141 research outputs found
Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing
No full textThe traditionally accepted relationships among basal jawed vertebrates have been challenged by some molecular phylogenetic analyses based on mitochondrial sequences. Those studies split extant gnathostomes into two monophyletic groups: tetrapods and piscine branch, including Chondrichthyes, Actinopterygii and sarcopterygian fishes. Lungfish and bichir are found in a basal position on the piscine branch. Based on transcriptomes of an armored bichir (Polypterus delhezi) and an African lungfish (Protopterus sp.) we generated, expressed sequences and whole genome sequences available from public databases, we obtained 111 genes to reconstruct the phylogenetic tree of basal jawed vertebrates and estimated their times of divergence. Our phylogenomic study supports the traditional relationship. We found that gnathostomes are divided into Chondrichthyes and the Osteichthyes, both with 100% support values (posterior probabilities and bootstrap values). Chimaeras were found to have a basal position among cartilaginous fishes with a 100% support value. Osteichthyes were divided into Actinopterygii and Sarcopterygii with 100% support value. Lungfish and tetrapods form a monophyletic group with 100% posterior probability. Bichir and two teleost species form a monophyletic group with 100% support value. The previous tree, based on mitochondrial data, was significantly rejected by an approximately unbiased test (AU test, p=0). The time of divergence between lungfish and tetrapods was estimated to be 391.8 Ma and the divergence of bichir from pufferfish and medaka was estimated to be 330.6 Ma. These estimates closely match the fossil record. In conclusion, our phylogenomic study successfully resolved the relationship of basal jawed vertebrates based on transtriptomes, EST and whole genome sequences.The traditionally accepted relationships among basal jawed vertebrates have been challenged by some molecular phylogenetic analyses based on mitochondrial sequences. Those studies split extant gnathostomes into two monophyletic groups: tetrapods and piscine branch, including Chondrichthyes, Actinopterygii and sarcopterygian fishes. Lungfish and bichir are found in a basal position on the piscine branch. Based on transcriptomes of an armored bichir (Polypterus delhezi) and an African lungfish (Protopterus sp.) we generated, expressed sequences and whole genome sequences available from public databases, we obtained 111 genes to reconstruct the phylogenetic tree of basal jawed vertebrates and estimated their times of divergence. Our phylogenomic study supports the traditional relationship. We found that gnathostomes are divided into Chondrichthyes and the Osteichthyes, both with 100% support values (posterior probabilities and bootstrap values). Chimaeras were found to have a basal position among cartilaginous fishes with a 100% support value. Osteichthyes were divided into Actinopterygii and Sarcopterygii with 100% support value. Lungfish and tetrapods form a monophyletic group with 100% posterior probability. Bichir and two teleost species form a monophyletic group with 100% support value. The previous tree, based on mitochondrial data, was significantly rejected by an approximately unbiased test (AU test, p=0). The time of divergence between lungfish and tetrapods was estimated to be 391.8 Ma and the divergence of bichir from pufferfish and medaka was estimated to be 330.6 Ma. These estimates closely match the fossil record. In conclusion, our phylogenomic study successfully resolved the relationship of basal jawed vertebrates based on transtriptomes, EST and whole genome sequences
Relationship between mercury concentration and size of long-jawed orb weaver spiders
No full textMethylmercury (MeHg) is an environmental contaminant that poses a serious threat to humans and wildlife. There are approximately 9 million water bodies in the United States alone that have all been contaminated with MeHg. Since there are so many water bodies, it is difficult to know the level of contamination for each, and whether or not they pose a threat to humans and/or wildlife. Ecologists use biosentinels, or a species that reflects the MeHg contamination of the aquatic ecosystem, in order to determine the level of contamination. In the present study, the author proposed the long-jawed orb weaver spider (Tetragnatha sp.) as a potential biosentinel for MeHg contamination of water bodies. The author collected spiders from 15 ponds in September and October of 2013, where she found a positive correlation between MeHg concentration and size of long-jawed orb weaver spiders. The author then found a positive relationship between MeHg concentration of the spiders and the overall MeHg contamination of the aquatic ecosystem, thus suggesting the long-jawed orb weaver spider is an effective biosentinel. This study proposes that long-jawed orb weaver spiders could be used as an efficient bioseninel to determine MeHg contamination in many of the 9 million water bodies across the United States
Ongoing Research in Jawed Fish Immunity: Structural and Functional Studies at the Protein and Cellular Levels
No full textThis eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contac
CYTOCHROME F FROM PLANTS AND CYANOBACTERIA
No full textExisting methods of isolation and purification of cytochrome f were modified to give extraction yields of close to 100 percent and purification yields of 80 to 90 percent. This procedure was successfully applied to cyanobacteria, a eukaryotic alga, and higher plants. In addition schemes were developed to obtain both monomeric and aggregated cytochrome f from the same organism. The first 81 residues of Spirulina maxima cytochrome f and the first 78 residues of spinach cytochrome f were determined by automated sequencing of fragments produced by chemical and proteolytic digestion. Fifty-nine of the eighty-one residues of the cyanobacterial cytochrome f are conserved in the eukaryotic protein. The heme binding site is located in this region. A low potential cytochrome, cytochrome c(,550), occasionally found in various species of cyanobacteria and eukaryotic algae and considered to be a proteolytic product of cytochrome f was isolated and purified by conventional and high performance liquid chromatography. N-Terminal amino acid sequence analysis proves the distinctness of this protein from cytochrome f. Indeed, cytochrome c(,550), the high potential cytochrome c(,553), and cyanobacterial cytochrome f are not antigenically related as determined by immunodiffusion experiments using antibodies raised against each cytochrome. Modification of intact and disrupted spinach thylakoid membranes with diazonium benzene sulfonic acid (DABS) was employed to investigate the location of plastocyanin and cytochrome f relative to the bilayer. The labeling patterns for plastocyanin and cytochrome f were dependent on the state of the membranes. Similar patterns were observed with thylakoids either incubated in the dark or exposed to light. Comparison with data obtained earlier for the labelling of cytochrome oxidase under similar conditions suggests that parts of the cytochrome f polypeptide chain are exposed at both sides of the photosynthetic membrane
Complete mitochondrial genome of saw-jawed monocle bream Scolopsis ciliata and its phylogenetic relationship in genus Scolopsis
No full textThe complete mitochondrial genome of the saw-jawed monocle bream, Scolopsis ciliata was deter�mined by the next generation sequencing (NGS) technique. The circular mitogenome of S. ciliata
(16,733 bp) encoded the canonical 37 genes including 13 proteins, 22 tRNA genes, 2 rRNAs (12S rRNA
and 16S rRNA), and two non-coding regions; the origin of light strand replication (OL) and the putative
control region (D-Loop). The gene arrangement of the S. ciliata mitogenome was identical to its rela�tive, Scolopsis vosmeri. Phylogenetic analysis based on the full mitochondrial genome sequences
showed that S. ciliata is most closely related to S. vosmeri with 83% nucleotide sequence identity. The
mitogenome information of S. ciliata would be the useful information to understand the evolutional
relationship of fishes in genus Scolopsi
Comparative genomic analysis of the proteasome β5t subunit gene : implications for the origin and evolution of thymoproteasomes
No full textThe thymoproteasome is a recently discovered, specialized form of 20S proteasomes expressed exclusively in the thymic cortex. Although the precise molecular mechanism by which the thymoproteasome exerts its function remains to be elucidated, accumulating evidence indicates that it plays a crucial role in positive selection of T cells. In the present study, we analyzed the evolution of the β5t subunit, a β-type catalytic subunit uniquely present in thymoproteasomes. The gene coding for the β5t subunit, designated PSMB11, was identified in the cartilaginous fish, the most divergent group of jawed vertebrates compared to the other jawed vertebrates, but not in jawless vertebrates or invertebrates. Interestingly, teleost fish have two copies of apparently functional PSMB11 genes, designated PSMB11a and PSMB11b, that encode β5t subunits with distinct amino acids in the S1 pocket. BLAST searches of genome databases suggest that birds such as chickens, turkey, and zebra finch lost the PSMB11 gene, and have neither thymoproteasomes nor immunoproteasomes. In mammals, reptiles, amphibians, and teleost fishes, the PSMB11 gene (the PSMB11a gene in teleost fish) is located next to the PSMB5 gene coding for the β5 subunit of the standard 20S proteasome, indicating that the PSMB11 gene arose by tandem duplication from the evolutionarily more ancient PSMB5 gene. The general absence of introns in PSMB11 and an unusual exon-intron structure of jawed vertebrate PSMB5 suggest that PSMB5 lost introns and duplicated in tandem in a common ancestor of jawed vertebrates, with PSMB5 subsequently gaining two introns and PSMB11 remaining intronless
Comparative genomic analysis of the proteasome β5t subunit gene : implications for the origin and evolution of thymoproteasomes.
No full textThe thymoproteasome is a recently discovered, specialized form of 20S proteasomes expressed exclusively in the thymic cortex. Although the precise molecular mechanism by which the thymoproteasome exerts its function remains to be elucidated, accumulating evidence indicates that it plays a crucial role in positive selection of T cells. In the present study, we analyzed the evolution of the β5t subunit, a β-type catalytic subunit uniquely present in thymoproteasomes. The gene coding for the β5t subunit, designated PSMB11, was identified in the cartilaginous fish, the most divergent group of jawed vertebrates compared to the other jawed vertebrates, but not in jawless vertebrates or invertebrates. Interestingly, teleost fish have two copies of apparently functional PSMB11 genes, designated PSMB11a and PSMB11b, that encode β5t subunits with distinct amino acids in the S1 pocket. BLAST searches of genome databases suggest that birds such as chickens, turkey, and zebra finch lost the PSMB11 gene, and have neither thymoproteasomes nor immunoproteasomes. In mammals, reptiles, amphibians, and teleost fishes, the PSMB11 gene (the PSMB11a gene in teleost fish) is located next to the PSMB5 gene coding for the β5 subunit of the standard 20S proteasome, indicating that the PSMB11 gene arose by tandem duplication from the evolutionarily more ancient PSMB5 gene. The general absence of introns in PSMB11 and an unusual exon-intron structure of jawed vertebrate PSMB5 suggest that PSMB5 lost introns and duplicated in tandem in a common ancestor of jawed vertebrates, with PSMB5 subsequently gaining two introns and PSMB11 remaining intronless.journal articl
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