scholarly journals Habitat-dependent diversification and parallel molecular evolution: Water scavenger beetles as a case study

2014 ◽  
Vol 60 (5) ◽  
pp. 561-570 ◽  
Author(s):  
Ke-Qing Song ◽  
Huai-Jun Xue ◽  
Rolf G. Beutel ◽  
Ming Bai ◽  
Dong-Ju Bian ◽  
...  
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Phylogenetic Trees ◽  
Habitat Type ◽  
Diversification Rate ◽  
Key Innovation ◽  
Evolutionary Changes ◽  
Habitat Factors ◽  
And Shifts

Abstract Habitat shift is a key innovation that has contributed to the extreme diversification of insects. Most groups are well-adapted to more or less specific environments and shifts usually only happen between similar habitats. To colonize a profoundly different habitat type does not only present ecological opportunities but also great challenges. We used Hydrophiloidea (water scavenger beetles) as a system to study transitions between terrestrial and aquatic environments. We estimated the diversification rate of different clades using phylogenetic trees based on a representative taxon sampling and six genes. We also investigated possible evolutionary changes in candidate genes following habitat shifts. Our results suggest that the diversification rate is relatively slow (0.039?0.050 sp/My) in the aquatic lineage, whereas it is distinctly increased in the secondarily terrestrial clade (0.055?0.075 sp/My). Our results also show that aquatic species have a G (Glycine) or S (Serine) amino acid at a given site of COI, while terrestrial species share an A (Alanine) amino acid with terrestrial outgroups. This indicates that habitat factors may create selection pressure on the evolution of functional genes and cause homoplasy in molecular evolution.

scholarly journals Molecular evolution of enolase.

2005 ◽  
Vol 52 (2) ◽  
pp. 507-513 ◽  
Author(s):  
Michał Piast ◽  
Irena Kustrzeba-Wójcicka ◽  
Małgorzata Matusiewicz ◽  
Teresa Banaś
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Functional Diversity ◽  
Phylogenetic Trees ◽  
Amino Acid Sequences ◽  
Evolutionary Relationships ◽  
Sort Intolerant From Tolerant ◽  
Alpha Beta ◽  
Gamma Enolase ◽  
Program Show

Enolase (EC 4.2.1.11) is an enzyme of the glycolytic pathway catalyzing the dehydratation reaction of 2-phosphoglycerate. In vertebrates the enzyme exists in three isoforms: alpha, beta and gamma. The amino-acid and nucleotide sequences deposited in the GenBank and SwissProt databases were subjected to analysis using the following bioinformatic programs: ClustalX, GeneDoc, MEGA2 and S.I.F.T. (sort intolerant from tolerant). Phylogenetic trees of enolases created with the use of the MEGA2 program show evolutionary relationships and functional diversity of the three isoforms of enolase in vertebrates. On the basis of calculations and the phylogenetic trees it can be concluded that vertebrate enolase has evolved according to the "birth and death" model of evolution. An analysis of amino acid sequences of enolases: non-neuronal (NNE), neuron specific (NSE) and muscle specific (MSE) using the S.I.F.T. program indicated non-uniform number of possible substitutions. Tolerated substitutions occur most frequently in alpha-enolase, while the lowest number of substitutions has accumulated in gamma-enolase, which may suggest that it is the most recently evolved isoenzyme of enolase in vertebrates.

scholarly journals ‘I’m not being paid for this conversation’: Uncovering the challenges of artist–academic collaborations in the neoliberal institution

2019 ◽  
Vol 23 (3) ◽  
pp. 317-333
Author(s):  
Alena Pfoser ◽  
Sara de Jong
Keyword(s):  
Collaborative Work ◽  
Knowledge Exchange ◽  
Academic Research ◽  
The Political ◽  
Institutional Pressures ◽  
Negative Effects ◽  
Collective Response ◽  
And Shifts ◽  
The Impact

Artist–academic collaborations are fuelled by increasing institutional pressures to show the impact of academic research. This article departs from the celebratory accounts of collaborative work and pragmatic toolkits for successful partnerships, which are dominant in existing scholarship, arguing for the need to critically interrogate the structural conditions under which collaborations take place. Based on a reflexive case study of a project developed in the context of Tate Exchange, one of the UK’s highest-profile platforms for knowledge exchange, we reveal three sets of (unequal) pressures, which mark artist–academic collaborations in the contemporary neoliberal academy: asymmetric funding and remuneration structures; uneven pressures of audit cultures; acceleration and temporal asymmetries. Innovations at the level of individual projects or partners can only mitigate the negative effects to a limited extent. Instead this article offers a systemic critique of the political economy of artist–academic collaborations and shifts the research agenda to developing a collective response.

Specific features of supramolecular organisation and hydrogen bonding in proline cocrystals: a case study of fenamates and diclofenac

CrystEngComm ◽  
2018 ◽  
Vol 20 (43) ◽  
pp. 6970-6981 ◽  
Author(s):  
Artem O. Surov ◽  
Alexander P. Voronin ◽  
Mikhail V. Vener ◽  
Andrei V. Churakov ◽  
German L. Perlovich
Keyword(s):  
Hydrogen Bonding ◽  
Amino Acid ◽  
Naturally Occurring ◽  
Supramolecular Organisation

New zwitterionic cocrystals of fenamate drugs and diclofenac with the naturally occurring amino acid l-proline have been obtained and thoroughly characterised by a variety of experimental and theoretical techniques.

scholarly journals Evolution and Adaptation of the Avian H7N9 Virus into the Human Host

2020 ◽  
Vol 8 (5) ◽  
pp. 778
Author(s):  
Andrew T. Bisset ◽  
Gerard F. Hoyne
Keyword(s):  
Amino Acid ◽  
Avian Influenza ◽  
Influenza A ◽  
Amino Acid Sequences ◽  
Influenza Viruses ◽  
Amino Acid Substitutions ◽  
Upper Respiratory Tract ◽  
Viral Polymerase ◽  
Evolutionary Changes ◽  
Avian Origin

Influenza viruses arise from animal reservoirs, and have the potential to cause pandemics. In 2013, low pathogenic novel avian influenza A(H7N9) viruses emerged in China, resulting from the reassortment of avian-origin viruses. Following evolutionary changes, highly pathogenic strains of avian influenza A(H7N9) viruses emerged in late 2016. Changes in pathogenicity and virulence of H7N9 viruses have been linked to potential mutations in the viral glycoproteins hemagglutinin (HA) and neuraminidase (NA), as well as the viral polymerase basic protein 2 (PB2). Recognizing that effective viral transmission of the influenza A virus (IAV) between humans requires efficient attachment to the upper respiratory tract and replication through the viral polymerase complex, experimental evidence demonstrates the potential H7N9 has for increased binding affinity and replication, following specific amino acid substitutions in HA and PB2. Additionally, the deletion of extended amino acid sequences in the NA stalk length was shown to produce a significant increase in pathogenicity in mice. Research shows that significant changes in transmissibility, pathogenicity and virulence are possible after one or a few amino acid substitutions. This review aims to summarise key findings from that research. To date, all strains of H7N9 viruses remain restricted to avian reservoirs, with no evidence of sustained human-to-human transmission, although mutations in specific viral proteins reveal the efficacy with which these viruses could evolve into a highly virulent and infectious, human-to-human transmitted virus.

scholarly journals Techniques for the verification of minimal phylogenetic trees illustrated with ten mammalian haemoglobin sequences

1980 ◽  
Vol 187 (1) ◽  
pp. 65-74 ◽  
Author(s):  
D Penny ◽  
M D Hendy ◽  
L R Foulds
Keyword(s):  
Amino Acid ◽  
Phylogenetic Tree ◽  
Protein Sequence ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Protein Sequences ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Minimal Tree ◽  
Protein Sequence Data

We have recently reported a method to identify the shortest possible phylogenetic tree for a set of protein sequences [Foulds Hendy & Penny (1979) J. Mol. Evol. 13. 127–150; Foulds, Penny & Hendy (1979) J. Mol. Evol. 13, 151–166]. The present paper discusses issues that arise during the construction of minimal phylogenetic trees from protein-sequence data. The conversion of the data from amino acid sequences into nucleotide sequences is shown to be advantageous. A new variation of a method for constructing a minimal tree is presented. Our previous methods have involved first constructing a tree and then either proving that it is minimal or transforming it into a minimal tree. The approach presented in the present paper progressively builds up a tree, taxon by taxon. We illustrate this approach by using it to construct a minimal tree for ten mammalian haemoglobin alpha-chain sequences. Finally we define a measure of the complexity of the data and illustrate a method to derive a directed phylogenetic tree from the minimal tree.

scholarly journals MOLECULAR AND GENETIC CHARACTERISTICS OF SURFACE AND NONSTRUCTURE PROTEINS OF PANDEMIC INFLUENZA VIRUSES A(H1N1)PDM09 IN 2015-2016 EPIDEMIC SEASON

2016 ◽  
Vol 72 (2) ◽  
pp. 44-48
Author(s):  
O. Smutko ◽  
L. Radchenko ◽  
A. Mironenko
Keyword(s):  
Amino Acid ◽  
Pandemic Influenza ◽  
Influenza A ◽  
Phylogenetic Trees ◽  
Influenza Viruses ◽  
Amino Acid Substitutions ◽  
Ns1 Protein ◽  
Genetic Characteristics ◽  
Epidemic Season ◽  
Influenza A H1n1

The aim of the present study was identifying of molecular and genetic changes in hemaglutinin (HA), neuraminidase (NA) and non-structure protein (NS1) genes of pandemic influenza A(H1N1)pdm09 strains, that circulated in Ukraine during 2015-2016 epidemic season. Samples (nasopharyngeal swabs from patients) were analyzed using real-time polymerase chain reaction (RTPCR). Phylogenetic trees were constructed using MEGA 7 software. 3D structures were constructed in Chimera 1.11.2rc software. Viruses were collected in 2015-2016 season fell into genetic group 6B and in two emerging subgroups, 6B.1 and 6B.2 by gene of HA and NA. Subgroups 6B.1 and 6B.2 are defined by the following amino acid substitutions. In the NS1 protein were identified new amino acid substitutions D2E, N48S, and E125D in 2015-2016 epidemic season. Specific changes were observed in HA protein antigenic sites, but viruses saved similarity to vaccine strain. NS1 protein acquired substitution associated with increased virulence of the influenza virus.

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