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Genome complexity in the coelacanth is reflected in its adaptive immune system.

ABSTRACT: We have analyzed the available genome and transcriptome resources from the coelacanth in order to characterize genes involved in adaptive immunity. Two highly distinctive IgW-encoding loci have been identified that exhibit a unique genomic organization, including a multiplicity of tandemly repeated constant region exons. The overall organization of the IgW loci precludes typical heavy chain class switching. A locus encoding IgM could not be identified either computationally or by using several different experimental strategies. Four distinct sets of genes encoding Ig light chains were identified. This includes a variant sigma-type Ig light chain previously identified only in cartilaginous fishes and which is now provisionally denoted sigma-2. Genes encoding ?/? and ?/? T-cell receptors, and CD3, CD4, and CD8 co-receptors also were characterized. Ig heavy chain variable region genes and TCR components are interspersed within the TCR ?/? locus; this organization previously was reported only in tetrapods and raises questions regarding evolution and functional cooption of genes encoding variable regions. The composition, organization and syntenic conservation of the major histocompatibility complex locus have been characterized. We also identified large numbers of genes encoding cytokines and their receptors, and other genes associated with adaptive immunity. In terms of sequence identity and organization, the adaptive immune genes of the coelacanth more closely resemble orthologous genes in tetrapods than those in teleost fishes, consistent with current phylogenomic interpretations. Overall, the work reported described herein highlights the complexity inherent in the coelacanth genome and provides a rich catalog of immune genes for future investigations.

SUBMITTER: Saha NR

PROVIDER: S-EPMC4110200 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature

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Genome complexity in the coelacanth is reflected in its adaptive immune system.

Saha Nil Ratan NR Ota Tatsuya T Litman Gary W GW Hansen John J Parra Zuly Z Hsu Ellen E Buonocore Francesco F Canapa Adriana A Cheng Jan-Fang JF Amemiya Chris T CT

Journal of experimental zoology. Part B, Molecular and developmental evolution 20140124 6

We have analyzed the available genome and transcriptome resources from the coelacanth in order to characterize genes involved in adaptive immunity. Two highly distinctive IgW-encoding loci have been identified that exhibit a unique genomic organization, including a multiplicity of tandemly repeated constant region exons. The overall organization of the IgW loci precludes typical heavy chain class switching. A locus encoding IgM could not be identified either computationally or by using several d ...[more]

PMID: 24464682

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Project description:BackgroundThe concept of complexity is used in palliative care (PC) to describe the nature of patients' situations and the extent of resulting needs and care demands. However, the term or concept is not clearly defined and operationalised with respect to its particular application in PC. As a complex problem, a care situation in PC is characterized by reciprocal, nonlinear relations and uncertainties. Dealing with complex problems necessitates problem-solving methods tailored to specific situations. The theory of complex adaptive systems (CAS) provides a framework for locating problems and solutions. This study aims to describe criteria contributing to complexity of PC situations from the professionals' view and to develop a conceptual framework to improve understanding of the concept of "complexity" and related elements of a PC situation by locating the complex problem "PC situation" in a CAS.MethodsQualitative interview study with 42 semi-structured expert (clinical/economical/political) interviews. Data was analysed using the framework method. The thematic framework was developed inductively. Categories were reviewed, subsumed and connected considering CAS theory.ResultsThe CAS of a PC situation consists of three subsystems: patient, social system, and team. Agents in the "system patient" are allocated to further subsystems on patient level: physical, psycho-spiritual, and socio-cultural. The "social system" and the "system team" are composed of social agents, who affect the CAS as carriers of characteristics, roles, and relationships. Environmental factors interact with the care situation from outside the system. Agents within subsystems and subsystems themselves interact on all hierarchical system levels and shape the system behaviour of a PC situation.ConclusionsThis paper provides a conceptual framework and comprehensive understanding of complexity in PC. The systemic view can help to understand and shape situations and dynamics of individual care situations; on higher hierarchical level, it can support an understanding and framework for the development of care structures and concepts. The framework provides a foundation for the development of a model to differentiate PC situations by complexity of patients and care needs. To enable an operationalisation and classification of complexity, relevant outcome measures mirroring the identified system elements should be identified and implemented in clinical practice.

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Genome complexity in the coelacanth is reflected in its adaptive immune system.

Publications

Genome complexity in the coelacanth is reflected in its adaptive immune system.

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