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- Babbitt, Patricia C., et al.
(författare)
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Creating a specialist protein resource network : a meeting report for the protein bioinformatics and community resources retreat
- 2015
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Ingår i: Database. - : Oxford University Press (OUP). - 1758-0463.
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Tidskriftsartikel (refereegranskat)abstract
- During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.
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| 2. |
- Pedersen, Julia, 1991-
(författare)
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Evolution of acetylcholine receptors and study of the anatomy of the mouse brain reward system
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis work is divided in two parts. In the first part, I make use of the transgenic TRPV1-Cre mouse line as a tool to investigate the midbrain ventral tegmental area (VTA). By using a ChR2-EYFP construct, detailed mapping of connectivity shows that TRPV1-Cre VTA neurons innervate many brain areas such as the prefrontal cortex (PFC), ventral pallidum, bed nucleus of stria terminalis and lateral habenula. Interestingly, a mainly excitatory subcircuit from the VTA to PFC in the TRPV1-Cre mouse was identified which suggests a fast modulatory mechanism of the PFC by a VTA subpopulation. These results are discussed in the light of behavioral and neurophysiological literature. In the second part, the evolution of the vertebrate acetylcholine (ACh) receptor gene families in relation to the whole genome duplications (WGDs), also called 1R and 2R, was investigated. The nicotinic ACh receptors (nAChRs) form a complex gene family, where the members have evolved with varying rates. Our analyses combined phylogeny, intron positions and chromosomal synteny in order to elucidate the nAChR evolution in relation to the vertebrate WGDs. We found that ten ancestral nAChR genes were present prior to the WGDs. 1R and 2R then expanded this set to 19 genes, of which 16 are present in mammals today. The teleost specific WGD, 3R, further expanded the repertoire into 31 genes, of which 27 genes are present in zebrafish. The muscarinic ACh receptors (mAChRs) on the other hand form a smaller receptor family. Using the same approach, our analyses show that there were two ancestral genes present prior to the WGDs, expanding to five genes following 1R and 2R. In zebrafish, all genes retained duplicates in 3R resulting in ten mAChR genes present today. Our analyses also showed that four mAChR teleost genes have gained introns, some up to six introns. The evolutionary analyses of the receptor gene families show that all vertebrate duplication events in the AChR families, except for two among the nAChR genes, occurred through 1R, 2R and 3R, displaying the substantial impact of the WGDs on the evolution of the AChR genes.
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