Comparison of Arctic and Antarctic teleost haemoglobins: primary structure, function and phytogeny

2004 ◽  
Vol 16 (1) ◽  
pp. 59-69 ◽  
Author(s):  
CINZIA VERDE ◽  
ELIO PARISI ◽  
GUIDO DI PRISCO

Organisms living in the Arctic and Antarctic are exposed to strong environmental constraints, especially temperature. Consequently, haemoglobin evolution has included adaptations with implications at the biochemical, physiological and molecular levels. The northern and southern polar oceans have very different oceanographic characteristics. Within the study of the molecular bases of cold adaptation in fish inhabiting polar habitats, and taking advantage of the information available on haemoglobin structure and function, we analysed the evolutionary history of the α and β globins of Antarctic and Arctic haemoglobins, under the assumption of the molecular-clock hypothesis, as a basis for reconstructing the phylogenetic relationships between species. Temperate fish, including two non-Antarctic notothenioids of special evolutionary interest, were also considered. Phylogenetic analysis was performed on the multiple sequence alignments constructed with the programme Clustal X. Tree topologies indicate that the chains of Antarctic major and minor haemoglobins cluster in two well separated groups and diverged prior to cold adaptation, forming a monophyletic group. In Arctic haemoglobins, the structure/function relationship reveals important differences in comparison with Antarctic ones, indicating a distinct evolutionary pathway. The Arctic ichthyofauna (unlike the Antarctic, dominated by one taxonomically uniform group) is characterized by high diversity, reflected in the phylogeny of a given trait. The constant physico-chemical conditions of the Antarctic waters are matched by a clear grouping of fish globin sequences, whereas the variability typical of the Arctic Ocean corresponds to high sequence variation, reflected in the trees by scattered intermediate positions between the Antarctic and non-Antarctic clades. The evolutionary history of the Root effect, an important physiological feature of fish haemoglobin, was investigated. Analysis of the fate of the residues of the β chains suggested to be correlated with the Root effect indicate that they should rather be regarded as ancestral characters, inherited by some species but not by others.

2020 ◽  
Vol 21 (2) ◽  
pp. 513 ◽  
Author(s):  
Marzia Tindara Venuto ◽  
Mathieu Decloquement ◽  
Joan Martorell Ribera ◽  
Maxence Noel ◽  
Alexander Rebl ◽  
...  

We identified and analyzed α2,8-sialyltransferases sequences among 71 ray-finned fish species to provide the first comprehensive view of the Teleost ST8Sia repertoire. This repertoire expanded over the course of Vertebrate evolution and was primarily shaped by the whole genome events R1 and R2, but not by the Teleost-specific R3. We showed that duplicated st8sia genes like st8sia7, st8sia8, and st8sia9 have disappeared from Tetrapods, whereas their orthologues were maintained in Teleosts. Furthermore, several fish species specific genome duplications account for the presence of multiple poly-α2,8-sialyltransferases in the Salmonidae (ST8Sia II-r1 and ST8Sia II-r2) and in Cyprinus carpio (ST8Sia IV-r1 and ST8Sia IV-r2). Paralogy and synteny analyses provided more relevant and solid information that enabled us to reconstruct the evolutionary history of st8sia genes in fish genomes. Our data also indicated that, while the mammalian ST8Sia family is comprised of six subfamilies forming di-, oligo-, or polymers of α2,8-linked sialic acids, the fish ST8Sia family, amounting to a total of 10 genes in fish, appears to be much more diverse and shows a patchy distribution among fish species. A focus on Salmonidae showed that (i) the two copies of st8sia2 genes have overall contrasted tissue-specific expressions, with noticeable changes when compared with human co-orthologue, and that (ii) st8sia4 is weakly expressed. Multiple sequence alignments enabled us to detect changes in the conserved polysialyltransferase domain (PSTD) of the fish sequences that could account for variable enzymatic activities. These data provide the bases for further functional studies using recombinant enzymes.


2021 ◽  
Author(s):  
Caitlin Cherryh ◽  
Bui Quang Minh ◽  
Rob Lanfear

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness


2009 ◽  
Vol 1 (1) ◽  
pp. 145-174
Author(s):  
David Leary

Abstract Bioprospecting is occurring in the Arctic and Antarctica. This paper considers evidence on the nature and scale of bioprospecting in the Polar Regions. The paper then aims to draw out some of the critical issues in this debate by examining recent developments in the context of the Antarctic Treaty System. After an introduction to the history of the debate on bioprospecting in the Antarctic context it examines the recent Report of the Antarctic Treaty Consultative Meeting (‘ATCM’) Intersessional Contact Group to examine the issue of Biologocal Prospecting in the Antarctic Treaty Area tabled at ATCM XVII in Kiev in June 2008. The paper then concludes with some brief thoughts on the relevance of the Arctic experience to the debate in relation to Antarctica and whether or not there is an ‘Arctic Model’ for a response to the bioprospecting question in Antarctica. It is argued that rather than there being one Arctic model there is in fact a spectrum of models and experiences to choose from.


2004 ◽  
Vol 85 (4) ◽  
pp. 601-610 ◽  
Author(s):  
Aren A. Eddingsaas ◽  
Brandy K. Jacobsen ◽  
Enrique P. Lessa ◽  
Joseph A. Cook

Parasitology ◽  
2017 ◽  
Vol 144 (11) ◽  
pp. 1426-1432 ◽  
Author(s):  
T. LEPORE ◽  
P. M. BARTLEY ◽  
F. CHIANINI ◽  
A. I. MACRAE ◽  
E. A. INNES ◽  
...  

SUMMARYNeck samples from 54 badgers and 32 tongue samples of the same badgers (Meles meles), collected in the Lothians and Borders regions of Scotland, were tested using polymerase chain reactions (PCRs) directed against the 18S ribosomal DNA and the internal transcribed spacer (ITS1) region of protozoan parasites of the family Sarcocystidae. Positive results were obtained from 36/54 (67%) neck and 24/32 (75%) tongue samples using an 18S rDNA PCR. A 468 base pair consensus sequence that was generated from the 18S rDNA PCR amplicons (KX229728) showed 100% identity to Sarcocystis lutrae. The ITS1 PCR results revealed that 12/20 (60%) neck and 10/20 (50%) tongue samples were positive for Sarcocystidae DNA. A 1074 bp consensus sequence was generated from the ITS1 PCR amplicons (KX431307) and showed 100% identity to S. lutrae. Multiple sequence alignments and phylogenetic analysis support the finding that the rDNA found in badgers is identical to that of S. lutrae. This parasite has not been previously reported in badgers or in the UK. Sarcocystis lutrae has previously only been detected in tongue, skeletal muscle and diaphragm samples of the Eurasian otter (Lutra lutra) in Norway and potentially in the Arctic fox (Vulpes lagopus).


Author(s):  
Yisong Li ◽  
Ying Huang

Sialic acids play essential roles in the physiology of humans and other metazoan animals, and microbial sialic acid catabolism (SAC) is one of the processes critical for pathogenesis. To date, microbial SAC is studied mainly in commensals and pathogens, while its distribution in free-living microbes and evolutionary pathway remain largely unexplored.


Polar Record ◽  
2003 ◽  
Vol 39 (4) ◽  
pp. 369-383 ◽  
Author(s):  
John S. Poland ◽  
Martin J. Riddle ◽  
Barbara A. Zeeb

Contaminants, in freezing ground or elsewhere in the world, are of concern not simply because of their presence but because of their potential for detrimental effects on human health, the biota, or other valued aspects of the environment. Understanding these effects is central to any attempt to manage or remediate contaminated land. The polar regions are different from other parts of the world, and it would be naïve to assume that the mass of information developed in temperate regions can be applied without modification to the polar regions. Despite their obvious environmental similarities, there are important differences between the Arctic and Antarctic. The landmass of the Arctic is much warmer than that of the Antarctic and as a result has a much greater diversity and abundance of flora. Because of its proximity to industrial areas in the Northern Hemisphere, the Arctic also experiences a higher input of contaminants via long-range aerial transport. In addition, the Arctic, with its indigenous population and generally undisputed territorial claims, has long been the subject of resource utilisation, including harvesting of living resources, mineral extraction, and the construction of military infrastructure. The history of human activity in Antarctica is relatively brief, but in this time there has been a series of quite distinct phases, culminating in the Antarctic now holding a unique position in the world. Activities in the Antarctic are governed by the Antarctic Treaty, which contains provisions dealing with environmental matters. The differences between the polar regions and the rest of the world, and between the Arctic and the Antarctic, significantly affect scientific and engineering approaches to the remediation of contamination in polar regions. This paper compares and contrasts the Arctic and Antarctic with respect to geography, configuration, habitation, logistics, environmental guidelines, regulations, and remediation protocols. Chemical contamination is also discussed in terms of its origin and major concerns and interests, particularly with reference to current remediation activities and site-restoration methodology.


2006 ◽  
Vol 2 (14) ◽  
pp. 683-685 ◽  
Author(s):  
Michael G. Burton

AbstractThe high, dry and stable climatic conditions on top of the Antarctic plateau offer exceptional conditions for a wide range of observational astronomy, from optical to millimetre wavelengths. This is principally on account of the greatly reduced thermal backgrounds, the improved atmospheric transmission and the supurb seeing, in comparison with conditions at temperate latitude sites. The polar plateaus in the Arctic may also offer excellent conditions for astronomy, though these have yet to be quantified. We briefly review the history of astronomy in Antarctica and outline some of the activities now taking place on the polar plateaus, and plans for the future.


2015 ◽  
Vol 7 (1) ◽  
pp. 1-54
Author(s):  
Akiho Shibata

This paper examines whether core foundational principles can be distilled from the 100 years of history of the legal order-making in the polar regions. Despite differences in geo-physical, socio-historical, and legal circumstances conditioning the Antarctic and the Arctic regions, the examination of the processes of legal order-making in both polar regions demonstrates that there are some foundational principles being assessed and applied in designing their respective legal regimes. The identification of those core foundational principles would not necessarily lead to similar end products, nor would such examination necessarily advocate, for example, an Arctic Treaty System. This paper, instead, submits that between the Antarctic and the Arctic there are mutual learning processes already discernible at the foundational level of process legitimacy in international legal order-making. This examination also provides a broader framework to assess the existing literature that sees certain interactions between the two regimes at the level of substantive principles and rules.


2021 ◽  
Author(s):  
Michel Edwar Mickael

Treg suppression of conventional T cells is a fundamental step in regulating the adaptive immune system function. It is known that Treg first appeared in vertebrates. However little is known about the evolutionary history of suppression pathways mediated by Tregs. We employed AI text mining system to highlight the suppression pathways currently known to be utilized by Tregs. Our system identified various pathways such as CTLA4, induction of apoptosis, calcium signaling, inhibition of NfkB and NFAT. After that we employed phylogenetic analysis including multiple sequence alignment, phylogenetic tree building, ancestral sequence reconstruction, neutrality tests and positive selection test to investigate the evolutionary history of Treg mediated pathways in more details. We found that CTLA4 first appeared in vertebrates possibly rising from an IGV containing protein in cartilaginous fish. Conversely, we found that Tregs repurposed ancient pathways such as Calcineurin and CAMP Response Element Modulator that both exists as far as amoeba. Interestingly we found that these two pathways were highly conserved between vertebrates and lower invertebrates indicating conservation of function. Taken together, our research indicate that Tregs evolved its regulatory systems that evolved in vertebrates as well as reused conserved ancient regulatory systems that are related to the innate immune system.


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