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Claudio V. Mello - One of the best experts on this subject based on the ideXlab platform.
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ZEBrA: Zebra finch Expression Brain Atlas-A resource for comparative molecular neuroanatomy and brain evolution studies.
Journal of Comparative Neurology, 2020Co-Authors: Peter V. Lovell, Morgan Wirthlin, Taylor Kaser, Alexa A. Buckner, Julia B. Carleton, Brian R. Snider, Anne Mchugh, Alexander Tolpygo, Partha P. Mitra, Claudio V. MelloAbstract:An in-depth understanding of the genetics and evolution of brain function and behavior requires detailed mapping of gene expression in functional brain circuits across major vertebrate clades. Here we present the Zebra finch Expression Brain Atlas (ZEBrA; www.zebrafinchatlas.org, RRID: SCR_012988), a web-based resource that maps the expression of genes linked to a broad range of functions onto the brain of zebra finches. ZEBrA is a first of its kind gene expression brain atlas for a bird species, and a first for any Sauropsid. ZEBrA's >3,200 high-resolution digital images of in situ hybridized sections for ~650 genes (as of June, 2019) are presented in alignment with an annotated histological atlas and can be browsed down to cellular resolution. An extensive relational database connects expression patterns to information about gene function, mouse expression patterns and phenotypes, and gene involvement in human diseases and communication disorders. By enabling brain-wide gene expression assessments in a bird, ZEBrA provides important substrates for comparative neuroanatomy and molecular brain evolution studies. ZEBrA also provides unique opportunities for linking genetic pathways to vocal learning and motor control circuits, as well as for novel insights into the molecular basis of sex steroids actions, brain dimorphisms, reproductive and social behaviors, sleep function, and adult neurogenesis, among other fundamental themes. This article is protected by copyright. All rights reserved.
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ZEBrA: Zebra finch Expression Brain Atlas—A resource for comparative molecular neuroanatomy and brain evolution studies
The Journal of comparative neurology, 2020Co-Authors: Peter V. Lovell, Morgan Wirthlin, Taylor Kaser, Alexa A. Buckner, Julia B. Carleton, Brian R. Snider, Anne Mchugh, Alexander Tolpygo, Partha P. Mitra, Claudio V. MelloAbstract:An in-depth understanding of the genetics and evolution of brain function and behavior requires detailed mapping of gene expression in functional brain circuits across major vertebrate clades. Here we present the Zebra finch Expression Brain Atlas (ZEBrA; www.zebrafinchatlas.org, RRID: SCR_012988), a web-based resource that maps the expression of genes linked to a broad range of functions onto the brain of zebra finches. ZEBrA is a first of its kind gene expression brain atlas for a bird species, and a first for any Sauropsid. ZEBrA's >3,200 high-resolution digital images of in situ hybridized sections for ~650 genes (as of June, 2019) are presented in alignment with an annotated histological atlas and can be browsed down to cellular resolution. An extensive relational database connects expression patterns to information about gene function, mouse expression patterns and phenotypes, and gene involvement in human diseases and communication disorders. By enabling brain-wide gene expression assessments in a bird, ZEBrA provides important substrates for comparative neuroanatomy and molecular brain evolution studies. ZEBrA also provides unique opportunities for linking genetic pathways to vocal learning and motor control circuits, as well as for novel insights into the molecular basis of sex steroids actions, brain dimorphisms, reproductive and social behaviors, sleep function, and adult neurogenesis, among other fundamental themes. This article is protected by copyright. All rights reserved.
Lorenzo Alibardi - One of the best experts on this subject based on the ideXlab platform.
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Molecular structure of Sauropsid β-keratins from tuatara (Sphenodon punctatus).
Journal of Structural Biology, 2019Co-Authors: David A. D. Parry, R.d. Bruce Fraser, Kim Rutherford, Lorenzo Alibardi, Neil John GemmellAbstract:Abstract The birds and reptiles, collectively known as the Sauropsids, can be subdivided phylogenetically into the archosaurs (birds, crocodiles), the testudines (turtles), the squamates (lizards, snakes) and the rhynchocephalia (tuatara). The structural framework of the epidermal appendages from the Sauropsids, which include feathers, claws and scales, has previously been characterised by electron microscopy, infrared spectroscopy and X-ray diffraction analyses, as well as by studies of the amino acid sequences of the constituent β-keratin proteins (also referred to as the corneous β-proteins). An important omission in this work, however, was the lack of sequence and structural data relating to the epidermal appendages of the rhynchocephalia (tuatara), one of the two branches of the lepidosaurs. Considerable effort has gone into sequencing the tuatara genome and while this is not yet complete, there are now sufficient sequence data for conclusions to be drawn on the similarity of the β-keratins from the tuatara to those of other members of the Sauropsids. These results, together with a comparison of the X-ray diffraction pattern of tuatara claw with those from seagull feather and goanna claw, confirm that there is a common structural plan in the β-keratins of all of the Sauropsids, and not just those that comprise the archosaurs (birds and crocodiles), the testudines (turtles) and the squamates (lizards and snakes).
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Granulocytes of reptilian Sauropsids contain beta-defensin-like peptides: a comparative ultrastructural survey.
Journal of Morphology, 2013Co-Authors: Lorenzo AlibardiAbstract:The ability of lizards to withstand infections after wounding or amputation of the tail or limbs has suggested the presence of antimicrobial peptides in their tissues. Previous studies on the lizard Anolis carolinensis have identified several beta-defensin-like peptides that may potentially be involved in protection from infections. The present ultrastructural immunocytochemical study has analyzed tissues in different reptilian species in order to localize the cellular source of one of the more expressed beta-defensins previously sequenced in lizard indicated as AcBD15. Beta-defensin-like immunoreactivity is present in some of the larger, nonspecific granules of granulocytes in two lizard species, a snake, the tuatara, and a turtle. The ultrastructural study indicates that only heterophilic and basophilic granulocytes contain this defensin while other cell types from the epidermis, mesenchyme, and dermis, muscles, nerves, cartilage or bone are immunonegative. The study further indicates that not all granules in reptilian granulocytes contain the beta-defensin peptide, suggesting the presence of granules with different content as previously indicated for mammalian neutrophilic leucocytes. No immunolabeling was instead observed in granulocytes of the alligator and chick using this antibody. The present immunocytochemical observations suggest a broad cross-reactivity and conservation of beta-defensin-like sequence or steric motif across lepidosaurians and likely in turtles while archosaurian granulocytes may contain different beta-defensin-like or other peptides. J. Morphol. 274:877–886, 2013. © 2013 Wiley Periodicals, Inc.
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Cell biology of adhesive setae in gecko lizards.
Zoology, 2009Co-Authors: Lorenzo AlibardiAbstract:Abstract Adhesive devices of digital pads of gecko lizards are formed by microscopic hair-like structures termed setae that derive from the interaction between the oberhautchen and the clear layer of the epidermis. The two layers form the shedding complex and permit skin shedding in lizards. Setae consist of a resistant but flexible corneous material largely made of keratin-associated beta-proteins (KAβPs, formerly called beta-keratins) of 8–22 kDa and of alpha-keratins of 45–60 kDa. In Gekko gecko , 19 Sauropsid keratin-associated beta-proteins (sKAβPs) and at least two larger alpha-keratins are expressed in the setae. Some sKAβPs are rich in cysteine (111–114 amino acids), while others are rich in glycine (169–219 amino acids). In the entire genome of Anolis carolinensis 40 KaβPs are present and participate in the formation of all types of scales, pad lamellae and claws. Nineteen sKAβPs comprise cysteine-rich 9.2–14.4 kDa proteins of 89–142 amino acids, and 19 are glycine-rich 16.5–22.0 kDa proteins containing 162–225 amino acids, and only two types of sKAβPs are cysteine- and glycine-poor proteins. Genes coding for these proteins contain an intron in the 5′-non-coding region, a typical characteristic of most Sauropsid KaβPs. Gecko KAβPs show a central amino acid region of high homology and a beta-pleated conformation that is likely responsible for the polymerization of KaβPs into long and resistant filaments. The association of numerous filaments, probably over a framework of alpha-keratins, permits the formation of bundles of corneous material for the elongation of setae, which may be over 100 μm long. The terminals branching off each seta may derive from the organization of the cytoskeleton and from the mechanical separation of keratin bundles located at the terminal apex of setae.
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evolution of hard proteins in the Sauropsid integument in relation to the cornification of skin derivatives in amniotes
Journal of Anatomy, 2009Co-Authors: Lorenzo Alibardi, Luisa Dalla Valle, Alessia Nardi, Mattia ToniAbstract:Hard skin appendages in amniotes comprise scales, feathers and hairs. The cell organization of these appendages probably derived from the localization of specialized areas of dermal–epidermal interaction in the integument. The horny scales and the other derivatives were formed from large areas of dermal–epidermal interaction. The evolution of these skin appendages was characterized by the production of specific coiled-coil keratins and associated proteins in the inter-filament matrix. Unlike mammalian keratin-associated proteins, those of Sauropsids contain a double beta-folded sequence of about 20 amino acids, known as the core-box. The core-box shows 60%–95% sequence identity with known reptilian and avian proteins. The core-box determines the polymerization of these proteins into filaments indicated as beta-keratin filaments. The nucleotide and derived amino acid sequences for these Sauropsid keratin-associated proteins are presented in conjunction with a hypothesis about their evolution in reptiles-birds compared to mammalian keratin-associated proteins. It is suggested that genes coding for ancestral glycine-serine-rich sequences of alpha-keratins produced a new class of small matrix proteins. In Sauropsids, matrix proteins may have originated after mutation and enrichment in proline, probably in a central region of the ancestral protein. This mutation gave rise to the core-box, and other regions of the original protein evolved differently in the various reptilians orders. In lepidosaurians, two main groups, the high glycine proline and the high cysteine proline proteins, were formed. In archosaurians and chelonians two main groups later diversified into the high glycine proline tyrosine, non-feather proteins, and into the glycine-tyrosine-poor group of feather proteins, which evolved in birds. The latter proteins were particularly suited for making the elongated barb/barbule cells of feathers. In therapsids-mammals, mutations of the ancestral proteins formed the high glycine-tyrosine or the high cysteine proteins but no core-box was produced in the matrix proteins of the hard corneous material of mammalian derivatives.
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Evolution of hard proteins in the Sauropsid integument in relation to the cornification of skin derivatives in amniotes
'Wiley', 2009Co-Authors: Lorenzo Alibardi, Luisa Dalla Valle, Alessia Nardi, Toni MattiaAbstract:Hard skin appendages in amniotes comprise scales, feathers and hairs. The cell organization of these appendages probably derived from the localization of specialized areas of dermal-epidermal interaction in the integument. The horny scales and the other derivatives were formed from large areas of dermal-epidermal interaction. The evolution of these skin appendages was characterized by the production of specific coiled-coil keratins and associated proteins in the inter-filament matrix. Unlike mammalian keratin-associated proteins, those of Sauropsids contain a double beta-folded sequence of about 20 amino acids, known as the core-box. The core-box shows 60%-95% sequence identity with known reptilian and avian proteins. The core-box determines the polymerization of these proteins into filaments indicated as beta-keratin filaments. The nucleotide and derived amino acid sequences for these Sauropsid keratin-associated proteins are presented in conjunction with a hypothesis about their evolution in reptiles-birds compared to mammalian keratin-associated proteins. It is suggested that genes coding for ancestral glycine-serine-rich sequences of alpha-keratins produced a new class of small matrix proteins. In Sauropsids, matrix proteins may have originated after mutation and enrichment in proline, probably in a central region of the ancestral protein. This mutation gave rise to the core-box, and other regions of the original protein evolved differently in the various reptilians orders. In lepidosaurians, two main groups, the high glycine proline and the high cysteine proline proteins, were formed. In archosaurians and chelonians two main groups later diversified into the high glycine proline tyrosine, non-feather proteins, and into the glycine-tyrosine-poor group of feather proteins, which evolved in birds. The latter proteins were particularly suited for making the elongated barb/barbule cells of feathers. In therapsids-mammals, mutations of the ancestral proteins formed the high glycine-tyrosine or the high cysteine proteins but no core-box was produced in the matrix proteins of the hard corneous material of mammalian derivatives. © 2009 The Authors Journal compilation © 2009 Anatomical Society of Great Britain and Ireland
Peter V. Lovell - One of the best experts on this subject based on the ideXlab platform.
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ZEBrA: Zebra finch Expression Brain Atlas-A resource for comparative molecular neuroanatomy and brain evolution studies.
Journal of Comparative Neurology, 2020Co-Authors: Peter V. Lovell, Morgan Wirthlin, Taylor Kaser, Alexa A. Buckner, Julia B. Carleton, Brian R. Snider, Anne Mchugh, Alexander Tolpygo, Partha P. Mitra, Claudio V. MelloAbstract:An in-depth understanding of the genetics and evolution of brain function and behavior requires detailed mapping of gene expression in functional brain circuits across major vertebrate clades. Here we present the Zebra finch Expression Brain Atlas (ZEBrA; www.zebrafinchatlas.org, RRID: SCR_012988), a web-based resource that maps the expression of genes linked to a broad range of functions onto the brain of zebra finches. ZEBrA is a first of its kind gene expression brain atlas for a bird species, and a first for any Sauropsid. ZEBrA's >3,200 high-resolution digital images of in situ hybridized sections for ~650 genes (as of June, 2019) are presented in alignment with an annotated histological atlas and can be browsed down to cellular resolution. An extensive relational database connects expression patterns to information about gene function, mouse expression patterns and phenotypes, and gene involvement in human diseases and communication disorders. By enabling brain-wide gene expression assessments in a bird, ZEBrA provides important substrates for comparative neuroanatomy and molecular brain evolution studies. ZEBrA also provides unique opportunities for linking genetic pathways to vocal learning and motor control circuits, as well as for novel insights into the molecular basis of sex steroids actions, brain dimorphisms, reproductive and social behaviors, sleep function, and adult neurogenesis, among other fundamental themes. This article is protected by copyright. All rights reserved.
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ZEBrA: Zebra finch Expression Brain Atlas—A resource for comparative molecular neuroanatomy and brain evolution studies
The Journal of comparative neurology, 2020Co-Authors: Peter V. Lovell, Morgan Wirthlin, Taylor Kaser, Alexa A. Buckner, Julia B. Carleton, Brian R. Snider, Anne Mchugh, Alexander Tolpygo, Partha P. Mitra, Claudio V. MelloAbstract:An in-depth understanding of the genetics and evolution of brain function and behavior requires detailed mapping of gene expression in functional brain circuits across major vertebrate clades. Here we present the Zebra finch Expression Brain Atlas (ZEBrA; www.zebrafinchatlas.org, RRID: SCR_012988), a web-based resource that maps the expression of genes linked to a broad range of functions onto the brain of zebra finches. ZEBrA is a first of its kind gene expression brain atlas for a bird species, and a first for any Sauropsid. ZEBrA's >3,200 high-resolution digital images of in situ hybridized sections for ~650 genes (as of June, 2019) are presented in alignment with an annotated histological atlas and can be browsed down to cellular resolution. An extensive relational database connects expression patterns to information about gene function, mouse expression patterns and phenotypes, and gene involvement in human diseases and communication disorders. By enabling brain-wide gene expression assessments in a bird, ZEBrA provides important substrates for comparative neuroanatomy and molecular brain evolution studies. ZEBrA also provides unique opportunities for linking genetic pathways to vocal learning and motor control circuits, as well as for novel insights into the molecular basis of sex steroids actions, brain dimorphisms, reproductive and social behaviors, sleep function, and adult neurogenesis, among other fundamental themes. This article is protected by copyright. All rights reserved.
Michel Laurin - One of the best experts on this subject based on the ideXlab platform.
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Exact distribution of divergence times from fossil ages and tree topologies
Systematic Biology, 2020Co-Authors: Gilles Didier, Michel LaurinAbstract:Being given a phylogenetic tree of both extant and extinct taxa in which the fossil ages are the only temporal information (namely, in which divergence times are considered unknown), we provide a method to compute the exact probability distribution of any divergence time of the tree with regard to any speciation (cladogenesis), extinction, and fossilization rates under the Fossilized Birth–Death model. We use this new method to obtain a probability distribution for the age of Amniota (the synapsid/Sauropsid or bird/mammal divergence), one of the most-frequently used dating constraints. Our results suggest an older age (between about 322 and 340 Ma) than has been assumed by most studies that have used this constraint (which typically assumed a best estimate around 310–315 Ma) and provide, for the first time, a method to compute the shape of the probability density for this divergence time.
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A Reassessment of the Taxonomic Position of Mesosaurs, and a Surprising Phylogeny of Early Amniotes
Frontiers in Earth Science, 2017Co-Authors: Michel Laurin, Graciela PiñeiroAbstract:We reassess the phylogenetic position of mesosaurs by using a data matrix that is updated and slightly expanded from a matrix that the first author published in 1995 with his former thesis advisor. The revised matrix, which incorporates anatomical information published in the last twenty years and observations on several mesosaur specimens (mostly from Uruguay) includes seventeen terminal taxa and 129 characters (four more taxa and five more characters than the original matrix from 1995). The new matrix also differs by incorporating more ordered characters (all morphoclines were ordered). Parsimony analyses in PAUP 4 using the branch and bound algorithm show that the new matrix supports a position of mesosaurs at the very base of Sauropsida, as suggested by the first author in 1995. The exclusion of mesosaurs from a less inclusive clade of Sauropsids is supported by a Bremer (Decay) index of 4 and a bootstrap frequency of 66%, both of which suggest that this result is moderately robust. The most parsimonious trees include some unexpected results, such as placing the anapsid reptile Paleothyris near the base of diapsids, and all of parareptiles as the sister-group of younginiforms (the most crownward diapsids included in the analyses). Turtles are placed among parareptiles, as the sister-group of pareiasaurs (and in diapsids, given that parareptiles are nested within diapsids). This unexpected result offers a potential solution to the long-lasting controversy about the position of turtles because previous studies viewed a position among diapsids and among parareptiles as mutually exclusive alternatives.
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A Reassessment of the Taxonomic Position of Mesosaurs, and a Surprising Phylogeny of Early Amniotes
Frontiers in Earth Science, 2017Co-Authors: Michel Laurin, Graciela PiñeiroAbstract:We reassess the phylogenetic position of mesosaurs by using a data matrix that is updated and slightly expanded from a matrix that the first author published in 1995 with his former thesis advisor. The revised matrix, which incorporates anatomical information published in the last 20 years and observations on several mesosaur specimens (mostly from Uruguay) includes 17 terminal taxa and 129 characters (four more taxa and five more characters than the original matrix from 1995). The new matrix also differs by incorporating more ordered characters (all morphoclines were ordered). Parsimony analyses in PAUP 4 using the branch and bound algorithm show that the new matrix supports a position of mesosaurs at the very base of Sauropsida, as suggested by the first author in 1995. The exclusion of mesosaurs from a less inclusive clade of Sauropsids is supported by a Bremer (Decay) index of 4 and a bootstrap frequency of 66%, both of which suggest that this result is moderately robust. The most parsimonious trees include some unexpected results, such as placing the anapsid reptile Paleothyris near the base of diapsids, and all of parareptiles as the sister-group of younginiforms (the most crownward diapsids included in the analyses). Turtles are placed among parareptiles, as the sister-group of pareiasaurs (and in diapsids, given that parareptiles are nested within diapsids). This unexpected result offers a potential solution to the long-lasting controversy about the position of turtles because previous studies viewed a position among diapsids and among parareptiles as mutually exclusive alternatives.
Jorge Mpodozis - One of the best experts on this subject based on the ideXlab platform.
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Anatomical organization of the visual dorsal ventricular ridge in the chick (Gallus gallus): Layers and columns in the avian pallium.
The Journal of comparative neurology, 2015Co-Authors: Patricio Ahumada-galleguillos, Máximo Fernández, Gonzalo Marín, Juan C. Letelier, Jorge MpodozisAbstract:The dorsal ventricular ridge (DVR) is one of the main components of the Sauropsid pallium. In birds, the DVR is formed by an inner region, the nidopallium, and a more dorsal region, the mesopallium. The nidopallium contains discrete areas that receive auditory, visual, and multisensory collothalamic projections. These nidopallial nuclei are known to sustain reciprocal, short-range projections with their overlying mesopallial areas. Recent findings on the anatomical organization of the auditory DVR have shown that these short-range projections have a columnar organization that closely resembles that of the mammalian neocortex. However, it is unclear whether this columnar organization generalizes to other areas within the DVR. Here we examine in detail the organization of the visual DVR, performing small, circumscribed deposits of neuronal tracers as well as intracellular fillings in brain slices. We show that the visual DVR is organized in three main laminae, the thalamorecipient nucleus entopallium; a dorsally adjacent nidopallial lamina, the intermediate nidopallium; and a contiguous portion of the ventral mesopallium, the mesopallium ventrale. As in the case of the auditory DVR, we found a highly topographically organized system of reciprocal interconnections among these layers, which was formed by dorsoventrally oriented, discrete columnar bundles of axons. We conclude that the columnar organization previously demonstrated in the auditory DVR is not a unique feature but a general characteristic of the avian sensory pallium. We discuss these results in the context of a comparison between Sauropsid and mammalian pallial organization. J. Comp. Neurol. 523:2618–2636, 2015. © 2015 Wiley Periodicals, Inc.
