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Search Results: 1 - 10 of 4622 matches for " Chordate evolution "
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Metaphylogeny of 82 gene families sheds a new light on chordate evolution
Vienne Alexandre,Pontarotti Pierre
International Journal of Biological Sciences , 2006,
Abstract: 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.
A neurochemical map of the developing amphioxus nervous system
Simona Candiani, Luca Moronti, Paola Ramoino, Michael Schubert, Mario Pestarino
BMC Neuroscience , 2012, DOI: 10.1186/1471-2202-13-59
Abstract: 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.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.
Evolutionary dynamics of olfactory receptor genes in chordates: interaction between environments and genomic contents
Yoshihito Niimura
Human Genomics , 2009, DOI: 10.1186/1479-7364-4-2-107
Abstract: There are a variety of odours in our environment. Detecting molecules of β-phenylethyl alcohol is recognised as the fragrance of rose in the human brain, while amyl acetate is perceived as a banana flavour. To humans, olfaction--the sense of smell-- may seem to be less important than vision or hearing. To most animals, however, olfaction is essential for their survival. It is used to find foods, avoid predators and identify mates and offspring. Odour molecules in the environment are detected by olfactory receptors (ORs). OR genes were first identified from rats by Buck and Axel in 1991[1]. They discovered a huge multigene family of G-protein-coupled receptors (GPCRs), of which expression is restricted to the olfactory epithelium in the nasal cavity, and suggested that there are ~ 1,000 different OR genes in mammalian genomes. The discovery opened the door to the molecular study of chemosensation, and these authors received the Nobel Prize in 2004 for this achievement. GPCRs are membrane proteins with seven transmembrane α-helical regions. The binding of a ligand to a receptor activates a G-protein and a subsequent signalling cascade. GPCRs are classified into at least five groups by sequence similarities[2]. OR genes belong to the largest group of them, the rhodopsin-like GPCR superfamily, which also includes opsin genes (which encode proteins that are photosensitive) and many other receptor genes, including those encoding neurotransmitters, peptide hormones, chemokines, lipids and nucleotides. OR genes are intronless in their coding regions, although the number of exons in the 5' untranslated region can be variable and these non-coding exons are often alternatively spliced.[3]It is generally thought that the olfactory system uses combinatorial coding[4]. The relationships between odour molecules and ORs are not one-to-one, but multiple-to-multiple; that is, one OR recognises multiple odorants, and one odorant is recognised by multiple ORs. Therefore, different odor
A SINE in the genome of the cephalochordate amphioxus is an Alu element
Holland Linda Z.
International Journal of Biological Sciences , 2006,
Abstract: 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.
A paleontological perspective of vertebrate origin
SHU Degan,
SHUDegan

科学通报(英文版) , 2003,
Abstract: 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.
Molecular evolution of a chordate specific family of G protein-coupled receptors
Stefan Kurtenbach, Christoph Mayer, Thomas Pelz, Hanns Hatt, Florian Leese, Eva M Neuhaus
BMC Evolutionary Biology , 2011, DOI: 10.1186/1471-2148-11-234
Abstract: 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.GPRC5 receptors, a class of G protein-coupled receptors with unique sequence characteristics, may represent a molecular novelty that helped non-chordates to become chordates.G protein-coupled receptors (GPCRs) are diverse in their primary structure, which has been used for their phylogenetic classification into subfamilies [1,2]. Most GPCRs belong to one of five subfamilies; Rhodopsin (also termed family A), Adhesion and Secretin (together formerly classified as family B), Glutamate (also termed family C) and Frizzled/Taste2. The Rhodopsin receptor family contains ~670 out of a total of ~800 full-length human receptor proteins [3] and is highly heterogeneous in primary structure and ligand specificity, although most Rhodopsin family receptors do share specific sequence motifs. Family C includes a total of 22 human proteins, m
A novel third complement component C3 gene of Ciona intestinalis expressed in the endoderm at the early developmental stages
T Hibino,M Nonaka
Invertebrate Survival Journal , 2013,
Abstract: The third complement component (C3) in ascidian was reported to function as an opsonin to enhance phagocytosis and as a chemotactic factor for phagocytes, indicating that ascidian C3 works in mesodermal cavity as a humoral factor like vertebrate C3s. In the basal Eumetazoa, Cnidaria lacking mesodermal tissues, C3 was reported to work in an endodermal cavity. Evolution of structure and function of C3 is still to be clarified. Here we report the identification of the third C3 gene, CiC3-3, in the genome of an ascidian, Ciona intestinalis. Phylogenetic analysis using the entire amino acid sequences of Eumetazoan C3s indicated that CiC3-3 possess a closer relationship to vertebrate C3, C4 and C5 than other ascidian C3s. Although CiC3-3 retained the α-β processing site and 6 cysteine residues in the C3a region, it lacked the intra-molecular thioester bond and the catalytic histidine residue. Instead, CiC3-3 had a unique insertion of about 70 residues long Lys/Arg-rich sequence. CiC3-3 was expressed highly in the embryonic stages, but little in the adult in contradistinction to CiC3-1 and CiC3-2. The expression of CiC3-3 in early embryonic stages was restricted to endoderm similar to cnidarian C3s. Thus, the ascidian complement system could represent a unique evolutionary stage sharing a primitive endodermal function with Cnidaria, and newly developed humoral function with vertebrates.
Role of Nitrite in Tumor Growth, Symbiogenetic Evolution of Cancer Cells, and China’s Successes in the War against Cancer  [PDF]
Kenneth J. Hsu, Chao S. Huangfu, Min Z. Qin
Journal of Cancer Therapy (JCT) , 2011, DOI: 10.4236/jct.2011.25080
Abstract: Statistics and experiments indicate a correlation between cancer mortality and nitrite in drinking water. Nitrite is a reductant that can deprive a cell of oxygen; it is also an oxidant that can be a substrate in anaerobic ammonium oxidation, the metabolic mode of the anammox bacteria. Eukaryote cells evolved through a fusion of anaerobic and aerobic bacteria. We postulate that an anammox bacterium sought refuge in a fusion with a membrane-bound cluster of aerobic bacteria. While the latter evolved into mitochondria organelles, the former became the nucleus of a prokaryote cell. Eventually, oxidative phosphorilation is the characteristic metabolic pathway of normal eukaryote cells, and we postulate that anammox is the protein-catabolism pathway for cancer cells. The metabolism consumes nitrite and explains thus the link between nitrite and cancer.
Long term clinical and dermoscopic follow-up of a child with a Spitz nevus  [PDF]
Massimiliano Scalvenzi, Maria Grazia Francia, Franco Palmisano, Claudia Costa
Open Journal of Pediatrics (OJPed) , 2012, DOI: 10.4236/ojped.2012.23040
Abstract: Background: Spitz nevus is uncommon, benign melanocytic neoplasm that may show some clinical, dermoscopical and histological features of melanoma. It occurs often in childhood, but may appear also in early adulthood. Rare congenital cases have been reported in literature. It is frequently located on the face and the lower extremities, but in some cases may appears on the trunk. Methods: We report a case of a 9-years-old girl presented to our Dermatology Unit because of the presence of a pigmented lesion on her right leg, 4 mm in diameter, which was clinically and dermoscopically diagnosed as Spitz nevus. We described the clinical and dermoscopic features that we observed every six months, over 11 years follow-up period. Objective: Our observation show that the globular, the starburst, the homogeneous patterns and diffuse brown colour with diffuse hypopigmented areas may be the different expression that correspond to possible evolutionary phases of pigmented Spitz nevus.
Charged Amino Acid Frequencies of Proteins over Macroevolutionary Time Scale  [PDF]
Yu-Juan Zhang, Jian-Jun Li, You-Jin Hao, Bin Chen
Engineering (ENG) , 2013, DOI: 10.4236/eng.2013.510B086
Abstract:

Charged amino acids (AAs) are targets for selective forces in protein evolution. To fully explore the trend of charged AA frequencies evolution in macroevolutionary process from prokaryotes to eukaryotes, we extend the analysis of five charged AAs separately and total basic and acidic AAs in protein sequences of 158 prokaryotic and 63 eukaryotic predicted proteomes and 456 clusters of orthologous groups (COGs). Also, we eliminate the biases that may caused by extreme organisms in both predicted proteomes and COGs analyses. More basic AAs, His,Lysand Glu were found in eukaryotic proteins compared with prokaryotic proteins by predicted proteomes analysis. By COGs analysis, we found that basic AAs andLysfrequencies are higher in eukaryotic orthologous proteins than their prokaryotic companions, while the trend of Arg frequency is the opposite. We discussed the agreements and disagreements of two analyses and gained a more credible trend of charged AAs evolution in macroevolutionary time scale.

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