The Experts below are selected from a list of 1023 Experts worldwide ranked by ideXlab platform
Masaaki Morisawa - One of the best experts on this subject based on the ideXlab platform.
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species specificity of sperm motility activation and chemotaxis a study on ascidian species
The Biological Bulletin, 2013Co-Authors: Manabu Yoshida, Noburu Sensui, Yuki Hiradate, Jacky Cosson, Masaaki MorisawaAbstract:Egg-derived sperm-activating factors and attractants activate sperm motility and attract the sperm, respectively. These phenomena constitute the first communication signaling between males and females in the process of fertilization in many animals and plants, and in many cases, these are species-specific events. Thus, sperm motility activation and chemotaxis may act as a safety process for the authentication between conspecific egg and sperm, and help to prevent crossbreeding. Here, we examine species-specificity of sperm motility activation and chemotaxis in the ascidians belonging to the order Phlebobranchiata: Ciona intestinalis, Ciona Savignyi, Phallusia mammillata, Phallusia nigra, and Ascidia sydneiensis. Cross-reactivity in both motility activation and chemotaxis of sperm was not observed between C. Savignyi and P. mammillata, or between A. sydneiensis and Phallusia spp. However, there is a “one way” (no reciprocity) cross-reaction between P. mammillata and P. nigra in sperm activation, and betwee...
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interaction between noradrenaline or adrenaline and the β1 adrenergic receptor in the nervous system triggers early metamorphosis of larvae in the ascidian Ciona Savignyi
Developmental Biology, 2003Co-Authors: Yukiko Kimura, Manabu Yoshida, Masaaki MorisawaAbstract:Abstract Molecular mechanisms underlying the metamorphosis of larvae, e.g., ligand and receptor interaction, have to be determined and roles for the nervous system in marine invertebrates are not well understood. We report here that treatment of swimming larvae of the ascidian Ciona Savignyi with noradrenaline or adrenaline promoted morphological changes in early metamorphosis, e.g., tail resorption. Antagonists of the β-adrenergic receptor, propranolol, and the β 1 -adrenergic receptor, metoprolol, inhibited the noradrenaline-induced tail resorption, while an antagonist of the α-adrenergic receptor, phentolamine, and of the β 2 - adrenergic receptor, butoxamine, had no inhibitory effects. In addition, a selective agonist of the β-adrenergic receptor, isoproterenol, the concentration of which was lower than the effective concentration of the neurotransmitters, facilitated tail resorption. Immunohistochemical studies, using an anti-dopamine-hydroxylase antibody, showed that neurotransmitters such as noradrenaline and adrenaline localized around the brain vesicle of the larvae during metamorphosis. The β 1 -adrenergic receptor stained with antibodies was localized on the nervous system. Temporal expression of the β 1 -adrenergic receptor was intense in the nervous system in the larvae competent for metamorphosis. We propose that interactions between noradrenaline or adrenaline and the β 1 -adrenergic receptor in the nervous system mediate the process of metamorphosis of Ciona larvae.
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Signaling pathway from [Ca2+]i transients to ooplasmic segregation involves small GTPase rho in the ascidian egg.
Development growth & differentiation, 2003Co-Authors: Manabu Yoshida, Noburu Sensui, Yuji Horiuchi, Masaaki MorisawaAbstract:Intracellular Ca2+ transients occur at fertilization in the eggs of all animal species and are thought to be critical for the initiation of several events in egg activation. The rho family of small GTPases are known to organize and maintain the actin filament-dependent cytoskeleton, and rho is involved in the control mechanism of cytokinesis. In the ascidian Ciona Savignyi, the first step of ooplasmic segregation observed just after fertilization is cortical contraction with egg deformation, mediated by the cortical actin filaments. C3 exoenzyme, a rho-specific inhibitor, did not affect the pattern of [Ca2+]i transients in the ascidian egg, but inhibited ooplasmic segregation and cytokinesis at the first cleavage. Injection of inositol 1,4,5-trisphosphate or treatment of Ca2+ ionophore induced deformation of the egg and extrusion of the first polar body, but these phenomena did not occur in the C3 exoenzyme-injected egg. These results suggest that rho proteins are involved in egg deformation, ooplasmic segregation and cytokinesis downstream of the [Ca2+]i transients.
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Store-operated calcium channel regulates the chemotactic behavior of ascidian sperm.
Proceedings of the National Academy of Sciences of the United States of America, 2002Co-Authors: Manabu Yoshida, Makiko Ishikawa, Hiroko Izumi, Rosaria De Santis, Masaaki MorisawaAbstract:The sperm-activating and -attracting factor released from the eggs of the ascidians Ciona intestinalis and Ciona Savignyi requires extracellular Ca(2+) for activating sperm motility and eliciting chemotactic behavior of the activated sperm toward the egg. Here, we show that modulators of the store-operated Ca(2+) channel, SKF on the other hand, blockers of voltage-dependent Ca(2+) channels did not inhibit the chemotaxis, even though they inhibited the sperm activation operated by voltage-dependent Ca(2+) channels. The blockers of store-operated Ca(2+) channels also inhibited the asymmetrical flagellar beating and turning movements of the ascidian sperm, which are typical signs of sperm chemotaxis. Depletion of internal Ca(2+) stores by thapsigargin induced capacitative Ca(2+) entry into the sperm, which was blocked by SK&F96365. These results suggest that the intracellular Ca(2+) concentration increase through the store-operated Ca(2+) channels induces asymmetrical flagellar movements to establish the chemotactic behavior of the sperm.
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Roles of MLCK and PI3 Kinase on Deformationand Ooplasmic Segregation at Fertilization in the Egg of Ciona Savignyi
The Biology of Ascidians, 2001Co-Authors: Noburu Sensui, Manabu Yoshida, Masaaki MorisawaAbstract:Deformation and ooplasmic segregation at fertilization in the egg of the ascidian Ciona Savignyi were suppressed by MLCK inhibitors (ML-7, ML-9 and high concentration of wortmannin), suggesting that MLCK plays a major part for the egg deformation and ooplasmic segregation. Studies using the PI3 kinase inhibitor also suggest participation of this kinase in the phenomena, High concentrations of wortmannin, an inhibitor common to MLCK and PI3-kinase did not inhibit Series I [Ca2+]i transients, suggesting that the MLCK- and PI3 kinase-related processes are active downstream of increase in intracellular Ca2+.
Arend Sidow - One of the best experts on this subject based on the ideXlab platform.
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SHRiMP: accurate mapping of short color-space reads,” PLoS
2013Co-Authors: Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend SidowAbstract:The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25–70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP- the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism. Our method is based upon a fast read mapping technique, separate thorough alignment methods for regular letter-space as well as AB SOLiD (color-space) reads, and a statistical model for false positive hits. We use SHRiMP to map reads from a newly sequenced Ciona Savignyi individual to the reference genome. We demonstrate that SHRiMP can accurately map reads to this highly polymorphic genome, while confirming high heterozygosity of C. Savignyi in this second individual. SHRiMP is freely available a
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shrimp accurate mapping of short color space reads
PLOS Computational Biology, 2009Co-Authors: Arend Sidow, Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Michael BrudnoAbstract:The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25–70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP - the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism. Our method is based upon a fast read mapping technique, separate thorough alignment methods for regular letter-space as well as AB SOLiD (color-space) reads, and a statistical model for false positive hits. We use SHRiMP to map reads from a newly sequenced Ciona Savignyi individual to the reference genome. We demonstrate that SHRiMP can accurately map reads to this highly polymorphic genome, while confirming high heterozygosity of C. Savignyi in this second individual. SHRiMP is freely available at http://compbio.cs.toronto.edu/shrimp.
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Shrimp: accurate mapping of short color-space reads
2009Co-Authors: Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend SidowAbstract:The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25–70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP- the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism. Our method is based upon a fast read mapping technique, separate thorough alignment methods for regular letter-space as well as AB SOLiD (color-space) reads, and a statistical model for false positive hits. We use SHRiMP to map reads from a newly sequenced Ciona Savignyi individual to the reference genome. We demonstrate that SHRiMP can accurately map reads to this highly polymorphic genome, while confirming high heterozygosity of C. Savignyi in this second individual. SHRiMP is freely available a
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a haplome alignment and reference sequence of the highly polymorphic Ciona Savignyi genome
Genome Biology, 2007Co-Authors: Kerrin S Small, Michael Brudno, Matthew M Hill, Arend SidowAbstract:The sequence of Ciona Savignyi was determined using a whole-genome shotgun strategy, but a high degree of polymorphism resulted in a fractured assembly wherein allelic sequences from the same genomic region assembled separately. We designed a multistep strategy to generate a nonredundant reference sequence from the original assembly by reconstructing and aligning the two 'haplomes' (haploid genomes). In the resultant 174 megabase reference sequence, each locus is represented once, misassemblies are corrected, and contiguity and continuity are dramatically improved.
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2007 Small et Volume al. 8, Issue 3, Article R41 Open Access Method
2007Co-Authors: Kerrin S Small, Michael Brudno, Matthew M Hill, Arend SidowAbstract:A haplome alignment and reference sequence of the highly polymorphic Ciona Savignyi genom
Manabu Yoshida - One of the best experts on this subject based on the ideXlab platform.
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species specificity of sperm motility activation and chemotaxis a study on ascidian species
The Biological Bulletin, 2013Co-Authors: Manabu Yoshida, Noburu Sensui, Yuki Hiradate, Jacky Cosson, Masaaki MorisawaAbstract:Egg-derived sperm-activating factors and attractants activate sperm motility and attract the sperm, respectively. These phenomena constitute the first communication signaling between males and females in the process of fertilization in many animals and plants, and in many cases, these are species-specific events. Thus, sperm motility activation and chemotaxis may act as a safety process for the authentication between conspecific egg and sperm, and help to prevent crossbreeding. Here, we examine species-specificity of sperm motility activation and chemotaxis in the ascidians belonging to the order Phlebobranchiata: Ciona intestinalis, Ciona Savignyi, Phallusia mammillata, Phallusia nigra, and Ascidia sydneiensis. Cross-reactivity in both motility activation and chemotaxis of sperm was not observed between C. Savignyi and P. mammillata, or between A. sydneiensis and Phallusia spp. However, there is a “one way” (no reciprocity) cross-reaction between P. mammillata and P. nigra in sperm activation, and betwee...
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fertilization and sperm chemotaxis in ascidians
Methods of Molecular Biology, 2004Co-Authors: Manabu YoshidaAbstract:Prior to fertilization, spermatozoa of many animals and plants show chemotactic behavior toward eggs. Chemotactic behavior was first described in ferns (1), and their attractant was identified as the bimalate ion (2). In animals, sperm chemotaxis to the egg was first observed in the hydrozoan Spirocodon saltatrix (3) and is now widely recognized in all species from cnidarians to human (for reviews, see refs. 4–6). Spermatozoa of the ascidians Ciona intestinalis and Ciona Savignyi were immotile or slightly motile when they were suspended in seawater, and if an unfertilized egg was placed in the sperm suspension, sperm near the egg were intensely activated and then showed chemotactic behavior toward the egg (7– 9). Egg seawater (ESW) that is a supernatant of seawater incubated with the ascidian egg has both sperm-activating and sperm-attracting activities, indicating that the ascidian egg releases some sperm-activating and sperm-attracting factors around the egg (9,10). The release of the attractant from the egg seems to stop after fertilization (9).
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interaction between noradrenaline or adrenaline and the β1 adrenergic receptor in the nervous system triggers early metamorphosis of larvae in the ascidian Ciona Savignyi
Developmental Biology, 2003Co-Authors: Yukiko Kimura, Manabu Yoshida, Masaaki MorisawaAbstract:Abstract Molecular mechanisms underlying the metamorphosis of larvae, e.g., ligand and receptor interaction, have to be determined and roles for the nervous system in marine invertebrates are not well understood. We report here that treatment of swimming larvae of the ascidian Ciona Savignyi with noradrenaline or adrenaline promoted morphological changes in early metamorphosis, e.g., tail resorption. Antagonists of the β-adrenergic receptor, propranolol, and the β 1 -adrenergic receptor, metoprolol, inhibited the noradrenaline-induced tail resorption, while an antagonist of the α-adrenergic receptor, phentolamine, and of the β 2 - adrenergic receptor, butoxamine, had no inhibitory effects. In addition, a selective agonist of the β-adrenergic receptor, isoproterenol, the concentration of which was lower than the effective concentration of the neurotransmitters, facilitated tail resorption. Immunohistochemical studies, using an anti-dopamine-hydroxylase antibody, showed that neurotransmitters such as noradrenaline and adrenaline localized around the brain vesicle of the larvae during metamorphosis. The β 1 -adrenergic receptor stained with antibodies was localized on the nervous system. Temporal expression of the β 1 -adrenergic receptor was intense in the nervous system in the larvae competent for metamorphosis. We propose that interactions between noradrenaline or adrenaline and the β 1 -adrenergic receptor in the nervous system mediate the process of metamorphosis of Ciona larvae.
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Signaling pathway from [Ca2+]i transients to ooplasmic segregation involves small GTPase rho in the ascidian egg.
Development growth & differentiation, 2003Co-Authors: Manabu Yoshida, Noburu Sensui, Yuji Horiuchi, Masaaki MorisawaAbstract:Intracellular Ca2+ transients occur at fertilization in the eggs of all animal species and are thought to be critical for the initiation of several events in egg activation. The rho family of small GTPases are known to organize and maintain the actin filament-dependent cytoskeleton, and rho is involved in the control mechanism of cytokinesis. In the ascidian Ciona Savignyi, the first step of ooplasmic segregation observed just after fertilization is cortical contraction with egg deformation, mediated by the cortical actin filaments. C3 exoenzyme, a rho-specific inhibitor, did not affect the pattern of [Ca2+]i transients in the ascidian egg, but inhibited ooplasmic segregation and cytokinesis at the first cleavage. Injection of inositol 1,4,5-trisphosphate or treatment of Ca2+ ionophore induced deformation of the egg and extrusion of the first polar body, but these phenomena did not occur in the C3 exoenzyme-injected egg. These results suggest that rho proteins are involved in egg deformation, ooplasmic segregation and cytokinesis downstream of the [Ca2+]i transients.
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Store-operated calcium channel regulates the chemotactic behavior of ascidian sperm.
Proceedings of the National Academy of Sciences of the United States of America, 2002Co-Authors: Manabu Yoshida, Makiko Ishikawa, Hiroko Izumi, Rosaria De Santis, Masaaki MorisawaAbstract:The sperm-activating and -attracting factor released from the eggs of the ascidians Ciona intestinalis and Ciona Savignyi requires extracellular Ca(2+) for activating sperm motility and eliciting chemotactic behavior of the activated sperm toward the egg. Here, we show that modulators of the store-operated Ca(2+) channel, SKF on the other hand, blockers of voltage-dependent Ca(2+) channels did not inhibit the chemotaxis, even though they inhibited the sperm activation operated by voltage-dependent Ca(2+) channels. The blockers of store-operated Ca(2+) channels also inhibited the asymmetrical flagellar beating and turning movements of the ascidian sperm, which are typical signs of sperm chemotaxis. Depletion of internal Ca(2+) stores by thapsigargin induced capacitative Ca(2+) entry into the sperm, which was blocked by SK&F96365. These results suggest that the intracellular Ca(2+) concentration increase through the store-operated Ca(2+) channels induces asymmetrical flagellar movements to establish the chemotactic behavior of the sperm.
Michael Brudno - One of the best experts on this subject based on the ideXlab platform.
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shrimp accurate mapping of short color space reads
PLOS Computational Biology, 2009Co-Authors: Arend Sidow, Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Michael BrudnoAbstract:The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25–70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP - the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism. Our method is based upon a fast read mapping technique, separate thorough alignment methods for regular letter-space as well as AB SOLiD (color-space) reads, and a statistical model for false positive hits. We use SHRiMP to map reads from a newly sequenced Ciona Savignyi individual to the reference genome. We demonstrate that SHRiMP can accurately map reads to this highly polymorphic genome, while confirming high heterozygosity of C. Savignyi in this second individual. SHRiMP is freely available at http://compbio.cs.toronto.edu/shrimp.
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Polymorphism Due to Multiple Amino Acid Substitutions at a Codon Site Within Ciona Savignyi
Genetics, 2008Co-Authors: Nilgun Donmez, Michael Brudno, Georgii A. Bazykin, Alexey S. KondrashovAbstract:We compared two haploid genotypes of one Ciona Savignyi individual and identified codons at which these genotypes differ by two nonsynonymous substitutions. Using the C. intestinalis genome as an outgroup, we showed that both substitutions tend to occur in the same genotype. Only in 53 (34.4%) of 154 codons, one substitution occurred in each of the two genotypes, although 77 (50%) of such codons are to be expected if substitutions were independent. We considered two feasible evolutionary causes for the observed pattern: substitutions driven by positive selection and compensatory substitutions, as well as several potential biases. However, none of these explanations is fully compelling, and data on multiple genotypes of C. Savignyi would help to elucidate the causes of this pattern.
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a haplome alignment and reference sequence of the highly polymorphic Ciona Savignyi genome
Genome Biology, 2007Co-Authors: Kerrin S Small, Michael Brudno, Matthew M Hill, Arend SidowAbstract:The sequence of Ciona Savignyi was determined using a whole-genome shotgun strategy, but a high degree of polymorphism resulted in a fractured assembly wherein allelic sequences from the same genomic region assembled separately. We designed a multistep strategy to generate a nonredundant reference sequence from the original assembly by reconstructing and aligning the two 'haplomes' (haploid genomes). In the resultant 174 megabase reference sequence, each locus is represented once, misassemblies are corrected, and contiguity and continuity are dramatically improved.
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2007 Small et Volume al. 8, Issue 3, Article R41 Open Access Method
2007Co-Authors: Kerrin S Small, Michael Brudno, Matthew M Hill, Arend SidowAbstract:A haplome alignment and reference sequence of the highly polymorphic Ciona Savignyi genom
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Extreme genomic variation in a natural population
2006Co-Authors: Kerrin S Small, Michael Brudno, Matthew M Hill, Arend SidowAbstract:Whole-genome sequence data from samples of natural populations provide fertile grounds for analyses of intraspecific variation and tests of population genetic theory. We show that the urochordate Ciona Savignyi, one of the species of ocean-dwelling broadcast spawners commonly known as sea squirts, exhibits the highest rates of single-nucleotide and structural polymorphism ever comprehensively quantified in a multicellular organism. We demonstrate that the cause for the extreme heterozygosity is a large effective population size, and, consistent with prediction by the neutral theory, we find evidence of strong purifying selection. These results constitute in-depth insight into the dynamics of highly polymorphic genomes and provide important empirical support of population genetic theory as it pertains to population size, heterozygosity, and natural selection.
Stephen M. Rumble - One of the best experts on this subject based on the ideXlab platform.
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SHRiMP: accurate mapping of short color-space reads,” PLoS
2013Co-Authors: Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend SidowAbstract:The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25–70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP- the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism. Our method is based upon a fast read mapping technique, separate thorough alignment methods for regular letter-space as well as AB SOLiD (color-space) reads, and a statistical model for false positive hits. We use SHRiMP to map reads from a newly sequenced Ciona Savignyi individual to the reference genome. We demonstrate that SHRiMP can accurately map reads to this highly polymorphic genome, while confirming high heterozygosity of C. Savignyi in this second individual. SHRiMP is freely available a
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shrimp accurate mapping of short color space reads
PLOS Computational Biology, 2009Co-Authors: Arend Sidow, Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Michael BrudnoAbstract:The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25–70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP - the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism. Our method is based upon a fast read mapping technique, separate thorough alignment methods for regular letter-space as well as AB SOLiD (color-space) reads, and a statistical model for false positive hits. We use SHRiMP to map reads from a newly sequenced Ciona Savignyi individual to the reference genome. We demonstrate that SHRiMP can accurately map reads to this highly polymorphic genome, while confirming high heterozygosity of C. Savignyi in this second individual. SHRiMP is freely available at http://compbio.cs.toronto.edu/shrimp.
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Shrimp: accurate mapping of short color-space reads
2009Co-Authors: Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend SidowAbstract:The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25–70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP- the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism. Our method is based upon a fast read mapping technique, separate thorough alignment methods for regular letter-space as well as AB SOLiD (color-space) reads, and a statistical model for false positive hits. We use SHRiMP to map reads from a newly sequenced Ciona Savignyi individual to the reference genome. We demonstrate that SHRiMP can accurately map reads to this highly polymorphic genome, while confirming high heterozygosity of C. Savignyi in this second individual. SHRiMP is freely available a