. The objective of this review is to help researchers who want to use phylogenetic analyses as a tool in virology and molecular epidemiology studies, presenting the most commonly used methodologies, describing the importance of the different techniques, their peculiar vocabulary and some examples of their use in virology.Review: This article starts presenting basic concepts of molecular epidemiology and molecular evolution, emphasizing their relevance in the context of viral infectious diseases. It presents a session on the vocabulary relevant to the subject, bringing readers to a minimum level of knowledge needed throughout this literature review. Within its main subject, the text explains what a molecular phylogenetic analysis is, starting from a multiple alignment of nucleotide or amino acid sequences. The different software used to perform multiple alignments may apply different algorithms. To build a phylogeny based on amino acid or nucleotide sequences it is necessary to produce a data matrix based on a model for nucleotide or amino acid replacement, also called evolutionary model. There are a number of evolutionary models available, varying in complexity according to the number of parameters (transition, transversion, GC content, nucleotide position in the codon, among others). Some papers presented herein provide techniques that can be used to choose evolutionary models. After the model is chosen, the next step is to opt for a phylogenetic reconstruction method that best fits the available data and the selected model. Here we present the most common reconstruction methods currently used, describing their principles, advantages and disadvantages. Distance methods, for example, are simpler and faster, however, they do not provide reliable estimations when the sequences are highly divergent. The accuracy of the analysis with probabilistic models (neighbour joining, maximum likelihood and bayesian inference) strongly depends on the adherence of the actual data to the chosen development model. Finally, we also explore topology confidence tests, especially the most used one, the bootstrap. To assist the reader, this review presents figures to explain specific situations discussed in the text and numerous examples of previously published scientific articles in virology that demonstrate the importance of the techniques discussed herein, as well as their judicious use.Conclusion: The DNA sequence is not only a record of phylogeny and divergence times, but also keeps signs of how the evolutionary process has shaped its history and also the elapsed time in the evolutionary process of the population. Analyses of genomic sequences by molecular phylogeny have demonstrated a broad spectrum of applications. It is important to note that for the different available data and different purposes of phylogenies, reconstruction methods and evolutionary models should be wisely chosen. This review provides theoretical basis for the choice of evolutionary models and phylogenetic reconstruction methods best suited to each situation. In addition, it presents examples of diverse applications of molecular phylogeny in virology.

scholarly journals Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 302
Author(s):  
Malik Sallam ◽  
Azmi Mahafzah
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Rapid Evolution ◽  
Molecular Signature ◽  
Special Focus ◽  
Genetic Lineage ◽  
Synonymous Mutation ◽  
Spike Gene ◽  
Genetic Lineages ◽  
The Uk

The rapid evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is manifested by the emergence of an ever-growing pool of genetic lineages. The aim of this study was to analyze the genetic variability of SARS-CoV-2 in Jordan, with a special focus on the UK variant of concern. A total of 579 SARS-CoV-2 sequences collected in Jordan were subjected to maximum likelihood and Bayesian phylogenetic analysis. Genetic lineage assignment was undertaken using the Pango system. Amino acid substitutions were investigated using the Protein Variation Effect Analyzer (PROVEAN) tool. A total of 19 different SARS-CoV-2 genetic lineages were detected, with the most frequent being the first Jordan lineage (B.1.1.312), first detected in August 2020 (n = 424, 73.2%). This was followed by the second Jordan lineage (B.1.36.10), first detected in September 2020 (n = 62, 10.7%), and the UK variant of concern (B.1.1.7; n = 36, 6.2%). In the spike gene region, the molecular signature for B.1.1.312 was the non-synonymous mutation A24432T resulting in a deleterious amino acid substitution (Q957L), while the molecular signature for B.1.36.10 was the synonymous mutation C22444T. Bayesian analysis revealed that the UK variant of concern (B.1.1.7) was introduced into Jordan in late November 2020 (mean estimate); four weeks earlier than its official reporting in the country. In Jordan, an exponential increase in COVID-19 cases due to B.1.1.7 lineage coincided with the new year 2021. The highest proportion of phylogenetic clustering was detected for the B.1.1.7 lineage. The amino acid substitution D614G in the spike glycoprotein was exclusively present in the country from July 2020 onwards. Two Jordanian lineages dominated infections in the country, with continuous introduction/emergence of new lineages. In Jordan, the rapid spread of the UK variant of concern should be monitored closely. The spread of SARS-CoV-2 mutants appeared to be related to the founder effect; nevertheless, the biological impact of certain mutations should be further investigated.

DIMENSIONING OF ORTHOTROPICALLY STIFFENED CFRP SHELLS OF LARGE LAUNCH VEHICLES FOR LOAD INTRODUCTION AND STABILITY

2010 ◽  
Vol 10 (04) ◽  
pp. 601-621 ◽  
Author(s):  
ANDREAS RITTWEGER ◽  
SUSANNE CHRISTIANSON ◽  
HUBA ÖRY
Keyword(s):  
Analytical Methods ◽  
Flux Distribution ◽  
Fe Analysis ◽  
Launch Vehicles ◽  
Local Instability ◽  
Axial Loads ◽  
Ring Frame ◽  
Final Design ◽  
Shell Equations ◽  
Analytical Approaches

The dimensioning of an orthotropically stiffened cylindrical CFRP shell subjected to the introduction of concentrated axial loads using rapid analytical methods is presented. For stress calculation the shell equations are simplified by applying the semibending theory and integrated by employing the transfer matrix method. Analytical approaches are used for stability verification. The dimensioning considers required constraints in the force flux distribution, strength of the laminate, general instability, panel instability (from ring frame to ring frame) and local instability. The rapid analytical methods allow mass optimization. The final design is confirmed by detailed FE analysis. A comparison of the FE analysis with the analytical results is shown.

Pincer ligands based on α-amino acids: V. New generation chiral receptors for the recognition of amino acid enantiomers in aqueous environment

2011 ◽  
Vol 47 (2) ◽  
pp. 193-201
Author(s):  
N. E. Borisova ◽  
F. E. Zhurkin ◽  
T. G. Gulevich ◽  
K. K. Babievskii ◽  
M. D. Reshetova ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Pincer Ligands ◽  
Aqueous Environment ◽  
Amino Acid Enantiomers ◽  
New Generation ◽  
Chiral Receptors

Targeting histidine for developing a new generation of covalent enzyme inhibitors

2021 ◽  
Vol 17 ◽  
Author(s):  
Donald Poirier
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Drug Development ◽  
Chemical Bond ◽  
Amino Acid Residue ◽  
Enzyme Inhibitors ◽  
Irreversible Inhibitors ◽  
Covalent Inhibitors ◽  
Targeted Inhibitors ◽  
New Generation

: Despite the significant number of irreversible inhibitors developed over the years, strong prejudices remain for this type of therapeutic molecule, particularly in the area of drug development. New generations of covalent targeted inhibitors are, however, in development, and interest is increasingly growing. In fact, the new generation of covalent inhibitors has a weakly reactive species (warhead) that is able, in a particular context, to selectively form a chemical bond with a given amino acid residue, which can be irreversible or reversible. In addition to new selective warheads, new amino acids are also targeted. In the following text, we will focus on covalent targeted inhibitors that selectively alkylate histidine.

Recent Developments of Micropattern Detectors

2014 ◽  
pp. 156-194
Keyword(s):  
Large Hadron Collider ◽  
Visible Light ◽  
Parallel Plate ◽  
Hadron Collider ◽  
Special Focus ◽  
Large Area ◽  
Special Place ◽  
Recent Developments ◽  
New Generation ◽  
Detector Technology

In this chapter, the exciting developments in micropattern detectors in recent years are described. This includes GEM and MICROMEGAS detectors combined with micropixel readout, some peculiar designs of GEM and GEM-like detectors sensitive to UV and visible light, large area (>1m2) GEM and MICROMEGAS prototypes developed for the upgrades of the experiments at the large hadron collider, etc. A special focus is put on a new generation of spark-proof micropattern detectors, using resistive electrodes instead of traditional metallic ones. These detectors operate as ordinary micropattern detectors. However, in the case of occasional sparks, their current is limited by the resistivity of the electrodes so that the energy of the discharge is reduced by several orders of magnitude. Various designs of such detectors have been developed and successfully tested, including resistive GEM, resistive MICROMEGAS, resistive MSGC, etc. Among this family of detectors, a special place belongs to resistive parallel-plate micropattern detectors allowing one to achieve at the same time excellent spatial (38 µm) and time (77 ps) resolutions. Finally, the potential of multilayer detector technology for further optimization of the detector operation is discussed.

Molecular and Cellular Pathogenesis of Depression and Mechanisms for Treatment Response

2013 ◽  
pp. 425-437
Author(s):  
Ronald S. Duman
Keyword(s):  
Amino Acid ◽  
Neurotrophic Factors ◽  
Limbic Structures ◽  
Brain Circuits ◽  
Antidepressant Agent ◽  
Treatment Of Depression ◽  
Cellular Pathogenesis ◽  
Gaba Transmission ◽  
Stress Models ◽  
New Generation

Early theories of depression were centered on the monoamines, but more recent work has focused on the amino acid neurotransmitters, glutamate and GABA. Imbalances of glutamate and GABA transmission in key cortical and limbic structures are thought to contribute to disruption of brain circuits that control emotion and mood. These imbalances, together with stress activated pathways that regulate neurotrophic factors and inflammatory cytokines could contribute to atrophy and loss of neurons observed in depressed patients and rodent stress models. The significance of synaptic connections in depression is highlighted by new studies demonstrating that a rapid acting, highly efficacious antidepressant agent increases synaptogenesis, paving the way for a new generation of medications for the treatment of depression.

Sign in / Sign up

Export Citation Format

Share Document