The Experts below are selected from a list of 540 Experts worldwide ranked by ideXlab platform
Petrus J De Vries - One of the best experts on this subject based on the ideXlab platform.
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evolution of the tsc1 tsc2 tor signaling pathway
Science Signaling, 2010Co-Authors: Jaco Serfontein, Ellen R R Nisbet, Christopher J. Howe, Petrus J De VriesAbstract:The TSC1/TSC2-TOR signaling pathway [the signaling pathway that includes the heterodimeric TSC1 (tuberous sclerosis 1 protein)–TSC2 (tuberous sclerosis 2 protein) complex and TOR (target of rapamycin)] regulates various cellular processes, including protein synthesis, in response to growth factors and nutrient availability. Homologs of some pathway components have been reported from animals, fungi, plants, and protozoa. These observations led to the perception that the whole pathway is evolutionarily conserved throughout eukaryotes. Using complete genome sequences, we show that, contrary to this view, the pathway was built up from a simpler one, present in the ancestral eukaryote, coupling cell growth to energy supplies. Additional elements, such as TSC1 and TSC2, were “bolted on” in particular eukaryotic lineages. Our results also suggest that unikonts [Opisthokonta (including animals and fungi) and Amoebozoa] form a monophyletic group with the Excavata and Chromalveolata. A previous proposal, that the root of the eukaryotic “tree of life” lies between the unikonts and other organisms, should therefore be reevaluated.
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Evolution of the TSC1/TSC2-TOR Signaling Pathway
Science Signaling, 2010Co-Authors: Jaco Serfontein, R. Ellen R. Nisbet, Christopher J. Howe, Petrus J De VriesAbstract:The TSC1/TSC2-TOR signaling pathway [the signaling pathway that includes the heterodimeric TSC1 (tuberous sclerosis 1 protein)-TSC2 (tuberous sclerosis 2 protein) complex and TOR (target of rapamycin)] regulates various cellular processes, including protein synthesis, in response to growth factors and nutrient availability. Homologs of some pathway components have been reported from animals, fungi, plants, and protozoa. These observations led to the perception that the whole pathway is evolutionarily conserved throughout eukaryotes. Using complete genome sequences, we show that, contrary to this view, the pathway was built up from a simpler one, present in the ancestral eukaryote, coupling cell growth to energy supplies. Additional elements, such as TSC1 and TSC2, were "bolted on" in particular eukaryotic lineages. Our results also suggest that unikonts [Opisthokonta (including animals and fungi) and Amoebozoa] form a monophyletic group with the Excavata and Chromalveolata. A previous proposal, that the root of the eukaryotic "tree of life" lies between the unikonts and other organisms, should therefore be reevaluated.
Jaco Serfontein - One of the best experts on this subject based on the ideXlab platform.
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evolution of the tsc1 tsc2 tor signaling pathway
Science Signaling, 2010Co-Authors: Jaco Serfontein, Ellen R R Nisbet, Christopher J. Howe, Petrus J De VriesAbstract:The TSC1/TSC2-TOR signaling pathway [the signaling pathway that includes the heterodimeric TSC1 (tuberous sclerosis 1 protein)–TSC2 (tuberous sclerosis 2 protein) complex and TOR (target of rapamycin)] regulates various cellular processes, including protein synthesis, in response to growth factors and nutrient availability. Homologs of some pathway components have been reported from animals, fungi, plants, and protozoa. These observations led to the perception that the whole pathway is evolutionarily conserved throughout eukaryotes. Using complete genome sequences, we show that, contrary to this view, the pathway was built up from a simpler one, present in the ancestral eukaryote, coupling cell growth to energy supplies. Additional elements, such as TSC1 and TSC2, were “bolted on” in particular eukaryotic lineages. Our results also suggest that unikonts [Opisthokonta (including animals and fungi) and Amoebozoa] form a monophyletic group with the Excavata and Chromalveolata. A previous proposal, that the root of the eukaryotic “tree of life” lies between the unikonts and other organisms, should therefore be reevaluated.
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Evolution of the TSC1/TSC2-TOR Signaling Pathway
Science Signaling, 2010Co-Authors: Jaco Serfontein, R. Ellen R. Nisbet, Christopher J. Howe, Petrus J De VriesAbstract:The TSC1/TSC2-TOR signaling pathway [the signaling pathway that includes the heterodimeric TSC1 (tuberous sclerosis 1 protein)-TSC2 (tuberous sclerosis 2 protein) complex and TOR (target of rapamycin)] regulates various cellular processes, including protein synthesis, in response to growth factors and nutrient availability. Homologs of some pathway components have been reported from animals, fungi, plants, and protozoa. These observations led to the perception that the whole pathway is evolutionarily conserved throughout eukaryotes. Using complete genome sequences, we show that, contrary to this view, the pathway was built up from a simpler one, present in the ancestral eukaryote, coupling cell growth to energy supplies. Additional elements, such as TSC1 and TSC2, were "bolted on" in particular eukaryotic lineages. Our results also suggest that unikonts [Opisthokonta (including animals and fungi) and Amoebozoa] form a monophyletic group with the Excavata and Chromalveolata. A previous proposal, that the root of the eukaryotic "tree of life" lies between the unikonts and other organisms, should therefore be reevaluated.
Ulrich Poschl - One of the best experts on this subject based on the ideXlab platform.
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size distributions and temporal variations of biological aerosol particles in the amazon rainforest characterized by microscopy and real time uv aps fluorescence techniques during amaze 08
Atmospheric Chemistry and Physics, 2012Co-Authors: J A Huffman, Baerbel Sinha, Rebecca M Garland, A Sneepollmann, Sachin S Gunthe, Paulo Artaxo, S T Martin, Meinrat O Andreae, Ulrich PoschlAbstract:Abstract. As a part of the AMAZE-08 campaign during the wet season in the rainforest of central Amazonia, an ultraviolet aerodynamic particle sizer (UV-APS) was operated for continuous measurements of fluorescent biological aerosol particles (FBAP). In the coarse particle size range (> 1 μm) the campaign median and quartiles of FBAP number and mass concentration were 7.3 × 104 m−3 (4.0–13.2 × 104 m−3) and 0.72 μg m−3 (0.42–1.19 μg m−3), respectively, accounting for 24% (11–41%) of total particle number and 47% (25–65%) of total particle mass. During the five-week campaign in February–March 2008 the concentration of coarse-mode Saharan dust particles was highly variable. In contrast, FBAP concentrations remained fairly constant over the course of weeks and had a consistent daily pattern, peaking several hours before sunrise, suggesting observed FBAP was dominated by nocturnal spore emission. This conclusion was supported by the consistent FBAP number size distribution peaking at 2.3 μm, also attributed to fungal spores and mixed biological particles by scanning electron microscopy (SEM), light microscopy and biochemical staining. A second primary biological aerosol particle (PBAP) mode between 0.5 and 1.0 μm was also observed by SEM, but exhibited little fluorescence and no true fungal staining. This mode may have consisted of single bacterial cells, brochosomes, various fragments of biological material, and small Chromalveolata (Chromista) spores. Particles liquid-coated with mixed organic-inorganic material constituted a large fraction of observations, and these coatings contained salts likely from primary biological origin. We provide key support for the suggestion that real-time laser-induce fluorescence (LIF) techniques using 355 nm excitation provide size-resolved concentrations of FBAP as a lower limit for the atmospheric abundance of biological particles in a pristine environment. We also show some limitations of using the instrument for ambient monitoring of weakly fluorescent particles
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Size distributions and temporal variations of biological aerosol particles in the Amazon rainforest characterized by microscopy and real-time UV-APS fluorescence techniques during AMAZE-08
Atmospheric Chemistry and Physics, 2012Co-Authors: J A Huffman, Baerbel Sinha, Rebecca M Garland, Sachin S Gunthe, Paulo Artaxo, S T Martin, Meinrat O Andreae, A. Snee-pollmann, Ulrich PoschlAbstract:Abstract. As a part of the AMAZE-08 campaign during the wet season in the rainforest of central Amazonia, an ultraviolet aerodynamic particle sizer (UV-APS) was operated for continuous measurements of fluorescent biological aerosol particles (FBAP). In the coarse particle size range (> 1 μm) the campaign median and quartiles of FBAP number and mass concentration were 7.3 × 104 m−3 (4.0–13.2 × 104 m−3) and 0.72 μg m−3 (0.42–1.19 μg m−3), respectively, accounting for 24% (11–41%) of total particle number and 47% (25–65%) of total particle mass. During the five-week campaign in February–March 2008 the concentration of coarse-mode Saharan dust particles was highly variable. In contrast, FBAP concentrations remained fairly constant over the course of weeks and had a consistent daily pattern, peaking several hours before sunrise, suggesting observed FBAP was dominated by nocturnal spore emission. This conclusion was supported by the consistent FBAP number size distribution peaking at 2.3 μm, also attributed to fungal spores and mixed biological particles by scanning electron microscopy (SEM), light microscopy and biochemical staining. A second primary biological aerosol particle (PBAP) mode between 0.5 and 1.0 μm was also observed by SEM, but exhibited little fluorescence and no true fungal staining. This mode may have consisted of single bacterial cells, brochosomes, various fragments of biological material, and small Chromalveolata (Chromista) spores. Particles liquid-coated with mixed organic-inorganic material constituted a large fraction of observations, and these coatings contained salts likely from primary biological origin. We provide key support for the suggestion that real-time laser-induce fluorescence (LIF) techniques using 355 nm excitation provide size-resolved concentrations of FBAP as a lower limit for the atmospheric abundance of biological particles in a pristine environment. We also show some limitations of using the instrument for ambient monitoring of weakly fluorescent particles < 2 μm. Our measurements confirm that primary biological particles, fungal spores in particular, are an important fraction of supermicron aerosol in the Amazon and that may contribute significantly to hydrological cycling, especially when coated by mixed inorganic material.
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Size distributions and temporal variations of biological aerosol particles in the Amazon rainforest characterized by microscopy and real-time UV-APS fluorescence techniques during AMAZE-08
Copernicus Publications, 2012Co-Authors: J A Huffman, Baerbel Sinha, Rebecca M Garland, Sachin S Gunthe, Paulo Artaxo, S T Martin, Meinrat O Andreae, A. Snee-pollmann, Ulrich PoschlAbstract:As a part of the AMAZE-08 campaign during the wet season in the rainforest of central Amazonia, an ultraviolet aerodynamic particle sizer (UV-APS) was operated for continuous measurements of fluorescent biological aerosol particles (FBAP). In the coarse particle size range (> 1 μm) the campaign median and quartiles of FBAP number and mass concentration were 7.3 × 10<sup>4</sup> m<sup>−3</sup> (4.0–13.2 × 10<sup>4</sup> m<sup>−3</sup>) and 0.72 μg m<sup>−3</sup> (0.42–1.19 μg m<sup>−3</sup>), respectively, accounting for 24% (11–41%) of total particle number and 47% (25–65%) of total particle mass. During the five-week campaign in February–March 2008 the concentration of coarse-mode Saharan dust particles was highly variable. In contrast, FBAP concentrations remained fairly constant over the course of weeks and had a consistent daily pattern, peaking several hours before sunrise, suggesting observed FBAP was dominated by nocturnal spore emission. This conclusion was supported by the consistent FBAP number size distribution peaking at 2.3 μm, also attributed to fungal spores and mixed biological particles by scanning electron microscopy (SEM), light microscopy and biochemical staining. A second primary biological aerosol particle (PBAP) mode between 0.5 and 1.0 μm was also observed by SEM, but exhibited little fluorescence and no true fungal staining. This mode may have consisted of single bacterial cells, brochosomes, various fragments of biological material, and small Chromalveolata (Chromista) spores. Particles liquid-coated with mixed organic-inorganic material constituted a large fraction of observations, and these coatings contained salts likely from primary biological origin. We provide key support for the suggestion that real-time laser-induce fluorescence (LIF) techniques using 355 nm excitation provide size-resolved concentrations of FBAP as a lower limit for the atmospheric abundance of biological particles in a pristine environment. We also show some limitations of using the instrument for ambient monitoring of weakly fluorescent particles < 2 μm. Our measurements confirm that primary biological particles, fungal spores in particular, are an important fraction of supermicron aerosol in the Amazon and that may contribute significantly to hydrological cycling, especially when coated by mixed inorganic material
Christopher J. Howe - One of the best experts on this subject based on the ideXlab platform.
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evolution of the tsc1 tsc2 tor signaling pathway
Science Signaling, 2010Co-Authors: Jaco Serfontein, Ellen R R Nisbet, Christopher J. Howe, Petrus J De VriesAbstract:The TSC1/TSC2-TOR signaling pathway [the signaling pathway that includes the heterodimeric TSC1 (tuberous sclerosis 1 protein)–TSC2 (tuberous sclerosis 2 protein) complex and TOR (target of rapamycin)] regulates various cellular processes, including protein synthesis, in response to growth factors and nutrient availability. Homologs of some pathway components have been reported from animals, fungi, plants, and protozoa. These observations led to the perception that the whole pathway is evolutionarily conserved throughout eukaryotes. Using complete genome sequences, we show that, contrary to this view, the pathway was built up from a simpler one, present in the ancestral eukaryote, coupling cell growth to energy supplies. Additional elements, such as TSC1 and TSC2, were “bolted on” in particular eukaryotic lineages. Our results also suggest that unikonts [Opisthokonta (including animals and fungi) and Amoebozoa] form a monophyletic group with the Excavata and Chromalveolata. A previous proposal, that the root of the eukaryotic “tree of life” lies between the unikonts and other organisms, should therefore be reevaluated.
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Evolution of the TSC1/TSC2-TOR Signaling Pathway
Science Signaling, 2010Co-Authors: Jaco Serfontein, R. Ellen R. Nisbet, Christopher J. Howe, Petrus J De VriesAbstract:The TSC1/TSC2-TOR signaling pathway [the signaling pathway that includes the heterodimeric TSC1 (tuberous sclerosis 1 protein)-TSC2 (tuberous sclerosis 2 protein) complex and TOR (target of rapamycin)] regulates various cellular processes, including protein synthesis, in response to growth factors and nutrient availability. Homologs of some pathway components have been reported from animals, fungi, plants, and protozoa. These observations led to the perception that the whole pathway is evolutionarily conserved throughout eukaryotes. Using complete genome sequences, we show that, contrary to this view, the pathway was built up from a simpler one, present in the ancestral eukaryote, coupling cell growth to energy supplies. Additional elements, such as TSC1 and TSC2, were "bolted on" in particular eukaryotic lineages. Our results also suggest that unikonts [Opisthokonta (including animals and fungi) and Amoebozoa] form a monophyletic group with the Excavata and Chromalveolata. A previous proposal, that the root of the eukaryotic "tree of life" lies between the unikonts and other organisms, should therefore be reevaluated.
Debashish Bhattacharya - One of the best experts on this subject based on the ideXlab platform.
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Support for Membership and Supergroup Monophyly from “Amoebozoa”-Targeted Molecular Genealogies
2013Co-Authors: Laura Wegener Parfrey, David J. Patterson, Debashish Bhattacharya, Erika Barbero, Elyse Lasser, Micah Dunthorn, Laura A. KatzAbstract:Membership: • indicates the member taxon falls within the supergroup Amoebozoa; ○ indicates that the member taxon is excluded from the Amoebozoa clade, or no clade is formed. Papers below blank line survey eukaryotic diversity [33,49,115] and are included in all analyses. Member taxa: My, Mycetozoa; Dc, Dictyosteliids; Tu, Tubulinea (Lobosea, Gymnamoebea sensu stricto); Am, Acanthamoebidae; Fl, Flabellinea (Discosea, Glycostylea); Pe, Pelomyxa; Ma, Mastigamoebidae; En, Entamoebidae; Rs, residua; Br, Breviata, “Mastigamoeba invertans sensu NCBI.” Supergroup Monophyly, + indicates monophyly; − indicates group is para- or polyphyletic, and blank indicates insufficient data available. Supergroup definition based on Adl et al. 2005 [4]: A, Amoebozoa; C, Chromalveolata; E, Excavata; O, Opisthokonta; P, Plantae; R, Rhizaria. The position of Breviata, Br, was not considered when scoring the monophyly of Amoebozoa as this organism was misidentified and affiliations are unknown (see text). Some nodes were constrained in reference [97]. References cited in this figure are [25,33,45,48,49,84,97,114,115].
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Trends in Supergroup Taxonomy
2013Co-Authors: Laura Wegener Parfrey, David J. Patterson, Debashish Bhattacharya, Erika Barbero, Elyse Lasser, Micah Dunthorn, Laura A. KatzAbstract:A comparison of three formal classifications illustrates trends within (A) “Amoebozoa” [7,45,47]; (B) “Excavata” [7,33,60]; (C) “Plantae” [2,6,7]; and (D) “Rhizaria” [6,7,33]. A majority of solid, horizontal lines would indicate temporal stability of supergroup classification. For visual simplicity we do not indicate groups newly included in the supergroups or taxonomic restructuring within subgroups. Asterisk indicates a newly introduced term. “Chromalveolata” and “Opisthokonta” are not included because only one formal taxonomy exists for both groups. See Figure 1 for further notes.
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The Chromalveolate Hypothesis
2012Co-Authors: Ahmed Moustafa, Debashish Bhattacharya, Adrian Reyes-prietoAbstract:Two putative “supergroups” of anciently derived photosynthetic eukaryotes exist in the tree of life, the Archaeplastida (i.e., Plantae; red, green [including plants], and glaucophyte algae) and the Chromalveolata (cryptophytes, haptophytes, and stramenopiles, alveolates). It is widely accepted that the photosynthetic organelle (plastid) of Plantae traces its origin to primary endosymbiosis, whereby a unicellular protist (the ‘host’) engulfed and retained a photosynthetic cyanobacterium (the endosymbiont). This momentous step in evolution likely occurred in the late Paleoproterozoic about 1.5 billion years ago with the resulting proto-alga being the putative common ancestor of this eukaryotic supergroup. Under the most parsimonious scenario, a single Plantae ancestor underwent the exceptional process of primary endosymbiosis described above that was ultimately driven by ecological pressures acting on the host genome. Once established, the primary plastid has apparently never been lost by Plantae hosts. In contrast to Plantae, the chromalveolates gained their widespread plastid through secondary endosymbiosis (i.e., eukaryote-eukaryote), whereby under the most prominent hypothesis, a red alga was engulfed and reduced to a secondary plastid. This event occurred about 1.2 billion years ago and gave rise to the putative photosynthetic ancestor of this supergroup.
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multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic
Current Biology, 2008Co-Authors: Adrian Reyesprieto, Ahmed A Moustafa, Debashish BhattacharyaAbstract:Plantae (as defined by Cavalier-Smith, 1981) plastids evolved via primary endosymbiosis whereby a heterotrophic protist enslaved a photosynthetic cyanobacterium. This "primary" plastid spread into other eukaryotes via secondary endosymbiosis. An important but contentious theory in algal evolution is the chromalveolate hypothesis that posits chromists (cryptophytes, haptophytes, and stramenopiles) and alveolates (ciliates, apicomplexans, and dinoflagellates) share a common ancestor that contained a red-algal-derived "secondary" plastid. Under this view, the existence of several later-diverging plastid-lacking chromalveolates such as ciliates and oomycetes would be explained by plastid loss in these lineages. To test the idea of a photosynthetic ancestry for ciliates, we used the 27,446 predicted proteins from the macronuclear genome of Tetrahymena thermophila to query prokaryotic and eukaryotic genomes. We identified 16 proteins of possible algal origin in the ciliates Tetrahymena and Paramecium tetraurelia. Fourteen of these are present in other chromalveolates. Here we compare and contrast the likely scenarios for algal-gene origin in ciliates either via multiple rounds of horizontal gene transfer (HGT) from algal prey or symbionts, or through endosymbiotic gene transfer (EGT) during a putative photosynthetic phase in their evolution.
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Broadly sampled multigene trees of eukaryotes
BMC Evolutionary Biology, 2008Co-Authors: Hwan Su Yoon, Jessica Grant, Benjamin C Chaon, Jeffrey C Cole, Jeanne M Logsdon, Yonas I. Tekle, David J. Patterson, Min Wu, Debashish Bhattacharya, Laura A. KatzAbstract:Background Our understanding of the eukaryotic tree of life and the tremendous diversity of microbial eukaryotes is in flux as additional genes and diverse taxa are sampled for molecular analyses. Despite instability in many analyses, there is an increasing trend to classify eukaryotic diversity into six major supergroups: the 'Amoebozoa', 'Chromalveolata', 'Excavata', 'Opisthokonta', 'Plantae', and 'Rhizaria'. Previous molecular analyses have often suffered from either a broad taxon sampling using only single-gene data or have used multigene data with a limited sample of taxa. This study has two major aims: (1) to place taxa represented by 72 sequences, 61 of which have not been characterized previously, onto a well-sampled multigene genealogy, and (2) to evaluate the support for the six putative supergroups using two taxon-rich data sets and a variety of phylogenetic approaches. Results The inferred trees reveal strong support for many clades that also have defining ultrastructural or molecular characters. In contrast, we find limited to no support for most of the putative supergroups as only the 'Opisthokonta' receive strong support in our analyses. The supergroup 'Amoebozoa' has only moderate support, whereas the 'Chromalveolata', 'Excavata', 'Plantae', and 'Rhizaria' receive very limited or no support. Conclusion Our analytical approach substantiates the power of increased taxon sampling in placing diverse eukaryotic lineages within well-supported clades. At the same time, this study indicates that the six supergroup hypothesis of higher-level eukaryotic classification is likely premature. The use of a taxon-rich data set with 105 lineages, which still includes only a small fraction of the diversity of microbial eukaryotes, fails to resolve deeper phylogenetic relationships and reveals no support for four of the six proposed supergroups. Our analyses provide a point of departure for future taxon- and gene-rich analyses of the eukaryotic tree of life, which will be critical for resolving their phylogenetic interrelationships.