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Martí Solans Josep - One of the best experts on this subject based on the ideXlab platform.

  • Oikopleura dioica com a model animal per investigar l'impacte de les pèrdues gèniques en l'Evo-Devo: les vies de senyalització de l'àcid retinoic i Wnt com a cas d'estudi
    'Edicions de la Universitat de Barcelona', 2018
    Co-Authors: Martí Solans Josep
    Abstract:

    [cat] El creixent nombre de genomes seqüenciats està posant de manifest que la pèrdua gènica és un fenomen recurrent que pot haver generat diversitat al llarg de la història evolutiva dels diferents grups d’organismes. En aquest sentit, un dels grans reptes en el camp de la EvoDevo és entendre l’impacte de la pèrdua gènica en l’evolució dels mecanismes del desenvolupament animal considerant diferents escenaris evolutius. En escenaris de selecció positiva, la pèrdua hauria comportat canvis morfològics o fisiològics que haurien permès l’adaptació de les espècies a noves condicions ambientals. En escenaris de selecció neutre (o quasi neutre), la pèrdua hauria afectat a gens que haurien esdevingut prescindibles per l’existència de robustesa mutacional o perquè les condicions ambientals haurien canviat. Saber si una pèrdua gènica ha estat adaptativa o neutre és generalment molt complex ja que molts cops es difícil establir relacions directes de causalitat entre la pèrdua d’un gen i l’aparició d’una nova característica evolutivament avantatjosa. Malgrat aquesta dificultat, en aquesta tesi doctoral vàrem voler estudiar l’impacte de la pèrdua gènica en l’EvoDevo a partir d’analitzar l’evolució de les vies de senyalització de l’àcid retinoic (RA) i de Wnt -vies essencials pel desenvolupament de tots els cordats- a l’urocordat Oikopleura. dioica com a sistema model de referència. Per establir O. dioica com a model animal, però, a més de les característiques biològiques que la fan atractiva per aquests tipus estudis –desenvolupament embrionari i cicle de vida extremadament ràpid, simplicitat i transparència corporal, genoma reduït i totalment seqüenciat, possibilitat de manipulació gènica per estudis funcionals– ha estat fonamental desenvolupar unes instal·lacions per cultivar-la en el laboratori, així com protocols de manteniment assequibles (low-cost) per qualsevol grup d’investigació. Gràcies a aquest sistema de cultiu, em pogut analitzar els components de la xarxa gènica del metabolisme de l’RA (RA-MGN), així com els lligands de la via de senyalització per Wnt. En referència a la RA-MGN, el nostre treball ens permet concloure que les pèrdues gèniques que han afectat a aquesta via durant l’evolució de O. dioica han tingut lloc en un sistema genètic no robust, on el desballestament de la via no han tingut un impacte dramàtic en el pla corporal típic de cordats que preserva aquest organisme. Per altre banda, l’anàlisi de la família Wnt a cordats, ens ha permès concloure que a més de la duplicació gènica o de la redundància funcional per processos d’evolució convergent, els fenòmens de reassignació de funcions (Function shuffling) augmenten també la robustesa mutacional i faciliten les pèrdues gèniques en les famílies de gens. En resum, els resultats d’aquesta tesi doctoral posen de manifest que O. dioica és un model animal atractiu per estudiar tant aspectes bàsics de l’impacte de les pèrdues gèniques en l’evolució dels mecanismes del desenvolupament, com en aspectes aplicats en que certes pèrdues confereixen a O. dioica la condició de knockout evolutiu que pot ser interessant per l’estudi de mecanismes moleculars concrets com la toxicitat de les PUAs en el desenvolupament embrionari d’organismes marins.[eng] The bloom of genomics is revealing gene loss as a pervasive Evolutionary force generating genetic diversity that shapes the Evolution of species. In this sense, one of the great challenges in the field of EvoDevo is to understand the impact of gene loss on the Evolution of animal developmental mechanisms. In this doctoral thesis we wanted to study the impact of gene loss in EvoDevo, using the analysis of the Evolution of retinoic acid (RA) and Wnt signaling pathways - essential pathways in the development of all the chordates- in the urochordate Oikopleura. dioica as a model reference system. To establish O. dioica as an animal model, in addition to the biological characteristics that make it attractive for his type of studies-embryonic development and extremely fast life cycle, simplicity and body transparency, reduced and fully sequenced genome, possibility of gene manipulation for Functional studies - It has been essential to develop a facility to grow O. dioica in the laboratory, as well as low-cost maintenance protocols affordable for any research group. Thanks to this culture system, we were able to analyze the components of the RA metabolic gene network (RA-MGN), as well as the ligands of the Wnt signaling pathway. In reference to the RA-MGN, our work allows us to conclude that the gene losses that have affected this pathway during the Evolution of O. dioica have taken place in a non-robust genetic system, where the dismantling of the network has not had a dramatic impact on the typical body plan of chordates that preserves this organism. On the other hand, the analysis of the Wnt family in chordates, has allowed us to conclude that in addition to gene duplication or Functional redundancy due to processes of convergent Evolution, Function shuffling also increase the mutational robustness and facilitate gene losses in gene families. In summary, the results of this doctoral thesis show that O. dioica is an attractive animal model for studying both basic aspects of the impact of gene losses in the Evolution of development mechanisms, and in applied aspects. For instance, certain losses give to O. dioica an Evolutionary knockout condition that may be interesting for the study of concrete molecular mechanisms such as the toxicity of PUAs in the embryonic development of marine organisms

  • Oikopleura dioica com a model animal per investigar l'impacte de les pèrdues gèniques en l'Evo-Devo: les vies de senyalització de l'àcid retinoic i Wnt com a cas d'estudi
    'Edicions de la Universitat de Barcelona', 2018
    Co-Authors: Martí Solans Josep
    Abstract:

    El creixent nombre de genomes seqüenciats està posant de manifest que la pèrdua gènica és un fenomen recurrent que pot haver generat diversitat al llarg de la història evolutiva dels diferents grups d’organismes. En aquest sentit, un dels grans reptes en el camp de la EvoDevo és entendre l’impacte de la pèrdua gènica en l’evolució dels mecanismes del desenvolupament animal considerant diferents escenaris evolutius. En escenaris de selecció positiva, la pèrdua hauria comportat canvis morfològics o fisiològics que haurien permès l’adaptació de les espècies a noves condicions ambientals. En escenaris de selecció neutre (o quasi neutre), la pèrdua hauria afectat a gens que haurien esdevingut prescindibles per l’existència de robustesa mutacional o perquè les condicions ambientals haurien canviat. Saber si una pèrdua gènica ha estat adaptativa o neutre és generalment molt complex ja que molts cops es difícil establir relacions directes de causalitat entre la pèrdua d’un gen i l’aparició d’una nova característica evolutivament avantatjosa. Malgrat aquesta dificultat, en aquesta tesi doctoral vàrem voler estudiar l’impacte de la pèrdua gènica en l’EvoDevo a partir d’analitzar l’evolució de les vies de senyalització de l’àcid retinoic (RA) i de Wnt -vies essencials pel desenvolupament de tots els cordats- a l’urocordat Oikopleura. dioica com a sistema model de referència. Per establir O. dioica com a model animal, però, a més de les característiques biològiques que la fan atractiva per aquests tipus estudis –desenvolupament embrionari i cicle de vida extremadament ràpid, simplicitat i transparència corporal, genoma reduït i totalment seqüenciat, possibilitat de manipulació gènica per estudis funcionals– ha estat fonamental desenvolupar unes instal·lacions per cultivar-la en el laboratori, així com protocols de manteniment assequibles (low-cost) per qualsevol grup d’investigació. Gràcies a aquest sistema de cultiu, em pogut analitzar els components de la xarxa gènica del metabolisme de l’RA (RA-MGN), així com els lligands de la via de senyalització per Wnt. En referència a la RA-MGN, el nostre treball ens permet concloure que les pèrdues gèniques que han afectat a aquesta via durant l’evolució de O. dioica han tingut lloc en un sistema genètic no robust, on el desballestament de la via no han tingut un impacte dramàtic en el pla corporal típic de cordats que preserva aquest organisme. Per altre banda, l’anàlisi de la família Wnt a cordats, ens ha permès concloure que a més de la duplicació gènica o de la redundància funcional per processos d’evolució convergent, els fenòmens de reassignació de funcions (Function shuffling) augmenten també la robustesa mutacional i faciliten les pèrdues gèniques en les famílies de gens. En resum, els resultats d’aquesta tesi doctoral posen de manifest que O. dioica és un model animal atractiu per estudiar tant aspectes bàsics de l’impacte de les pèrdues gèniques en l’evolució dels mecanismes del desenvolupament, com en aspectes aplicats en que certes pèrdues confereixen a O. dioica la condició de knockout evolutiu que pot ser interessant per l’estudi de mecanismes moleculars concrets com la toxicitat de les PUAs en el desenvolupament embrionari d’organismes marins.The bloom of genomics is revealing gene loss as a pervasive Evolutionary force generating genetic diversity that shapes the Evolution of species. In this sense, one of the great challenges in the field of EvoDevo is to understand the impact of gene loss on the Evolution of animal developmental mechanisms. In this doctoral thesis we wanted to study the impact of gene loss in EvoDevo, using the analysis of the Evolution of retinoic acid (RA) and Wnt signaling pathways - essential pathways in the development of all the chordates- in the urochordate Oikopleura. dioica as a model reference system. To establish O. dioica as an animal model, in addition to the biological characteristics that make it attractive for his type of studies-embryonic development and extremely fast life cycle, simplicity and body transparency, reduced and fully sequenced genome, possibility of gene manipulation for Functional studies - It has been essential to develop a facility to grow O. dioica in the laboratory, as well as low-cost maintenance protocols affordable for any research group. Thanks to this culture system, we were able to analyze the components of the RA metabolic gene network (RA-MGN), as well as the ligands of the Wnt signaling pathway. In reference to the RA-MGN, our work allows us to conclude that the gene losses that have affected this pathway during the Evolution of O. dioica have taken place in a non-robust genetic system, where the dismantling of the network has not had a dramatic impact on the typical body plan of chordates that preserves this organism. On the other hand, the analysis of the Wnt family in chordates, has allowed us to conclude that in addition to gene duplication or Functional redundancy due to processes of convergent Evolution, Function shuffling also increase the mutational robustness and facilitate gene losses in gene families. In summary, the results of this doctoral thesis show that O. dioica is an attractive animal model for studying both basic aspects of the impact of gene losses in the Evolution of development mechanisms, and in applied aspects. For instance, certain losses give to O. dioica an Evolutionary knockout condition that may be interesting for the study of concrete molecular mechanisms such as the toxicity of PUAs in the embryonic development of marine organisms

G S Mourad - One of the best experts on this subject based on the ideXlab platform.

  • the nicotiana sylvestris nucleobase cation symporter 1 retains a dicot solute specificity profile
    Plant Gene, 2020
    Co-Authors: J N Nguyen, J R Schein, K A Hunt, J A Tippmannfeightner, Micah Rapp, A J Stofferbittner, V J Nalam, A M Funk, Neil P Schultes, G S Mourad
    Abstract:

    Abstract Nucleobase Cation Symporter 1 proteins are present in bacteria, fungi and among plants. Microbes often contain numerous NCS1 proteins that have evolved specific solute specificity profiles (solute transport and binding). Conversely, most members of Viridiplantae have a unique NCS1 that shows a broad, yet species –specific, solute specificity profile. Properties of NCS1 from Nicotiana sylvestris Speg. & Comes (NsNCS1) have been determined as part of an ongoing Evolution-Function analysis through heterologous expression studies in ncs1-deficient Saccharomyces cerevisiae Meyen ex E.C. Hansen as well as Functional assays and subcellular localization studies in planta. NsNCS1 transports the purine adenine with high affinity and moves guanine, uracil, cytosine and hypoxanthine. Xanthine, uric acid and 5-flourocytosine act as competitive inhibitors for NsNCS1. When expressed in Arabidopsis, NsNCS1 locates to the chloroplast and facilitates the transport of guanine and 8-azaguanine. The NsNCS1 solute specificity profile is very similar, yet distinct, from AtNCS1 (A. thaliana (L.) Heynh. NCS1) and indicates that despite Evolutionary divergence in the Eudicots - Nicotiana, an Astrid, and Arabidopsis, a Rosid, − little Functional difference evolved. The alignment of select plant NCS1 amino acid sequences coupled with a detailed knowledge of each solute specificity profile facilitates identifying residues that may contribute to subtle solute discrimination. Such an Evolution-Function analysis will complement recent molecular model based site-directed mutagenesis analysis of select microbial and plant NCS1.

J N Nguyen - One of the best experts on this subject based on the ideXlab platform.

  • the nicotiana sylvestris nucleobase cation symporter 1 retains a dicot solute specificity profile
    Plant Gene, 2020
    Co-Authors: J N Nguyen, J R Schein, K A Hunt, J A Tippmannfeightner, Micah Rapp, A J Stofferbittner, V J Nalam, A M Funk, Neil P Schultes, G S Mourad
    Abstract:

    Abstract Nucleobase Cation Symporter 1 proteins are present in bacteria, fungi and among plants. Microbes often contain numerous NCS1 proteins that have evolved specific solute specificity profiles (solute transport and binding). Conversely, most members of Viridiplantae have a unique NCS1 that shows a broad, yet species –specific, solute specificity profile. Properties of NCS1 from Nicotiana sylvestris Speg. & Comes (NsNCS1) have been determined as part of an ongoing Evolution-Function analysis through heterologous expression studies in ncs1-deficient Saccharomyces cerevisiae Meyen ex E.C. Hansen as well as Functional assays and subcellular localization studies in planta. NsNCS1 transports the purine adenine with high affinity and moves guanine, uracil, cytosine and hypoxanthine. Xanthine, uric acid and 5-flourocytosine act as competitive inhibitors for NsNCS1. When expressed in Arabidopsis, NsNCS1 locates to the chloroplast and facilitates the transport of guanine and 8-azaguanine. The NsNCS1 solute specificity profile is very similar, yet distinct, from AtNCS1 (A. thaliana (L.) Heynh. NCS1) and indicates that despite Evolutionary divergence in the Eudicots - Nicotiana, an Astrid, and Arabidopsis, a Rosid, − little Functional difference evolved. The alignment of select plant NCS1 amino acid sequences coupled with a detailed knowledge of each solute specificity profile facilitates identifying residues that may contribute to subtle solute discrimination. Such an Evolution-Function analysis will complement recent molecular model based site-directed mutagenesis analysis of select microbial and plant NCS1.

Bing Zhang - One of the best experts on this subject based on the ideXlab platform.

  • grb 080503 late afterglow re brightening signature of a magnetar powered merger nova
    The Astrophysical Journal, 2015
    Co-Authors: He Gao, Xuan Ding, Zigao Dai, Bing Zhang
    Abstract:

    GRB 080503 is a short gamma-ray burst (GRB) detected by Swift and has been classified as a GRB originating from a compact star merger. The soft extended emission and the simultaneous late re-brightening in both the X-ray and optical afterglow light curves raise interesting questions regarding its physical origin. We show that the broadband data of GRB 080503 can be well explained within the framework of the double neutron star merger model, provided that the merger remnant is a rapidly rotating massive neutron star with an extremely high magnetic field (i.e., a millisecond magnetar). We show that the late optical re-brightening is consistent with the emission from a magnetar-powered "merger-nova." This adds one more case to the growing sample of merger-novae associated with short GRBs. The soft extended emission and the late X-ray excess emission are well connected through a magnetar dipole spin-down luminosity Evolution Function, suggesting that direct magnetic dissipation is the mechanism to produce these X-rays. The X-ray emission initially leaks from a hole in the merger ejecta pierced by the short GRB jet. The hole subsequently closes after the magnetar spins down and the magnetic pressure drops below ram pressure. The X-ray photons are then trapped behind the merger-nova ejecta until the ejecta becomes optically thin at a later time. This explains the essentially simultaneous re-brightening in both the optical and X-ray light curves. Within this model, future gravitational-wave sources could be associated with a bright X-ray counterpart along with the merger-nova, even if the short GRB jet beams away from Earth.

  • grb 080503 late afterglow re brightening signature of a magnetar powered merger nova
    arXiv: High Energy Astrophysical Phenomena, 2015
    Co-Authors: He Gao, Xuan Ding, Zigao Dai, Bing Zhang
    Abstract:

    GRB 080503 is a short gamma-ray burst (GRB) detected by \emph{Swift} and has been classified as a compact-star-merger-origin GRB. The soft extended emission and the simultaneous late re-brightening in both the X-ray and optical afterglow lightcurves raise interesting questions regarding its physical origin. We show that the broad-band data of GRB 080503 can be well explained within the framework of the double neutron star merger model, provided that the merger remnant is a rapidly-rotating massive neutron star with an extremely high magnetic field (i.e. a millisecond magnetar). We show that the late optical re-brightening is consistent with the emission from a magnetar-powered "merger-nova". This adds one more case to the growing sample of merger-novae associated with short GRBs. The soft extended emission and the late X-ray excess emission are well connected through a magnetar dipole spin-down luminosity Evolution Function, suggesting that direct magnetic dissipation is the mechanism to produce these X-rays. The X-ray emission initially leaks from a hole in the merger ejecta pierced by the short GRB jet. The hole subsequently closes after the magnetar spins down and the magnetic pressure drops below ram pressure. The X-ray photons are then trapped behind the mergernova ejecta until the ejecta becomes optically thin at a later time. This explains the essentially simultaneous re-brightening in both the optical and X-ray lightcurves. Within this model, future gravitational wave sources could be associated with a bright X-ray counterpart along with the mergernova, even if the short GRB jet beams away from Earth.

Mourad George - One of the best experts on this subject based on the ideXlab platform.

  • Heterologous Complementation Studies Reveal the Solute Transport Profiles of a Two-Member Nucleobase Cation Symporter 1 (NCS1) Family in Physcomitrella Patens
    Opus: Research \u26 Creativity at IPFW, 2016
    Co-Authors: Minton Janet, Rapp Micah, Schultes, Neil P, Stoffer Amanda, Mourad George
    Abstract:

    As part of an Evolution-Function analysis, two nucleobase cation symporter 1 (NCS1) from the moss Physcomitrella patens (PpNCS1A and PpNCS1B) are examined – the first such analysis of nucleobase transporters from early land plants. The solute specificity profiles for the moss NCS1 were determined through heterologous expression, growth and radiolabeled uptake experiments in NCS1-deficient Saccharomyces cerevisiae. Both PpNCS1A and 1B, share the same profiles as high affinity transporters of adenine and transport uracil, guanine, 8-azaguanine, 8-azaadenine, cytosine, 5-fluorocytosine, hypoxanthine, and xanthine. Despite sharing the same solute specificity profile, PpNCS1A and PpNCS1B move nucleobase compounds with different efficiencies. The broad nucleobase transport profile of PpNCS1A and 1B differs from the recently-characterized Viridiplantae NCS1 in breadth, revealing a flexibility in solute interactions with NCS1 across plant Evolution

  • Heterologous Complementation Studies Reveal the Solute Transport Profiles of a Two-Member Nucleobase Cation Symporter 1 (NCS1) Family in Physcomitrella Patens
    Opus: Research \u26 Creativity at IPFW, 2015
    Co-Authors: Minton, Janet A, Rapp Micah, Stoffer, Amanda J, Schultes, Neil P, Mourad George
    Abstract:

    As part of an Evolution-Function analysis, two nucleobase cation symporter 1 (NCS1) from the moss Physcomitrella patens (PpNCS1A and PpNCS1B) are examined e the first such analysis of nucleobase transporters from early land plants. The solute specificity profiles for the moss NCS1 were determined through heterologous expression, growth and radiolabeled uptake experiments in NCS1-deficient Saccharomyces cerevisiae. Both PpNCS1A and 1B, share the same profiles as high affinity transporters of adenine and transport uracil, guanine, 8-azaguanine, 8-azaadenine, cytosine, 5-fluorocytosine, hypoxanthine, and xanthine. Despite sharing the same solute specificity profile, PpNCS1A and PpNCS1B move nucleobase compounds with different efficiencies. The broad nucleobase transport profile of PpNCS1A and 1B differs from the recently-characterized Viridiplantae NCS1 in breadth, revealing a flexibility in solute interactions with NCS1 across plant Evolution