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Sample records for chordates

  1. Developmental genetics in primitive chordates.

    OpenAIRE

    P. SORDINO; L. Belluzzi; De Santis, R; Smith, W.C.

    2001-01-01

    Recent advances in the study of the genetics and genomics of urochordates testify to a renewed interest in this chordate subphylum, believed to be the most primitive extant chordate relatives of the vertebrates. In addition to their primitive nature, many features of their reproduction and early development make the urochordates ideal model chordates for developmental genetics. Many urochordates spawn large numbers of transparent and externally developing embryos on a daily basis. Additionall...

  2. Hemichordates and the origin of chordates

    Science.gov (United States)

    Gerhart, John; Lowe, Christopher; Kirschner, Marc

    2005-01-01

    Hemichordates, the phylum of bilateral animals most closely related to chordates, could reveal the evolutionary origins of chordate traits such as the nerve cord, notochord, gill slits and tail. The anteroposterior maps of gene expression domains for 38 genes of chordate neural patterning are highly similar for hemichordates and chordates, even though hemichordates have a diffuse nerve-net. About 40% of the domains are not present in protostome maps. We propose that this map, the gill slits and the tail date to the deuterostome ancestor. The map of dorsoventral expression domains, centered on a Bmp-Chordin axis, differs between the two groups; hemichordates resemble protostomes more than they do chordates. The dorsoventral axis might have undergone extensive modification in the chordate line, including centralization of the nervous system, segregation of epidermis, derivation of the notochord, and an inversion of organization.

  3. Seeing chordate evolution through the Ciona genome sequence

    OpenAIRE

    Cañestro, Cristian; Bassham, Susan; Postlethwait, John H.

    2003-01-01

    A draft sequence of the compact genome of the sea squirt Ciona intestinalis, a non-vertebrate chordate that diverged very early from other chordates, including vertebrates, illuminates how chordates originated and how vertebrate developmental innovations evolved.

  4. The Evolution of Dopamine Systems in Chordates

    OpenAIRE

    Philippe Vernier

    2011-01-01

    Dopamine (DA) neurotransmission in the central nervous system (CNS) is found throughout chordates, and its emergence predates the divergence of chordates. Many of the molecular components of DA systems, such as biosynthetic enzymes, transporters, and receptors, are shared with those of other monoamine systems, suggesting the common origin of these systems. In the mammalian CNS, the DA neurotransmitter systems are diversified and serve for visual and olfactory perception, sensory–motor program...

  5. Hemichordates and the Origin of Chordates

    Science.gov (United States)

    Gerhart, John; Kirschner, Marc; Lowe, Chris

    2002-01-01

    At the start of the period of the NASA grant three years ago, we had no information on the organization and development of the body axis of the hemichordate, Saccoglossus kowalevskii. Now we have substantial findings about the anteroposterior axis and dorsoventral axis, and based on this information, we have new insights about the origin of chordates from ancestral deuterostomes. We found ways to obtain and preserve large numbers of embryos and hatched juveniles. We can now collect about 40,000 embryos in the month of September, the time of S. kowalevskii spawning at Woods Hole. Excellent cDNA libraries were prepared from three developmental stages. From these libraries, we directly isolated about 30 gene ortholog sequences by screening and pcr techniques, all of these sequences of interest in the inquiry about the animal's organization and development. We also performed a mid-sized EST project (60,000 randomly picked clones, many of these arrayed). About half of these have been analyzed so far by blastx and are suitable for direct use of clones. We have obtained about 50 interesting sequences from this set. The rest still await analysis. Thus, at this time we have isolated orthologs of 80 genes that are known to be expressed in chordates in conserved domains and known to have interesting roles in chordate organization and development. The orthology of the S. kowalevskii sequences has been verified by neighbor joining and parsimony methods, with bootstrap estimates of validity. The S. kowalevskii sequences cluster with other deuterostome sequences, namely, other hemichordates, echinoderms, ascidians, amphioxus, or vertebrates, depending on what sequences are available in the database for comparison. We have used these sequences to do high quality in situ hybridization on S. kowalevskii embryos, and the results can be divided into three sections-those concerning the anteroposterior axis of S. kowalevskii in comparison to the same axis of chordates, those concerning

  6. New Early Cambrian Chordates from Haikou, Kunming

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Two new chordates, Cathaymyrus haikouensis Luo et Hu sp. nov. andZhongxiniscus intermedius Luo et Hu gen. et sp. nov. are studied in this paper. Both display numerous S-shaped myomeres on their trunk. C. haikouensis shows a long and slim body similar to that of Cathaymyrus diadexus Shu et al., Zhongxiniscus approaches to Myllokunmingia and Haikouichthvs in the dorsal fin, but differs in the myomeres. Zhongxiniscus may be the intermediate form between Ca thaymyrus and Myllokunmingia and Haikouichthys.

  7. The evolution of dopamine systems in chordates

    Directory of Open Access Journals (Sweden)

    Kei eYamamoto

    2011-03-01

    Full Text Available Dopamine (DA neurotransmission in the central nervous system (CNS is found throughout chordates, and its emergence predates the divergence of chordates. Many of the molecular components of DA systems, such as biosynthetic enzymes, transporters and receptors, are shared with those of other monoamine systems, suggesting the common origin of these systems. In the mammalian CNS, the DA neurotransmitter systems are diversified and serve for visual and olfactory perception, sensory-motor programming, motivation, memory, emotion, and endocrine regulations. Some of the functions are conserved among different vertebrate groups, while others are not, and this is reflected in the anatomical aspects of DA systems in the forebrain and midbrain. Recent findings concerning a second tyrosine hydroxylase gene (TH2 revealed new populations of DA synthesizing cells, as evidenced in the periventricular hypothalamic zones of teleost fish. It is likely that the ancestor of vertebrates possessed TH2 DA-synthesizing cells, and the TH2 gene has been lost secondarily in placental mammals. All the vertebrates possess DA cells in the olfactory bulb, retina and in the diencephalon. Midbrain DA cells are abundant in amniotes while absent in some groups, e.g. teleosts. Studies of protochordate DA cells suggest that the diencephalic DA cells were present before the divergence of the chordate lineage. In contrast, the midbrain cell populations have probably emerged in the vertebrate lineage following the development of the midbrain-hindbrain boundary. The functional flexibility of the DA systems, and the evolvability provided by duplication of the corresponding genes permitted a large diversification of these systems. These features were instrumental in the adaptation of brain functions to the very variable way of life of vertebrates.

  8. The amphioxus genome and the evolution of the chordate karyotype

    Energy Technology Data Exchange (ETDEWEB)

    Putnam, Nicholas H.; Butts, Thomas; Ferrier, David E.K.; Furlong, Rebecca F.; Hellsten, Uffe; Kawashima, Takeshi; Robinson-Rechavi, Marc; Shoguchi, Eiichi; Terry, Astrid; Yu, Jr-Kai; Benito-Gutierrez, Elia; Dubchak, Inna; Garcia-Fernandez, Jordi; Gibson-Brown, Jeremy J.; Grigoriev, Igor V.; Horton, Amy C.; de Jong, Pieter J.; Jurka, Jerzy; Kapitonov, Vladimir; Kohara, Yuji; Kuroki, Yoko; Lindquist, Erika; Lucas, Susan; Osoegawa, Kazutoyo; Pennacchio, Len A.; Salamov, Asaf A.; Satou, Yutaka; Sauka-Spengler, Tatjana; Schmutz[, Jeremy; Shin-I, Tadasu; Toyoda, Atsushi; Bronner-Fraser, Marianne; Fujiyama, Asao; Holland, Linda Z.; Holland, Peter W. H.; Satoh, Nori; Rokhsar, Daniel S.

    2008-04-01

    Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage with a fossil record dating back to the Cambrian. We describe the structure and gene content of the highly polymorphic {approx}520 million base pair genome of the Florida lancelet Branchiostoma floridae, and analyze it in the context of chordate evolution. Whole genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets, and vertebrates), and allow reconstruction of not only the gene complement of the last common chordate ancestor, but also a partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.

  9. Retinoic acid signaling and the evolution of chordates

    OpenAIRE

    Marlétaz, Ferdinand; Holland, Linda Z; Laudet, Vincent; Schubert, Michael

    2006-01-01

    In chordates, which comprise urochordates, cephalochordates and vertebrates, the vitamin A-derived morphogen retinoic acid (RA) has a pivotal role during development. Altering levels of endogenous RA signaling during early embryology leads to severe malformations, mainly due to incorrect positional codes specifying the embryonic anteroposterior body axis. In this review, we present our current understanding of the RA signaling pathway and its roles during chordate development. In particular, ...

  10. Inversion of the chordate body axis: are there alternatives?

    Science.gov (United States)

    Gerhart, J.

    2000-01-01

    One major morphological difference between chordates and annelids or arthropods is the opposite orientation of the nerve cord and heart. A long-standing proposal is that the chordate axis evolved by inverting the body of an ancestor with the annelid/arthropod orientation. However, the data can also be explained by a common ancestor with diffuse dorsoventral organization, followed by oppositely directed condensation of the nerve cord and relocation of the heart in the two lines.

  11. Ascidians and the plasticity of the chordate developmental program

    OpenAIRE

    Lemaire, Patrick; Smith, William C.; Nishida, Hiroki

    2008-01-01

    Little is known about the ancient chordates that gave rise to the first vertebrates, but the descendants of other invertebrate chordates extant at the time still flourish in the ocean. These invertebrates include the cephalochordates and tunicates, whose larvae share with vertebrate embryos a common body plan with a central notochord and a dorsal nerve cord. Tunicates are now thought to be the sister group of vertebrates. However, research based on several species of ascidians, a diverse and ...

  12. Inversion of the chordate body axis: Are there alternatives?

    OpenAIRE

    Gerhart, J.

    2000-01-01

    One major morphological difference between chordates and annelids or arthropods is the opposite orientation of the nerve cord and heart. A long-standing proposal is that the chordate axis evolved by inverting the body of an ancestor with the annelid/arthropod orientation. However, the data can also be explained by a common ancestor with diffuse dorsoventral organization, followed by oppositely directed condensation of the nerve cord and relocation of the heart in the t...

  13. Unique Development in Hemichordates Suggest Some Unique Features of Chordates

    OpenAIRE

    Lowe, Christopher J.; Mark Terasaki; Michael Wu; Freeman, Robert M.; Linda Runft; Kristen Kwan; Saori Haigo; Jochanan Aronowicz; Eric Lander; Chris Gruber; Mark Smith; Marc Kirschner; John Gerhart

    2006-01-01

    We have compared the dorsoventral development of hemichordates and chordates to deduce the organization of their common ancestor, and hence to identify the evolutionary modifications of the chordate body axis after the lineages split. In the hemichordate embryo, genes encoding bone morphogenetic proteins (Bmp) 2/4 and 5/8, as well as several genes for modulators of Bmp activity, are expressed in a thin stripe of ectoderm on one midline, historically called "dorsal." On the opposite midline, t...

  14. Chordate evolution and the three-phylum system

    OpenAIRE

    Satoh, Noriyuki; Rokhsar, Daniel; Nishikawa, Teruaki

    2014-01-01

    Traditional metazoan phylogeny classifies the Vertebrata as a subphylum of the phylum Chordata, together with two other subphyla, the Urochordata (Tunicata) and the Cephalochordata. The Chordata, together with the phyla Echinodermata and Hemichordata, comprise a major group, the Deuterostomia. Chordates invariably possess a notochord and a dorsal neural tube. Although the origin and evolution of chordates has been studied for more than a century, few authors have intimately discussed taxonomi...

  15. Dorsoventral patterning in hemichordates: insights into early chordate evolution.

    Directory of Open Access Journals (Sweden)

    Christopher J Lowe

    2006-09-01

    Full Text Available We have compared the dorsoventral development of hemichordates and chordates to deduce the organization of their common ancestor, and hence to identify the evolutionary modifications of the chordate body axis after the lineages split. In the hemichordate embryo, genes encoding bone morphogenetic proteins (Bmp 2/4 and 5/8, as well as several genes for modulators of Bmp activity, are expressed in a thin stripe of ectoderm on one midline, historically called "dorsal." On the opposite midline, the genes encoding Chordin and Anti-dorsalizing morphogenetic protein (Admp are expressed. Thus, we find a Bmp-Chordin developmental axis preceding and underlying the anatomical dorsoventral axis of hemichordates, adding to the evidence from Drosophila and chordates that this axis may be at least as ancient as the first bilateral animals. Numerous genes encoding transcription factors and signaling ligands are expressed in the three germ layers of hemichordate embryos in distinct dorsoventral domains, such as pox neuro, pituitary homeobox, distalless, and tbx2/3 on the Bmp side and netrin, mnx, mox, and single-minded on the Chordin-Admp side. When we expose the embryo to excess Bmp protein, or when we deplete endogenous Bmp by small interfering RNA injections, these expression domains expand or contract, reflecting their activation or repression by Bmp, and the embryos develop as dorsalized or ventralized limit forms. Dorsoventral patterning is independent of anterior/posterior patterning, as in Drosophila but not chordates. Unlike both chordates and Drosophila, neural gene expression in hemichordates is not repressed by high Bmp levels, consistent with their development of a diffuse rather than centralized nervous system. We suggest that the common ancestor of hemichordates and chordates did not use its Bmp-Chordin axis to segregate epidermal and neural ectoderm but to pattern many other dorsoventral aspects of the germ layers, including neural cell fates

  16. Retinoic acid signaling and the evolution of chordates

    Directory of Open Access Journals (Sweden)

    2006-04-01

    Full Text Available In chordates, which comprise urochordates, cephalochordates and vertebrates, the vitamin A-derived morphogen retinoic acid (RA has a pivotal role during development. Altering levels of endogenous RA signaling during early embryology leads to severe malformations, mainly due to incorrect positional codes specifying the embryonic anteroposterior body axis. In this review, we present our current understanding of the RA signaling pathway and its roles during chordate development. In particular, we focus on the conserved roles of RA and its downstream mediators, the Hox genes, in conveying positional patterning information to different embryonic tissues, such as the endoderm and the central nervous system. We find that some of the control mechanisms governing RA-mediated patterning are well conserved between vertebrates and invertebrate chordates, such as the cephalochordate amphioxus. In contrast, outside the chordates, evidence for roles of RA signaling is scarce and the evolutionary origin of the RA pathway itself thus remains elusive. In sum, to fully understand the evolutionary history of the RA pathway, future research should focus on identification and study of components of the RA signaling cascade in non-chordate deuterostomes (such as hemichordates and echinoderms and other invertebrates, such as insects, mollusks and cnidarians.

  17. Evolution of the organizer and the chordate body plan

    Science.gov (United States)

    Gerhart, J.

    2001-01-01

    The discovery of the organizer by Spemann and Mangold in 1924 raised two kinds of questions: those about the means of patterning the chordate body axis and those about the mechanisms of cell determination by induction. Some researchers, stressing the second, have suggested over the years that the organizer is poorly named and doesn't really organize because inducers act permissively, because they are not unique to the organizer, and because multipotent responsive cells develop complex local differentiations under artificial conditions. Furthermore, with the discovery of meso-endoderm induction in 1969, the possibility arose that this earlier induction generates as much organization as, or more than, does the organizer itself. Evidence is summarized in this article that the organizer does fulfill its title with regard to pattern formation: it adds greatly to embryonic organization by providing information about time, place, scale, and orientation for development by nearby members of the large multipotent competence groups surrounding the organizer. Embryos having smaller or larger organizers due to experimental intervention develop defective axial organization. Without an organizer the embryo develops no body axis and none of the four chordate characters: the notochord, gill slits, dorsal hollow nerve chord, and post-anal tail. For normal axis formation, the organizer's tripartite organization is needed. Each part differs in inducers, morphogenesis, and self-differentiation. The organizer is a trait of development of all members of the chordate phylum. In comparison to hemichordates, which constitute a phylum with some similarities to chordates, the chordamesoderm part is unique to the chordate organizer (the trunk-tail organizer). Its convergent extension displaces the gastrula posterior pole from alignment with the animal-vegetal axis and generates a new anteroposterior axis orthogonal to this old one. Once it has extended to full length, its signaling modifies

  18. Anteroposterior patterning in hemichordates and the origins of the chordate nervous system

    Science.gov (United States)

    Lowe, Christopher J.; Wu, Mike; Salic, Adrian; Evans, Louise; Lander, Eric; Stange-Thomann, Nicole; Gruber, Christian E.; Gerhart, John; Kirschner, Marc

    2003-01-01

    The chordate central nervous system has been hypothesized to originate from either a dorsal centralized, or a ventral centralized, or a noncentralized nervous system of a deuterostome ancestor. In an effort to resolve these issues, we examined the hemichordate Saccoglossus kowalevskii and studied the expression of orthologs of genes that are involved in patterning the chordate central nervous system. All 22 orthologs studied are expressed in the ectoderm in an anteroposterior arrangement nearly identical to that found in chordates. Domain topography is conserved between hemichordates and chordates despite the fact that hemichordates have a diffuse nerve net, whereas chordates have a centralized system. We propose that the deuterostome ancestor may have had a diffuse nervous system, which was later centralized during the evolution of the chordate lineage.

  19. Amphioxus: a peaceful anchovy fillet to illuminate Chordate Evolution (II

    Directory of Open Access Journals (Sweden)

    Jordi Garcia-Fernàndez

    2006-01-01

    Full Text Available The genome of the amphioxus is on the horizon. With Linda Holland and Jeremy Gibson-Brown at the forefront, with all the amphioxus community behind, and with the Joint Genome Institute, the amphioxus genome will see the light this year, 2006. Hope that it will reflect the “prototypical” preduplicative genome of vertebrates. It may answer definitively what the human genome did not: Are we vertebrates octaploid? Will it shed light on the novelties that helped non-chordates to be chordates? And more, will amphioxus, with a simpler genome, be developed to a senior “experimental model system”, allowing the testing of molecular functions in a non-duplicated genome background and allowing genetic modification to “recapitulate” evolution? Thanks to an outstanding collaboration between labs, the laboratory culture of amphioxus is underway after years of hard work in the field. 2007 looks promising for amphioxus research.

  20. Genetic and Genomic Toolbox of the Chordate Ciona intestinalis

    OpenAIRE

    Stolfi, Alberto; Christiaen, Lionel

    2012-01-01

    The experimental malleability and unique phylogenetic position of the sea squirt Ciona intestinalis as part of the sister group to the vertebrates have helped establish these marine chordates as model organisms for the study of developmental genetics and evolution. Here we summarize the tools, techniques, and resources available to the Ciona geneticist, citing examples of studies that employed such strategies in the elucidation of gene function in Ciona. Genetic screens, germline transgenesis...

  1. Vertebrate-like regeneration in the invertebrate chordate amphioxus

    OpenAIRE

    Somorjai, Ildikó M. L.; Rajmund L. Somorjai; Garcia-Fernàndez, Jordi; Escrivà, Hector

    2011-01-01

    An important question in biology is why some animals are able to regenerate, whereas others are not. The basal chordate amphioxus is uniquely positioned to address the evolution of regeneration. We report here the high regeneration potential of the European amphioxus Branchiostoma lanceolatum. Adults regenerate both anterior and posterior structures, including neural tube, notochord, fin, and muscle. Development of a classifier based on tail regeneration profiles predicts the assignment of yo...

  2. Conservation of Notochord Gene Expression Across Chordates: Insights From the Leprecan Gene Family

    OpenAIRE

    Capellini, Terence D.; Dunn, Matthew P.; Yale J Passamaneck; Selleri, Licia; Di Gregorio, Anna

    2008-01-01

    The notochord is a defining character of the chordates, and the T-box transcription factor Brachyury has been shown to be required for notochord development in all chordates examined. In the ascidian Ciona intestinalis, at least 44 notochord genes have been identified as bona fide transcriptional targets of Brachyury. We examined the embryonic expression of a subset of murine orthologs of Ciona Brachyury target genes in the notochord to assess its conservation throughout chordate evolution. W...

  3. rRNA genes from the lower chordate Herdmania momus: structural similarity with higher eukaryotes.

    OpenAIRE

    Degnan, B M; Yan, J.; Hawkins, C J; Lavin, M F

    1990-01-01

    Ascidians, primitive chordates that have retained features of the likely progenitors to all vertebrates, are a useful model to study the evolutionary relationship of chordates to other animals. We have selected the well characterized ribosomal RNA (rRNA) genes to investigate this relationship, and we describe here the cloning and characterization of an entire ribosomal DNA (rDNA) tandem repeat unit from a lower chordate, the ascidian Herdmania momus. rDNA copy number and considerable sequence...

  4. The Middle Cambrian fossil Pikaia and the evolution of chordate swimming

    OpenAIRE

    Lacalli Thurston

    2012-01-01

    Abstract Conway Morris and Caron (2012) have recently published an account of virtually all the available information on Pikaia gracilens, a well-known Cambrian fossil and supposed basal chordate, and propose on this basis some new ideas about Pikaia’s anatomy and evolutionary significance. Chief among its chordate-like features are the putative myomeres, a regular series of vertical bands that extends the length of the body. These differ from the myomeres of living chordates in that boundari...

  5. Acquisition of the dorsal structures in chordate amphioxus

    Science.gov (United States)

    Morov, Arseniy R.; Ukizintambara, Tharcisse; Sabirov, Rushan M.

    2016-01-01

    Acquisition of dorsal structures, such as notochord and hollow nerve cord, is likely to have had a profound influence upon vertebrate evolution. Dorsal formation in chordate development thus has been intensively studied in vertebrates and ascidians. However, the present understanding does not explain how chordates acquired dorsal structures. Here we show that amphioxus retains a key clue to answer this question. In amphioxus embryos, maternal nodal mRNA distributes asymmetrically in accordance with the remodelling of the cortical cytoskeleton in the fertilized egg, and subsequently lefty is first expressed in a patch of blastomeres across the equator where wnt8 is expressed circularly and which will become the margin of the blastopore. The lefty domain co-expresses zygotic nodal by the initial gastrula stage on the one side of the blastopore margin and induces the expression of goosecoid, not-like, chordin and brachyury1 genes in this region, as in the oral ectoderm of sea urchin embryos, which provides a basis for the formation of the dorsal structures. The striking similarity in the gene regulations and their respective expression domains when comparing dorsal formation in amphioxus and the determination of the oral ectoderm in sea urchin embryos suggests that chordates derived from an ambulacrarian-type blastula with dorsoventral inversion. PMID:27307516

  6. Acquisition of the dorsal structures in chordate amphioxus.

    Science.gov (United States)

    Morov, Arseniy R; Ukizintambara, Tharcisse; Sabirov, Rushan M; Yasui, Kinya

    2016-06-01

    Acquisition of dorsal structures, such as notochord and hollow nerve cord, is likely to have had a profound influence upon vertebrate evolution. Dorsal formation in chordate development thus has been intensively studied in vertebrates and ascidians. However, the present understanding does not explain how chordates acquired dorsal structures. Here we show that amphioxus retains a key clue to answer this question. In amphioxus embryos, maternal nodal mRNA distributes asymmetrically in accordance with the remodelling of the cortical cytoskeleton in the fertilized egg, and subsequently lefty is first expressed in a patch of blastomeres across the equator where wnt8 is expressed circularly and which will become the margin of the blastopore. The lefty domain co-expresses zygotic nodal by the initial gastrula stage on the one side of the blastopore margin and induces the expression of goosecoid, not-like, chordin and brachyury1 genes in this region, as in the oral ectoderm of sea urchin embryos, which provides a basis for the formation of the dorsal structures. The striking similarity in the gene regulations and their respective expression domains when comparing dorsal formation in amphioxus and the determination of the oral ectoderm in sea urchin embryos suggests that chordates derived from an ambulacrarian-type blastula with dorsoventral inversion. PMID:27307516

  7. Evolution of the reproductive endocrine system in chordates.

    Science.gov (United States)

    Kubokawa, Kaoru; Tando, Yukiko; Roy, Sonali

    2010-07-01

    The cephalochordate, amphioxus, is phylogenetically placed at the most primitive position in the chordate clade. Despite many studies on the endocrine system of amphioxus, definitive evidence has not been reported for the presence an endocrine system comparable to the pituitary-gonadal axis, which is important in the regulation of reproduction in vertebrates. Recent genome analyses in the amphioxus, Branchiostoma floridae, showed that it does not have any pituitary hormone genes except the thyrostimulin gene. Thyrostimulin is a heterodimeric glycoprotein hormone consisting of α and β subunits, and is present in various organs of vertebrates. Analyses of a phylogenetic tree and a synteny suggest that amphioxus' thyrostimulin is an ancestral type of the glycoprotein hormones in chordates. In addition, genes for sex steroidogenic enzymes belonging to the CYP family were found in the genome sequences. The conversion pathway of sex steroids from cholesterol to estrogen, androgen, and major sex steroids was also identified in the gonads of amphioxus in vitro. Furthermore, we demonstrated the expression of genes encoding thyrostimulin and sex steroidogenic enzymes by an in situ hybridization technique. Here, we discuss the evolution of hormones and reproductive functions in the neuroendocrine control system of chordates.

  8. Roles of retinoic acid and Tbx1/10 in pharyngeal segmentation: amphioxus and the ancestral chordate condition

    OpenAIRE

    Koop, Demian; Chen, Jie; Theodosiou, Maria; Carvalho, João E; Alvarez, Susana; de Lera, Angel R.; Holland, Linda Z.; Schubert, Michael

    2014-01-01

    Background Although chordates descend from a segmented ancestor, the evolution of head segmentation has been very controversial for over 150 years. Chordates generally possess a segmented pharynx, but even though anatomical evidence and gene expression analyses suggest homologies between the pharyngeal apparatus of invertebrate chordates, such as the cephalochordate amphioxus, and vertebrates, these homologies remain contested. We, therefore, decided to study the evolution of the chordate hea...

  9. Evolution of anterior Hox regulatory elements among chordates

    Directory of Open Access Journals (Sweden)

    Natale Alfonso

    2011-11-01

    Full Text Available Abstract Background The Hox family of transcription factors has a fundamental role in segmentation pathways and axial patterning of embryonic development and their clustered organization is linked with the regulatory mechanisms governing their coordinated expression along embryonic axes. Among chordates, of particular interest are the Hox paralogous genes in groups 1-4 since their expression is coupled to the control of regional identity in the anterior nervous system, where the highest structural diversity is observed. Results To investigate the degree of conservation in cis-regulatory components that form the basis of Hox expression in the anterior nervous system, we have used assays for transcriptional activity in ascidians and vertebrates to compare and contrast regulatory potential. We identified four regulatory sequences located near the CiHox1, CiHox2 and CiHox4 genes of the ascidian Ciona intestinalis which direct neural specific domains of expression. Using functional assays in Ciona and vertebrate embryos in combination with sequence analyses of enhancer fragments located in similar positions adjacent to Hox paralogy group genes, we compared the activity of these four Ciona cis-elements with a series of neural specific enhancers from the amphioxus Hox1-3 genes and from mouse Hox paralogous groups 1-4. Conclusions This analysis revealed that Kreisler and Krox20 dependent enhancers critical in segmental regulation of the hindbrain appear to be specific for the vertebrate lineage. In contrast, neural enhancers that function as Hox response elements through the action of Hox/Pbx binding motifs have been conserved during chordate evolution. The functional assays reveal that these Hox response cis-elements are recognized by the regulatory components of different and extant species. Together, our results indicate that during chordate evolution, cis-elements dependent upon Hox/Pbx regulatory complexes, are responsible for key aspects of

  10. Ciona as a Simple Chordate Model for Heart Development and Regeneration

    Directory of Open Access Journals (Sweden)

    Heather Evans Anderson

    2016-08-01

    Full Text Available Cardiac cell specification and the genetic determinants that govern this process are highly conserved among Chordates. Recent studies have established the importance of evolutionarily-conserved mechanisms in the study of congenital heart defects and disease, as well as cardiac regeneration. As a basal Chordate, the Ciona model system presents a simple scaffold that recapitulates the basic blueprint of cardiac development in Chordates. Here we will focus on the development and cellular structure of the heart of the ascidian Ciona as compared to other Chordates, principally vertebrates. Comparison of the Ciona model system to heart development in other Chordates presents great potential for dissecting the genetic mechanisms that underlie congenital heart defects and disease at the cellular level and might provide additional insight into potential pathways for therapeutic cardiac regeneration.

  11. Facts and fancies about early fossil chordates and vertebrates.

    Science.gov (United States)

    Janvier, Philippe

    2015-04-23

    The interrelationships between major living vertebrate, and even chordate, groups are now reasonably well resolved thanks to a large amount of generally congruent data derived from molecular sequences, anatomy and physiology. But fossils provide unexpected combinations of characters that help us to understand how the anatomy of modern groups was progressively shaped over millions of years. The dawn of vertebrates is documented by fossils that are preserved as either soft-tissue imprints, or minute skeletal fragments, and it is sometimes difficult for palaeontologists to tell which of them are reliable vertebrate remains and which merely reflect our idea of an ancestral vertebrate.

  12. Amphioxus: a peaceful anchovy fillet to illuminate Chordate Evolution (II)

    OpenAIRE

    Jordi Garcia-Fernàndez

    2006-01-01

    The genome of the amphioxus is on the horizon. With Linda Holland and Jeremy Gibson-Brown at the forefront, with all the amphioxus community behind, and with the Joint Genome Institute, the amphioxus genome will see the light this year, 2006. Hope that it will reflect the “prototypical” preduplicative genome of vertebrates. It may answer definitively what the human genome did not: Are we vertebrates octaploid? Will it shed light on the novelties that helped non-chordates to be cho...

  13. Origins of anteroposterior patterning and Hox gene regulation during chordate evolution.

    OpenAIRE

    Schilling, T. F.; Knight, R D

    2001-01-01

    All chordates share a basic body plan and many common features of early development. Anteroposterior (AP) regions of the vertebrate neural tube are specified by a combinatorial pattern of Hox gene expression that is conserved in urochordates and cephalochordates. Another primitive feature of Hox gene regulation in all chordates is a sensitivity to retinoic acid during embryogenesis, and recent developmental genetic studies have demonstrated the essential role for retinoid signalling in verteb...

  14. How much does the amphioxus genome represent the ancestor of chordates?

    OpenAIRE

    Louis A.; Roest Crollius H.; Robinson-Rechavi M.

    2012-01-01

    One of the main motivations to study amphioxus is its potential for understanding the last common ancestor of chordates, which notably gave rise to the vertebrates. An important feature in this respect is the slow evolutionary rate that seems to have characterized the cephalochordate lineage, making amphioxus an interesting proxy for the chordate ancestor, as well as a key lineage to include in comparative studies. Whereas slow evolution was first noticed at the phenotypic level, it has also ...

  15. Evolutionary Patterns of RNA-Based Duplication in Non-Mammalian Chordates

    OpenAIRE

    Ming Chen; Ming Zou; Beide Fu; Xin Li; Vibranovski, Maria D.; Xiaoni Gan; Dengqiang Wang; Wen Wang; Manyuan Long; Shunping He

    2011-01-01

    The role of RNA-based duplication, or retroposition, in the evolution of new gene functions in mammals, plants, and Drosophila has been widely reported. However, little is known about RNA-based duplication in non-mammalian chordates. In this study, we screened ten non-mammalian chordate genomes for retrocopies and investigated their evolutionary patterns. We identified numerous retrocopies in these species. Examination of the age distribution of these retrocopies revealed no burst of young re...

  16. Characterization of an individual neural crest-like cell lineage in the invertebrate chordate Ciona intestinalis

    OpenAIRE

    Cone, Angela C.

    2008-01-01

    During embryogenesis, all chordate embryos undergo neurulation to form a dorsal, hollow nerve cord. Neural crest cells (NCC), considered a vertebrate innovation, arise during neurulation and later differentiate into a multitude of tissues that account for much of the structural complexity that distinguishes craniates from invertebrate chordates [1, 2]. NCCs are induced and specified at the border of the neural and non-neural ectoderm by a complex network of inductive signals and transcription...

  17. Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny.

    OpenAIRE

    Loya Yossi; Shenkar Noa; Blanquart Samuel; Delsuc Frédéric; Tsagkogeorga Georgia; Singh Tiratha; Douzery Emmanuel JP; Huchon Dorothée

    2009-01-01

    Abstract Background Tunicates represent a key metazoan group as the sister-group of vertebrates within chordates. The six complete mitochondrial genomes available so far for tunicates have revealed distinctive features. Extensive gene rearrangements and particularly high evolutionary rates have been evidenced with regard to other chordates. This peculiar evolutionary dynamics has hampered the reconstruction of tunicate phylogenetic relationships within chordates based on mitogenomic data. Res...

  18. The genome sequence of the colonial chordate, Botryllus schlosseri

    Science.gov (United States)

    Voskoboynik, Ayelet; Neff, Norma F; Sahoo, Debashis; Newman, Aaron M; Pushkarev, Dmitry; Koh, Winston; Passarelli, Benedetto; Fan, H Christina; Mantalas, Gary L; Palmeri, Karla J; Ishizuka, Katherine J; Gissi, Carmela; Griggio, Francesca; Ben-Shlomo, Rachel; Corey, Daniel M; Penland, Lolita; White, Richard A; Weissman, Irving L; Quake, Stephen R

    2013-01-01

    Botryllus schlosseri is a colonial urochordate that follows the chordate plan of development following sexual reproduction, but invokes a stem cell-mediated budding program during subsequent rounds of asexual reproduction. As urochordates are considered to be the closest living invertebrate relatives of vertebrates, they are ideal subjects for whole genome sequence analyses. Using a novel method for high-throughput sequencing of eukaryotic genomes, we sequenced and assembled 580 Mbp of the B. schlosseri genome. The genome assembly is comprised of nearly 14,000 intron-containing predicted genes, and 13,500 intron-less predicted genes, 40% of which could be confidently parceled into 13 (of 16 haploid) chromosomes. A comparison of homologous genes between B. schlosseri and other diverse taxonomic groups revealed genomic events underlying the evolution of vertebrates and lymphoid-mediated immunity. The B. schlosseri genome is a community resource for studying alternative modes of reproduction, natural transplantation reactions, and stem cell-mediated regeneration. DOI: http://dx.doi.org/10.7554/eLife.00569.001 PMID:23840927

  19. Evolution of a core gene network for skeletogenesis in chordates.

    Directory of Open Access Journals (Sweden)

    Jochen Hecht

    2008-03-01

    Full Text Available The skeleton is one of the most important features for the reconstruction of vertebrate phylogeny but few data are available to understand its molecular origin. In mammals the Runt genes are central regulators of skeletogenesis. Runx2 was shown to be essential for osteoblast differentiation, tooth development, and bone formation. Both Runx2 and Runx3 are essential for chondrocyte maturation. Furthermore, Runx2 directly regulates Indian hedgehog expression, a master coordinator of skeletal development. To clarify the correlation of Runt gene evolution and the emergence of cartilage and bone in vertebrates, we cloned the Runt genes from hagfish as representative of jawless fish (MgRunxA, MgRunxB and from dogfish as representative of jawed cartilaginous fish (ScRunx1-3. According to our phylogenetic reconstruction the stem species of chordates harboured a single Runt gene and thereafter Runt locus duplications occurred during early vertebrate evolution. All newly isolated Runt genes were expressed in cartilage according to quantitative PCR. In situ hybridisation confirmed high MgRunxA expression in hard cartilage of hagfish. In dogfish ScRunx2 and ScRunx3 were expressed in embryonal cartilage whereas all three Runt genes were detected in teeth and placoid scales. In cephalochordates (lancelets Runt, Hedgehog and SoxE were strongly expressed in the gill bars and expression of Runt and Hedgehog was found in endo- as well as ectodermal cells. Furthermore we demonstrate that the lancelet Runt protein binds to Runt binding sites in the lancelet Hedgehog promoter and regulates its activity. Together, these results suggest that Runt and Hedgehog were part of a core gene network for cartilage formation, which was already active in the gill bars of the common ancestor of cephalochordates and vertebrates and diversified after Runt duplications had occurred during vertebrate evolution. The similarities in expression patterns of Runt genes support the view

  20. Symmetry breaking and convergent extension in early chordate development.

    Science.gov (United States)

    Schiffmann, Yoram

    2006-10-01

    The initiation of axis, polarity, cell differentiation, and gastrulation in the very early chordate development is due to the breaking of radial symmetry. It is believed that this occurs by an external signal. We suggest instead spontaneous symmetry breaking through the agency of the Turing-Child field. Increased size or decreased diffusivity, both brought about by mitotic activity, cause the spontaneous loss of stability of the homogeneous state and the evolution of the metabolic pattern during development. The polar metabolic pattern is the cause of polar gene expression, polar morphogenesis (gastrulation), and polar mitotic activity. The Turing-Child theory explains not only the spontaneous formation of the invagination in gastrulation but also the coherent cell movement observed in convergence and extension during gastrulation and neurulation. The theory is demonstrated with respect to experimental observations on the early development of fish, amphibian, and the chick. The theory can explain a multitude of experimental details. For example, it explains the splayed polar progression of reduction in the fish blastoderm. Reduction starts on that side of the blastoderm margin, which will initiate invagination several hours later. It progresses toward the blastoderm center and somewhat laterally from this future "dorsal lip". This is precisely as predicted by a Turing-Child system in a circle. And for a fish like zebrafish with a blastoderm that is slightly oval, reduction is observed to progress along the long axis of the ellipse, which is what Turing-Child theory predicts. In general the shape and the chemical nature of the experimental patterns are the same as predicted by the Turing couple (cAMP, ATP). Embryological polarity and convergent extension are based on polar eigenfunction and saddle-shaped eigenfunction, respectively.

  1. Molecular evolution of a chordate specific family of G protein-coupled receptors

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    Leese Florian

    2011-08-01

    Full Text Available Abstract Background Chordate evolution is a history of innovations that is marked by physical and behavioral specializations, which led to the development of a variety of forms from a single ancestral group. Among other important characteristics, vertebrates obtained a well developed brain, anterior sensory structures, a closed circulatory system and gills or lungs as blood oxygenation systems. The duplication of pre-existing genes had profound evolutionary implications for the developmental complexity in vertebrates, since mutations modifying the function of a duplicated protein can lead to novel functions, improving the evolutionary success. Results We analyzed here the evolution of the GPRC5 family of G protein-coupled receptors by comprehensive similarity searches and found that the receptors are only present in chordates and that the size of the receptor family expanded, likely due to genome duplication events in the early history of vertebrate evolution. We propose that a single GPRC5 receptor coding gene originated in a stem chordate ancestor and gave rise by duplication events to a gene family comprising three receptor types (GPRC5A-C in vertebrates, and a fourth homologue present only in mammals (GPRC5D. Additional duplications of GPRC5B and GPRC5C sequences occurred in teleost fishes. The finding that the expression patterns of the receptors are evolutionarily conserved indicates an important biological function of these receptors. Moreover, we found that expression of GPRC5B is regulated by vitamin A in vivo, confirming previous findings that linked receptor expression to retinoic acid levels in tumor cell lines and strengthening the link between the receptor expression and the development of a complex nervous system in chordates, known to be dependent on retinoic acid signaling. Conclusions GPRC5 receptors, a class of G protein-coupled receptors with unique sequence characteristics, may represent a molecular novelty that helped non-chordates

  2. Evolutionary patterns of RNA-based duplication in non-mammalian chordates.

    Directory of Open Access Journals (Sweden)

    Ming Chen

    Full Text Available The role of RNA-based duplication, or retroposition, in the evolution of new gene functions in mammals, plants, and Drosophila has been widely reported. However, little is known about RNA-based duplication in non-mammalian chordates. In this study, we screened ten non-mammalian chordate genomes for retrocopies and investigated their evolutionary patterns. We identified numerous retrocopies in these species. Examination of the age distribution of these retrocopies revealed no burst of young retrocopies in ancient chordate species. Upon comparing these non-mammalian chordate species to the mammalian species, we observed that a larger fraction of the non-mammalian retrocopies was under strong evolutionary constraints than mammalian retrocopies are, as evidenced by signals of purifying selection and expression profiles. For the Western clawed frog, Medaka, and Sea squirt, many retrogenes have evolved gonad and brain expression patterns, similar to what was observed in human. Testing of retrogene movement in the Medaka genome, where the nascent sex chrosomes have been well assembled, did not reveal any significant gene movement. Taken together, our analyses demonstrate that RNA-based duplication generates many functional genes and can make a significant contribution to the evolution of non-mammalian genomes.

  3. Phylostratigraphic profiles in zebrafish uncover chordate origins of the vertebrate brain.

    Science.gov (United States)

    Šestak, Martin Sebastijan; Domazet-Lošo, Tomislav

    2015-02-01

    An elaborated tripartite brain is considered one of the important innovations of vertebrates. Other extant chordate groups have a more basic brain organization. For instance, cephalochordates possess a relatively simple brain possibly homologous to the vertebrate forebrain and hindbrain, whereas tunicates display the tripartite organization, but without the specialized brain centers. The difference in anatomical complexity is even more pronounced if one compares chordates with other deuterostomes that have only a diffuse nerve net or alternatively a rather simple central nervous system. To gain a new perspective on the evolutionary roots of the complex vertebrate brain, we made here a phylostratigraphic analysis of gene expression patterns in the developing zebrafish (Danio rerio). The recovered adaptive landscape revealed three important periods in the evolutionary history of the zebrafish brain. The oldest period corresponds to preadaptive events in the first metazoans and the emergence of the nervous system at the metazoan-eumetazoan transition. The origin of chordates marks the next phase, where we found the overall strongest adaptive imprint in almost all analyzed brain regions. This finding supports the idea that the vertebrate brain evolved independently of the brains within the protostome lineage. Finally, at the origin of vertebrates we detected a pronounced signal coming from the dorsal telencephalon, in agreement with classical theories that consider this part of the cerebrum a genuine vertebrate innovation. Taken together, these results reveal a stepwise adaptive history of the vertebrate brain where most of its extant organization was already present in the chordate ancestor. PMID:25415965

  4. Modeling RNA polymerase interaction in mitochondria of chordates

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    Lyubetsky Vassily A

    2012-08-01

    selected genes only relative RNA concentrations have been experimentally determined. Conversely, these characteristics and absolute transcription levels can be obtained using relative RNA concentrations and RNA half-lives known from various experimental studies. In this case, the “inverse problem” is solved with multi-objective optimization. Conclusions In this study, we demonstrate that our model accurately reproduces all relevant experimental data available for plant plastids, as well as the mitochondria of chordates. Using experimental data, the model is applied to estimate binding intensities of phage-type RNA polymerases to their promoters as well as predicting terminator characteristics, including polarization. In addition, one can predict characteristics of phage-type RNA polymerases and the transcription process that are difficult to measure directly, e.g., the association between the promoter’s nucleotide composition and the intensity of polymerase binding. To illustrate the application of our model in functional predictions, we propose a possible mechanism for MELAS syndrome development in human involving a decrease of Phe-tRNA, Val-tRNA and rRNA concentrations in the cell. In addition, we describe how changes in methylation patterns of the mTERF binding site and three promoters in hypothyroid rat correlate with changes in intensities of the mTERF binding and transcription initiations. Finally, we introduce an auxiliary model to describe the interaction between polysomal mRNA and ribonucleases.

  5. Essential role of Bmp signaling and its positive feedback loop in the early cell fate evolution of chordates

    OpenAIRE

    Kozmiková, I. (Iryna); S Candiani; P. Fabian; Gurská, D. (Daniela); Kozmik, Z

    2013-01-01

    In chordates, early separation of cell fate domains occurs prior to the final specification of ectoderm to neural and non-neural as well as mesoderm to dorsal and ventral during development. Maintaining such division with the establishment of an exact border between the domains is required for the formation of highly differentiated structures such as neural tube and notochord. We hypothesized that the key condition for efficient cell fate separation in a chordate embryo is the presence of a p...

  6. Evolution of retinoic acid receptors in chordates: insights from three lamprey species, Lampetra fluviatilis, Petromyzon marinus, and Lethenteron japonicum

    OpenAIRE

    Campo-Paysaa, Florent; Jandzik, David; Takio-Ogawa, Yoko; Cattell, Maria V; Neef, Haley C; Langeland, James A.; Kuratani, Shigeru; Medeiros, Daniel M.; Mazan, Sylvie; Kuraku, Shigehiro; Laudet, Vincent; Schubert, Michael

    2015-01-01

    Background Retinoic acid (RA) signaling controls many developmental processes in chordates, from early axis specification to late organogenesis. The functions of RA are chiefly mediated by a subfamily of nuclear hormone receptors, the retinoic acid receptors (RARs), that act as ligand-activated transcription factors. While RARs have been extensively studied in jawed vertebrates (that is, gnathostomes) and invertebrate chordates, very little is known about the repertoire and developmental role...

  7. Ancient homeobox gene loss and the evolution of chordate brain and pharynx development : deductions from amphioxus gene expression

    OpenAIRE

    Butts, Thomas; Holland, Peter W. H.; Ferrier, David Ellard Keith

    2010-01-01

    Homeobox genes encode a large superclass of transcription factors with widespread roles in animal development. Within chordates there are over 100 homeobox genes in the invertebrate cephalochordate amphioxus and over 200 in humans. Set against this general trend of increasing gene number in vertebrate evolution, some ancient homeobox genes that were present in the last common ancestor of chordates have been lost from vertebrates. Here, we describe the embryonic expression of four amphioxus de...

  8. Retinoic acid influences anteroposterior positioning of epidermal sensory neurons and their gene expression in a developing chordate (amphioxus)

    OpenAIRE

    Schubert, Michael; Holland, Nicholas D; Escriva, Hector; Holland, Linda Z; Laudet, Vincent

    2004-01-01

    In developing chordates, retinoic acid (RA) signaling patterns the rostrocaudal body axis globally and affects gene expression locally in some differentiating cell populations. Here we focus on development of epidermal sensory neurons in an invertebrate chordate (amphioxus) to determine how RA signaling influences their rostrocaudal distribution and gene expression (for AmphiCoe, a neural precursor gene; for amphioxus islet and AmphiERR, two neural differentiation genes; and for AmphiHox1, -3...

  9. The Middle Cambrian fossil Pikaia and the evolution of chordate swimming

    Directory of Open Access Journals (Sweden)

    Lacalli Thurston

    2012-07-01

    Full Text Available Abstract Conway Morris and Caron (2012 have recently published an account of virtually all the available information on Pikaia gracilens, a well-known Cambrian fossil and supposed basal chordate, and propose on this basis some new ideas about Pikaia’s anatomy and evolutionary significance. Chief among its chordate-like features are the putative myomeres, a regular series of vertical bands that extends the length of the body. These differ from the myomeres of living chordates in that boundaries between them (the myosepta are gently curved, with minimal overlap, whereas amphioxus and vertebrates have strongly overlapping V- and W-shaped myomeres. The implication, on biomechanical grounds, is that myomeres in Pikaia exerted much less tension on the myosepta, so the animal would have been incapable of swimming as rapidly as living chordates operating in the fast-twitch mode used for escape and attack. Pikaia either lacked the fast-twitch fibers necessary for such speeds, having instead only slow-twitch fibers, or it had an ancestral fiber type with functional capabilities more like modern slow fibers than fast ones. The first option is supported by the sequence of development in zebrafish, where both myoseptum formation and fast fiber deployment show a dependence on slow fibers, which develop first. For Pikaia, the absence of fast fibers has both behavioral and anatomical implications, which are discussed. Among the latter is the possibility that a notochord may not have been needed as a primary stiffening device if other structures (for example, the dorsal organ could perform that role.

  10. Evolution of the role of RA and FGF signals in the control of somitogenesis in chordates

    OpenAIRE

    Stéphanie Bertrand; Daniel Aldea; Silvan Oulion; Lucie Subirana; de Lera, Angel R.; Ildiko Somorjai; Hector Escriva

    2015-01-01

    During vertebrate development, the paraxial mesoderm becomes segmented, forming somites that will give rise to dermis, axial skeleton and skeletal muscles. Although recently challenged, the "clock and wavefront" model for somitogenesis explains how interactions between several cell-cell communication pathways, including the FGF, RA, Wnt and Notch signals, control the formation of these bilateral symmetric blocks. In the cephalochordate amphioxus, which belongs to the chordate phylum together ...

  11. Evolution of anterior Hox regulatory elements among chordates

    OpenAIRE

    Natale Alfonso; Sims Carrie; Chiusano Maria L; Amoroso Alessandro; D'Aniello Enrico; Fucci Laura; Krumlauf Robb; Branno Margherita; Locascio Annamaria

    2011-01-01

    Abstract Background The Hox family of transcription factors has a fundamental role in segmentation pathways and axial patterning of embryonic development and their clustered organization is linked with the regulatory mechanisms governing their coordinated expression along embryonic axes. Among chordates, of particular interest are the Hox paralogous genes in groups 1-4 since their expression is coupled to the control of regional identity in the anterior nervous system, where the highest struc...

  12. The synapsin gene family in basal chordates: evolutionary perspectives in metazoans

    OpenAIRE

    De Bernardi Fiorenza; Pennati Roberta; Moronti Luca; Candiani Simona; Benfenati Fabio; Pestarino Mario

    2010-01-01

    Abstract Background Synapsins are neuronal phosphoproteins involved in several functions correlated with both neurotransmitter release and synaptogenesis. The comprehension of the basal role of the synapsin family is hampered in vertebrates by the existence of multiple synapsin genes. Therefore, studying homologous genes in basal chordates, devoid of genome duplication, could help to achieve a better understanding of the complex functions of these proteins. Results In this study we report the...

  13. Diversification of the expression patterns and developmental functions of the Dishevelled gene family during chordate evolution

    OpenAIRE

    Gray, Ryan S.; Bayly, Robbie D.; Green, Stephen A.; Agarwala, Seema; Lowe, Christopher J.; Wallingford, John B.

    2009-01-01

    Dishevelled (Dvl) proteins are key transducers of Wnt signaling encoded by members of a multi-gene family in vertebrates. We report here the divergent, tissue-specific expression patterns for all three Dvl genes in Xenopus embryos, which contrast dramatically with their expression patterns in mice. Moreover, we find that the expression patterns of Dvl genes in the chick diverge significantly from those of Xenopus. In addition, in hemichordates, an outgroup to chordates, we find that the one D...

  14. Molecular evolution of a chordate specific family of G protein-coupled receptors

    OpenAIRE

    Leese Florian; Hatt Hanns; Pelz Thomas; Mayer Christoph; Kurtenbach Stefan; Neuhaus Eva M

    2011-01-01

    Abstract Background Chordate evolution is a history of innovations that is marked by physical and behavioral specializations, which led to the development of a variety of forms from a single ancestral group. Among other important characteristics, vertebrates obtained a well developed brain, anterior sensory structures, a closed circulatory system and gills or lungs as blood oxygenation systems. The duplication of pre-existing genes had profound evolutionary implications for the developmental ...

  15. The Transcriptome of an Amphioxus, Asymmetron lucayanum, from the Bahamas: A Window into Chordate Evolution

    OpenAIRE

    Yue, Jia-Xing; Yu, Jr-Kai; Putnam, Nicholas H.; Holland, Linda Z

    2014-01-01

    Cephalochordates, the sister group of tunicates plus vertebrates, have been called “living fossils” due to their resemblance to fossil chordates from Cambrian strata. The genome of the cephalochordate Branchiostoma floridae shares remarkable synteny with vertebrates and is free from whole-genome duplication. We performed RNA sequencing from larvae and adults of Asymmetron lucayanum, a cephalochordate distantly related to B. floridae. Comparisons of about 430 orthologous gene groups among both...

  16. Evolution of the chordate body plan: New insights from phylogenetic analyses of deuterostome phyla

    OpenAIRE

    Cameron, Chris B.; Garey, James R.; Swalla, Billie J.

    2000-01-01

    The deuterostome phyla include Echinodermata, Hemichordata, and Chordata. Chordata is composed of three subphyla, Vertebrata, Cephalochordata (Branchiostoma), and Urochordata (Tunicata). Careful analysis of a new 18S rDNA data set indicates that deuterostomes are composed of two major clades: chordates and echinoderms + hemichordates. This analysis strongly supports the monophyly of each of the four major deuterostome taxa: Vertebrata + Cephalochordata, Urochordata, Hemichordata, and Echinode...

  17. Evolution of the Role of RA and FGF Signals in the Control of Somitogenesis in Chordates.

    Directory of Open Access Journals (Sweden)

    Stéphanie Bertrand

    Full Text Available During vertebrate development, the paraxial mesoderm becomes segmented, forming somites that will give rise to dermis, axial skeleton and skeletal muscles. Although recently challenged, the "clock and wavefront" model for somitogenesis explains how interactions between several cell-cell communication pathways, including the FGF, RA, Wnt and Notch signals, control the formation of these bilateral symmetric blocks. In the cephalochordate amphioxus, which belongs to the chordate phylum together with tunicates and vertebrates, the dorsal paraxial mesendoderm also periodically forms somites, although this process is asymmetric and extends along the whole body. It has been previously shown that the formation of the most anterior somites in amphioxus is dependent upon FGF signalling. However, the signals controlling somitogenesis during posterior elongation in amphioxus are still unknown. Here we show that, contrary to vertebrates, RA and FGF signals act independently during posterior elongation and that they are not mandatory for posterior somites to form. Moreover, we show that RA is not able to buffer the left/right asymmetry machinery that is controlled through the asymmetric expression of Nodal pathway actors. Our results give new insights into the evolution of the somitogenesis process in chordates. They suggest that RA and FGF pathways have acquired specific functions in the control of somitogenesis in vertebrates. We propose that the "clock and wavefront" system was selected specifically in vertebrates in parallel to the development of more complex somite-derived structures but that it was not required for somitogenesis in the ancestor of chordates.

  18. LRRCE: a leucine-rich repeat cysteine capping motif unique to the chordate lineage

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    Bishop Paul N

    2008-12-01

    Full Text Available Abstract Background The small leucine-rich repeat proteins and proteoglycans (SLRPs form an important family of regulatory molecules that participate in many essential functions. They typically control the correct assembly of collagen fibrils, regulate mineral deposition in bone, and modulate the activity of potent cellular growth factors through many signalling cascades. SLRPs belong to the group of extracellular leucine-rich repeat proteins that are flanked at both ends by disulphide-bonded caps that protect the hydrophobic core of the terminal repeats. A capping motif specific to SLRPs has been recently described in the crystal structures of the core proteins of decorin and biglycan. This motif, designated as LRRCE, differs in both sequence and structure from other, more widespread leucine-rich capping motifs. To investigate if the LRRCE motif is a common structural feature found in other leucine-rich repeat proteins, we have defined characteristic sequence patterns and used them in genome-wide searches. Results The LRRCE motif is a structural element exclusive to the main group of SLRPs. It appears to have evolved during early chordate evolution and is not found in protein sequences from non-chordate genomes. Our search has expanded the family of SLRPs to include new predicted protein sequences, mainly in fishes but with intriguing putative orthologs in mammals. The chromosomal locations of the newly predicted SLRP genes would support the large-scale genome or gene duplications that are thought to have occurred during vertebrate evolution. From this expanded list we describe a new class of SLRP sequences that could be representative of an ancestral SLRP gene. Conclusion Given its exclusivity the LRRCE motif is a useful annotation tool for the identification and classification of new SLRP sequences in genome databases. The expanded list of members of the SLRP family offers interesting insights into early vertebrate evolution and suggests an

  19. mRNA 5′-leader trans-splicing in the chordates

    OpenAIRE

    Vandenberghe, Amanda E.; Meedel, Thomas H.; Hastings, Kenneth E.M.

    2001-01-01

    We report the discovery of mRNA 5′-leader trans-splicing (SL trans-splicing) in the chordates. In the ascidian protochordate Ciona intestinalis, the mRNAs of at least seven genes undergo trans-splicing of a 16-nucleotide 5′-leader apparently derived from a 46-nucleotide RNA that shares features with previously characterized splice donor SL RNAs. SL trans-splicing was known previously to occur in several protist and metazoan phyla, however, this is the first report of SL trans-splicing within ...

  20. Evolutionary history of chordate PAX genes: dynamics of change in a complex gene family.

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    Vanessa Rodrigues Paixão-Côrtes

    Full Text Available Paired box (PAX genes are transcription factors that play important roles in embryonic development. Although the PAX gene family occurs in animals only, it is widely distributed. Among the vertebrates, its 9 genes appear to be the product of complete duplication of an original set of 4 genes, followed by an additional partial duplication. Although some studies of PAX genes have been conducted, no comprehensive survey of these genes across the entire taxonomic unit has yet been attempted. In this study, we conducted a detailed comparison of PAX sequences from 188 chordates, which revealed restricted variation. The absence of PAX4 and PAX8 among some species of reptiles and birds was notable; however, all 9 genes were present in all 74 mammalian genomes investigated. A search for signatures of selection indicated that all genes are subject to purifying selection, with a possible constraint relaxation in PAX4, PAX7, and PAX8. This result indicates asymmetric evolution of PAX family genes, which can be associated with the emergence of adaptive novelties in the chordate evolutionary trajectory.

  1. A conserved non-reproductive GnRH system in chordates.

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    Takehiro G Kusakabe

    Full Text Available Gonadotropin-releasing hormone (GnRH is a neuroendocrine peptide that plays a central role in the vertebrate hypothalamo-pituitary axis. The roles of GnRH in the control of vertebrate reproductive functions have been established, while its non-reproductive function has been suggested but less well understood. Here we show that the tunicate Ciona intestinalis has in its non-reproductive larval stage a prominent GnRH system spanning the entire length of the nervous system. Tunicate GnRH receptors are phylogenetically closest to vertebrate GnRH receptors, yet functional analysis of the receptors revealed that these simple chordates have evolved a unique GnRH system with multiple ligands and receptor heterodimerization enabling complex regulation. One of the gnrh genes is conspicuously expressed in the motor ganglion and nerve cord, which are homologous structures to the hindbrain and spinal cord of vertebrates. Correspondingly, GnRH receptor genes were found to be expressed in the tail muscle and notochord of embryos, both of which are phylotypic axial structures along the nerve cord. Our findings suggest a novel non-reproductive role of GnRH in tunicates. Furthermore, we present evidence that GnRH-producing cells are present in the hindbrain and spinal cord of the medaka, Oryzias latipes, thereby suggesting the deep evolutionary origin of a non-reproductive GnRH system in chordates.

  2. Ontology for the asexual development and anatomy of the colonial chordate Botryllus schlosseri.

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    Lucia Manni

    Full Text Available Ontologies provide an important resource to integrate information. For developmental biology and comparative anatomy studies, ontologies of a species are used to formalize and annotate data that are related to anatomical structures, their lineage and timing of development. Here, we have constructed the first ontology for anatomy and asexual development (blastogenesis of a bilaterian, the colonial tunicate Botryllus schlosseri. Tunicates, like Botryllus schlosseri, are non-vertebrates and the only chordate taxon species that reproduce both sexually and asexually. Their tadpole larval stage possesses structures characteristic of all chordates, i.e. a notochord, a dorsal neural tube, and gill slits. Larvae settle and metamorphose into individuals that are either solitary or colonial. The latter reproduce both sexually and asexually and these two reproductive modes lead to essentially the same adult body plan. The Botryllus schlosseri Ontology of Development and Anatomy (BODA will facilitate the comparison between both types of development. BODA uses the rules defined by the Open Biomedical Ontologies Foundry. It is based on studies that investigate the anatomy, blastogenesis and regeneration of this organism. BODA features allow the users to easily search and identify anatomical structures in the colony, to define the developmental stage, and to follow the morphogenetic events of a tissue and/or organ of interest throughout asexual development. We invite the scientific community to use this resource as a reference for the anatomy and developmental ontology of B. schlosseri and encourage recommendations for updates and improvements.

  3. The transcriptome of an amphioxus, Asymmetron lucayanum, from the Bahamas: a window into chordate evolution.

    Science.gov (United States)

    Yue, Jia-Xing; Yu, Jr-Kai; Putnam, Nicholas H; Holland, Linda Z

    2014-10-01

    Cephalochordates, the sister group of tunicates plus vertebrates, have been called "living fossils" due to their resemblance to fossil chordates from Cambrian strata. The genome of the cephalochordate Branchiostoma floridae shares remarkable synteny with vertebrates and is free from whole-genome duplication. We performed RNA sequencing from larvae and adults of Asymmetron lucayanum, a cephalochordate distantly related to B. floridae. Comparisons of about 430 orthologous gene groups among both cephalochordates and 10 vertebrates using an echinoderm, a hemichordate, and a mollusk as outgroups showed that cephalochordates are evolving more slowly than the slowest evolving vertebrate known (the elephant shark), with A. lucayanum evolving even more slowly than B. floridae. Against this background of slow evolution, some genes, notably several involved in innate immunity, stand out as evolving relatively quickly. This may be due to the lack of an adaptive immune system and the relatively high levels of bacteria in the inshore waters cephalochordates inhabit. Molecular dating analysis including several time constraints revealed a divergence time of ∼120 Ma for A. lucayanum and B. floridae. The divisions between cephalochordates and vertebrates, and that between chordates and the hemichordate plus echinoderm clade likely occurred before the Cambrian. PMID:25240057

  4. The synapsin gene family in basal chordates: evolutionary perspectives in metazoans

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    De Bernardi Fiorenza

    2010-01-01

    Full Text Available Abstract Background Synapsins are neuronal phosphoproteins involved in several functions correlated with both neurotransmitter release and synaptogenesis. The comprehension of the basal role of the synapsin family is hampered in vertebrates by the existence of multiple synapsin genes. Therefore, studying homologous genes in basal chordates, devoid of genome duplication, could help to achieve a better understanding of the complex functions of these proteins. Results In this study we report the cloning and characterization of the Ciona intestinalis and amphioxus Branchiostoma floridae synapsin transcripts and the definition of their gene structure using available C. intestinalis and B. floridae genomic sequences. We demonstrate the occurrence, in both model organisms, of a single member of the synapsin gene family. Full-length synapsin genes were identified in the recently sequenced genomes of phylogenetically diverse metazoans. Comparative genome analysis reveals extensive conservation of the SYN locus in several metazoans. Moreover, developmental expression studies underline that synapsin is a neuronal-specific marker in basal chordates and is expressed in several cell types of PNS and in many, if not all, CNS neurons. Conclusion Our study demonstrates that synapsin genes are metazoan genes present in a single copy per genome, except for vertebrates. Moreover, we hypothesize that, during the evolution of synapsin proteins, new domains are added at different stages probably to cope up with the increased complexity in the nervous system organization. Finally, we demonstrate that protochordate synapsin is restricted to the post-mitotic phase of CNS development and thereby is a good marker of postmitotic neurons.

  5. Conservation and diversification of an ancestral chordate gene regulatory network for dorsoventral patterning.

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    Iryna Kozmikova

    Full Text Available Formation of a dorsoventral axis is a key event in the early development of most animal embryos. It is well established that bone morphogenetic proteins (Bmps and Wnts are key mediators of dorsoventral patterning in vertebrates. In the cephalochordate amphioxus, genes encoding Bmps and transcription factors downstream of Bmp signaling such as Vent are expressed in patterns reminiscent of those of their vertebrate orthologues. However, the key question is whether the conservation of expression patterns of network constituents implies conservation of functional network interactions, and if so, how an increased functional complexity can evolve. Using heterologous systems, namely by reporter gene assays in mammalian cell lines and by transgenesis in medaka fish, we have compared the gene regulatory network implicated in dorsoventral patterning of the basal chordate amphioxus and vertebrates. We found that Bmp but not canonical Wnt signaling regulates promoters of genes encoding homeodomain proteins AmphiVent1 and AmphiVent2. Furthermore, AmphiVent1 and AmphiVent2 promoters appear to be correctly regulated in the context of a vertebrate embryo. Finally, we show that AmphiVent1 is able to directly repress promoters of AmphiGoosecoid and AmphiChordin genes. Repression of genes encoding dorsal-specific signaling molecule Chordin and transcription factor Goosecoid by Xenopus and zebrafish Vent genes represents a key regulatory interaction during vertebrate axis formation. Our data indicate high evolutionary conservation of a core Bmp-triggered gene regulatory network for dorsoventral patterning in chordates and suggest that co-option of the canonical Wnt signaling pathway for dorsoventral patterning in vertebrates represents one of the innovations through which an increased morphological complexity of vertebrate embryo is achieved.

  6. A glycine receptor is involved in the organization of swimming movements in an invertebrate chordate

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    Okamura Yasushi

    2010-01-01

    Full Text Available Abstract Background Rhythmic motor patterns for locomotion in vertebrates are generated in spinal cord neural networks known as spinal Central Pattern Generators (CPGs. A key element in pattern generation is the role of glycinergic synaptic transmission by interneurons that cross the cord midline and inhibit contralaterally-located excitatory neurons. The glycinergic inhibitory drive permits alternating and precisely timed motor output during locomotion such as walking or swimming. To understand better the evolution of this system we examined the physiology of the neural network controlling swimming in an invertebrate chordate relative of vertebrates, the ascidian larva Ciona intestinalis. Results A reduced preparation of the larva consisting of nerve cord and motor ganglion generates alternating swimming movements. Pharmacological and genetic manipulation of glycine receptors shows that they are implicated in the control of these locomotory movements. Morphological molecular techniques and heterologous expression experiments revealed that glycine receptors are inhibitory and are present on both motoneurones and locomotory muscle while putative glycinergic interneurons were identified in the nerve cord by labeling with an anti-glycine antibody. Conclusions In Ciona intestinalis, glycine receptors, glycinergic transmission and putative glycinergic interneurons, have a key role in coordinating swimming movements through a simple CPG that is present in the motor ganglion and nerve cord. Thus, the strong association between glycine receptors and vertebrate locomotory networks may now be extended to include the phylum chordata. The results suggest that the basic network for 'spinal-like' locomotion is likely to have existed in the common ancestor of extant chordates some 650 M years ago.

  7. Cell signaling and transcription factor genes expressed during whole body regeneration in a colonial chordate

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    Rinkevich Baruch

    2008-10-01

    Full Text Available Abstract Background The restoration of adults from fragments of blood vessels in botryllid ascidians (termed whole body regeneration [WBR] represents an inimitable event in the chordates, which is poorly understood on the mechanistic level. Results To elucidate mechanisms underlying this phenomenon, a subtracted EST library for early WBR stages was previously assembled, revealing 76 putative genes belonging to major signaling pathways, including Notch/Delta, JAK/STAT, protein kinases, nuclear receptors, Ras oncogene family members, G-Protein coupled receptor (GPCR and transforming growth factor beta (TGF-β signaling. RT-PCR on selected transcripts documented specific up-regulation in only regenerating fragments, pointing to a broad activation of these signaling pathways at onset of WBR. The followed-up expression pattern of seven representative transcripts from JAK/STAT signaling (Bl-STAT, the Ras oncogene family (Bl-Rap1A, Bl-Rab-33, the protein kinase family (Bl-Mnk, Bl-Cnot, Bl-Slit and Bl-Bax inhibitor, revealed systemic and site specific activations during WBR in a sub-population of circulatory cells. Conclusion WBR in the non-vertebrate chordate Botrylloides leachi is a multifaceted phenomenon, presided by a complex array of cell signaling and transcription factors. Above results, provide a first insight into the whole genome molecular machinery of this unique regeneration process, and reveal the broad participation of cell signaling and transcription factors in the process. While regeneration involves the participation of specific cell populations, WBR signals are systemically expressed at the organism level.

  8. A new vetulicolian from Australia and its bearing on the chordate affinities of an enigmatic Cambrian group

    OpenAIRE

    García-Bellido, Diego C.; Lee, Michael S. Y.; Gregory D. Edgecombe; Jago, James B; Gehling, James G; Paterson, John R

    2014-01-01

    Background Vetulicolians are one of the most problematic and controversial Cambrian fossil groups, having been considered as arthropods, chordates, kinorhynchs, or their own phylum. Mounting evidence suggests that vetulicolians are deuterostomes, but affinities to crown-group phyla are unresolved. Results A new vetulicolian from the Emu Bay Shale Konservat-Lagerstätte, South Australia, Nesonektris aldridgei gen. et sp. nov., preserves an axial, rod-like structure in the posterior body region ...

  9. DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants

    OpenAIRE

    Barta, Endre; Sebestyén, Endre; Pálfy, Tamás B.; Tóth, Gábor; Ortutay, Csaba P.; Patthy, László

    2004-01-01

    DoOP (http://doop.abc.hu/) is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species. The annotated first exons of human and Arabidopsis thaliana genes were used as queries in BLAST searches to collect the most closely related orthologous first exon sequences from Chordata and Viridiplantae species. Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and pl...

  10. Molecular signatures that are distinctive characteristics of the vertebrates and chordates and supporting a grouping of vertebrates with the tunicates.

    Science.gov (United States)

    Gupta, Radhey S

    2016-01-01

    Members of the phylum Chordata and the subphylum Vertebrata are presently distinguished solely on the basis of morphological characteristics. The relationship of the vertebrates to the two non-vertebrate chordate subphyla is also a subject of debate. Analyses of protein sequences have identified multiple conserved signature indels (CSIs) that are specific for Chordata or for Vertebrata. Five CSIs in 4 important proteins are specific for the Vertebrata, whereas two other CSIs are uniquely found in all sequenced chordate species including Ciona intestinalis and Oikapleura dioica (Tunicates) as well as Branchiostoma floridae (Cephalochordates). The shared presence of these molecular signatures by all vertebrates/chordate species, but in no other animal taxa, strongly indicates that the genetic changes represented by the identified CSIs diagnose monophyletic groups. Two other discovered CSIs are uniquely shared by different vertebrate species and by either one (Ciona intestinalis) or both tunicate (Ciona and Oikapleura) species, but they are not found in Branchiostoma or other animal species. Specific presence of these CSIs in different vertebrates and either one or both tunicate species provides strong independent evidence that the vertebrate species are more closely related to the urochordates (tunicates) than to the cephalochordates. PMID:26419477

  11. Ion channel clustering at the axon initial segment and node of Ranvier evolved sequentially in early chordates.

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    Alexis S Hill

    2008-12-01

    Full Text Available In many mammalian neurons, dense clusters of ion channels at the axonal initial segment and nodes of Ranvier underlie action potential generation and rapid conduction. Axonal clustering of mammalian voltage-gated sodium and KCNQ (Kv7 potassium channels is based on linkage to the actin-spectrin cytoskeleton, which is mediated by the adaptor protein ankyrin-G. We identified key steps in the evolution of this axonal channel clustering. The anchor motif for sodium channel clustering evolved early in the chordate lineage before the divergence of the wormlike cephalochordate, amphioxus. Axons of the lamprey, a very primitive vertebrate, exhibited some invertebrate features (lack of myelin, use of giant diameter to hasten conduction, but possessed narrow initial segments bearing sodium channel clusters like in more recently evolved vertebrates. The KCNQ potassium channel anchor motif evolved after the divergence of lampreys from other vertebrates, in a common ancestor of shark and humans. Thus, clustering of voltage-gated sodium channels was a pivotal early innovation of the chordates. Sodium channel clusters at the axon initial segment serving the generation of action potentials evolved long before the node of Ranvier. KCNQ channels acquired anchors allowing their integration into pre-existing sodium channel complexes at about the same time that ancient vertebrates acquired myelin, saltatory conduction, and hinged jaws. The early chordate refinements in action potential mechanisms we have elucidated appear essential to the complex neural signaling, active behavior, and evolutionary success of vertebrates.

  12. Evolutionary dynamics of olfactory receptor genes in chordates: interaction between environments and genomic contents

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    Niimura Yoshihito

    2009-12-01

    Full Text Available Abstract Olfaction is essential for the survival of animals. Versatile odour molecules in the environment are received by olfactory receptors (ORs, which form the largest multigene family in vertebrates. Identification of the entire repertories of OR genes using bioinformatics methods from the whole-genome sequences of diverse organisms revealed that the numbers of OR genes vary enormously, ranging from ~1,200 in rats and ~400 in humans to ~150 in zebrafish and ~15 in pufferfish. Most species have a considerable fraction of pseudogenes. Extensive phylogenetic analyses have suggested that the numbers of gene gains and losses are extremely large in the OR gene family, which is a striking example of the birth-and-death evolution. It appears that OR gene repertoires change dynamically, depending on each organism's living environment. For example, higher primates equipped with a well-developed vision system have lost a large number of OR genes. Moreover, two groups of OR genes for detecting airborne odorants greatly expanded after the time of terrestrial adaption in the tetrapod lineage, whereas fishes retain diverse repertoires of genes that were present in aquatic ancestral species. The origin of vertebrate OR genes can be traced back to the common ancestor of all chordate species, but insects, nematodes and echinoderms utilise distinctive families of chemoreceptors, suggesting that chemoreceptor genes have evolved many times independently in animal evolution.

  13. Metaphylogeny of 82 gene families sheds a new light on chordate evolution

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    2006-04-01

    Full Text Available Achieving a better comprehension of the evolution of species has always been an important matter for evolutionary biologists. The deuterostome phylogeny has been described for many years, and three phyla are distinguishable: Echinodermata (including sea stars, sea urchins, etc…, Hemichordata (including acorn worms and pterobranchs, and Chordata (including urochordates, cephalochordates and extant vertebrates. Inside the Chordata phylum, the position of vertebrate species is quite unanimously accepted. Nonetheless, the position of urochordates in regard with vertebrates is still the subject of debate, and has even been suggested by some authors to be a separate phylum from cephalochordates and vertebrates. It was also the case for agnathans species –myxines and hagfish– for which phylogenetic evidence was recently given for a controversial monophyly. This raises the following question: which one of the cephalochordata or urochordata is the sister group of vertebrates and what are their relationships? In the present work, we analyzed 82 protein families presenting homologs between urochordata and other deuterostomes and focused on two points: 1 testing accurately the position of urochordata and cephalochordata phyla in regard with vertebrates as well as chordates monophyly, 2 performing an estimation of the rate of gene loss in the Ciona intestinalis genome. We showed that the urochordate phyla is the vertebrate sister group and that gene loss played a major role in structuring the urochordate genome.

  14. Revaluation of deuterostome phylogeny and evolutionary relationships among chordate subphyla using mitogenome data.

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    Zhong, Jing; Zhang, Juyong; Mukwaya, Emmanuel; Wang, Yiquan

    2009-03-01

    The traditional knowledge in textbooks indicated that cephalochordates were the closest relatives to vertebrates among all extant organisms. However, this opinion was challenged by several recent phylogenetic studies using hundreds of nuclear genes. The researchers suggested that urochordates, but not cephalochordates, should be the closest living relatives to vertebrates. In the present study, by using data generated from hundreds of mtDNA sequences, we revalue the deuterostome phylogeny in terms of whole mitochondrial genomes (mitogenomes). Our results firmly demonstrate that each of extant deuterostome phyla and chordate subphyla is monophyletic. But the results present several alternative phylogenetic trees depending on different sequence datasets used in the analysis. Although no clear phylogenetic relationships are obtained, those trees indicate that the ancient common ancestor diversified rapidly soon after their appearance in the early Cambrian and generated all major deuterostome lineages during a short historical period, which is consistent with "Cambrian explosion" revealed by paleontologists. It was the 520-million-year's evolution that obscured the phylogenetic relationships of extant deuterostomes. Thus, we conclude that an integrative analysis approach rather than simply using more DNA sequences should be employed to address the distant evolutionary relationship. PMID:19302971

  15. The Simple Chordate Ciona intestinalis Has a Reduced Complement of Genes Associated with Fanconi Anemia

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    Stanley, Edward C.; Azzinaro, Paul A.; Vierra, David A.; Howlett, Niall G.; Irvine, Steven Q.

    2016-01-01

    Fanconi anemia (FA) is a human genetic disease characterized by congenital defects, bone marrow failure, and increased cancer risk. FA is associated with mutation in one of 24 genes. The protein products of these genes function cooperatively in the FA pathway to orchestrate the repair of DNA interstrand cross-links. Few model organisms exist for the study of FA. Seeking a model organism with a simpler version of the FA pathway, we searched the genome of the simple chordate Ciona intestinalis for homologs of the human FA-associated proteins. BLAST searches, sequence alignments, hydropathy comparisons, maximum likelihood phylogenetic analysis, and structural modeling were used to infer the likelihood of homology between C. intestinalis and human FA proteins. Our analysis indicates that C. intestinalis indeed has a simpler and potentially functional FA pathway. The C. intestinalis genome was searched for candidates for homology to 24 human FA and FA-associated proteins. Support was found for the existence of homologs for 13 of these 24 human genes in C. intestinalis. Members of each of the three commonly recognized FA gene functional groups were found. In group I, we identified homologs of FANCE, FANCL, FANCM, and UBE2T/FANCT. Both members of group II, FANCD2 and FANCI, have homologs in C. intestinalis. In group III, we found evidence for homologs of FANCJ, FANCO, FANCQ/ERCC4, FANCR/RAD51, and FANCS/BRCA1, as well as the FA-associated proteins ERCC1 and FAN1. Evidence was very weak for the existence of homologs in C. intestinalis for any other recognized FA genes. This work supports the notion that C. intestinalis, as a close relative of vertebrates, but having a much reduced complement of FA genes, offers a means of studying the function of certain FA proteins in a simpler pathway than that of vertebrate cells. PMID:27279728

  16. Lifespan extension in a semelparous chordate occurs via developmental growth arrest just prior to meiotic entry.

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    Gunasekaran Subramaniam

    Full Text Available It is proposed that the ageing process is linked to signaling from the germline such that the rate of ageing can be adjusted to the state of the reproductive system, allowing these two processes to co-evolve. Mechanistic insight into this link has been primarily derived from iteroparous reproductive models, the nematode C. elegans, and the arthropod Drosophila. Here, we examined to what extent these mechanisms are evolutionarily conserved in a semelparous chordate, Oikopleura dioica, where we identify a developmental growth arrest (GA in response to crowded, diet-restricted conditions, which can extend its lifespan at least three-fold. Under nutritional stress, the iteroparative models sacrifice germ cells that have entered meiosis, while maintaining a reduced pool of active germline stem cells (GSCs. In contrast, O. dioica only entered GA prior to meiotic entry. Stress conditions encountered after this point led to maturation in a normal time frame but with reduced reproductive output. During GA, TOR signaling was inhibited, whereas MAPK, ERK1/2 and p38 pathways were activated, and under such conditions, activation of these pathways was shown to be critical for survival. Direct inhibition of TOR signaling alone was sufficient to prevent meiotic entry and germline differentiation. This inhibition activated the p38 pathway, but did not activate the ERK1/2 pathway. Thus, the link between reproductive status and lifespan extension in response to nutrient-limited conditions is interpreted in a significantly different manner in these iteroparative versus semelparous models. In the latter case, meiotic entry is a definitive signal that lifespan extension can no longer occur, whereas in the former, meiotic entry is not a unique chronological event, and can be largely erased during lifespan extension in response to nutrient stress, and reactivated from a pool of maintained GSCs when conditions improve.

  17. The candidate histocompatibility locus of a Basal chordate encodes two highly polymorphic proteins.

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    Marie L Nydam

    Full Text Available The basal chordate Botryllus schlosseri undergoes a natural transplantation reaction governed by a single, highly polymorphic locus called the fuhc. Our initial characterization of this locus suggested it encoded a single gene alternatively spliced into two transcripts: a 555 amino acid-secreted form containing the first half of the gene, and a full-length, 1008 amino acid transmembrane form, with polymorphisms throughout the ectodomain determining outcome. We have now found that the locus encodes two highly polymorphic genes which are separated by a 227 bp intergenic region: first, the secreted form as previously described, and a second gene encoding a 531 amino acid membrane-bound gene containing three extracellular immunoglobulin domains. While northern blotting revealed only these two mRNAs, both PCR and mRNA-seq detect a single capped and polyadenylated transcript that encodes processed forms of both genes linked by the intergenic region, as well as other transcripts in which exons of the two genes are spliced together. These results might suggest that the two genes are expressed as an operon, during which both genes are co-transcribed and then trans-spliced into two separate messages. This type of transcriptional regulation has been described in tunicates previously; however, the membrane-bound gene does not encode a typical Splice Leader (SL sequence at the 5' terminus that usually accompanies trans-splicing. Thus, the presence of stable transcripts encoding both genes may suggest a novel mechanism of regulation, or conversely may be rare but stable transcripts in which the two mRNAs are linked due to a small amount of read-through by RNA polymerase. Both genes are highly polymorphic and co-expressed on tissues involved in histocompatibility. In addition, polymorphisms on both genes correlate with outcome, although we have found a case in which it appears that the secreted form may be major allorecognition determinant.

  18. Evolutionary origin of GnIH and NPFF in chordates: insights from novel amphioxus RFamide peptides.

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    Tomohiro Osugi

    Full Text Available Gonadotropin-inhibitory hormone (GnIH is a newly identified hypothalamic neuropeptide that inhibits pituitary hormone secretion in vertebrates. GnIH has an LPXRFamide (X = L or Q motif at the C-terminal in representative species of gnathostomes. On the other hand, neuropeptide FF (NPFF, a neuropeptide characterized as a pain-modulatory neuropeptide, in vertebrates has a PQRFamide motif similar to the C-terminal of GnIH, suggesting that GnIH and NPFF have diverged from a common ancestor. Because GnIH and NPFF belong to the RFamide peptide family in vertebrates, protochordate RFamide peptides may provide important insights into the evolutionary origin of GnIH and NPFF. In this study, we identified a novel gene encoding RFamide peptides and two genes of their putative receptors in the amphioxus Branchiostoma japonicum. Molecular phylogenetic analysis and synteny analysis indicated that these genes are closely related to the genes of GnIH and NPFF and their receptors of vertebrates. We further identified mature RFamide peptides and their receptors in protochordates. The identified amphioxus RFamide peptides inhibited forskolin induced cAMP signaling in the COS-7 cells with one of the identified amphioxus RFamide peptide receptors expressed. These results indicate that the identified protochordate RFamide peptide gene is a common ancestral form of GnIH and NPFF genes, suggesting that the origin of GnIH and NPFF may date back to the time of the emergence of early chordates. GnIH gene and NPFF gene may have diverged by whole-genome duplication in the course of vertebrate evolution.

  19. Pax258 and Pax6 alternative splicing events in basal chordates and vertebrates: a focus on paired box domain

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    Peter eFabian

    2015-07-01

    Full Text Available Paired box transcription factors play important role in development and tissue morphogenesis. The number of Pax homologs varies among species studied so far, due to genome and gene duplications that have affected PAX family to a great extent. Based on sequence similarity and functional domains, four Pax classes have been identified in chordates, namely Pax1/9, Pax2/5/8, Pax3/7 and Pax4/6. Numerous splicing events have been reported mainly for Pax2/5/8 and Pax6 genes. Of significant interest are those events that lead to Pax proteins with presumed novel properties, such as altered DNA-binding or transcriptional activity. In the current study, a thorough analysis of Pax2/5/8 splicing events from cephalochordate and vertebrates was performed. We focused more on Pax2/5/8 and Pax6 splicing events in which the paired domain is involved. Three new splicing events were identified in Oryzias latipes, one of which seems to be conserved in Acanthomorphata. Using representatives from deuterostome and protostome phyla, a comparative analysis of the Pax6 exon-intron structure of the paired domain was performed, during an attempt to estimate the time of appearance of the Pax6(5a mRNA isoform. As shown in our analysis, this splicing event is absent in basal chordates and is characteristic of Gnathostomata. Moreover, expression pattern of alternative spliced variants was compared between basal chordates and fish species. In summary, our data indicate expansion of alternative mRNA variants in paired box region of Pax2/5/8 and Pax6 genes during the course of vertebrate evolution.

  20. The central nervous system of sea cucumbers (Echinodermata: Holothuroidea shows positive immunostaining for a chordate glial secretion

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    Grondona Jesus M

    2009-06-01

    Full Text Available Abstract Background Echinoderms and chordates belong to the same monophyletic taxon, the Deuterostomia. In spite of significant differences in body plan organization, the two phyla may share more common traits than was thought previously. Of particular interest are the common features in the organization of the central nervous system. The present study employs two polyclonal antisera raised against bovine Reissner's substance (RS, a secretory product produced by glial cells of the subcomissural organ, to study RS-like immunoreactivity in the central nervous system of sea cucumbers. Results In the ectoneural division of the nervous system, both antisera recognize the content of secretory vacuoles in the apical cytoplasm of the radial glia-like cells of the neuroepithelium and in the flattened glial cells of the non-neural epineural roof epithelium. The secreted immunopositive material seems to form a thin layer covering the cell apices. There is no accumulation of the immunoreactive material on the apical surface of the hyponeural neuroepithelium or the hyponeural roof epithelium. Besides labelling the supporting cells and flattened glial cells of the epineural roof epithelium, both anti-RS antisera reveal a previously unknown putative glial cell type within the neural parenchyma of the holothurian nervous system. Conclusion Our results show that: a the glial cells of the holothurian tubular nervous system produce a material similar to Reissner's substance known to be synthesized by secretory glial cells in all chordates studied so far; b the nervous system of sea cucumbers shows a previously unrealized complexity of glial organization. Our findings also provide significant clues for interpretation of the evolution of the nervous system in the Deuterostomia. It is suggested that echinoderms and chordates might have inherited the RS-producing radial glial cell type from the central nervous system of their common ancestor, i.e., the last common

  1. Retinoic acid signaling acts via Hox1 to establish the posterior limit of the pharynx in the chordate amphioxus

    OpenAIRE

    Schubert, Michael; Yu, Jr-Kai; Holland, Nicholas D; Escriva, Hector; Laudet, Vincent; Holland, Linda Z

    2004-01-01

    In the invertebrate chordate amphioxus, as in vertebrates, retinoic acid (RA) specifies position along the anterior/posterior axis with elevated RA signaling in the middle third of the endoderm setting the posterior limit of the pharynx. Here we show that AmphiHox1 is also expressed in the middle third of the developing amphioxus endoderm and is activated by RA signaling. Knockdown of AmphiHox1 function with an antisense morpholino oligonucleotide shows that AmphiHox1 mediates the role of RA ...

  2. Testing putative hemichordate homologues of the chordate dorsal nervous system and endostyle: expression of NK2.1 (TTF-1) in the acorn worm Ptychodera flava (Hemichordata, Ptychoderidae)

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    Takacs, Carter M.; Moy, Vanessa N.; Peterson, Kevin J.

    2002-01-01

    Recent phylogenetic investigations have confirmed that hemichordates and echinoderms are sister taxa. However, hemichordates share several cardinal characterstics with chordates and are thus an important taxon for testing hypotheses of homology between key chordate characters and their putative hemichordate antecedents. The chordate dorsal nervous system (DNS) and endostyle are intriguing characters because both hemichordate larval and adult structures have been hypothesized as homologues. This study attempts to test these purported homologies through examination of the expression pattem of a Ptychodera flava NK2 gene, PfNK2.1, because this gene is expressed both in the DNS and endostyle/thyroid in a wide range of chordate taxa. We found that PfNK2.1 is expressed in both neuronal and pharyngeal structures, but its expression pattem is broken up into distinct embryonic and juvenile phases. During embryogenesis, PfNK2.1 is expressed in the apical ectoderm, with transcripts later detected in presumable neuronal structures, including the apical organ and ciliated feeding band. In the developing juvenile we detected PfNK2.1 signal throughout the pharynx, including the stomochord, and later in the hindgut. We conclude that the similar utilization of NK2.1 in apical organ development and chordate DNS is probably due to a more general role for NK2.1 in neurogenesis and that hemichordates do not possess a homologue of the chordate DNS. In addition, we conclude that P. flava most likely does not possess a true endostyle; rather during the evolution of the endostyle NK2.1 was recruited from its more general role in pharynx development.

  3. Phylogenetic analysis of the tenascin gene family: evidence of origin early in the chordate lineage

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    Tucker RP

    2006-08-01

    suggests that tenascins may be specific to chordates. Later genomic duplication events led to the appearance of four family members in vertebrates: tenascin-C, tenascin-R, tenascin-W and tenascin-X.

  4. Developmental Control of Cell-Cycle Compensation Provides a Switch for Patterned Mitosis at the Onset of Chordate Neurulation.

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    Ogura, Yosuke; Sasakura, Yasunori

    2016-04-18

    During neurulation of chordate ascidians, the 11th mitotic division within the epidermal layer shows a posterior-to-anterior wave that is precisely coordinated with the unidirectional progression of the morphogenetic movement. Here we show that the first sign of this patterned mitosis is an asynchronous anterior-to-posterior S-phase length and that mitotic synchrony is reestablished by a compensatory asynchronous G2-phase length. Live imaging combined with genetic experiments demonstrated that compensatory G2-phase regulation requires transcriptional activation of the G2/M regulator cdc25 by the patterning genes GATA and AP-2. The downregulation of GATA and AP-2 at the onset of neurulation leads to loss of compensatory G2-phase regulation and promotes the transition to patterned mitosis. We propose that such developmentally regulated cell-cycle compensation provides an abrupt switch to spatially patterned mitosis in order to achieve the coordination between mitotic timing and morphogenesis.

  5. CiMT-1, an unusual chordate metallothionein gene in Ciona intestinalis genome: structure and expression studies.

    Science.gov (United States)

    Franchi, Nicola; Boldrin, Francesco; Ballarin, Loriano; Piccinni, Ester

    2011-02-01

    The present article reports on the characterization of the urochordate metallothionein (MT) gene, CiMT-1, from the solitary ascidian Ciona intestinalis. The predicted protein is shorter than other known deuterostome MTs, having only 39 amino acids. The gene has the same tripartite structure as vertebrate MTs, with some features resembling those of echinoderm MTs. The promoter region shows the canonical cis-acting elements recognized by transcription factors that respond to metal, ROS, and cytokines. Unusual sequences, described in fish and echinoderms, are also present. In situ hybridization suggests that only a population of hemocytes involved in immune responses, i.e. granular amebocytes, express CiMT-1 mRNA. These observations support the idea that urochordates perform detoxification through hemocytes, and that MTs may play important roles in inflammatory humoral responses in tunicates. The reported data offer new clues for better understanding the evolution of these multivalent proteins from non-vertebrate to vertebrate chordates and reinforce their functions in detoxification and immunity. PMID:21328559

  6. Photoresponse and Learning Behavior of Ascidian Larvae, a Primitive Chordate, to Repeated Stimuli of Step-Up and Step-Down of Light

    OpenAIRE

    Kawakami, I.; Shiraishi, S; Tsuda, M

    2002-01-01

    Ascidians are lower chordates and their simple tadpole-like larvae share a basic body plan with vertebrates. Newly hatched larvae show no response to a stimulus of light. 4 h after hatching, the larvae were induced to swim upon a step-down of light and stop swimming upon a step-up of light. At weaker intensity of light, the larvae show the same response to a stimulus after presentation of repeated stimuli. When intensity of actinic light was increased, the larvae show sensitization and habitu...

  7. Pax2/5/8 and Pax6 alternative splicing events in basal chordates and vertebrates: a focus on paired box domain

    OpenAIRE

    Fabian, Peter; Kozmikova, Iryna; Kozmik, Zbynek; Pantzartzi, Chrysoula N.

    2015-01-01

    Paired box transcription factors play important role in development and tissue morphogenesis. The number of Pax homologs varies among species studied so far, due to genome and gene duplications that have affected PAX family to a great extent. Based on sequence similarity and functional domains, four Pax classes have been identified in chordates, namely Pax1/9, Pax2/5/8, Pax3/7, and Pax4/6. Numerous splicing events have been reported mainly for Pax2/5/8 and Pax6 genes. Of significant interest ...

  8. Characterization of bbtTICAM from amphioxus suggests the emergence of a MyD88-independent pathway in basal chordates

    Institute of Scientific and Technical Information of China (English)

    ManyiYang; ShaochunYuan; Shengfeng Huang; Jun Li; Liqun Xu; Huiqing Huang; Xin Tao; Jian peng; Anlong Xu

    2011-01-01

    The MyD88-independent pathway,one of the two crucial TLR signaling routes,Is thought to be a vertebrate innovation.However,a novel Toll/interleukin-1 receptor (TIR) adaptor,designated bbtTICAM,which was identified in the basal chordate amphioxus,links this pathway to invertebrates.The protein architecture of bbtTICAM is similar to that of vertebrate TICAM1 (TIR-containing adaptor molecule-1,also known as TRIF),while phylogenetic analysis based on the TIR domain indicated that bbtTICAM is the oldest ortholog of vertebrate TICAMI and TICAM2(TIR-containing adaptor molecule-2,also known as TRAM).Similar to human TICAM1,bbtTICAM activates NF-κB in a MyD88-independent manner by interacting with receptor interacting protein (RIP) via its RHIM motif.Such activation requires bbtTICAM to form homodimers in endosomes,and it may be negatively regulated by amphioxus SARM (sterile a and armadillo motif-containing protein) and TRAF2.However,bbtTICAM did not induce the production of type I interferon.Thus,our study not only presents the ancestral features of vertebrate TICAM I and TICAM2,but also reveals the evolutionary origin of the MyD88-independent pathway from basal chordates,which will aid in understanding the development of the vertebrate TLR network.

  9. Retinoic acid signaling targets Hox genes during the amphioxus gastrula stage: insights into early anterior-posterior patterning of the chordate body plan.

    Science.gov (United States)

    Koop, Demian; Holland, Nicholas D; Sémon, Marie; Alvarez, Susana; de Lera, Angel Rodriguez; Laudet, Vincent; Holland, Linda Z; Schubert, Michael

    2010-02-01

    Previous studies of vertebrate development have shown that retinoic acid (RA) signaling at the gastrula stage strongly influences anterior-posterior (A-P) patterning of the neurula and later stages. However, much less is known about the more immediate effects of RA signaling on gene transcription and developmental patterning at the gastrula stage. To investigate the targets of RA signaling during the gastrula stage, we used the basal chordate amphioxus, in which gastrulation involves very minimal tissue movements. First, we determined the effect of altered RA signaling on expression of 42 genes (encoding transcription factors and components of major signaling cascades) known to be expressed in restricted domains along the A-P axis during the gastrula and early neurula stage. Of these 42 genes, the expression domains during gastrulation of only four (Hox1, Hox3, HNF3-1 and Wnt3) were spatially altered by exposure of the embryos to excess RA or to the RA antagonist BMS009. Moreover, blocking protein synthesis with puromycin before adding RA or BMS009 showed that only three of these genes (Hox1, Hox3 and HNF3-1) are direct RA targets at the gastrula stage. From these results we conclude that in the amphioxus gastrula RA signaling primarily acts via regulation of Hox transcription to establish positional identities along the A-P axis and that Hox1, Hox3, HNF3-1 and Wnt3 constitute a basal module of RA action during chordate gastrulation. PMID:19914237

  10. Evolutionary conservation of the presumptive neural plate markers AmphiSox1/2/3 and AmphiNeurogenin in the invertebrate chordate amphioxus

    Science.gov (United States)

    Holland, L. Z.; Schubert, M.; Holland, N. D.; Neuman, T.

    2000-01-01

    Amphioxus, as the closest living invertebrate relative of the vertebrates, can give insights into the evolutionary origin of the vertebrate body plan. Therefore, to investigate the evolution of genetic mechanisms for establishing and patterning the neuroectoderm, we cloned and determined the embryonic expression of two amphioxus transcription factors, AmphiSox1/2/3 and AmphiNeurogenin. These genes are the earliest known markers for presumptive neuroectoderm in amphioxus. By the early neurula stage, AmphiNeurogenin expression becomes restricted to two bilateral columns of segmentally arranged neural plate cells, which probably include precursors of motor neurons. This is the earliest indication of segmentation in the amphioxus nerve cord. Later, expression extends to dorsal cells in the nerve cord, which may include precursors of sensory neurons. By the midneurula, AmphiSox1/2/3 expression becomes limited to the dorsal part of the forming neural tube. These patterns resemble those of their vertebrate and Drosophila homologs. Taken together with the evolutionarily conserved expression of the dorsoventral patterning genes, BMP2/4 and chordin, in nonneural and neural ectoderm, respectively, of chordates and Drosophila, our results are consistent with the evolution of the chordate dorsal nerve cord and the insect ventral nerve cord from a longitudinal nerve cord in a common bilaterian ancestor. However, AmphiSox1/2/3 differs from its vertebrate homologs in not being expressed outside the CNS, suggesting that additional roles for this gene have evolved in connection with gene duplication in the vertebrate lineage. In contrast, expression in the midgut of AmphiNeurogenin together with the gene encoding the insulin-like peptide suggests that amphioxus may have homologs of vertebrate pancreatic islet cells, which express neurogenin3. In addition, AmphiNeurogenin, like its vertebrate and Drosophila homologs, is expressed in apparent precursors of epidermal chemosensory and

  11. Distinctive expression patterns of Hedgehog pathway genes in the Ciona intestinalis larva: implications for a role of Hedgehog signaling in postembryonic development and chordate evolution.

    Science.gov (United States)

    Islam, A F M Tariqul; Moly, Pricila Khan; Miyamoto, Yuki; Kusakabe, Takehiro G

    2010-02-01

    Members of the Hedgehog (Hh) family are soluble ligands that orchestrate a wide spectrum of developmental processes ranging from left-right axis determination of the embryo to tissue patterning and organogenesis. Tunicates, including ascidians, are the closest relatives of vertebrates, and elucidation of Hh signaling in ascidians should provide an important clue towards better understanding the role of this pathway in development. In previous studies, expression patterns of genes encoding Hh and its downstream factor Gli have been examined up to the tailbud stage in the ascidian embryo, but their expression in the larva has not been reported. Here we show the spatial expression patterns of hedgehog (Ci-hh1, Ci-hh2), patched (Ci-ptc), smoothened (Ci-smo), and Gli (Ci-Gli) orthologs in larvae of the ascidian Ciona intestinalis. The expression patterns of Ci-hh2 and Ci-Gli dramatically change during the period between the late tailbud embryo and the swimming larva. At the larval stage, expression of Ci-Gli was found in a central part of the endoderm and in the visceral ganglion, while Ci-hh2 was expressed in two discrete endodermal regions, anteriorly and posteriorly adjacent to the cells expressing Gli. The expression patterns of these genes suggest that the Hh ligand controls postembryonic development of the endoderm and the central nervous system. Expression of a gene encoding Hh in the anterior and/or pharyngeal endoderm is probably an ancient chordate character; diversification of regulation and targets of the Hh signaling in this region may have played a major role in the evolution of chordate body structures.

  12. Structural and functional insights into the ligand-binding domain of a nonduplicated retinoid X nuclear receptor from the invertebrate chordate amphioxus.

    Science.gov (United States)

    Tocchini-Valentini, Giuseppe D; Rochel, Natacha; Escriva, Hector; Germain, Pierre; Peluso-Iltis, Carole; Paris, Mathilde; Sanglier-Cianferani, Sarah; Van Dorsselaer, Alain; Moras, Dino; Laudet, Vincent

    2009-01-16

    Retinoid X nuclear receptors (RXRs), as well as their insect orthologue, ultraspiracle protein (USP), play an important role in the transcription regulation mediated by the nuclear receptors as the common partner of many other nuclear receptors. Phylogenetic and structural studies have shown that the several evolutionary shifts have modified the ligand binding ability of RXRs. To understand the vertebrate-specific character of RXRs, we have studied the RXR ligand-binding domain of the cephalochordate amphioxus (Branchiostoma floridae), an invertebrate chordate that predates the genome duplication that produced the three vertebrates RXRs (alpha, beta, and gamma). Here we report the crystal structure of a novel apotetramer conformation of the AmphiRXR ligand-binding domain, which shows some similarity with the structures of the arthropods RXR/USPs. AmphiRXR adopts an apo antagonist conformation with a peculiar conformation of helix H11 filling the binding pocket. In contrast to the arthropods RXR/USPs, which cannot be activated by any RXR ligands, our functional data show that AmphiRXR, like the vertebrates/mollusk RXRs, is able to bind and be activated by RXR ligands but less efficiently than vertebrate RXRs. Our data suggest that amphioxus RXR is, functionally, an intermediate between arthropods RXR/USPs and vertebrate RXRs. PMID:18986992

  13. The retinoic acid signaling pathway regulates anterior/posterior patterning in the nerve cord and pharynx of amphioxus, a chordate lacking neural crest

    Science.gov (United States)

    Escriva, Hector; Holland, Nicholas D.; Gronemeyer, Hinrich; Laudet, Vincent; Holland, Linda Z.

    2002-01-01

    Amphioxus, the closest living invertebrate relative of the vertebrates, has a notochord, segmental axial musculature, pharyngeal gill slits and dorsal hollow nerve cord, but lacks neural crest. In amphioxus, as in vertebrates, exogenous retinoic acid (RA) posteriorizes the embryo. The mouth and gill slits never form, AmphiPax1, which is normally downregulated where gill slits form, remains upregulated and AmphiHox1 expression shifts anteriorly in the nerve cord. To dissect the role of RA signaling in patterning chordate embryos, we have cloned the single retinoic acid receptor (AmphiRAR), retinoid X receptor (AmphiRXR) and an orphan receptor (AmphiTR2/4) from amphioxus. AmphiTR2/4 inhibits AmphiRAR-AmphiRXR-mediated transactivation in the presence of RA by competing for DR5 or IR7 retinoic acid response elements (RAREs). The 5' untranslated region of AmphiTR2/4 contains an IR7 element, suggesting possible auto- and RA-regulation. The patterns of AmphiTR2/4 and AmphiRAR expression during embryogenesis are largely complementary: AmphiTR2/4 is strongly expressed in the cerebral vesicle (homologous to the diencephalon plus anterior midbrain), while AmphiRAR expression is high in the equivalent of the hindbrain and spinal cord. Similarly, while AmphiTR2/4 is expressed most strongly in the anterior and posterior thirds of the endoderm, the highest AmphiRAR expression is in the middle third. Expression of AmphiRAR is upregulated by exogenous RA and completely downregulated by the RA antagonist BMS009. Moreover, BMS009 expands the pharynx posteriorly; the first three gill slit primordia are elongated and shifted posteriorly, but do not penetrate, and additional, non-penetrating gill slit primordia are induced. Thus, in an organism without neural crest, initiation and penetration of gill slits appear to be separate events mediated by distinct levels of RA signaling in the pharyngeal endoderm. Although these compounds have little effect on levels of AmphiTR2/4 expression, RA

  14. The evolutionary differentiation of two histone H2A.Z variants in chordates (H2A.Z-1 and H2A.Z-2 is mediated by a stepwise mutation process that affects three amino acid residues

    Directory of Open Access Journals (Sweden)

    Ausió Juan

    2009-02-01

    Full Text Available Abstract Background The histone H2A family encompasses the greatest number of core histone variants of which the replacement variant H2A.Z is currently one of the most heavily studied. No clear mechanism for the functional variability that H2A.Z imparts to chromatin has yet been proposed. While most of the past studies have referred to H2A.Z generically as a single protein, in vertebrates it is a mixture of two protein forms H2A.Z-1 (previously H2A.Z and H2A.Z-2 (previously H2A.F/Z or H2A.V that differ by three amino acids. Results We have performed an extensive study on the long-term evolution of H2A.Z across metazoans with special emphasis on the possible selective mechanisms responsible for the differentiation between H2A.Z-1 and H2A.Z-2. Our results reveal a common origin of both forms early in chordate evolution. The evolutionary process responsible for the differentiation involves refined stepwise mutation change within the codons of the three differential residues. This eventually led to differences in the intensity of the selective constraints acting upon the different H2A.Z forms in vertebrates. Conclusion The results presented in this work definitively reveal that the existence of H2A.Z-1 and H2A.Z-2 is not a whim of random genetic drift. Our analyses demonstrate that H2A.Z-2 is not only subject to a strong purifying selection but it is significantly more evolutionarily constrained than H2A.Z-1. Whether or not the evolutionary drift between H2A.Z-1 and H2A.Z-2 has resulted in a functional diversification of these proteins awaits further research. Nevertheless, the present work suggests that in the process of their differently constrained evolutionary pathways, these two forms may have acquired new or complementary functions.

  15. Identification of a Colonial Chordate Histocompatibility Gene

    Science.gov (United States)

    Voskoboynik, Ayelet; Newman, Aaron M.; Corey, Daniel M.; Sahoo, Debashis; Pushkarev, Dmitry; Neff, Norma F.; Passarelli, Benedetto; Koh, Winston; Ishizuka, Katherine J.; Palmeri, Karla J.; Dimov, Ivan K.; Keasar, Chen; Fan, H. Christina; Mantalas, Gary L.; Sinha, Rahul; Penland, Lolita; Quake, Stephen R.; Weissman, Irving L.

    2013-01-01

    Histocompatibility is the basis by which multicellular organisms of the same species distinguish self from non-self. Relatively little is known about the mechanisms underlying histocompatibility reactions in lower organisms. Botryllus schlosseri is a colonial urochordate, a sister group of vertebrates, that exhibits a genetically determined natural transplantation reaction, whereby self-recognition between colonies leads to formation of parabionts with a common vasculature, whereas rejection occurs between incompatible colonies. Using genetically defined lines, whole-transcriptome sequencing, and genomics, we identified a single gene that encodes self/non-self and determines “graft” outcomes in this organism. This gene is significantly upregulated in colonies poised to undergo fusion or rejection, is highly expressed in the vasculature, and is functionally linked to histocompatibility outcomes. These findings establish a platform for advancing the science of allorecognition. PMID:23888037

  16. Evolution of a core gene network for skeletogenesis in chordates

    OpenAIRE

    Jochen Hecht; Sigmar Stricker; Ulrike Wiecha; Asita Stiege; Georgia Panopoulou; Lars Podsiadlowski; Poustka, Albert J.; Christoph Dieterich; Siegfried Ehrich; Julia Suvorova; Stefan Mundlos; Volkhard Seitz

    2008-01-01

    The skeleton is one of the most important features for the reconstruction of vertebrate phylogeny but few data are available to understand its molecular origin. In mammals the Runt genes are central regulators of skeletogenesis. Runx2 was shown to be essential for osteoblast differentiation, tooth development, and bone formation. Both Runx2 and Runx3 are essential for chondrocyte maturation. Furthermore, Runx2 directly regulates Indian hedgehog expression, a master coordinator of skeletal dev...

  17. Structure and anticoagulant properties of sulfated glycosaminoglycans from primitive Chordates

    Directory of Open Access Journals (Sweden)

    PAVÃO MAURO S. G.

    2002-01-01

    Full Text Available Dermatan sulfates and heparin, similar to the mammalian glycosaminoglycans, but with differences in the degree and position of sulfation were previously isolated from the body of the ascidian Styela plicata and Ascidia nigra. These differences produce profound effects on their anticoagulant properties. S. plicata dermatan sulfate composed by 2-O-sulfatedalpha-L-iduronic acid and 4-O-sulfated N-acetyl-beta-D-galactosamine residues is a potent anticoagulant due to a high heparin cofactor II activity. Surprisingly, it has a lower potency to prevent thrombus formation on an experimental model and a lower bleeding effect in rats than the mammalian dermatan sulfate. In contrast, A. nigra dermatan sulfate, also enriched in 2-O-sulfated alpha-L-iduronic acid, but in this case sulfated at O-6 of the N-acetyl-beta-D-galactosamine units, has no in vitro or in vivo anticoagulant activity, does not prevent thrombus formation but shows a bleeding effect similar to the mammalian glycosaminoglycan. Ascidian heparin, composed by 2-O-sulfated alpha-L-iduronic acid, N- and 6-O-sulfated glucosamine (75% and alpha-L-iduronic acid, N- and 6-O-sulfated glucosamine (25% disaccharide units has an anticoagulant activity 10 times lower than the mammalian heparin, is about 20 times less potent in the inhibition of thrombin by antithrombin, but has the same heparin cofactor II activity as mammalian heparin.

  18. Marine radionuclide transfer factors in chordates and a phylogenetic hypothesis

    International Nuclear Information System (INIS)

    Previous radiotracer experiments that compared multi-elemental whole organism: water transfer factors among chondrichthyan and teleost fishes, including an ICRP reference flatfish Psetta maxima, demonstrated distinctive contrasts in their bioaccumulation characteristics, with generally elevated bioaccumulation in chondrichthyans. These results supported a hypothesis that phylogenetic divergence may influence marine radionuclide transfer factors. This notion has been further evaluated in an amphioxus species Branchiostoma lanceolatum, sub-phylum Cephalochordata. This taxon diverged about 800 MYBP from a common ancestor of the teleosts and the chondrichthyans, which in turn diverged from each other around 500 MYBP. Our experimental results indicate that amphioxus is indeed more divergent in its multi-elemental bioaccumulation patterns from teleosts and chondrichthyans than they are from each other, consistent with our hypothesis. The experimental comparisons with the ICRP reference flatfish P. maxima also revealed an unexpectedly enhanced capacity in amphioxus to accumulate all eight tested trace elements from seawater, and for some by more than two orders of magnitude. These results have practical applications for the strategic selection of marine biota for further radioecological investigations to better guarantee the radiological protection of marine biodiversity. Such seemingly anomalous results for understudied biota like amphioxus and chondrichthyans suggest that more effort in marine radioecology be directed to assessing the bioaccumulatory capacities of other phylogenetic groups that have received less attention so far, particularly those that are phylogenetically more remote from commonly investigated taxa and those nominated as ICRP marine reference organisms

  19. Amphioxus: a peaceful anchovy fillet to illuminate Chordate Evolution (I

    Directory of Open Access Journals (Sweden)

    2006-04-01

    Full Text Available The cephalochordate amphioxus occupies a central place in evolutionary thoughts to the origin of Vertebrates. With a prototypical vertebrate-like body plan and a preduplicative genome, the friendly lancelet seems to be in morphological and genetic motionless since its separation from the major branch of evolution that eventually ended up in our corner in the Animal Kingdom. This makes it an ideal model system with which, with the current development of genomic and experimental tools, an Evo-Devo approach to the understanding of the origin of vertebrates looks proper, reliable, and excitingly promising.

  20. Arsenic (+3 oxidation state) methyltransferase and the methylation of arsenicals in the invertebrate chordate Ciona intestinalis

    Science.gov (United States)

    Biotransformation of inorganic arsenic (iAs) involves methylation catalyzed by arsenic (+3 oxidation state) methyltransferase (As3mt), yielding mono- , di- , and trimethylated arsenicals. To investigate the evolution of molecular mechanisms that mediate arsenic biotransformation,...

  1. Expansion of the Hox gene family and the evolution of chordates.

    OpenAIRE

    Pendleton, J W; Nagai, B K; Murtha, M T; Ruddle, F H

    1993-01-01

    Homeobox genes encode DNA-binding transcription regulators that participate in the formation of embryonic pattern or contribute to cell-type specificity during metazoan development. Homeobox genes that regulate axial patterning and segmental identity (Hox/HOM genes) share a conserved clustered genomic organization. Mammals have four clusters that have likely arisen from the duplication of a single ancestral cluster. The number of Hox-type genes in other deuterostomes was estimated by using a ...

  2. Wnt affects symmetry and morphogenesis during post-embryonic development in colonial chordates

    OpenAIRE

    Di Maio, Alessandro; Setar, Leah; Tiozzo, Stefano; De Tomaso, Anthony W

    2015-01-01

    Background Wnt signaling is one of the earliest and most highly conserved regulatory pathways for the establishment of the body axes during regeneration and early development. In regeneration, body axes determination occurs independently of tissue rearrangement and early developmental cues. Modulation of the Wnt signaling in either process has shown to result in unusual body axis phenotypes. Botryllus schlosseri is a colonial ascidian that can regenerate its entire body through asexual buddin...

  3. Evolutionary Origin of GnIH and NPFF in Chordates: Insights from Novel Amphioxus RFamide Peptides

    OpenAIRE

    Tomohiro Osugi; Tomoki Okamura; You Lee Son; Makoto Ohkubo; Takayoshi Ubuka; Yasuhisa Henmi; Kazuyoshi Tsutsui

    2014-01-01

    Gonadotropin-inhibitory hormone (GnIH) is a newly identified hypothalamic neuropeptide that inhibits pituitary hormone secretion in vertebrates. GnIH has an LPXRFamide (X = L or Q) motif at the C-terminal in representative species of gnathostomes. On the other hand, neuropeptide FF (NPFF), a neuropeptide characterized as a pain-modulatory neuropeptide, in vertebrates has a PQRFamide motif similar to the C-terminal of GnIH, suggesting that GnIH and NPFF have diverged from a common ancestor. Be...

  4. Was the tail bud the ancestral centre where the fin developmental program evolved in chordates?

    OpenAIRE

    Cotoras, D.D.; M.L. Allende

    2015-01-01

    The structural origin of the vertebrates’ paired limbs is still an unsolved problem. Historically, two hypotheses have been raised to explain the origin of vertebrate limbs: the Archipterygium Hypothesis and the Fin Fold Hypothesis. Current knowledge provides support for both ideas. In the recent years, it has been also suggested that (1) all appendages correspond to body axis duplications and (2) they are originated by the ventralization of the developmental program present in the median fin...

  5. Evolutionary functional elaboration of the Elovl2/5 gene family in chordates

    OpenAIRE

    Óscar Monroig; Mónica Lopes-Marques; Navarro, Juan C.; Francisco Hontoria; Raquel Ruivo; Miguel M. Santos; Byrappa Venkatesh; Tocher, Douglas R.; L Filipe C Castro

    2016-01-01

    The biosynthesis of long-chain polyunsaturated fatty acids (LC-PUFA) provides an intriguing example on how multi-enzymatic cascades evolve. Essential LC-PUFA, such as arachidonic, eicosapentaenoic, and docosahexaenoic acids (DHA), can be acquired from the diet but are also endogenously retailored from C18 precursors through consecutive elongations and desaturations catalyzed, respectively, by fatty acyl elongase and desaturase enzymes. The molecular wiring of this enzymatic pathway defines th...

  6. Comparative genomics of Hedgehog loci in chordates and the origin of Shh regulatory novelties

    OpenAIRE

    Manuel Irimia; Jose L. Royo; Demian Burguera; Ignacio Maeso; Gómez-Skarmeta, José L.; Jordi Garcia-Fernandez

    2012-01-01

    The origin and evolution of the complex regulatory landscapes of some vertebrate developmental genes, often spanning hundreds of Kbp and including neighboring genes, remain poorly understood. The Sonic Hedgehog (Shh) genomic regulatory block (GRB) is one of the best functionally characterized examples, with several discrete enhancers reported within its introns, vast upstream gene-free region and neighboring genes (Lmbr1 and Rnf32). To investigate the origin and evolution of this GRB, we sequ...

  7. Evolutionary dynamics of olfactory receptor genes in chordates: interaction between environments and genomic contents

    OpenAIRE

    Niimura Yoshihito

    2009-01-01

    Abstract Olfaction is essential for the survival of animals. Versatile odour molecules in the environment are received by olfactory receptors (ORs), which form the largest multigene family in vertebrates. Identification of the entire repertories of OR genes using bioinformatics methods from the whole-genome sequences of diverse organisms revealed that the numbers of OR genes vary enormously, ranging from ~1,200 in rats and ~400 in humans to ~150 in zebrafish and ~15 in pufferfish. Most specie...

  8. A Conserved Non-Reproductive GnRH System in Chordates

    OpenAIRE

    Kusakabe, Takehiro G.; Tsubasa Sakai; Masato Aoyama; Yuka Kitajima; Yuki Miyamoto; Toru Takigawa; Yutaka Daido; Kentaro Fujiwara; Yasuko Terashima; Yoko Sugiuchi; Giorgio Matassi; Hitoshi Yagisawa; Min Kyun Park; Honoo Satake; Motoyuki Tsuda

    2012-01-01

    Gonadotropin-releasing hormone (GnRH) is a neuroendocrine peptide that plays a central role in the vertebrate hypothalamo-pituitary axis. The roles of GnRH in the control of vertebrate reproductive functions have been established, while its non-reproductive function has been suggested but less well understood. Here we show that the tunicate Ciona intestinalis has in its non-reproductive larval stage a prominent GnRH system spanning the entire length of the nervous system. Tunicate GnRH recept...

  9. Metaphylogeny of 82 gene families sheds a new light on chordate evolution

    OpenAIRE

    Vienne, Alexandre; Pontarotti, Pierre

    2006-01-01

    Achieving a better comprehension of the evolution of species has always been an important matter for evolutionary biologists. The deuterostome phylogeny has been described for many years, and three phyla are distinguishable: Echinodermata (including sea stars, sea urchins, etc…), Hemichordata (including acorn worms and pterobranchs), and Chordata (including urochordates, cephalochordates and extant vertebrates). Inside the Chordata phylum, the position of vertebrate species is quite unanimous...

  10. The evolution and regulation of the mucosal immune complexity in the basal chordate amphioxus.

    Science.gov (United States)

    Huang, Shengfeng; Wang, Xin; Yan, Qingyu; Guo, Lei; Yuan, Shaochun; Huang, Guangrui; Huang, Huiqing; Li, Jun; Dong, Meiling; Chen, Shangwu; Xu, Anlong

    2011-02-15

    Both amphioxus and the sea urchin encode a complex innate immune gene repertoire in their genomes, but the composition and mechanisms of their innate immune systems, as well as the fundamental differences between two systems, remain largely unexplored. In this study, we dissect the mucosal immune complexity of amphioxus into different evolutionary-functional modes and regulatory patterns by integrating information from phylogenetic inferences, genome-wide digital expression profiles, time course expression dynamics, and functional analyses. With these rich data, we reconstruct several major immune subsystems in amphioxus and analyze their regulation during mucosal infection. These include the TNF/IL-1R network, TLR and NLR networks, complement system, apoptosis network, oxidative pathways, and other effector genes (e.g., peptidoglycan recognition proteins, Gram-negative binding proteins, and chitin-binding proteins). We show that beneath the superficial similarity to that of the sea urchin, the amphioxus innate system, despite preserving critical invertebrate components, is more similar to that of the vertebrates in terms of composition, expression regulation, and functional strategies. For example, major effectors in amphioxus gut mucous tissue are the well-developed complement and oxidative-burst systems, and the signaling network in amphioxus seems to emphasize signal transduction/modulation more than initiation. In conclusion, we suggest that the innate immune systems of amphioxus and the sea urchin are strategically different, possibly representing two successful cases among many expanded immune systems that arose at the age of the Cambrian explosion. We further suggest that the vertebrate innate immune system should be derived from one of these expanded systems, most likely from the same one that was shared by amphioxus. PMID:21248255

  11. A glycine receptor is involved in the organization of swimming movements in an invertebrate chordate

    OpenAIRE

    Okamura Yasushi; Nishino Atsuo; Piscopo Stefania; Brown Euan R

    2010-01-01

    Abstract Background Rhythmic motor patterns for locomotion in vertebrates are generated in spinal cord neural networks known as spinal Central Pattern Generators (CPGs). A key element in pattern generation is the role of glycinergic synaptic transmission by interneurons that cross the cord midline and inhibit contralaterally-located excitatory neurons. The glycinergic inhibitory drive permits alternating and precisely timed motor output during locomotion such as walking or swimming. To unders...

  12. An amphioxus Gli gene reveals conservation of midline patterning and the evolution of hedgehog signalling diversity in chordates.

    Directory of Open Access Journals (Sweden)

    Sebastian M Shimeld

    Full Text Available BACKGROUND: Hedgehog signalling, interpreted in receiving cells by Gli transcription factors, plays a central role in the development of vertebrate and Drosophila embryos. Many aspects of the signalling pathway are conserved between these lineages, however vertebrates have diverged in at least one key aspect: they have evolved multiple Gli genes encoding functionally-distinct proteins, increasing the complexity of the hedgehog-dependent transcriptional response. Amphioxus is one of the closest living relatives of the vertebrates, having split from the vertebrate lineage prior to the widespread gene duplication prominent in early vertebrate evolution. PRINCIPAL FINDINGS: We show that amphioxus has a single Gli gene, which is deployed in tissues adjacent to sources of hedgehog signalling derived from the midline and anterior endoderm. This shows the duplication and divergence of the Gli gene family, and hence the origin of vertebrate Gli functional diversity, was specific to the vertebrate lineage. However we also show that the single amphioxus Gli gene produces two distinct transcripts encoding different proteins. We utilise three tests of Gli function to examine the transcription regulatory capacities of these different proteins, demonstrating one has activating activity similar to Gli2, while the other acts as a weak repressor, similar to Gli3. CONCLUSIONS: These data show that vertebrates and amphioxus have evolved functionally-similar repertoires of Gli proteins using parallel molecular routes; vertebrates via gene duplication and divergence, and amphioxus via alternate splicing of a single gene. Our results demonstrate that similar functional complexity of intercellular signalling can be achieved via different evolutionary pathways.

  13. TCF/Lef regulates the Gsx ParaHox gene in central nervous system development in chordates

    OpenAIRE

    Garstang, Myles Grant; Osborne, Peter; Ferrier, David Ellard Keith

    2016-01-01

    Background The ParaHox genes play an integral role in the anterior-posterior (A-P) patterning of the nervous system and gut of most animals. The ParaHox cluster is an ideal system in which to study the evolution and regulation of developmental genes and gene clusters, as it displays similar regulatory phenomena to its sister cluster, the Hox cluster, but offers a much simpler system with only three genes. Results Using Ciona intestinalis transgenics, we isolated a regulatory element upstream ...

  14. Conserved developmental expression of Fezf in chordates and Drosophila and the origin of the Zona Limitans Intrathalamica (ZLI) brain organizer

    OpenAIRE

    Irimia Manuel; Piñeiro Cristina; Maeso Ignacio; Gómez-Skarmeta José; Casares Fernando; Garcia-Fernàndez Jordi

    2010-01-01

    Abstract Background The zona limitans intrathalamica (ZLI) and the isthmus organizer (IsO) are two major secondary organizers of vertebrate brain development. These organizers are located at the interface of the expression domains of key patterning genes (Fezf-Irx and Otx-Gbx, respectively). To gain insights into the evolutionary origin of the ZLI, we studied Fezf in bilaterians. Results In this paper, we identified a conserved sequence motif (Fezf box) in all bilaterians. We report the expre...

  15. Sequence analysis and phylogenetic study of some toxin proteins of snakes and related non-toxin proteins of chordates

    OpenAIRE

    Panda, Subhamay; Chandra, Goutam

    2013-01-01

    Snakes are equipped with their venomic armory to tackle different prey and predators in adverse natural world. The venomic composition of snakes is a mix of biologically active proteins and polypeptides. Among different components snake venom cytotoxins and short neurotoxin are non-enzymatic polypeptide candidates with in the venom. These two components structurally resembled to three-finger protein superfamily specific scaffold. Different non-toxin family members of three-finger protein supe...

  16. Conserved developmental expression of Fezf in chordates and Drosophila and the origin of the Zona Limitans Intrathalamica (ZLI brain organizer

    Directory of Open Access Journals (Sweden)

    Irimia Manuel

    2010-09-01

    Full Text Available Abstract Background The zona limitans intrathalamica (ZLI and the isthmus organizer (IsO are two major secondary organizers of vertebrate brain development. These organizers are located at the interface of the expression domains of key patterning genes (Fezf-Irx and Otx-Gbx, respectively. To gain insights into the evolutionary origin of the ZLI, we studied Fezf in bilaterians. Results In this paper, we identified a conserved sequence motif (Fezf box in all bilaterians. We report the expression pattern of Fezf in amphioxus and Drosophila and compare it with those of Gbx, Otx and Irx. We found that the relative expression patterns of these genes in vertebrates are fully conserved in amphioxus and flies, indicating that the genetic subdivisions defining the location of both secondary organizers in early vertebrate brain development were probably present in the last common ancestor of extant bilaterians. However, in contrast to vertebrates, we found that Irx-defective flies do not show an affected Fezf expression pattern. Conclusions The absence of expression of the corresponding morphogens from cells at these conserved genetic boundaries in invertebrates suggests that the organizing properties might have evolved specifically in the vertebrate lineage by the recruitment of key morphogens to these conserved genetic locations.

  17. Physicochemical characterization and functional analysis of some snake venom toxin proteins and related non-toxin proteins of other chordates

    OpenAIRE

    Panda, Subhamay; Chandra, Goutam

    2012-01-01

    Snake venom contains a diverse array of proteins and polypeptides. Cytotoxins and short neurotoxins are non-enzymatic polypeptide components of snake venom. The three-dimensional structure of cytotoxin and short neurotoxin resembles a three finger appearance of three-finger protein super family. Different family members of three-finger protein super family are employed in diverse biological functions. In this work we analyzed the cytotoxin, short neurotoxin and related non-toxin proteins of o...

  18. Ion channel clustering at the axon initial segment and node of Ranvier evolved sequentially in early chordates.

    OpenAIRE

    Hill, Alexis S.; Atsuo Nishino; Koichi Nakajo; Giuxin Zhang; Fineman, Jaime R.; Selzer, Michael E.; Yasushi Okamura; Cooper, Edward C.

    2008-01-01

    In many mammalian neurons, dense clusters of ion channels at the axonal initial segment and nodes of Ranvier underlie action potential generation and rapid conduction. Axonal clustering of mammalian voltage-gated sodium and KCNQ (Kv7) potassium channels is based on linkage to the actin–spectrin cytoskeleton, which is mediated by the adaptor protein ankyrin-G. We identified key steps in the evolution of this axonal channel clustering. The anchor motif for sodium channel clustering evolved earl...

  19. Differential regulation of ParaHox genes by retinoic acid in the invertebrate chordate amphioxus (Branchiostoma floridae).

    Science.gov (United States)

    Osborne, Peter W; Benoit, Gérard; Laudet, Vincent; Schubert, Michael; Ferrier, David E K

    2009-03-01

    The ParaHox cluster is the evolutionary sister to the Hox cluster. Like the Hox cluster, the ParaHox cluster displays spatial and temporal regulation of the component genes along the anterior/posterior axis in a manner that correlates with the gene positions within the cluster (a feature called collinearity). The ParaHox cluster is however a simpler system to study because it is composed of only three genes. We provide a detailed analysis of the amphioxus ParaHox cluster and, for the first time in a single species, examine the regulation of the cluster in response to a single developmental signalling molecule, retinoic acid (RA). Embryos treated with either RA or RA antagonist display altered ParaHox gene expression: AmphiGsx expression shifts in the neural tube, and the endodermal boundary between AmphiXlox and AmphiCdx shifts its anterior/posterior position. We identified several putative retinoic acid response elements and in vitro assays suggest some may participate in RA regulation of the ParaHox genes. By comparison to vertebrate ParaHox gene regulation we explore the evolutionary implications. This work highlights how insights into the regulation and evolution of more complex vertebrate arrangements can be obtained through studies of a simpler, unduplicated amphioxus gene cluster. PMID:19103191

  20. Genomic organization and gene expression of the multiple globins in Atlantic cod: conservation of globin-flanking genes in chordates infers the origin of the vertebrate globin clusters

    OpenAIRE

    Jakobsen Kjetill S; Wilson Robert C; Nederbragt Alexander J; Wetten Ola F; Edvardsen Rolf B; Andersen Øivind

    2010-01-01

    Abstract Background The vertebrate globin genes encoding the α- and β-subunits of the tetrameric hemoglobins are clustered at two unlinked loci. The highly conserved linear order of the genes flanking the hemoglobins provides a strong anchor for inferring common ancestry of the globin clusters. In fish, the number of α-β-linked globin genes varies considerably between different sublineages and seems to be related to prevailing physico-chemical conditions. Draft sequences of the Atlantic cod g...

  1. Structural and functional insights into the ligand-binding domain of a nonduplicated retinoid X nuclear receptor from the invertebrate chordate amphioxus

    OpenAIRE

    Tocchini-Valentini, Guiseppe D.; Rochel, Natacha; Escriva, Hector; Germain, Pierre; Peluso-Iltis, Carole; Paris, Mathilde; Sanglier-Cianferani, Sarah; Van Dorsselaer, Alain; Moras, Dino; Laudet, Vincent

    2009-01-01

    Retinoid X nuclear receptors (RXRs), as well as their insect orthologue, ultraspiracle protein (USP), play an important role in the transcription regulation mediated by the nuclear receptors as the common partner of many other nuclear receptors. Phylogenetic and structural studies have shown that the several evolutionary shifts have modified the ligand binding ability of RXRs. To understand the vertebrate-specific character of RXRs, we have studied the RXR ligand-binding domain of the cephalo...

  2. The Clinicaling of Echocardiographic Diagnosis of Anylisis in Left Ventricle False Chordate Tendinae%左心室假腱索的超声诊断分析及临床意义

    Institute of Scientific and Technical Information of China (English)

    张锦怡

    2010-01-01

    目的 探讨超声心动图对左室假腱索的诊断价值.方法 对106例患者,用2.5~3.5MHz超声探头检查.结果 本组106例患者中,共检出左宣假腱索患者68例,其中1条50例,2条12例,3条4例.结论 左室假腱索的超声检出率可能与操作技术,观察的仔细程度,仪器的分辨率有关,左室假腱索临床上可能与健康人的心脏杂音及引起室性期前收缩有关.

  3. The evolutionary differentiation of two histone H2A.Z variants in chordates (H2A.Z-1 and H2A.Z-2) is mediated by a stepwise mutation process that affects three amino acid residues

    OpenAIRE

    Ausió Juan; Ishibashi Toyotaka; Dryhurst Deanna; González-Romero Rodrigo; Eirín-López José M

    2009-01-01

    Abstract Background The histone H2A family encompasses the greatest number of core histone variants of which the replacement variant H2A.Z is currently one of the most heavily studied. No clear mechanism for the functional variability that H2A.Z imparts to chromatin has yet been proposed. While most of the past studies have referred to H2A.Z generically as a single protein, in vertebrates it is a mixture of two protein forms H2A.Z-1 (previously H2A.Z) and H2A.Z-2 (previously H2A.F/Z or H2A.V)...

  4. Isolation of key retinoid signalling and metabolic modules in invertebrates

    OpenAIRE

    Ana André; L. Filipe Castro

    2014-01-01

    Retinoids are a class of molecules related to vitamin A (Retinol) that are required for regulation of critical chordate ndocrine-mediated process, such as embryonic development, reproduction, and vision. To maintain such physiological process, chordates have a complex mechanism to regulate the spatial and temporal distribution of retinoids that includes metabolic and signalling modules. Initially, retinoid modules were seen as a chordate novelty. However, emerging biochemical and genomic evid...

  5. Ciona intestinalis as an emerging model organism: its regeneration under controlled conditions and methodology for egg dechorionation*

    OpenAIRE

    Liu, Li-Ping; Xiang, Jian-hai; Dong, Bo; Natarajan, Pavanasam; Yu, Kui-jie; Cai, Nan-er

    2006-01-01

    The ascidian Ciona intestinalis is a model organism of developmental and evolutionary biology and may provide crucial clues concerning two fundamental matters, namely, how chordates originated from the putative deuterostome ancestor and how advanced chordates originated from the simplest chordates. In this paper, a whole-life-span culture of C. intestinalis was conducted. Fed with the diet combination of dry Spirulina, egg yolk, Dicrateria sp., edible yeast and weaning diet for shrimp, C. int...

  6. Embryology of a planktonic tunicate reveals traces of sessility

    OpenAIRE

    Stach, Thomas; Winter, Jonas; Bouquet, Jean-Marie; Chourrout, Daniel; Schnabel, Ralf

    2008-01-01

    A key problem in understanding deuterostome evolution has been the origin of the chordate body plan. A biphasic life cycle with a sessile adult and a free-swimming larva is traditionally considered ancestral in chordates with subsequent neotenic loss of the sessile adult stage. Molecular phylogenies challenged this view, suggesting that the primitive life cycle in chordates was entirely free-living as in modern day larvaceans. Here, we report the precise cell lineage and fate map in the norma...

  7. The Autopsy of Squirrel Doe

    Science.gov (United States)

    Dick, Timothy T.; Watson, Jason

    2005-01-01

    Introductory biology laboratory experiences frequently rely on preserved chordates for anatomical study. Unfortunately, these preserved organisms rarely reflect the appearance of a living creature. Since community colleges are generally prohibited the use of live chordates, this paper describes the autopsy of a "road kill" squirrel to facilitate…

  8. Isolation of key retinoid signalling and metabolic modules in invertebrates

    Directory of Open Access Journals (Sweden)

    Ana André

    2014-05-01

    Full Text Available Retinoids are a class of molecules related to vitamin A (Retinol that are required for regulation of critical chordate ndocrine-mediated process, such as embryonic development, reproduction, and vision. To maintain such physiological process, chordates have a complex mechanism to regulate the spatial and temporal distribution of retinoids that includes metabolic and signalling modules. Initially, retinoid modules were seen as a chordate novelty. However, emerging biochemical and genomic evidences have challenged this view, clearly pointing to a more basal ancestry than previously thought. However, for the majority of non-chordate invertebrate lineages a clearly characterization of the main enzymatic/molecular players is still missing. Despite limited, the available evidence supports the presence of biologically active retinoid pathways in invertebrates. In order to enhance our insights on retinoid biology, evolution, and its putative disruption by environmental chemicals, the isolation and functional characterization of key retinoid metabolic players in marine invertebrates has been carried out.

  9. Molecular Phylogeny of the Animal Kingdom.

    Science.gov (United States)

    Field, Katharine G.; And Others

    1988-01-01

    A rapid sequencing method for ribosomal RNA was applied to the resolution of evolutionary relationships among Metazoa. Describes the four groups (chordates, echinoderms, arthropods, and eucoelomate protostomes) that radiated from the coelomates. (TW)

  10. Germ-line transgenesis of the Tc1/mariner superfamily transposon Minos in Ciona intestinalis

    OpenAIRE

    Sasakura, Yasunori; Awazu, Satoko; Chiba, Shota; Satoh, Nori

    2003-01-01

    The tadpole larva of the basal chordate Ciona intestinalis has the most simplified, basic body-plan of chordates. Because it has a compact genome with a complete draft sequence, a large quantity of EST/cDNA information, and a short generation time, Ciona is a suitable model for future genetics. We establish here a transgenic technique in Ciona that uses the Tc1/mariner superfamily transposon Minos. Minos was integrated efficiently into the genome of germ cells and transmitted stably to ...

  11. Coelomata and Not Ecdysozoa: Evidence From Genome-Wide Phylogenetic Analysis

    OpenAIRE

    Wolf, Yuri I.; Rogozin, Igor B.; Koonin, Eugene V.

    2004-01-01

    Relative positions of nematodes, arthropods, and chordates in animal phylogeny remain uncertain. The traditional tree topology joins arthropods with chordates in a coelomate clade, whereas nematodes, which lack a coelome, occupy a basal position. However, the current leading hypothesis, based on phylogenetic trees for 18S ribosomal RNA and several proteins, joins nematodes with arthropods in a clade of molting animals, Ecdysozoa. We performed a phylogenetic analysis of over 500 sets of orthol...

  12. Phylogenomic Analyses of Echinodermata Support the Sister Groups of Asterozoa and Echinozoa

    OpenAIRE

    Adrian Reich; Casey Dunn; Koji Akasaka; Gary Wessel

    2015-01-01

    Echinoderms (sea urchins, sea stars, brittle stars, sea lilies and sea cucumbers) are a group of diverse organisms, second in number within deuterostome species to only the chordates. Echinoderms serve as excellent model systems for developmental biology due to their diverse developmental mechanisms, tractable laboratory use, and close phylogenetic distance to chordates. In addition, echinoderms are very well represented in the fossil record, including some larval features, making echinoderms...

  13. Evolution of bilaterian central nervous systems: a single origin?

    OpenAIRE

    Carvalho, Joao E.; Escriva, Hector; Laudet, Vincent; Schubert, Michael; Shimeld, Sebastian M; Yu, Jr-Kai

    2013-01-01

    Abstract The question of whether the ancestral bilaterian had a central nervous system (CNS) or a diffuse ectodermal nervous system has been hotly debated. Considerable evidence supports the theory that a CNS evolved just once. However, an alternative view proposes that the chordate CNS evolved from the ectodermal nerve net of a hemichordate-like ancestral deuterostome, implying independent evolution of the CNS in chordates and protostomes. To specify morphological divisions along the ...

  14. New genes in the evolution of the neural crest differentiation program

    OpenAIRE

    Martínez-Morales, Juan Ramón; Henrich, Thorsten; Ramialison, Mirana; Wittbrodt, Joachim

    2007-01-01

    BACKGROUND: Development of the vertebrate head depends on the multipotency and migratory behavior of neural crest derivatives. This cell population is considered a vertebrate innovation and, accordingly, chordate ancestors lacked neural crest counterparts. The identification of neural crest specification genes expressed in the neural plate of basal chordates, in addition to the discovery of pigmented migratory cells in ascidians, has challenged this hypothesis. These new findings revive th...

  15. Evolutionary mitogenomics of Chordata: the strange case of ascidians and vertebrates

    OpenAIRE

    C Gissi; F. Griggio; F Iannelli

    2009-01-01

    The availability of almost one thousand complete mitochondrial genome (mtDNA) sequences of chordates provides an almost unique opportunity to analyse the evolution of this genome in the phylum Chordata, and to identify possible divergent evolutionary trends followed by the three chordate subphyla: Vertebrata, Cephalochordata and Tunicata.Here, we review some genome-level features of mtDNA, such as genetic code, gene content, genome architecture and gene strand asymmetry, mostly focusing on di...

  16. Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus

    OpenAIRE

    Cattaneo Elena; Pesole Graziano; Gissi Carmela; Tartari Marzia

    2006-01-01

    Abstract Background To gain insight into the evolutionary features of the huntingtin (htt) gene in Chordata, we have sequenced and characterized the full-length htt mRNA in the ascidian Ciona intestinalis, a basal chordate emerging as new invertebrate model organism. Moreover, taking advantage of the availability of genomic and EST sequences, the htt gene structure of a number of chordate species, including the cogeneric ascidian Ciona savignyi, and the vertebrates Xenopus and Gallus was reco...

  17. An Early Cambrian tunicate from China.

    Science.gov (United States)

    Shu, D G; Chen, L; Han, J; Zhang, X L

    2001-05-24

    Like the Burgess Shales of Canada, the Chengjiang Lagerstätte from the Lower Cambrian of China is renowned for the detailed preservation as fossils of delicate, soft-bodied creatures, providing an insight into the Cambrian explosion. The fossils of possible hemichordate chordates and vertebrates have attracted particular attention. Tunicates, or urochordates, comprise the most basal chordate clade, and details of their evolution could be important in understanding the sequence of character acquisition that led to the emergence of chordates and vertebrates. However, definitive fossils of tunicates from the Cambrian are scarce or debatable. Here we report a probable tunicate Cheungkongella ancestralis from the Chengjiang fauna. It resembles the extant ascidian tunicate genus Styela whose morphology could be useful in understanding the origin of the vertebrates. PMID:11373678

  18. Identification of differentially expressed genes from multipotent epithelia at the onset of an asexual development

    Science.gov (United States)

    Ricci, Lorenzo; Chaurasia, Ankita; Lapébie, Pascal; Dru, Philippe; Helm, Rebecca R.; Copley, Richard R.; Tiozzo, Stefano

    2016-01-01

    Organisms that have evolved alternative modes of reproduction, complementary to the sexual mode, are found across metazoans. The chordate Botryllus schlosseri is an emerging model for asexual development studies. Botryllus can rebuild its entire body from a portion of adult epithelia in a continuous and stereotyped process called blastogenesis. Anatomy and ontogenies of blastogenesis are well described, however molecular signatures triggering this developmental process are entirely unknown. We isolated tissues at the site of blastogenesis onset and from the same epithelia where this process is never triggered. We linearly amplified an ultra-low amount of mRNA (chordate. PMID:27264734

  19. Dispersal of NK homeobox gene clusters in amphioxus and humans

    OpenAIRE

    Luke, Graham N.; L Filipe C Castro; McLay, Kirsten; Bird, Christine; Coulson, Alan; Holland, Peter W. H.

    2003-01-01

    The Drosophila melanogaster genome has six physically clustered NK-related homeobox genes in just 180 kb. Here we show that the NK homeobox gene cluster was an ancient feature of bilaterian animal genomes, but has been secondarily split in chordate ancestry. The NK homeobox gene clusters of amphioxus and vertebrates are each split and dispersed at two equivalent intergenic positions. From the ancestral NK gene cluster, only the Tlx–Lbx and NK3–NK4 linkages have been retained in chordates. Thi...

  20. Observations on the Evolution of the Melanocortin Receptor Gene Family: Distinctive Features of the Melanocortin-2 Receptor

    OpenAIRE

    RobertMichaelDores

    2013-01-01

    The melanocortin receptors are a gene family in the rhodopsin class of G protein-coupled receptors. Based on the analysis of several metazoan genome databases it appears that the melanocortin receptors are only found in chordates. The presence of five genes in the family (i.e., MC1R, MC2R, MC3R, MC4R, MC5R) in representatives of the tetrapods indicates that the gene family is the result of two genome duplication events and one local gene duplication event during the evolution of the chordates...

  1. Ascidian gene-expression profiles

    OpenAIRE

    William R Jeffery

    2002-01-01

    With the advent of gene-expression profiling, a large number of genes can now be investigated simultaneously during critical stages of development. This approach will be particularly informative in studies of ascidians, basal chordates whose genomes and embryology are uniquely suited for mapping developmental gene networks.

  2. How the sea squirt nucleus tells mesoderm Not to be endoderm

    OpenAIRE

    Parton, Richard M.; Davis, Ilan

    2010-01-01

    Sea squirts are simple invertebrate chordates. In this issue, Takatori et al show nuclear migration within ascidian mesendodermal cells enables polarized localization of Not mRNA, which encodes a homeobox protein that distinguishes mesoderm from endoderm fates. The link between nuclear migration and mRNA localization suggests exciting parallels with protostomes.

  3. A second form of collagenous lectin from the tunicate, Styela plicata.

    NARCIS (Netherlands)

    Green, P.; Luty, J.F.; Nair, S.; Radford, J.; Raftos, D.

    2006-01-01

    This study characterised a 90 kDa lectin from an invertebrate chordate, the tunicate Styela plicata. One- and two-dimensional electrophoresis showed that the apparent molecular weight of this protein is maintained under both reducing and non-reducing conditions, suggesting that its native form is a

  4. Evolutionary mitogenomics of Chordata: the strange case of ascidians and vertebrates

    Directory of Open Access Journals (Sweden)

    C Gissi

    2009-03-01

    Full Text Available The availability of almost one thousand complete mitochondrial genome (mtDNA sequences of chordates provides an almost unique opportunity to analyse the evolution of this genome in the phylum Chordata, and to identify possible divergent evolutionary trends followed by the three chordate subphyla: Vertebrata, Cephalochordata and Tunicata.Here, we review some genome-level features of mtDNA, such as genetic code, gene content, genome architecture and gene strand asymmetry, mostly focusing on differences existing between tunicates and remaining chordates. Indeed, tunicate mtDNAs show a surprisingly high variability in several genome-level features, even though the current tunicate taxon sampling is absolutely insufficient and is focused mainly on the class Ascidiacea. On the contrary, a stabilization of the mtDNA structural and evolutionary features is observed in both cephalochordates and vertebrates, where genome-level features are almost invariant. Thus, different evolutionary dynamics, probably related to divergent functional constraints, have modelled the overall mtDNA structure and organization of the three chordate subphyla.

  5. Crafting a gene expression timeline for the thyroid in the early-life stages of fathead minnows (Pimephales promelas)

    Science.gov (United States)

    The hypothalamic-pituitary-thyroid (HPT) axis plays a number of critical roles in chordate physiology including regulation of metabolism, growth, and development. While the role of the HPT axis and thyroid hormone signaling in mammalian and amphibian development is well establis...

  6. Evolution of bilaterian central nervous systems: a single origin?

    Science.gov (United States)

    Holland, Linda Z; Carvalho, João E; Escriva, Hector; Laudet, Vincent; Schubert, Michael; Shimeld, Sebastian M; Yu, Jr-Kai

    2013-01-01

    The question of whether the ancestral bilaterian had a central nervous system (CNS) or a diffuse ectodermal nervous system has been hotly debated. Considerable evidence supports the theory that a CNS evolved just once. However, an alternative view proposes that the chordate CNS evolved from the ectodermal nerve net of a hemichordate-like ancestral deuterostome, implying independent evolution of the CNS in chordates and protostomes. To specify morphological divisions along the anterior/posterior axis, this ancestor used gene networks homologous to those patterning three organizing centers in the vertebrate brain: the anterior neural ridge, the zona limitans intrathalamica and the isthmic organizer, and subsequent evolution of the vertebrate brain involved elaboration of these ancestral signaling centers; however, all or part of these signaling centers were lost from the CNS of invertebrate chordates. The present review analyzes the evidence for and against these theories. The bulk of the evidence indicates that a CNS evolved just once - in the ancestral bilaterian. Importantly, in both protostomes and deuterostomes, the CNS represents a portion of a generally neurogenic ectoderm that is internalized and receives and integrates inputs from sensory cells in the remainder of the ectoderm. The expression patterns of genes involved in medio/lateral (dorso/ventral) patterning of the CNS are similar in protostomes and chordates; however, these genes are not similarly expressed in the ectoderm outside the CNS. Thus, their expression is a better criterion for CNS homologs than the expression of anterior/posterior patterning genes, many of which (for example, Hox genes) are similarly expressed both in the CNS and in the remainder of the ectoderm in many bilaterians. The evidence leaves hemichordates in an ambiguous position - either CNS centralization was lost to some extent at the base of the hemichordates, or even earlier, at the base of the hemichordates

  7. Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus

    Directory of Open Access Journals (Sweden)

    Cattaneo Elena

    2006-11-01

    Full Text Available Abstract Background To gain insight into the evolutionary features of the huntingtin (htt gene in Chordata, we have sequenced and characterized the full-length htt mRNA in the ascidian Ciona intestinalis, a basal chordate emerging as new invertebrate model organism. Moreover, taking advantage of the availability of genomic and EST sequences, the htt gene structure of a number of chordate species, including the cogeneric ascidian Ciona savignyi, and the vertebrates Xenopus and Gallus was reconstructed. Results The C. intestinalis htt transcript exhibits some peculiar features, such as spliced leader trans-splicing in the 98 nt-long 5' untranslated region (UTR, an alternative splicing in the coding region, eight alternative polyadenylation sites, and no similarities of both 5' and 3'UTRs compared to homologs of the cogeneric C. savignyi. The predicted protein is 2946 amino acids long, shorter than its vertebrate homologs, and lacks the polyQ and the polyP stretches found in the the N-terminal regions of mammalian homologs. The exon-intron organization of the htt gene is almost identical among vertebrates, and significantly conserved between Ciona and vertebrates, allowing us to hypothesize an ancestral chordate gene consisting of at least 40 coding exons. Conclusion During chordate diversification, events of gain/loss, sliding, phase changes, and expansion of introns occurred in both vertebrate and ascidian lineages predominantly in the 5'-half of the htt gene, where there is also evidence of lineage-specific evolutionary dynamics in vertebrates. On the contrary, the 3'-half of the gene is highly conserved in all chordates at the level of both gene structure and protein sequence. Between the two Ciona species, a fast evolutionary rate and/or an early divergence time is suggested by the absence of significant similarity between UTRs, protein divergence comparable to that observed between mammals and fishes, and different distribution of repetitive

  8. Evolution of retinoid and steroid signaling: vertebrate diversification from an amphioxus perspective.

    Science.gov (United States)

    Albalat, Ricard; Brunet, Frédéric; Laudet, Vincent; Schubert, Michael

    2011-01-01

    Although the physiological relevance of retinoids and steroids in vertebrates is very well established, the origin and evolution of the genetic machineries implicated in their metabolic pathways is still very poorly understood. We investigated the evolution of these genetic networks by conducting an exhaustive survey of components of the retinoid and steroid pathways in the genome of the invertebrate chordate amphioxus (Branchiostoma floridae). Due to its phylogenetic position at the base of chordates, amphioxus is a very useful model to identify and study chordate versus vertebrate innovations, both on a morphological and a genomic level. We have characterized more than 220 amphioxus genes evolutionarily related to vertebrate components of the retinoid and steroid pathways and found that, globally, amphioxus has orthologs of most of the vertebrate components of these two pathways, with some very important exceptions. For example, we failed to identify a vertebrate-like machinery for retinoid storage, transport, and delivery in amphioxus and were also unable to characterize components of the adrenal steroid pathway in this invertebrate chordate. The absence of these genes from the amphioxus genome suggests that both an elaboration and a refinement of the retinoid and steroid pathways took place at the base of the vertebrate lineage. In stark contrast, we also identified massive amplifications in some amphioxus gene families, most extensively in the short-chain dehydrogenase/reductase superfamily, which, based on phylogenetic and genomic linkage analyses, were likely the result of duplications specific to the amphioxus lineage. In sum, this detailed characterization of genes implicated in retinoid and steroid signaling in amphioxus allows us not only to reconstruct an outline of these pathways in the ancestral chordate but also to discuss functional innovations in retinoid homeostasis and steroid-dependent regulation in both cephalochordate and vertebrate evolution

  9. Evolution of developmental roles of Pax2/5/8 paralogs after independent duplication in urochordate and vertebrate lineages

    Directory of Open Access Journals (Sweden)

    Cañestro Cristian

    2008-08-01

    Full Text Available Abstract Background Gene duplication provides opportunities for lineage diversification and evolution of developmental novelties. Duplicated genes generally either disappear by accumulation of mutations (nonfunctionalization, or are preserved either by the origin of positively selected functions in one or both duplicates (neofunctionalization, or by the partitioning of original gene subfunctions between the duplicates (subfunctionalization. The Pax2/5/8 family of important developmental regulators has undergone parallel expansion among chordate groups. After the divergence of urochordate and vertebrate lineages, two rounds of independent gene duplications resulted in the Pax2, Pax5, and Pax8 genes of most vertebrates (the sister group of the urochordates, and an additional duplication provided the pax2a and pax2b duplicates in teleost fish. Separate from the vertebrate genome expansions, a duplication also created two Pax2/5/8 genes in the common ancestor of ascidian and larvacean urochordates. Results To better understand mechanisms underlying the evolution of duplicated genes, we investigated, in the larvacean urochordate Oikopleura dioica, the embryonic gene expression patterns of Pax2/5/8 paralogs. We compared the larvacean and ascidian expression patterns to infer modular subfunctions present in the single pre-duplication Pax2/5/8 gene of stem urochordates, and we compared vertebrate and urochordate expression to infer the suite of Pax2/5/8 gene subfunctions in the common ancestor of olfactores (vertebrates + urochordates. Expression pattern differences of larvacean and ascidian Pax2/5/8 orthologs in the endostyle, pharynx and hindgut suggest that some ancestral gene functions have been partitioned differently to the duplicates in the two urochordate lineages. Novel expression in the larvacean heart may have resulted from the neofunctionalization of a Pax2/5/8 gene in the urochordates. Expression of larvacean Pax2/5/8 in the endostyle, in

  10. The Evolution of Sensory Placodes

    Directory of Open Access Journals (Sweden)

    Francoise Mazet

    2006-01-01

    Full Text Available The vertebrate cranial sensory placodes are ectodermal embryonic patches that give rise to sensory receptor cells of the peripheral paired sense organs and to neurons in the cranial sensory ganglia. Their differentiation and the genetic pathways that underlay their development are now well understood. Their evolutionary history, however, has remained obscure. Recent molecular work, performed on close relatives of the vertebrates, demonstrated that some sensory placodes (namely the adenohypophysis, the olfactory, and accoustico-lateralis placodes first evolved at the base of the chordate lineage, while others might be specific to vertebrates. Combined with morphological and cellular fate data, these results also suggest that the sensory placodes of the ancestor of all chordates differentiated into a wide range of structures, most likely to fit the lifestyle and environment of each species.

  11. The vertebrate Hox gene regulatory network for hindbrain segmentation: Evolution and diversification: Coupling of a Hox gene regulatory network to hindbrain segmentation is an ancient trait originating at the base of vertebrates.

    Science.gov (United States)

    Parker, Hugo J; Bronner, Marianne E; Krumlauf, Robb

    2016-06-01

    Hindbrain development is orchestrated by a vertebrate gene regulatory network that generates segmental patterning along the anterior-posterior axis via Hox genes. Here, we review analyses of vertebrate and invertebrate chordate models that inform upon the evolutionary origin and diversification of this network. Evidence from the sea lamprey reveals that the hindbrain regulatory network generates rhombomeric compartments with segmental Hox expression and an underlying Hox code. We infer that this basal feature was present in ancestral vertebrates and, as an evolutionarily constrained developmental state, is fundamentally important for patterning of the vertebrate hindbrain across diverse lineages. Despite the common ground plan, vertebrates exhibit neuroanatomical diversity in lineage-specific patterns, with different vertebrates revealing variations of Hox expression in the hindbrain that could underlie this diversification. Invertebrate chordates lack hindbrain segmentation but exhibit some conserved aspects of this network, with retinoic acid signaling playing a role in establishing nested domains of Hox expression. PMID:27027928

  12. Evidence of G.O.D.'s Miracle: Unearthing a RAG Transposon.

    Science.gov (United States)

    Flajnik, Martin F

    2016-06-30

    Diversity of antibodies and T cell receptors is generated by gene rearrangement dependent on RAG1 and RAG2, enzymes predicted to have been derived from a transposable element (TE) that invaded an immunoglobulin superfamily gene early in the evolution of jawed vertebrates. Now, Huang et al. report the discovery of ProtoRAG in the lower chordate Amphioxus, the long-anticipated TE related to the RAG transposon. PMID:27368095

  13. Echinoderm immunity

    OpenAIRE

    JE García-Arrarás; F Ramírez-Gómez

    2010-01-01

    Echinoderms are exclusively marine animals that, after the chordates, represent the second largest group of deuterostomes. Their diverse species composition and singular ecological niches provide at the same time challenges and rewards when studying the broad range of responses that make up their immune mechanisms. Two types of responses comprise the immune system of echinoderms: a cellular response and a humoral one. Cell-based immunity is carried by the celomocytes, a morphologically hetero...

  14. Evolutionary conservation of the mature oocyte proteome

    Directory of Open Access Journals (Sweden)

    Tamar Lotan

    2014-06-01

    Significance: The current study provides the first proteomic profile of an oocyte of a cnidarian organism the starlet sea anemone N. vectensis and gives new insights on the ancient origin of an oocyte proteome template. The comparative analysis with a chordate oocyte suggests that the oocyte proteome predates the divergence of the cnidarian and bilaterian lineages. In addition, the data generated in the study will serve as a valuable resource for further developmental and evolutional studies.

  15. Embryonic Cleavage Cycles: How Is a Mouse Like a Fly?

    OpenAIRE

    O’Farrell, Patrick H.; Stumpff, Jason; Su, Tin Tin

    2004-01-01

    The evolutionary advent of uterine support of embryonic growth in mammals is relatively recent. Nonetheless, striking differences in the earliest steps of embryogenesis make it difficult to draw parallels even with other chordates. We suggest that use of fertilization as a reference point misaligns the earliest stages and masks parallels that are evident when development is aligned at conserved stages surrounding gastrulation. In externally deposited eggs from representatives of all the major...

  16. Analysis of coelom development in the sea urchin Holopneustes purpurescens yielding a deuterostome body plan

    OpenAIRE

    Morris, Valerie B.

    2016-01-01

    ABSTRACT An analysis of early coelom development in the echinoid Holopneustes purpurescens yields a deuterostome body plan that explains the disparity between the pentameral plan of echinoderms and the bilateral plans of chordates and hemichordates, the three major phyla of the monophyletic deuterostomes. The analysis shows an early separation into a medial hydrocoele and lateral coelomic mesoderm with an enteric channel between them before the hydrocoele forms the pentameral plan of five pri...

  17. Perforin evolved from a gene duplication of MPEG1, followed by a complex pattern of gene gain and loss within Euteleostomi

    OpenAIRE

    D’Angelo Michael E; Dunstone Michelle A; Whisstock James C; Trapani Joseph A; Bird Phillip I

    2012-01-01

    Abstract Background The pore-forming protein perforin is central to the granule-exocytosis pathway used by cytotoxic lymphocytes to kill abnormal cells. Although this mechanism of killing is conserved in bony vertebrates, cytotoxic cells are present in other chordates and invertebrates, and their cytotoxic mechanism has not been elucidated. In order to understand the evolution of this pathway, here we characterize the origins and evolution of perforin. Results We identified orthologs and homo...

  18. A Genomic View of the Sea Urchin Nervous System

    OpenAIRE

    Burke, RD; Angerer, LM; Elphick, MR; Humphrey, GW; Yaguchi, S; Kiyama, T.; Liang, S.; Mu, X.; Agca, C; Klein, WH; Brandhorst, BP; Rowe, M.; Wilson, K.; Churcher, AM; Taylor, JS

    2006-01-01

    The sequencing of the Strongylocentrotus purpuratus genome provides a unique opportunity to investigate the function and evolution of neural genes. The neurobiology of sea urchins is of particular interest because they have a close phylogenetic relationship with chordates, yet a distinctive pentaradiate body plan and unusual neural organization. Orthologues of transcription factors that regulate neurogenesis in other animals have been identified and several are expressed in neurogenic domains...

  19. Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response

    OpenAIRE

    Asiel Arturo Benitez; Laura Adrienne Spanko; Mehdi Bouhaddou; David Sachs; Benjamin Robert tenOever

    2015-01-01

    While the intrinsic antiviral cell defenses of many kingdoms utilize pathogen-specific small RNAs, the antiviral response of chordates is primarily protein-based and not uniquely tailored to the incoming microbe. In an effort to explain this evolutionary bifurcation, we determined whether antiviral RNA interference (RNAi) was sufficient to replace the protein-based type I interferon (IFN-I) system of mammals. To this end, we recreated an RNAi-like response in mammals and determined its effect...

  20. Molecular evolution of the vertebrate immune system

    OpenAIRE

    Bartl, S; Baltimore, D; Weissman, I L

    1994-01-01

    An understanding of the evolution of vertebrate immunity is slowly emerging from studies of chordates that share distant ancestors with mammals. In higher vertebrates, such as birds and mammals, we know that two receptor systems are operative. B cells use immunoglobulins to bind foreign agents (the functionally defined antigens). T cells use T-cell receptors (TCRs) to respond to antigen in the form of processed peptides bound to cell surface proteins encoded in the major histocompatibility...

  1. Ciona Genetics

    OpenAIRE

    Veeman, Michael T.; Chiba, Shota; Smith, William C.

    2011-01-01

    Ascidians, such as Ciona, are invertebrate chordates with simple embryonic body plans and small, relatively non-redundant genomes. Ciona genetics is in its infancy compared to many other model systems, but it provides a powerful method for studying this important vertebrate outgroup. Here we give basic methods for genetic analysis of Ciona, including protocols for controlled crosses both by natural spawning and by the surgical isolation of gametes; the identification and propagation of mutant...

  2. Proteomics based approach to understand tissue regeneration

    OpenAIRE

    Franco, Catarina de Matos Ferraz

    2011-01-01

    Most echinoderm species share an outstanding capacity for regeneration that is maintained throughout the adult animal lifespan. Regeneration allows these deuterostomes to recover from predation injuries or selfinduced arm autotomy, which are known to occur frequently in nature. Although echinoderms are extremely interesting in terms of their phylogenetic proximity to chordates, most areas of echinoderm research have been neglected in recent years. These wonderful animals quickly s...

  3. Evolution of arylalkylamine N-acetyltransferase: Emergence and divergence

    OpenAIRE

    Coon, Steven L.; Klein, David C.

    2006-01-01

    The melatonin rhythm-generating enzyme, arylalkylamine N-acetyltransferase (AANAT) is known to have recognizable ancient homologs in bacteria and fungi, but not in other eukaryotes. Analysis of new cDNA and genomic sequences has identified several additional homologs in other groupings. First, an AANAT homolog has been found in the genome of the cephalochordate amphioxus, representing the oldest homolog in chordates. Second, two AANAT homologs have been identified in unicellular green algae. ...

  4. How Fast Is the Sessile Ciona?

    OpenAIRE

    Giuseppe D'Onofrio; Fernando Alvarez-Valin; Luisa Berná

    2009-01-01

    Genomewide analyses of distances between orthologous gene pairs from the ascidian species Ciona intestinalis and Ciona savignyi were compared with those of vertebrates. Combining this data with a detailed and careful use of vertebrate fossil records, we estimated the time of divergence between the two ascidians nearly 180 My. This estimation was obtained after correcting for the different substitution rates found comparing several groups of chordates; indeed we determine here that on average ...

  5. Deciphering deuterostome phylogeny: molecular, morphological and palaeontological perspectives

    OpenAIRE

    Swalla, Billie J.; Smith, Andrew B.

    2008-01-01

    Deuterostomes are a monophyletic group of animals that include the vertebrates, invertebrate chordates, ambulacrarians and xenoturbellids. Fossil representatives from most major deuterostome groups, including some phylum-level crown groups, are found in the Lower Cambrian, suggesting that evolutionary divergence occurred in the Late Precambrian, in agreement with some molecular clock estimates. Molecular phylogenies, larval morphology and the adult heart/kidney complex all support echinoderms...

  6. Biota of a Pennsylvanian muddy coast: habitat within the Mazonian delta complex, northeast Illinois

    Energy Technology Data Exchange (ETDEWEB)

    Baird, G.C.

    1985-03-01

    The Mazon Creek biota (Westphalian D) is composed of plants and animals from terrestrial fresh water and marginal marine habitats. Fossil animals, including jellyfish, worms, crustaceans, holothurians, insects, chordates, and problematica occur in sideritic concretions on spoilpiles of more than 100 abandoned coal mines in a five county region (Mazon Creek area) of northeast Illinois. These fossils record rapid burial and early diagenesis in a muddy, delta-influenced coastal setting submerged during marine transgression.

  7. The identification of transcription factors expressed in the notochord of Ciona intestinalis adds new potential players to the Brachyury gene regulatory network

    OpenAIRE

    Diana S José-Edwards; Kerner, Pierre; Kugler, Jamie E.; Deng, Wei; Jiang, Di; Di Gregorio, Anna

    2011-01-01

    The notochord is the distinctive characteristic of chordates; however, the knowledge of the complement of transcription factors governing the development of this structure is still incomplete. Here we present the expression patterns of seven transcription factor genes detected in the notochord of the ascidian Ciona intestinalis at various stages of embryonic development. Four of these transcription factors, Fos-a, NFAT5, AFF and Klf15, have not been directly associated with the notochord in p...

  8. Evolution of the notochord

    OpenAIRE

    Annona, Giovanni; Holland, Nicholas D.; D’Aniello, Salvatore

    2015-01-01

    A notochord is characteristic of developing chordates (which comprise amphioxus, tunicates and vertebrates), and, more arguably, is also found in some other animals. Although notochords have been well reviewed from a developmental genetic point of view, there has heretofore been no adequate survey of the dozen or so scenarios accounting for their evolutionary origin. Advances in molecular phylogenetics and developmental genetics have, on the one hand, failed to support many of these ideas (al...

  9. Trait-based diversification shifts reflect differential extinction among fossil taxa

    OpenAIRE

    Wagner, Peter J; Estabrook, George F.

    2014-01-01

    Shifts in biological diversity often are associated with particular anatomical traits. Anatomical data from over 300 clades of brachiopods, molluscs, arthropods, echinoderms, and chordates show that trait-based diversification shifts are common at even fairly low (genus and species) taxonomic levels. Cambrian taxa present the lone major exception. Among post-Cambrian taxa, diversification shifts correlate strongly with elevated net extinction of primitive taxa rather than elevated net speciat...

  10. The Amphioxus SoxB Family: Implications for the Evolution of Vertebrate Placodes

    OpenAIRE

    Meulemans, Daniel; Bronner-Fraser, Marianne

    2007-01-01

    Cranial placodes are regions of thickened ectoderm that give rise to sense organs and ganglia in the vertebrate head. Homologous structures are proposed to exist in urochordates, but have not been found in cephalochordates, suggesting the first chordates lacked placodes. SoxB genes are expressed in discrete subsets of vertebrate placodes. To investigate how placodes arose and diversified in the vertebrate lineage we isolated the complete set of SoxB genes from amphioxus and analyzed their exp...

  11. Development and Evolution of the Pharyngeal Apparatus

    OpenAIRE

    Frisdal, Aude; Trainor, Paul A.

    2014-01-01

    The oral or pharyngeal apparatus facilitates the dual functions of respiration and feeding. It develops during embryogenesis from transient structures called pharyngeal arches, which comprise a reiterated series of outgrowths on the lateral side of the head. The pharyngeal arches and their segmental arrangement are highly conserved throughout evolution from invertebrate chordates such as amphioxus, through to vertebrate agnathans including avians, squamates and mammals. The structural organiz...

  12. ORGANIZATION AND FUNCTION OF THE FKBP52 AND FKBP51 GENES

    OpenAIRE

    Cioffi, Donna L.; Hubler, Tina R.; Scammell, Jonathan G.

    2011-01-01

    Best established as components of steroid hormone receptor complexes, it is now clear that the large molecular weight immunophilins, FKBP52 and FKBP51, play important regulatory roles elsewhere in the cell. This review outlines what is known about the organization of the genes, FKBP4 and FKBP5 respectively, encoding these proteins and describes their diverse actions in the nervous system, reproduction, and cancer. The organization of FKBP4 and FKBP5 is very similar among the chordates, and ge...

  13. Characterization of two Dscam orthologues in Hirudo medicinalis

    OpenAIRE

    Kym, Eunice Seunga

    2011-01-01

    Dscam is a transmembrane protein of the Ig superfamily that has been shown to play critical roles in the developing nervous system. Its known functions include isoneuronal dendritic and axonal self-avoidance, heteroneuronal avoidance in a process called "tiling", heteroneuronal synapse formation, and axon guidance. The importance of Dscam is further demonstrated by its high degree of sequence, structural and functional conservation in organisms across several phyla, including chordates, mollu...

  14. Origin of the metazoan phyla: Molecular clocks confirm paleontological estimates

    OpenAIRE

    Ayala, Francisco José; Rzhetsky, Andrey; Ayala, Francisco J.

    1998-01-01

    The time of origin of the animal phyla is controversial. Abundant fossils from the major animal phyla are found in the Cambrian, starting 544 million years ago. Many paleontologists hold that these phyla originated in the late Neoproterozoic, during the 160 million years preceding the Cambrian fossil explosion. We have analyzed 18 protein-coding gene loci and estimated that protostomes (arthropods, annelids, and mollusks) diverged from deuterostomes (echinoderms and chordates) about 670 milli...

  15. Ciona intestinalis as an emerging model organism: its regeneration under controlled conditions and methodology for egg dechorionation

    Institute of Scientific and Technical Information of China (English)

    LIU Li-ping; XIANG Jian-hai; DONG Bo; NATARAJAN Pavanasam; YU Kui-jie; CAI Nan-er

    2006-01-01

    The ascidian Ciona intestinalis is a model organism of developmental and evolutionary biology and may provide crucial clues concerning two fundamental matters, namely, how chordates originated from the putative deuterostome ancestor and how advanced chordates originated from the simplest chordates. In this paper, a whole-life-span culture of C. intestinalis was conducted. Fed with the diet combination of dry Spirulina, egg yolk, Dicrateria sp., edible yeast and weaning diet for shrimp, C.intestinalis grew up to average 59 mm and matured after 60 d cultivation. This culture process could be repeated using the artificially cultured mature ascidians as material. When the fertilized eggs were maintained under 10, 15, 20, 25 ℃, they hatched within 30 h, 22 h, 16 h and 12 h 50 min respectively experiencing cleavage, blastulation, gastrulation, neurulation, tailbud stage and tadpole stage. The tadpole larvae were characterized as typical but simplified chordates because of their dorsal nerve cord, notochord and primordial brain. After 8~24 h freely swimming, the tadpole larvae settled on the substrates and metamorphosized within 1~2 d into filter feeding sessile juvenile ascidians. In addition, unfertilized eggs were successfully dechorionated in filtered seawater containing 1% Tripsin, 0.25% EDTA at pH of 10.5 within 40 min. After fertilization, the dechorionated eggs developed well and hatched at normal hatching rate. In conclusion, this paper presented feasible methodology for rearing the tadpole larvae of C. intestinalis into sexual maturity under controlled conditions and detailed observations on the embryogenesis of the laboratory cultured ascidians, which will facilitate developmental and genetic research using this model system.

  16. An Otx/Nodal Regulatory Signature for Posterior Neural Development in Ascidians

    OpenAIRE

    Agnès Roure; Patrick Lemaire; Sébastien Darras

    2014-01-01

    In chordates, neural induction is the first step of a complex developmental process through which ectodermal cells acquire a neural identity. In ascidians, FGF-mediated neural induction occurs at the 32-cell stage in two blastomere pairs, precursors respectively of anterior and posterior neural tissue. We combined molecular embryology and cis-regulatory analysis to unveil in the ascidian Ciona intestinalis the remarkably simple proximal genetic network that controls posterior neural fate acqu...

  17. The last common bilaterian ancestor

    OpenAIRE

    Erwin, Douglas H.; Davidson, Eric H.

    2002-01-01

    Many regulatory genes appear to be utilized in at least superficially similar ways in the development of particular body parts in Drosophila and in chordates. These similarities have been widely interpreted as functional homologies, producing the conventional view of the last common protostome-deuterostome ancestor (PDA) as a complex organism that possessed some of the same body parts as modern bilaterians. Here we discuss an alternative view, in which the last common PDA had a less complex b...

  18. An enigmatic fourth runt domain gene in the fugu genome: ancestral gene loss versus accelerated evolution

    OpenAIRE

    Hood Leroy; Kaur Amardeep; Glusman Gustavo; Rowen Lee

    2004-01-01

    Abstract Background The runt domain transcription factors are key regulators of developmental processes in bilaterians, involved both in cell proliferation and differentiation, and their disruption usually leads to disease. Three runt domain genes have been described in each vertebrate genome (the RUNX gene family), but only one in other chordates. Therefore, the common ancestor of vertebrates has been thought to have had a single runt domain gene. Results Analysis of the genome draft of the ...

  19. Domain shuffling and the evolution of vertebrates

    OpenAIRE

    Kawashima, Takeshi; Kawashima, Shuichi; Tanaka, Chisaki; Murai, Miho; Yoneda, Masahiko; Putnam, Nicholas H.; Rokhsar, Daniel S.; Kanehisa, Minoru; Satoh, Nori; Wada, Hiroshi

    2009-01-01

    The evolution of vertebrates has included a number of important events: the development of cartilage, the immune system, and complicated craniofacial structures. Here, we examine domain shuffling as one of the mechanisms that contributes novel genetic material required for vertebrate evolution. We mapped domain-shuffling events during the evolution of deuterostomes with a focus on how domain shuffling contributed to the evolution of vertebrate- and chordate-specific characteristics. We identi...

  20. Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes

    OpenAIRE

    Huang, Shengfeng; Chen, Zelin; Yan, Xinyu; Yu, Ting; Huang, Guangrui; Yan, Qingyu; Pontarotti, Pierre Antoine; Zhao, Hongchen; Li, Jie; Yang, Ping; Wang, Ruihua; Li, Rui; Tao, Xin; Deng, Ting; Wang, Yiquan

    2014-01-01

    Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancel...

  1. Emergence and evolution of the renin-angiotensin-aldosterone system

    OpenAIRE

    Fournier, D.; Luft, F C; Bader, M.; Ganten, D; Andrade-Navarro, M A

    2012-01-01

    The renin–angiotensin–aldosterone system (RAAS) is not the sole, but perhaps the most important volume regulator in vertebrates. To gain insights into the function and evolution of its components, we conducted a phylogenetic analysis of its main related genes. We found that important parts of the system began to appear with primitive chordates and tunicates and that all major components were present at the divergence of bony fish, with the exception of the Mas receptor. The Mas receptor first...

  2. Molecular genetic insights into deuterostome evolution from the direct-developing hemichordate Saccoglossus kowalevskii

    OpenAIRE

    Lowe, Christopher J.

    2008-01-01

    Progress in developmental biology, phylogenomics and palaeontology over the past five years are all making major contributions to a long-enduring problem in comparative biology: the early origins of the deuterostome phyla. Recent advances in the developmental biology of hemichordates have given a unique insight into developmental similarities between this phylum and chordates. Transcriptional and signalling gene expression patterns between the two groups during the early development of the an...

  3. The origin and evolution of the neural crest

    OpenAIRE

    Donoghue, Philip C. J.; Graham, Anthony; Kelsh, Robert N.

    2008-01-01

    Many of the features that distinguish the vertebrates from other chordates are derived from the neural crest, and it has long been argued that the emergence of this multipotent embryonic population was a key innovation underpinning vertebrate evolution. More recently, however, a number of studies have suggested that the evolution of the neural crest was less sudden than previously believed. This has exposed the fact that neural crest, as evidenced by its repertoire of derivative cell types, h...

  4. Identical genomic organization of two hemichordate Hox clusters

    OpenAIRE

    Freeman, Robert; Ikuta, Tetsuro; Wu, Michael; Koyanagi, Ryo; Kawashima, Takeshi; Tagawa, Kunifumi; Humphreys, Tom; Fang, Guang-Chen; Fujiyama, Asao; Saiga, Hidetoshi; Lowe, Christopher.; Worley, Kim; Jenkins, Jerry; Schmutz, Jeremy; Kirschner, Marc

    2012-01-01

    Genomic comparisons of chordates, hemichordates, and echinoderms can inform hypotheses for the evolution of these strikingly different phyla from the last common deuterostome ancestor [1–5]. Since hox genes play pivotal developmental roles in bilaterian animals [6–8], we analyzed the Hox complexes of two hemichordate genomes. We find that Saccoglossus kowalevskii and Ptychodera flava both possess 12-gene clusters, with mir10 between hox4 and hox5, in 550kb and 452kb intervals, respectively. G...

  5. Tbx4/5 gene duplication and the origin of vertebrate paired appendages

    OpenAIRE

    Minguillon, Carolina; Gibson-Brown, Jeremy J.; Logan, Malcolm P.

    2009-01-01

    Paired fins/limbs are one of the most successful vertebrate innovations, since they are used for numerous fundamental activities, including locomotion, feeding, and breeding. Gene duplication events generate new genes with the potential to acquire novel functions, and two rounds of genome duplication took place during vertebrate evolution. The cephalochordate amphioxus diverged from other chordates before these events and is widely used to deduce the functions of ancestral genes, present in s...

  6. Modularity of gene-regulatory networks revealed in sea-star development

    OpenAIRE

    Degnan Bernard M; McDougall Carmel

    2011-01-01

    Abstract Evidence that conserved developmental gene-regulatory networks can change as a unit during deutersostome evolution emerges from a study published in BMC Biology. This shows that genes consistently expressed in anterior brain patterning in hemichordates and chordates are expressed in a similar spatial pattern in another deuterostome, an asteroid echinoderm (sea star), but in a completely different developmental context (the animal-vegetal axis). This observation has implications for h...

  7. Tunicates push the limits of animal evo-devo

    OpenAIRE

    Ferrier David EK

    2011-01-01

    Abstract The phylum to which humans belong, Chordata, takes its name from one of the major shared derived features of the group, the notochord. All chordates have a notochord, at least during embryogenesis, and there is little doubt about notochord homology at the morphological level. A study in BMC Evolutionary Biology now shows that there is greater variability in the molecular genetics underlying notochord development than previously appreciated. See research article: http://www.biomedcent...

  8. Metal Dealing at the Origin of the Chordata Phylum: The Metallothionein System and Metal Overload Response in Amphioxus

    OpenAIRE

    Maria Guirola; Sílvia Pérez-Rafael; Mercè Capdevila; Oscar Palacios; Sílvia Atrian

    2012-01-01

    Non-vertebrate chordates, specifically amphioxus, are considered of the utmost interest for gaining insight into the evolutionary trends, i.e. differentiation and specialization, of gene/protein systems. In this work, MTs (metallothioneins), the most important metal binding proteins, are characterized for the first time in the cephalochordate subphylum at both gene and protein level, together with the main features defining the amphioxus response to cadmium and copper overload. Two MT genes (...

  9. Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

    OpenAIRE

    Denoeud, F.; Henriet, S.; Mungpakdee, S.; Aury, J.; da Silva, C.; Brinkmann, H; Mikhaleva, J.; Olsen, L.; Jubin, C.; Canestro, C.; Bouquet, J; Danks, G.; Poulain, J.; Campsteijn, C.; Adamski, M

    2010-01-01

    International audience Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely non...

  10. Structural and cell adhesion properties of zebrafish syndecan-4 are shared with higher vertebrates

    DEFF Research Database (Denmark)

    Whiteford, James; Ko, Sunggeon; Lee, Weontae;

    2008-01-01

    The syndecan proteoglycans are an ancient class of receptor, bearing heparan sulfate chains that interact with numerous potential ligands including growth factors, morphogens, and extracellular matrix molecules. The single syndecan of invertebrates appears not to have cell adhesion roles, but the......-4 are consistent across the vertebrate spectrum and reflect an early acquisition of specialization after syndecan gene duplication events at the invertebrate/early chordate boundary....

  11. Gene and genome duplications in vertebrates : the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions

    OpenAIRE

    Meyer, Axel; Schartl, Manfred

    1999-01-01

    One important mechanism for functional innovation during evolution is the duplication of genes and entire genomes. Evidence is accumulating that during the evolution of vertebrates from early deuterostome ancestors entire genomes were duplicated through two rounds of duplications (the oneto- two-to-four rule). The first genome duplication in chordate evolution might predate the Cambrian explosion. The second genome duplication possibly dates back to the early Devonian. Recent data suggest t...

  12. Osmotic/ionic status of body fluids in the euryhaline cephalopod suggest possible parallel evolution of osmoregulation

    OpenAIRE

    Tatsuya Sakamoto; Satoshi Ogawa; Yudai Nishiyama; Chiaki Akada; Hideya Takahashi; Taro Watanabe; Hiroyuki Minakata; Hirotaka Sakamoto

    2015-01-01

    Acclimation from marine to dilute environments constitutes among the dramatic evolutionary transitions in the history of life. Such adaptations have evolved in multiple lineages, but studies of the blood/hemolymph homeostasis mechanisms are limited to those using evolutionarily advanced Deuterostome (chordates) and Ecdysozoa (crustaceans). Here, we examined hemolymph homeostasis in the advanced Lophotrochozoa/mollusc, the other unexplored taxa, and its possible regulation by the vasopressin/o...

  13. Hemichordate neurulation and the origin of the neural tube

    OpenAIRE

    Miyamoto, Norio; Wada, Hiroshi

    2013-01-01

    The origin of the body plan of our own phylum, Chordata, is one of the most fascinating questions in evolutionary biology. Yet, after more than a century of debate, the evolutionary origins of the neural tube and notochord remain unclear. Here we examine the development of the collar nerve cord in the hemichordate Balanoglossus simodensis and find shared gene expression patterns between hemichordate and chordate neurulation. Moreover, we show that the dorsal endoderm of the buccal tube and th...

  14. Functional Brachyury binding sites establish a temporal read-out of gene expression in the Ciona notochord.

    OpenAIRE

    Lavanya Katikala; Hitoshi Aihara; Passamaneck, Yale J.; Stefan Gazdoiu; José-Edwards, Diana S.; Kugler, Jamie E.; Izumi Oda-Ishii; Janice H Imai; Yutaka Nibu; Anna Di Gregorio

    2013-01-01

    Author Summary Transcription factors control where and when gene expression is switched on by binding to specific stretches of DNA known as cis-regulatory modules (CRMs). In this study, we investigated the architecture and composition of CRMs that direct gene expression in the notochord—a transient rod-like structure found in all embryos that belong to the phylum chordata, which includes humans. Here we used the sea squirt Ciona, a simple chordate, and analyzed how the transcription factor Br...

  15. Neofunctionalization in vertebrates: the example of retinoic acid receptors.

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    Hector Escriva

    2006-07-01

    Full Text Available Understanding the role of gene duplications in establishing vertebrate innovations is one of the main challenges of Evo-Devo (evolution of development studies. Data on evolutionary changes in gene expression (i.e., evolution of transcription factor-cis-regulatory elements relationships tell only part of the story; protein function, best studied by biochemical and functional assays, can also change. In this study, we have investigated how gene duplication has affected both the expression and the ligand-binding specificity of retinoic acid receptors (RARs, which play a major role in chordate embryonic development. Mammals have three paralogous RAR genes--RAR alpha, beta, and gamma--which resulted from genome duplications at the origin of vertebrates. By using pharmacological ligands selective for specific paralogues, we have studied the ligand-binding capacities of RARs from diverse chordates species. We have found that RAR beta-like binding selectivity is a synapomorphy of all chordate RARs, including a reconstructed synthetic RAR representing the receptor present in the ancestor of chordates. Moreover, comparison of expression patterns of the cephalochordate amphioxus and the vertebrates suggests that, of all the RARs, RAR beta expression has remained most similar to that of the ancestral RAR. On the basis of these results together, we suggest that while RAR beta kept the ancestral RAR role, RAR alpha and RAR gamma diverged both in ligand-binding capacity and in expression patterns. We thus suggest that neofunctionalization occurred at both the expression and the functional levels to shape RAR roles during development in vertebrates.

  16. Evolution of Retinoid and Steroid Signaling: Vertebrate Diversification from an Amphioxus Perspective

    OpenAIRE

    Albalat, Ricard; Brunet, Frédéric; Laudet, Vincent; Schubert, Michael

    2011-01-01

    Although the physiological relevance of retinoids and steroids in vertebrates is very well established, the origin and evolution of the genetic machineries implicated in their metabolic pathways is still very poorly understood. We investigated the evolution of these genetic networks by conducting an exhaustive survey of components of the retinoid and steroid pathways in the genome of the invertebrate chordate amphioxus (Branchiostoma floridae). Due to its phylogenetic position at the base of ...

  17. The amphioxus genome illuminates vertebrate origins and cephalochordate biology

    Science.gov (United States)

    Holland, Linda Z.; Albalat, Ricard; Azumi, Kaoru; Benito-Gutiérrez, Èlia; Blow, Matthew J.; Bronner-Fraser, Marianne; Brunet, Frederic; Butts, Thomas; Candiani, Simona; Dishaw, Larry J.; Ferrier, David E.K.; Garcia-Fernàndez, Jordi; Gibson-Brown, Jeremy J.; Gissi, Carmela; Godzik, Adam; Hallböök, Finn; Hirose, Dan; Hosomichi, Kazuyoshi; Ikuta, Tetsuro; Inoko, Hidetoshi; Kasahara, Masanori; Kasamatsu, Jun; Kawashima, Takeshi; Kimura, Ayuko; Kobayashi, Masaaki; Kozmik, Zbynek; Kubokawa, Kaoru; Laudet, Vincent; Litman, Gary W.; McHardy, Alice C.; Meulemans, Daniel; Nonaka, Masaru; Olinski, Robert P.; Pancer, Zeev; Pennacchio, Len A.; Pestarino, Mario; Rast, Jonathan P.; Rigoutsos, Isidore; Robinson-Rechavi, Marc; Roch, Graeme; Saiga, Hidetoshi; Sasakura, Yasunori; Satake, Masanobu; Satou, Yutaka; Schubert, Michael; Sherwood, Nancy; Shiina, Takashi; Takatori, Naohito; Tello, Javier; Vopalensky, Pavel; Wada, Shuichi; Xu, Anlong; Ye, Yuzhen; Yoshida, Keita; Yoshizaki, Fumiko; Yu, Jr-Kai; Zhang, Qing; Zmasek, Christian M.; de Jong, Pieter J.; Osoegawa, Kazutoyo; Putnam, Nicholas H.; Rokhsar, Daniel S.; Satoh, Noriyuki; Holland, Peter W.H.

    2008-01-01

    Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding components of the endocrine and immune systems, and conserved cis-regulatory enhancers. The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene. This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity. However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events. In addition, several transcriptional enhancers are conserved between amphioxus and vertebrates—a very wide phylogenetic distance. In contrast, urochordate genomes have lost many genes, including a diversity of homeobox families and genes involved in steroid hormone function. The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems. Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates. PMID:18562680

  18. Experimental taphonomy and the anatomy and diversity of the earliest fossil vertebrates (Chengjiang Biota, Cambrian, China)

    Science.gov (United States)

    Purnell, Mark; Gabbott, Sarah; Murdock, Duncan; Cong, Peiyun

    2016-04-01

    The oldest fossil vertebrates are from the Lower Cambrian Chengjiang biota of China, which contains four genera of fish-like, primitive vertebrates: Haikouichthys, Myllokunmingia, Zhongjianichthys and Zhongxiniscus. These fossils play key roles in calibrating molecular clocks and informing our view of the anatomy of animals close to the origin of vertebrates, potentially including transitional forms between vertebrates and their nearest relatives. Despite the evident importance of these fossils, the degree to which taphonomic processes have affected their anatomical completeness has not been investigated. For example, some or all might have been affected by stemward slippage - the pattern observed in experimental decay of non-biomineralised chordates in which preferential decay of synapomorphies and retention of plesiomorphic characters would cause fossil taxa to erroneously occupy more basal positions than they should. This hypothesis is based on experimental data derived from decay of non-biomineralised chordates under laboratory conditions. We have expanded this analysis to include a broader range of potentially significant environmental variables; we have also compared and combined the results of experiments from several taxa to identify general patterns of chordate decay. Examination of the Chengjiang vertebrates in the light of these results demonstrates that, contrary to some assertions, experimentally derived models of phylogenetic bias are applicable to fossils. Anatomical and phylogenetic interpretations of early vertebrates that do not take taphonomic biases into account risk overestimating diversity and the evolutionary significance of differences between fossil specimens.

  19. Analysis of coelom development in the sea urchin Holopneustes purpurescens yielding a deuterostome body plan.

    Science.gov (United States)

    Morris, Valerie B

    2016-01-01

    An analysis of early coelom development in the echinoid Holopneustes purpurescens yields a deuterostome body plan that explains the disparity between the pentameral plan of echinoderms and the bilateral plans of chordates and hemichordates, the three major phyla of the monophyletic deuterostomes. The analysis shows an early separation into a medial hydrocoele and lateral coelomic mesoderm with an enteric channel between them before the hydrocoele forms the pentameral plan of five primary podia. The deuterostome body plan thus has a single axial or medial coelom and a pair of lateral coeloms, all surrounding an enteric channel, the gut channel. Applied to the phyla, the medial coelom is the hydrocoele in echinoderms, the notochord in chordates and the proboscis coelom in hemichordates: the lateral coeloms are the coelomic mesoderm in echinoderms, the paraxial mesoderm in chordates and the lateral coeloms in hemichordates. The plan fits frog and chick development and the echinoderm fossil record, and predicts genes involved in coelomogenesis as the source of deuterostome macroevolution.

  20. Development of oral and branchial muscles in lancelet larvae of Branchiostoma japonicum.

    Science.gov (United States)

    Yasui, Kinya; Kaji, Takao; Morov, Arseniy R; Yonemura, Shigenobu

    2014-04-01

    The perforated pharynx has generally been regarded as a shared characteristic of chordates. However, there still remains phylogenetic ambiguity between the cilia-driven system in invertebrate chordates and the muscle-driven system in vertebrates. Giant larvae of the genus Asymmetron were reported to develop an orobranchial musculature similar to that of vertebrates more than 100 years ago. This discovery might represent an evolutionary link for the chordate branchial system, but few investigations of the lancelet orobranchial musculature have been completed since. We studied staged larvae of a Japanese population of Branchiostoma japonicum to characterize the developmental property of the orobranchial musculature. The larval mouth and the unpaired primary gills develop well-organized muscles. These muscles function only as obturators of the openings without antagonistic system. As the larval mouth enlarged posteriorly to the level of the ninth myomere, the oral musculature was fortified accordingly without segmental patterning. In contrast, the iterated branchial muscles coincided with the dorsal myomeric pattern before metamorphosis, but the pharynx was remodeled dynamically irrespective of the myomeric pattern during metamorphosis. The orobranchial musculature disappeared completely during metamorphosis, and adult muscles in the oral hood and velum, as well as on the pterygial coeloms developed independently. The lancelet orobranchial musculature is apparently a larval adaptation to prevent harmful intake. However, vestigial muscles appeared transiently with the secondary gill formation suggest a bilateral ancestral state of muscular gills, and a segmental pattern of developing branchial muscles without neural crest and placodal contributions is suggestive of a precursor of vertebrate branchiomeric pattern.

  1. Functional Brachyury binding sites establish a temporal read-out of gene expression in the Ciona notochord.

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    Lavanya Katikala

    2013-10-01

    Full Text Available The appearance of the notochord represented a milestone in Deuterostome evolution. The notochord is necessary for the development of the chordate body plan and for the formation of the vertebral column and numerous organs. It is known that the transcription factor Brachyury is required for notochord formation in all chordates, and that it controls transcription of a large number of target genes. However, studies of the structure of the cis-regulatory modules (CRMs through which this control is exerted are complicated in vertebrates by the genomic complexity and the pan-mesodermal expression territory of Brachyury. We used the ascidian Ciona, in which the single-copy Brachyury is notochord-specific and CRMs are easily identifiable, to carry out a systematic characterization of Brachyury-downstream notochord CRMs. We found that Ciona Brachyury (Ci-Bra controls most of its targets directly, through non-palindromic binding sites that function either synergistically or individually to activate early- and middle-onset genes, respectively, while late-onset target CRMs are controlled indirectly, via transcriptional intermediaries. These results illustrate how a transcriptional regulator can efficiently shape a shallow gene regulatory network into a multi-tiered transcriptional output, and provide insights into the mechanisms that establish temporal read-outs of gene expression in a fast-developing chordate embryo.

  2. Analysis of coelom development in the sea urchin Holopneustes purpurescens yielding a deuterostome body plan

    Directory of Open Access Journals (Sweden)

    Valerie B. Morris

    2016-03-01

    Full Text Available An analysis of early coelom development in the echinoid Holopneustes purpurescens yields a deuterostome body plan that explains the disparity between the pentameral plan of echinoderms and the bilateral plans of chordates and hemichordates, the three major phyla of the monophyletic deuterostomes. The analysis shows an early separation into a medial hydrocoele and lateral coelomic mesoderm with an enteric channel between them before the hydrocoele forms the pentameral plan of five primary podia. The deuterostome body plan thus has a single axial or medial coelom and a pair of lateral coeloms, all surrounding an enteric channel, the gut channel. Applied to the phyla, the medial coelom is the hydrocoele in echinoderms, the notochord in chordates and the proboscis coelom in hemichordates: the lateral coeloms are the coelomic mesoderm in echinoderms, the paraxial mesoderm in chordates and the lateral coeloms in hemichordates. The plan fits frog and chick development and the echinoderm fossil record, and predicts genes involved in coelomogenesis as the source of deuterostome macroevolution.

  3. Expression of Fox genes in the cephalochordate Branchiostoma lanceolatum

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    Daniel eAldea

    2015-07-01

    Full Text Available Forkhead box (Fox genes code for transcription factors that play important roles in different biological processes. They are found in a wide variety of organisms and appeared in unicellular eukaryotes. In metazoans, the gene family includes many members that can be subdivided into 24 classes. Cephalochordates are key organisms to understand the functional evolution of gene families in the chordate lineage due to their phylogenetic position as an early divergent chordate, their simple anatomy and genome structure. In the genome of the cephalochordate amphioxus Branchiostoma floridae, 32 Fox genes were identified, with at least one member for each of the classes that were present in the ancestor of bilaterians. In this work we describe the expression pattern of 13 of these genes during the embryonic development of the Mediterranean amphioxus, Branchiostoma lanceolatum. We found that FoxK and FoxM genes present an ubiquitous expression while all the others show specific expression patterns restricted to diverse embryonic territories. Many of these expression patterns are conserved with vertebrates, suggesting that the main functions of Fox genes in chordates were present in their common ancestor.

  4. Evolution of retinoic acid receptors and retinoic acid signaling.

    Science.gov (United States)

    Gutierrez-Mazariegos, Juliana; Schubert, Michael; Laudet, Vincent

    2014-01-01

    Retinoic acid (RA) is a vitamin A-derived morphogen controlling important developmental processes in vertebrates, and more generally in chordates, including axial patterning and tissue formation and differentiation. In the embryo, endogenous RA levels are controlled by RA synthesizing and degrading enzymes and the RA signal is transduced by two retinoid receptors: the retinoic acid receptor (RAR) and the retinoid X receptor (RXR). Both RAR and RXR are members of the nuclear receptor superfamily of ligand-activated transcription factors and mainly act as heterodimers to activate the transcription of target genes in the presence of their ligand, all-trans RA. This signaling pathway was long thought to be a chordate innovation, however, recent findings of gene homologs involved in RA signaling in the genomes of a wide variety of non-chordate animals, including ambulacrarians (sea urchins and acorn worms) and lophotrochozoans (annelids and mollusks), challenged this traditional view and suggested that the RA signaling pathway might have a more ancient evolutionary origin than previously thought. In this chapter, we discuss the evolutionary history of the RA signaling pathway, and more particularly of the RARs, which might have experienced independent gene losses and duplications in different animal lineages. In sum, the available data reveal novel insights into the origin of the RA signaling pathway as well as into the evolutionary history of the RARs. PMID:24962881

  5. A neurotropic herpesvirus infecting the gastropod, abalone, shares ancestry with oyster herpesvirus and a herpesvirus associated with the amphioxus genome

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    Sawbridge Tim

    2010-11-01

    Full Text Available Abstract Background With the exception of the oyster herpesvirus OsHV-1, all herpesviruses characterized thus far infect only vertebrates. Some cause neurological disease in their hosts, while others replicate or become latent in neurological tissues. Recently a new herpesvirus causing ganglioneuritis in abalone, a gastropod, was discovered. Molecular analysis of new herpesviruses, such as this one and others, still to be discovered in invertebrates, will provide insight into the evolution of herpesviruses. Results We sequenced the genome of a neurotropic virus linked to a fatal ganglioneuritis devastating parts of a valuable wild abalone fishery in Australia. We show that the newly identified virus forms part of an ancient clade with its nearest relatives being a herpesvirus infecting bivalves (oyster and, unexpectedly, one we identified, from published data, apparently integrated within the genome of amphioxus, an invertebrate chordate. Predicted protein sequences from the abalone virus genome have significant similarity to several herpesvirus proteins including the DNA packaging ATPase subunit of (putative terminase and DNA polymerase. Conservation of amino acid sequences in the terminase across all herpesviruses and phylogenetic analysis using the DNA polymerase and terminase proteins demonstrate that the herpesviruses infecting the molluscs, oyster and abalone, are distantly related. The terminase and polymerase protein sequences from the putative amphioxus herpesvirus share more sequence similarity with those of the mollusc viruses than with sequences from any of the vertebrate herpesviruses analysed. Conclusions A family of mollusc herpesviruses, Malacoherpesviridae, that was based on a single virus infecting oyster can now be further established by including a distantly related herpesvirus infecting abalone, which, like many vertebrate viruses is neurotropic. The genome of Branchiostoma floridae (amphioxus provides evidence for the

  6. In silico identification of the sea squirt selenoproteome

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    Jiang Liang

    2010-05-01

    Full Text Available Abstract Background Computational methods for identifying selenoproteins have been developed rapidly in recent years. However, it is still difficult to identify the open reading frame (ORF of eukaryotic selenoprotein gene, because the TGA codon for a selenocysteine (Sec residue in the active centre of selenoprotein is traditionally a terminal signal of protein translation. Although the identification of selenoproteins from genomes through bioinformatics methods has been conducted in bacteria, unicellular eukaryotes, insects and several vertebrates, only a few results have been reported on the ancient chordate selenoproteins. Results A gene assembly algorithm SelGenAmic has been constructed and presented in this study for identifying selenoprotein genes from eukaryotic genomes. A method based on this algorithm was developed to build an optimal TGA-containing-ORF for each TGA in a genome, followed by protein similarity analysis through conserved sequence alignments to screen out selenoprotein genes form these ORFs. This method improved the sensitivity of detecting selenoproteins from a genome due to the design that all TGAs in the genome were investigated for its possibility of decoding as a Sec residue. Using this method, eighteen selenoprotein genes were identified from the genome of Ciona intestinalis, leading to its member of selenoproteome up to 19. Among them a selenoprotein W gene was found to have two SECIS elements in the 3'-untranslated region. Additionally, the disulfide bond formation protein A (DsbA was firstly identified as a selenoprotein in the ancient chordates of Ciona intestinalis, Ciona savignyi and Branchiostoma floridae, while selenoprotein DsbAs had only been found in bacteria and green algae before. Conclusion The method based on SelGenAmic algorithm is capable of identifying eukaryotic selenoprotein genes from their genomes. Application of this method to Ciona intestinalis proves its successes in finding Sec-decoding TGA

  7. Nodal signaling is required for mesodermal and ventral but not for dorsal fates in the indirect developing hemichordate, Ptychodera flava

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    Eric Röttinger

    2015-07-01

    Full Text Available Nodal signaling plays crucial roles in vertebrate developmental processes such as endoderm and mesoderm formation, and axial patterning events along the anteroposterior, dorsoventral and left-right axes. In echinoderms, Nodal plays an essential role in the establishment of the dorsoventral axis and left-right asymmetry, but not in endoderm or mesoderm induction. In protostomes, Nodal signaling appears to be involved only in establishing left-right asymmetry. Hence, it is hypothesized that Nodal signaling has been co-opted to pattern the dorsoventral axis of deuterostomes and for endoderm, mesoderm formation as well as anteroposterior patterning in chordates. Hemichordata, together with echinoderms, represent the sister taxon to chordates. In this study, we analyze the role of Nodal signaling in the indirect developing hemichordate Ptychodera flava. In particular, we show that during gastrulation nodal transcripts are detected in a ring of cells at the vegetal pole that gives rise to endomesoderm and in the ventral ectoderm at later stages of development. Inhibition of Nodal function disrupts dorsoventral fates and also blocks formation of the larval mesoderm. Interestingly, molecular analysis reveals that only mesodermal, apical and ventral gene expression is affected while the dorsal side appears to be patterned correctly. Taken together, this study suggests that the co-option of Nodal signaling in mesoderm formation and potentially in anteroposterior patterning has occurred prior to the emergence of chordates and that Nodal signaling on the ventral side is uncoupled from BMP signaling on the dorsal side, representing a major difference from the molecular mechanisms of dorsoventral patterning events in echinoderms.

  8. Perforin evolved from a gene duplication of MPEG1, followed by a complex pattern of gene gain and loss within Euteleostomi

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    D’Angelo Michael E

    2012-05-01

    Full Text Available Abstract Background The pore-forming protein perforin is central to the granule-exocytosis pathway used by cytotoxic lymphocytes to kill abnormal cells. Although this mechanism of killing is conserved in bony vertebrates, cytotoxic cells are present in other chordates and invertebrates, and their cytotoxic mechanism has not been elucidated. In order to understand the evolution of this pathway, here we characterize the origins and evolution of perforin. Results We identified orthologs and homologs of human perforin in all but one species analysed from Euteleostomi, and present evidence for an earlier ortholog in Gnathostomata but not in more primitive chordates. In placental mammals perforin is a single copy gene, but there are multiple perforin genes in all lineages predating marsupials, except birds. Our comparisons of these many-to-one homologs of human perforin show that they mainly arose from lineage-specific gene duplications in multiple taxa, suggesting acquisition of new roles or different modes of regulation. We also present evidence that perforin arose from duplication of the ancient MPEG1 gene, and that it shares a common ancestor with the functionally related complement proteins. Conclusions The evolution of perforin in vertebrates involved a complex pattern of gene, as well as intron, gain and loss. The primordial perforin gene arose at least 500 million years ago, at around the time that the major histocompatibility complex-T cell receptor antigen recognition system was established. As it is absent from primitive chordates and invertebrates, cytotoxic cells from these lineages must possess a different effector molecule or cytotoxic mechanism.

  9. Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord.

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    Diana S José-Edwards

    2015-12-01

    Full Text Available A main challenge of modern biology is to understand how specific constellations of genes are activated to differentiate cells and give rise to distinct tissues. This study focuses on elucidating how gene expression is initiated in the notochord, an axial structure that provides support and patterning signals to embryos of humans and all other chordates. Although numerous notochord genes have been identified, the regulatory DNAs that orchestrate development and propel evolution of this structure by eliciting notochord gene expression remain mostly uncharted, and the information on their configuration and recurrence is still quite fragmentary. Here we used the simple chordate Ciona for a systematic analysis of notochord cis-regulatory modules (CRMs, and investigated their composition, architectural constraints, predictive ability and evolutionary conservation. We found that most Ciona notochord CRMs relied upon variable combinations of binding sites for the transcription factors Brachyury and/or Foxa2, which can act either synergistically or independently from one another. Notably, one of these CRMs contains a Brachyury binding site juxtaposed to an (AC microsatellite, an unusual arrangement also found in Brachyury-bound regulatory regions in mouse. In contrast, different subsets of CRMs relied upon binding sites for transcription factors of widely diverse families. Surprisingly, we found that neither intra-genomic nor interspecific conservation of binding sites were reliably predictive hallmarks of notochord CRMs. We propose that rather than obeying a rigid sequence-based cis-regulatory code, most notochord CRMs are rather unique. Yet, this study uncovered essential elements recurrently used by divergent chordates as basic building blocks for notochord CRMs.

  10. Amphioxus: beginning of vertebrate and end of invertebrate type GnRH receptor lineage.

    Science.gov (United States)

    Tello, Javier A; Sherwood, Nancy M

    2009-06-01

    In vertebrates, activation of the GnRH receptor is necessary to initiate the reproductive cascade. However, little is known about the characteristics of GnRH receptors before the vertebrates evolved. Recently genome sequencing was completed for amphioxus, Branchiostoma floridae. To understand the GnRH receptors (GnRHR) from this most basal chordate, which is also classified as an invertebrate, we cloned and characterized four GnRHR cDNAs encoded in the amphioxus genome. We found that incubation of GnRH1 (mammalian GnRH) and GnRH2 (chicken GnRH II) with COS7 cells heterologously expressing the amphioxus GnRHRs caused potent intracellular inositol phosphate turnover in two of the receptors. One of the two receptors displayed a clear preference for GnRH1 over GnRH2, a characteristic not previously seen outside the type I mammalian GnRHRs. Phylogenetic analysis grouped the four receptors into two paralogous pairs, with one pair grouping basally with the vertebrate GnRH receptors and the other grouping with the octopus GnRHR-like sequence and the related receptor for insect adipokinetic hormone. Pharmacological studies showed that octopus GnRH-like peptide and adipokinetic hormone induced potent inositol phosphate turnover in one of these other two amphioxus receptors. These data demonstrate the functional conservation of two distinct types of GnRH receptors at the base of chordates. We propose that one receptor type led to vertebrate GnRHRs, whereas the other type, related to the mollusk GnRHR-like receptor, was lost in the vertebrate lineage. This is the first report to suggest that distinct invertebrate and vertebrate GnRHRs are present simultaneously in a basal chordate, amphioxus. PMID:19264870

  11. The evolution of tenascins and fibronectin.

    Science.gov (United States)

    Adams, Josephine C; Chiquet-Ehrismann, Ruth; Tucker, Richard P

    2015-01-01

    Tenascins are extracellular matrix glycoproteins that act both as integrin ligands and as modifiers of fibronectin-integrin interactions to regulate cell adhesion, migration, proliferation and differentiation. In tetrapods, both tenascins and fibronectin bind to integrins via RGD and LDV-type tripeptide motifs found in exposed loops in their fibronectin-type III domains. We previously showed that tenascins appeared early in the chordate lineage and are represented by single genes in extant cephalochordates and tunicates. Here we have examined the genomes of the coelacanth Latimeria chalumnae, the elephant shark Callorhinchus milii as well as the lampreys Petromyzon marinus and Lethenteron japonicum to learn more about the evolution of the tenascin gene family as well as the timing of the appearance of fibronectin during chordate evolution. The coelacanth has 4 tenascins that are more similar to tetrapod tenascins than are tenascins from ray-finned fishes. In contrast, only 2 tenascins were identified in the elephant shark and the Japanese lamprey L. japonicum. An RGD motif exposed to integrin binding is observed in tenascins from many, but not all, classes of chordates. Tetrapods that lack this RGD motif in tenascin-C have a similar motif in the paralog tenascin-W, suggesting the potential for some overlapping function. A predicted fibronectin with the same domain organization as the fibronectin from tetrapods is found in the sea lamprey P. marinus but not in tunicates, leading us to infer that fibronectin first appeared in vertebrates. The motifs that recognize LDV-type integrin receptors are conserved in fibronectins from a broad spectrum of vertebrates, but the RGD integrin-binding motif may have evolved in gnathostomes.

  12. Metastatic Chordoma: A Diagnostic Challenge on Fine Needle Aspiration

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    Ghassan Tranesh

    2016-01-01

    Full Text Available Chordomas are primary low grade malignant tumors of bone that usually arise within both ends of axial skeleton. The Notochord is a midline, ectoderm-derived structure that defines the phylum of chordates. Chordomas may pose difficult diagnostic challenges when encountered in secondary locations, such as lungs or other parenchymatous organs. We report the cytologic findings of a metastatic chordoma sampled through CT-scan guided fine needle aspiration (FNA of lower lobe lung nodule in a 54-year-old man diagnosed with recurrent chordoma involving the lumber spine and paraspinal region.

  13. Metastatic Chordoma: A Diagnostic Challenge on Fine Needle Aspiration

    Science.gov (United States)

    Tranesh, Ghassan; Nassar, Aziza

    2016-01-01

    Chordomas are primary low grade malignant tumors of bone that usually arise within both ends of axial skeleton. The Notochord is a midline, ectoderm-derived structure that defines the phylum of chordates. Chordomas may pose difficult diagnostic challenges when encountered in secondary locations, such as lungs or other parenchymatous organs. We report the cytologic findings of a metastatic chordoma sampled through CT-scan guided fine needle aspiration (FNA) of lower lobe lung nodule in a 54-year-old man diagnosed with recurrent chordoma involving the lumber spine and paraspinal region. PMID:26881166

  14. How Fast Is the Sessile Ciona?

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    Luisa Berná

    2009-01-01

    Full Text Available Genomewide analyses of distances between orthologous gene pairs from the ascidian species Ciona intestinalis and Ciona savignyi were compared with those of vertebrates. Combining this data with a detailed and careful use of vertebrate fossil records, we estimated the time of divergence between the two ascidians nearly 180 My. This estimation was obtained after correcting for the different substitution rates found comparing several groups of chordates; indeed we determine here that on average Ciona species evolve 50% faster than vertebrates.

  15. Modularity of gene-regulatory networks revealed in sea-star development

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    Degnan Bernard M

    2011-01-01

    Full Text Available Abstract Evidence that conserved developmental gene-regulatory networks can change as a unit during deutersostome evolution emerges from a study published in BMC Biology. This shows that genes consistently expressed in anterior brain patterning in hemichordates and chordates are expressed in a similar spatial pattern in another deuterostome, an asteroid echinoderm (sea star, but in a completely different developmental context (the animal-vegetal axis. This observation has implications for hypotheses on the type of development present in the deuterostome common ancestor. See research article: http://www.biomedcentral.com/1741-7007/8/143/abstract

  16. The last common bilaterian ancestor

    Science.gov (United States)

    Erwin, Douglas H.; Davidson, Eric H.

    2002-01-01

    Many regulatory genes appear to be utilized in at least superficially similar ways in the development of particular body parts in Drosophila and in chordates. These similarities have been widely interpreted as functional homologies, producing the conventional view of the last common protostome-deuterostome ancestor (PDA) as a complex organism that possessed some of the same body parts as modern bilaterians. Here we discuss an alternative view, in which the last common PDA had a less complex body plan than is frequently conceived. This reconstruction alters expectations for Neoproterozoic fossil remains that could illustrate the pathways of bilaterian evolution.

  17. Evolution of developmental regulation in the vertebrate FgfD subfamily

    OpenAIRE

    Jovelin, Richard; Yan, Yi-Lin; He, Xinjun; Catchen, Julian; Amores, Angel; Canestro, Cristian; Yokoi, Hayato; Postlethwait, John H.

    2010-01-01

    Fibroblast growth factors (Fgfs) encode small signaling proteins that help regulate embryo patterning. Fgfs fall into seven families, including FgfD. Non-vertebrate chordates have a single FgfD gene; mammals have three (Fgf8, Fgf17, and Fgf18); and teleosts have six (fgf8a, fgf8b, fgf17, fgf18a, fgf18b, and fgf24). What are the evolutionary processes that led to the structural duplication and functional diversification of FgfD genes during vertebrate phylogeny? To study this question, we inve...

  18. Tunicates push the limits of animal evo-devo

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    Ferrier David EK

    2011-01-01

    Full Text Available Abstract The phylum to which humans belong, Chordata, takes its name from one of the major shared derived features of the group, the notochord. All chordates have a notochord, at least during embryogenesis, and there is little doubt about notochord homology at the morphological level. A study in BMC Evolutionary Biology now shows that there is greater variability in the molecular genetics underlying notochord development than previously appreciated. See research article: http://www.biomedcentral.com/1471-2148/11/21

  19. Larval nervous systems

    DEFF Research Database (Denmark)

    Nielsen, Claus

    2015-01-01

    as the adult central nervous system (CNS). Two structures can be recognized, viz. a pair of cerebral ganglia, which form the major part of the adult brain, and a blastoporal (circumblastoporal) nerve cord, which becomes differentiated into a perioral loop, paired or secondarily fused ventral nerve cords......, and the nervous systems of echinoderms and enteropneusts appear completely enigmatic. The ontogeny of the chordate CNS can perhaps be interpreted as a variation of the ontogeny of the blastoporal nerve cord of the protostomes, and this is strongly supported by patterns of gene expression. The presence...

  20. The repertoire of heterotrimeric G proteins and RGS proteins in Ciona intestinalis.

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    R Prasobh

    Full Text Available BACKGROUND: Heterotrimeric G proteins and regulators of G protein signaling (RGS proteins are key downstream interacting partners in the G protein coupled receptor (GPCR signaling pathway. The highly versatile GPCR transmembrane signaling system is a consequence of the coupling of a diverse set of receptors to downstream partners that include multiple subforms of G proteins and regulatory proteins including RGS proteins, among others. While the GPCR repertoire of Ciona intestinalis, representing the basal chordate is known, the repertoire of the heterotrimeric G proteins and RGS proteins is unknown. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we performed an in-silico genome-wide search of C. intestinalis for its complement of G proteins and RGS proteins. The identification of several one-to-one orthologs of human G proteins at the levels of families, subfamilies and types and of homologs of the human RGS proteins suggests an evolutionarily conserved structure function relationship of the GPCR signaling mechanism in the chordates. CONCLUSIONS: The C. intestinalis genome encodes a highly conserved, albeit, limited repertoire of the heterotrimeric G protein complexes with the size of subunit types comparable with that in lower eukaryotes.

  1. Are we degenerate tetraploids? More genomes, new facts

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    Abbasi Amir

    2008-12-01

    Full Text Available Abstract Background Within the bilaterians, the appearance and evolution of vertebrates is accompanied by enormous changes in anatomical, morphological and developmental features. This evolution of increased complexity has been associated with two genome duplications (2R hypothesis at the origin of vertebrates. However, in spite of extensive debate the validity of the 2R hypothesis remains controversial. The paucity of sequence data in early years of genomic era was an intrinsic obstacle in tracking the genome evolutionary history of chordates. Hypothesis In this article I review the 2R hypothesis by taking into account the recent availability of genomic sequence data for an expanding range of animals. I argue here that genetic architecture of lower metazoans and representatives of major vertebrate and invertebrate lineages provides no support for the hypothesis relating the origin of vertebrates with widespread gene or genome duplications. Conclusion It appears that much of the genomic complexity of modern vertebrates is very ancient likely predating the origin of chordates or even the Bilaterian-Nonbilaterian divergence. The origin and evolution of vertebrates is partly accompanied by an increase in gene number. However, neither can we take this subtle increase in gene number as an only causative factor for evolution of phenotypic complexity in modern vertebrates nor we can take it as a reflection of polyplodization events early in their history. Reviewers This article was reviewed by Eugene Koonin, Joshua Cherry (nominated by David Lipman, and Jerzy Jurka.

  2. Pre-bilaterian origin of the blastoporal axial organizer

    Science.gov (United States)

    Kraus, Yulia; Aman, Andy; Technau, Ulrich; Genikhovich, Grigory

    2016-01-01

    The startling capacity of the amphibian Spemann organizer to induce naïve cells to form a Siamese twin embryo with a second set of body axes is one of the hallmarks of developmental biology. However, the axis-inducing potential of the blastopore-associated tissue is commonly regarded as a chordate feature. Here we show that the blastopore lip of a non-bilaterian metazoan, the anthozoan cnidarian Nematostella vectensis, possesses the same capacity and uses the same molecular mechanism for inducing extra axes as chordates: Wnt/β-catenin signaling. We also demonstrate that the establishment of the secondary, directive axis in Nematostella by BMP signaling is sensitive to an initial Wnt signal, but once established the directive axis becomes Wnt-independent. By combining molecular analysis with experimental embryology, we provide evidence that the emergence of the Wnt/β-catenin driven blastopore-associated axial organizer predated the cnidarian-bilaterian split over 600 million years ago. PMID:27229764

  3. The Amphioxus SoxB Family: Implications for the Evolution of Vertebrate Placodes

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    Daniel Meulemans, Marianne Bronner-Fraser

    2007-01-01

    Full Text Available Cranial placodes are regions of thickened ectoderm that give rise to sense organs and ganglia in the vertebrate head. Homologous structures are proposed to exist in urochordates, but have not been found in cephalochordates, suggesting the first chordates lacked placodes. SoxB genes are expressed in discrete subsets of vertebrate placodes. To investigate how placodes arose and diversified in the vertebrate lineage we isolated the complete set of SoxB genes from amphioxus and analyzed their expression in embryos and larvae. We find that while amphioxus possesses a single SoxB2 gene, it has three SoxB1 paralogs. Like vertebrate SoxB1 genes, one of these paralogs is expressed in non-neural ectoderm destined to give rise to sensory cells. When considered in the context of other amphioxus placode marker orthologs, amphioxus SoxB1 expression suggests a diversity of sensory cell types utilizing distinct placode-type gene programs was present in the first chordates. Our data supports a model for placode evolution and diversification whereby the full complement of vertebrate placodes evolved by serial recruitment of distinct sensory cell specification programs to anterior pre-placodal ectoderm.

  4. Ordered expression pattern of Hox and ParaHox genes along the alimentary canal in the ascidian juvenile.

    Science.gov (United States)

    Nakayama, Satoshi; Satou, Kunihiro; Orito, Wataru; Ogasawara, Michio

    2016-07-01

    The Hox and ParaHox genes of bilateria share a similar expression pattern along the body axis and are known to be associated with anterior-posterior patterning. In vertebrates, the Hox genes are also expressed in presomitic mesoderm and gut endoderm and the ParaHox genes show a restricted expression pattern in the gut-related derivatives. Regional expression patterns in the embryonic central nervous system of the basal chordates amphioxus and ascidian have been reported; however, little is known about their endodermal expression in the alimentary canal. We focus on the Hox and ParaHox genes in the ascidian Ciona intestinalis and investigate the gene expression patterns in the juvenile, which shows morphological regionality in the alimentary canal. Gene expression analyses by using whole-mount in situ hybridization reveal that all Hox genes have a regional expression pattern along the alimentary canal. Expression of Hox1 to Hox4 is restricted to the posterior region of pharyngeal derivatives. Hox5 to Hox13 show an ordered expression pattern correlated with each Hox gene number along the postpharyngeal digestive tract. This expression pattern along the anterior-posterior axis has also been observed in Ciona ParaHox genes. Our observations suggest that ascidian Hox and ParaHox clusters are dispersed; however, the ordered expression patterns along the alimentary canal appear to be conserved among chordates. PMID:26837224

  5. Coherent Raman scattering microscopy for label-free imaging of live amphioxus

    Science.gov (United States)

    Yu, Zhilong; Chen, Tao; Zhang, Xiannian; Shen, Jie; Chen, Junyuan; Huang, Yanyi

    2012-03-01

    The existence of notochord distinguishes chordates from other phyla. Amphioxus is the only animal that keeps notochord during the whole life. Notochord is a unique organ for amphioxus, with its vertically arranged muscular notochordal plates, which is different from notochords in embryos of other chordates. We use stimulated Raman scattering (SRS) microscopy as a non-invasive technique to image the chemical components in amphioxus notochord. SRS provides chemical specificity as spontaneous Raman does and offers a higher sensitivity for fast acquisition. Unlike coherent anti- Stokes Raman scattering (CARS) microscopy, SRS microscopy doesn't have non-resonant background and can better differentiate different components in the specimen. We verify that the notochord is a protein-rich organ, which agrees well with the result of conventional staining methods. Detailed structures in notochordal plates and notochordal sheath are revealed by SRS microscopy with diffraction limited resolution. Our experiment shows that SRS microscopy is an excellent imaging tool for biochemical research with its intrinsic chemical selectivity, high spatiotemporal resolution and native 3D optical sectioning ability.

  6. An otx/nodal regulatory signature for posterior neural development in ascidians.

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    Agnès Roure

    2014-08-01

    Full Text Available In chordates, neural induction is the first step of a complex developmental process through which ectodermal cells acquire a neural identity. In ascidians, FGF-mediated neural induction occurs at the 32-cell stage in two blastomere pairs, precursors respectively of anterior and posterior neural tissue. We combined molecular embryology and cis-regulatory analysis to unveil in the ascidian Ciona intestinalis the remarkably simple proximal genetic network that controls posterior neural fate acquisition downstream of FGF. We report that the combined action of two direct FGF targets, the TGFβ factor Nodal, acting via Smad- and Fox-binding sites, and the transcription factor Otx suffices to trigger ascidian posterior neural tissue formation. Moreover, we found that this strategy is conserved in the distantly related ascidian Phallusia mammillata, in spite of extreme sequence divergence in the cis-regulatory sequences involved. Our results thus highlight that the modes of gene regulatory network evolution differ with the evolutionary scale considered. Within ascidians, developmental regulatory networks are remarkably robust to genome sequence divergence. Between ascidians and vertebrates, major fate determinants, such as Otx and Nodal, can be co-opted into different networks. Comparative developmental studies in ascidians with divergent genomes will thus uncover shared ascidian strategies, and contribute to a better understanding of the diversity of developmental strategies within chordates.

  7. Gonadotropin-releasing hormone and Adipokinetic hormone signaling systems share a common evolutionary origin

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    Marleen eLindemans

    2011-07-01

    Full Text Available Gonadotropin-releasing hormone (GnRH is a critical and central hormone that regulates vertebrate reproduction. The high conservation of GnRH signaling within the chordates (deuterostomians raises the important question as to whether its appearance might date back prior to the divergence of protostomian and deuterostomian lineages, about 700 million years ago. This leads to several important questions regarding the evolution of the GnRH family. Has GnRH been retained in most protostomian lineages? And was regulation of reproduction already a function of ancestral GnRH? The first question can undoubtedly be answered affirmatively since several GnRH-like sequences have been found in wide variety of protostomian and deuterostomian phyla. However, based on their different primary functions in different phyla – which implies a less unanimous answer on the second question – consistency in the nomenclature of this peptide family has been lost. A comparative and phylogenetic approach shows that the ecdysozoan adipokinetic hormones (AKHs, lophotrozoan GnRHs and chordate GnRHs are structurally related and that they all originate from a common ancestor. This review supports the view that the AKH-GnRH signaling system probably arose very early in metazoan evolution, prior to the divergence of protostomians and deuterostomians.

  8. Filter Feeding Mechanism Simulated Machine Paradigms – A Theoretical Approach

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    Channaveerappa. H,

    2014-01-01

    Full Text Available Bionics is the emerging branch of bio engineering where in the structures and functions of organism are utilized to construct a gadget that resembles the structure and performs similar function. The functional principles are also used to construct special gadgets to perform functions in the form of simulated robots. Animal models have also been used in creation of many structures/machines, for example the organization and flight mechanism of birds, echolocation in bats, and internal ear of mammals have been taken as blue prints to design aero planes, radars and telegraphic systems respectively. Here we are using ciliary feeding mechanisms in animals to create a machine that can be used for a particular purpose. Cilia are minute finger like protoplasmic extensions serve different functions like movement, creation of water current propelling and filter feeding in animals. In many invertebrates and lower chordates rotor movements of cilia create whirl pool of water current to obtain food material. Animals those use cilia for feeding are referred to ciliary feeders or filter feeders. The filter feeders are highly diverse in their habit but share common requirements. The filter feeders may be sessile or free swimming forms but the principles of feeding remains the same. In lower chordates the pharngometry of pharynx plays a decisive role in filter feeding. The filter feeding mechanism is highly evolved in animals through well designed evolutionary paradigms.

  9. Discovery of germline-related genes in Cephalochordate amphioxus: A genome wide survey using genome annotation and transcriptome data.

    Science.gov (United States)

    Yue, Jia-Xing; Li, Kun-Lung; Yu, Jr-Kai

    2015-12-01

    The generation of germline cells is a critical process in the reproduction of multicellular organisms. Studies in animal models have identified a common repertoire of genes that play essential roles in primordial germ cell (PGC) formation. However, comparative studies also indicate that the timing and regulation of this core genetic program vary considerably in different animals, raising the intriguing questions regarding the evolution of PGC developmental mechanisms in metazoans. Cephalochordates (commonly called amphioxus or lancelets) represent one of the invertebrate chordate groups and can provide important information about the evolution of developmental mechanisms in the chordate lineage. In this study, we used genome and transcriptome data to identify germline-related genes in two distantly related cephalochordate species, Branchiostoma floridae and Asymmetron lucayanum. Branchiostoma and Asymmetron diverged more than 120 MYA, and the most conspicuous difference between them is their gonadal morphology. We used important germline developmental genes in several model animals to search the amphioxus genome and transcriptome dataset for conserved homologs. We also annotated the assembled transcriptome data using Gene Ontology (GO) terms to facilitate the discovery of putative genes associated with germ cell development and reproductive functions in amphioxus. We further confirmed the expression of 14 genes in developing oocytes or mature eggs using whole mount in situ hybridization, suggesting their potential functions in amphioxus germ cell development. The results of this global survey provide a useful resource for testing potential functions of candidate germline-related genes in cephalochordates and for investigating differences in gonad developmental mechanisms between Branchiostoma and Asymmetron species.

  10. Observations on the evolution of the melanocortin receptor gene family: distinctive features of the melanocortin-2 receptor

    Directory of Open Access Journals (Sweden)

    Robert Michael Dores

    2013-04-01

    Full Text Available The melanocortin receptors are a gene family in the rhodopsin class of G protein-coupled receptors. Based on the analysis of several metazoan genome databases it appears that the melanocortin receptors are only found in chordates. The presence of five genes in the family (i.e., MC1R, MC2R, MC3R, MC4R, MC5R in representatives of the tetrapods indicates that the gene family is the result of two genome duplication events and one local gene duplication event during the evolution of the chordates. The melanocortin receptors are activated by melanocortin ligands (i.e., ACTH, α-MSH, β-MSH, γ-MSH, δ-MSH which are all derived from the polypeptide hormone/neuropeptide precursor, POMC, and as a result the functional evolution of the melanocortin receptors is intimately associated with the co-evolution of POMC endocrine and neuronal circuits. This review will consider the origin of the melanocortin receptors, and discuss the evolutionary relationship between MC2R, MC5R, and MC4R. In addition, this review will analyze the functional evolution of the mc2r gene in light of the co-evolution of the MRAP (Melanocortin-2 Receptor Accessory Protein gene family.

  11. Diverse ETS transcription factors mediate FGF signaling in the Ciona anterior neural plate.

    Science.gov (United States)

    Gainous, T Blair; Wagner, Eileen; Levine, Michael

    2015-03-15

    The ascidian Ciona intestinalis is a marine invertebrate belonging to the sister group of the vertebrates, the tunicates. Its compact genome and simple, experimentally tractable embryos make Ciona well-suited for the study of cell-fate specification in chordates. Tunicate larvae possess a characteristic chordate body plan, and many developmental pathways are conserved between tunicates and vertebrates. Previous studies have shown that FGF signals are essential for neural induction and patterning at sequential steps of Ciona embryogenesis. Here we show that two different ETS family transcription factors, Ets1/2 and Elk1/3/4, have partially redundant activities in the anterior neural plate of gastrulating embryos. Whereas Ets1/2 promotes pigment cell formation in lateral lineages, both Ets1/2 and Elk1/3/4 are involved in the activation of Myt1L in medial lineages and the restriction of Six3/6 expression to the anterior-most regions of the neural tube. We also provide evidence that photoreceptor cells arise from posterior regions of the presumptive sensory vesicle, and do not depend on FGF signaling. Cells previously identified as photoreceptor progenitors instead form ependymal cells and neurons of the larval brain. Our results extend recent findings on FGF-dependent patterning of anterior-posterior compartments in the Ciona central nervous system.

  12. Molecular phylogeny of metazoan intermediate filament proteins.

    Science.gov (United States)

    Erber, A; Riemer, D; Bovenschulte, M; Weber, K

    1998-12-01

    We have cloned cytoplasmic intermediate filament (IF) proteins from a large number of invertebrate phyla using cDNA probes, the monoclonal antibody IFA, peptide sequence information, and various RT-PCR procedures. Novel IF protein sequences reported here include the urochordata and nine protostomic phyla, i.e., Annelida, Brachiopoda, Chaetognatha, Echiura, Nematomorpha, Nemertea, Platyhelminthes, Phoronida, and Sipuncula. Taken together with the wealth of data on IF proteins of vertebrates and the results on IF proteins of Cephalochordata, Mollusca, Annelida, and Nematoda, two IF prototypes emerge. The L-type, which includes 35 sequences from 11 protostomic phyla, shares with the nuclear lamins the long version of the coil 1b subdomain and, in most cases, a homology segment of some 120 residues in the carboxyterminal tail domain. The S-type, which includes all four subfamilies (types I to IV) of vertebrate IF proteins, lacks 42 residues in the coil 1b subdomain and the carboxyterminal lamin homology segment. Since IF proteins from all three phyla of the chordates have the 42-residue deletion, this deletion arose in a progenitor prior to the divergence of the chordates into the urochordate, cephalochordate, and vertebrate lineages, possibly already at the origin of the deuterostomic branch. Four phyla recently placed into the protostomia on grounds of their 18S rDNA sequences (Brachiopoda, Nemertea, Phoronida, and Platyhelminthes) show IF proteins of the L-type and fit by sequence identity criteria into the lophotrochozoic branch of the protostomia. PMID:9847417

  13. Coelomogenesis during the abbreviated development of the echinoid Heliocidaris erythrogramma and the developmental origin of the echinoderm pentameral body plan.

    Science.gov (United States)

    Morris, Valerie B

    2011-01-01

    The development of the coeloms is described in an echinoid with an abbreviated larval development and shows the early morphogenesis of the coeloms of the adult stage. The development is described from images obtained by laser scanning confocal microscopy. The development in Heliocidaris erythrogramma is asymmetric with a larger left coelom forming on the larval-left side and a smaller right coelom forming on the larval-right side. The right coelom forms after the development of the left coelom is well advanced. The hydrocoele forms from the anterior part of the left coelom. The five lobes of the hydrocoele from which the pentamery of the adult derives take shape on the outer, distal wall of the anterior part of the left coelom. The hydrocoele separates from the more posterior part of the left coelom, which becomes the left posterior coelom. The lobes of the hydrocoele are named, based on the site of the connexion of the stone canal to the hydrocoele. The mouth is assumed to form by penetration through only the outer, distal wall of the hydrocoele and the ectoderm. Both larval and adult polarities are evident in this larva. A comparison with coelomogenesis in the asteroid Parvulastra exigua, which also has an abbreviated development, leads to predictions of homology between the echinoderm and chordate phyla that do not require the hypothesis of a dorsoventral inversion event in chordates.

  14. Structural shifts of aldehyde dehydrogenase enzymes were instrumental for the early evolution of retinoid-dependent axial patterning in metazoans.

    Science.gov (United States)

    Sobreira, Tiago J P; Marlétaz, Ferdinand; Simões-Costa, Marcos; Schechtman, Deborah; Pereira, Alexandre C; Brunet, Frédéric; Sweeney, Sarah; Pani, Ariel; Aronowicz, Jochanan; Lowe, Christopher J; Davidson, Bradley; Laudet, Vincent; Bronner, Marianne; de Oliveira, Paulo S L; Schubert, Michael; Xavier-Neto, José

    2011-01-01

    Aldehyde dehydrogenases (ALDHs) catabolize toxic aldehydes and process the vitamin A-derived retinaldehyde into retinoic acid (RA), a small diffusible molecule and a pivotal chordate morphogen. In this study, we combine phylogenetic, structural, genomic, and developmental gene expression analyses to examine the evolutionary origins of ALDH substrate preference. Structural modeling reveals that processing of small aldehydes, such as acetaldehyde, by ALDH2, versus large aldehydes, including retinaldehyde, by ALDH1A is associated with small versus large substrate entry channels (SECs), respectively. Moreover, we show that metazoan ALDH1s and ALDH2s are members of a single ALDH1/2 clade and that during evolution, eukaryote ALDH1/2s often switched between large and small SECs after gene duplication, transforming constricted channels into wide opened ones and vice versa. Ancestral sequence reconstructions suggest that during the evolutionary emergence of RA signaling, the ancestral, narrow-channeled metazoan ALDH1/2 gave rise to large ALDH1 channels capable of accommodating bulky aldehydes, such as retinaldehyde, supporting the view that retinoid-dependent signaling arose from ancestral cellular detoxification mechanisms. Our analyses also indicate that, on a more restricted evolutionary scale, ALDH1 duplicates from invertebrate chordates (amphioxus and ascidian tunicates) underwent switches to smaller and narrower SECs. When combined with alterations in gene expression, these switches led to neofunctionalization from ALDH1-like roles in embryonic patterning to systemic, ALDH2-like roles, suggesting functional shifts from signaling to detoxification. PMID:21169504

  15. Thyroid hormones and postembryonic development in amniotes.

    Science.gov (United States)

    Holzer, Guillaume; Laudet, Vincent

    2013-01-01

    In chordates, metamorphosis is a developmental event well described in amphibians in which thyroid hormone triggers this event. Interestingly, among amphibians, several variations upon the eggs/tadpole/frog developmental sequence are observed such as direct development or neoteny. The fact that TH-regulated metamorphosis is conserved in invertebrate chordates such as amphioxus implies that this event is an ancient feature of all vertebrates. This allows us to propose that TH may play an important role in coordinating the postembryonic development of apparently nonmetamorphosing vertebrates such as mammals or sauropsids. Indeed, the observations of thyroid hormone levels in mammals and sauropsids draw interesting parallels with what is observed during amphibian metamorphosis. At the physiological level, the increase of thyroid hormone signaling is required for the normal development particularly for the intestine and the brain. At the behavioral level, a peak of TH often precedes the autonomy of the young from parental care. At the ecological level, offspring with a TH peak close to birth/hatching tends to be precocial young whereas offspring with a TH peak long after birth/hatching tends to be altricial young. Taken together, these observations in amniotes, which are not considered as undergoing metamorphosis during their development, are consistent with the idea of a late developmental step controlled by TH and allowing the accession to the adult ecological niche. Thus, according to this view, at the molecular level all vertebrates undergo a period of remodeling controlled by TH that is reminiscent of metamorphosis. PMID:23347527

  16. The origins and evolution of vertebrate metamorphosis.

    Science.gov (United States)

    Laudet, Vincent

    2011-09-27

    Metamorphosis, classically defined as a spectacular post-embryonic transition, is well exemplified by the transformation of a tadpole into a frog. It implies the appearance of new body parts (such as the limbs), the resorption of larval features (such as the tail) and the remodelling of many organs (such as the skin or the intestine). In vertebrates, metamorphosis has been well characterized in anuran amphibians, where thyroid hormones orchestrate the intricate and seemingly contradictory changes observed at the cellular and tissue levels. Thyroid hormones control a complex hierarchical cascade of target genes via binding to specific receptors, TRα and TRβ, ligand-activated transcription factors belonging to the nuclear receptor superfamily. Metamorphosis is actually widespread in the vertebrates, though quite diverse in the way it manifests in a particular species. Furthermore, evolutionary and ecological variations of this key event, from paedomorphosis to direct development, provide an excellent illustration of how tinkering with a control pathway can lead to divergent life histories. The study of invertebrate chordates has also shed light on the origin of metamorphosis. The available data suggest that post-embryonic remodelling governed by thyroid hormones is an ancestral feature of chordates. According to this view, metamorphosis of the anurans is an extreme example of a widespread life history transition. PMID:21959163

  17. Identification of differentially expressed genes from multipotent epithelia at the onset of an asexual development.

    Science.gov (United States)

    Ricci, Lorenzo; Chaurasia, Ankita; Lapébie, Pascal; Dru, Philippe; Helm, Rebecca R; Copley, Richard R; Tiozzo, Stefano

    2016-01-01

    Organisms that have evolved alternative modes of reproduction, complementary to the sexual mode, are found across metazoans. The chordate Botryllus schlosseri is an emerging model for asexual development studies. Botryllus can rebuild its entire body from a portion of adult epithelia in a continuous and stereotyped process called blastogenesis. Anatomy and ontogenies of blastogenesis are well described, however molecular signatures triggering this developmental process are entirely unknown. We isolated tissues at the site of blastogenesis onset and from the same epithelia where this process is never triggered. We linearly amplified an ultra-low amount of mRNA (strategies with a de novo assembled transcriptome and partially assembled genome as references, additionally a self-mapping strategy on the dataset. A subset of differentially expressed genes were analyzed and validated by in situ hybridization. The comparison of different analyses allowed us to isolate stringent sets of target genes, including transcripts with potential involvement in the onset of a non-embryonic developmental pathway. The results provide a good entry point to approach regenerative event in a basal chordate. PMID:27264734

  18. Review: Evolution of GnIH structure and function

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    Tomohiro eOsugi

    2014-08-01

    Full Text Available Discovery of gonadotropin-inhibitory hormone (GnIH in the Japanese quail in 2000 was the first to demonstrate the existence of a hypothalamic neuropeptide inhibiting gonadotropin release. We now know that GnIH regulates reproduction by inhibiting gonadotropin synthesis and release via action on the gonadotropin-releasing hormone (GnRH system and the gonadotrope in various vertebrates. GnIH peptides identified in birds and mammals have a common LPXRF-amide (X = L or Q motif at the C-terminus and inhibits pituitary gonadotropin secretion. However, the function and structure of GnIH peptides were diverse in fish. Goldfish GnIHs possessing a C-terminal LPXRF-amide motif had both stimulatory and inhibitory effects on gonadotropin synthesis or release. The C-terminal sequence of grass puffer and medaka GnIHs were MPQRF-amide. To investigate the evolutionary origin of GnIH and its ancestral structure and function, we searched for GnIH in agnathans, the most ancient lineage of vertebrates. We identified GnIH precursor gene and mature GnIH peptides with C-terminal QPQRF-amide or RPQRF-amide from the brain of sea lamprey. Lamprey GnIH fibers were in close proximity to GnRH-III neurons. Further, one of lamprey GnIHs stimulated the expression of lamprey GnRH-III peptide in the hypothalamus and gonadotropic hormone β mRNA expression in the pituitary. We further identified the ancestral form of GnIH, which had a C-terminal RPQRF-amide, and its receptors in amphioxus, the most basal chordate species. The amphioxus GnIH inhibited cAMP signaling in vitro. In sum, the original forms of GnIH may date back to the time of the emergence of early chordates. GnIH peptides may have had various C-terminal structures slightly different from LPXRF-amide in basal chordates, which had stimulatory and/or inhibitory functions on reproduction. The C-terminal LPXRF-amide structure and its inhibitory function on reproduction may be selected in later-evolved vertebrates, such as

  19. Evolutionary changes in the notochord genetic toolkit: a comparative analysis of notochord genes in the ascidian Ciona and the larvacean Oikopleura

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    Jiang Di

    2011-01-01

    Full Text Available Abstract Background The notochord is a defining feature of the chordate clade, and invertebrate chordates, such as tunicates, are uniquely suited for studies of this structure. Here we used a well-characterized set of 50 notochord genes known to be targets of the notochord-specific Brachyury transcription factor in one tunicate, Ciona intestinalis (Class Ascidiacea, to begin determining whether the same genetic toolkit is employed to build the notochord in another tunicate, Oikopleura dioica (Class Larvacea. We identified Oikopleura orthologs of the Ciona notochord genes, as well as lineage-specific duplicates for which we determined the phylogenetic relationships with related genes from other chordates, and we analyzed their expression patterns in Oikopleura embryos. Results Of the 50 Ciona notochord genes that were used as a reference, only 26 had clearly identifiable orthologs in Oikopleura. Two of these conserved genes appeared to have undergone Oikopleura- and/or tunicate-specific duplications, and one was present in three copies in Oikopleura, thus bringing the number of genes to test to 30. We were able to clone and test 28 of these genes. Thirteen of the 28 Oikopleura orthologs of Ciona notochord genes showed clear expression in all or in part of the Oikopleura notochord, seven were diffusely expressed throughout the tail, six were expressed in tissues other than the notochord, while two probes did not provide a detectable signal at any of the stages analyzed. One of the notochord genes identified, Oikopleura netrin, was found to be unevenly expressed in notochord cells, in a pattern reminiscent of that previously observed for one of the Oikopleura Hox genes. Conclusions A surprisingly high number of Ciona notochord genes do not have apparent counterparts in Oikopleura, and only a fraction of the evolutionarily conserved genes show clear notochord expression. This suggests that Ciona and Oikopleura, despite the morphological similarities

  20. Extensive intron gain in the ancestor of placental mammals

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    Kordiš Dušan

    2011-11-01

    Full Text Available Abstract Background Genome-wide studies of intron dynamics in mammalian orthologous genes have found convincing evidence for loss of introns but very little for intron turnover. Similarly, large-scale analysis of intron dynamics in a few vertebrate genomes has identified only intron losses and no gains, indicating that intron gain is an extremely rare event in vertebrate evolution. These studies suggest that the intron-rich genomes of vertebrates do not allow intron gain. The aim of this study was to search for evidence of de novo intron gain in domesticated genes from an analysis of their exon/intron structures. Results A phylogenomic approach has been used to analyse all domesticated genes in mammals and chordates that originated from the coding parts of transposable elements. Gain of introns in domesticated genes has been reconstructed on well established mammalian, vertebrate and chordate phylogenies, and examined as to where and when the gain events occurred. The locations, sizes and amounts of de novo introns gained in the domesticated genes during the evolution of mammals and chordates has been analyzed. A significant amount of intron gain was found only in domesticated genes of placental mammals, where more than 70 cases were identified. De novo gained introns show clear positional bias, since they are distributed mainly in 5' UTR and coding regions, while 3' UTR introns are very rare. In the coding regions of some domesticated genes up to 8 de novo gained introns have been found. Intron densities in Eutheria-specific domesticated genes and in older domesticated genes that originated early in vertebrates are lower than those for normal mammalian and vertebrate genes. Surprisingly, the majority of intron gains have occurred in the ancestor of placentals. Conclusions This study provides the first evidence for numerous intron gains in the ancestor of placental mammals and demonstrates that adequate taxon sampling is crucial for

  1. Tubular Heart Pumping Mechanisms in Ciona Intestinalis

    Science.gov (United States)

    Battista, Nicholas; Miller, Laura

    2015-11-01

    In vertebrate embryogenesis, the first organ to form is the heart, beginning as a primitive heart tube. However, many invertebrates have tubular hearts from infancy through adulthood. Heart tubes have been described as peristaltic and impedance pumps. Impedance pumping assumes a single actuation point of contraction, while traditional peristalsis assumes a traveling wave of actuation. In addition to differences in flow, this inherently implies differences in the conduction system. It is possible to transition from pumping mechanism to the other with a change in the diffusivity of the action potential. In this work we consider the coupling between the fluid dynamics and electrophysiology of both mechanisms, within a basal chordate, the tunicate. Using CFD with a neuro-mechanical model of tubular pumping, we discuss implications of the both mechanisms. Furthermore, we discuss the implications of the pumping mechanism on evolution and development.

  2. AmphiFoxQ2, a novel winged helix/forkhead gene, exclusively marks the anterior end of the amphioxus embryo

    Science.gov (United States)

    Yu, Jr-Kai; Holland, Nicholas D.; Holland, Linda Z.

    2003-01-01

    A full-length FoxQ-related gene (AmphiFoxQ2) was isolated from amphioxus. Expression is first detectable in the animal/anterior hemisphere at the mid blastula stage. The midpoint of this expression domain coincides with the anterior pole of the embryo and is offset dorsally by about 20 degrees from the animal pole. During the gastrula stage, expression is limited to the anterior ectoderm. By the early neurula stage, expression remains in the anterior ectoderm and also appears in the adjacent anterior mesendoderm. By the early larval stages, expression is detectable in the anteriormost ectoderm and in the rostral tip of the notochord. AmphiFoxQ2 is never expressed anywhere except at the anterior tip of amphioxus embryos and larvae. This is the first gene known that exclusively marks the anterior pole of chordate embryos. It may, therefore, play an important role in establishing and/or maintaining the anterior/posterior axis.

  3. Development of Bipotent Cardiac/Skeletal Myogenic Progenitors from MESP1+ Mesoderm

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    Sunny Sun-Kin Chan

    2016-01-01

    Full Text Available The branchiomeric skeletal muscles co-evolved with new chambers of the heart to enable predatory feeding in chordates. These co-evolved tissues develop from a common population in anterior splanchnic mesoderm, referred to as cardiopharyngeal mesoderm (CPM. The regulation and development of CPM are poorly understood. We describe an embryonic stem cell-based system in which MESP1 drives a PDGFRA+ population with dual cardiac and skeletal muscle differentiation potential, and gene expression resembling CPM. Using this system, we investigate the regulation of these bipotent progenitors, and find that cardiac specification is governed by an antagonistic TGFβ-BMP axis, while skeletal muscle specification is enhanced by Rho kinase inhibition. We define transcriptional signatures of the first committed CPM-derived cardiac and skeletal myogenic progenitors, and discover surface markers to distinguish cardiac (PODXL+ from the skeletal muscle (CDH4+ CPM derivatives. These tools open an accessible window on this developmentally and evolutionarily important population.

  4. Reconstructing Ancient Forms of Life

    Science.gov (United States)

    Benner, Steven A.

    1998-01-01

    Progress in the past three months has occurred in two areas, reconstruction of ancestral proteins and improved understanding of chemical features that are likely to be universal in generic matter regardless of its genesis. Ancestral ribonucleases have been reconstructed, and an example has been developed that shows how physiological function can be assigned to in vitro behaviors observed in biological systems. Sequence data have been collected to permit the reconstruction of src homology 2 domains that underwent radiative divergence at the time of the radiative divergence of chordates. New studies have been completed that show how genetic matter (or its remnants) might be detected on Mars (or other non-terrean locations.) Last, the first in vitro selection experiments have been completed using a nucleoside library carrying positively charged functionality, illustrating the importance of non-standard nucleotides to those attempting to obtain evidence for an "RNA world" as an early episode of life on earth.

  5. Bio-inspired flow sensor from printed PEDOT:PSS micro-hairs

    International Nuclear Information System (INIS)

    This paper reports on the creation of a low-cost, disposable sensor for low flow velocities, constructed from extruded micro-sized ‘hair’ of conducting polymer PEDOT. These microstructures are inspired by hair strands found in many arthropods and chordates, which play a prime role in sensing air flows. The paper describes the fabrication techniques and the initial prototype testing results toward employing this sensing mechanism in applications requiring sensing of low flow rates such as a flow sensor in neonatal resuscitators. The fabricated 1000 μm long, 6 μm diameter micro-hairs mimic the bending movement of tactile hair strands to sense the velocity of air flow. The prototype sensor developed is a four-level direct digital-output sensor and is capable of detecting flow velocities of up to 0.97 m s−1. (paper)

  6. Differential mesodermal expression of two amphioxus MyoD family members (AmphiMRF1 and AmphiMRF2)

    Science.gov (United States)

    Schubert, Michael; Meulemans, Daniel; Bronner-Fraser, Marianne; Holland, Linda Z.; Holland, Nicholas D.

    2003-01-01

    To explore the evolution of myogenic regulatory factors in chordates, we isolated two MyoD family genes (AmphiMRF1 and AmphiMRF2) from amphioxus. AmphiMRF1 is first expressed at the late gastrula in the paraxial mesoderm. As the first somites form, expression is restricted to their myotomal region. In the early larva, expression is strongest in the most anterior and most posterior somites. AmphiMRF2 transcription begins at mid/late gastrula in the paraxial mesoderm, but never spreads into its most anterior region. Through much of the neurula stage, AmphiMRF2 expression is strong in the myotomal region of all somites except the most anterior pair; by late neurula expression is downregulated except in the most posterior somites forming just rostral to the tail bud. These two MRF genes of amphioxus have partly overlapping patterns of mesodermal expression and evidently duplicated independent of the diversification of the vertebrate MRF family.

  7. 3D model of amphioxus steroid receptor complexed with estradiol

    International Nuclear Information System (INIS)

    The origins of signaling by vertebrate steroids are not fully understood. An important advance was the report that an estrogen-binding steroid receptor [SR] is present in amphioxus, a basal chordate with a similar body plan as vertebrates. To investigate the evolution of estrogen-binding to steroid receptors, we constructed a 3D model of amphioxus SR complexed with estradiol. This 3D model indicates that although the SR is activated by estradiol, some interactions between estradiol and human ERα are not conserved in the SR, which can explain the low affinity of estradiol for the SR. These differences between the SR and ERα in the steroid-binding domain are sufficient to suggest that another steroid is the physiological regulator of the SR. The 3D model predicts that mutation of Glu-346 to Gln will increase the affinity of testosterone for amphioxus SR and elucidate the evolution of steroid-binding to nuclear receptors.

  8. An amphioxus Krox gene: insights into vertebrate hindbrain evolution.

    Science.gov (United States)

    Knight, R D; Panopoulou, G D; Holland, P W; Shimeld, S M

    2000-10-01

    The transcription factor Krox-20 has roles in the maintenance of segmentation and specification of segment identity in the vertebrate hindbrain. Overt hindbrain segmentation is a vertebrate novelty, and is not seen in invertebrate chordates such as amphioxus and tunicates. To test if the roles of Krox-20 are also derived, we cloned a Krox-20 related gene, AmphiKrox, from amphioxus. AmphiKrox is related to a small family of vertebrate Krox genes and is expressed in the most anterior region of the amphioxus brain and in the club shaped gland, a secretory organ that develops in the anterior pharynx. Neither expression domain overlaps with the expression of AmphiHox-1, -2, -3 or -4, suggesting that the roles of Krox-20 in hindbrain segmentation and in Hox gene regulation were acquired concomitant with the duplication of Krox genes in vertebrate evolution. PMID:11180801

  9. Blurring Borders: Innate Immunity with Adaptive Features

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    K. Kvell

    2007-01-01

    Full Text Available Adaptive immunity has often been considered the penultimate of immune capacities. That system is now being deconstructed to encompass less stringent rules that govern its initiation, actual effector activity, and ambivalent results. Expanding the repertoire of innate immunity found in all invertebrates has greatly facilitated the relaxation of convictions concerning what actually constitutes innate and adaptive immunity. Two animal models, incidentally not on the line of chordate evolution (C. elegans and Drosophila, have contributed enormously to defining homology. The characteristics of specificity and memory and whether the antigen is pathogenic or nonpathogenic reveal considerable information on homology, thus deconstructing the more fundamentalist view. Senescence, cancer, and immunosuppression often associated with mammals that possess both innate and adaptive immunity also exist in invertebrates that only possess innate immunity. Strict definitions become blurred casting skepticism on the utility of creating rigid definitions of what innate and adaptive immunity are without considering overlaps.

  10. Homeobox gene expression in Brachiopoda

    DEFF Research Database (Denmark)

    Altenburger, Andreas; Martinez, Pedro; Wanninger, Andreas

    2011-01-01

    The molecular control that underlies brachiopod ontogeny is largely unknown. In order to contribute to this issue we analyzed the expression pattern of two homeobox containing genes, Not and Cdx, during development of the rhynchonelliform (i.e., articulate) brachiopod Terebratalia transversa....... Not is a homeobox containing gene that regulates the formation of the notochord in chordates, while Cdx (caudal) is a ParaHox gene involved in the formation of posterior tissues of various animal phyla. The T. transversa homolog, TtrNot, is expressed in the ectoderm from the beginning of gastrulation until...... formation. TtrNot expression is absent in unfertilized eggs, in embryos prior to gastrulation, and in settled individuals during and after metamorphosis. Comparison with the expression patterns of Not genes in other metazoan phyla suggests an ancestral role for this gene in gastrulation and germ layer...

  11. A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis

    Energy Technology Data Exchange (ETDEWEB)

    Keys, David N.; Lee, Byung-in; Di Gregorio, Anna; Harafuji, Naoe; Detter, Chris; Wang, Mei; Kahsai, Orsalem; Ahn, Sylvia; Arellano, Andre; Zhang, Quin; Trong, Stephan; Doyle, Sharon A.; Satoh, Noriyuki; Satou, Yutaka; Saiga, Hidetoshi; Christian, Allen; Rokhsar, Dan; Hawkins, Trevor L.; Levine, Mike; Richardson, Paul

    2005-01-05

    A screen for the systematic identification of cis-regulatory elements within large (>100 kb) genomic domains containing Hox genes was performed by using the basal chordate Ciona intestinalis. Randomly generated DNA fragments from bacterial artificial chromosomes containing two clusters of Hox genes were inserted into a vector upstream of a minimal promoter and lacZ reporter gene. A total of 222 resultant fusion genes were separately electroporated into fertilized eggs, and their regulatory activities were monitored in larvae. In sum, 21 separable cis-regulatory elements were found. These include eight Hox linked domains that drive expression in nested anterior-posterior domains of ectodermally derived tissues. In addition to vertebrate-like CNS regulation, the discovery of cis-regulatory domains that drive epidermal transcription suggests that C. intestinalis has arthropod-like Hox patterning in the epidermis.

  12. Expression pattern of the Brachyury gene in the arrow worm paraspadella gotoi (chaetognatha).

    Science.gov (United States)

    Takada, Norio; Goto, Taichiro; Satoh, Nori

    2002-03-01

    Arrow worms (the phylum Chaetognatha), which are among the major marine planktonic animals, are direct developers and exhibit features characteristic of both deuterostomes and protostomes. In particular, the embryonic development of arrow worms appears to be of the deuterostome type. Brachyury functions critically in the formation of the notochord in chordates, whereas the gene is expressed in both the blastopore and stomodeum invagination regions in embryos of hemichordates and echinoderms. Here we analyzed the expression of Brachyury (Pg-Bra) in the arrow worm Paraspadella gotoi and showed that Pg-Bra is expressed in the blastopore region and the stomodeum region in the embryo and then around the mouth opening region at the time of hatching. The expression of Pg-Bra in the embryo resembles that of Brachyury in embryos of hemichordates and echinoderms, whereas that in the mouth opening region in the hatchling appears to be novel. PMID:11892013

  13. A new phyllopod bed-like assemblage from the Burgess Shale of the Canadian Rockies.

    Science.gov (United States)

    Caron, Jean-Bernard; Gaines, Robert R; Aria, Cédric; Mángano, M Gabriela; Streng, Michael

    2014-01-01

    Burgess Shale-type fossil assemblages provide the best evidence of the 'Cambrian explosion'. Here we report the discovery of an extraordinary new soft-bodied fauna from the Burgess Shale. Despite its proximity (ca. 40 km) to Walcott's original locality, the Marble Canyon fossil assemblage is distinct, and offers new insights into the initial diversification of metazoans, their early morphological disparity, and the geographic ranges and longevity of many Cambrian taxa. The arthropod-dominated assemblage is remarkable for its high density and diversity of soft-bodied fossils, as well as for its large proportion of new species (22% of total diversity) and for the preservation of hitherto unreported anatomical features, including in the chordate Metaspriggina and the arthropod Mollisonia. The presence of the stem arthropods Misszhouia and Primicaris, previously known only from the early Cambrian of China, suggests that the palaeogeographic ranges and longevity of Burgess Shale taxa may be underestimated. PMID:24513643

  14. Otx1 gene-controlled morphogenesis of the horizontal semicircular canal and the origin of the gnathostome characteristics.

    Science.gov (United States)

    Mazan, S; Jaillard, D; Baratte, B; Janvier, P

    2000-01-01

    The horizontal semicircular canal of the inner ear is a unique feature of gnathostomes and is predated by the two vertical semicircular canals, which are already present in lampreys and some fossil, armored jawless vertebrates regarded as close relatives of gnathostomes. Inactivation in mice of the orthodenticle-related gene Otx1 results in the absence of this structure. In bony fishes and tetrapods (osteichthyans), this gene belongs to a small multigene family comprising at least two orthology classes, Otx1 and Otx2. We report that, as in the mouse, xenopus and zebrafish, Otx1- and Otx2-related genes are present in a chondrichthyan, the dogfish Scyliorhinus canicula, with an Otx1 expression domain in the otocyst very similar to those observed in osteichthyans. A strong correlation is thus observed in extant vertebrates between the distribution of the horizontal semicircular canal and the presence of an Otx1 ortholog expressed in the inner ear, which supports the hypothesis that the absence of this characteristic in Otx1-/- mice may correspond to an atavism. The same conclusion applies to two other gnathostome-specific characteristics also deleted in Otx1-/- mice, the utriculosaccular duct and the ciliary process. Together with functional analyses of Otx1 and Otx2 genes in mice and comparative analyses of the Otx gene families characterized in chordates, these discoveries lead to the hypothesis that some of the anatomic characteristics of gnathostomes have appeared quite suddenly and almost simultaneously in vertebrate evolution, possibly as a consequence of gene functional diversifications following duplications of an ancestral chordate gene. PMID:11252561

  15. Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis.

    Science.gov (United States)

    Yokomori, Rui; Shimai, Kotaro; Nishitsuji, Koki; Suzuki, Yutaka; Kusakabe, Takehiro G; Nakai, Kenta

    2016-01-01

    The tunicate Ciona intestinalis, an invertebrate chordate, has recently emerged as a powerful model organism for gene regulation analysis. However, few studies have been conducted to identify and characterize its transcription start sites (TSSs) and promoters at the genome-wide level. Here, using TSS-seq, we identified TSSs at the genome-wide scale and characterized promoters in C. intestinalis. Specifically, we identified TSS clusters (TSCs), high-density regions of TSS-seq tags, each of which appears to originate from an identical promoter. TSCs were found not only at known TSSs but also in other regions, suggesting the existence of many unknown transcription units in the genome. We also identified candidate promoters of 79 ribosomal protein (RP) genes, each of which had the major TSS in a polypyrimidine tract and showed a sharp TSS distribution like human RP gene promoters. Ciona RP gene promoters, however, did not appear to have typical TATA boxes, unlike human RP gene promoters. In Ciona non-RP promoters, two pyrimidine-purine dinucleotides, CA and TA, were frequently used as TSSs. Despite the absence of CpG islands, Ciona TATA-less promoters showed low expression specificity like CpG-associated human TATA-less promoters. By using TSS-seq, we also predicted trans-spliced gene TSSs and found that their downstream regions had higher G+T content than those of non-trans-spliced gene TSSs. Furthermore, we identified many putative alternative promoters, some of which were regulated in a tissue-specific manner. Our results provide valuable information about TSSs and promoter characteristics in C. intestinalis and will be helpful in future analysis of transcriptional regulation in chordates.

  16. The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s.

    Science.gov (United States)

    Nelson, David R; Goldstone, Jared V; Stegeman, John J

    2013-02-19

    The neighbourhoods of cytochrome P450 (CYP) genes in deuterostome genomes, as well as those of the cnidarians Nematostella vectensis and Acropora digitifera and the placozoan Trichoplax adhaerens were examined to find clues concerning the evolution of CYP genes in animals. CYP genes created by the 2R whole genome duplications in chordates have been identified. Both microsynteny and macrosynteny were used to identify genes that coexisted near CYP genes in the animal ancestor. We show that all 11 CYP clans began in a common gene environment. The evidence implies the existence of a single locus, which we term the 'cytochrome P450 genesis locus', where one progenitor CYP gene duplicated to create a tandem set of genes that were precursors of the 11 animal CYP clans: CYP Clans 2, 3, 4, 7, 19, 20, 26, 46, 51, 74 and mitochondrial. These early CYP genes existed side by side before the origin of cnidarians, possibly with a few additional genes interspersed. The Hox gene cluster, WNT genes, an NK gene cluster and at least one ARF gene were close neighbours to this original CYP locus. According to this evolutionary scenario, the CYP74 clan originated from animals and not from land plants nor from a common ancestor of plants and animals. The CYP7 and CYP19 families that are chordate-specific belong to CYP clans that seem to have originated in the CYP genesis locus as well, even though this requires many gene losses to explain their current distribution. The approach to uncovering the CYP genesis locus overcomes confounding effects because of gene conversion, sequence divergence, gene birth and death, and opens the way to understanding the biodiversity of CYP genes, families and subfamilies, which in animals has been obscured by more than 600 Myr of evolution.

  17. Broken colinearity of the amphioxus Hox cluster

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    Pascual-Anaya Juan

    2012-12-01

    Full Text Available Abstract Background In most eumetazoans studied so far, Hox genes determine the identity of structures along the main body axis. They are usually linked in genomic clusters and, in the case of the vertebrate embryo, are expressed with spatial and temporal colinearity. Outside vertebrates, temporal colinearity has been reported in the cephalochordate amphioxus (the least derived living relative of the chordate ancestor but only for anterior and central genes, namely Hox1 to Hox4 and Hox6. However, most of the Hox gene expression patterns in amphioxus have not been reported. To gain global insights into the evolution of Hox clusters in chordates, we investigated a more extended expression profile of amphioxus Hox genes. Results Here we report an extended expression profile of the European amphioxus Branchiostoma lanceolatum Hox genes and describe that all Hox genes, except Hox13, are expressed during development. Interestingly, we report the breaking of both spatial and temporal colinearity for at least Hox6 and Hox14, which thus have escaped from the classical Hox code concept. We show a previously unidentified Hox6 expression pattern and a faint expression for posterior Hox genes in structures such as the posterior mesoderm, notochord, and hindgut. Unexpectedly, we found that amphioxus Hox14 had the most divergent expression pattern. This gene is expressed in the anterior cerebral vesicle and pharyngeal endoderm. Amphioxus Hox14 expression represents the first report of Hox gene expression in the most anterior part of the central nervous system. Nevertheless, despite these divergent expression patterns, amphioxus Hox6 and Hox14 seem to be still regulated by retinoic acid. Conclusions Escape from colinearity by Hox genes is not unusual in either vertebrates or amphioxus and we suggest that those genes escaping from it are probably associated with the patterning of lineage-specific morphological traits, requiring the loss of those developmental

  18. The sea lamprey Petromyzon marinus genome reveals the early origin of several chemosensory receptor families in the vertebrate lineage

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    Zhang Ziping

    2009-07-01

    Full Text Available Abstract Background In gnathostomes, chemosensory receptors (CR expressed in olfactory epithelia are encoded by evolutionarily dynamic gene families encoding odorant receptors (OR, trace amine-associated receptors (TAAR, V1Rs and V2Rs. A limited number of OR-like sequences have been found in invertebrate chordate genomes. Whether these gene families arose in basal or advanced vertebrates has not been resolved because these families have not been examined systematically in agnathan genomes. Results Petromyzon is the only extant jawless vertebrate whose genome has been sequenced. Known to be exquisitely sensitive to several classes of odorants, lampreys detect fewer amino acids and steroids than teleosts. This reduced number of detectable odorants is indicative of reduced numbers of CR gene families or a reduced number of genes within CR families, or both, in the sea lamprey. In the lamprey genome we identified a repertoire of 59 intact single-exon CR genes, including 27 OR, 28 TAAR, and four V1R-like genes. These three CR families were expressed in the olfactory organ of both parasitic and adult life stages. Conclusion An extensive search in the lamprey genome failed to identify potential orthologs or pseudogenes of the multi-exon V2R family that is greatly expanded in teleost genomes, but did find intact calcium-sensing receptors (CASR and intact metabotropic glutamate receptors (MGR. We conclude that OR and V1R arose in chordates after the cephalochordate-urochordate split, but before the diversification of jawed and jawless vertebrates. The advent and diversification of V2R genes from glutamate receptor-family G protein-coupled receptors, most likely the CASR, occurred after the agnathan-gnathostome divergence.

  19. Origin and evolution of retinoid isomerization machinery in vertebrate visual cycle: hint from jawless vertebrates.

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    Eugenia Poliakov

    Full Text Available In order to maintain visual sensitivity at all light levels, the vertebrate eye possesses a mechanism to regenerate the visual pigment chromophore 11-cis retinal in the dark enzymatically, unlike in all other taxa, which rely on photoisomerization. This mechanism is termed the visual cycle and is localized to the retinal pigment epithelium (RPE, a support layer of the neural retina. Speculation has long revolved around whether more primitive chordates, such as tunicates and cephalochordates, anticipated this feature. The two key enzymes of the visual cycle are RPE65, the visual cycle all-trans retinyl ester isomerohydrolase, and lecithin:retinol acyltransferase (LRAT, which generates RPE65's substrate. We hypothesized that the origin of the vertebrate visual cycle is directly connected to an ancestral carotenoid oxygenase acquiring a new retinyl ester isomerohydrolase function. Our phylogenetic analyses of the RPE65/BCMO and N1pC/P60 (LRAT superfamilies show that neither RPE65 nor LRAT orthologs occur in tunicates (Ciona or cephalochordates (Branchiostoma, but occur in Petromyzon marinus (Sea Lamprey, a jawless vertebrate. The closest homologs to RPE65 in Ciona and Branchiostoma lacked predicted functionally diverged residues found in all authentic RPE65s, but lamprey RPE65 contained all of them. We cloned RPE65 and LRATb cDNAs from lamprey RPE and demonstrated appropriate enzymatic activities. We show that Ciona ß-carotene monooxygenase a (BCMOa (previously annotated as an RPE65 has carotenoid oxygenase cleavage activity but not RPE65 activity. We verified the presence of RPE65 in lamprey RPE by immunofluorescence microscopy, immunoblot and mass spectrometry. On the basis of these data we conclude that the crucial transition from the typical carotenoid double bond cleavage functionality (BCMO to the isomerohydrolase functionality (RPE65, coupled with the origin of LRAT, occurred subsequent to divergence of the more primitive chordates

  20. Prospective protochordate homologs of vertebrate midbrain and MHB, with some thoughts on MHB origins

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    Thurston C. Lacalli

    2006-01-01

    Full Text Available The MHB (midbrain-hindbrain boundary is a key organizing center in the vertebrate brain characterized by highly conserved patterns of gene expression. The evidence for an MHB homolog in protochordates is equivocal, the "neck" region immediately caudal to the sensory vesicle in ascidian larvae being the best accepted candidate. It is argued here that similarities in expression patterns between the MHB and the ascidian neck region are more likely due to the latter being the principal source of neurons in the adult brain, and hence where all the genes involved in patterning the latter will necessarily be expressed. The contrast with amphioxus is exemplified by pax2/5/8, expressed in the neck region in ascidian larvae, but more caudally, along much of the nerve cord in amphioxus. The zone of expression in each case corresponds with that part of the nerve cord ultimately responsible for innervating the adult body, which suggests the spatially restricted MHB-like expression pattern in ascidians is secondarily reduced from a condition more like that in amphioxus. Patterns resembling those of the vertebrate MHB are nevertheless found elsewhere among metazoans. This suggests that, irrespective of its modern function, the MHB marks the site of an organizing center of considerable antiquity. Any explanation for how such a center became incorporated into the chordate brain must take account of the dorsoventral inversion chordates have experienced relative to other metazoans. Especially relevant here is a concept developed by Claus Nielsen, in which the brain is derived from a neural center located behind the ancestral mouth. While this is somewhat counterintuitive, it accords well with emerging molecular data.

  1. SNPs and Hox gene mapping in Ciona intestinalis

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    Biffali Elio

    2008-01-01

    Full Text Available Abstract Background The tunicate Ciona intestinalis (Enterogona, Ascidiacea, a major model system for evolutionary and developmental genetics of chordates, harbours two cryptic species. To assess the degree of intra- and inter-specific genetic variability, we report the identification and analysis of C. intestinalis SNP (Single Nucleotide Polymorphism markers. A SNP subset was used to determine the genetic distance between Hox-5 and -10 genes. Results DNA fragments were amplified from 12 regions of C. intestinalis sp. A. In total, 128 SNPs and 32 one bp indels have been identified within 8 Kb DNA. SNPs in coding regions cause 4 synonymous and 12 non-synonymous substitutions. The highest SNP frequency was detected in the Hox5 and Hox10 intragenic regions. In C. intestinalis, these two genes have lost their archetypal topology within the cluster, such that Hox10 is located between Hox4 and Hox5. A subset of the above primers was used to perform successful amplification in C. intestinalis sp. B. In this cryptic species, 62 SNPs were identified within 3614 bp: 41 in non-coding and 21 in coding regions. The genetic distance of the Hox-5 and -10 loci, computed combining a classical backcross approach with the application of SNP markers, was found to be 8.4 cM (Haldane's function. Based on the physical distance, 1 cM corresponds to 39.5 Kb. Linkage disequilibrium between the aforementioned loci was calculated in the backcross generation. Conclusion SNPs here described allow analysis and comparisons within and between C. intestinalis cryptic species. We provide the first reliable computation of genetic distance in this important model chordate. This latter result represents an important platform for future studies on Hox genes showing deviations from the archetypal topology.

  2. Annelid Distal-less/Dlx duplications reveal varied post-duplication fates

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    Korchagina Natalia

    2011-08-01

    Full Text Available Abstract Background Dlx (Distal-less genes have various developmental roles and are widespread throughout the animal kingdom, usually occurring as single copy genes in non-chordates and as multiple copies in most chordate genomes. While the genomic arrangement and function of these genes is well known in vertebrates and arthropods, information about Dlx genes in other organisms is scarce. We investigate the presence of Dlx genes in several annelid species and examine Dlx gene expression in the polychaete Pomatoceros lamarckii. Results Two Dlx genes are present in P. lamarckii, Capitella teleta and Helobdella robusta. The C. teleta Dlx genes are closely linked in an inverted tail-to-tail orientation, reminiscent of the arrangement of vertebrate Dlx pairs, and gene conversion appears to have had a role in their evolution. The H. robusta Dlx genes, however, are not on the same genomic scaffold and display divergent sequences, while, if the P. lamarckii genes are linked in a tail-to-tail orientation they are a minimum of 41 kilobases apart and show no sign of gene conversion. No expression in P. lamarckii appendage development has been observed, which conflicts with the supposed conserved role of these genes in animal appendage development. These Dlx duplications do not appear to be annelid-wide, as the polychaete Platynereis dumerilii likely possesses only one Dlx gene. Conclusions On the basis of the currently accepted annelid phylogeny, we hypothesise that one Dlx duplication occurred in the annelid lineage after the divergence of P. dumerilii from the other lineages and these duplicates then had varied evolutionary fates in different species. We also propose that the ancestral role of Dlx genes is not related to appendage development.

  3. A neurochemical map of the developing amphioxus nervous system

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    Candiani Simona

    2012-06-01

    Full Text Available Abstract Background Amphioxus, representing the most basal group of living chordates, is the best available proxy for the last invertebrate ancestor of the chordates. Although the central nervous system (CNS of amphioxus comprises only about 20,000 neurons (as compared to billions in vertebrates, the developmental genetics and neuroanatomy of amphioxus are strikingly vertebrate-like. In the present study, we mapped the distribution of amphioxus CNS cells producing distinctive neurochemicals. To this end, we cloned genes encoding biosynthetic enzymes and/or transporters of the most common neurotransmitters and assayed their developmental expression in the embryo and early larva. Results By single and double in situ hybridization experiments, we identified glutamatergic, GABAergic/glycinergic, serotonergic and cholinergic neurons in developing amphioxus. In addition to characterizing the distribution of excitatory and inhibitory neurons in the developing amphioxus CNS, we observed that cholinergic and GABAergic/glycinergic neurons are segmentally arranged in the hindbrain, whereas serotonergic, glutamatergic and dopaminergic neurons are restricted to specific regions of the cerebral vesicle and the hindbrain. We were further able to identify discrete groups of GABAergic and glutamatergic interneurons and cholinergic motoneurons at the level of the primary motor center (PMC, the major integrative center of sensory and motor stimuli of the amphioxus nerve cord. Conclusions In this study, we assessed neuronal differentiation in the developing amphioxus nervous system and compiled the first neurochemical map of the amphioxus CNS. This map is a first step towards a full characterization of the neurotransmitter signature of previously described nerve cell types in the amphioxus CNS, such as motoneurons and interneurons.

  4. The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida is ancestral within the deuterostomes

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    Lanfear Robert

    2009-05-01

    Full Text Available Abstract Background Mitochondrial genome comparisons contribute in multiple ways when inferring animal relationships. As well as primary sequence data, rare genomic changes such as gene order, shared gene boundaries and genetic code changes, which are unlikely to have arisen through convergent evolution, are useful tools in resolving deep phylogenies. Xenoturbella bocki is a morphologically simple benthic marine worm recently found to belong among the deuterostomes. Here we present analyses comparing the Xenoturbella bocki mitochondrial gene order, genetic code and control region to those of other metazoan groups. Results The complete mitochondrial genome sequence of Xenoturbella bocki was determined. The gene order is most similar to that of the chordates and the hemichordates, indicating that this conserved mitochondrial gene order might be ancestral to the deuterostome clade. Using data from all phyla of deuterostomes, we infer the ancestral mitochondrial gene order for this clade. Using inversion and breakpoint analyses of metazoan mitochondrial genomes, we test conflicting hypotheses for the phylogenetic placement of Xenoturbella and find a closer affinity to the hemichordates than to other metazoan groups. Comparative analyses of the control region reveal similarities in the transcription initiation and termination sites and origin of replication of Xenoturbella with those of the vertebrates. Phylogenetic analyses of the mitochondrial sequence indicate a weakly supported placement as a basal deuterostome, a result that may be the effect of compositional bias. Conclusion The mitochondrial genome of Xenoturbella bocki has a very conserved gene arrangement in the deuterostome group, strikingly similar to that of the hemichordates and the chordates, and thus to the ancestral deuterostome gene order. Similarity to the hemichordates in particular is suggested by inversion and breakpoint analysis. Finally, while phylogenetic analyses of the

  5. 60 YEARS OF POMC: Melanocortin receptors: evolution of ligand selectivity for melanocortin peptides.

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    Dores, Robert M; Liang, Liang; Davis, Perry; Thomas, Alexa L; Petko, Bogdana

    2016-05-01

    The evolution of the melanocortin receptors (MCRs) is linked to the evolution of adrenocorticotrophic hormone (ACTH), the melanocyte-stimulating hormones (MSHs), and their common precursor pro-opiomelanocortin (POMC). The origin of the MCRs and POMC appears to be grounded in the early radiation of the ancestral protochordates. During the genome duplications that have occurred during the evolution of the chordates, the organization plan for POMC was established, and features that have been retained include, the high conservation of the amino acid sequences of α-MSH and ACTH, and the presence of the HFRW MCR activation motif in all of the melanocortin peptides (i.e. ACTH, α-MSH, β-MSH, γ-MSH, and δ-MSH). For the MCRs, the chordate genome duplication events resulted in the proliferation of paralogous receptor genes, and a divergence in ligand selectivity. While most gnathostome MCRs can be activated by either ACTH or the MSHs, teleost and tetrapod MC2R orthologs can only be activated by ACTH. The appearance of the accessory protein, MRAP1, paralleled the emergence of teleost and tetrapods MC2R ligand selectivity, and the dependence of these orthologs on MRAP1 for trafficking to the plasma membrane. The accessory protein, MRAP2, does not affect MC2R ligand selectivity, but does influence the functionality of MC4R orthologs. In this regard, the roles that these accessory proteins may play in the physiology of the five MCRs (i.e. MC1R, MC2R, MC3R, MC4R, and MC5R) are discussed. PMID:26792827

  6. Migratory neuronal progenitors arise from the neural plate borders in tunicates.

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    Stolfi, Alberto; Ryan, Kerrianne; Meinertzhagen, Ian A; Christiaen, Lionel

    2015-11-19

    The neural crest is an evolutionary novelty that fostered the emergence of vertebrate anatomical innovations such as the cranium and jaws. During embryonic development, multipotent neural crest cells are specified at the lateral borders of the neural plate before delaminating, migrating and differentiating into various cell types. In invertebrate chordates (cephalochordates and tunicates), neural plate border cells express conserved factors such as Msx, Snail and Pax3/7 and generate melanin-containing pigment cells, a derivative of the neural crest in vertebrates. However, invertebrate neural plate border cells have not been shown to generate homologues of other neural crest derivatives. Thus, proposed models of neural crest evolution postulate vertebrate-specific elaborations on an ancestral neural plate border program, through acquisition of migratory capabilities and the potential to generate several cell types. Here we show that a particular neuronal cell type in the tadpole larva of the tunicate Ciona intestinalis, the bipolar tail neuron, shares a set of features with neural-crest-derived spinal ganglia neurons in vertebrates. Bipolar tail neuron precursors derive from caudal neural plate border cells, delaminate and migrate along the paraxial mesoderm on either side of the neural tube, eventually differentiating into afferent neurons that form synaptic contacts with both epidermal sensory cells and motor neurons. We propose that the neural plate borders of the chordate ancestor already produced migratory peripheral neurons and pigment cells, and that the neural crest evolved through the acquisition of a multipotent progenitor regulatory state upstream of multiple, pre-existing neural plate border cell differentiation programs. PMID:26524532

  7. An enigmatic fourth runt domain gene in the fugu genome: ancestral gene loss versus accelerated evolution

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    Hood Leroy

    2004-11-01

    Full Text Available Abstract Background The runt domain transcription factors are key regulators of developmental processes in bilaterians, involved both in cell proliferation and differentiation, and their disruption usually leads to disease. Three runt domain genes have been described in each vertebrate genome (the RUNX gene family, but only one in other chordates. Therefore, the common ancestor of vertebrates has been thought to have had a single runt domain gene. Results Analysis of the genome draft of the fugu pufferfish (Takifugu rubripes reveals the existence of a fourth runt domain gene, FrRUNT, in addition to the orthologs of human RUNX1, RUNX2 and RUNX3. The tiny FrRUNT packs six exons and two putative promoters in just 3 kb of genomic sequence. The first exon is located within an intron of FrSUPT3H, the ortholog of human SUPT3H, and the first exon of FrSUPT3H resides within the first intron of FrRUNT. The two gene structures are therefore "interlocked". In the human genome, SUPT3H is instead interlocked with RUNX2. FrRUNT has no detectable ortholog in the genomes of mammals, birds or amphibians. We consider alternative explanations for an apparent contradiction between the phylogenetic data and the comparison of the genomic neighborhoods of human and fugu runt domain genes. We hypothesize that an ancient RUNT locus was lost in the tetrapod lineage, together with FrFSTL6, a member of a novel family of follistatin-like genes. Conclusions Our results suggest that the runt domain family may have started expanding in chordates much earlier than previously thought, and exemplify the importance of detailed analysis of whole-genome draft sequence to provide new insights into gene evolution.

  8. The mitochondrial genome of Phallusia mammillata and Phallusia fumigata (Tunicata, Ascidiacea: high genome plasticity at intra-genus level

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    Pesole Graziano

    2007-08-01

    Full Text Available Abstract Background Within Chordata, the subphyla Vertebrata and Cephalochordata (lancelets are characterized by a remarkable stability of the mitochondrial (mt genome, with constancy of gene content and almost invariant gene order, whereas the limited mitochondrial data on the subphylum Tunicata suggest frequent and extensive gene rearrangements, observed also within ascidians of the same genus. Results To confirm this evolutionary trend and to better understand the evolutionary dynamics of the mitochondrial genome in Tunicata Ascidiacea, we have sequenced and characterized the complete mt genome of two congeneric ascidian species, Phallusia mammillata and Phallusia fumigata (Phlebobranchiata, Ascidiidae. The two mtDNAs are surprisingly rearranged, both with respect to one another and relative to those of other tunicates and chordates, with gene rearrangements affecting both protein-coding and tRNA genes. The new data highlight the extraordinary variability of ascidian mt genome in base composition, tRNA secondary structure, tRNA gene content, and non-coding regions (number, size, sequence and location. Indeed, both Phallusia genomes lack the trnD gene, show loss/acquisition of DHU-arm in two tRNAs, and have a G+C content two-fold higher than other ascidians. Moreover, the mt genome of P. fumigata presents two identical copies of trnI, an extra tRNA gene with uncertain amino acid specificity, and four almost identical sequence regions. In addition, a truncated cytochrome b, lacking a C-terminal tail that commonly protrudes into the mt matrix, has been identified as a new mt feature probably shared by all tunicates. Conclusion The frequent occurrence of major gene order rearrangements in ascidians both at high taxonomic level and within the same genus makes this taxon an excellent model to study the mechanisms of gene rearrangement, and renders the mt genome an invaluable phylogenetic marker to investigate molecular biodiversity and speciation

  9. No more than 14: the end of the amphioxus Hox cluster

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    2005-01-01

    Full Text Available The Hox gene cluster has been a key paradigm for a generation of developmental and evolutionary biologists. Since its discovery in the mid-1980's, the identification, genomic organization, expression, colinearity, and regulation of Hox genes have been immediate targets for study in any new model organism, and metazoan genome projects always refer to the structure of the particular Hox cluster(s. Since the early 1990's, it has been dogma that vertebrate Hox clusters are composed of thirteen paralogous groups. Nonetheless, we showed that in the otherwise prototypical cephalochordate amphioxus (Branchiostoma floridae, the Hox cluster contains a fourteenth Hox gene, and very recently, a 14th Hox paralogous group has been found in the coelacanth and the horn shark, suggesting that the amphioxus cluster was anticipating the finding of Hox 14 in some vertebrate lineages. In view of the pivotal place that amphioxus occupies in vertebrate evolution, we thought it of considerable interest to establish the limits of its Hox gene cluster, namely resolution of whether more Hox genes are present in the amphioxus cluster (e.g., Hox 15. Using two strategies, here we report the completion and characterization of the Hox gene content of the single amphioxus Hox cluster, which encompasses 650 kb from Hox1 to Evx. Our data have important implications for the primordial Hox gene cluster of chordates: the prototypical nature of the single amphioxus Hox cluster makes it unlikely that additional paralogous groups will be found in any chordate lineage. We suggest that 14 is the end.

  10. Conodont body size and diversity trends after the end-Permian extinction: implications for the recovery of pelagic vs. benthic marine ecosystems

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    Schaal, E. K.; Morgan, D. J.; Clapham, M.; Rego, B. L.; Wang, S. C.; Payne, J.

    2012-12-01

    Many marine clades decreased in size across the end-Permian extinction horizon, but the pattern and timing of subsequent size increase during recovery is poorly constrained. The tempo of recovery from the end-Permian extinction is key to understanding the role of evolutionary and environmental constraints in the recovery of ecosystems. However, not all marine organisms share the same recovery pattern. In this study, we document Late Permian to Late Triassic trends in size distribution of conodonts, pelagic chordates that exhibit much more rapid diversification in the Early Triassic compared to benthic clades. Because tooth size correlates with body weight in chordates over many orders of magnitude and is commonly used to predict body size in fossils, conodont elements can serve as a proxy for the size of the conodont animal. Our dataset includes both specimens from high-resolution samples through an exceptionally exposed carbonate platform in south China and size measurements from the published literature for conodonts and seven other marine clades. In platform slope sections of south China, we observe a size decrease across the P/Tr boundary, but in platform interior sections, large conodonts are prolific in the earliest Triassic. Comparison with global data shows that while there is decrease in median conodont size across the P/Tr boundary, there is little change in maximum conodont size, and pre-extinction size distributions return by the Smithian. While benthic clades show Early Triassic size reduction and slow recovery, pelagic clades such as conodonts and ammonoids show large size and rapid diversification after the extinction event. This decoupling of recovery between benthic and pelagic marine ecosystems could reflect a depth gradient in environmental parameters such as oxygen availability or intrinsic differences in the evolutionary dynamics of these clades.

  11. Evolutionary relationships of Aurora kinases: Implications for model organism studies and the development of anti-cancer drugs

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    Patrick Denis R

    2004-10-01

    Full Text Available Abstract Background As key regulators of mitotic chromosome segregation, the Aurora family of serine/threonine kinases play an important role in cell division. Abnormalities in Aurora kinases have been strongly linked with cancer, which has lead to the recent development of new classes of anti-cancer drugs that specifically target the ATP-binding domain of these kinases. From an evolutionary perspective, the species distribution of the Aurora kinase family is complex. Mammals uniquely have three Aurora kinases, Aurora-A, Aurora-B, and Aurora-C, while for other metazoans, including the frog, fruitfly and nematode, only Aurora-A and Aurora-B kinases are known. The fungi have a single Aurora-like homolog. Based on the tacit assumption of orthology to human counterparts, model organism studies have been central to the functional characterization of Aurora kinases. However, the ortholog and paralog relationships of these kinases across various species have not been rigorously examined. Here, we present comprehensive evolutionary analyses of the Aurora kinase family. Results Phylogenetic trees suggest that all three vertebrate Auroras evolved from a single urochordate ancestor. Specifically, Aurora-A is an orthologous lineage in cold-blooded vertebrates and mammals, while structurally similar Aurora-B and Aurora-C evolved more recently in mammals from a duplication of an ancestral Aurora-B/C gene found in cold-blooded vertebrates. All so-called Aurora-A and Aurora-B kinases of non-chordates are ancestral to the clade of chordate Auroras and, therefore, are not strictly orthologous to vertebrate counterparts. Comparisons of human Aurora-B and Aurora-C sequences to the resolved 3D structure of human Aurora-A lends further support to the evolutionary scenario that vertebrate Aurora-B and Aurora-C are closely related paralogs. Of the 26 residues lining the ATP-binding active site, only three were variant and all were specific to Aurora-A. Conclusions In

  12. Proteomic characterization and evolutionary analyses of zona pellucida domain-containing proteins in the egg coat of the cephalochordate, Branchiostoma belcheri

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    Xu Qianghua

    2012-12-01

    Full Text Available Abstract Background Zona pellucida domain-containing proteins (ZP proteins have been identified as the principle constituents of the egg coat (EC of diverse metazoan taxa, including jawed vertebrates, urochordates and molluscs that span hundreds of millions of years of evolutionary divergence. Although ZP proteins generally contain the zona pellucida (ZP structural modules to fulfill sperm recognition and EC polymerization functions during fertilization, the primary sequences of the ZP proteins from the above-mentioned animal classes are drastically different, which makes it difficult to assess the evolutionary relationships of ZP proteins. To understand the origin of vertebrate ZP proteins, we characterized the egg coat components of Branchiostoma belcheri, an invertebrate species that belongs to the chordate subphylum Cephalochordata. Results Five ZP proteins (BbZP1-5 were identified by mass spectrometry analyses using the egg coat extracts from both unfertilized and fertilized eggs. In addition to the C-terminal ZP module in each of the BbZPs, the majority contain a low-density lipoprotein receptor domain and a von Willebrand factor type A (vWFA domain, but none possess an EGF-like domain that is frequently observed in the ZP proteins of urochordates. Fluorescence in situ hybridization and immuno-histochemical analyses of B. belcheri ovaries showed that the five BbZPs are synthesized predominantly in developing eggs and deposited around the extracellular space of the egg, which indicates that they are bona fide egg coat ZP proteins. BbZP1, BbZP3 and BbZP4 are significantly more abundant than BbZP2 and BbZP5 in terms of gene expression levels and the amount of mature proteins present on the egg coats. The major ZP proteins showed high polymorphism because multiple variants are present with different molecular weights. Sequence comparison and phylogenetic analysis between the ZP proteins from cephalochordates, urochordates and vertebrates

  13. Introduction to 'Homology and convergence in nervous system evolution'.

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    Strausfeld, Nicholas J; Hirth, Frank

    2016-01-01

    The origin of brains and central nervous systems (CNSs) is thought to have occurred before the Palaeozoic era 540 Ma. Yet in the absence of tangible evidence, there has been continued debate whether today's brains and nervous systems derive from one ancestral origin or whether similarities among them are due to convergent evolution. With the advent of molecular developmental genetics and genomics, it has become clear that homology is a concept that applies not only to morphologies, but also to genes, developmental processes, as well as to behaviours. Comparative studies in phyla ranging from annelids and arthropods to mammals are providing evidence that corresponding developmental genetic mechanisms act not only in dorso-ventral and anterior-posterior axis specification but also in segmentation, neurogenesis, axogenesis and eye/photoreceptor cell formation that appear to be conserved throughout the animal kingdom. These data are supported by recent studies which identified Mid-Cambrian fossils with preserved soft body parts that present segmental arrangements in brains typical of modern arthropods, and similarly organized brain centres and circuits across phyla that may reflect genealogical correspondence and control similar behavioural manifestations. Moreover, congruence between genetic and geological fossil records support the notion that by the 'Cambrian explosion' arthropods and chordates shared similarities in brain and nervous system organization. However, these similarities are strikingly absent in several sister- and outgroups of arthropods and chordates which raises several questions, foremost among them: what kind of natural laws and mechanisms underlie the convergent evolution of such similarities? And, vice versa: what are the selection pressures and genetic mechanisms underlying the possible loss or reduction of brains and CNSs in multiple lineages during the course of evolution? These questions were addressed at a Royal Society meeting to discuss

  14. Introduction to 'Homology and convergence in nervous system evolution'.

    Science.gov (United States)

    Strausfeld, Nicholas J; Hirth, Frank

    2016-01-01

    The origin of brains and central nervous systems (CNSs) is thought to have occurred before the Palaeozoic era 540 Ma. Yet in the absence of tangible evidence, there has been continued debate whether today's brains and nervous systems derive from one ancestral origin or whether similarities among them are due to convergent evolution. With the advent of molecular developmental genetics and genomics, it has become clear that homology is a concept that applies not only to morphologies, but also to genes, developmental processes, as well as to behaviours. Comparative studies in phyla ranging from annelids and arthropods to mammals are providing evidence that corresponding developmental genetic mechanisms act not only in dorso-ventral and anterior-posterior axis specification but also in segmentation, neurogenesis, axogenesis and eye/photoreceptor cell formation that appear to be conserved throughout the animal kingdom. These data are supported by recent studies which identified Mid-Cambrian fossils with preserved soft body parts that present segmental arrangements in brains typical of modern arthropods, and similarly organized brain centres and circuits across phyla that may reflect genealogical correspondence and control similar behavioural manifestations. Moreover, congruence between genetic and geological fossil records support the notion that by the 'Cambrian explosion' arthropods and chordates shared similarities in brain and nervous system organization. However, these similarities are strikingly absent in several sister- and outgroups of arthropods and chordates which raises several questions, foremost among them: what kind of natural laws and mechanisms underlie the convergent evolution of such similarities? And, vice versa: what are the selection pressures and genetic mechanisms underlying the possible loss or reduction of brains and CNSs in multiple lineages during the course of evolution? These questions were addressed at a Royal Society meeting to discuss

  15. D- and L-lactate dehydrogenases during invertebrate evolution

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    Stillman Jonathon H

    2008-10-01

    Full Text Available Abstract Background The L-lactate and D-lactate dehydrogenases, which are involved in the reduction of pyruvate to L(--lactate and D(+-lactate, belong to evolutionarily unrelated enzyme families. The genes encoding L-LDH have been used as a model for gene duplication due to the multiple paralogs found in eubacteria, archaebacteria, and eukaryotes. Phylogenetic studies have suggested that several gene duplication events led to the main isozymes of this gene family in chordates, but little is known about the evolution of L-Ldh in invertebrates. While most invertebrates preferentially oxidize L-lactic acid, several species of mollusks, a few arthropods and polychaetes were found to have exclusively D-LDH enzymatic activity. Therefore, it has been suggested that L-LDH and D-LDH are mutually exclusive. However, recent characterization of putative mammalian D-LDH with significant similarity to yeast proteins showing D-LDH activity suggests that at least mammals have the two naturally occurring forms of LDH specific to L- and D-lactate. This study describes the phylogenetic relationships of invertebrate L-LDH and D-LDH with special emphasis on crustaceans, and discusses gene duplication events during the evolution of L-Ldh. Results Our phylogenetic analyses of L-LDH in vertebrates are consistent with the general view that the main isozymes (LDH-A, LDH-B and LDH-C evolved through a series of gene duplications after the vertebrates diverged from tunicates. We report several gene duplication events in the crustacean, Daphnia pulex, and the leech, Helobdella robusta. Several amino acid sequences with strong similarity to putative mammalian D-LDH and to yeast DLD1 with D-LDH activity were found in both vertebrates and invertebrates. Conclusion The presence of both L-Ldh and D-Ldh genes in several chordates and invertebrates suggests that the two enzymatic forms are not necessarily mutually exclusive. Although, the evolution of L-Ldh has been punctuated by

  16. Amphioxus (Branchiostoma floridae has orthologs of vertebrate odorant receptors

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    Taylor John S

    2009-10-01

    Full Text Available Abstract Background A common feature of chemosensory systems is the involvement of G protein-coupled receptors (GPCRs in the detection of environmental stimuli. Several lineages of GPCRs are involved in vertebrate olfaction, including trace amine-associated receptors, type 1 and 2 vomeronasal receptors and odorant receptors (ORs. Gene duplication and gene loss in different vertebrate lineages have lead to an enormous amount of variation in OR gene repertoire among species; some fish have fewer than 100 OR genes, while some mammals possess more than 1000. Fascinating features of the vertebrate olfactory system include allelic exclusion, where each olfactory neuron expresses only a single OR gene, and axonal guidance where neurons expressing the same receptor project axons to common glomerulae. By identifying homologous ORs in vertebrate and in non-vertebrate chordates, we hope to expose ancestral features of the chordate olfactory system that will help us to better understand the evolution of the receptors themselves and of the cellular components of the olfactory system. Results We have identified 50 full-length and 11 partial ORs in Branchiostoma floridae. No ORs were identified in Ciona intestinalis. Phylogenetic analysis places the B. floridae OR genes in a monophyletic clade with the vertebrate ORs. The majority of OR genes in amphioxus are intronless and many are also tandemly arrayed in the genome. By exposing conserved amino acid motifs and testing the ability of those motifs to discriminate between ORs and non-OR GPCRs, we identified three OR-specific amino acid motifs common in cephalochordate, fish and mammalian and ORs. Conclusion Here, we show that amphioxus has orthologs of vertebrate ORs. This conclusion demonstrates that the receptors, and perhaps other components of vertebrate olfaction, evolved at least 550 million years ago. We have also identified highly conserved amino acid motifs that may be important for maintaining

  17. Conodonts, Calcichordates and the Origin of Vertebrates

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    J. Bergström

    1998-01-01

    Full Text Available Interpretation of early deuterostome evolution and relationships has been hampered by the lack of soft-part preservation in most groups. In addition, a recently revealed upside-down life orientation of vertebrates (the only real notoneuralians compared to other bilateral animals has been misinterpreted as evidence for a unique body design in all deuterostomes, misleading any search for relatives. Regarding echinoderms, the variety of body plans is confusing. The interpretation of some fossils with echinoderm-type calcite skeletons as “calcichordate” ancestors of chordates, however, involves a hypothetical reconstruction of an unusual body plan and a long series of hypothetical transitions. The number of necessary steps is much lower if cephalochordates (amphioxus or lancelet are derived directly from hemichordate enteropneusts. “Sensation interpretations” of fossils (Yunnanozoon, Cathaymyrus from Burgess Shale type deposits have added further confusion. Soft-part preservation of conodont animals, with V-shaped myomeres and a notochord, shows that they were segmented chordates, while probable eyes and teeth suggest that they were already on the vertebrate side. Die Interpretation früher Deuterostomia hinsichtlich ihrer Evolution und verwandtschaftlichen Beziehungen ist in den meisten Gruppen durch den Mangel an Weichkörpererhaltung sehr erschwert. Die kürzlich entdeckte Tatsache, daß Vertebraten, d. h. die einzigen echten Notoneuralia, im Gegensatz zu anderen bilateral symmetrischen Organismen eine mit ihrer ursprünglichen Oberseite nach unten gerichtete Lebensstellung einnehmen, hat zu der irrtümlichen Ansicht geführt, daß alle Deuostomia über einen im Tierreich einzigartigen Bauplan verfügen. Diese Interpretation brachte naturgemäß jede Suche nach Verwandtschaftsverhältnissen auf Abwege. Hinsichtlich der Echinodermata ist die bauplanmäßige Variation in der Tat verwirrend. Die Interpretation einiger Fossilien mit

  18. Molecular cloning and analysis of zebrafish voltage-gated sodium channel beta subunit genes: implications for the evolution of electrical signaling in vertebrates

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    Zhong Tao P

    2007-07-01

    Full Text Available Abstract Background Action potential generation in excitable cells such as myocytes and neurons critically depends on voltage-gated sodium channels. In mammals, sodium channels exist as macromolecular complexes that include a pore-forming alpha subunit and 1 or more modulatory beta subunits. Although alpha subunit genes have been cloned from diverse metazoans including flies, jellyfish, and humans, beta subunits have not previously been identified in any non-mammalian species. To gain further insight into the evolution of electrical signaling in vertebrates, we investigated beta subunit genes in the teleost Danio rerio (zebrafish. Results We identified and cloned single zebrafish gene homologs for beta1-beta3 (zbeta1-zbeta3 and duplicate genes for beta4 (zbeta4.1, zbeta4.2. Sodium channel beta subunit loci are similarly organized in fish and mammalian genomes. Unlike their mammalian counterparts, zbeta1 and zbeta2 subunit genes display extensive alternative splicing. Zebrafish beta subunit genes and their splice variants are differentially-expressed in excitable tissues, indicating tissue-specific regulation of zbeta1-4 expression and splicing. Co-expression of the genes encoding zbeta1 and the zebrafish sodium channel alpha subunit Nav1.5 in Chinese Hamster Ovary cells increased sodium current and altered channel gating, demonstrating functional interactions between zebrafish alpha and beta subunits. Analysis of the synteny and phylogeny of mammalian, teleost, amphibian, and avian beta subunit and related genes indicated that all extant vertebrate beta subunits are orthologous, that beta2/beta4 and beta1/beta3 share common ancestry, and that beta subunits are closely related to other proteins sharing the V-type immunoglobulin domain structure. Vertebrate sodium channel beta subunit genes were not identified in the genomes of invertebrate chordates and are unrelated to known subunits of the para sodium channel in Drosophila. Conclusion The

  19. A forkhead gene related to HNF-3beta is required for gastrulation and axis formation in the ascidian embryo.

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    Olsen, C L; Jeffery, W R

    1997-09-01

    We have isolated a member of the HNF-3/forkhead gene family in ascidians as a means to determine the role of winged-helix genes in chordate development. The MocuFH1 gene, isolated from a Molgula oculata cDNA library, exhibits a forkhead DNA-binding domain most similar to zebrafish axial and rodent HNF-3beta. MocuFH1 is a single copy gene but there is at least one other related forkhead gene in the M. oculata genome. The MocuFH1 gene is expressed in the presumptive endoderm, mesenchyme and notochord cells beginning during the late cleavage stages. During gastrulation, MocuFH1 expression occurs in the prospective endoderm cells, which invaginate at the vegetal pole, and in the presumptive notochord and mesenchyme cells, which involute over the anterior and lateral lips of the blastopore, respectively. However, this gene is not expressed in the presumptive muscle cells, which involute over the posterior lip of the blastopore. MocuFH1 expression continues in the same cell lineages during neurulation and axis formation, however, during the tailbud stage, MocuFH1 is also expressed in ventral cells of the brain and spinal cord. The functional role of the MocuFH1 gene was studied using antisense oligodeoxynucleotides (ODNs), which transiently reduce MocuFH1 transcript levels during gastrulation. Embryos treated with antisense ODNs cleave normally and initiate gastrulation. However, gastrulation is incomplete, some of the endoderm and notochord cells do not enter the embryo and undergo subsequent movements, and axis formation is abnormal. In contrast, the prospective muscle cells, which do not express MocuFH1, undergo involution and later express muscle actin and acetylcholinesterase, markers of muscle cell differentiation. The results suggest that MocuFH1 is required for morphogenetic movements of the endoderm and notochord precursor cells during gastrulation and axis formation. The effects of inhibiting MocuFH1 expression on embryonic axis formation in ascidians are

  20. Evidence for gill slits and a pharynx in Cambrian vetulicolians: implications for the early evolution of deuterostomes

    Directory of Open Access Journals (Sweden)

    Ou Qiang

    2012-10-01

    members of the stem-group deuterostomes; a group best known as the chordates (amphioxus, tunicates, vertebrates, but also including the ambulacrarians (echinoderms, hemichordates, and xenoturbellids. If the latter, first they demonstrate that these members of the stem group show few similarities to the descendant crown group representatives. Second, of the key innovations that underpinned deuterostome success, the earliest and arguably most seminal was the evolution of openings that define the pharyngeal gill slits of hemichordates (and some extinct echinoderms and chordates.

  1. Melanopsin-expressing amphioxus photoreceptors transduce light via a phospholipase C signaling cascade.

    Directory of Open Access Journals (Sweden)

    Juan Manuel Angueyra

    Full Text Available Melanopsin, the receptor molecule that underlies light sensitivity in mammalian 'circadian' receptors, is homologous to invertebrate rhodopsins and has been proposed to operate via a similar signaling pathway. Its downstream effectors, however, remain elusive. Melanopsin also expresses in two distinct light-sensitive cell types in the neural tube of amphioxus. This organism is the most basal extant chordate and can help outline the evolutionary history of different photoreceptor lineages and their transduction mechanisms; moreover, isolated amphioxus photoreceptors offer unique advantages, because they are unambiguously identifiable and amenable to single-cell physiological assays. In the present study whole-cell patch clamp recording, pharmacological manipulations, and immunodetection were utilized to investigate light transduction in amphioxus photoreceptors. A G(q was identified and selectively localized to the photosensitive microvillar membrane, while the pivotal role of phospholipase C was established pharmacologically. The photocurrent was profoundly depressed by IP₃ receptor antagonists, highlighting the importance of IP₃ receptors in light signaling. By contrast, surrogates of diacylglycerol (DAG, as well as poly-unsaturated fatty acids failed to activate a membrane conductance or to alter the light response. The results strengthen the notion that calcium released from the ER via IP₃-sensitive channels may fulfill a key role in conveying--directly or indirectly--the melanopsin-initiated light signal to the photoconductance; moreover, they challenge the dogma that microvillar photoreceptors and phoshoinositide-based light transduction are a prerogative of invertebrate eyes.

  2. LPS injection reprograms the expression and the 3' UTR of a CAP gene by alternative polyadenylation and the formation of a GAIT element in Ciona intestinalis.

    Science.gov (United States)

    Vizzini, Aiti; Bonura, Angela; Longo, Valeria; Sanfratello, Maria Antonietta; Parrinello, Daniela; Cammarata, Matteo; Colombo, Paolo

    2016-09-01

    The diversification of cellular functions is one of the major characteristics of multicellular organisms which allow cells to modulate their gene expression, leading to the formation of transcripts and proteins with different functions and concentrations in response to different stimuli. CAP genes represent a widespread family of proteins belonging to the cysteine-rich secretory protein, antigen 5 and pathogenesis-related 1 superfamily which, it has been proposed, play key roles in the infection process and the modulation of immune responses in host animals. The ascidian Ciona intestinalis represents a group of proto-chordates with an exclusively innate immune system that has been widely studied in the field of comparative and developmental immunology. Using this biological system, we describe the identification of a novel APA mechanism by which an intronic polyadenylation signal is activated by LPS injection, leading to the formation of a shorter CAP mRNA capable of expressing the first CAP exon plus 19 amino acid residues whose sequence is contained within the first intron of the annotated gene. Furthermore, such an APA event causes the expression of a translational controlling cis-acting GAIT element which is not present in the previously isolated CAP isoform and identified in the 3'-UTR of other immune-related genes, suggesting an intriguing scenario in which both transcriptional and post-transcriptional control mechanisms are involved in the activation of the CAP gene during inflammatory response in C. intestinalis.

  3. Protochordate amphioxus is an emerging model organism for comparative immunology

    Institute of Scientific and Technical Information of China (English)

    Shicui Zhang; Yujun Liang; Guangdong Jia; Zhimeng Zhuang

    2009-01-01

    Protochordate amphioxus is an extant invertebrate regarded quite recently as a basal chordate. It has a vertebrate-like body plan including a circulation system with an organization similar to that of vertebrates. However, amphioxus is less complex than vertebrates for having a genome uncomplicated by extensive genomic duplication, and lacking lymphoid organs and free circulating blood cells.Recent studies on immunity have demonstrated the presence in amphioxus of both the constituent elements of key molecules involved in adaptive immunity such as proto-major histocompatibility complex (proto-MHC), V region-containing chitin-binding protein (VCBP)and V and C domain-bearing protein (VCP), and the complement system operating via the alternative and lectin pathways resembling those seen in vertebrates. In addition, the acute phase response profile in amphioxus has been shown to be similar to that observed in vertebrates. These findings together with the relative structural and genomic simplicity make amphioxus an ideal organism for gaining insights into the origin and evolution of the vertebrate immune system, especially adaptive immunity, and the composition and mech-anisms of the vertebrate innate immunity.

  4. Molecular cloning and expression patterns of the Vasa gene from Rana nigromaculata (Amphibia: Anura

    Directory of Open Access Journals (Sweden)

    Rui Jia

    2009-06-01

    Full Text Available The Vasa protein is a member of the DEAD (Asp-Glu-Alu-Asp box family of ATP-dependent RNA helicases. The Vasa gene is specifically expressed in germ-line cells of many metazoans and is known to play a critical role in gametogenesis and reproductive regulation. In this paper, we isolate the full length cDNA sequence of the Vasa gene from the frog Rana nigromaculata Hallowell, 1861. The open reading frame (ORF encoding 398 amino acid residues has nine conserved motifs. According to the similarities at the amino acid sequenceythe phylogenetic analysis of Vasa gene was consistent with the evolution relationships from chordates to mammals. Furthermore, the expression pattern analysis of RnVasa mRNA, using the technique of Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR, showed a high level of transcripts in testis, ovary and kidney, whereas little to no signal was detected in other tissues, which suggests that it may play a role during gametogenesis.

  5. The bijection from data to parameter space with the standard DEB model quantifies the supply–demand spectrum

    DEFF Research Database (Denmark)

    Lika, Konstadia; Augustine, Starrlight; Pecquerie, Laure;

    2014-01-01

    The standard Dynamic Energy Budget (DEB) model assumes that food is converted to reserve and a fraction κ of mobilised reserve of an individual is allocated to somatic maintenance plus growth, while the rest is allocated to maturity maintenance plus maturation (in embryos and juveniles) or reprod......The standard Dynamic Energy Budget (DEB) model assumes that food is converted to reserve and a fraction κ of mobilised reserve of an individual is allocated to somatic maintenance plus growth, while the rest is allocated to maturity maintenance plus maturation (in embryos and juveniles......) or reproduction (in adults). The add_my_pet collection of over 300 animal species from most larger phyla, and all chordate classes, shows that this model fits energy data very well. Nine parameters determine nine data points at abundant food: dry/wet weight ratio, age at birth, puberty, death, weight at birth......, metamorphosis, puberty, ultimate weight and ultimate reproduction rate. We demonstrate that, given a few other parameters, these nine data points also determine the nine parameters uniquely that are independent of food availability: maturity at birth, metamorphosis and puberty, specific assimilation, somatic...

  6. Developmental transcriptome of Aplysia californica'

    KAUST Repository

    Heyland, Andreas

    2010-12-06

    Genome-wide transcriptional changes in development provide important insight into mechanisms underlying growth, differentiation, and patterning. However, such large-scale developmental studies have been limited to a few representatives of Ecdysozoans and Chordates. Here, we characterize transcriptomes of embryonic, larval, and metamorphic development in the marine mollusc Aplysia californica and reveal novel molecular components associated with life history transitions. Specifically, we identify more than 20 signal peptides, putative hormones, and transcription factors in association with early development and metamorphic stages-many of which seem to be evolutionarily conserved elements of signal transduction pathways. We also characterize genes related to biomineralization-a critical process of molluscan development. In summary, our experiment provides the first large-scale survey of gene expression in mollusc development, and complements previous studies on the regulatory mechanisms underlying body plan patterning and the formation of larval and juvenile structures. This study serves as a resource for further functional annotation of transcripts and genes in Aplysia, specifically and molluscs in general. A comparison of the Aplysia developmental transcriptome with similar studies in the zebra fish Danio rerio, the fruit fly Drosophila melanogaster, the nematode Caenorhabditis elegans, and other studies on molluscs suggests an overall highly divergent pattern of gene regulatory mechanisms that are likely a consequence of the different developmental modes of these organisms. © 2010 Wiley-Liss, Inc., A Wiley Company.

  7. A RALDH-like enzyme involved in Fusarium verticillioides development

    KAUST Repository

    Díaz-Sánchez, Violeta

    2015-12-11

    Retinaldehyde dehydrogenases (RALDHs) convert retinal to retinoic acid, an important chordate morphogen. Retinal also occurs in some fungi, such as Fusarium and Ustilago spp., evidenced by the presence of rhodopsins and β–carotene cleaving, retinal-forming dioxygenases. Based on the assumption that retinoic acid may also be formed in fungi, we searched the Fusarium protein databases for RALDHs homologs, focusing on Fusarium verticillioides. Using crude lysates of Escherichia coli cells expressing the corresponding cDNAs, we checked the capability of best matches to convert retinal into retinoic acid in vitro. Thereby, we identified an aldehyde dehydrogenase, termed CarY, as a retinoic acid-forming enzyme, an activity that was also exerted by purified CarY. Targeted mutation of the carY gene in F. verticillioides resulted in alterations of mycelia development and conidia morphology in agar cultures, and reduced capacity to produce perithecia as a female in sexual crosses. Complementation of the mutant with a wild-type carY allele demonstrated that these alterations are caused by the lack of CarY. However, retinoic acid could not be detected by LC-MS analysis either in the wild type or the complemented carY strain in vivo, making elusive the connection between CarY enzymatic activity and retinoic acid formation in the fungus.

  8. THE COMPOSITION OF FLUIDS AND SERA OF SOME MARINE ANIMALS AND OF THE SEA WATER IN WHICH THEY LIVE.

    Science.gov (United States)

    Cole, W H

    1940-05-20

    1. The electrolyte composition, the pH, and freezing points of the fluids of several invertebrates and one primitive chordate are reported. 2. Fluids of the worms, echinoderms, and the clam Venus were isotonic with sea water; fluids of the Arthropoda were hypertonic to sea water. 3. The pH of all fluids was below that of sea water. In the Arthropoda and Myxine less individual variation in pH appeared than in the echinoderms and worms. 4. Ratios of ionic concentrations in the fluid to those in the sea water indicated (1) uniform distribution of ions between the internal and external media for the echinoderms and Venus, (2) differential distribution of potassium and magnesium in the worms; (3) differential distribution of sulfate, magnesium, potassium, and calcium in the Arthropoda; and (4) differential distribution of calcium, magnesium, and sulfate in Myxine. 5. The unequal distribution of ions implies the expenditure of energy against a concentration gradient across the absorbing or excreting membranes, a capacity frequently overlooked in the invertebrates. 6. The sera of the Arthropoda from diluted sea water showed higher concentrations of sodium, potassium, calcium, and chloride ions relative to the respective concentrations in the external medium than in normal sea water, and also showed different orders for those ions. 7. The increase in osmotic pressure of the sera of the animals moving into brackish water is caused by unequal accumulation of sodium, potassium, calcium, and chloride ions. Sulfate and magnesium ionic ratios do not change.

  9. Echinoderm immunity

    Directory of Open Access Journals (Sweden)

    JE García-Arrarás

    2010-09-01

    Full Text Available Echinoderms are exclusively marine animals that, after the chordates, represent the second largest group of deuterostomes. Their diverse species composition and singular ecological niches provide at the same time challenges and rewards when studying the broad range of responses that make up their immune mechanisms. Two types of responses comprise the immune system of echinoderms: a cellular response and a humoral one. Cell-based immunity is carried by the celomocytes, a morphologically heterogeneous population of free roaming cells that are capable of recognizing and neutralizing pathogens. Celomocytes present diverse morphologies and functions, which include phagocytosis, encapsulation, clotting, cytotoxicity, wound healing among others. Humoral immunity is mediated by a wide variety of secreted compounds that can be found in the celomic fluid and play important roles in defense against infection. Compounds such as lectins, agglutinins, perforins, complement and some cytokines make up some of the humoral responses of echinoderms. Recent advances in the field of molecular biology, genomics and transcriptomics have allowed for the discovery of new immune genes and their products. These discoveries have expanded our knowledge of echinoderm immunity and are setting up the stage for future experiments to better understand the evolution of the immune mechanisms of deuterostomes

  10. Body Size Evolution in Conodonts from the Cambrian through the Triassic

    Science.gov (United States)

    Schaal, E. K.; Morgan, D. J.; Payne, J.

    2013-12-01

    The size of an organism exercises tremendous control over its physiology, life history, and ecology, yet the factors that influence body size evolution remain poorly understood. One major limitation is the lack of appropriate datasets spanning long intervals of evolutionary time. Here, we document size trends in conodonts (tooth-like microfossils from marine chordates) because they evolved rapidly and are known to change size during intervals of environmental change. By measuring photographs from the Catalogue of Conodonts (Ziegler 1982), we compiled a database of conodont P1 element measurements for 575 species and subspecies from the Cambrian through Triassic periods. Because tooth size correlates with body size in conodont animals and their extant relatives, conodont element length can serve as a proxy for the size of the conodont animal. We find that mean and maximum size across species increased during the early Paleozoic, peaked during the Devonian-Mississippian, and then generally decreased until conodonts went extinct at the end of the Triassic. We used regression analyses to compare conodont mean size trends to potential environmental predictors, such as changing atmospheric pO2, atmospheric pCO2, and sea level. Conodont size exhibited poor correlation with these environmental factors, suggesting that conodont evolution may have been more strongly influenced by other environmental covariates or ecological variables such as predation and competition.

  11. The functional relationship between ectodermal and mesodermal segmentation in the crustacean, Parhyale hawaiensis.

    Science.gov (United States)

    Hannibal, Roberta L; Price, Alivia L; Patel, Nipam H

    2012-01-15

    In arthropods, annelids and chordates, segmentation of the body axis encompasses both ectodermal and mesodermal derivatives. In vertebrates, trunk mesoderm segments autonomously and induces segmental arrangement of the ectoderm-derived nervous system. In contrast, in the arthropod Drosophila melanogaster, the ectoderm segments autonomously and mesoderm segmentation is at least partially dependent on the ectoderm. While segmentation has been proposed to be a feature of the common ancestor of vertebrates and arthropods, considering vertebrates and Drosophila alone, it is impossible to conclude whether the ancestral primary segmented tissue was the ectoderm or the mesoderm. Furthermore, much of Drosophila segmentation occurs before gastrulation and thus may not accurately represent the mechanisms of segmentation in all arthropods. To better understand the relationship between segmented germ layers in arthropods, we asked whether segmentation is an intrinsic property of the ectoderm and/or the mesoderm in the crustacean Parhyale hawaiensis by ablating either the ectoderm or the mesoderm and then assaying for segmentation in the remaining tissue layer. We found that the ectoderm segments autonomously. However, mesoderm segmentation requires at least a permissive signal from the ectoderm. Although mesodermal stem cells undergo normal rounds of division in the absence of ectoderm, they do not migrate properly in respect to migration direction and distance. In addition, their progeny neither divide nor express the mesoderm segmentation markers Ph-twist and Ph-Even-skipped. As segmentation is ectoderm-dependent in both Parhyale and holometabola insects, we hypothesize that segmentation is primarily a property of the ectoderm in pancrustacea.

  12. Natural variation of model mutant phenotypes in Ciona intestinalis.

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    Paolo Sordino

    Full Text Available BACKGROUND: The study of ascidians (Chordata, Tunicata has made a considerable contribution to our understanding of the origin and evolution of basal chordates. To provide further information to support forward genetics in Ciona intestinalis, we used a combination of natural variation and neutral population genetics as an approach for the systematic identification of new mutations. In addition to the significance of developmental variation for phenotype-driven studies, this approach can encompass important implications in evolutionary and population biology. METHODOLOGY/PRINCIPAL FINDINGS: Here, we report a preliminary survey for naturally occurring mutations in three geographically interconnected populations of C. intestinalis. The influence of historical, geographical and environmental factors on the distribution of abnormal phenotypes was assessed by means of 12 microsatellites. We identified 37 possible mutant loci with stereotyped defects in embryonic development that segregate in a way typical of recessive alleles. Local populations were found to differ in genetic organization and frequency distribution of phenotypic classes. CONCLUSIONS/SIGNIFICANCE: Natural genetic polymorphism of C. intestinalis constitutes a valuable source of phenotypes for studying embryonic development in ascidians. Correlating genetic structure and the occurrence of abnormal phenotypes is a crucial focus for understanding the selective forces that shape natural finite populations, and may provide insights of great importance into the evolutionary mechanisms that generate animal diversity.

  13. The gut of geographically disparate Ciona intestinalis harbors a core microbiota.

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    Larry J Dishaw

    Full Text Available It is now widely understood that all animals engage in complex interactions with bacteria (or microbes throughout their various life stages. This ancient exchange can involve cooperation and has resulted in a wide range of evolved host-microbial interdependencies, including those observed in the gut. Ciona intestinalis, a filter-feeding basal chordate and classic developmental model that can be experimentally manipulated, is being employed to help define these relationships. Ciona larvae are first exposed internally to microbes upon the initiation of feeding in metamorphosed individuals; however, whether or not these microbes subsequently colonize the gut and whether or not Ciona forms relationships with specific bacteria in the gut remains unknown. In this report, we show that the Ciona gut not only is colonized by a complex community of bacteria, but also that samples from three geographically isolated populations reveal striking similarity in abundant operational taxonomic units (OTUs consistent with the selection of a core community by the gut ecosystem.

  14. Evolutionary developmental pathology and anthropology: A new field linking development, comparative anatomy, human evolution, morphological variations and defects, and medicine.

    Science.gov (United States)

    Diogo, Rui; Smith, Christopher M; Ziermann, Janine M

    2015-11-01

    We introduce a new subfield of the recently created field of Evolutionary-Developmental-Anthropology (Evo-Devo-Anth): Evolutionary-Developmental-Pathology-and-Anthropology (Evo-Devo-P'Anth). This subfield combines experimental and developmental studies of nonhuman model organisms, biological anthropology, chordate comparative anatomy and evolution, and the study of normal and pathological human development. Instead of focusing on other organisms to try to better understand human development, evolution, anatomy, and pathology, it places humans as the central case study, i.e., as truly model organism themselves. We summarize the results of our recent Evo-Devo-P'Anth studies and discuss long-standing questions in each of the broader biological fields combined in this subfield, paying special attention to the links between: (1) Human anomalies and variations, nonpentadactyly, homeotic transformations, and "nearest neighbor" vs. "find and seek" muscle-skeleton associations in limb+facial muscles vs. other head muscles; (2) Developmental constraints, the notion of "phylotypic stage," internalism vs. externalism, and the "logic of monsters" vs. "lack of homeostasis" views about human birth defects; (3) Human evolution, reversions, atavisms, paedomorphosis, and peromorphosis; (4) Scala naturae, Haeckelian recapitulation, von Baer's laws, and parallelism between phylogeny and development, here formally defined as "Phylo-Devo parallelism"; and (5) Patau, Edwards, and Down syndrome (trisomies 13, 18, 21), atavisms, apoptosis, heart malformations, and medical implications.

  15. An endocrine disruptor, bisphenol A, affects development in the protochordate Ciona intestinalis: Hatching rates and swimming behavior alter in a dose-dependent manner

    International Nuclear Information System (INIS)

    Bisphenol A (BPA) is widely used industrially to produce polycarbonate plastics and epoxy resins. Numerous studies document the harmful effects caused by low-dose BPA exposure especially on nervous systems and behavior in experimental animals such as mice and rats. Here, we exposed embryos of a model chordate, Ciona intestinalis, to seawater containing BPA to evaluate adverse effects on embryonic development and on the swimming behavior of subsequent larvae. Ciona is ideal because its larva develops rapidly and has few cells. The rate of larval hatching decreased in a dose-dependent manner with exposures to BPA above 3 μM; swimming behavior was also affected in larvae emerging from embryos exposed to 1 μM BPA. Adverse effects were most severe on fertilized eggs exposed to BPA within 7 h post-fertilization. Ciona shares twelve nuclear receptors with mammals, and BPA is proposed to disturb the physiological functions of one or more of these. - Highlights: ► Embryos of Ciona intestinalis were exposed to BPA to evaluate its developmental effects. ► The rate of larval hatching decreased in a dose-dependent manner. ► Swimming behavior was affected in larvae that emerge from embryos exposed to 1 μM BPA. ► Our findings will support a new strategy to analyze the developmental effects induced by BPA. - Exposure of fertilized Ciona embryos to BPA decreased their hatch rate in a dose-dependent manner and led to abnormal larval swimming behavior.

  16. [Structure-functional organization of eukaryotic high-affinity copper importer CTR1 determines its ability to transport copper, silver and cisplatin].

    Science.gov (United States)

    Skvortsov, A N; Zatulovskiĭ, E A; Puchkova, L V

    2012-01-01

    It was shown recently, that high affinity Cu(I) importer eukaryotic protein CTR1 can also transport in vitro abiogenic Ag(I) ions and anticancer drug cisplatin. At present there is no rational explanation how CTR1 can transfer platinum group, which is different by coordination properties from highly similar Cu(I) and Ag(I). To understand this phenomenon we analyzed 25 sequences of chordate CTR1 proteins, and found out conserved patterns of organization of N-terminal extracellular part of CTR1 which correspond to initial metal binding. Extracellular copper-binding motifs were qualified by their coordination properties. It was shown that relative position of Met- and His-rich copper-binding motifs in CTR1 predisposes the extracellular CTR1 part to binding of copper, silver and cisplatin. Relation between tissue-specific expression of CTR1 gene, steady-state copper concentration, and silver and platinum accumulation in organs of mice in vivo was analyzed. Significant positive but incomplete correlation exists between these variables. Basing on structural and functional peculiarities of N-terminal part of CTR1 a hypothesis of coupled transport of copper and cisplatin has been suggested, which avoids the disagreement between CTR1-mediated cisplatin transport in vitro, and irreversible binding of platinum to Met-rich peptides.

  17. GC skew is a conserved property of unmethylated CpG island promoters across vertebrates.

    Science.gov (United States)

    Hartono, Stella R; Korf, Ian F; Chédin, Frédéric

    2015-11-16

    GC skew is a measure of the strand asymmetry in the distribution of guanines and cytosines. GC skew favors R-loops, a type of three stranded nucleic acid structures that form upon annealing of an RNA strand to one strand of DNA, creating a persistent RNA:DNA hybrid. Previous studies show that GC skew is prevalent at thousands of human CpG island (CGI) promoters and transcription termination regions, which correspond to hotspots of R-loop formation. Here, we investigated the conservation of GC skew patterns in 60 sequenced chordates genomes. We report that GC skew is a conserved sequence characteristic of the CGI promoter class in vertebrates. Furthermore, we reveal that promoter GC skew peaks at the exon 1/ intron1 junction and that it is highly correlated with gene age and CGI promoter strength. Our data also show that GC skew is predictive of unmethylated CGI promoters in a range of vertebrate species and that it imparts significant DNA hypomethylation for promoters with intermediate CpG densities. Finally, we observed that terminal GC skew is conserved for a subset of vertebrate genes that tend to be located significantly closer to their downstream neighbors, consistent with a role for R-loop formation in transcription termination. PMID:26253743

  18. Phylogenetic analysis of Amphioxus genes of the proprotein convertase family, including aPC6C, a marker of epithelial fusions during embryology

    Directory of Open Access Journals (Sweden)

    Stéphanie Bertrand, Alain Camasses, Mathilde Paris, Nicholas D. Holland, Hector Escriva

    2006-01-01

    Full Text Available The proprotein convertases (PCs comprise a family of subtilisin-like endoproteases that activate precursor proteins (including, prohormones, growth factors, and adhesion molecules during their transit through secretory pathways or at the cell surface. To explore the evolution of the PC gene family in chordates, we made a phylogenetic analysis of PC genes found in databases, with special attention to three PC genes of the cephalochordate amphioxus, the closest living invertebrate relative to the vertebrates. Since some vertebrate PC genes are essential for early development, we investigated the expression pattern of the C isoform of the amphioxus PC6 gene (aPC6C. In amphioxus embryos and larvae, aPC6C is expressed at places where epithelia fuse. Several kinds of fusions occur: ectoderm-to-ectoderm during neurulation; mesoderm-to-ectoderm during formation of the preoral ciliated pit; and endoderm-to-ectoderm during formation of the mouth, pharyngeal slits, anus, and external opening of the club-shaped gland. Presumably, at all these sites, aPC6C is activating proteins favoring association between previously disjunct cell populations.

  19. Expression analysis of eight amphioxus genes involved in the Wnt/β-catenin signaling pathway

    Science.gov (United States)

    WANG, Jing; LI, Guang; QIAN, Guang-Hui; HUA, Jun-Hao; WANG, Yi-Quan

    2016-01-01

    The Wnt/β-catenin signaling pathway plays a crucial role in the embryonic development of metazoans. Although the pathway has been studied extensively in many model animals, its function in amphioxus, the most primitive chordate, remains largely uncharacterized. To obtain basic data for functional analysis, we identified and isolated seven genes (Lrp5/6, Dvl, APC, CkIα, CkIδ, Gsk3β, and Gro) of the Wnt/β-catenin signaling pathway from the amphioxus (Branchiostoma floridae) genome. Phylogenetic analysis revealed that amphioxus had fewer members of each gene family than that found in vertebrates. Whole-mount in situ hybridization showed that the genes were maternally expressed and broadly distributed throughout the whole embryo at the cleavage and blastula stages. Among them, Dvl was expressed asymmetrically towards the animal pole, while the others were evenly distributed in all blastomeres. At the mid-gastrula stage, the genes were specifically expressed in the primitive endomesoderm, but displayed different patterns. When the embryo developed into the neurula stage, the gene expressions were mainly detected in either paraxial somites or the tail bud. With the development of the embryo, the expression levels further decreased gradually and remained only in some pharyngeal regions or the tail bud at the larva stage. Our results suggest that the Wnt/β-catenin pathway might be involved in amphioxus somite formation and posterior growth, but not in endomesoderm specification. PMID:27265651

  20. Evolutionary Analysis of the B56 Gene Family of PP2A Regulatory Subunits

    Directory of Open Access Journals (Sweden)

    Lauren M. Sommer

    2015-05-01

    Full Text Available Protein phosphatase 2A (PP2A is an abundant serine/threonine phosphatase that functions as a tumor suppressor in numerous cell-cell signaling pathways, including Wnt, myc, and ras. The B56 subunit of PP2A regulates its activity, and is encoded by five genes in humans. B56 proteins share a central core domain, but have divergent amino- and carboxy-termini, which are thought to provide isoform specificity. We performed phylogenetic analyses to better understand the evolution of the B56 gene family. We found that B56 was present as a single gene in eukaryotes prior to the divergence of animals, fungi, protists, and plants, and that B56 gene duplication prior to the divergence of protostomes and deuterostomes led to the origin of two B56 subfamilies, B56αβε and B56γδ. Further duplications led to three B56αβε genes and two B56γδ in vertebrates. Several nonvertebrate B56 gene names are based on distinct vertebrate isoform names, and would best be renamed. B56 subfamily genes lack significant divergence within primitive chordates, but each became distinct in complex vertebrates. Two vertebrate lineages have undergone B56 gene loss, Xenopus and Aves. In Xenopus, B56δ function may be compensated for by an alternatively spliced transcript, B56δ/γ, encoding a B56δ-like amino-terminal region and a B56γ core.

  1. MicroRNA-Offset RNA Alters Gene Expression and Cell Proliferation

    Science.gov (United States)

    Zhao, Jin; Schnitzler, Gavin R.; Iyer, Lakshmanan K.; Aronovitz, Mark J.; Baur, Wendy E.; Karas, Richard H.

    2016-01-01

    MicroRNA-offset RNAs (moRs) were first identified in simple chordates and subsequently in mouse and human cells by deep sequencing of short RNAs. MoRs are derived from sequences located immediately adjacent to microRNAs (miRs) in the primary miR (pri-miR). Currently moRs are considered to be simply a by-product of miR biosynthesis that lack biological activity. Here we show for the first time that a moR is biologically active. We demonstrate that endogenous or over-expressed moR-21 significantly alters gene expression and inhibits the proliferation of vascular smooth muscle cells (VSMC). In addition, we find that miR-21 and moR-21 may regulate different genes in a given pathway and can oppose each other in regulating certain genes. We report that there is a “seed region” of moR-21 as well as a “seed match region” in the target gene 3’UTR that are indispensable for moR-21-mediated gene down-regulation. We further demonstrate that moR-21-mediated gene repression is Argonaute 2 (Ago2) dependent. Taken together, these findings provide the first evidence that microRNA offset RNA alters gene expression and is biologically active. PMID:27276022

  2. What Can Domesticated Genes Tell Us about the Intron Gain in Mammals?

    Directory of Open Access Journals (Sweden)

    Dušan Kordiš

    2012-01-01

    Full Text Available Domesticated genes, originating from retroelements or from DNA-transposons, constitute an ideal system for testing the hypothesis on the absence of intron gain in mammals. Since single-copy domesticated genes originated from the intronless multicopy transposable elements, the ancestral intron state for domesticated genes is zero. A phylogenomic approach has been used to analyse all domesticated genes in mammals and chordates that originated from the coding parts of transposable elements. A significant amount of intron gain was found only in domesticated genes of placental mammals, where more than 70 cases were identified. De novo gained introns show clear positional bias, since they are distributed mainly in 5′ UTR and coding regions, while 3′ UTR introns are very rare. In the coding regions of some domesticated genes up to 8 de novo gained introns have been found. Surprisingly, the majority of intron gains have occurred in the ancestor of placental mammals. Domesticated genes could constitute an excellent system on which to analyse the mechanisms of intron gain. This paper summarizes the current understanding of intron gain in mammals.

  3. Emerging functional similarities and divergences between Drosophila Spargel /dPGC-1 and mammalian PGC-1 protein

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    Subhas eMukherjee

    2014-07-01

    Full Text Available Peroxisome Proliferator Activated Receptor Gamma Co-activator-1 (PGC-1 is a well- conserved protein among all chordates. Entire Drosophila species subgroup carries a PGC-1 homolog in their genome called spargel/dPGC-1 showing very little divergence. Recent studies have reported that significant functional similarities are shared between vertebrate and invertebrate PGC-1’s based on their role in mitochondrial functions and biogenesis, gluconeogenesis, and most likely in transcription and RNA processing. With the help of genetic epistasis analysis, we established that Drosophila Spargel/dPGC-1 affects cell growth process as a terminal effector in the Insulin-TOR signaling pathway. The association between Spargel and Insulin signaling could also explain its role in the aging process. Here we provided a further comparison between Spargel/dPGC-1 and PGC-1 focusing on nuclear localization, oxidative stress resistance and a possible role of Spargel/dPGC-1 in oogenesis reminiscing the role of Spargel in reproductive aging like many Insulin signaling partners. This led us to hypothesize that the discovery of newer biological functions in Drosophila Spargel/dPGC-1 will pave the way to uncover novel functional equivalents in mammals.

  4. A SINE in the genome of the cephalochordate amphioxus is an Alu element

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    2006-04-01

    Full Text Available Transposable elements of about 300 bp, termed “short interspersed nucleotide elements or SINEs are common in eukaryotes. However, Alu elements, SINEs containing restriction sites for the AluI enzyme, have been known only from primates. Here I report the first SINE found in the genome of the cephalochordate, amphioxus. It is an Alu element of 375 bp that does not share substantial identity with any genomic sequences in vertebrates. It was identified because it was located in the FoxD regulatory region in a cosmid derived from one individual, but absent from the two FoxD alleles of BACs from a second individual. However, searches of sequences of BACs and genomic traces from this second individual gave an estimate of 50-100 copies in the amphioxus genome. The finding of an Alu element in amphioxus raises the question of whether Alu elements in amphioxus and primates arose by convergent evolution or by inheritance from a common ancestor. Genome-wide analyses of transposable elements in amphioxus and other chordates such as tunicates, agnathans and cartilaginous fishes could well provide the answer.

  5. Evolutionary paths of the cAMP-dependent protein kinase (PKA catalytic subunits.

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    Kristoffer Søberg

    Full Text Available 3',5'-cyclic adenosine monophosphate (cAMP dependent protein kinase or protein kinase A (PKA has served as a prototype for the large family of protein kinases that are crucially important for signal transduction in eukaryotic cells. The PKA catalytic subunits Cα and Cβ, encoded by the two genes PRKACA and PRKACB, respectively, are among the best understood and characterized human kinases. Here we have studied the evolution of this gene family in chordates, arthropods, mollusks and other animals employing probabilistic methods and show that Cα and Cβ arose by duplication of an ancestral PKA catalytic subunit in a common ancestor of vertebrates. The two genes have subsequently been duplicated in teleost fishes. The evolution of the PRKACG retroposon in simians was also investigated. Although the degree of sequence conservation in the PKA Cα/Cβ kinase family is exceptionally high, a small set of signature residues defining Cα and Cβ subfamilies were identified. These conserved residues might be important for functions that are unique to the Cα or Cβ clades. This study also provides a good example of a seemingly simple phylogenetic problem which, due to a very high degree of sequence conservation and corresponding weak phylogenetic signals, combined with problematic nonphylogenetic signals, is nontrivial for state-of-the-art probabilistic phylogenetic methods.

  6. Evolutionary loss of 8-oxo-G repair components among eukaryotes

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    Jansson Kristina

    2010-09-01

    Full Text Available Abstract Background We have examined the phylogenetic pattern among eukaryotes of homologues of the E. coli 7,8-dihydro-8-oxoguanine (8-oxo-G repair enzymes MutY, MutM, and MutT. Results These DNA repair enzymes are present in all large phylogenetic groups, with MutM homologues being the most universally conserved. All chordates and echinoderms were found to possess all three 8-oxo-G repair components. Likewise, the red and green algae examined have all three repair enzymes, while all land-living plants have MutY and MutM homologues, but lack MutT. However, for some phyla, e.g. protostomes, a more patchy distribution was found. Nematodes provide a striking example, where Caenorhabditis is the only identified example of an organism group having none of the three repair enzymes, while the genome of another nematode, Trichinella spiralis, instead encodes all three. The most complex distribution exists in fungi, where many different patterns of retention or loss of the three repair components are found. In addition, we found sequence insertions near or within the catalytic sites of MutY, MutM, and MutT to be present in some subgroups of Ascomycetes. Conclusion The 8-oxo-G repair enzymes are ancient in origin, and loss of individual 8-oxo-G repair components at several distinct points in evolution appears to be the most likely explanation for the phylogenetic pattern among eukaryotes.

  7. VKORC1 and VKORC1L1: Why do Vertebrates Have Two Vitamin K 2,3-Epoxide Reductases?

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    Johannes Oldenburg

    2015-07-01

    Full Text Available Among all cellular life on earth, with the exception of yeasts, fungi, and some prokaryotes, VKOR family homologs are ubiquitously encoded in nuclear genomes, suggesting ancient and important biological roles for these enzymes. Despite single gene and whole genome duplications on the largest evolutionary timescales, and the fact that most gene duplications eventually result in loss of one copy, it is surprising that all jawed vertebrates (gnathostomes have retained two paralogous VKOR genes. Both VKOR paralogs function as entry points for nutritionally acquired and recycled K vitamers in the vitamin K cycle. Here we present phylogenetic evidence that the human paralogs likely arose earlier than gnathostomes, possibly in the ancestor of crown chordates. We ask why gnathostomes have maintained these paralogs throughout evolution and present a current summary of what we know. In particular, we look to published studies about tissue- and developmental stage-specific expression, enzymatic function, phylogeny, biological roles and associated pathways that together suggest subfunctionalization as a major influence in evolutionary fixation of both paralogs. Additionally, we investigate on what evolutionary timescale the paralogs arose and under what circumstances in order to gain insight into the biological raison d’être for both VKOR paralogs in gnathostomes.

  8. Evolutionary patterns of RNA-based gene duplicates in Caenorhabditis nematodes coincide with their genomic features

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    Zou Ming

    2012-08-01

    Full Text Available Abstract Background RNA-based gene duplicates (retrocopies played pivotal roles in many physiological processes. Nowadays, functional retrocopies have been systematically identified in several mammals, fruit flies, plants, zebrafish and other chordates, etc. However, studies about this kind of duplication in Caenorhabditis nematodes have not been reported. Findings We identified 43, 48, 43, 9, and 42 retrocopies, of which 6, 15, 18, 3, and 13 formed chimeric genes in C. brenneri, C. briggsae, C. elegans, C. japonica, and C. remanei, respectively. At least 5 chimeric types exist in Caenorhabditis species, of which retrocopy recruiting both N and C terminus is the commonest one. Evidences from different analyses demonstrate many retrocopies and almost all chimeric genes may be functional in these species. About half of retrocopies in each species has coordinates in other species, and we suggest that retrocopies in closely related species may be helpful in identifying retrocopies for one certain species. Conclusions A number of retrocopies and chimeric genes exist in Caenorhabditis genomes, and some of them may be functional. The evolutionary patterns of these genes may correlate with their genomic features, such as the activity of retroelements, the high rate of mutation and deletion rate, and a large proportion of genes subject to trans-splicing.

  9. T-type Calcium Channel Regulation of Neural Tube Closure and EphrinA/EPHA Expression

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    Sarah Abdul-Wajid

    2015-10-01

    Full Text Available A major class of human birth defects arise from aberrations during neural tube closure (NTC. We report on a NTC signaling pathway requiring T-type calcium channels (TTCCs that is conserved between primitive chordates (Ciona and Xenopus. With loss of TTCCs, there is a failure to seal the anterior neural folds. Accompanying loss of TTCCs is an upregulation of EphrinA effectors. Ephrin signaling is known to be important in NTC, and ephrins can affect both cell adhesion and repulsion. In Ciona, ephrinA-d expression is downregulated at the end of neurulation, whereas, with loss of TTCC, ephrinA-d remains elevated. Accordingly, overexpression of ephrinA-d phenocopied TTCC loss of function, while overexpression of a dominant-negative Ephrin receptor was able to rescue NTC in a Ciona TTCC mutant. We hypothesize that signaling through TTCCs is necessary for proper anterior NTC through downregulation of ephrins, and possibly elimination of a repulsive signal.

  10. Mapping Association between Long-Range Cis-Regulatory Regions and Their Target Genes Using Comparative Genomics

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    Mongin, Emmanuel; Dewar, Ken; Blanchette, Mathieu

    In chordates, long-range cis-regulatory regions are involved in the control of transcription initiation (either as repressors or enhancers). They can be located as far as 1 Mb from the transcription start site of the target gene and can regulate more than one gene. Therefore, proper characterization of functional interactions between long-range cis-regulatory regions and their target genes remains problematic. We present a novel method to predict such interactions based on the analysis of rearrangements between the human and 16 other vertebrate genomes. Our method is based on the assumption that genome rearrangements that would disrupt the functional interaction between a cis-regulatory region and its target gene are likely to be deleterious. Therefore, conservation of synteny through evolution would be an indication of a functional interaction. We use our algorithm to classify a set of 1,406,084 putative associations from the human genome. This genome-wide map of interactions has many potential applications, including the selection of candidate regions prior to in vivo experimental characterization, a better characterization of regulatory regions involved in position effect diseases, and an improved understanding of the mechanisms and importance of long-range regulation.

  11. Geographically conserved microbiomes of four temperate water tunicates.

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    Cahill, Patrick L; Fidler, Andrew E; Hopkins, Grant A; Wood, Susanna A

    2016-08-01

    Tunicates are useful models for exploring microbiomes because they have an innate immune system resembling that of chordates. Automated ribosomal RNA intergenic spacer analysis and High-Throughput Sequencing were used to compare the tunic microbiomes of Ciona robusta (formerly Ciona intestinalis type A), Ciona savignyi, Botrylloides leachi and Botryllus schlosseri sampled from three distinct locations with limited genetic connectivity. Bacterial phylotype profiles were conserved within each species, and there were no detectable differences between tunic and tunic + cuticle subsamples from an individual. Bacterial operational taxonomic unit (OTU) diversity was lowest for C. savignyi (320 ± 190 OTUs) and highest for B. schlosseri (1260 ± 190 OTUs). Each species had a distinct set of bacterial OTUs (pseudo-F = 3.0, p > 0.001), with the exception of B. leachi and B. schlosseri from one sampling location (t = 1.2, p = 0.09). Of note were OTUs assigned to Alphaproteobacteria from C. robusta plus Phyllobacteriaceae and Endozoicomonas from C. savignyi. These OTUs contributed 51, 22 and 10% of sequence reads, respectively, and are related to known bacterial symbionts. The within-species conservation of core OTUs across three distinct and co-occurring populations of tunicates provides compelling evidence that these tunicates foster defined microbiomes. PMID:26929150

  12. Immunobiology of compound ascidians, with particular reference to Botryllus schlosseri: state of art

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    L Ballarin

    2008-05-01

    Full Text Available The phylogenetic position of invertebrate chordates closely related to vertebrates explains the increasing interest towards tunicate immunobiology. Most of the tunicates are ascidians which, like all other invertebrates, rely only on innate immunity for their defense. Compound ascidians differ from solitary species for the presence of colony specificity, i.e. the ability for intraspecific non-self recognition. The immunobiology of compound ascidians has been particularly studied in Botryllus schlosseri, which is an emerging model organism for this kind of studies. In B. schlosseri and related species, immunocytes are represented by phagocytes and cytotoxic morula cells, the former able to ingest foreign cell and particles, the latter representing the effectors of the inflammatory reaction which follows the contact between genetically incompatible colonies. Activated phagocytes release lectins with opsonic activity and are involved in the clearance of apoptotic cells during the colonial generational change. Morula cells recognize the presence of foreign molecules as well as allogeneic soluble factors diffusing from an alien colony and as a consequence they: i release cytokines in the medium which have chemotactic activity and activate phagocytes; ii degranulate and release phenoloxidase which induces necrotic cell death by oxidative stress. A better knowledge of Botryllus genome will allow a deeper insight into open problems in immunobiology of compound ascidians.

  13. Functional Expression in Escherichia coli of the Disulfide-Rich Sea Anemone Peptide APETx2, a Potent Blocker of Acid-Sensing Ion Channel 3

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    Glenn F. King

    2012-07-01

    Full Text Available Acid-sensing ion channels (ASICs are proton-gated sodium channels present in the central and peripheral nervous system of chordates. ASIC3 is highly expressed in sensory neurons and plays an important role in inflammatory and ischemic pain. Thus, specific inhibitors of ASIC3 have the potential to be developed as novel analgesics. APETx2, isolated from the sea anemone Anthopleura elegantissima, is the most potent and selective inhibitor of ASIC3-containing channels. However, the mechanism of action of APETx2 and the molecular basis for its interaction with ASIC3 is not known. In order to assist in characterizing the ASIC3-APETx2 interaction, we developed an efficient and cost-effective Escherichia coli periplasmic expression system for the production of APETx2. NMR studies on uniformly 13C/15N-labelled APETx2 produced in E. coli showed that the recombinant peptide adopts the native conformation. Recombinant APETx2 is equipotent with synthetic APETx2 at inhibiting ASIC3 channels expressed in Xenopus oocytes. Using this system we mutated Phe15 to Ala, which caused a profound loss of APETx2’s activity on ASIC3. These findings suggest that this expression system can be used to produce mutant versions of APETx2 in order to facilitate structure-activity relationship studies.

  14. Hypothesis and Theory: Revisiting Views on the Co-evolution of the Melanocortin Receptors and the Accessory Proteins, MRAP1 and MRAP2

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    Dores, Robert M.

    2016-01-01

    The evolution of the melanocortin receptors (MCRs) is closely associated with the evolution of the melanocortin-2 receptor accessory proteins (MRAPs). Recent annotation of the elephant shark genome project revealed the sequence of a putative MRAP1 ortholog. The presence of this sequence in the genome of a cartilaginous fish raises the possibility that the mrap1 and mrap2 genes in the genomes of gnathostome vertebrates were the result of the chordate 2R genome duplication event. The presence of a putative MRAP1 ortholog in a cartilaginous fish genome is perplexing. Recent studies on melanocortin-2 receptor (MC2R) in the genomes of the elephant shark and the Japanese stingray indicate that these MC2R orthologs can be functionally expressed in CHO cells without co-expression of an exogenous mrap1 cDNA. The novel ligand selectivity of these cartilaginous fish MC2R orthologs is discussed. Finally, the origin of the mc2r and mc5r genes is reevaluated. The distinctive primary sequence conservation of MC2R and MC5R is discussed in light of the physiological roles of these two MCR paralogs.

  15. Growth patterns in Onychophora (velvet worms: lack of a localised posterior proliferation zone

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    Landman Kerry A

    2010-11-01

    Full Text Available Abstract Background During embryonic development of segmented animals, body segments are thought to arise from the so-called "posterior growth zone" and the occurrence of this "zone" has been used to support the homology of segmentation between arthropods, annelids, and vertebrates. However, the term "posterior growth zone" is used ambiguously in the literature, mostly referring to a region of increased proliferation at the posterior end of the embryo. To determine whether such a localised posterior proliferation zone is an ancestral feature of Panarthropoda (Onychophora + Tardigrada + Arthropoda, we examined cell division patterns in embryos of Onychophora. Results Using in vivo incorporation of the DNA replication marker BrdU (5-bromo-2'-deoxyuridine and anti-phospho-histone H3 immunolabelling, we found that a localised posterior region of proliferating cells does not occur at any developmental stage in onychophoran embryos. This contrasts with a localised pattern of cell divisions at the posterior end of annelid embryos, which we used as a positive control. Based on our data, we present a mathematical model, which challenges the paradigm that a localised posterior proliferation zone is necessary for segment patterning in short germ developing arthropods. Conclusions Our findings suggest that a posterior proliferation zone was absent in the last common ancestor of Onychophora and Arthropoda. By comparing our data from Onychophora with those from annelids, arthropods, and chordates, we suggest that the occurrence of a "posterior growth zone" currently cannot be used to support the homology of segmentation between these three animal groups.

  16. Two lamprey Hedgehog genes share non-coding regulatory sequences and expression patterns with gnathostome Hedgehogs.

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    Shungo Kano

    Full Text Available Hedgehog (Hh genes play major roles in animal development and studies of their evolution, expression and function point to major differences among chordates. Here we focused on Hh genes in lampreys in order to characterize the evolution of Hh signalling at the emergence of vertebrates. Screening of a cosmid library of the river lamprey Lampetra fluviatilis and searching the preliminary genome assembly of the sea lamprey Petromyzon marinus indicate that lampreys have two Hh genes, named Hha and Hhb. Phylogenetic analyses suggest that Hha and Hhb are lamprey-specific paralogs closely related to Sonic/Indian Hh genes. Expression analysis indicates that Hha and Hhb are expressed in a Sonic Hh-like pattern. The two transcripts are expressed in largely overlapping but not identical domains in the lamprey embryonic brain, including a newly-described expression domain in the nasohypophyseal placode. Global alignments of genomic sequences and local alignment with known gnathostome regulatory motifs show that lamprey Hhs share conserved non-coding elements (CNE with gnathostome Hhs albeit with sequences that have significantly diverged and dispersed. Functional assays using zebrafish embryos demonstrate gnathostome-like midline enhancer activity for CNEs contained in intron2. We conclude that lamprey Hh genes are gnathostome Shh-like in terms of expression and regulation. In addition, they show some lamprey-specific features, including duplication and structural (but not functional changes in the intronic/regulatory sequences.

  17. Discovery of an Active RAG Transposon Illuminates the Origins of V(D)J Recombination.

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    Huang, Shengfeng; Tao, Xin; Yuan, Shaochun; Zhang, Yuhang; Li, Peiyi; Beilinson, Helen A; Zhang, Ya; Yu, Wenjuan; Pontarotti, Pierre; Escriva, Hector; Le Petillon, Yann; Liu, Xiaolong; Chen, Shangwu; Schatz, David G; Xu, Anlong

    2016-06-30

    Co-option of RAG1 and RAG2 for antigen receptor gene assembly by V(D)J recombination was a crucial event in the evolution of jawed vertebrate adaptive immunity. RAG1/2 are proposed to have arisen from a transposable element, but definitive evidence for this is lacking. Here, we report the discovery of ProtoRAG, a DNA transposon family from lancelets, the most basal extant chordates. A typical ProtoRAG is flanked by 5-bp target site duplications and a pair of terminal inverted repeats (TIRs) resembling V(D)J recombination signal sequences. Between the TIRs reside tail-to-tail-oriented, intron-containing RAG1-like and RAG2-like genes. We demonstrate that ProtoRAG was recently active in the lancelet germline and that the lancelet RAG1/2-like proteins can mediate TIR-dependent transposon excision, host DNA recombination, transposition, and low-efficiency TIR rejoining using reaction mechanisms similar to those used by vertebrate RAGs. We propose that ProtoRAG represents a molecular "living fossil" of the long-sought RAG transposon. PMID:27293192

  18. The isochore patterns of invertebrate genomes

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    Costantini Maria

    2009-11-01

    Full Text Available Abstract Background Previous investigations from our laboratory were largely focused on the genome organization of vertebrates. We showed that these genomes are mosaics of isochores, megabase-size DNA sequences that are fairly homogeneous in base composition yet belong to a small number of families that cover a wide compositional spectrum. A question raised by these results concerned how far back in evolution an isochore organization of the eukaryotic genome arose. Results The present investigation deals with the compositional patterns of the invertebrates for which full genome sequences, or at least scaffolds, are available. We found that (i a mosaic of isochores is the long-range organization of all the genomes that we investigated; (ii the isochore families from the invertebrate genomes matched the corresponding families of vertebrates in GC levels; (iii the relative amounts of isochore families were remarkably different for different genomes, except for those from phylogenetically close species, such as the Drosophilids. Conclusion This work demonstrates not only that an isochore organization is present in all metazoan genomes analyzed that included Nematodes, Arthropods among Protostomia, Echinoderms and Chordates among Deuterostomia, but also that the isochore families of invertebrates share GC levels with the corresponding families of vertebrates.

  19. Preservation and phylogeny of Cambrian ecdysozoans tested by experimental decay of Priapulus.

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    Sansom, Robert S

    2016-01-01

    The exceptionally preserved Cambrian fossil record provides unique insight into the early evolutionary history of animals. Understanding of the mechanisms of exceptional soft tissue preservation frames all interpretations of the fauna and its evolutionary significance. This is especially true for recent interpretations of preserved nervous tissues in fossil ecdysozoans. However, models of soft tissue preservation lack empirical support from actualistic studies. Here experimental decay of the priapulid Priapulus reveal consistent bias towards rapid loss of internal non-cuticular anatomy compared with recalcitrant cuticular anatomy. This is consistent with models of Burgess Shale-type preservation and indicates that internal tissues are unlikely to be preserved with fidelity if organically preserved. This pattern, along with extreme body margin distortion, is consistent with onychophoran decay, and is therefore resolved as general for early ecdysozoans. Application of these patterns to phylogenetic data finds scalidophoran taxa to be very sensitive to taphonomically informed character coding, but not panarthropodan taxa. Priapulid decay also have unexpected relevance for interpretation of myomeres in fossil chordates. The decay data presented serve not only as a test of models of preservation but also a framework with which to interpret ecdysozoan fossil anatomies, and the subsequent evolutionary inferences drawn from them. PMID:27595908

  20. Evolution of signal multiplexing by 14-3-3-binding 2R-ohnologue protein families in the vertebrates

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    Tinti, Michele; Johnson, Catherine; Toth, Rachel; Ferrier, David E. K.; MacKintosh, Carol

    2012-01-01

    14-3-3 proteins regulate cellular responses to stimuli by docking onto pairs of phosphorylated residues on target proteins. The present study shows that the human 14-3-3-binding phosphoproteome is highly enriched in 2R-ohnologues, which are proteins in families of two to four members that were generated by two rounds of whole genome duplication at the origin of the vertebrates. We identify 2R-ohnologue families whose members share a ‘lynchpin’, defined as a 14-3-3-binding phosphosite that is conserved across members of a given family, and aligns with a Ser/Thr residue in pro-orthologues from the invertebrate chordates. For example, the human receptor expression enhancing protein (REEP) 1–4 family has the commonest type of lynchpin motif in current datasets, with a phosphorylatable serine in the –2 position relative to the 14-3-3-binding phosphosite. In contrast, the second 14-3-3-binding sites of REEPs 1–4 differ and are phosphorylated by different kinases, and hence the REEPs display different affinities for 14-3-3 dimers. We suggest a conceptual model for intracellular regulation involving protein families whose evolution into signal multiplexing systems was facilitated by 14-3-3 dimer binding to lynchpins, which gave freedom for other regulatory sites to evolve. While increased signalling complexity was needed for vertebrate life, these systems also generate vulnerability to genetic disorders. PMID:22870394

  1. Characteristic and functional analysis of toll-like receptors (TLRs in the lophotrocozoan, Crassostrea gigas, reveals ancient origin of TLR-mediated innate immunity.

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    Yang Zhang

    Full Text Available The evolution of TLR-mediated innate immunity is a fundamental question in immunology. Here, we report the characterization and functional analysis of four TLR members in the lophotrochozoans Crassostreagigas (CgTLRs. All CgTLRs bear a conserved domain organization and have a close relationship with TLRs in ancient non-vertebrate chordates. In HEK293 cells, every CgTLR could constitutively activate NF-κB responsive reporter, but none of the PAMPs tested could stimulate CgTLR-activated NF-κB induction. Subcellular localization showed that CgTLR members have similar and dual distribution on late endosomes and plasma membranes. Moreover, CgTLRs and CgMyD88 mRNA show a consistent response to multiple PAMP challenges in oyster hemocytes. As CgTLR-mediated NF-κB activation is dependent on CgMyD88, we designed a blocking peptide for CgTLR signaling that would inhibit CgTLR-CgMyD88 dependent NF-κB activation. This was used to demonstrate that a Vibrio parahaemolyticus infection-induced enhancement of degranulation and increase of cytokines TNF mRNA in hemocytes, could be inhibited by blocking CgTLR signaling. In summary, our study characterized the primitive TLRs in the lophotrocozoan C. gigas and demonstrated a fundamental role of TLR signaling in infection-induced hemocyte activation. This provides further evidence for an ancient origin of TLR-mediated innate immunity.

  2. Experimental analysis of decay biases in the fossil record of lobopodians

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    Murdock, Duncan; Gabbott, Sarah; Purnell, Mark

    2016-04-01

    If fossils are to realize their full potential in reconstructing the tree of life we must understand how our view of ancient organisms is obscured by taphonomic filters of decay and preservation. In most cases, processes of decay will leave behind either nothing or only the most decay resistant body parts, and even in those rare instances where soft tissues are fossilized we cannot assume that the resulting fossil, however exquisite, represents a faithful anatomical representation of the animal as it was in life.Recent experiments have shown that the biases introduced by decay can be far from random; in chordates, for example, the most phylogenetically informative characters are also the most decay-prone, resulting in 'stemward slippage'. But how widespread is this phenomenon, and are there other non-random biases linked to decay? Intuitively, we make assumptions about the likelihood of different kinds of characters to survive and be preserved, with knock-on effects for anatomical and phylogenetic interpretations. To what extent are these assumptions valid? We combine our understanding of the fossil record of lobopodians with insights from decay experiments of modern onychophorans (velvet worms) to test these assumptions. Our analysis demonstrates that taphonomically informed tests of character interpretations have the potential to improve phylogenetic resolution. This approach is widely applicable to the fossil record - allowing us to ground-truth some of the assumptions involved in describing exceptionally preserved fossil material.

  3. Unusually long palindromes are abundant in mitochondrial control regions of insects and nematodes.

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    K P Arunkumar

    Full Text Available BACKGROUND: Palindromes are known to be involved in a variety of biological processes. In the present investigation we carried out a comprehensive analysis of palindromes in the mitochondrial control regions (CRs of several animal groups to study their frequency, distribution and architecture to gain insights into the origin of replication of mtDNA. METHODOLOGY/PRINCIPAL FINDINGS: Many species of Arthropoda, Nematoda, Mollusca and Annelida harbor palindromes and inverted repeats (IRs in their CRs. Lower animals like cnidarians and higher animal groups like chordates are almost devoid of palindromes and IRs. The study revealed that palindrome occurrence is positively correlated with the AT content of CRs, and that IRs are likely to give rise to longer palindromes. CONCLUSIONS/SIGNIFICANCE: The present study attempts to explain possible reasons and gives in silico evidence for absence of palindromes and IRs from CR of vertebrate mtDNA and acquisition and retention of the same in insects. Study of CRs of different animal phyla uncovered unique architecture of this locus, be it high abundance of long palindromes and IRs in CRs of Insecta and Nematoda, or short IRs of 10-20 nucleotides with a spacer region of 12-14 bases in subphylum Chelicerata, or nearly complete of absence of any long palindromes and IRs in Vertebrata, Cnidaria and Echinodermata.

  4. Heterogeneous generation of new cells in the adult echinoderm nervous system

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    Vladimir S. Mashanov

    2015-09-01

    Full Text Available Adult neurogenesis, generation of new functional cells in the mature central nervous system (CNS, has been documented in a number of diverse organisms, ranging from humans to invertebrates. However, the origin and evolution of this phenomenon is still poorly understood for many of the key phylogenetic groups. Echinoderms are one such phylum, positioned as a sister group to chordates within the monophyletic clade Deuterostomia. They are well known for the ability of their adult organs, including the CNS, to completely regenerate after injury. Nothing is known, however, about production of new cells in the nervous tissue under normal physiological conditions in these animals. In this study, we show that new cells are continuously generated in the mature radial nerve cord (RNC of the sea cucumber Holothuria glaberrima. Importantly, this neurogenic activity is not evenly distributed, but is significantly more extensive in the lateral regions of the RNC than along the midline. Some of the new cells generated in the apical region of the ectoneural neuroepithelium leave their place of origin and migrate basally to populate the neural parenchyma. Gene expression analysis showed that generation of new cells in the adult sea cucumber CNS is associated with transcriptional activity of genes known to be involved in regulation of various aspects of neurogenesis in other animals. Further analysis of one of those genes, the transcription factor Myc showed that it is expressed, in some, but not all radial glial cells, suggesting heterogeneity of this CNS progenitor cell population in echinoderms.

  5. A RALDH-like enzyme involved in Fusarium verticillioides development.

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    Díaz-Sánchez, Violeta; Limón, M Carmen; Schaub, Patrick; Al-Babili, Salim; Avalos, Javier

    2016-01-01

    Retinaldehyde dehydrogenases (RALDHs) convert retinal to retinoic acid, an important chordate morphogen. Retinal also occurs in some fungi, such as Fusarium and Ustilago spp., evidenced by the presence of rhodopsins and β-carotene cleaving, retinal-forming dioxygenases. Based on the assumption that retinoic acid may also be formed in fungi, we searched the Fusarium protein databases for RALDHs homologs, focusing on Fusarium verticillioides. Using crude lysates of Escherichia coli cells expressing the corresponding cDNAs, we checked the capability of best matches to convert retinal into retinoic acid in vitro. Thereby, we identified an aldehyde dehydrogenase, termed CarY, as a retinoic acid-forming enzyme, an activity that was also exerted by purified CarY. Targeted mutation of the carY gene in F. verticillioides resulted in alterations of mycelia development and conidia morphology in agar cultures, and reduced capacity to produce perithecia as a female in sexual crosses. Complementation of the mutant with a wild-type carY allele demonstrated that these alterations are caused by the lackof CarY. However, retinoic acid could not be detected by LC-MS analysis either in the wild type or the complemented carY strain in vivo, making elusive the connection between CarY enzymatic activity and retinoic acid formation in the fungus.

  6. Ensembl regulation resources.

    Science.gov (United States)

    Zerbino, Daniel R; Johnson, Nathan; Juetteman, Thomas; Sheppard, Dan; Wilder, Steven P; Lavidas, Ilias; Nuhn, Michael; Perry, Emily; Raffaillac-Desfosses, Quentin; Sobral, Daniel; Keefe, Damian; Gräf, Stefan; Ahmed, Ikhlak; Kinsella, Rhoda; Pritchard, Bethan; Brent, Simon; Amode, Ridwan; Parker, Anne; Trevanion, Steven; Birney, Ewan; Dunham, Ian; Flicek, Paul

    2016-01-01

    New experimental techniques in epigenomics allow researchers to assay a diversity of highly dynamic features such as histone marks, DNA modifications or chromatin structure. The study of their fluctuations should provide insights into gene expression regulation, cell differentiation and disease. The Ensembl project collects and maintains the Ensembl regulation data resources on epigenetic marks, transcription factor binding and DNA methylation for human and mouse, as well as microarray probe mappings and annotations for a variety of chordate genomes. From this data, we produce a functional annotation of the regulatory elements along the human and mouse genomes with plans to expand to other species as data becomes available. Starting from well-studied cell lines, we will progressively expand our library of measurements to a greater variety of samples. Ensembl's regulation resources provide a central and easy-to-query repository for reference epigenomes. As with all Ensembl data, it is freely available at http://www.ensembl.org, from the Perl and REST APIs and from the public Ensembl MySQL database server at ensembldb.ensembl.org. Database URL: http://www.ensembl.org. PMID:26888907

  7. Pigmented anatomy in Carboniferous cyclostomes and the evolution of the vertebrate eye.

    Science.gov (United States)

    Gabbott, Sarah E; Donoghue, Philip C J; Sansom, Robert S; Vinther, Jakob; Dolocan, Andrei; Purnell, Mark A

    2016-08-17

    The success of vertebrates is linked to the evolution of a camera-style eye and sophisticated visual system. In the absence of useful data from fossils, scenarios for evolutionary assembly of the vertebrate eye have been based necessarily on evidence from development, molecular genetics and comparative anatomy in living vertebrates. Unfortunately, steps in the transition from a light-sensitive 'eye spot' in invertebrate chordates to an image-forming camera-style eye in jawed vertebrates are constrained only by hagfish and lampreys (cyclostomes), which are interpreted to reflect either an intermediate or degenerate condition. Here, we report-based on evidence of size, shape, preservation mode and localized occurrence-the presence of melanosomes (pigment-bearing organelles) in fossil cyclostome eyes. Time of flight secondary ion mass spectrometry analyses reveal secondary ions with a relative intensity characteristic of melanin as revealed through principal components analyses. Our data support the hypotheses that extant hagfish eyes are degenerate, not rudimentary, that cyclostomes are monophyletic, and that the ancestral vertebrate had a functional visual system. We also demonstrate integument pigmentation in fossil lampreys, opening up the exciting possibility of investigating colour patterning in Palaeozoic vertebrates. The examples we report add to the record of melanosome preservation in Carboniferous fossils and attest to surprising durability of melanosomes and biomolecular melanin. PMID:27488650

  8. Developmental expression of a class IV POU gene in the gastropod Haliotis asinina supports a conserved role in sensory cell development in bilaterians.

    Science.gov (United States)

    O'Brien, Elizabeth K; Degnan, Bernard M

    2002-09-01

    POU-IV genes regulate neuronal development in a number of deuterostomes (chordates) and ecdysozoans (arthropods and nematodes). Currently their function and expression in the third bilaterian clade, the Lophotrochozoa, comprising molluscs, annelids and their affiliates, is unclear. Herein we characterise the developmental expression of HasPOU-IV in the gastropod mollusc, Haliotis asinina. The POU-IV gene is transiently expressed in 11 distinct larval territories during the first 3 days of development. HasPOU-IV is first expressed in sets of ventral epidermal cells in the newly hatched trochophore larvae. As larval morphogenesis proceeds, we observe HasPOU-IV transcripts in cells that putatively form a range of sensory systems including chemo- and mechanosensory cells in the foot, cephalic tentacles, the ctenidia, the geosensory statocyst and the eyes. By comparing HasPOU-IV expression with POU-IV genes in other bilaterians we infer that this class of POU-domain genes had an ancestral role in regulating sensory cell development.

  9. Developmental cell death programs license cytotoxic cells to eliminate histocompatible partners.

    Science.gov (United States)

    Corey, Daniel M; Rosental, Benyamin; Kowarsky, Mark; Sinha, Rahul; Ishizuka, Katherine J; Palmeri, Karla J; Quake, Stephen R; Voskoboynik, Ayelet; Weissman, Irving L

    2016-06-01

    In a primitive chordate model of natural chimerism, one chimeric partner is often eliminated in a process of allogeneic resorption. Here, we identify the cellular framework underlying loss of tolerance to one partner within a natural Botryllus schlosseri chimera. We show that the principal cell type mediating chimeric partner elimination is a cytotoxic morula cell (MC). Proinflammatory, developmental cell death programs render MCs cytotoxic and, in collaboration with activated phagocytes, eliminate chimeric partners during the "takeover" phase of blastogenic development. Among these genes, the proinflammatory cytokine IL-17 enhances cytotoxicity in allorecognition assays. Cellular transfer of FACS-purified MCs from allogeneic donors into recipients shows that the resorption response can be adoptively acquired. Transfer of 1 × 10(5) allogeneic MCs eliminated 33 of 78 (42%) recipient primary buds and 20 of 76 (20.5%) adult parental adult organisms (zooids) by 14 d whereas transfer of allogeneic cell populations lacking MCs had only minimal effects on recipient colonies. Furthermore, reactivity of transferred cells coincided with the onset of developmental-regulated cell death programs and disproportionately affected developing tissues within a chimera. Among chimeric partner "losers," severe developmental defects were observed in asexually propagating tissues, reflecting a pathologic switch in gene expression in developmental programs. These studies provide evidence that elimination of one partner in a chimera is an immune cell-based rejection that operates within histocompatible pairs and that maximal allogeneic responses involve the coordination of both phagocytic programs and the "arming" of cytotoxic cells. PMID:27217570

  10. Acoel flatworms are not platyhelminthes: evidence from phylogenomics.

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    Hervé Philippe

    Full Text Available Acoel flatworms are small marine worms traditionally considered to belong to the phylum Platyhelminthes. However, molecular phylogenetic analyses suggest that acoels are not members of Platyhelminthes, but are rather extant members of the earliest diverging Bilateria. This result has been called into question, under suspicions of a long branch attraction (LBA artefact. Here we re-examine this problem through a phylogenomic approach using 68 different protein-coding genes from the acoel Convoluta pulchra and 51 metazoan species belonging to 15 different phyla. We employ a mixture model, named CAT, previously found to overcome LBA artefacts where classical models fail. Our results unequivocally show that acoels are not part of the classically defined Platyhelminthes, making the latter polyphyletic. Moreover, they indicate a deuterostome affinity for acoels, potentially as a sister group to all deuterostomes, to Xenoturbellida, to Ambulacraria, or even to chordates. However, the weak support found for most deuterostome nodes, together with the very fast evolutionary rate of the acoel Convoluta pulchra, call for more data from slowly evolving acoels (or from its sister-group, the Nemertodermatida to solve this challenging phylogenetic problem.

  11. Multiple independent fusions of glucose-6-phosphate dehydrogenase with enzymes in the pentose phosphate pathway.

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    Nicholas A Stover

    Full Text Available Fusions of the first two enzymes in the pentose phosphate pathway, glucose-6-phosphate dehydrogenase (G6PD and 6-phosphogluconolactonase (6PGL, have been previously described in two distant clades, chordates and species of the malarial parasite Plasmodium. We have analyzed genome and expressed sequence data from a variety of organisms to identify the origins of these gene fusion events. Based on the orientation of the domains and range of species in which homologs can be found, the fusions appear to have occurred independently, near the base of the metazoan and apicomplexan lineages. Only one of the two metazoan paralogs of G6PD is fused, showing that the fusion occurred after a duplication event, which we have traced back to an ancestor of choanoflagellates and metazoans. The Plasmodium genes are known to contain a functionally important insertion that is not seen in the other apicomplexan fusions, highlighting this as a unique characteristic of this group. Surprisingly, our search revealed two additional fusion events, one that combined 6PGL and G6PD in an ancestor of the protozoan parasites Trichomonas and Giardia, and another fusing G6PD with phosphogluconate dehydrogenase (6PGD in a species of diatoms. This study extends the range of species known to contain fusions in the pentose phosphate pathway to many new medically and economically important organisms.

  12. Lessons from evolution: developmental plasticity in vertebrates with complex life cycles.

    Science.gov (United States)

    Denver, R J; Middlemis-Maher, J

    2010-10-01

    Developmental plasticity is the property of a given genotype to produce different phenotypes in response to the environmental conditions experienced during development. Chordates have two basic modes of development, direct and indirect. Direct development (mode of humans) was derived evolutionarily from indirect development (mode of many amphibians), the major difference being the presence of a larval stage with indirect development; larvae undergo metamorphosis to the juvenile adult. In amphibians, environmental conditions experienced during the larval stage can lead to extreme plasticity in behaviour, morphology and the timing of metamorphosis and can cause variation in adult phenotypic expression (carry-over effects, or developmental programming). Hormones of the neuroendocrine stress axis play pivotal roles in mediating environmental effects on animal development. Stress hormones, produced in response to a deteriorating larval habitat, accelerate amphibian metamorphosis; in mammals, stress hormones hasten the onset of parturition and play an important role in pre-term birth caused by intra-uterine stress. While stress hormones can promote survival in a deteriorating larval or intra-uterine habitat, costs may be incurred, such as reduced growth and size at metamorphosis or birth. Furthermore, exposure to elevated stress hormones during the tadpole or foetal stage can cause permanent neurological changes, leading to altered physiology and behaviour later in life. The actions of stress hormones in animal development are evolutionarily conserved, and therefore amphibians can serve as important model organisms for research on the mechanisms of developmental plasticity.

  13. Self/non-self recognition mechanisms in sexual reproduction: new insight into the self-incompatibility system shared by flowering plants and hermaphroditic animals.

    Science.gov (United States)

    Sawada, Hitoshi; Morita, Masaya; Iwano, Megumi

    2014-08-01

    Sexual reproduction is an essential process for generating a genetic variety in the next generation. However, most flowering plants and hermaphroditic animals potentially allow self-fertilization. Approximately 60% of angiosperms possess a self-incompatibility (SI) system to avoid inbreeding. The SI system functions at a process of interaction between pollen (or pollen tube) and the pistil. These SI-responsible factors (S-determinants) in pollen and the pistil are encoded by highly polymorphic multiallelic genes in the S-locus, which are tightly linked making a single haplotype. Different taxonomic families utilize different types of S-determinant proteins. In contrast to the plant system, the mechanisms of SI in simultaneously hermaphroditic animals are largely unknown. Among them, promising candidates for SI in ascidians (primitive chordates) were recently identified. The SI system in the ascidian Cionaintestinalis was found to be very similar to those in flowering plants: The products of sperm- and egg-side multiallelic SI genes, which are tight linked and highly polymorphic, appear to be responsible for the SI system as revealed by genetic analysis. These findings led us to speculate that the SI systems in plants and animals evolved in a manner of convergent evolution. Here, we review the current understanding of the molecular mechanisms of the SI system in flowering plants, particularly Brassicacea, and in ascidians from the viewpoint of common mechanisms shared by plants and animals.

  14. On the Origin of Cells and Derivation of Thyroid Cancer: C Cell Story Revisited.

    Science.gov (United States)

    Nilsson, Mikael; Williams, Dillwyn

    2016-07-01

    We will highlight and put into perspective new lineage tracing data from genetic studies in mice indicating that the genuine progenitors to C cells arise in the endoderm germ layer. This overturns the current concept of a neural crest origin of thyroid C cells referred to in every textbook and dedicated paper to this very day. As will become apparent, except for a single experiment, the neural crest theory has little or no support when the evolution and development of calcitonin-producing cells in the entire chordate family are considered. Instead, a unifying origin of all cells of the ultimobranchial bodies reopens questions on the histogenesis of certain thyroid pathologies previously difficult to explain. On this aspect, medullary thyroid cancer shows a stronger connection to gut neuroendocrine tumours than previously recognized. It is envisaged that novel factors implicated in C cell-derived tumour growth and progression will be discovered as the mechanisms that regulate lineage expansion of embryonic C cell precursors from pharyngeal endoderm are uncovered. We will not discuss why C cells go to the bother of burying themselves in the thyroid - this remains a mystery. PMID:27493881

  15. Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages.

    Directory of Open Access Journals (Sweden)

    2006-03-01

    Full Text Available Hemiascomycete yeasts cover an evolutionary span comparable to that of the entire phylum of chordates. Since this group currently contains the largest number of complete genome sequences it presents unique opportunities to understand the evolution of genome organization in eukaryotes. We inferred rates of genome instability on all branches of a phylogenetic tree for 11 species and calculated species-specific rates of genome rearrangements. We characterized all inversion events that occurred within synteny blocks between six representatives of the different lineages. We show that the rates of macro- and microrearrangements of gene order are correlated within individual lineages but are highly variable across different lineages. The most unstable genomes correspond to the pathogenic yeasts Candida albicans and Candida glabrata. Chromosomal maps have been intensively shuffled by numerous interchromosomal rearrangements, even between species that have retained a very high physical fraction of their genomes within small synteny blocks. Despite this intensive reshuffling of gene positions, essential genes, which cluster in low recombination regions in the genome of Saccharomyces cerevisiae, tend to remain syntenic during evolution. This work reveals that the high plasticity of eukaryotic genomes results from rearrangement rates that vary between lineages but also at different evolutionary times of a given lineage.

  16. Forming a tough shell via an intracellular matrix and cellular junctions in the tail epidermis of Oikopleura dioica (Chordata: Tunicata: Appendicularia)

    Science.gov (United States)

    Nakashima, Keisuke; Nishino, Atsuo; Hirose, Euichi

    2011-08-01

    A postanal tail is a major synapomorphy of the phylum Chordata, which is composed of three subphyla: Vertebrata, Cephalochordata, and Tunicata (Urochordata). Among tunicates, appendicularians are the only group that retains the tail in the adult, and the adult tail functions in locomotion and feeding in combination with a cellulose-based house structure. Given the phylogenetic position of tunicates, the appendicularian adult tail may possess ancestral features of the chordate tail. We assess the ultrastructural development of the tail epidermis of the appendicularian Oikopleura dioica. The epidermis of the larval tail is enclosed by the larval envelope, which is a thin sheet similar to the outer tunic layer of ascidian larvae. The epidermis of the adult tail seems to bear no tunic-like cellulosic integuments, and the tail fin is a simple folding of the epidermis. Every epidermal cell, except for the triangular cells at the edge of the tail fin, has a conspicuous matrix layer of fibrous content in the apical cytoplasm without enclosing membranes. The epidermis of the larval tail does not have a fibrous matrix layer, suggesting the production of the layer during larval development and metamorphosis. Zonulae adhaerentes firmly bind the epidermal cells of the adult tail to one another, and the dense microfilaments lining the cell borders constitute a mechanical support for the cell membranes. The intracellular matrix, cell junctions, and cytoskeletons probably make the tail epidermis a tough, flexible shell supporting the active beating of the oikopleuran adult tail.

  17. Notochord morphogenesis in mice: Current understanding & open questions.

    Science.gov (United States)

    Balmer, Sophie; Nowotschin, Sonja; Hadjantonakis, Anna-Katerina

    2016-05-01

    The notochord is a structure common to all chordates, and the feature that the phylum Chordata has been named after. It is a rod-like mesodermal structure that runs the anterior-posterior length of the embryo, adjacent to the ventral neural tube. The notochord plays a critical role in embryonic tissue patterning, for example the dorsal-ventral patterning of the neural tube. The cells that will come to form the notochord are specified at gastrulation. Axial mesodermal cells arising at the anterior primitive streak migrate anteriorly as the precursors of the notochord and populate the notochordal plate. Yet, even though a lot of interest has centered on investigating the functional and structural roles of the notochord, we still have a very rudimentary understanding of notochord morphogenesis. The events driving the formation of the notochord are rapid, taking place over the period of approximately a day in mice. In this commentary, we provide an overview of our current understanding of mouse notochord morphogenesis, from the initial specification of axial mesendodermal cells at the primitive streak, the emergence of these cells at the midline on the surface of the embryo, to their submergence and organization of the stereotypically positioned notochord. We will also discuss some key open questions. Developmental Dynamics 245:547-557, 2016. © 2016 Wiley Periodicals, Inc. PMID:26845388

  18. Hypothesis and Theory: Revisiting Views on the Co-evolution of the Melanocortin Receptors and the Accessory Proteins, MRAP1 and MRAP2.

    Science.gov (United States)

    Dores, Robert M

    2016-01-01

    The evolution of the melanocortin receptors (MCRs) is closely associated with the evolution of the melanocortin-2 receptor accessory proteins (MRAPs). Recent annotation of the elephant shark genome project revealed the sequence of a putative MRAP1 ortholog. The presence of this sequence in the genome of a cartilaginous fish raises the possibility that the mrap1 and mrap2 genes in the genomes of gnathostome vertebrates were the result of the chordate 2R genome duplication event. The presence of a putative MRAP1 ortholog in a cartilaginous fish genome is perplexing. Recent studies on melanocortin-2 receptor (MC2R) in the genomes of the elephant shark and the Japanese stingray indicate that these MC2R orthologs can be functionally expressed in CHO cells without co-expression of an exogenous mrap1 cDNA. The novel ligand selectivity of these cartilaginous fish MC2R orthologs is discussed. Finally, the origin of the mc2r and mc5r genes is reevaluated. The distinctive primary sequence conservation of MC2R and MC5R is discussed in light of the physiological roles of these two MCR paralogs. PMID:27445982

  19. Evolutionary developmental pathology and anthropology: A new field linking development, comparative anatomy, human evolution, morphological variations and defects, and medicine.

    Science.gov (United States)

    Diogo, Rui; Smith, Christopher M; Ziermann, Janine M

    2015-11-01

    We introduce a new subfield of the recently created field of Evolutionary-Developmental-Anthropology (Evo-Devo-Anth): Evolutionary-Developmental-Pathology-and-Anthropology (Evo-Devo-P'Anth). This subfield combines experimental and developmental studies of nonhuman model organisms, biological anthropology, chordate comparative anatomy and evolution, and the study of normal and pathological human development. Instead of focusing on other organisms to try to better understand human development, evolution, anatomy, and pathology, it places humans as the central case study, i.e., as truly model organism themselves. We summarize the results of our recent Evo-Devo-P'Anth studies and discuss long-standing questions in each of the broader biological fields combined in this subfield, paying special attention to the links between: (1) Human anomalies and variations, nonpentadactyly, homeotic transformations, and "nearest neighbor" vs. "find and seek" muscle-skeleton associations in limb+facial muscles vs. other head muscles; (2) Developmental constraints, the notion of "phylotypic stage," internalism vs. externalism, and the "logic of monsters" vs. "lack of homeostasis" views about human birth defects; (3) Human evolution, reversions, atavisms, paedomorphosis, and peromorphosis; (4) Scala naturae, Haeckelian recapitulation, von Baer's laws, and parallelism between phylogeny and development, here formally defined as "Phylo-Devo parallelism"; and (5) Patau, Edwards, and Down syndrome (trisomies 13, 18, 21), atavisms, apoptosis, heart malformations, and medical implications. PMID:26293597

  20. Functional evolution of ADAMTS genes: Evidence from analyses of phylogeny and gene organization

    Directory of Open Access Journals (Sweden)

    Van Meir Erwin G

    2005-02-01

    Full Text Available Abstract Background The ADAMTS (A Disintegrin-like and Metalloprotease with Thrombospondin motifs proteins are a family of metalloproteases with sequence similarity to the ADAM proteases, that contain the thrombospondin type 1 sequence repeat motifs (TSRs common to extracellular matrix proteins. ADAMTS proteins have recently gained attention with the discovery of their role in a variety of diseases, including tissue and blood disorders, cancer, osteoarthritis, Alzheimer's and the genetic syndromes Weill-Marchesani syndrome (ADAMTS10, thrombotic thrombocytopenic purpura (ADAMTS13, and Ehlers-Danlos syndrome type VIIC (ADAMTS2 in humans and belted white-spotting mutation in mice (ADAMTS20. Results Phylogenetic analysis and comparison of the exon/intron organization of vertebrate (Homo, Mus, Fugu, chordate (Ciona and invertebrate (Drosophila and Caenorhabditis ADAMTS homologs has elucidated the evolutionary relationships of this important gene family, which comprises 19 members in humans. Conclusions The evolutionary history of ADAMTS genes in vertebrate genomes has been marked by rampant gene duplication, including a retrotransposition that gave rise to a distinct ADAMTS subfamily (ADAMTS1, -4, -5, -8, -15 that may have distinct aggrecanase and angiogenesis functions.

  1. On the contribution of the soil fauna to the macropores

    Science.gov (United States)

    Barontini, Stefano; Vitale, Paolo; Comincini, Mattia; Pezzotti, Dario; Peli, Marco; Armiraglio, Stefano; Tomirotti, Massimo; Ranzi, Roberto

    2016-04-01

    Soil fauna play an important role in characterizing the soil structure, and they are one of the main macropore sources, together with roots, swelling and local erosion. In an hydrological perspective, according to most of the authors, macropores are meati with meaningfully small capillary action, that is with a characteristic transverse-length greater than some tens of micrometers. Macropores importance is crucial for the hydrological cycle, as they are seat of preferential flow and they contribute to key hydrological processes, viz infiltration, percolation and subsurface runoff. In the framework of a wider investigation which aims at deepening the comprehension of the role played by the macropores in characterising the soil hydrological response (at spatial scales from the local to the slope one), we present a literature reanalysis focused on the capability of soil fauna to dig nests, holes, burrows, and subsoil tunnels and rooms. Particularly we examinated data about fauna with dimensions ranging from small arthropods and anellids to some big chordates. As a result we present a classification approach which aims at enlightening the hydrological features of the holes, e.g. structure, length, main direction, tortuosity, transverse section, displaced soil volume, hydraulic radius, digging technique, affected soil layers, in view of comparing the hydrological fallouts of different soil diggers.

  2. Insights from amphioxus into the evolution of vertebrate cartilage.

    Directory of Open Access Journals (Sweden)

    Daniel Meulemans

    Full Text Available Central to the story of vertebrate evolution is the origin of the vertebrate head, a problem difficult to approach using paleontology and comparative morphology due to a lack of unambiguous intermediate forms. Embryologically, much of the vertebrate head is derived from two ectodermal tissues, the neural crest and cranial placodes. Recent work in protochordates suggests the first chordates possessed migratory neural tube cells with some features of neural crest cells. However, it is unclear how and when these cells acquired the ability to form cellular cartilage, a cell type unique to vertebrates. It has been variously proposed that the neural crest acquired chondrogenic ability by recruiting proto-chondrogenic gene programs deployed in the neural tube, pharynx, and notochord. To test these hypotheses we examined the expression of 11 amphioxus orthologs of genes involved in neural crest chondrogenesis. Consistent with cellular cartilage as a vertebrate novelty, we find that no single amphioxus tissue co-expresses all or most of these genes. However, most are variously co-expressed in mesodermal derivatives. Our results suggest that neural crest-derived cartilage evolved by serial cooption of genes which functioned primitively in mesoderm.

  3. N-Methyl-D-aspartic Acid (NMDA in the nervous system of the amphioxus Branchiostoma lanceolatum

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    Garcia-Fernàndez Jordi

    2007-12-01

    Full Text Available Abstract Background NMDA (N-methyl-D-aspartic acid is a widely known agonist for a class of glutamate receptors, the NMDA type. Synthetic NMDA elicits very strong activity for the induction of hypothalamic factors and hypophyseal hormones in mammals. Moreover, endogenous NMDA has been found in rat, where it has a role in the induction of GnRH (Gonadotropin Releasing Hormone in the hypothalamus, and of LH (Luteinizing Hormone and PRL (Prolactin in the pituitary gland. Results In this study we show evidence for the occurrence of endogenous NMDA in the amphioxus Branchiostoma lanceolatum. A relatively high concentration of NMDA occurs in the nervous system of this species (3.08 ± 0.37 nmol/g tissue in the nerve cord and 10.52 ± 1.41 nmol/g tissue in the cephalic vesicle. As in rat, in amphioxus NMDA is also biosynthesized from D-aspartic acid (D-Asp by a NMDA synthase (also called D-aspartate methyl transferase. Conclusion Given the simplicity of the amphioxus nervous and endocrine systems compared to mammalian, the discovery of NMDA in this protochordate is important to gain insights into the role of endogenous NMDA in the nervous and endocrine systems of metazoans and particularly in the chordate lineage.

  4. Refining the Ciona intestinalis model of central nervous system regeneration.

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    Carl Dahlberg

    Full Text Available BACKGROUND: New, practical models of central nervous system regeneration are required and should provide molecular tools and resources. We focus here on the tunicate Ciona intestinalis, which has the capacity to regenerate nerves and a complete adult central nervous system, a capacity unusual in the chordate phylum. We investigated the timing and sequence of events during nervous system regeneration in this organism. METHODOLOGY/PRINCIPAL FINDINGS: We developed techniques for reproducible ablations and for imaging live cellular events in tissue explants. Based on live observations of more than 100 regenerating animals, we subdivided the regeneration process into four stages. Regeneration was functional, as shown by the sequential recovery of reflexes that established new criteria for defining regeneration rates. We used transgenic animals and labeled nucleotide analogs to describe in detail the early cellular events at the tip of the regenerating nerves and the first appearance of the new adult ganglion anlage. CONCLUSIONS/SIGNIFICANCE: The rate of regeneration was found to be negatively correlated with adult size. New neural structures were derived from the anterior and posterior nerve endings. A blastemal structure was implicated in the formation of new neural cells. This work demonstrates that Ciona intestinalis is as a useful system for studies on regeneration of the brain, brain-associated organs and nerves.

  5. Regulation of pre-otic brain development by the cephalic neural crest.

    Science.gov (United States)

    Creuzet, Sophie E

    2009-09-15

    Emergence of the neural crest (NC) is considered an essential asset in the evolution of the chordate phylum, as specific vertebrate traits such as peripheral nervous system, cephalic skeletal tissues, and head development are linked to the NC and its derivatives. It has been proposed that the emergence of the NC was responsible for the formation of a "new head" characterized by the spectacular development of the forebrain and associated sense organs. It was previously shown that removal of the cephalic NC (CNC) prevents the formation of the facial structures but also results in anencephaly. This article reports on the molecular mechanisms whereby the CNC controls cephalic neurulation and brain morphogenesis. This study demonstrates that molecular variations of Gremlin and Noggin level in CNC account for morphological changes in brain size and development. CNC cells act in these processes through a multi-step control and exert cumulative effects counteracting bone morphogenetic protein signaling produced by the neighboring tissues (e.g., adjacent neuroepithelium, ventro-medial mesoderm, superficial ectoderm). These data provide an explanation for the fact that acquisition of the NC during the protochordate-to-vertebrate transition has coincided with a large increase of brain vesicles. PMID:19720987

  6. Spliced leader trapping reveals widespread alternative splicing patterns in the highly dynamic transcriptome of Trypanosoma brucei.

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    Daniel Nilsson

    Full Text Available Trans-splicing of leader sequences onto the 5'ends of mRNAs is a widespread phenomenon in protozoa, nematodes and some chordates. Using parallel sequencing we have developed a method to simultaneously map 5'splice sites and analyze the corresponding gene expression profile, that we term spliced leader trapping (SLT. The method can be applied to any organism with a sequenced genome and trans-splicing of a conserved leader sequence. We analyzed the expression profiles and splicing patterns of bloodstream and insect forms of the parasite Trypanosoma brucei. We detected the 5' splice sites of 85% of the annotated protein-coding genes and, contrary to previous reports, found up to 40% of transcripts to be differentially expressed. Furthermore, we discovered more than 2500 alternative splicing events, many of which appear to be stage-regulated. Based on our findings we hypothesize that alternatively spliced transcripts present a new means of regulating gene expression and could potentially contribute to protein diversity in the parasite. The entire dataset can be accessed online at TriTrypDB or through: http://splicer.unibe.ch/.

  7. Solitary ascidians embryos (Chordata, Tunicata as model organisms for testing coastal pollutant toxicity

    Directory of Open Access Journals (Sweden)

    G Zega

    2009-03-01

    Full Text Available Marine coastal communities are daily exposed to several chemical compounds commonly used in agriculture and industrial activities. Therefore, toxicological studies evaluating the effects of these compounds on marine organisms are of primary importance for marine environment preservation. Different model organisms are used to perform toxicity tests with potential pollutants, under laboratory conditions. In last decades, solitary ascidians have been selected as valuable model organisms to run bioassays with embryos and larvae. In fact, by in vitro fertilization, it is easy to obtain thousands of embryos, rapidly developing and therefore allowing a fast screen of pollutant toxicity.The aim of this review was to summarize results from toxicity tests, run with heavy metals, organo-metal and organic compounds, on solitary ascidian development and settlement to evidence that these animals offer several advantages as models to perform these kind of studies. First of all, they have a sensitiveness directly comparable to that of other marine model organisms. Moreover, the effects of toxicants on exposed embryos and larvae could be studied using different approaches, from ultrastructure to genetic analysis. Finally, since ascidians are chordates morphological and gene expression analyses could provide data for comparative studies with vertebrates.

  8. Active metabolism of thyroid hormone during metamorphosis of amphioxus.

    Science.gov (United States)

    Paris, Mathilde; Hillenweck, Anne; Bertrand, Stéphanie; Delous, Georges; Escriva, Hector; Zalko, Daniel; Cravedi, Jean-Pierre; Laudet, Vincent

    2010-07-01

    Thyroid hormones (THs), and more precisely the 3,3',5-triiodo-l-thyronine (T(3)) acetic derivative 3,3',5-triiodothyroacetic acid (TRIAC), have been shown to activate metamorphosis in amphioxus. However, it remains unknown whether TRIAC is endogenously synthesized in amphioxus and more generally whether an active TH metabolism is regulating metamorphosis. Here we show that amphioxus naturally produces TRIAC from its precursors T(3) and l-thyroxine (T(4)), supporting its possible role as the active TH in amphioxus larvae. In addition, we show that blocking TH production inhibits metamorphosis and that this effect is compensated by exogenous T(3), suggesting that a peak of TH production is important for advancement of proper metamorphosis. Moreover, several amphioxus genes encoding proteins previously proposed to be involved in the TH signaling pathway display expression profiles correlated with metamorphosis. In particular, thyroid hormone receptor (TR) and deiodinases gene expressions are either up- or down-regulated during metamorphosis and by TH treatments. Overall, these results suggest that an active TH metabolism controls metamorphosis in amphioxus, and that endogenous TH production and metabolism as well as TH-regulated metamorphosis are ancestral in the chordate lineage. PMID:21558188

  9. 3D-printed microwell arrays for Ciona microinjection and timelapse imaging.

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    Clint Gregory

    Full Text Available Ascidians such as Ciona are close chordate relatives of the vertebrates with small, simple embryonic body plans and small, simple genomes. The tractable size of the embryo offers considerable advantages for in toto imaging and quantitative analysis of morphogenesis. For functional studies, Ciona eggs are considerably more challenging to microinject than the much larger eggs of other model organisms such as zebrafish and Xenopus. One of the key difficulties is in restraining the eggs so that the microinjection needle can be easily introduced and withdrawn. Here we develop and test a device to cast wells in agarose that are each sized to hold a single egg. This injection mold is fabricated by micro-resolution stereolithography with a grid of egg-sized posts that cast corresponding wells in agarose. This 3D printing technology allows the rapid and inexpensive testing of iteratively refined prototypes. In addition to their utility in microinjection, these grids of embryo-sized wells are also valuable for timelapse imaging of multiple embryos.

  10. The retinoic acid machinery in invertebrates: ancestral elements and vertebrate innovations.

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    Albalat, Ricard

    2009-12-10

    Recent discoveries have changed our view of the evolutionary history of retinoic acid (RA) machinery. It is no longer considered a vertebrate or chordate invention but rather a common genetic toolkit of diverse lineages of metazoans. In particular, the basic machinery of RA-metabolizing enzymes, retinoid-binding proteins and RA-binding nuclear receptors has been identified in protostome and deuterostome lineages. Moreover, the retinoid content and the effects of RA treatment have been described in a number of invertebrates, although the physiological role of RA signaling outside vertebrates is still not fully understood. This review summarizes the evidence gathered over many years on the invertebrate RA system, highlighting the ancient origin of the RA genetic machinery and a basic role in neuronal differentiation. Comparison of invertebrate and vertebrate RA toolkits suggests some innovations in the RA machinery of vertebrates that might have contributed to improving the physiological control of retinoid homeostasis, compensating for vitamin A fluctuations in this lineage. Analysis of the RA machinery in invertebrates also reveals independent losses of RA components during evolution, which might be related to changes in embryonic developmental modes and the absence of the temporal collinearity of hox clusters. Additional studies analyzing the biochemical and functional characteristics of the invertebrate RA genetic machinery are warranted to lend experimental support to the hypotheses sketched in this review. These hypotheses open, however, new perspectives toward understanding how the RA genetic machinery evolved to suit the physiological and developmental requirements of metazoans.

  11. Clupeiformes' Egg Envelope Proteins characterization: The case of Engraulis encrasicolus as a proxy for stock assessment through a novel molecular tool.

    Science.gov (United States)

    Miccoli, Andrea; Leonori, Iole; Estonba, Andone; De Felice, Andrea; Piccinetti, Chiara Carla; Carnevali, Oliana

    2016-07-01

    Zona radiata proteins are essential for ensuring bactericidal resistance, oocyte nutrients uptake and functional buoyancy, sperm binding and guidance to the micropyle, and protection to the growing oocyte or embryo from the physical environment. Such glycoproteins have been characterized in terms of molecular structure, protein composition and phylogenetics in several chordate models. Nevertheless, research on teleost has not been extensive. In Clupeiformes, one of the most biologically relevant and commercially important order which accounts for over 400 species and totally contributes to more than a quarter of the world fish catch, Egg Envelope Protein (EEP) information exist only for the Clupea pallasii and Engraulis japonicus species. The European anchovy, Engraulis encrasicolus, the target of a well-consolidated fishery in the Mediterranean Sea, has been ignored until now and the interest on the Otocephala superorder has been fragmentally limited to some Cypriniformes and Gonorynchiformes, as well. The aim of the present study was to fill the ZP protein-wise gap of knowledge afflicting the understanding of the European anchovy's reproductive process and to expand the background on Clupeiformes. We cloned the five Engraulis encrasicolus' zp genes and deduced their products, determined their tissue distribution, quantified their mRNA expression throughout the reproductive cycle and provided an insight into their evolution through phylogenetic tools. Furthermore, we proposed a multivariate statistics-based method to objectively infer and/or confirm the classification of Engraulis encrasicolus' sexual maturity stages by analyzing data of zp mRNAs' relative abundance. PMID:27060425

  12. p63 in Mytilus galloprovincialis and p53 family members in the phylum Mollusca.

    Science.gov (United States)

    Stifanić, Mauro; Micić, Milena; Ramsak, Andreja; Blasković, Sanja; Ruso, Ana; Zahn, Rudolf K; Batel, Renato

    2009-11-01

    Genes of the p53 family are known to be critical regulators of the cell cycle. They have already been established as possible biomarkers. Elaborate regulation mechanisms result in numerous cDNA and protein isoforms being expressed from each gene of the p53 family. Their similarity caused an often misleading nomenclature in non-vertebrate species. The aim of the present work is a clarification of the nomenclature of molluscan p53 family sequences, an essential prerequisite for reliable interpretation of gene expression and protein function studies. Here, we report five partial cDNA and one partial genomic p63 sequences, all originating from two Mytilus galloprovincialis individuals. DNA, deduced protein sequences, and the exon/intron architecture were analyzed and compared to p53, p63 and p73 sequences from other organisms. Along with our sequences, we analyzed all similar molluscan sequences found in the GenBank database. The analysis showed our cDNA sequences code for the TAp63gamma isoform of the p63 protein, and identified all other molluscan p53 family sequences as p63 genes or their expression isoforms. Our results also indicate p63 as the ancestral gene of the p53 family as well as the only gene of the family present in non-chordate metazoan species.

  13. A conserved cluster of three PRD-class homeobox genes (homeobrain, rx and orthopedia in the Cnidaria and Protostomia

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    Mazza Maureen E

    2010-07-01

    Full Text Available Abstract Background Homeobox genes are a superclass of transcription factors with diverse developmental regulatory functions, which are found in plants, fungi and animals. In animals, several Antennapedia (ANTP-class homeobox genes reside in extremely ancient gene clusters (for example, the Hox, ParaHox, and NKL clusters and the evolution of these clusters has been implicated in the morphological diversification of animal bodyplans. By contrast, similarly ancient gene clusters have not been reported among the other classes of homeobox genes (that is, the LIM, POU, PRD and SIX classes. Results Using a combination of in silico queries and phylogenetic analyses, we found that a cluster of three PRD-class homeobox genes (Homeobrain (hbn, Rax (rx and Orthopedia (otp is present in cnidarians, insects and mollusks (a partial cluster comprising hbn and rx is present in the placozoan Trichoplax adhaerens. We failed to identify this 'HRO' cluster in deuterostomes; in fact, the Homeobrain gene appears to be missing from the chordate genomes we examined, although it is present in hemichordates and echinoderms. To illuminate the ancestral organization and function of this ancient cluster, we mapped the constituent genes against the assembled genome of a model cnidarian, the sea anemone Nematostella vectensis, and characterized their spatiotemporal expression using in situ hybridization. In N. vectensis, these genes reside in a span of 33 kb with the same gene order as previously reported in insects. Comparisons of genomic sequences and expressed sequence tags revealed the presence of alternative transcripts of Nv-otp and two highly unusual protein-coding polymorphisms in the terminal helix of the Nv-rx homeodomain. A population genetic survey revealed the Rx polymorphisms to be widespread in natural populations. During larval development, all three genes are expressed in the ectoderm, in non-overlapping territories along the oral-aboral axis, with distinct

  14. Functional Authentication of a Novel Gastropod Gonadotropin-Releasing Hormone Receptor Reveals Unusual Features and Evolutionary Insight

    Science.gov (United States)

    Kavanaugh, Scott I.

    2016-01-01

    A gonadotropin-releasing hormone (GnRH)-like molecule was previously identified in a gastropod, Aplysia californica, and named ap-GnRH. In this study, we cloned the full-length cDNA of a putative ap-GnRH receptor (ap-GnRHR) and functionally authenticated this receptor as a bona fide ap-GnRHR. This receptor contains two potential translation start sites, each accompanied by a Kozak sequence, suggesting the translation of a long and a short form of the receptor is possible. The putative ap-GnRHR maintains the conserved structural motifs of GnRHR-like receptors and shares 45% sequence identity with the octopus GnRHR. The expression of the putative ap-GnRHR short form is ubiquitous in all tissues examined, whereas the long form is only expressed in parts of the central nervous system, osphradium, small hermaphroditic duct, and ovotestis. The cDNA encoding the long or the short receptor was transfected into the Drosophila S2 cell line and subject to a radioreceptor assay using 125I-labeled ap-GnRH as the radioligand. Further, the transfected cells were treated with various concentrations of ap-GnRH and measured for the accumulation of cAMP and inositol monophosphate (IP1). Radioreceptor assay revealed that only the long receptor bound specifically to the radioligand. Further, only the long receptor responded to ap-GnRH with an increased accumulation of IP1, but not cAMP. Our studies show that despite the more prevalent expression of the short receptor, only the long receptor is the functional ap-GnRHR. Importantly, this is only the second report on the authentication of a protostome GnRHR, and based on the function and the phylogenetic grouping of ap-GnRHR, we suggest that this receptor is more similar to protostome corazonin receptors than chordate GnRHRs. PMID:27467252

  15. The complex multidomain organization of SCO-spondin protein is highly conserved in mammals.

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    Meiniel, Olivier; Meiniel, Annie

    2007-02-01

    The multidomain organization of SCO-spondin protein is a special feature of the chordate phylum. This protein is expressed in the central nervous system (CNS) from the time a dorsal neural tube appears in the course of phylogenetical evolution. With the advance of the systematic whole genomes sequencing, we were able to determine the SCO-spondin amino acid sequence in four mammalian species using the Wise2 software. From the ClustalW alignment of bovine (Bos taurus), human (Homo sapiens), murine (Mus musculus) and rat (Rattus norvegicus) proteins, a consensus sequence for mammalian SCO-spondin was determined and further validated with the dog (Canis familiaris) SCO-spondin sequence. The analysis of this consensus sequence is consistent with a very high degree of conservation in the amino acids composition and multidomain organization of SCO-spondin in mammals. In addition, the identification of conserved domains, namely, Emilin (EMI), von Willebrand factor D (vWD), low-density lipoprotein receptor type A (LDLrA) domains, SCO repeats (SCOR), thrombospondin type 1 repeats (TSR), a coagulation factor 5/8 type C (FA5-8C) or discoidin motif and a C-terminal cystine knot (CTCK) domain, provides a greater insight into the putative function of this multidomain protein. SCO-spondin belongs to the TSR superfamily given the presence of a great number of TSR (26). A finer classification of the TSR motifs in groups 1, 2 and 3 is proposed on the basis of different cysteine patterns. Interestingly, group 2 TSR are present in a number of CNS developmental proteins including R-spondins, F-spondins and Mindins.

  16. Ensembl variation resources

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    Marin-Garcia Pablo

    2010-05-01

    Full Text Available Abstract Background The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics. Description The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl. Conclusions Variation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org.

  17. Expression of a retinoic acid receptor (RAR)-like protein in the embryonic and adult nervous system of a protostome species.

    Science.gov (United States)

    Carter, Christopher J; Rand, Christopher; Mohammad, Imtiaz; Lepp, Amanda; Vesprini, Nicholas; Wiebe, Olivia; Carlone, Robert; Spencer, Gaynor E

    2015-01-01

    The vitamin A metabolite, retinoic acid, is an important molecule in nervous system development and regeneration in vertebrates. Retinoic acid signaling in vertebrates is mediated by two classes of nuclear receptors, the retinoid X receptors (RXRs) and the retinoic acid receptors (RARs). Recently, evidence has emerged to suggest that many effects of retinoic acid are conserved between vertebrate and invertebrate nervous systems, even though the RARs were previously thought to be a vertebrate innovation and to not exist in non-chordates. We have cloned a full-length putative RAR from the CNS of the mollusc Lymnaea stagnalis (LymRAR). Immunoreactivity for the RAR protein was found in axons of adult neurons in the central nervous system and in growth cones of regenerating neurons in vitro. A vertebrate RAR antagonist blocked growth cone turning induced by exogenous all-trans retinoic acid, possibly suggesting a role for this receptor in axon guidance. We also provide immunostaining evidence for the presence of RAR protein in the developing, embryonic CNS, where it is also found in axonal processes. Using qPCR, we determined that LymRAR mRNA is detectable in the early veliger stage embryo and that mRNA levels increase significantly during embryonic development. Putative disruption of retinoid signaling in Lymnaea embryos using vertebrate RAR antagonists resulted in abnormal eye and shell development and in some instances completely halted development, resembling the effects of all-trans retinoic acid. This study provides evidence for RAR functioning in a protostome species. PMID:25504929

  18. Comparative toxicity of cis-cypermethrin in rainbow trout, frog, mouse, and quail.

    Science.gov (United States)

    Edwards, R; Millburn, P; Hutson, D H

    1986-07-01

    The synthetic alpha-cyano-phenoxybenzyl-containing pyrethroid insecticides act on the CNS of vertebrates and show a species-selective toxicity in the order fish greater than amphibians much greater than mammals greater than birds. Concentrations of [14C]cis-cypermethrin in the brains of representative members of each of these classes of chordates were measured at toxic signs (an onset of hyperactivity followed by seizures and loss of balance/equilibrium) as an indicator of target organ sensitivity. The concentration of cis-cypermethrin in brain, associated with toxic signs, in micrograms per gram (mean +/- SE) as determined by high-performance liquid chromatography was 0.08 +/- 0.03 (frog), 0.23 +/- 0.05 (trout), 1.71 +/- 0.33 (mouse), and 3.94 +/- 0.88 (quail). Trout brain was equally sensitive to the cis and trans isomers of cypermethrin. In both mouse and quail, some 90% of the radioactivity in the brain was parent pyrethroid. Trout and frog, however, afforded only 56 and 32%, respectively, of the brain 14C as cypermethrin, with the remaining radioactivity in both extractable and nonextractable metabolites, including 4'-hydroxy-cis-cypermethrin, which is potentially neuroactive. Following oral administration, cis-cypermethrin was readily absorbed and metabolized by quail. Intestinal uptake was far less rapid in trout and mouse, with unchanged cypermethrin dispersed in secreted bile, being readily eliminated from the intestines of fish. The uptake and metabolism of cis-cypermethrin and the brain sensitivities of these animals to the pyrethroid account for the observed differences in acute toxicity.

  19. Observing Evolutionary Entropy in Relation to Body Size Over Time

    Science.gov (United States)

    Idgunji, S.; Zhang, H.; Payne, J.; Heim, N. A.

    2015-12-01

    The Second Law of Thermodynamics, according to Clausius, states that entropy will always increase in the universe, meaning systems will break down and become simple and chaotic. However, this is seemingly contradicted by the existence of living organisms, which can have highly complex and organized systems. Furthermore, there is a greater contradiction in the theory of evolution, which sees organisms growing larger and becoming more complex over time. Our research project revolved around whether organisms actually became more complex over time, and correlating these findings with the body size of these organisms. We analyzed the relationship between body size and cell types of five different marine phyla: arthropods, brachiopods, chordates, echinoderms, and mollusks. We attempted to find a relation between the biovolume of these different phyla and the number of specialized cell types that they had, which is a common measure of biocomplexity. In addition, we looked at the metabolic intensity, which is the mass-specific rate of energy processing applied to an organism's size, because it is also correlated to genetic complexity. Using R programming, we tested for correlations between these factors. After applying a Pearson correlation test, we discovered a generally positive correlation between the body sizes, number of cell types, and metabolic intensities of these phyla. However, one exception is that there is a negative correlation between the body size and metabolic intensity of echinoderms. Overall, we can see that marine organisms tend to evolve larger and more complex over time, and that is a very interesting find. Our discovery yielded many research questions and problems that we would like to solve, such as how the environment is thermodynamically affected by these organisms.

  20. NK4 antagonizes Tbx1/10 to promote cardiac versus pharyngeal muscle fate in the ascidian second heart field.

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    Wei Wang

    2013-12-01

    Full Text Available The heart and head muscles share common developmental origins and genetic underpinnings in vertebrates, including humans. Parts of the heart and cranio-facial musculature derive from common mesodermal progenitors that express NKX2-5, ISL1, and TBX1. This ontogenetic kinship is dramatically reflected in the DiGeorge/Cardio-Velo-Facial syndrome (DGS/CVFS, where mutations of TBX1 cause malformations in the pharyngeal apparatus and cardiac outflow tract. Cardiac progenitors of the first heart field (FHF do not require TBX1 and segregate precociously from common progenitors of the second heart field (SHF and pharyngeal muscles. However, the cellular and molecular mechanisms that govern heart versus pharyngeal muscle specification within this lineage remain elusive. Here, we harness the simplicity of the ascidian larva to show that, following asymmetric cell division of common progenitors, NK4/NKX2-5 promotes GATAa/GATA4/5/6 expression and cardiac specification in the second heart precursors by antagonizing Tbx1/10-mediated inhibition of GATAa and activation of Collier/Olf/EBF (COE, the determinant of atrial siphon muscle (ASM specification. Our results uncover essential regulatory connections between the conserved cardio-pharyngeal factor Tbx1/10 and muscle determinant COE, as well as a mutual antagonism between NK4 and Tbx1/10 activities upstream of GATAa and COE. The latter cross-antagonism underlies a fundamental heart versus pharyngeal muscle fate choice that occurs in a conserved lineage of cardio-pharyngeal progenitors. We propose that this basic ontogenetic motif underlies cardiac and pharyngeal muscle development and evolution in chordates.

  1. Evolutionary history of the iroquois/Irx genes in metazoans

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    Ikmi Aissam

    2009-04-01

    Full Text Available Abstract Background The iroquois (iro/Irx genes encode transcriptional regulators that belong to the TALE superclass of homeodomain proteins and have key functions during development in both vertebrates and insects. The Irx genes occur in one or two genomic clusters containing three genes each within the Drosophila and several vertebrate genomes, respectively. The similar genomic organization in Drosophila and vertebrates is widely considered as a result of convergent evolution, due to independent tandem gene duplications. In this study, we investigate the evolutionary history of the Irx genes at the scale of the whole metazoan kingdom. Results We identified in silico the putative full complement of Irx genes in the sequenced genomes of 36 different species representative of the main metazoan lineages, including non bilaterian species, several arthropods, non vertebrate chordates, and a basal vertebrate, the sea lamprey. We performed extensive phylogenetic analyses of the identified Irx genes and defined their genomic organizations. We found that, in most species, there are several Irx genes, these genes form two to four gene clusters, and the Irx genes are physically linked to a structurally and functionally unrelated gene known as CG10632 in Drosophila. Conclusion Three main conclusions can be drawn from our study. First, an Irx cluster composed of two genes, araucan/caupolican and mirror, is ancestral to the crustaceans+insects clade and has been strongly conserved in this clade. Second, three Irx genes were probably present in the last common ancestor of vertebrates and the duplication that has given rise to the six genes organized into two clusters found in most vertebrates, likely occurred in the gnathostome lineage after its separation from sea lampreys. Third, the clustered organization of the Irx genes in various evolutionary lineages may represent an exceptional case of convergent evolution or may point to the existence of an Irx gene

  2. Evolution of a new function by degenerative mutation in cephalochordate steroid receptors.

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    Jamie T Bridgham

    Full Text Available Gene duplication is the predominant mechanism for the evolution of new genes. Major existing models of this process assume that duplicate genes are redundant; degenerative mutations in one copy can therefore accumulate close to neutrally, usually leading to loss from the genome. When gene products dimerize or interact with other molecules for their functions, however, degenerative mutations in one copy may produce repressor alleles that inhibit the function of the other and are therefore exposed to selection. Here, we describe the evolution of a duplicate repressor by simple degenerative mutations in the steroid hormone receptors (SRs, a biologically crucial vertebrate gene family. We isolated and characterized the SRs of the cephalochordate Branchiostoma floridae, which diverged from other chordates just after duplication of the ancestral SR. The B. floridae genome contains two SRs: BfER, an ortholog of the vertebrate estrogen receptors, and BfSR, an ortholog of the vertebrate receptors for androgens, progestins, and corticosteroids. BfSR is specifically activated by estrogens and recognizes estrogen response elements (EREs in DNA; BfER does not activate transcription in response to steroid hormones but binds EREs, where it competitively represses BfSR. The two genes are partially coexpressed, particularly in ovary and testis, suggesting an ancient role in germ cell development. These results corroborate previous findings that the ancestral steroid receptor was estrogen-sensitive and indicate that, after duplication, BfSR retained the ancestral function, while BfER evolved the capacity to negatively regulate BfSR. Either of two historical mutations that occurred during BfER evolution is sufficient to generate a competitive repressor. Our findings suggest that after duplication of genes whose functions depend on specific molecular interactions, high-probability degenerative mutations can yield novel functions, which are then exposed to positive

  3. Characterization and transcription studies of a phytochelatin synthase gene from the solitary tunicate Ciona intestinalis exposed to cadmium

    International Nuclear Information System (INIS)

    Highlights: • Ciona intestinalis have a functional phytochelatin synthase (PCS) gene (cipcs). • CiPCS amino acid sequence is phylogentically related to other metazoan PCSs. • CiPCS catalyze the synthesis of PC2. • cipcs are mostly transcribed in circulating hemocytes, in both tunic and blood lacunae. • Cadmium exposure results in a significant increase of cipcs and cipcna transcription. - Abstract: The major thiol-containing molecules involved in controlling the level of intracellular ROS in eukaryotes, acting as a nonenzymatic detoxification system, are metallothioneins (MTs), glutathione (GSH) and phytochelatins (PCs). Both MTs and GSH are well-known in the animal kingdom. PC was considered a prerogative of the plant kingdom but, in 2001, a phytochelatin synthase (PCS) gene was described in the nematode Caenorhabditis elegans; additional genes encoding this enzyme were later described in the earthworm Eisenia fetida and in the parasitic nematode Schistosoma mansoni but scanty data are available, up to now, for Deuterostomes. Here, we describe the molecular characteristics and transcription pattern, in the presence of Cd, of a PCS gene from the invertebrate chordate Ciona intestinalis, a ubiquitous solitary tunicate and demonstrate the presence of PCs in tissue extracts. We also studied mRNA localization by in situ hybridization. In addition, we analyzed the behavior of hemocytes and tunic cells consequent to Cd exposure as well as the transcription pattern of the Ciona orthologous for proliferating cell nuclear antigen (PCNA), usually considered a proliferation marker, and observed that cell proliferation occurs after 96 h of Cd treatment. This matches the hypothesis of Cd-induced cell proliferation, as already suggested by previous data on the expression of a metallothionein gene in the same animal

  4. Early Neurodevelopment of Sea Urchin and Neurotoxic Effects of Organophosphate Pesticides on It%海胆早期神经发育及有机磷农药对其神经毒性作用的研究进展

    Institute of Scientific and Technical Information of China (English)

    汝少国; 许磊

    2012-01-01

    早期发育阶段是有机磷农药神经毒性作用最敏感的时期,海胆的胚胎和幼虫为研究有机磷农药对早期发育阶段的神经毒性作用提供了一种理想的模型.本文介绍了海胆的早期神经发育过程,综述了神经系统对海胆早期发育的调控作用,结合近年来国内外的研究,阐述了有机磷农药对海胆早期发育的影响及其神经毒性作用机制,并展望了该领域的研究方向.%Despite their widespread use, organophosphate pesticides cause developmental neurotoxicity through a mechanism based on their function as an acetylcholinesterase inhibitor. Animals in early developmental stages are especially vulnerable to developmental neurotoxicity induced by organophosphate pesticides. The embryos and larvae of sea urchin provide a promising invertebrate model system for evaluating developmental neurotoxicity induced by organophosphate pesticides, as they develop quickly with well -characterized morphological and biochemical features, possess similar processes of neurogenesis and signaling cascades to chordates, and are vulnerable to pollutants. Both the neurodevelpment of sea urchin during early development stage and the regulation on the early development were included. Particularly, the neurotoxic effects of organophosphate pesticides on the early development and its potential neurotoxicity mechanism for sea urchin are discussed, and future prospects of this field are provided.

  5. A study of neural-related microRNAs in the developing amphioxus

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    Candiani Simona

    2011-07-01

    Full Text Available Abstract Background MicroRNAs are small noncoding RNAs regulating expression of protein coding genes at post-transcriptional level and controlling several biological processes. At present microRNAs have been identified in various metazoans and seem also to be involved in brain development, neuronal differentiation and subtypes specification. An approach to better understand the role of microRNAs in animal gene expression is to determine temporal and tissue-specific expression patterns of microRNAs in different model organisms. Therefore, we have investigated the expression of six neural related microRNAs in amphioxus, an organism having an important phylogenetic position in terms of understanding the origin and evolution of chordates. Results In amphioxus, all the microRNAs we examined are expressed in specific regions of the CNS, and some of them are correlated with specific cell types. In addition, miR-7, miR-137 and miR-184 are also expressed in endodermal and mesodermal tissues. Several potential targets expressed in the nervous system of amphioxus have been identified by computational prediction and some of them are coexpressed with one or more miRNAs. Conclusion We identified six miRNAs that are expressed in the nervous system of amphioxus in a variety of patterns. miR-124 is found in both differentiating and mature neurons, miR-9 in differentiated neurons, miR-7, miR-137 and miR-184 in restricted CNS regions, and miR-183 in cells of sensory organs. Therefore, such amphioxus miRNAs may play important roles in regional patterning and/or specification of neuronal cell types.

  6. Nme gene family evolutionary history reveals pre-metazoan origins and high conservation between humans and the sea anemone, Nematostella vectensis.

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    Thomas Desvignes

    Full Text Available BACKGROUND: The Nme gene family is involved in multiple physiological and pathological processes such as cellular differentiation, development, metastatic dissemination, and cilia functions. Despite the known importance of Nme genes and their use as clinical markers of tumor aggressiveness, the associated cellular mechanisms remain poorly understood. Over the last 20 years, several non-vertebrate model species have been used to investigate Nme functions. However, the evolutionary history of the family remains poorly understood outside the vertebrate lineage. The aim of the study was thus to elucidate the evolutionary history of the Nme gene family in Metazoans. METHODOLOGY/PRINCIPAL FINDINGS: Using a total of 21 eukaryote species including 14 metazoans, the evolutionary history of Nme genes was reconstructed in the metazoan lineage. We demonstrated that the complexity of the Nme gene family, initially thought to be restricted to chordates, was also shared by the metazoan ancestor. We also provide evidence suggesting that the complexity of the family is mainly a eukaryotic innovation, with the exception of Nme8 that is likely to be a choanoflagellate/metazoan innovation. Highly conserved gene structure, genomic linkage, and protein domains were identified among metazoans, some features being also conserved in eukaryotes. When considering the entire Nme family, the starlet sea anemone is the studied metazoan species exhibiting the most conserved gene and protein sequence features with humans. In addition, we were able to show that most of the proteins known to interact with human NME proteins were also found in starlet sea anemone. CONCLUSION/SIGNIFICANCE: Together, our observations further support the association of Nme genes with key cellular functions that have been conserved throughout metazoan evolution. Future investigations of evolutionarily conserved Nme gene functions using the starlet sea anemone could shed new light on a wide variety of

  7. Early evolution of ionotropic GABA receptors and selective regimes acting on the mammalian-specific theta and epsilon subunits.

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    Christopher J Martyniuk

    Full Text Available BACKGROUND: The amino acid neurotransmitter GABA is abundant in the central nervous system (CNS of both invertebrates and vertebrates. Receptors of this neurotransmitter play a key role in important processes such as learning and memory. Yet, little is known about the mode and tempo of evolution of the receptors of this neurotransmitter. Here, we investigate the phylogenetic relationships of GABA receptor subunits across the chordates and detail their mode of evolution among mammals. PRINCIPAL FINDINGS: Our analyses support two major monophyletic clades: one clade containing GABA(A receptor alpha, gamma, and epsilon subunits, and another one containing GABA(A receptor rho, beta, delta, theta, and pi subunits. The presence of GABA receptor subunits from each of the major clades in the Ciona intestinalis genome suggests that these ancestral duplication events occurred before the divergence of urochordates. However, while gene divergence proceeded at similar rates on most receptor subunits, we show that the mammalian-specific subunits theta and epsilon experienced an episode of positive selection and of relaxed constraints, respectively, after the duplication event. Sites putatively under positive selection are placed on a three-dimensional model obtained by homology-modeling. CONCLUSIONS: Our results suggest an early divergence of the GABA receptor subunits, before the split from urochordates. We show that functional changes occurred in the lineages leading to the mammalian-specific subunit theta, and we identify the amino acid sites putatively responsible for the functional divergence. We discuss potential consequences for the evolution of mammals and of their CNS.

  8. FGFRL1 is a neglected putative actor of the FGF signalling pathway present in all major metazoan phyla

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    Lamonerie Thomas

    2009-09-01

    Full Text Available Abstract Background Fibroblast Growth Factors (FGF and their receptors are well known for having major implications in cell signalling controlling embryonic development. Recently, a gene coding for a protein closely related to FGFRs (Fibroblast Growth Factor Receptors called FGFR5 or FGFR-like 1 (FGFRL1, has been described in vertebrates. An orthologous gene was also found in the cephalochordate amphioxus, but no orthologous genes were found by the authors in other non-vertebrate species, even if a FGFRL1 gene was identified in the sea urchin genome, as well as a closely related gene, named nou-darake, in the planarian Dugesia japonica. These intriguing data of a deuterostome-specific gene that might be implicated in FGF signalling prompted us to search for putative FGFRL1 orthologues in the completely sequenced genomes of metazoans. Results We found FGFRL1 genes in the cnidarian Nematostella vectensis as well as in many bilaterian species. Our analysis also shows that FGFRL1 orthologous genes are linked in the genome with other members of the FGF signalling pathway from cnidarians to bilaterians (distance in situ hybridization. We show that some homologous expression territories can be defined, and we propose that FGFRL1 and FGF8/17/18 were already co-expressed in the pharyngeal endoderm in the ancestor of chordates. Conclusion Our work sheds light on the existence of a putative FGF signalling pathway actor present in the ancestor of probably all metazoans, the function of which has received little attention until now.

  9. Widespread presence of human BOULE homologs among animals and conservation of their ancient reproductive function.

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    Chirag Shah

    2010-07-01

    Full Text Available Sex-specific traits that lead to the production of dimorphic gametes, sperm in males and eggs in females, are fundamental for sexual reproduction and accordingly widespread among animals. Yet the sex-biased genes that underlie these sex-specific traits are under strong selective pressure, and as a result of adaptive evolution they often become divergent. Indeed out of hundreds of male or female fertility genes identified in diverse organisms, only a very small number of them are implicated specifically in reproduction in more than one lineage. Few genes have exhibited a sex-biased, reproductive-specific requirement beyond a given phylum, raising the question of whether any sex-specific gametogenesis factors could be conserved and whether gametogenesis might have evolved multiple times. Here we describe a metazoan origin of a conserved human reproductive protein, BOULE, and its prevalence from primitive basal metazoans to chordates. We found that BOULE homologs are present in the genomes of representative species of each of the major lineages of metazoans and exhibit reproductive-specific expression in all species examined, with a preponderance of male-biased expression. Examination of Boule evolution within insect and mammalian lineages revealed little evidence for accelerated evolution, unlike most reproductive genes. Instead, purifying selection was the major force behind Boule evolution. Furthermore, loss of function of mammalian Boule resulted in male-specific infertility and a global arrest of sperm development remarkably similar to the phenotype in an insect boule mutation. This work demonstrates the conservation of a reproductive protein throughout eumetazoa, its predominant testis-biased expression in diverse bilaterian species, and conservation of a male gametogenic requirement in mice. This shows an ancient gametogenesis requirement for Boule among Bilateria and supports a model of a common origin of spermatogenesis.

  10. Testis-specific glyceraldehyde-3-phosphate dehydrogenase: origin and evolution

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    Frishman Dmitrij

    2011-06-01

    Full Text Available Abstract Background Glyceraldehyde-3-phosphate dehydrogenase (GAPD catalyses one of the glycolytic reactions and is also involved in a number of non-glycolytic processes, such as endocytosis, DNA excision repair, and induction of apoptosis. Mammals are known to possess two homologous GAPD isoenzymes: GAPD-1, a well-studied protein found in all somatic cells, and GAPD-2, which is expressed solely in testis. GAPD-2 supplies energy required for the movement of spermatozoa and is tightly bound to the sperm tail cytoskeleton by the additional N-terminal proline-rich domain absent in GAPD-1. In this study we investigate the evolutionary history of GAPD and gain some insights into specialization of GAPD-2 as a testis-specific protein. Results A dataset of GAPD sequences was assembled from public databases and used for phylogeny reconstruction by means of the Bayesian method. Since resolution in some clades of the obtained tree was too low, syntenic analysis was carried out to define the evolutionary history of GAPD more precisely. The performed selection tests showed that selective pressure varies across lineages and isoenzymes, as well as across different regions of the same sequences. Conclusions The obtained results suggest that GAPD-1 and GAPD-2 emerged after duplication during the early evolution of chordates. GAPD-2 was subsequently lost by most lineages except lizards, mammals, as well as cartilaginous and bony fishes. In reptilians and mammals, GAPD-2 specialized to a testis-specific protein and acquired the novel N-terminal proline-rich domain anchoring the protein in the sperm tail cytoskeleton. This domain is likely to have originated by exonization of a microsatellite genomic region. Recognition of the proline-rich domain by cytoskeletal proteins seems to be unspecific. Besides testis, GAPD-2 of lizards was also found in some regenerating tissues, but it lacks the proline-rich domain due to tissue-specific alternative splicing.

  11. Evolution of the CNS myelin gene regulatory program.

    Science.gov (United States)

    Li, Huiliang; Richardson, William D

    2016-06-15

    Myelin is a specialized subcellular structure that evolved uniquely in vertebrates. A myelinated axon conducts action potentials many times faster than an unmyelinated axon of the same diameter; for the same conduction speed, the unmyelinated axon would need a much larger diameter and volume than its myelinated counterpart. Hence myelin speeds information transfer and saves space, allowing the evolution of a powerful yet portable brain. Myelination in the central nervous system (CNS) is controlled by a gene regulatory program that features a number of master transcriptional regulators including Olig1, Olig2 and Myrf. Olig family genes evolved from a single ancestral gene in non-chordates. Olig2, which executes multiple functions with regard to oligodendrocyte identity and development in vertebrates, might have evolved functional versatility through post-translational modification, especially phosphorylation, as illustrated by its evolutionarily conserved serine/threonine phospho-acceptor sites and its accumulation of serine residues during more recent stages of vertebrate evolution. Olig1, derived from a duplicated copy of Olig2 in early bony fish, is involved in oligodendrocyte development and is critical to remyelination in bony vertebrates, but is lost in birds. The origin of Myrf orthologs might be the result of DNA integration between an invading phage or bacterium and an early protist, producing a fusion protein capable of self-cleavage and DNA binding. Myrf seems to have adopted new functions in early vertebrates - initiation of the CNS myelination program as well as the maintenance of mature oligodendrocyte identity and myelin structure - by developing new ways to interact with DNA motifs specific to myelin genes. This article is part of a Special Issue entitled SI: Myelin Evolution. PMID:26474911

  12. Characterization, developmental expression and evolutionary features of the huntingtin gene in the amphioxus Branchiostoma floridae

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    Cattaneo Elena

    2007-11-01

    Full Text Available Abstract Background Huntington's disease is an inherited neurodegenerative disorder that is caused by the expansion of an N-terminal polyQ stretch in the huntingtin protein. In order to investigate the hypothesis that huntingtin was already involved in development of the nervous system in the last common ancestor of chordates, we isolated and characterised the huntingtin homologue from the amphioxus Branchiostoma floridae. In the present paper the amphioxus general term must be referred to Branchiostoma floridae. Results In this report, we show that the exon-intron organization of the amphioxus huntingtin gene is highly conserved with that of other vertebrates species. The AmphiHtt protein has two glutamine residues in the position of the typical vertebrate polyQ tract. Sequence conservation is greater along the entire length of the protein than in a previously identified Ciona huntingtin. The first three N-terminal HEAT repeats are highly conserved in vertebrates and amphioxus, although exon rearrangement has occurred in this region. AmphiHtt expression is detectable by in situ hybridization starting from the early neurula stage, where it is found in cells of the neural plate. At later stages, it is retained in the neural compartment but also it appears in limited and well-defined groups of non-neural cells. At subsequent larval stages, AmphiHtt expression is detected in the neural tube, with the strongest signal being present in the most anterior part. Conclusion The cloning of amphioxus huntingtin allows to infer that the polyQ in huntingtin was already present 540 million years ago and provides a further element for the study of huntingtin function and its evolution along the deuterostome branch.

  13. Calcium-insensitive splice variants of mammalian E1 subunit of 2-oxoglutarate dehydrogenase complex with tissue-specific patterns of expression.

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    Denton, Richard M; Pullen, Timothy J; Armstrong, Craig T; Heesom, Kate J; Rutter, Guy A

    2016-05-01

    The 2-oxoglutarate dehydrogenase (OGDH) complex is an important control point in vertebrate mitochondrial oxidative metabolism, including in the citrate cycle and catabolism of alternative fuels including glutamine. It is subject to allosteric regulation by NADH and the ATP/ADP ratio, and by Ca(2+) through binding to the E1 subunit. The latter involves a unique Ca(2+)-binding site which includes D(114)ADLD (site 1). Here, we describe three splice variants of E1 in which either the exon expressing this site is replaced with another exon (loss of site 1, LS1) or an additional exon is expressed leading to the insertion of 15 amino acids just downstream of site 1 (Insert), or both changes occur together (LS1/Insert). We show that all three variants are essentially Ca(2+)-insensitive. Comparison of massive parallel sequence (RNA-Seq) databases demonstrates predominant expression of the Ca(2+)-sensitive archetype form in heart and skeletal muscle, but substantial expression of the Ca(2+)-insensitive variants in brain, pancreatic islets and other tissues. Detailed proteomic and activity studies comparing OGDH complexes from rat heart and brain confirmed the substantial difference in expression between these tissues. The evolution of OGDH variants was explored using bioinformatics, and this indicated that Ca(2+)-sensitivity arose with the emergence of chordates. In all species examined, this was associated with the co-emergence of Ca(2+)-insensitive variants suggesting a retained requirement for the latter in some settings. Tissue-specific expression of OGDH splice variants may thus provide a mechanism that tunes the control of the enzyme to the specialized metabolic and signalling needs of individual cell types. PMID:26936970

  14. Elongated polyproline motifs facilitate enamel evolution through matrix subunit compaction.

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    Tianquan Jin

    2009-12-01

    repeat fragment assemblies and the evolution and the design of vertebrate mineralized tissue microstructures. Our findings reveal that in the greater context of chordate evolution, the biological control of apatite growth by polyproline-based matrix assemblies provides a molecular basis for the evolution of the vertebrate body plan.

  15. Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species.

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    Emese Meglécz

    Full Text Available Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within groups has been conducted. In this study, we examined microsatellite coverage and motif patterns from 454 shotgun sequences of 154 Eukaryote species from eight distantly related phyla (Cnidaria, Arthropoda, Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and Streptophyta to test if a consistent phylogenetic pattern emerges from the microsatellite composition of these species. It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.

  16. Sociocultural Variables That Impact High School Students' Perceptions of Native Fauna: a Study on the Species Component of the Biodiversity Concept

    Science.gov (United States)

    Bermudez, Gonzalo M. A.; Battistón, Luisina V.; García Capocasa, María C.; De Longhi, Ana L.

    2015-11-01

    This study investigates the influence of school sector (private versus state schools) and student gender on knowledge of native fauna. Our main objectives were (a) to describe the knowledge of high school students from the province of Cordoba, Argentina with respect to native animal species, (b) to determine if any exotic species (introduced or domestic) are considered native, and (c) to analyze the effects of school sector and gender on the students' knowledge of the native fauna. In total, 321 students aged 15-18 from 14 urban schools (8 state and 6 private schools) were asked to write down ten animals native to Córdoba, Argentina, in a free-list questionnaire. Relative frequencies and Generalized Linear Mixed Models (GLMM) were used to analyze the categorized (animal names) and continuous answers (quantity of responses, number of native animals, etc.), with the 25 most frequently mentioned species showing a predominance of native ones, of which "Puma" (Puma concolor) and "Andean condor" (Vultur gryphus) were the most prominent. An overrepresentation of mammalian species compared to other classes of chordates was also found, with high school students mentioning native and domestic species higher on the free-list. Using GLMM, we found that school sector had a significant effect on the number of native animals mentioned at both national and local levels, and on domestic and mixed species. Finally, male students mentioned more species and more native animals than their female counterparts. These findings were interpreted and discussed in light of sociocultural and traditional ecological knowledge theories, from which several implications arose related to research and practice.

  17. Evolutionary origins of C-terminal (GPPn 3-hydroxyproline formation in vertebrate tendon collagen.

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    David M Hudson

    Full Text Available Approximately half the proline residues in fibrillar collagen are hydroxylated. The predominant form is 4-hydroxyproline, which helps fold and stabilize the triple helix. A minor form, 3-hydroxyproline, still has no clear function. Using peptide mass spectrometry, we recently revealed several previously unknown molecular sites of 3-hydroxyproline in fibrillar collagen chains. In fibril-forming A-clade collagen chains, four new partially occupied 3-hydroxyproline sites were found (A2, A3, A4 and (GPPn in addition to the fully occupied A1 site at Pro986. The C-terminal (GPPn motif has five consecutive GPP triplets in α1(I, four in α2(I and three in α1(II, all subject to 3-hydroxylation. The evolutionary origins of this substrate sequence were investigated by surveying the pattern of its 3-hydroxyproline occupancy from early chordates through amphibians, birds and mammals. Different tissue sources of type I collagen (tendon, bone and skin and type II collagen (cartilage and notochord were examined by mass spectrometry. The (GPPn domain was found to be a major substrate for 3-hydroxylation only in vertebrate fibrillar collagens. In higher vertebrates (mouse, bovine and human, up to five 3-hydroxyproline residues per (GPPn motif were found in α1(I and four in α2(I, with an average of two residues per chain. In vertebrate type I collagen the modification exhibited clear tissue specificity, with 3-hydroxyproline prominent only in tendon. The occupancy also showed developmental changes in Achilles tendon, with increasing 3-hydroxyproline levels with age. The biological significance is unclear but the level of 3-hydroxylation at the (GPPn site appears to have increased as tendons evolved and shows both tendon type and developmental variations within a species.

  18. The central nervous system of ascidian larvae.

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    Hudson, Clare

    2016-09-01

    Ascidians are marine invertebrate chordates. Their tadpole larvae contain a dorsal tubular nervous system, resulting from the rolling up of a neural plate. Along the anterior-posterior (A-P) axis, the central nervous system (CNS) is organized into a sensory vesicle, neck, trunk ganglion, and tail nerve cord and consists of approximately only 330 cells, of which around 100 are thought to be neurons. The organization of distinct neuronal cell types and neurotransmitter gene expression within the CNS has been described. The unique developmental mode of ascidians, with a small number of cells and a fixed cell division pattern, allows individual cells to be traced throughout development. This feature has led to the complete documentation of the cell lineages of certain cell types in the CNS. Thus, a step-by-step understanding of nervous system development from the initial stages of neural induction to the neurogenesis of individual neurons is a feasible goal. The genetic control of neural fate induction and early neural plate patterning are now well understood. The molecular mechanisms specifying the cholinergic neurons of the trunk ganglion as well as the pigment cells of the sensory organs are also well elucidated. In addition, studies have begun on the morphogenetic processes of neurulation. Remaining challenges include building an embryonic atlas integrating gene expression patterns, cell lineage, and neuronal cell types as well as developing the gene regulatory networks of cell fate specification and integrating them with the genetic control of morphogenesis. WIREs Dev Biol 2016, 5:538-561. doi: 10.1002/wdev.239 For further resources related to this article, please visit the WIREs website. PMID:27328318

  19. Pm-miR-133 hosting in one potential lncRNA regulates RhoA expression in pearl oyster Pinctada martensii.

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    Zheng, Zhe; Huang, RongLian; Tian, RongRong; Jiao, Yu; Du, Xiaodong

    2016-10-15

    Long non-coding RNAs (LncRNAs) are abundant in the genome of higher forms of eukaryotes and implicated in regulating the diversity of biological processes partly because they host microRNAs (miRNAs), which are repressors of target gene expression. In vertebrates, miR-133 regulates the differentiation and proliferation of cardiac and skeletal muscles. Pinctada martensii miR-133 (pm-miR-133) was identified in our previous research through Solexa deep sequencing. In the present study, the precise sequence of mature pm-miR-133 was validated through miR-RACE. Stem loop qRT-PCR analysis demonstrated that mature pm-miR-133 was constitutively expressed in the adductor muscle, gonad, hepatopancreas, mantle, foot, and gill of P. martensii. Among these tissues, the adductor muscle exhibited the highest pm-miR-133 expression. Target analysis indicated that pm-RhoA was the potential regulatory target of pm-miR-133. Bioinformatics analyses revealed that a potential LncRNA (designated as Lnc133) with a mature pm-miR-133 could generate a hairpin structure that was highly homologous to that of Lottia gigantea. Lnc133 was also highly expressed in the adductor muscle, gill, hepatopancreas, and gonad. Phylogenetic analysis further showed that the miR-133s derived from chordate and achordate were separated into two classes. Therefore, Lnc133 hosting pm-miR-133 could be involved in regulating the cell proliferation of adductor muscles by targeting pm-RhoA.

  20. Immunolocalization of arthropsin in the onychophoran Euperipatoides rowelli (Peripatopsidae

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    Isabell Schumann

    2016-08-01

    Full Text Available Opsins are light-sensitive proteins that play a key role in animal vision and are related to the ancient photoreceptive molecule rhodopsin found in unicellular organisms. In general, opsins involved in vision comprise two major groups: the rhabdomeric (r-opsins and the ciliary opsins (c-opsins. The functionality of opsins, which is dependent on their protein structure, may have changed during evolution. In arthropods, typically r-opsins are responsible for vision, whereas in vertebrates c-opsins are components of visual photoreceptors. Recently, an enigmatic r-opsin-like protein called arthropsin has been identified in various bilaterian taxa, including arthropods, lophotrochozoans and chordates, by performing transcriptomic and genomic analyses. Since the role of arthropsin and its distribution within the body are unknown, we immunolocalized this protein in a representative of Onychophora – Euperipatoides rowelli – an ecdysozoan taxon which is regarded as one of the closest relatives of Arthropoda. Our data show that arthropsin is expressed in the central nervous system of E. rowelli, including the brain and the ventral nerve cords, but not in the eyes. These findings are consistent with previous results based on reverse transcription PCR in a closely related onychophoran species and suggest that arthropsin is a non-visual protein. Based on its distribution in the central brain region and the mushroom bodies, we speculate that the onychophoran arthropsin might be either a photosensitive molecule playing a role in the circadian clock, or a non-photosensitive protein involved in olfactory pathways, or both.

  1. A new mechanistic scenario for the origin and evolution of vertebrate cartilage.

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    Maria Cattell

    Full Text Available The appearance of cellular cartilage was a defining event in vertebrate evolution because it made possible the physical expansion of the vertebrate "new head". Despite its central role in vertebrate evolution, the origin of cellular cartilage has been difficult to understand. This is largely due to a lack of informative evolutionary intermediates linking vertebrate cellular cartilage to the acellular cartilage of invertebrate chordates. The basal jawless vertebrate, lamprey, has long been considered key to understanding the evolution of vertebrate cartilage. However, histological analyses of the lamprey head skeleton suggest it is composed of modern cellular cartilage and a putatively unrelated connective tissue called mucocartilage, with no obvious transitional tissue. Here we take a molecular approach to better understand the evolutionary relationships between lamprey cellular cartilage, gnathostome cellular cartilage, and lamprey mucocartilage. We find that despite overt histological similarity, lamprey and gnathostome cellular cartilage utilize divergent gene regulatory networks (GRNs. While the gnathostome cellular cartilage GRN broadly incorporates Runx, Barx, and Alx transcription factors, lamprey cellular cartilage does not express Runx or Barx, and only deploys Alx genes in certain regions. Furthermore, we find that lamprey mucocartilage, despite its distinctive mesenchymal morphology, deploys every component of the gnathostome cartilage GRN, albeit in different domains. Based on these findings, and previous work, we propose a stepwise model for the evolution of vertebrate cellular cartilage in which the appearance of a generic neural crest-derived skeletal tissue was followed by a phase of skeletal tissue diversification in early agnathans. In the gnathostome lineage, a single type of rigid cellular cartilage became dominant, replacing other skeletal tissues and evolving via gene cooption to become the definitive cellular cartilage of

  2. A new mechanistic scenario for the origin and evolution of vertebrate cartilage.

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    Cattell, Maria; Lai, Su; Cerny, Robert; Medeiros, Daniel Meulemans

    2011-01-01

    The appearance of cellular cartilage was a defining event in vertebrate evolution because it made possible the physical expansion of the vertebrate "new head". Despite its central role in vertebrate evolution, the origin of cellular cartilage has been difficult to understand. This is largely due to a lack of informative evolutionary intermediates linking vertebrate cellular cartilage to the acellular cartilage of invertebrate chordates. The basal jawless vertebrate, lamprey, has long been considered key to understanding the evolution of vertebrate cartilage. However, histological analyses of the lamprey head skeleton suggest it is composed of modern cellular cartilage and a putatively unrelated connective tissue called mucocartilage, with no obvious transitional tissue. Here we take a molecular approach to better understand the evolutionary relationships between lamprey cellular cartilage, gnathostome cellular cartilage, and lamprey mucocartilage. We find that despite overt histological similarity, lamprey and gnathostome cellular cartilage utilize divergent gene regulatory networks (GRNs). While the gnathostome cellular cartilage GRN broadly incorporates Runx, Barx, and Alx transcription factors, lamprey cellular cartilage does not express Runx or Barx, and only deploys Alx genes in certain regions. Furthermore, we find that lamprey mucocartilage, despite its distinctive mesenchymal morphology, deploys every component of the gnathostome cartilage GRN, albeit in different domains. Based on these findings, and previous work, we propose a stepwise model for the evolution of vertebrate cellular cartilage in which the appearance of a generic neural crest-derived skeletal tissue was followed by a phase of skeletal tissue diversification in early agnathans. In the gnathostome lineage, a single type of rigid cellular cartilage became dominant, replacing other skeletal tissues and evolving via gene cooption to become the definitive cellular cartilage of modern jawed

  3. A paleontological perspective of vertebrate origin

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The Early Cambrian Haikouichthys and Haikouella have been claimed to be related to contribute in an important way to our understanding of vertebrate origin, but there have been heated debates about how exactly they are to be interpreted. New discoveries of numerous specimens of Haikouichthys not only confirm the identity of previously described structures such as the dorsal and the ventral fins, and chevron-shaped myomeres, but also reveal many new important characteristics, including sensory organs of the head (e.g. large eyes), and a prominent notochord with differentiated vertebral elements. This "first fish" appears, however, to retain primitive reproductive features of acraniates, suggesting that it is a stem-group craniates. A new order (Myllokunmingiida) and a new family (Myllokunmingiidae) are erected, and a new species, Zhongjianichthys rostratus (gen. et sp. nov.), is described herein. Over 1400 newly-discovered specimens of Haikouella provide a wealth of anatomical information on this organism. It differs from chordates in many organs and organ systems, including the skin, muscles, respiratory, circulatory and nervous systems. In contrast, its body-design resembles that of vetulicolians, and the presence of a "transitional" nervous system with both dorsal and ventral nerve cords suggests an affinity with living hemichordates. On the basis of these and other recent findings of fossil deuterostomes, a five-step hypothesis for vertebrate origin is proposed, intended to bridge the long- standing gap between protostomes and vertebrates. Four of the five steps accord with established ideas current in modern evolutionary zoology. Evidence for the first step is obtainable only from fossils, and specifically from fossils found from South China, hence the crucial importance of S. China sites for our understanding of early vertebrate origins and evolution. Accordingly, South China is suggested as the oldest-known birthplace of the whole vertebrates.

  4. A new mechanistic scenario for the origin and evolution of vertebrate cartilage.

    Science.gov (United States)

    Cattell, Maria; Lai, Su; Cerny, Robert; Medeiros, Daniel Meulemans

    2011-01-01

    The appearance of cellular cartilage was a defining event in vertebrate evolution because it made possible the physical expansion of the vertebrate "new head". Despite its central role in vertebrate evolution, the origin of cellular cartilage has been difficult to understand. This is largely due to a lack of informative evolutionary intermediates linking vertebrate cellular cartilage to the acellular cartilage of invertebrate chordates. The basal jawless vertebrate, lamprey, has long been considered key to understanding the evolution of vertebrate cartilage. However, histological analyses of the lamprey head skeleton suggest it is composed of modern cellular cartilage and a putatively unrelated connective tissue called mucocartilage, with no obvious transitional tissue. Here we take a molecular approach to better understand the evolutionary relationships between lamprey cellular cartilage, gnathostome cellular cartilage, and lamprey mucocartilage. We find that despite overt histological similarity, lamprey and gnathostome cellular cartilage utilize divergent gene regulatory networks (GRNs). While the gnathostome cellular cartilage GRN broadly incorporates Runx, Barx, and Alx transcription factors, lamprey cellular cartilage does not express Runx or Barx, and only deploys Alx genes in certain regions. Furthermore, we find that lamprey mucocartilage, despite its distinctive mesenchymal morphology, deploys every component of the gnathostome cartilage GRN, albeit in different domains. Based on these findings, and previous work, we propose a stepwise model for the evolution of vertebrate cellular cartilage in which the appearance of a generic neural crest-derived skeletal tissue was followed by a phase of skeletal tissue diversification in early agnathans. In the gnathostome lineage, a single type of rigid cellular cartilage became dominant, replacing other skeletal tissues and evolving via gene cooption to become the definitive cellular cartilage of modern jawed

  5. Characterization of an Alpha Type Carbonic Anhydrase from Paracentrotus lividus Sea Urchin Embryos.

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    Karakostis, Konstantinos; Costa, Caterina; Zito, Francesca; Brümmer, Franz; Matranga, Valeria

    2016-06-01

    Carbonic anhydrases (CA) are zinc metalloenzymes that catalyze the reversible hydration of carbon dioxide to bicarbonate. In the sea urchin, CA has a role in the formation of the calcitic skeleton during embryo development. Here, we report a newly identified mRNA sequence from embryos of the sea urchin Paracentrotus lividus, referred to as Pl-can. The complete coding sequence was identified with the aid of both EST databases and experimental procedures. Pl-CAN is a 447 aa-long protein, with an estimated molecular mass of 48.5 kDa and an isoelectric point of 6.83. The in silico study of functional domains showed, in addition to the alpha type CA-specific domain, the presence of an unexpected glycine-rich region at the N-terminal of the molecule. This is not found in any other species described so far, but probably it is restricted to the sea urchins. The phylogenetic analysis indicated that Pl-CAN is evolutionarily closer to human among chordates than to other species. The putative role(s) of the identified domains is discussed. The Pl-can temporal and spatial expression profiles, analyzed throughout embryo development by comparative qPCR and whole-mount in situ hybridization (WMISH), showed that Pl-can mRNA is specifically expressed in the primary mesenchyme cells (PMC) of the embryo and levels increase along with the growth of the embryonic skeleton, reaching a peak at the pluteus stage. A recombinant fusion protein was produced in E. coli and used to raise specific antibodies in mice recognized the endogenous Pl-CAN by Western blot in embryo extracts from gastrula and pluteus. PMID:27230618

  6. Comparative genomic analysis of slc39a12/ZIP12: insight into a zinc transporter required for vertebrate nervous system development.

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    Winyoo Chowanadisai

    Full Text Available The zinc transporter ZIP12, which is encoded by the gene slc39a12, has previously been shown to be important for neuronal differentiation in mouse Neuro-2a neuroblastoma cells and primary mouse neurons and necessary for neurulation during Xenopus tropicalis embryogenesis. However, relatively little is known about the biochemical properties, cellular regulation, or the physiological role of this gene. The hypothesis that ZIP12 is a zinc transporter important for nervous system function and development guided a comparative genetics approach to uncover the presence of ZIP12 in various genomes and identify conserved sequences and expression patterns associated with ZIP12. Ortholog detection of slc39a12 was conducted with reciprocal BLAST hits with the amino acid sequence of human ZIP12 in comparison to the human paralog ZIP4 and conserved local synteny between genomes. ZIP12 is present in the genomes of almost all vertebrates examined, from humans and other mammals to most teleost fish. However, ZIP12 appears to be absent from the zebrafish genome. The discrimination of ZIP12 compared to ZIP4 was unsuccessful or inconclusive in other invertebrate chordates and deuterostomes. Splice variation, due to the inclusion or exclusion of a conserved exon, is present in humans, rats, and cows and likely has biological significance. ZIP12 also possesses many putative di-leucine and tyrosine motifs often associated with intracellular trafficking, which may control cellular zinc uptake activity through the localization of ZIP12 within the cell. These findings highlight multiple aspects of ZIP12 at the biochemical, cellular, and physiological levels with likely biological significance. ZIP12 appears to have conserved function as a zinc uptake transporter in vertebrate nervous system development. Consequently, the role of ZIP12 may be an important link to reported congenital malformations in numerous animal models and humans that are caused by zinc deficiency.

  7. Comparative genomic analysis of slc39a12/ZIP12: insight into a zinc transporter required for vertebrate nervous system development.

    Science.gov (United States)

    Chowanadisai, Winyoo

    2014-01-01

    The zinc transporter ZIP12, which is encoded by the gene slc39a12, has previously been shown to be important for neuronal differentiation in mouse Neuro-2a neuroblastoma cells and primary mouse neurons and necessary for neurulation during Xenopus tropicalis embryogenesis. However, relatively little is known about the biochemical properties, cellular regulation, or the physiological role of this gene. The hypothesis that ZIP12 is a zinc transporter important for nervous system function and development guided a comparative genetics approach to uncover the presence of ZIP12 in various genomes and identify conserved sequences and expression patterns associated with ZIP12. Ortholog detection of slc39a12 was conducted with reciprocal BLAST hits with the amino acid sequence of human ZIP12 in comparison to the human paralog ZIP4 and conserved local synteny between genomes. ZIP12 is present in the genomes of almost all vertebrates examined, from humans and other mammals to most teleost fish. However, ZIP12 appears to be absent from the zebrafish genome. The discrimination of ZIP12 compared to ZIP4 was unsuccessful or inconclusive in other invertebrate chordates and deuterostomes. Splice variation, due to the inclusion or exclusion of a conserved exon, is present in humans, rats, and cows and likely has biological significance. ZIP12 also possesses many putative di-leucine and tyrosine motifs often associated with intracellular trafficking, which may control cellular zinc uptake activity through the localization of ZIP12 within the cell. These findings highlight multiple aspects of ZIP12 at the biochemical, cellular, and physiological levels with likely biological significance. ZIP12 appears to have conserved function as a zinc uptake transporter in vertebrate nervous system development. Consequently, the role of ZIP12 may be an important link to reported congenital malformations in numerous animal models and humans that are caused by zinc deficiency.

  8. Pattern and morphogenesis of presumptive superficial mesoderm in two closely related species, Xenopus laevis and Xenopus tropicalis.

    Science.gov (United States)

    Shook, David R; Majer, Christina; Keller, Ray

    2004-06-01

    The mesoderm, comprising the tissues that come to lie entirely in the deep layer, originates in both the superficial epithelial and the deep mesenchymal layers of the early amphibian embryo. Here, we characterize the mechanisms by which the superficial component of the presumptive mesoderm ingresses into the underlying deep mesenchymal layer in Xenopus tropicalis and extend our previous findings for Xenopus laevis. Fate mapping the superficial epithelium of pregastrula stage embryos demonstrates ingression of surface cells into both paraxial and axial mesoderm (including hypochord), in similar patterns and amounts in both species. Superficial presumptive notochord lies medially, flanked by presumptive hypochord and both overlie the deep region of the presumptive notochord. These tissues are flanked laterally by superficial presumptive somitic mesoderm, the anterior tip of which also appears to overlay the presumptive deep notochord. Time-lapse recordings show that presumptive somitic and notochordal cells move out of the roof of the gastrocoel and into the deep region during neurulation, whereas hypochordal cells ingress after neurulation. Scanning electron microscopy at the stage and position where ingression occurs suggests that superficial presumptive somitic cells in X. laevis ingress into the deep region as bottle cells whereas those in X. tropicalis ingress by "relamination" (e.g., [Dev. Biol. 174 (1996) 92]). In both species, the superficially derived presumptive somitic cells come to lie in the medial region of the presumptive somites during neurulation. By the early tailbud stages, these cells lie at the horizontal myoseptum of the somites. The morphogenic pathway of these cells strongly resembles that of the primary slow muscle pioneer cells of the zebrafish. We present a revised fate map of Xenopus, and we discuss the conservation of superficial mesoderm within amphibians and across the chordates and its implications for the role of this tissue in

  9. Characterization and transcription studies of a phytochelatin synthase gene from the solitary tunicate Ciona intestinalis exposed to cadmium

    Energy Technology Data Exchange (ETDEWEB)

    Franchi, Nicola [Department of Biology, University of Padova, Padova (Italy); Department of Biological, Chemical, Pharmaceutical Science and Technology, University of Palermo, Palermo (Italy); Piccinni, Ester [Department of Biology, University of Padova, Padova (Italy); Ferro, Diana [Department of Biology, University of Padova, Padova (Italy); Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität, Münster (Germany); Basso, Giuseppe [Department of Woman and Child Health, University of Padova, Padova (Italy); Spolaore, Barbara [CRIBI Biotechnology Centre, University of Padova, Padova (Italy); Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova (Italy); Santovito, Gianfranco, E-mail: gianfranco.santovito@unipd.it [Department of Biology, University of Padova, Padova (Italy); Ballarin, Loriano [Department of Biology, University of Padova, Padova (Italy)

    2014-07-01

    Highlights: • Ciona intestinalis have a functional phytochelatin synthase (PCS) gene (cipcs). • CiPCS amino acid sequence is phylogentically related to other metazoan PCSs. • CiPCS catalyze the synthesis of PC2. • cipcs are mostly transcribed in circulating hemocytes, in both tunic and blood lacunae. • Cadmium exposure results in a significant increase of cipcs and cipcna transcription. - Abstract: The major thiol-containing molecules involved in controlling the level of intracellular ROS in eukaryotes, acting as a nonenzymatic detoxification system, are metallothioneins (MTs), glutathione (GSH) and phytochelatins (PCs). Both MTs and GSH are well-known in the animal kingdom. PC was considered a prerogative of the plant kingdom but, in 2001, a phytochelatin synthase (PCS) gene was described in the nematode Caenorhabditis elegans; additional genes encoding this enzyme were later described in the earthworm Eisenia fetida and in the parasitic nematode Schistosoma mansoni but scanty data are available, up to now, for Deuterostomes. Here, we describe the molecular characteristics and transcription pattern, in the presence of Cd, of a PCS gene from the invertebrate chordate Ciona intestinalis, a ubiquitous solitary tunicate and demonstrate the presence of PCs in tissue extracts. We also studied mRNA localization by in situ hybridization. In addition, we analyzed the behavior of hemocytes and tunic cells consequent to Cd exposure as well as the transcription pattern of the Ciona orthologous for proliferating cell nuclear antigen (PCNA), usually considered a proliferation marker, and observed that cell proliferation occurs after 96 h of Cd treatment. This matches the hypothesis of Cd-induced cell proliferation, as already suggested by previous data on the expression of a metallothionein gene in the same animal.

  10. Evolution of the CNS myelin gene regulatory program.

    Science.gov (United States)

    Li, Huiliang; Richardson, William D

    2016-06-15

    Myelin is a specialized subcellular structure that evolved uniquely in vertebrates. A myelinated axon conducts action potentials many times faster than an unmyelinated axon of the same diameter; for the same conduction speed, the unmyelinated axon would need a much larger diameter and volume than its myelinated counterpart. Hence myelin speeds information transfer and saves space, allowing the evolution of a powerful yet portable brain. Myelination in the central nervous system (CNS) is controlled by a gene regulatory program that features a number of master transcriptional regulators including Olig1, Olig2 and Myrf. Olig family genes evolved from a single ancestral gene in non-chordates. Olig2, which executes multiple functions with regard to oligodendrocyte identity and development in vertebrates, might have evolved functional versatility through post-translational modification, especially phosphorylation, as illustrated by its evolutionarily conserved serine/threonine phospho-acceptor sites and its accumulation of serine residues during more recent stages of vertebrate evolution. Olig1, derived from a duplicated copy of Olig2 in early bony fish, is involved in oligodendrocyte development and is critical to remyelination in bony vertebrates, but is lost in birds. The origin of Myrf orthologs might be the result of DNA integration between an invading phage or bacterium and an early protist, producing a fusion protein capable of self-cleavage and DNA binding. Myrf seems to have adopted new functions in early vertebrates - initiation of the CNS myelination program as well as the maintenance of mature oligodendrocyte identity and myelin structure - by developing new ways to interact with DNA motifs specific to myelin genes. This article is part of a Special Issue entitled SI: Myelin Evolution.

  11. The repertoire of G protein-coupled receptors in the sea squirt Ciona intestinalis

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    Manoj Narayanan

    2008-05-01

    Full Text Available Abstract Background G protein-coupled receptors (GPCRs constitute a large family of integral transmembrane receptor proteins that play a central role in signal transduction in eukaryotes. The genome of the protochordate Ciona intestinalis has a compact size with an ancestral complement of many diversified gene families of vertebrates and is a good model system for studying protochordate to vertebrate diversification. An analysis of the Ciona repertoire of GPCRs from a comparative genomic perspective provides insight into the evolutionary origins of the GPCR signalling system in vertebrates. Results We have identified 169 gene products in the Ciona genome that code for putative GPCRs. Phylogenetic analyses reveal that Ciona GPCRs have homologous representatives from the five major GRAFS (Glutamate, Rhodopsin, Adhesion, Frizzled and Secretin families concomitant with other vertebrate GPCR repertoires. Nearly 39% of Ciona GPCRs have unambiguous orthologs of vertebrate GPCR families, as defined for the human, mouse, puffer fish and chicken genomes. The Rhodopsin family accounts for ~68% of the Ciona GPCR repertoire wherein the LGR-like subfamily exhibits a lineage specific gene expansion of a group of receptors that possess a novel domain organisation hitherto unobserved in metazoan genomes. Conclusion Comparison of GPCRs in Ciona to that in human reveals a high level of orthology of a protochordate repertoire with that of vertebrate GPCRs. Our studies suggest that the ascidians contain the basic ancestral complement of vertebrate GPCR genes. This is evident at the subfamily level comparisons since Ciona GPCR sequences are significantly analogous to vertebrate GPCR subfamilies even while exhibiting Ciona specific genes. Our analysis provides a framework to perform future experimental and comparative studies to understand the roles of the ancestral chordate versions of GPCRs that predated the divergence of the urochordates and the vertebrates.

  12. Hox gene clusters in the Indonesian coelacanth, Latimeria menadoensis.

    Science.gov (United States)

    Koh, Esther G L; Lam, Kevin; Christoffels, Alan; Erdmann, Mark V; Brenner, Sydney; Venkatesh, Byrappa

    2003-02-01

    The Hox genes encode transcription factors that play a key role in specifying body plans of metazoans. They are organized into clusters that contain up to 13 paralogue group members. The complex morphology of vertebrates has been attributed to the duplication of Hox clusters during vertebrate evolution. In contrast to the single Hox cluster in the amphioxus (Branchiostoma floridae), an invertebrate-chordate, mammals have four clusters containing 39 Hox genes. Ray-finned fishes (Actinopterygii) such as zebrafish and fugu possess more than four Hox clusters. The coelacanth occupies a basal phylogenetic position among lobe-finned fishes (Sarcopterygii), which gave rise to the tetrapod lineage. The lobe fins of sarcopterygians are considered to be the evolutionary precursors of tetrapod limbs. Thus, the characterization of Hox genes in the coelacanth should provide insights into the origin of tetrapod limbs. We have cloned the complete second exon of 33 Hox genes from the Indonesian coelacanth, Latimeria menadoensis, by extensive PCR survey and genome walking. Phylogenetic analysis shows that 32 of these genes have orthologs in the four mammalian HOX clusters, including three genes (HoxA6, D1, and D8) that are absent in ray-finned fishes. The remaining coelacanth gene is an ortholog of hoxc1 found in zebrafish but absent in mammals. Our results suggest that coelacanths have four Hox clusters bearing a gene complement more similar to mammals than to ray-finned fishes, but with an additional gene, HoxC1, which has been lost during the evolution of mammals from lobe-finned fishes.

  13. Molecular evolutionary analysis of ABCB5: the ancestral gene is a full transporter with potentially deleterious single nucleotide polymorphisms.

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    Karobi Moitra

    Full Text Available BACKGROUND: ABCB5 is a member of the ABC protein superfamily, which includes the transporters ABCB1, ABCC1 and ABCG2 responsible for causing drug resistance in cancer patients and also several other transporters that have been linked to human disease. The ABCB5 full transporter (ABCB5.ts is expressed in human testis and its functional significance is presently unknown. Another variant of this transporter, ABCB5 beta possess a "half-transporter-like" structure and is expressed in melanoma stem cells, normal melanocytes, and other types of pigment cells. ABCB5 beta has important clinical implications, as it may be involved with multidrug resistance in melanoma stem cells, allowing these stem cells to survive chemotherapeutic regimes. METHODOLOGY/PRINCIPAL FINDINGS: We constructed and examined in detail topological structures of the human ABCB5 protein and determined in-silico the cSNPs (coding single nucleotide polymorphisms that may affect its function. Evolutionary analysis of ABCB5 indicated that ABCB5, ABCB1, ABCB4, and ABCB11 share a common ancestor, which began duplicating early in the evolutionary history of chordates. This suggests that ABCB5 has evolved as a full transporter throughout its evolutionary history. CONCLUSIONS/SIGNIFICANCE: From our in-silco analysis of cSNPs we found that a large number of non-synonymous cSNPs map to important functional regions of the protein suggesting that these SNPs if present in human populations may play a role in diseases associated with ABCB5. From phylogenetic analyses, we have shown that ABCB5 evolved as a full transporter throughout its evolutionary history with an absence of any major shifts in selection between the various lineages suggesting that the function of ABCB5 has been maintained during mammalian evolution. This finding would suggest that ABCB5 beta may have evolved to play a specific role in human pigment cells and/or melanoma cells where it is predominantly expressed.

  14. Thyroid hormone receptor orthologues from invertebrate species with emphasis on Schistosoma mansoni

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    Niles Edward G

    2007-08-01

    Full Text Available Abstract Background: Thyroid hormone receptors (TRs function as molecular switches in response to thyroid hormone to regulate gene transcription. TRs were previously believed to be present only in chordates. Results: We isolated two TR genes from the Schistosoma mansoni and identified TR orthologues from other invertebrates: the platyhelminths, S. japonium and Schmidtea mediterranea, the mollusc, Lottia gigantean and the arthropod Daphnia pulex. Phylogenetic analysis of the DNA binding domain and/or ligand binding domain shows that invertebrate and vertebrate TRs cluster together, TRs from the vertebrates and from the jawless vertebrate (lamprey clustered within separate subgroups, Platyhelminth TRs cluster outside of the vertebrate TR subgroups and that the schistosome TRs and S. mediterranea TRs clustered within separate subgroups. Alignment of the C-terminus of the A/B domain revealed a conserved TR-specific motif, termed TR 'N-terminus signature sequence', with a consensus sequence of (G/PYIPSY(M/LXXXGPE(D/EX. Heterodimer formation between S. mansoni TRs and SmRXR1 suggests that the invertebrate TR protein gained the ability to form a heterodimer with RXR. ESMA analysis showed that SmTRα could bind to a conserved DNA core motif as a monomer or homodimer. Conclusion: Vertebrate TR genes originated from a common ancestor of the Bilateria. TR genes underwent duplication independently in the Protostomia and Deuterostomia. The duplication of TRs in deuterostomes occurred after the split of jawless and jawed vertebrates. In protostomes, TR genes underwent duplication in Platyhelminths, occurring independently in trematode and turbellarian lineages. Using S. mansoni TRs as an example, invertebrate TRs exhibited the ability to form a dimer with RXR prior to the emergence of the vertebrate TRs and were able to bind to vertebrate TR core DNA elements as a monomer or homodimer.

  15. SETDB1 is involved in postembryonic DNA methylation and gene silencing in Drosophila.

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    Dawei Gou

    Full Text Available DNA methylation is fundamental for the stability and activity of genomes. Drosophila melanogaster and vertebrates establish a global DNA methylation pattern of their genome during early embryogenesis. Large-scale analyses of DNA methylation patterns have uncovered revealed that DNA methylation patterns are dynamic rather than static and change in a gene-specific fashion during development and in diseased cells. However, the factors and mechanisms involved in dynamic, postembryonic DNA methylation remain unclear. Methylation of lysine 9 in histone H3 (H3-K9 by members of the Su(var3-9 family of histone methyltransferases (HMTs triggers embryonic DNA methylation in Arthropods and Chordates. Here, we demonstrate that Drosophila SETDB1 (dSETDB1 can mediate DNA methylation and silencing of genes and retrotransposons. We found that dSETDB1 tri-methylates H3-K9 and binds methylated CpA motifs. Tri-methylation of H3-K9 by dSETDB1 mediates recruitment of DNA methyltransferase 2 (Dnmt2 and Su(var205, the Drosophila ortholog of mammalian "Heterochromatin Protein 1", to target genes for dSETDB1. By enlisting Dnmt2 and Su(var205, dSETDB1 triggers DNA methylation and silencing of genes and retrotransposons in Drosophila cells. DSETDB1 is involved in postembryonic DNA methylation and silencing of Rt1b{} retrotransposons and the tumor suppressor gene retinoblastoma family protein 1 (Rb in imaginal discs. Collectively, our findings implicate dSETDB1 in postembryonic DNA methylation, provide a model for silencing of the tumor suppressor Rb, and uncover a role for cell type-specific DNA methylation in Drosophila development.

  16. The bijection from data to parameter space with the standard DEB model quantifies the supply-demand spectrum.

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    Lika, Konstadia; Augustine, Starrlight; Pecquerie, Laure; Kooijman, Sebastiaan A L M

    2014-08-01

    The standard Dynamic Energy Budget (DEB) model assumes that food is converted to reserve and a fraction κ of mobilised reserve of an individual is allocated to somatic maintenance plus growth, while the rest is allocated to maturity maintenance plus maturation (in embryos and juveniles) or reproduction (in adults). The add_my_pet collection of over 300 animal species from most larger phyla, and all chordate classes, shows that this model fits energy data very well. Nine parameters determine nine data points at abundant food: dry/wet weight ratio, age at birth, puberty, death, weight at birth, metamorphosis, puberty, ultimate weight and ultimate reproduction rate. We demonstrate that, given a few other parameters, these nine data points also determine the nine parameters uniquely that are independent of food availability: maturity at birth, metamorphosis and puberty, specific assimilation, somatic maintenance and costs for structure, allocation fraction of mobilised reserve to soma, energy conductance, and ageing acceleration. We provide an efficient algorithm for mapping between data and parameter space in both directions and found expressions for the boundaries of the parameter and data spaces. One of them quantifies the position of species in the supply-demand spectrum, which reflects the internalisation of energetic control. We link eco-physiological properties of species to their position in this spectrum and discuss it in the context of homeostasis. Invertebrates and ray-finned fish turn out to be close to the supply end of the spectrum, while other vertebrates, including cartilaginous fish, have stronger demand tendencies. We explain why birds and mammals up-regulate metabolism during reproduction. We study some properties of the bijection using elasticity coefficients. The properties have applications in parameter estimation and in the analysis of evolutionary constraints on parameter values; the relationship between DEB parameters and data has similarities

  17. Conservation of linkage and evolution of developmental function within the Tbx2/3/4/5 subfamily of T-box genes: implications for the origin of vertebrate limbs.

    Science.gov (United States)

    Horton, Amy C; Mahadevan, Navin R; Minguillon, Carolina; Osoegawa, Kazutoyo; Rokhsar, Daniel S; Ruvinsky, Ilya; de Jong, Pieter J; Logan, Malcolm P; Gibson-Brown, Jeremy J

    2008-12-01

    T-box genes encode a family of DNA-binding transcription factors implicated in numerous developmental processes in all metazoans. The Tbx2/3/4/5 subfamily genes are especially interesting because of their key roles in the evolution of vertebrate appendages, eyes, and the heart, and, like the Hox genes, the longevity of their chromosomal linkage. A BAC library derived from the single male amphioxus (Branchiostoma floridae) used to sequence the amphioxus genome was screened for AmphiTbx2/3 and AmphiTbx4/5, yielding two independent clones containing both genes. Using comparative expression, genomic linkage, and phylogenetic analyses, we have reconstructed the evolutionary histories of these members of the T-box gene family. We find that the Tbx2-Tbx4 and Tbx3-Tbx5 gene pairs have maintained tight linkage in most animal lineages since their birth by tandem duplication, long before the divergence of protostomes and deuterostomes (e.g., arthropods and vertebrates) at least 600 million years ago, and possibly before the divergence of poriferans and cnidarians (e.g., sponges and jellyfish). Interestingly, we find that the gene linkage detected in all vertebrate genomes has been maintained in the primitively appendage-lacking, basal chordate, amphioxus. Although all four genes have been involved in the evolution of developmental programs regulating paired fin and (later) limb outgrowth and patterning, and most are also implicated in eye and heart development, linkage maintenance--often considered due to regulatory constraints imposed by limb, eye, and/or heart associated gene expression--is undoubtedly a consequence of other, much more ancient functional constraints. PMID:18815807

  18. On the Phylum Vetulicolia

    Institute of Scientific and Technical Information of China (English)

    SHU Degan

    2005-01-01

    The origins and radiations of metazoans, bilaterians, deuterostomes and vertebrates have been recognized as the four most important milestone events in animal history and, conversely four of the toughest and puzzling questions in evolutionary biology. Among them, the first two occurred in the deep time of the Precambrian and have left little information in the fossil records. Fortunately, intensive investigation into the Early Cambrian Chengjiang faunas in the past two decades have revealed numerous significant data on the main episode of the Cambrian Explosion, particularly information on the various earliest-known deuterostomes, leading to a much better understanding of the last two events. The "first fish" Haikouichthys and Myllokunmingia have been proved the oldest-known vertebrates, and to be among the most primitive ones, representing a key transitional group from acraniates to craniates. Indeed, "Paleontological work of Shu and collaborators is revising our understanding of the early evolution of chordates". Moreover, the discovery of the Phylum Vetulicolia may also throw new light on the origin of deuterostomes. This extinct group with simple gill slits might represent one of the roots in the deuterostome lineage, as the evidence of molecular biology and developmental biology has predicted. Here the first discovery of tiny vetulicolians from the Chengjiang Lagerst(a)tte is reported. The evolutionary trend from the giant to the small might represent a special adaptation in early animal history. Since all vetulicolians share similar characters in their anterior section (pharynx), and on the basis of differences in their posterior section, a new classification system is proposed, with a new class, the Heteromorphida erected. As both the "root" group vetulicolians and the "top" group vertebrates in the early deuterostome lineage, as well as those members in between, such as vetulocystids, yunnanozoans, cephalochordates and urochordates, have been recovered, a

  19. Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining.

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    Etienne G J Danchin

    2013-10-01

    Full Text Available Root-knot nematodes are globally the most aggressive and damaging plant-parasitic nematodes. Chemical nematicides have so far constituted the most efficient control measures against these agricultural pests. Because of their toxicity for the environment and danger for human health, these nematicides have now been banned from use. Consequently, new and more specific control means, safe for the environment and human health, are urgently needed to avoid worldwide proliferation of these devastating plant-parasites. Mining the genomes of root-knot nematodes through an evolutionary and comparative genomics approach, we identified and analyzed 15,952 nematode genes conserved in genomes of plant-damaging species but absent from non target genomes of chordates, plants, annelids, insect pollinators and mollusks. Functional annotation of the corresponding proteins revealed a relative abundance of putative transcription factors in this parasite-specific set compared to whole proteomes of root-knot nematodes. This may point to important and specific regulators of genes involved in parasitism. Because these nematodes are known to secrete effector proteins in planta, essential for parasitism, we searched and identified 993 such effector-like proteins absent from non-target species. Aiming at identifying novel targets for the development of future control methods, we biologically tested the effect of inactivation of the corresponding genes through RNA interference. A total of 15 novel effector-like proteins and one putative transcription factor compatible with the design of siRNAs were present as non-redundant genes and had transcriptional support in the model root-knot nematode Meloidogyne incognita. Infestation assays with siRNA-treated M. incognita on tomato plants showed significant and reproducible reduction of the infestation for 12 of the 16 tested genes compared to control nematodes. These 12 novel genes, showing efficient reduction of parasitism when

  20. Amphioxus spawning behavior in an artificial seawater facility.

    Science.gov (United States)

    Theodosiou, Maria; Colin, Audrey; Schulz, Jasmin; Laudet, Vincent; Peyrieras, Nadine; Nicolas, Jean-François; Schubert, Michael; Hirsinger, Estelle

    2011-06-15

    Owing to its phylogenetic position at the base of the chordates, the cephalochordate amphioxus is an emerging model system carrying immense significance for understanding the evolution of vertebrate development. One important shortcoming of amphioxus as a model organism has been the unavailability of animal husbandry protocols to maintain amphioxus adults away from the field. Here, we present the first report of successful maintenance and spawning of Branchiostoma lanceolatum adults in a facility run on artificial seawater. B. lanceolatum has been chosen for this study because it is the only amphioxus species that can be induced to spawn. We provide a step-by-step guide for the assembly of such a facility and discuss the day-to-day operations required for successful animal husbandry of B. lanceolatum adults. This work also includes a detailed description of the B. lanceolatum spawning behavior in captivity. Our analysis shows that the induced spawning efficiency is not sex biased, but increases as the natural spawning season progresses. We find that a minor fraction of the animals undergo phases of spontaneous spawning in the tanks and that this behavior is not affected by the treatment used to induce spawning. Moreover, the induced spawning efficiency is not discernibly correlated with spontaneous spawning in the facility. Last, we describe a protocol for long-term cryopreservation of B. lanceolatum sperm. Taken together, this work represents an important step toward further establishing amphioxus as a laboratory animal making it more amenable to experimental research, and hence assists the coming of age of this emerging model. PMID:21271675

  1. The cephalochordate amphioxus: a key to reveal the secrets of nuclear receptor evolution.

    Science.gov (United States)

    Lecroisey, Claire; Laudet, Vincent; Schubert, Michael

    2012-03-01

    The members of the nuclear receptor (NR) superfamily are transcription factors characterized by a particular mode of function, which is related to the conserved nature of their molecular structure. NR proteins usually contain a DNA-binding domain (DBD) and a ligand-binding domain (LBD) allowing them to directly bind to DNA and regulate target gene expression in a ligand-dependent manner. In this review, we are summarizing our current understanding of the NR diversity in the cephalochordate amphioxus, which represents the best available proxy for the last common chordate ancestor both in terms of morphology and genome organization. The amphioxus genome encodes 33 NRs, which is more than expected based on its phylogenetic position, with at least one representative of all major NR groups, excepting NR1E and NR1I/J. This elevated number of receptor genes shows that the amphioxus NR complement has experienced some secondary modifications that are most evident in the NR1H group, which is characterized by three members in humans and ten representatives in amphioxus. By highlighting specific examples of the NR repertoire, including the receptors for retinoic acid, thyroid hormone, estrogen and steroids as well as the bile acid and oxysterol receptors of the NR1H group, we are illustrating the functional diversity of these receptors in amphioxus. We conclude that the amphioxus NRs are valuable models for assessing the evolutionary interplay between receptors and their ligands and that more integrative and comparative approaches are required for assessment of the evolutionary plasticity of receptor-ligand interactions revealed by the studies of amphioxus NRs. PMID:22441553

  2. Evolution of Vertebrate Phototransduction: Cascade Activation.

    Science.gov (United States)

    Lamb, Trevor D; Patel, Hardip; Chuah, Aaron; Natoli, Riccardo C; Davies, Wayne I L; Hart, Nathan S; Collin, Shaun P; Hunt, David M

    2016-08-01

    We applied high-throughput sequencing to eye tissue from several species of basal vertebrates (a hagfish, two species of lamprey, and five species of gnathostome fish), and we analyzed the mRNA sequences for the proteins underlying activation of the phototransduction cascade. The molecular phylogenies that we constructed from these sequences are consistent with the 2R WGD model of two rounds of whole genome duplication. Our analysis suggests that agnathans retain an additional representative (that has been lost in gnathostomes) in each of the gene families we studied; the evidence is strong for the G-protein α subunit (GNAT) and the cGMP phosphodiesterase (PDE6), and indicative for the cyclic nucleotide-gated channels (CNGA and CNGB). Two of the species (the hagfish Eptatretus cirrhatus and the lamprey Mordacia mordax) possess only a single class of photoreceptor, simplifying deductions about the composition of cascade protein isoforms utilized in their photoreceptors. For the other lamprey, Geotria australis, analysis of the ratios of transcript levels in downstream and upstream migrant animals permits tentative conclusions to be drawn about the isoforms used in four of the five spectral classes of photoreceptor. Overall, our results suggest that agnathan rod-like photoreceptors utilize the same GNAT1 as gnathostomes, together with a homodimeric PDE6 that may be agnathan-specific, whereas agnathan cone-like photoreceptors utilize a GNAT that may be agnathan-specific, together with the same PDE6C as gnathostomes. These findings help elucidate the evolution of the vertebrate phototransduction cascade from an ancestral chordate phototransduction cascade that existed prior to the vertebrate radiation. PMID:27189541

  3. Zebrafish brd2a and brd2b are paralogous members of the bromodomain-ET (BET family of transcriptional coregulators that show structural and expression divergence

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    Bee Katharine J

    2008-04-01

    Full Text Available Abstract Background Brd2 belongs to the bromodomain-extraterminal domain (BET family of transcriptional co-regulators, and functions as a pivotal histone-directed recruitment scaffold in chromatin modification complexes affecting signal-dependent transcription. Brd2 facilitates expression of genes promoting proliferation and is implicated in apoptosis and in egg maturation and meiotic competence in mammals; it is also a susceptibility gene for juvenile myoclonic epilepsy (JME in humans. The brd2 ortholog in Drosophila is a maternal effect, embryonic lethal gene that regulates several homeotic loci, including Ultrabithorax. Despite its importance, there are few systematic studies of Brd2 developmental expression in any organism. To help elucidate both conserved and novel gene functions, we cloned and characterized expression of brd2 cDNAs in zebrafish, a vertebrate system useful for genetic analysis of development and disease, and for study of the evolution of gene families and functional diversity in chordates. Results We identify cDNAs representing two paralogous brd2 loci in zebrafish, brd2a on chromosome 19 and brd2b on chromosome 16. By sequence similarity, syntenic and phylogenetic analyses, we present evidence for structural divergence of brd2 after gene duplication in fishes. brd2 paralogs show potential for modular domain combinations, and exhibit distinct RNA expression patterns throughout development. RNA in situ hybridizations in oocytes and embryos implicate brd2a and brd2b as maternal effect genes involved in egg polarity and egg to embryo transition, and as zygotic genes important for development of the vertebrate nervous system and for morphogenesis and differentiation of the digestive tract. Patterns of brd2 developmental expression in zebrafish are consistent with its proposed role in Homeobox gene regulation. Conclusion Expression profiles of zebrafish brd2 paralogs support a role in vertebrate developmental patterning and

  4. Circuits regulating pleasure and happiness: the evolution of reward-seeking and misery-fleeing behavioral mechanisms in vertebrates.

    Science.gov (United States)

    Loonen, Anton J M; Ivanova, Svetlana A

    2015-01-01

    The very first free-moving animals in the oceans over 540 million years ago must have been able to obtain food, territory, and shelter, as well as reproduce. Therefore, they would have needed regulatory mechanisms to induce movements enabling achievement of these prerequisites for survival. It can be useful to consider these mechanisms in primitive chordates, which represent our earliest ancestors, to develop hypotheses addressing how these essential parts of human behavior are regulated and relate to more sophisticated behavioral manifestations such as mood. An animal comparable to lampreys was the earliest known vertebrate with a modern forebrain consisting of old and new cortical parts. Lampreys have a separate dorsal pallium, the forerunner of the most recently developed part of the cerebral cortex. In addition, the lamprey extrapyramidal system (EPS), which regulates movement, is modern. However, in lampreys and their putative forerunners, the hagfishes, the striatum, which is the input part of this EPS, probably corresponds to the human centromedial amygdala, which in higher vertebrates is part of a system mediating fear and anxiety. Both animals have well-developed nuclear habenulae, which are involved in several critical behaviors; in lampreys this system regulates the reward system that reinforces appetitive-seeking behavior or the avoidance system that reinforces flight behavior resulting from negative inputs. Lampreys also have a distinct glutamatergic nucleus, the so-called habenula-projection globus pallidus, which receives input from glutamatergic and GABAergic signals and gives output to the lateral habenula. Via this route, this nucleus influences midbrain monoaminergic nuclei and regulates the food acquisition system. These various structures involved in motor regulation in the lampreys may be conserved in humans and include two complementary mechanisms for reward reinforcement and avoidance behaviors. The first system is associated with

  5. Characterization and metal-induced gene transcription of two new copper zinc superoxide dismutases in the solitary ascidian Ciona intestinalis

    International Nuclear Information System (INIS)

    Highlights: •Ciona intestinalis express two copper-zinc superoxide dismutases (Cu,Zn SODs), one extracellular (Ci-SODa) and one intracellular isoform (Ci-SODb). •Promoters contain consensus sequences similar to mammalian MRE. •Metal exposure results in a significant increase of gene transcription: ci-soda is induced especially by copper and zinc, the increase of ci-sodb transcription is more evident after cadmium exposure. •Genes are mostly transcribed in circulating hemocytes and in ovarian follicular cells. -- Abstract: Antioxidant enzymes are known to protect living organisms against the oxidative stress risk, also induced by metals. In the present study, we describe the purification and molecular characterization of two Cu,Zn superoxide dismutases (SODs), referred to as Ci-SODa and Ci-SODb, from Ciona intestinalis, a basal chordate widely distributed in temperate shallow seawater. The putative amino acid sequences were compared with Cu,Zn SODs from other metazoans and phylogenetic analyses indicate that the two putative Ci-SODs are more related to invertebrate SODs than vertebrate ones. Both phylogenetic and preliminary homology modeling analyses suggest that Ci-SODa and Ci-SODb are extracellular and intracellular isoform, respectively. The mRNA of the two Cu,Zn SODs was localized in hemocytes and in ovarian follicular cells, as revealed by in situ hybridization. The time course of SOD mRNA levels in the presence of three different metals showed upregulation of ci-soda and inhibition of ci-sodb. Spectrophotometric analysis confirms the presence of SOD activity in Ciona tissues. Our in silico analyses of the ci-soda promoter region revealed putative consensus sequences similar to mammalian metal-responsive elements (MRE), suggesting that the transcription of these genes directly depends on metals. These data emphasize the importance of complex metal regulation of ci-soda and ci-sodb transcription, as components of an efficient detoxification pathway

  6. Developmental Expression of an Amphioxus (Branchiostoma belcheri) Gene Encoding a GATA Transcription Factor%文昌鱼一个GATA基因在胚胎发育中的表达图式

    Institute of Scientific and Technical Information of China (English)

    张煜; 毛炳宇

    2009-01-01

    GATA factors are evolutionarily conserved and play crucial roles during embryonic development in both vertebrates and invertebrates. Vertebrate GATAs can be divided into two subgroups, the GATA1/2/3 and the GATA4/5/6 classes. Through genomic analysis, we have identified three GATA factors, representing the GATA1/2/3 and GATA4/5/6 subfamilies respectively, and one GATA like protein in the genome of the basal chordate amphioxus (Branchiostoma floridae, cephalochordata). Partial sequence of GATA123 in the amphioxus Branchiostoma belcheri (BbGATA123) was cloned and its expression pattern during early embryonic development was studied. Expression of BbGATA123 is first detected in the mesendoderm during gastrulation. Interestingly, in the late neurula and early larva stages, it is expressed strongly in the cerebral vesicle and the mid gut region. Its expression is compared to Otx, a gene known crucial for the development of anterior structures. Our observations suggest that GATA123, together with Otx, might play an important role in the development of amphioxus cerebral vesicle, the counterpart of the vertebrate brain.%GATA基因在脊椎动物和非脊椎动物的发育中行使重要的功能,该家族的成员在进化上也足非常保守的.脊椎动物的GATA基因分为两个亚群:GATA1/2/3和GATA4/5/6.通过生物信息分析,在文吕鱼的基因缓中找到了3个GATA基因:一个GATA1/2/3业家族基因,两个GATA4/5/6亚家族基因:还找到一个类GATA基因.还克隆了白氏文昌鱼(Branchiostoma belcheri)GATA123的一段序列,并研究了它在早期胚胎发育中的表达图式.结果表明GATA123在原肠胚的中内胚层表达,而在神经胚晚期和幼体早期,GATA123在脑泡和消化道中部区域表达.这种表达模式与头部发育的重要基因Otx相类似.结果提示在文吕鱼脑泡的发育过程中GATA123和Otx很可能共同发挥着重要的作用.

  7. 日本血吸虫反式剪接前导RNA的鉴定%Identification and Characterization of an mRNA Trans-splicing Leader in Schistosoma Japonicum

    Institute of Scientific and Technical Information of China (English)

    李锐; 贺亮; 郝力力

    2012-01-01

    RNA trans-splicing occurs in a wide range of eukaryotes, from protozoa to chordates. To investigate the SL RNA-mediated trans-splicing in the zoonotic trematode Schistosoma japonicum, a spliced-leader (SL) RNA was cloned in adults using race. The 36-nucleotide SL in S. Japonicum was derived from a 90-nucleotide nonpolyadenylylated RNA transcript encoded by 55 copies of SL genes dispersed in the genome confirmed by blot and real time PCR. Differential transcription patterns of the SL gene in the parasite developmental stages were observed using real time PCR. Predominant expression of SL RNA was found in the two developmental stages, egg and cercariae. Expression of SL RNA transcripts in female was the least. No significant expression difference between male and schistosomulum (3 d and 14 d) was observed. In summary, trans-splicing of spliced leader might acted as an important mechanism of post-transcriptional gene regulation in S. Japonicum.%RNA反式剪接现象广泛存在于真核生物中,包括单细胞原虫以及低等脊索动物.为鉴定日本血吸虫中是否存在SL RNA介导的反式剪接,运用Race方法从成虫中克隆出了1个90 nt的SL RNA基因,36 nt的RNA前导序列正是来源于此90 nt的无PolyA结构的SL RNA,并通过Northern进一步证实了该基因的存在.同时采用荧光定量和Southern对其拷贝数、基因组上的分布方式以及虫体不同阶段的表达量进行了鉴定,发现SL RNA具有55个拷贝并在基因组上呈散在分布;在虫卵和尾蚴时期SL RNA基因的转录丰度最高,雌虫阶段最低,雄虫、3天童虫以及14天童虫阶段无明显差别.结果表明,SL RNA介导的反式剪接可能是日本血吸虫基因转录后重要的调控机制之一.

  8. Distribution, abundance and trail characteristics of acorn worms at Australian continental margins

    Science.gov (United States)

    Anderson, T. J.; Przeslawski, R.; Tran, M.

    2011-04-01

    Acorn worms (Enteropneusta), which were previously thought to be a missing link in understanding the evolution of chordates, are an unusual and potentially important component of many deep-sea benthic environments, particularly for nutrient cycling. Very little is known about their distribution, abundance, or behaviour in deep-sea environments around the world, and almost nothing is known about their distribution within Australian waters. In this study, we take advantage of two large-scale deep-sea mapping surveys along the eastern (northern Lord Howe Rise) and western continental margins of Australia to quantify the distribution, abundance and trail-forming behaviour of this highly unusual taxon. This is the first study to quantify the abundance and trail behaviour of acorn worms within Australian waters and provides the first evidence of strong depth-related distributions. Acorn worm densities and trail activity were concentrated between transect-averaged depths of 1600 and 3000 m in both eastern and western continental margins. The shallow limit of their depth distribution was 1600 m. The deeper limit was less well-defined, as individuals were found in small numbers below 3000 down to 4225 m. This distributional pattern may reflect a preference for these depths, possibly due to higher availability of nutrients, rather than a physiological constraint to greater depths. Sediment characteristics alone were poor predictors of acorn worm densities and trail activity. High densities of acorn worms and trails were associated with sandy-mud sediments, but similar sediment characteristics in either shallower or deeper areas did not support similar densities of acorn worms or trails. Trail shapes varied between eastern and western margins, with proportionally more meandering trails recorded in the east, while spiral and meandering trails were both common in the west. Trail shape varied by depth, with spiral-shaped trails dominant in areas of high acorn worm densities

  9. The evolutionary history of mitochondrial porins

    Directory of Open Access Journals (Sweden)

    Hausner Georg

    2007-02-01

    Full Text Available Abstract Background Mitochondrial porins, or voltage-dependent anion-selective channels (VDAC allow the passage of small molecules across the mitochondrial outer membrane, and are involved in complex interactions regulating organellar and cellular metabolism. Numerous organisms possess multiple porin isoforms, and initial studies indicated an intriguing evolutionary history for these proteins and the genes that encode them. Results In this work, the wealth of recent sequence information was used to perform a comprehensive analysis of the evolutionary history of mitochondrial porins. Fungal porin sequences were well represented, and newly-released sequences from stramenopiles, alveolates, and seed and flowering plants were analyzed. A combination of Neighbour-Joining and Bayesian methods was used to determine phylogenetic relationships among the proteins. The aligned sequences were also used to reassess the validity of previously described eukaryotic porin motifs and to search for signature sequences characteristic of VDACs from plants, animals and fungi. Secondary structure predictions were performed on the aligned VDAC primary sequences and were used to evaluate the sites of intron insertion in a representative set of the corresponding VDAC genes. Conclusion Our phylogenetic analysis clearly shows that paralogs have appeared several times during the evolution of VDACs from the plants, metazoans, and even the fungi, suggesting that there are no "ancient" paralogs within the gene family. Sequence motifs characteristic of the members of the crown groups of organisms were identified. Secondary structure predictions suggest a common 16 β-strand framework for the transmembrane arrangement of all porin isoforms. The GLK (and homologous or analogous motifs and the eukaryotic porin motifs in the four representative Chordates tend to be in exons that appear to have changed little during the evolution of these metazoans. In fact there is phase

  10. FEZ2 has acquired additional protein interaction partners relative to FEZ1: functional and evolutionary implications.

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    Marcos R Alborghetti

    Full Text Available BACKGROUND: The FEZ (fasciculation and elongation protein zeta family designation was purposed by Bloom and Horvitz by genetic analysis of C. elegans unc-76. Similar human sequences were identified in the expressed sequence tag database as FEZ1 and FEZ2. The unc-76 function is necessary for normal axon fasciculation and is required for axon-axon interactions. Indeed, the loss of UNC-76 function results in defects in axonal transport. The human FEZ1 protein has been shown to rescue defects caused by unc-76 mutations in nematodes, indicating that both UNC-76 and FEZ1 are evolutionarily conserved in their function. Until today, little is known about FEZ2 protein function. METHODOLOGY/PRINCIPAL FINDINGS: Using the yeast two-hybrid system we demonstrate here conserved evolutionary features among orthologs and non-conserved features between paralogs of the FEZ family of proteins, by comparing the interactome profiles of the C-terminals of human FEZ1, FEZ2 and UNC-76 from C. elegans. Furthermore, we correlate our data with an analysis of the molecular evolution of the FEZ protein family in the animal kingdom. CONCLUSIONS/SIGNIFICANCE: We found that FEZ2 interacted with 59 proteins and that of these only 40 interacted with FEZ1. Of the 40 FEZ1 interacting proteins, 36 (90%, also interacted with UNC-76 and none of the 19 FEZ2 specific proteins interacted with FEZ1 or UNC-76. This together with the duplication of unc-76 gene in the ancestral line of chordates suggests that FEZ2 is in the process of acquiring new additional functions. The results provide also an explanation for the dramatic difference between C. elegans and D. melanogaster unc-76 mutants on one hand, which cause serious defects in the nervous system, and the mouse FEZ1 -/- knockout mice on the other, which show no morphological and no strong behavioural phenotype. Likely, the ubiquitously expressed FEZ2 can completely compensate the lack of neuronal FEZ1, since it can interact with all FEZ

  11. The evolution of core proteins involved in microRNA biogenesis

    Directory of Open Access Journals (Sweden)

    Brown James R

    2008-03-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are a recently discovered class of non-coding RNAs (ncRNAs which play important roles in eukaryotic gene regulation. miRNA biogenesis and activation is a complex process involving multiple protein catalysts and involves the large macromolecular RNAi Silencing Complex or RISC. While phylogenetic analyses of miRNA genes have been previously published, the evolution of miRNA biogenesis itself has been little studied. In order to better understand the origin of miRNA processing in animals and plants, we determined the phyletic occurrences and evolutionary relationships of four major miRNA pathway protein components; Dicer, Argonaute, RISC RNA-binding proteins, and Exportin-5. Results Phylogenetic analyses show that all four miRNA pathway proteins were derived from large multiple protein families. As an example, vertebrate and invertebrate Argonaute (Ago proteins diverged from a larger family of PIWI/Argonaute proteins found throughout eukaryotes. Further gene duplications among vertebrates after the evolution of chordates from urochordates but prior to the emergence of fishes lead to the evolution of four Ago paralogues. Invertebrate RISC RNA-binding proteins R2D2 and Loquacious are related to other RNA-binding protein families such as Staufens as well as vertebrate-specific TAR (HIV trans-activator RNA RNA-binding protein (TRBP and protein kinase R-activating protein (PACT. Export of small RNAs from the nucleus, including miRNA, is facilitated by three closely related karyopherin-related nuclear transporters, Exportin-5, Exportin-1 and Exportin-T. While all three exportins have direct orthologues in deutrostomes, missing exportins in arthropods (Exportin-T and nematodes (Exportin-5 are likely compensated by dual specificities of one of the other exportin paralogues. Conclusion Co-opting particular isoforms from large, diverse protein families seems to be a common theme in the evolution of miRNA biogenesis

  12. Unravelling the Evolution of the Allatostatin-Type A, KISS and Galanin Peptide-Receptor Gene Families in Bilaterians: Insights from Anopheles Mosquitoes.

    Directory of Open Access Journals (Sweden)

    Rute C Felix

    synteny revealed that AST-AR and KISSR emerged after GALR gene divergence. AST-AR genes were present in the hemichordates but were lost from the chordates. In protostomes, AST-ARs persisted and evolved through lineage-specific events and duplicated in the arthropod radiation. Diptera acquired and maintained functionally divergent duplicate AST-AR genes.

  13. The molecular evolution of the p120-catenin subfamily and its functional associations.

    Directory of Open Access Journals (Sweden)

    Robert H Carnahan

    Full Text Available BACKGROUND: p120-catenin (p120 is the prototypical member of a subclass of armadillo-related proteins that includes δ-catenin/NPRAP, ARVCF, p0071, and the more distantly related plakophilins 1-3. In vertebrates, p120 is essential in regulating surface expression and stability of all classical cadherins, and directly interacts with Kaiso, a BTB/ZF family transcription factor. METHODOLOGY/PRINCIPAL FINDINGS: To clarify functional relationships between these proteins and how they relate to the classical cadherins, we have examined the proteomes of 14 diverse vertebrate and metazoan species. The data reveal a single ancient δ-catenin-like p120 family member present in the earliest metazoans and conserved throughout metazoan evolution. This single p120 family protein is present in all protostomes, and in certain early-branching chordate lineages. Phylogenetic analyses suggest that gene duplication and functional diversification into "p120-like" and "δ-catenin-like" proteins occurred in the urochordate-vertebrate ancestor. Additional gene duplications during early vertebrate evolution gave rise to the seven vertebrate p120 family members. Kaiso family members (i.e., Kaiso, ZBTB38 and ZBTB4 are found only in vertebrates, their origin following that of the p120-like gene lineage and coinciding with the evolution of vertebrate-specific mechanisms of epigenetic gene regulation by CpG island methylation. CONCLUSIONS/SIGNIFICANCE: The p120 protein family evolved from a common δ-catenin-like ancestor present in all metazoans. Through several rounds of gene duplication and diversification, however, p120 evolved in vertebrates into an essential, ubiquitously expressed protein, whereas loss of the more selectively expressed δ-catenin, p0071 and ARVCF are tolerated in most species. Together with phylogenetic studies of the vertebrate cadherins, our data suggest that the p120-like and δ-catenin-like genes co-evolved separately with non-neural (E- and P

  14. An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

    Directory of Open Access Journals (Sweden)

    Shenkar Noa

    2009-08-01

    suggest a sister-group relationship between Salpida and Pyrosomatida within Thaliacea. Conclusion An updated phylogenetic framework for tunicates is provided based on phylogenetic analyses using the most realistic evolutionary models currently available for ribosomal molecules and an unprecedented taxonomic sampling. Detailed analyses of the 18S rRNA gene allowed a clear definition of the major tunicate groups and revealed contrasting evolutionary dynamics among major lineages. The resolving power of this gene nevertheless appears limited within the clades composed of Phlebobranchia + Thaliacea + Aplousobranchia and Pyuridae + Styelidae, which were delineated as spots of low resolution. These limitations underline the need to develop new nuclear markers in order to further resolve the phylogeny of this keystone group in chordate evolution.

  15. Circuits regulating pleasure and happiness:the evolution of reward-seeking and misery-fleeing behavioral mechanisms in vertebrates

    Directory of Open Access Journals (Sweden)

    Anton J.M. Loonen

    2015-10-01

    Full Text Available The very first free-moving animals in the oceans over 540 million years ago must have been able to obtain food, territory and shelter, as well as reproduce. Therefore, they would have needed regulatory mechanisms to induce movements enabling achievement of these prerequisites for survival. It can be useful to consider these mechanisms in primitive chordates, which represent our earliest ancestors, to develop hypotheses addressing how these essential parts of human behavior are regulated and relate to more sophisticated behavioral manifestations such as mood. An animal comparable to lampreys was the earliest known vertebrate with a modern forebrain consisting of old and new cortical parts. Lampreys have a separate dorsal pallium, the forerunner of the most recently developed part of the cerebral cortex. In addition, the lamprey extrapyramidal system, which regulates movement, is modern. However, in lampreys and their putative forerunners, the hagfishes, the striatum, which is the input part of this extrapyramidal system, probably corresponds to the human centromedial amygdala, which in higher vertebrates is part of a system mediating fear and anxiety. Both animals have well-developed nuclear habenulae, which are involved in several critical behaviors; in lampreys this system regulates the reward system that reinforces appetitive-seeking behavior or the avoidance system that reinforces flight behavior resulting from negative inputs. Lampreys also have a distinct glutamatergic nucleus, the so-called habenula-projection globus pallidus, which receives input from glutamatergic and GABAergic signals and gives output to the lateral habenula. Via this route, this nucleus influences midbrain monoaminergic nuclei and regulates the food acquisition system. These various structures involved in motor regulation in the lampreys may be conserved in humans and include two complementary mechanisms for reward reinforcement and avoidance behaviors. The first

  16. Circuits regulating pleasure and happiness: the evolution of reward-seeking and misery-fleeing behavioral mechanisms in vertebrates.

    Science.gov (United States)

    Loonen, Anton J M; Ivanova, Svetlana A

    2015-01-01

    The very first free-moving animals in the oceans over 540 million years ago must have been able to obtain food, territory, and shelter, as well as reproduce. Therefore, they would have needed regulatory mechanisms to induce movements enabling achievement of these prerequisites for survival. It can be useful to consider these mechanisms in primitive chordates, which represent our earliest ancestors, to develop hypotheses addressing how these essential parts of human behavior are regulated and relate to more sophisticated behavioral manifestations such as mood. An animal comparable to lampreys was the earliest known vertebrate with a modern forebrain consisting of old and new cortical parts. Lampreys have a separate dorsal pallium, the forerunner of the most recently developed part of the cerebral cortex. In addition, the lamprey extrapyramidal system (EPS), which regulates movement, is modern. However, in lampreys and their putative forerunners, the hagfishes, the striatum, which is the input part of this EPS, probably corresponds to the human centromedial amygdala, which in higher vertebrates is part of a system mediating fear and anxiety. Both animals have well-developed nuclear habenulae, which are involved in several critical behaviors; in lampreys this system regulates the reward system that reinforces appetitive-seeking behavior or the avoidance system that reinforces flight behavior resulting from negative inputs. Lampreys also have a distinct glutamatergic nucleus, the so-called habenula-projection globus pallidus, which receives input from glutamatergic and GABAergic signals and gives output to the lateral habenula. Via this route, this nucleus influences midbrain monoaminergic nuclei and regulates the food acquisition system. These various structures involved in motor regulation in the lampreys may be conserved in humans and include two complementary mechanisms for reward reinforcement and avoidance behaviors. The first system is associated with

  17. Functional evolution of the vitamin D and pregnane X receptors

    Directory of Open Access Journals (Sweden)

    Ou Junhai

    2007-11-01

    Full Text Available Abstract Background The vitamin D receptor (VDR and pregnane X receptor (PXR are nuclear hormone receptors of the NR1I subfamily that show contrasting patterns of cross-species variation. VDR and PXR are thought to have arisen from duplication of an ancestral gene, evident now as a single gene in the genome of the chordate invertebrate Ciona intestinalis (sea squirt. VDR genes have been detected in a wide range of vertebrates including jawless fish. To date, PXR genes have not been found in cartilaginous fish. In this study, the ligand selectivities of VDRs were compared in detail across a range of vertebrate species and compared with those of the Ciona VDR/PXR. In addition, several assays were used to search for evidence of PXR-mediated hepatic effects in three model non-mammalian species: sea lamprey (Petromyzon marinus, zebrafish (Danio rerio, and African clawed frog (Xenopus laevis. Results Human, mouse, frog, zebrafish, and lamprey VDRs were found to have similar ligand selectivities for vitamin D derivatives. In contrast, using cultured primary hepatocytes, only zebrafish showed evidence of PXR-mediated induction of enzyme expression, with increases in testosterone 6β-hydroxylation activity (a measure of cytochrome P450 3A activity in other species and flurbiprofen 4-hydroxylation activity (measure of cytochrome P450 2C activity following exposure to known PXR activators. A separate assay in vivo using zebrafish demonstrated increased hepatic transcription of another PXR target, multidrug resistance gene (ABCB5, following injection of the major zebrafish bile salt, 5α-cyprinol 27-sulfate. The PXR target function, testosterone hydroxylation, was detected in frog and sea lamprey primary hepatocytes, but was not inducible in these two species by a wide range of PXR activators in other animals. Analysis of the sea lamprey draft genome also did not show evidence of a PXR gene. Conclusion Our results show tight conservation of ligand

  18. Metal dealing at the origin of the Chordata phylum: the metallothionein system and metal overload response in amphioxus.

    Directory of Open Access Journals (Sweden)

    Maria Guirola

    Full Text Available Non-vertebrate chordates, specifically amphioxus, are considered of the utmost interest for gaining insight into the evolutionary trends, i.e. differentiation and specialization, of gene/protein systems. In this work, MTs (metallothioneins, the most important metal binding proteins, are characterized for the first time in the cephalochordate subphylum at both gene and protein level, together with the main features defining the amphioxus response to cadmium and copper overload. Two MT genes (BfMT1 and BfMT2 have been identified in a contiguous region of the genome, as well as several ARE (antioxidant response element and MRE (metal response element located upstream the transcribed region. Their corresponding cDNAs exhibit identical sequence in the two lancelet species (B. floridae and B. lanceolatum, BfMT2 cDNA resulting from an alternative splicing event. BfMT1 is a polyvalent metal binding peptide that coordinates any of the studied metal ions (Zn, Cd or Cu rendering complexes stable enough to last in physiological environments, which is fully concordant with the constitutive expression of its gene, and therefore, with a metal homeostasis housekeeping role. On the contrary, BfMT2 exhibits a clear ability to coordinate Cd(II ions, while it is absolutely unable to fold into stable Cu (I complexes, even as mixed species. This identifies it as an essential detoxification agent, which is consequently only induced in emergency situations. The cephalochordate MTs are not directly related to vertebrate MTs, neither by gene structure, protein similarity nor metal-binding behavior of the encoded peptides. The closest relative is the echinoderm MT, which confirm proposed phylogenetic relationships between these two groups. The current findings support the existence in most organisms of two types of MTs as for their metal binding preferences, devoted to different biological functions: multivalent MTs for housekeeping roles, and specialized MTs that evolve

  19. Gonadotrophin-releasing hormone in winter flounder (Pseudopleuronectes americanus): molecular characterization, distribution and effects of fasting.

    Science.gov (United States)

    Tuziak, Sarah M; Volkoff, Hélène

    2013-04-01

    Gonadotrophin-releasing hormone (GnRH) is primarily related to reproductive processes in vertebrates. However other physiological roles, including functions in food intake regulation and energy status, have been demonstrated for GnRH in animals. The ten amino acid active peptide is relatively conserved throughout chordates, more specifically in fish species. Teleosts generally have at least two variants of GnRH present in their genomes. GnRH2 (commonly termed chicken-GnRH) is common to all fish, whereas other prevalent forms include GnRH1 and/or GnRH3 (also known as salmon-GnRH). The mRNAs of all three forms were identified in winter flounder (Pseudopleuronectes americanus). Winter flounder GnRH1 appears to be ubiquitously and strongly expressed throughout the brain. GnRH2 mRNA is highly expressed in the optic tectum/thalamus. Finally, GnRH3 mRNA is expressed throughout the brain, but not in the pituitary, with apparent highest expression in the telencephalon/preoptic area. Flounder GnRH1 mRNA is found in most peripheral tissues examined, including the foregut, midgut and gonads. GnRH2 mRNA appears to be expressed throughout the periphery, with apparent highest transcript expression in male gonads. Finally, winter flounder GnRH3 transcript is found at low levels in the skin, heart, and gonads. The effect of fasting on the expression of each of the three isoforms was assessed. Fasting reduces GnRH2 and GnRH3 mRNA expression in the optic tectum/thalamus and hypothalamus, and telencephalon/preoptic area, respectively, compared with fed fish. GnRH1 mRNA expression does not appear to be altered by feeding status. GnRH mRNAs do not seem to regulate food intake peripherally through the gut based on our preliminary findings. Our preliminary results suggest that the GnRH system could play a central role in food intake regulation of winter flounder. PMID:23298570

  20. Characterization of the neurohypophysial hormone gene loci in elephant shark and the Japanese lamprey: origin of the vertebrate neurohypophysial hormone genes

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    Brenner Sydney

    2009-02-01

    Full Text Available Abstract Background Vasopressin and oxytocin are mammalian neurohypophysial hormones with distinct functions. Vasopressin is involved mainly in osmoregulation and oxytocin is involved primarily in parturition and lactation. Jawed vertebrates contain at least one homolog each of vasopressin and oxytocin, whereas only a vasopressin-family hormone, vasotocin, has been identified in jawless vertebrates. The genes encoding vasopressin and oxytocin are closely linked tail-to-tail in eutherian mammals whereas their homologs in chicken, Xenopus and coelacanth (vasotocin and mesotocin are linked tail-to-head. In contrast, their pufferfish homologs, vasotocin and isotocin, are located on the same strand of DNA with isotocin located upstream of vasotocin and separated by five genes. These differences in the arrangement of the two genes in different bony vertebrate lineages raise questions about their origin and ancestral arrangement. To trace the origin of these genes, we have sequenced BAC clones from the neurohypophysial gene loci in a cartilaginous fish, the elephant shark (Callorhinchus milii, and in a jawless vertebrate, the Japanese lamprey (Lethenteron japonicum. We have also analyzed the neurohypophysial hormone gene locus in an invertebrate chordate, the amphioxus (Branchiostoma floridae. Results The elephant shark neurohypophysial hormone genes encode vasotocin and oxytocin, and are linked tail-to-head like their homologs in coelacanth and non-eutherian tetrapods. Besides the hypothalamus, the two genes are also expressed in the ovary. In addition, the vasotocin gene is expressed in the kidney, rectal gland and intestine. These expression profiles indicate a paracrine role for the two hormones. The lamprey locus contains a single neurohypophysial hormone gene, the vasotocin. The synteny of genes in the lamprey locus is conserved in elephant shark, coelacanth and tetrapods but disrupted in teleost fishes. The amphioxus locus encodes a single

  1. Regulation and functions of the lms homeobox gene during development of embryonic lateral transverse muscles and direct flight muscles in Drosophila.

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    Dominik Müller

    Full Text Available BACKGROUND: Patterning and differentiation of developing musculatures require elaborate networks of transcriptional regulation. In Drosophila, significant progress has been made into identifying the regulators of muscle development and defining their interactive networks. One major family of transcription factors involved in these processes consists of homeodomain proteins. In flies, several members of this family serve as muscle identity genes to specify the fates of individual muscles, or groups thereof, during embryonic and/or adult muscle development. Herein, we report on the expression and function of a new Drosophila homeobox gene during both embryonic and adult muscle development. METHODOLOGY/PRINCIPAL FINDINGS: The newly described homeobox gene, termed lateral muscles scarcer (lms, which has yet uncharacterized orthologs in other invertebrates and primitive chordates but not in vertebrates, is expressed exclusively in subsets of developing muscle tissues. In embryos, lms is expressed specifically in the four lateral transverse (LT muscles and their founder cells in each hemisegment, whereas in larval wing imaginal discs, it is expressed in myoblasts that develop into direct flight muscles (DFMs, which are important for proper wing positioning. We have analyzed the regulatory inputs of various other muscle identity genes with overlapping or complementary expression patterns towards the cell type specific regulation of lms expression. Further we demonstrate that lms null mutants exhibit reduced numbers of embryonic LT muscles, and null mutant adults feature held-out-wing phenotypes. We provide a detailed description of the pattern and morphology of the direct flight muscles in the wild type and lms mutant flies by using the recently-developed ultramicroscopy and show that, in the mutants, all DFMs are present and present normal morphologies. CONCLUSIONS/SIGNIFICANCE: We have identified the homeobox gene lms as a new muscle identity gene

  2. Bioinformatic analysis of the neprilysin (M13 family of peptidases reveals complex evolutionary and functional relationships

    Directory of Open Access Journals (Sweden)

    Pinney John W

    2008-01-01

    Full Text Available Abstract Background The neprilysin (M13 family of endopeptidases are zinc-metalloenzymes, the majority of which are type II integral membrane proteins. The best characterised of this family is neprilysin, which has important roles in inactivating signalling peptides involved in modulating neuronal activity, blood pressure and the immune system. Other family members include the endothelin converting enzymes (ECE-1 and ECE-2, which are responsible for the final step in the synthesis of potent vasoconstrictor endothelins. The ECEs, as well as neprilysin, are considered valuable therapeutic targets for treating cardiovascular disease. Other members of the M13 family have not been functionally characterised, but are also likely to have biological roles regulating peptide signalling. The recent sequencing of animal genomes has greatly increased the number of M13 family members in protein databases, information which can be used to reveal evolutionary relationships and to gain insight into conserved biological roles. Results The phylogenetic analysis successfully resolved vertebrate M13 peptidases into seven classes, one of which appears to be specific to mammals, and insect genes into five functional classes and a series of expansions, which may include inactive peptidases. Nematode genes primarily resolved into groups containing no other taxa, bar the two nematode genes associated with Drosophila DmeNEP1 and DmeNEP4. This analysis reconstructed only one relationship between chordate and invertebrate clusters, that of the ECE sub-group and the DmeNEP3 related genes. Analysis of amino acid utilisation in the active site of M13 peptidases reveals a basis for their biochemical properties. A relatively invariant S1' subsite gives the majority of M13 peptidases their strong preference for hydrophobic residues in P1' position. The greater variation in the S2' subsite may be instrumental in determining the specificity of M13 peptidases for their substrates

  3. Body Size Preference of Marine Animals in Relation to Extinction Selectivity

    Science.gov (United States)

    Sriram, A.; Idgunji, S.; Heim, N. A.; Payne, J.

    2014-12-01

    Our project encompasses an extremely specific aspect in relation to the five mass extinctions in geologic history. We asked ourselves whether larger or smaller body sizes would be better suited for surviving a mass extinction. To conduct research for our project, we used the body sizes of 17,172 marine animal genera as our primary data. These animals include echinoderms, arthropods, chordates, mollusks, and brachiopods. These creatures are perfect model organisms in terms of finding data on them because they have an excellent fossil record, and are well documented. We focused on the mean body size of these animals before and after each of the five mass extinctions (end-Ordovician, Late Devonian, end-Permian, end-Triassic, and end-Cretaceous). Our hypothesis was that the average biovolume of animals increased after each of the extinctions, with the mean size being greater after than it was before. Our size data is from the Ellis & Messina Catalogue of Ostracoda and the Treatise on Invertebrate Paleontology. We obtained stratigraphic range data The Treatise and Sepkoski (2002). In our analyses, we compared the mean size of the different animal genera before and after each extinction event. We further partitioned size change across mass extinction boundaries into three categories: the surviving genera, the extinct genera, and the newly originating genera that came about after the extinction. According to our analyses, the mean sizes did not change significantly from the genera living during the stages before the extinctions and after the extinctions. From our results, we can assume that there were not enough major increases in the overall volume of the organisms to warrant a definite conclusion that extinctions lead to larger body sizes. Further support for our findings came from the T-tests in our R code. Only the Cretaceous period showed true evidence for size changing because of the extinction; in this case, the mean size decreased. T-tests for the Cretaceous

  4. Matrotrophy and placentation in invertebrates: a new paradigm.

    Science.gov (United States)

    Ostrovsky, Andrew N; Lidgard, Scott; Gordon, Dennis P; Schwaha, Thomas; Genikhovich, Grigory; Ereskovsky, Alexander V

    2016-08-01

    histophagy are rarer, plausibly evolving through heterochronous development of the embryonic mouthparts and digestive system. During gestation, matrotrophic modes can shift, intergrade, and be performed simultaneously. Invertebrate matrotrophic adaptations are less complex structurally than in chordates, but they are more diverse, being formed either by a parent, embryo, or both. In a broad and still preliminary sense, there are indications of trends or grades of evolutionarily increasing complexity of nutritive structures: formation of (i) local zones of enhanced nutritional transport (placental analogues), including specialized parent-offspring cell complexes and various appendages increasing the entire secreting and absorbing surfaces as well as the contact surface between embryo and parent, (ii) compartmentalization of the common incubatory space into more compact and 'isolated' chambers with presumably more effective nutritional relationships, and (iii) internal secretory ('milk') glands. Some placental analogues in onychophorans and arthropods mimic the simplest placental variants in vertebrates, comprising striking examples of convergent evolution acting at all levels-positional, structural and physiological. PMID:25925633

  5. Thyroid hormone and retinoid X receptor function and expression during sea lamprey (Petromyzon marinus) metamorphosis.

    Science.gov (United States)

    Manzon, Lori A; Youson, John H; Holzer, Guillaume; Staiano, Leopoldo; Laudet, Vincent; Manzon, Richard G

    2014-08-01

    Sea lampreys (Petromyzon marinus) are members of the ancient class Agnatha and undergo a metamorphosis that transforms blind, sedentary, filter-feeding larvae into free-swimming, parasitic juveniles. Thyroid hormones (THs) appear to be important for lamprey metamorphosis, however, serum TH concentrations are elevated in the larval phase, decline rapidly during early metamorphosis and remain low until metamorphosis is complete; these TH fluctuations are contrary to those of other metamorphosing vertebrates. Moreover, thyroid hormone synthesis inhibitors (goitrogens) induce precocious metamorphosis and exogenous TH treatments disrupt natural metamorphosis in P. marinus. Given that THs exert their effects by binding to TH nuclear receptors (TRs) that often act as heterodimers with retinoid X receptors (RXRs), we cloned and characterized these receptors from P. marinus and examined their expression during metamorphosis. Two TRs (PmTR1 and PmTR2) and three RXRs (PmRXRs) were isolated from P. marinus cDNA. Phylogenetic analyses group the PmTRs together on a branch prior to the gnathostome TRα/β split. The three RXRs also group together, but our data indicated that these transcripts are most likely either allelic variants of the same gene locus, or the products of a lamprey-specific duplication event. Importantly, these P. marinus receptors more closely resemble vertebrate as opposed to invertebrate chordate receptors. Functional analysis revealed that PmTR1 and PmTR2 can activate transcription of TH-responsive genes when treated with nanomolar concentrations of TH and they have distinct pharmacological profiles reminiscent of vertebrate TRβ and TRα, respectively. Also similar to other metamorphosing vertebrates, expression patterns of the PmTRs during lamprey metamorphosis suggest that PmTR1 has a dynamic, tissue-specific expression pattern that correlates with tissue morphogenesis and biochemical changes and PmTR2 has a more uniform expression pattern. This TR

  6. 文昌鱼SMYD家族基因的系统进化分析%Phylogenetic Analysis of the Amphioxus SMYD Gene Family

    Institute of Scientific and Technical Information of China (English)

    郭泉阳; 李红岩

    2015-01-01

    SMYD( SET and MYND domain containing,SMYD)是一类含有SET功能域的蛋白,在染色体的调节、基因的表达、细胞生长周期的控制、细胞的分裂、分化及发育等方面具有重要作用。目前已知在果蝇、脊椎动物中均含有Smyd基因,且这些基因的进化、表达及功能均有很多研究,但关于脊索动物SMYD家族基因的研究则很少。本文对头索动物文昌鱼的基因组进行搜索,发现文昌鱼有6个可能的Smyd基因。对Smyd基因在染色体上的位置分析结果显示:文昌鱼Smyd相关基因同其他已经研究过的物种如爪蟾、小鼠、人等一样,均是散在分布于不同的染色体上。对这些基因的功能域的分析结果显示:文昌鱼的3个Smyd基因,斑马鱼的2个Smyd基因和人的4个Smyd基因除了含有SET功能域之外,还有另外一个SCOP功能域。基因结构的分析表明:脊椎动物的基因结构比较保守,但无脊椎动物及脊索动物的基因结构则保守性较差。而系统进化分析的结果则显示,文昌鱼Smyd相关的6个基因中只有两个与其他物种同源性较高,其余四个则相对较低。本文旨在对文昌鱼SMYD家族基因进行初步的系统进化分析,但脊索动物文昌鱼的Smyd基因在体内到底执行什么样的功能,其功能又是如何实现的,都有待于进一步研究。%SMYD( SET and MYND domain containing,SMYD) are a class of proteins containing the SET func-tional domains. They play an important role in the regulation of chromosomal gene expression,cell cycle con-trol, cell division, differentiation and development. It is known that drosophila and vertebrates contain Smyd genes and scholars have done much research on the expression, function and evolution of these genes. Howev-er, research on the chordate SMYD family genes is limited. This article searched the cephalochordate amphioxus genome and found that amphioxus had six possible Smyd genes. Analysis of the functional

  7. 文昌鱼SMYD家族基因的系统进化分析%Phylogenetic Analysis of the Amphioxus SMYD Gene Family

    Institute of Scientific and Technical Information of China (English)

    郭泉阳; 李红岩

    2015-01-01

    SMYD( SET and MYND domain containing,SMYD) are a class of proteins containing the SET func-tional domains. They play an important role in the regulation of chromosomal gene expression,cell cycle con-trol, cell division, differentiation and development. It is known that drosophila and vertebrates contain Smyd genes and scholars have done much research on the expression, function and evolution of these genes. Howev-er, research on the chordate SMYD family genes is limited. This article searched the cephalochordate amphioxus genome and found that amphioxus had six possible Smyd genes. Analysis of the functional domains of these Smyd genes showed that:amphioxus-related genes and those of other studied species,such as drosophi-la,xenopus,mouse,human are alike,all in different chromosomes. Analysis of gene structures shows that 3 Smyd genes of the amphioxus,2 of zebrafish and 4 of human have a SCOP functional domain in addition to the SET functional domains. Analysis of gene structure show that the genetic structure of vertebrates is conserva-tive,but invertebrates and chordata are less conservative. The results of phylogenetic analysis show that only two of the six amphioxus Smyd genes are high homologous with other species and the other four are relatively low. This paper aims to conduct a preliminary phylogenetic analysis of amphioxus SMYD family. What roles the Smyd genes in chordate amphioxus perform,and how they realize their functions still need further studies.%SMYD( SET and MYND domain containing,SMYD)是一类含有SET功能域的蛋白,在染色体的调节、基因的表达、细胞生长周期的控制、细胞的分裂、分化及发育等方面具有重要作用。目前已知在果蝇、脊椎动物中均含有Smyd基因,且这些基因的进化、表达及功能均有很多研究,但关于脊索动物SMYD家族基因的研究则很少。本文对头索动物文昌鱼的基因组进行搜索,发现文昌鱼有6个可能的Smyd基因。对Smyd基因在

  8. Evolution of Innate Immunity: Clues from Invertebrates via Fish to Mammals

    Science.gov (United States)

    Buchmann, Kurt

    2014-01-01

    Host responses against invading pathogens are basic physiological reactions of all living organisms. Since the appearance of the first eukaryotic cells, a series of defense mechanisms have evolved in order to secure cellular integrity, homeostasis, and survival of the host. Invertebrates, ranging from protozoans to metazoans, possess cellular receptors, which bind to foreign elements and differentiate self from non-self. This ability is in multicellular animals associated with presence of phagocytes, bearing different names (amebocytes, hemocytes, coelomocytes) in various groups including animal sponges, worms, cnidarians, mollusks, crustaceans, chelicerates, insects, and echinoderms (sea stars and urchins). Basically, these cells have a macrophage-like appearance and function and the repair and/or fight functions associated with these cells are prominent even at the earliest evolutionary stage. The cells possess pathogen recognition receptors recognizing pathogen-associated molecular patterns, which are well-conserved molecular structures expressed by various pathogens (virus, bacteria, fungi, protozoans, helminths). Scavenger receptors, Toll-like receptors, and Nod-like receptors (NLRs) are prominent representatives within this group of host receptors. Following receptor–ligand binding, signal transduction initiates a complex cascade of cellular reactions, which lead to production of one or more of a wide array of effector molecules. Cytokines take part in this orchestration of responses even in lower invertebrates, which eventually may result in elimination or inactivation of the intruder. Important innate effector molecules are oxygen and nitrogen species, antimicrobial peptides, lectins, fibrinogen-related peptides, leucine rich repeats (LRRs), pentraxins, and complement-related proteins. Echinoderms represent the most developed invertebrates and the bridge leading to the primitive chordates, cephalochordates, and urochordates, in which many autologous genes

  9. Clinical use of transthoracic echocardiography in patients with mitral valve prolapse%经胸超声心动图定位诊断二尖瓣脱垂的临床应用

    Institute of Scientific and Technical Information of China (English)

    袁媛; 谢明星; 马小静; 王静; 袁莉; 杨亚利

    2012-01-01

    Objective:To evaluate the clinical value of transthoracic echocardiography (TTE) in patients with mitral valve prolapse before operation. Method: One hundred and twenty-six patients who underwent mitral valve repair for mitral valve proplapse were retrospectively reviewed. TTE and transesophageal echocardiography (TEE) were performed in all patients by using standardized imaging views for identifying the location of flail or prolapsed segments and functional analysis of mitral valve prolapse according to Carpentier' s functional classification. Compared with surgical findings, the accuracy and specificity of TTE and TEE for locating the segments of MVP was indentified. Result: The difference between TTE and TEE to detect vegetations, ruptured chordate, tendinae or annular calcium was not significant. The incremental value of TEE or TTE for the identification of flail or prolapsed segments according to Carpentier classification was not significant. In the group of MVP, agreement with surgical findings for the localization of prolapsed segments by TTE was 89% — 98% (Kappa value 0. 68 — 0. 90), by TEE was 92% —99% (Kappa value 0. 77-0. 95). Before operation, TTE and TEE study indentified that respectively, 93% and 95% of patients had severe mitral regurgitation respectively, while 95% of patients were considered as severe mitral regurgitation during surgical procedure. The difference between TTE, TEE and surgical findings was not significant. Conclusion: TTE can accurately evaluate the function and anatomy of the mitral complex, and precisely positioning the MVP before surgery.%目的:探讨经胸超声心动图(TTE)在术中二尖瓣脱垂(MVP)定位诊断中的临床应用价值.方法:回顾性分析126例经手术确诊为MVP并行二尖瓣成形术患者,利用术前TTE及术中经食管超声心动图(TEE)分别对二尖瓣复合装置的解剖、功能进行评估,并定位瓣叶脱垂部位,将超声诊断结果分别与外科直视下诊断结果对

  10. 长江口北支大型底栖动物群落周年变化特征%Anniversary variation characteristics of benthic animal community in the north branch of the Yangtze River estuary

    Institute of Scientific and Technical Information of China (English)

    赵开彬; 刘婧; 吴惠仙; 边佳胤; 王宝强; 薛俊增

    2014-01-01

    分析了长江口北支滩涂大型底栖动物的群落结构和多样性变化特征。共采集大型底栖动物78种,包括环节动物7种、软体动物23种、节肢动物28种、脊索动物18种、其它两种,全年优势种有8种。密度为0.08 ind/m2(1月)-1.24 ind/m2(7月),生物量为0.006 g/m2(2月)-0.58 g/m2(5月),Margalef丰富度指数(D)为0.82(1月)-3.88(7月),Pielou均匀度指数(J)为0.60(9月)-0.86(1月),Shannon-Wiener多样性指数(H′)为1.59(2月)-2.76(10月)。底栖动物密度与环境因子进行相关性分析显示,北支潮间带的大型底栖动物群落按照盐度、沉积特征等不同可分为3组,盐度和温度是影响底栖动物群落分布的主导因子。%The community structure and diversity characteristics of large benthic animal in the north branch of the Yangtze River estuary were analyzed .The collected 78 species included 23 species of mollusks , 7 species of annelids , 28 species of arthropods , 18 species of chordates, and 2 others.Also eight dominant species were found throughout the year .The density was from 0.08 ind/m2(Jan.)to 1.24 ind/m2(July).The biomass was from 0.006 g/m2(Feb.) to 0.58 g/m2(May).The Margalef index (D) was from 0.82(Jan.)to 3.88 (July).The Pielou index (J) was from 0.60(Sep.)to 0.86(Jan.).The Shannon-Wiener index (H′) was from 1.59(Feb.)to 2.76 (Oct.).Based on the analysis between density and environmental factors , there were three groups according to the salinity , sedimentary characteristics and other aspects .Moreover , salinity and temperature played a main role on the benthic species distribution .

  11. Retinoid X Receptor in Mollusc%软体动物维甲酸X受体研究进展

    Institute of Scientific and Technical Information of China (English)

    李维; 王淑红; 王艺磊; 王国栋; 邹志华

    2013-01-01

    维甲酸X受体(retinoid X receptor,RXR)作为配体依赖的转录因子,是核受体超家族重要的一员.脊椎动物RXR与配体及其辅调节因子相互作用,调控基因的协调表达,在胚胎发育、细胞分化、新陈代谢等许多生理过程中起着重要作用.软体动物RXR的研究因其与腹足类性畸变的关系越来越受到关注.本文综述了目前获得的软体动物RXR基因的结构,比较了软体动物RXR基因各功能结构域与人类和其他动物RXR的相似性.以RXR编码区的氨基酸序列为基础,构建了系统进化树,发现软体动物RXR与脊索动物而不是其他无脊椎动物的RXR聚成一支.软体动物和甲壳动物不同RXR亚型的氨基酸序列比较发现,两类动物可能存在不同的剪切酶或剪切位点.此外论文还针对软体动物RXR的配体、二聚体伙伴以及生理功能等方面的研究进行了综述.%Retinoid X receptor (RXR) is a member of the nuclear receptor superfamily of ligand-activated transcription factors that have been characterized in a wide variety of species.In vertebrates,RXR functions as either homo-or hetero-dimers to regulate expression of target genes.RXR is important in a variety of physiological events including embryo development,cell-proliferation,metabolism and regeneration.The investigation of molluscan RXR is of particular interest due to its involvement in neogastropods imposex.In this review,we compared the amino acid sequence of molluscan RXRs with human RXRo and other vertebrate RXRs and performed phylogenetic analyses.Parsimony analyses of 22 invertebrate and vertebrate RXRs indicated that the molluscan RXRs were analogous to chordate RXRs.The alignment of amino acid of different isoforms of molluscs and crustaceans indicated that different cutting enzymes or splice sites should exist in Tbox.In addition,we discussed the ligand,dimer partner,and physiological function of molluscan RXRs.

  12. 鱼类黑素皮质素受体(MCR)研究进展%Advances in fish melanocortin receptor family research

    Institute of Scientific and Technical Information of China (English)

    董晶晶; 谢骏; 习丙文

    2014-01-01

    The melanocortin receptor family, with seven transmembrane alpha-helixs, is a member of the smallest G-protein-coupled receptor and of great importance in chordate physiological function. The melanocortin receptor fam-ily has five subtypes (MC1R, MC2R, MC3R, MC4R and MC5R) in mammalian and tetrapod, with rather diverse func-tions. It has been confirmed that MCRs are involved in diverse number of physiological functions, including pigmenta-tion, steroidogenesis, energy homeostasis, inflammation and sexual function. In recent years, fish MCRs have gained more and more concern of researchers. Different MCR subtypes have been cloned and analyzed in several fish species. The MCRs of fish, the earliest vertebrates in evolution, is highly conserved compared with mammalian in molecular characterization and physiology fuction. Meanwhile they have some special features of their own. Thorough research on MCRs will contribute to our understanding of vertebrate MCRs evolution and its regulation functions in fish physiology. To facilitate the study on MCRs, we provide a review about clone, molecular characterization, pharmacology and phys-iological function of fish melanocortin receptors and highlight progress made in these areas.%黑素皮质素受体(melanocortin receptor, MCR)家族属于最小的G蛋白偶联受体家族之一,具有7个跨膜的α螺旋,在脊索动物生理活动中具有重要作用。在哺乳类及四肢类动物的MCR研究中共发现有5种不同功能的同源基因(MC1R、MC2R、MC3R、MC4R、MC5R),它们在机体色素沉积、摄食行为、能量平衡、类固醇合成和性行为等方面发挥重要功能。近年来,鱼类 MCRs 的研究逐渐得到学者们的普遍关注,一些鱼类的 MCRs 亚型相继被克隆,并对其功能进行了分析。鱼类作为脊椎动物进化中较为原始的类群,具有与哺乳动物 MCRs 相似的保守特征,同时也具有其特殊性。对鱼类MCRs的深入研究有利于揭示MCRs在脊椎动物

  13. 二尖瓣成形术在二尖瓣关闭不全中的应用%Application of mitral valvuloplasty in mitral insufficiency

    Institute of Scientific and Technical Information of China (English)

    陈红卫; 潘砚鹏; 陈文宽

    2015-01-01

    Objective To summarize and analyze the operation method and clinical effect of the mitral valvuloplas-ty. Methods The clinical data of 42 patients with mitral valvuloplasty from Jan. 2006 to Jun. 2013 were retrospectively analyzed. The operations were performed under low temperature during cardiopulmonary bypass. And among these ,8 cases adopted repairment of the cleft of the mitral leaflet,lobes rectangular resection and suture in 12 cases,chordate tendineae folded or transfer molding in 2 cases,valve annulus of the back lobe ring contraction and placation of the commeasure in 7 cases. Mitral valvuloplasty mitral valve perforation and repairmen in 4 cases. “ Edge-to-Edge”technique for method of double holes in 7 cases,prosthetic ring for mitral annuloplasty in 2 cases. The above method of forming at the same time the application of artificial valve ring annuloplasty in 28 cases,during the operation,to adopt water injection test and Tran esophageal echocardiography,after the operation,to ultrasound assessment of the forming effect. Results There was no death case,and after the operation,through ultrasonography showed no tricuspid regurgitation was in 27 cases(64. 29% ), mild reflux in 12 cases(28. 57% ),slight to middle degree in 3 cases(7. 14% ),and after the operation,due to hemoglo-binuria to have another operation in 1 case,the rate of re-resection was 2. 38% . The mean follow- up time was 1 - 6 (3. 5 ± 1. 6)years. All the patients return to normal life and work,I degree of NYHA in 32 cases,Ⅱ degree in 10 cases. Conclusions For the patients with mitral insufficiency with high quality leaflets,during the operation,according to the patient’s mitral morphology,to adopt corresponding operation forming and have good clinical results.%目的:总结分析二尖瓣成形术患者的手术方法和临床疗效。方法回顾性分析2006年1月至2013年6月行二尖瓣成形术患者42例,手术在体外循环中低温下施行,采用瓣叶裂缺修补8

  14. Comparison of three techniques of anterior mitral valve repair in treatment of mitral insufficiency%应用三种二尖瓣前叶成形技术治疗二尖瓣关闭不全的对照研究

    Institute of Scientific and Technical Information of China (English)

    张卫; 方亮; 叶伟

    2013-01-01

    Objective To compare the effects of chordal transfer, edge-to-edge suture and artificial chordae techniques in treatment of mitral insufficiency induced by anterior mitral valve diseases. Methods According to different surgical methods, 171 patients with anterior mitral valve diseases were divided into chordal transfer group (group I ), edge-to-edge suture group ( group II ) and artificial chordate group ( group IE) , with 57 patients in each group. The mitral valve close was examined by transesophageal echocardiography ( TEE) , the effective mitral valve areas and parameters related to left ventricular function were measured by transthoracic echo, and the short and middle term data of mitral valve close were followed up. Results The percentages of patients with satisfied mitral valve revealed by postoperative TEE in group I , group II and group 1 were 82. 46% (47/57), 85.96% (49/57) and 84. 21% (48/57), respectively. The postoperative effective mitral valve areas of all three groups were significantly smaller than those before operation (P < 0. 05). The postoperative left ventricular end diastolic diameters in all three groups were significantly shorter than those before operation (P<0. 05). After follow up for 1 to 11 years (3.28 years in average), the percentages of satisfied mitral valve close in group I, group II and group HI were 82.46% (47/57), 85.96% (49/57) and 82.46% (47/57), respectively. Conclusion Ghordal transfer, edge-to-edge suture and artificial chordae techniques are effective in treatment of anterior mitral valve diseases, and the choice of surgical procedure should be based on the age and disease condition.%目的 比较腱索转移、缘对缘缝合和人工腱索置入三种方法治疗二尖瓣前叶病变引起的二尖瓣关闭不全的效果.方法 将因二尖瓣前叶病变接受手术治疗的171例患者按手术方式不同分为腱索转移组(Ⅰ组)、缘对缘技术组(Ⅱ组)和人工腱索置入组(Ⅲ组),每组各57例.

  15. Secondary productivity of benthic macrofaunal community in intertidal zone of Lianzhou Bay, China%廉州湾滨海湿地潮间带大型底栖动物群落次级生产力

    Institute of Scientific and Technical Information of China (English)

    何斌源; 赖廷和; 王欣; 潘良浩; 曹庆先

    2013-01-01

    A seasonal investigation was conducted on the dynamic changes of benthic macrofaunal community in the three types of intertidal habitats,i.e.,bare flat,mangrove forest,and Cyperus malaccensis saltmarsh,in Lianzhou Bay in January,April,July,and October,2011,and the Brey's empirical formula was applied to estimate the secondary productivity of benthic macrofaunal community in the three habitats.A total 156 species belonging to 8 phyla of intertidal benthic macrofauna were collected,among which,136,85,and 29 species were recorded in bare flat,mangrove forest,and saltmarsh habitats,respectively.The average species abundance per sampling station was 9.5±4.8 species in bare flat,9.5±3.9 species in mangrove forest,and 5.9±1.9 species in saltmarsh,respectively.In all the three habitats,the percentages of different categories to total species followed the same decreasing order of Mollusk > Arthropod > Annelid >Chordate > other categories.The community structure of the benthic macrofauna in saltmarsh had smaller change,with Ilyoplax ningpoensis significantly dominated.In mangrove forest and bare flat,the dominant species changed with the water salinity.In the intertidal zone of Lianzhou Bay,the average secondary productivity of the benthic macrofaunal community was 15.88 g· m-2· a-1,and that in bare flat,mangrove forest,and saltmarsh was 16.16 g · m-2· a-1,9.97 g · m-2 · a-1,and 3.88 g · m-2 · a-1,respectively.The average P/B ratio in the intertidal zone was 0.70,and that in bare flat,mangrove forest,and saltmarsh was 0.70,0.65,and 1.02,respectively.The annual secondary production in the intertidal zone was 14623 t (FM).Water salinity and vegetation type were the major factors affecting the community structure of the intertidal benthic macrofauna,and further,the spatial distribution of the secondary productivity of the benthic macrofauna in Lianzhou Bay.%于2011年1月、4月、7月和10月开展广西廉州湾的

  16. 贵州董背洞和水江洞内动物群落结构与部分环境因子的相关性%Correlation Between the Animal Community Structure and Environmental Factors in Dongbei Cave and Shuijiang Cave of Guizhou Province

    Institute of Scientific and Technical Information of China (English)

    黎道洪

    2006-01-01

    Mollusks, arthropods and chordates which were visible to the naked eye were observed and collected in Dongbei and Shuijiang caves of Libo county five times between February and July from 2002 to 2005. Four hundred and forty samples from Dongbei Cave were classified into three phyla, five classes, 10 orders, 20 families and 39 species or groups of species. Four hundred and ninety-eight samples from Shuijiang Cave were classified into three phyla, six classes, 11 orders, 20 families and 25 species or groups of species. Six animal communities were identified in the light belt of the two caves according to their species types and numbers of individuals in the light belt of two cave. The communities which have the highest values of species richness community diversity, maximum diversity, evenness, dominance and community similarity are respectively: B (4.1059), H (2.4716), B (3.3322), E (0.9042), C (0.3442) and A-C (0.5251). The community diversity and correlation of environmental factors were also studied. The temperature, humidity, content of CO2 and N2, content of organic matter and some inorganic salts in soil were analyzed by Pearson correlation. The results showed that the content of organic matter in soil is positively related to species number, species richness and maximum community diversity, with correlations of 0.885, 0.909, 0.868 respectively (two-tailed significance test, P≤0.05), and significantly positively related to diversity, with the coefficient of 0.611, (two-tailed significance test, P≤ 0.1). This suggests that the content of organic matter in soil is one of the important elements influencing the community variation of cave animals. Outside the cave, temperature and humidity are important factors impacting on community diversity. As the temperature in all seasons in the cave is stable and the humidity is always high (above 90%), the temperature and humidity have weak correlation to community diversity in caves.%在2002-2005年的2月和7月共5

  17. Assessment of left ventricular radial systolic function of rat models with chronic heart failure by two-dimensional speckle tracking imaging%二维斑点追踪成像技术评价实验性大鼠慢性心力衰竭模型左心室径向收缩功能

    Institute of Scientific and Technical Information of China (English)

    覃小娟; 谢明星; 王静; 吕清; 方凌云; 付倩; 黄桂

    2012-01-01

    (PWT), fraction shortening (FS) and ejection fraction (EF) were measured at the left ventricular chordate level before operation and 2, 4 and 8 weeks after operation with M-mode echocardiography. High frame rate dynamic 2D images were recorded from the left ventricular short-axis views at the papillary muscle level. Peak systolic radial strains (PRS) of 6 segments and global peak radial strain (GPRS) were measured with 2D-STI. All the parameters were compared between the two groups at the same time points, and the changes of values were observed in each group at the different time points. Results Compared with the values of pro-surgical and sham-surgical group at the same time point, there was no significant difference of each value in 2 weeks after operation (all P>0. 05). Four weeks after operation, IVST, PWT in operation group increased, but PRS and GPRS decreased (all P0. 05). PRS obtained in intra- and inter-group both showed high agreement. Conclusion 2D-STI can observe left ventricular myocardial fibers radial remodeling and the progress of contraction function changes induced by after-load increasing. It is an efficient method to evaluate left ventricular function in CHF rat models.