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Daniel Prieur - One of the best experts on this subject based on the ideXlab platform.
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thermococcus barophilus sp nov a new barophilic and hyperthermophilic archaeon isolated under high hydrostatic pressure from a deep sea hydrothermal vent
International Journal of Systematic and Evolutionary Microbiology, 1999Co-Authors: Viggo Thor Marteinsson, Annalouise Reysenbach, Jeanlouis Birrien, M Vernet, Dominique Marie, Paul Messner, Uwe B Sleytr, Daniel PrieurAbstract:A novel barophilic, hyperthermophilic, anaerobic sulfur-metabolizing archaeon, strain MPT(T = type strain), was isolated from a hydrothermal vent site (Snakepit) on the Mid-Atlantic Ridge (depth, 3550 m). Enrichments and isolation were done under 40 MPa hydrostatic pressure at 95°C. Strain MPTwas barophilic at 75, 80, 85, 90, 95 and 98°C, and was an obligate Barophile between 95 and 100°C (T max). For growth above 95°C a pressure of 15·0-17·5 MPa was required. The strain grew at 48-95°C under atmospheric pressure. The optimal temperature for growth was 85°C at both high (40 MPa) and low (0·3 MPa) pressures. The growth rate was twofold higher at 85°C under in situ hydrostatic pressure compared to at low pressure. Strain MPTcells were motile, coccoid, 0·8-2·0 μm in diameter and covered by a hexagonal S-layer lattice. The optimum pH and NaCI concentration for growth at low pressure were 7·0 and 20-30 gl-1, respectively. The new isolate was an obligate heterotroph and utilized yeast extract, beef extract and peptone for growth. Growth was optimal in the presence of elemental sulfur. Rifampicin and chloramphenicol inhibited growth. The core lipids consisted of a major archaeol and a complex lipid pattern consisting of a major phospholipid. The DNA G+C content was 37·1 mol%. Sequencing of the 16S rRNA gene revealed that strain MPTbelonged to the genus Thermococcus and it is proposed that this isolate should be designated as a new species, Thermococcus barophilus.
Gustavo Caetanoanolles - One of the best experts on this subject based on the ideXlab platform.
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comparative analysis of barophily related amino acid content in protein domains of pyrococcus abyssi and pyrococcus furiosus
Archaea, 2013Co-Authors: Liudmila S Yafremava, Massimo Di Giulio, Gustavo CaetanoanollesAbstract:Amino acid substitution patterns between the nonbarophilic Pyrococcus furiosus and its barophilic relative P. abyssi confirm that hydrostatic pressure asymmetry indices reflect the extent to which amino acids are preferred by barophilic archaeal organisms. Substitution patterns in entire protein sequences, shared protein domains defined at fold superfamily level, domains in homologous sequence pairs, and domains of very ancient and very recent origin now provide further clues about the environment that led to the genetic code and diversified life. The pyrococcal proteomes are very similar and share a very early ancestor. Relative amino acid abundance analyses showed that biases in the use of amino acids are due to their shared fold superfamilies. Within these repertoires, only two of the five amino acids that are preferentially barophilic, aspartic acid and arginine, displayed this preference significantly and consistently across structure and in domains appearing in the ancestor. The more primordial asparagine, lysine and threonine displayed a consistent preference for nonbarophily across structure and in the ancestor. Since barophilic preferences are already evident in ancient domains that are at least ~3 billion year old, we conclude that barophily is a very ancient trait that unfolded concurrently with genetic idiosyncrasies in convergence towards a universal code.
Massimo Di Giulio - One of the best experts on this subject based on the ideXlab platform.
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Research Article Comparative Analysis of Barophily-Related Amino Acid Content in Protein Domains of Pyrococcus abyssi and
2016Co-Authors: Pyrococcus Furiosus, Massimo Di Giulio, Liudmila S Yafremava, Gustavo Caetano-anollésAbstract:License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Amino acid substitution patterns between the nonbarophilic Pyrococcus furiosus and its barophilic relative P. abyssi confirm that hydrostatic pressure asymmetry indices reflect the extent to which amino acids are preferred by barophilic archaeal organisms. Substitution patterns in entire protein sequences, shared protein domains defined at fold superfamily level, domains in homologous sequence pairs, and domains of very ancient and very recent origin now provide further clues about the environment that led to the genetic code and diversified life.The pyrococcal proteomes are very similar and share a very early ancestor. Relative amino acid abundance analyses showed that biases in the use of amino acids are due to their shared fold superfamilies.Within these repertoires, only two of the five amino acids that are preferentially barophilic, aspartic acid and arginine, displayed this preference significantly and consistently across structure and in domains appearing in the ancestor. The more primordial asparagine, lysine and threonine displayed a consistent preference for nonbarophily across structure and in the ancestor. Since barophilic preferences are already evident in ancient domains that are at least ∼3 billion year old, we conclude that barophily is a very ancient trait that unfolde
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comparative analysis of barophily related amino acid content in protein domains of pyrococcus abyssi and pyrococcus furiosus
Archaea, 2013Co-Authors: Liudmila S Yafremava, Massimo Di Giulio, Gustavo CaetanoanollesAbstract:Amino acid substitution patterns between the nonbarophilic Pyrococcus furiosus and its barophilic relative P. abyssi confirm that hydrostatic pressure asymmetry indices reflect the extent to which amino acids are preferred by barophilic archaeal organisms. Substitution patterns in entire protein sequences, shared protein domains defined at fold superfamily level, domains in homologous sequence pairs, and domains of very ancient and very recent origin now provide further clues about the environment that led to the genetic code and diversified life. The pyrococcal proteomes are very similar and share a very early ancestor. Relative amino acid abundance analyses showed that biases in the use of amino acids are due to their shared fold superfamilies. Within these repertoires, only two of the five amino acids that are preferentially barophilic, aspartic acid and arginine, displayed this preference significantly and consistently across structure and in domains appearing in the ancestor. The more primordial asparagine, lysine and threonine displayed a consistent preference for nonbarophily across structure and in the ancestor. Since barophilic preferences are already evident in ancient domains that are at least ~3 billion year old, we conclude that barophily is a very ancient trait that unfolded concurrently with genetic idiosyncrasies in convergence towards a universal code.
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A comparison of proteins from Pyrococcus furiosus and Pyrococcus abyssi: barophily in the physicochemical properties of amino acids and in the genetic code.
Gene, 2004Co-Authors: Massimo Di GiulioAbstract:A comparison is made between orthologous proteins from a nonBarophile (Pyrococcus furiosus) and a Barophile (Pyrococcus abyssi) organism. The pattern of asymmetries in the amino acid substitution process identifies the amino acids arginine, serine, glycine, valine and aspartic acid as those having the most barophilic behaviour, and tyrosine and glutamine as the least barophilic. The construction of a hydrostatic pressure asymmetry index (PAI) which orders the amino acids from the most barophilic to the least barophilic makes it possible to visualise the amino acid properties that best explain barophily. The polarity of amino acids is positively correlated to the PAI values, i.e., on average, the more polar amino acids possess a higher PAI value, that is to say they are more barophilic. Moreover, the "size" of amino acids (molecular weight) is negatively correlated to the PAI value, that is to say that, on average, high PAI values are associated to "small" amino acids which are therefore more barophilic than "larger" ones. These two amino acid properties are the same ones that are known for having been important in affecting the origin of genetic code organisation. All the above, as well as the significant and positive correlation between the number of codons attributed to the amino acids in the genetic code and the PAI values, seem to favour the hypothesis that genetic code structuring took place under high hydrostatic pressure.
A. Giorgi - One of the best experts on this subject based on the ideXlab platform.
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A contribution to the knowledge of Linaria tonzigii Lona, a steno-endemic species of the Orobie Bergamasche Regional Park (Italian Alps)
eco.mont (Journal on Protected Mountain Areas Research), 2019Co-Authors: L. Giupponi, A. GiorgiAbstract:Linaria tonzigii is a rare steno-endemic species of Community interest that grows on some limestone screes in the Orobie Bergamasche Regional Park (Italian Alps). In- formation is scarce regarding its ecology (and especially synecology) and its Grime\u2019s CSR functional strategy. For this reason, this research, as well as analysing the floristic composition and ecology of the L. tonzigii community by means of traditional methods, also evaluated the Grime\u2019s CSR strategy of this endemic species using the latest methods and tools. Analysis of the phytosociological relev\ue9s conducted in five different areas revealed that the species constitutes a single plant community (the Linaria tonzigii-Hornungia alpina community) consisting of basophile and xerophile species mostly typical of limestone screes. The analysis of the CSR strategy revealed that the mean strategy of L. tonzigii is R / CSR, although the species presents slightly different strategies in the different sampling areas. This article reports the first ever data regarding inter-population variation in plant functional strategies in nature and suggests that the functional variability of the species is much wider than had been thought. The analysis of plant height of L. tonzigii also showed that the population isolated at the northern limit of the species\u2019 distribution range has significantly taller and less stress-tolerant individuals than those in other areas, suggesting that it may be a different ecotype. This article aims to stimulate researchers to study little-known endemic species in order to protect and valorize the biodiversity of protected areas
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Plant community, ecology and functional strategy of Linaria tonzigii Lona, a steno-endemic species of the Italian pre-Alps
Società Botanica Italiana, 2018Co-Authors: L. Giupponi, A. GiorgiAbstract:Linaria tonzigii is a rare steno-endemic species of Community interest that grows on some limestone screes in the Orobie Bergamasche Regional Park (Italian Alps) (Fig. 1). Currently, its presence is certain in just a few sites of the Orobic pre-Alps. Many of these sites were refuge areas during the glaciations of the Quaternary Age: Mt. Arera/Mt. Corna Quadra group (locus classicus), Mt. Menna, Mt. Secco, Mt. Ferrante/Mt. Presolana group and Mt. Cavallo/Mt. Pegherolo group. According to the IUCN Red List of threatened species, Linaria tonzigii belongs to the category \u2018Endangered D\u2019, and it is therefore subject to strict protection under law LR10/2008 in Lombardy. Information on its ecology (and synecology), and on its Grime's CSR functional strategy are scarce. This study, other than analyzing the floristic composition and ecology of the communities hosting Linaria tonzigii by means of traditional methods (ecological indices), also evaluated its Grime's CSR strategy using the latest methods and tools. Analysis of 24 phytosociological relev\ue9s conducted in five different areas revealed that this species is part of a single plant community (Linaria tonzigii-Hornungia alpina community), consisting of basophile and xerophile species, mostly typical of limestone screes. The analysis of the CSR strategy revealed that the main strategy of Linaria tonzigii is R/CSR (Fig. 2), although the species adopts slightly different strategies in different sampling areas. The analysis of plant height showed that the isolated population at the northern limit of the distribution range has significantly taller, and less stress-tolerant individuals, than those in other areas, suggesting that this population may be a different ecotype (1). This study aims at stimulating researchers to study poorly known endemic species, in order to preserve and valorize the biodiversity of protected areas, and hence that of the planet
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Plant community, ecology and CSR functional strategy of Linaria tonzigii Lona, a steno-endemic species of the Italian pre-Alps
2018Co-Authors: A. Giorgi, L. GiupponiAbstract:Linaria tonzigiii is a rare steno-endemic species of Community interest that grows on some limestone screes in the Orobie Bergamasche Regional Park (Italian Alps). Currently, its presence is certain in just a few sites of the Orobic pre-Alps many of which were refuge zones during the glaciations of the Quaternary Age. Information is scarce regarding its ecology (and especially synecology) and its Grime's CSR functional strategy. For this reason, this study, as well as analyzing the floristic composition and ecology of the Linaria tonzigiicommunity by means of traditional methods (ecological indices), also evaluated the Grime's CSR strategy of this endemic species using the latest methods and tools. Analysis of 24 phytosociological relev\ue9s conducted in five different areas revealed that this species constitutes a single plant community consisting of basophile species mostly typical of limestone screes. The analysis of the CSR strategy revealed that the mean strategy of Linaria tonzigii is R/CSR although the species presents slightly different strategies in the different sampling areas. This research suggests that the functional variability of the species is much wider than is currently known. The analysis of plant height of Linaria tonzigiialso showed that the population isolated at the northern limit of the distribution range of the species has significantly taller and less stress-tolerant individuals than those in other areas, suggesting that it may be a different ecotype. This study aims to stimulate researchers to study the little-known endemic species in order to protect and valorize the biodiversity of the planet
Liudmila S Yafremava - One of the best experts on this subject based on the ideXlab platform.
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Research Article Comparative Analysis of Barophily-Related Amino Acid Content in Protein Domains of Pyrococcus abyssi and
2016Co-Authors: Pyrococcus Furiosus, Massimo Di Giulio, Liudmila S Yafremava, Gustavo Caetano-anollésAbstract:License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Amino acid substitution patterns between the nonbarophilic Pyrococcus furiosus and its barophilic relative P. abyssi confirm that hydrostatic pressure asymmetry indices reflect the extent to which amino acids are preferred by barophilic archaeal organisms. Substitution patterns in entire protein sequences, shared protein domains defined at fold superfamily level, domains in homologous sequence pairs, and domains of very ancient and very recent origin now provide further clues about the environment that led to the genetic code and diversified life.The pyrococcal proteomes are very similar and share a very early ancestor. Relative amino acid abundance analyses showed that biases in the use of amino acids are due to their shared fold superfamilies.Within these repertoires, only two of the five amino acids that are preferentially barophilic, aspartic acid and arginine, displayed this preference significantly and consistently across structure and in domains appearing in the ancestor. The more primordial asparagine, lysine and threonine displayed a consistent preference for nonbarophily across structure and in the ancestor. Since barophilic preferences are already evident in ancient domains that are at least ∼3 billion year old, we conclude that barophily is a very ancient trait that unfolde
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comparative analysis of barophily related amino acid content in protein domains of pyrococcus abyssi and pyrococcus furiosus
Archaea, 2013Co-Authors: Liudmila S Yafremava, Massimo Di Giulio, Gustavo CaetanoanollesAbstract:Amino acid substitution patterns between the nonbarophilic Pyrococcus furiosus and its barophilic relative P. abyssi confirm that hydrostatic pressure asymmetry indices reflect the extent to which amino acids are preferred by barophilic archaeal organisms. Substitution patterns in entire protein sequences, shared protein domains defined at fold superfamily level, domains in homologous sequence pairs, and domains of very ancient and very recent origin now provide further clues about the environment that led to the genetic code and diversified life. The pyrococcal proteomes are very similar and share a very early ancestor. Relative amino acid abundance analyses showed that biases in the use of amino acids are due to their shared fold superfamilies. Within these repertoires, only two of the five amino acids that are preferentially barophilic, aspartic acid and arginine, displayed this preference significantly and consistently across structure and in domains appearing in the ancestor. The more primordial asparagine, lysine and threonine displayed a consistent preference for nonbarophily across structure and in the ancestor. Since barophilic preferences are already evident in ancient domains that are at least ~3 billion year old, we conclude that barophily is a very ancient trait that unfolded concurrently with genetic idiosyncrasies in convergence towards a universal code.