77 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
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
Parallel Expansions of Sox Transcription Factor Group B Predating the Diversifications of the Arthropods and Jawed Vertebrates
No full textGroup B of the Sox transcription factor family is crucial in embryo development in the insects and vertebrates. Sox group B, unlike the other Sox groups, has an unusually enlarged functional repertoire in insects, but the timing and mechanism of the expansion of this group were unclear. We collected and analyzed data for Sox group B from 36 species of 12 phyla representing the major metazoan clades, with an emphasis on arthropods, to reconstruct the evolutionary history of SoxB in bilaterians and to date the expansion of Sox group B in insects. We found that the genome of the bilaterian last common ancestor probably contained one SoxB1 and one SoxB2 gene only and that tandem duplications of SoxB2 occurred before the arthropod diversification but after the arthropod-nematode divergence, resulting in the basal repertoire of Sox group B in diverse arthropod lineages. The arthropod Sox group B repertoire expanded differently from the vertebrate repertoire, which resulted from genome duplications. The parallel increases in the Sox group B repertoires of the arthropods and vertebrates are consistent with the parallel increases in the complexity and diversification of these two important organismal groups
Predation success by a plant-ant indirectly favours the growth and fitness of its host myrmecophyte
No full textMutualisms, or interactions between species that lead to net fitness benefits for each species involved, are stable and
ubiquitous in nature mostly due to "byproduct benefits" stemming from the intrinsic traits of one partner that generate an indirect and positive outcome for the other. Here we verify if myrmecotrophy (where plants obtain nutrients from the refuse of their associated ants) can explain the stability of the tripartite association between the myrmecophyte Hirtella physophora, the ant Allomerus decemarticulatus and an Ascomycota fungus. The plant shelters and provides the ants with extrafloral nectar. The ants protect the plant from herbivores and integrate the fungus into the construction of a trap that they use to capture prey; they also provide the fungus and their host plant with nutrients. During a 9-month field study, we
over-provisioned experimental ant colonies with insects, enhancing colony fitness (i.e., more winged females were
produced). The rate of partial castration of the host plant, previously demonstrated, was not influenced by the experiment. Experimental plants showed higher δ¹⁵N values (confirming myrmecotrophy), plus enhanced vegetative growth (e.g., more leaves produced increased the possibility of lodging ants in leaf pouches) and fitness (i.e., more fruits produced and more flowers that matured into fruit). This study highlights the importance of myrmecotrophy on host plant fitness and the stability of ant-myrmecophyte mutualisms
Evaluating relationships between organisational core competencies and individuals' competencies.
No full textDetermining core competence has been increasingly considered as a vital strategic approach towards a sustainable competitive advantage by researchers and decisionmakers. Although its importance is widely recognised, the identification process appears complex. Therefore, sound theoretical systematic identification processes are still sought. In addition, the underlying components of core competence such as individuals' competencies have implications and need to be investigated. The contribution made by individuals' competencies in the content and form of organisational core competences is critical. In response, this research aims to examine the potential link between core competences and individuals' competencies. To meet this goal, this thesis complements and extends a previous work (Hafeez et al, 2002a-c) which introduced a structured framework to identify core competence. In particular, it intends to develop the Hafeez et al (2002a) core competence identification framework at the individuals' level. In addition, the CIPD (2004) competency headings framework comprising seven competencies is used. Therefore, an integrated structured framework to link the relevant individuals' competences with the identified core competences is developed. The context of this study is the utility, construction, oil services, and manufacturing industries. A combined methodology of structured questionnaire-based interviews and a postal survey involving fifteen organisations is performed. Data is at times subjectively collected and analysed. However, the AHP technique with its related software (EXPERT CHOICE) is used through all the stages of the proposed framework to eliminate subjective inconsistencies and enable this author to obtain solid results and conclusions.The study recognised that the composition of core competences for the majority of surveyed organisations leans towards the human contribution. In addition, individuals' competencies influence and contribute towards the core competences. This confirms a strong relationship between individuals' competencies and core competences. However, the relative importance of the examined individuals' competencies against the identified core competences was rather different. On average, the prevalence of Team orientation followed by People management competencies was relatively the highest. The research concluded that the nature of the industry and the organisation's context has an impact on the portfolio of individuals' competencies to be linked with core competences. This research has made four main contributions to knowledge. First, the Hafeez et al. (2002a-c) framework is re-tested within other industries, namely, utility, construction, oil services, and manufacturing. Second, the framework is developed at the individuals' competencies level. Third, the composition of identified core competences in terms of human, organisational, and technological contributions is evaluated. Fourth, the relevant portfolio of related individuals' competencies to be linked with core competences is determined. The outcomes of this research may help organisations to make key strategic decisions such as how to invest to develop particular organisational core competences and individuals' competencies
The internal cranial anatomy of Romundina stellina Orvig, 1975 (Vertebrata, Placodermi, Acanthothoraci) and the origin of jawed vertebrates-Anatomical atlas of a primitive gnathostome
No full textPlacoderms are considered as the first jawed vertebrates and constitute a paraphyletic group in the stem-gnathostome grade. The acanthothoracid placoderms are among the phylogenetically most basal and morphologically primitive gnathostomes, but their neurocranial anatomy is poorly understood. Here we present a near-complete three-dimensional skull of Romundina stellina, a small Early Devonian acanthothoracid from the Canadian Arctic Archipelago, scanned with propagation phase contrast microtomography at a 7.46 mu m isotropic voxel size at the European Synchrotron Radiation Facility, Grenoble, France. This is the first model of an early gnathostome skull produced using this technique, and as such represents a major advance in objectivity compared to past descriptions of placoderm neurocrania on the basis of grinding series. Despite some loss of material along an oblique crack, most of the internal structures are remarkably preserved, and most of the missing structures can be reconstructed by symmetry. This virtual approach offers the possibility to connect with certainty all the external foramina to the blood and nerve canals and the central structures, and thus identify accurate homologies without destroying the specimen. The high level of detail enables description of the main arterial, venous and nerve canals of the skull, and other perichondrally ossified endocranial structures such as the palatoquadrate articulations, the endocranial cavity and the inner ear cavities. The braincase morphology appears less extreme than that of Brindabellaspis, and is in some respects more reminiscent of a basal arthrodire such as Kujdanowiaspis.This work was funded by European
Research Council Advanced Investigator Grant
233111 (https://erc.europa.eu/)-funding only;
Wallenberg Scholarship from the Knut and Alice
Wallenberg Foundation (https://www.wallenberg.
com/)-funding only; and ESRF (https://www.esrf.
eu)-data collection (microtromography). The Museum National d’Histoire Naturelle provided
support in the form of salaries for author DG, but
did not have any additional role in the study design,
data collection and analysis, decision to publish, or
preparation of the manuscript
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