| 1. |
- Clark, Andrew G., et al.
(författare)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Tidskriftsartikel (refereegranskat)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 2. |
- Horvatovich, Peter, et al.
(författare)
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Quest for Missing Proteins : Update 2015 on Chromosome-Centric Human Proteome Project
- 2015
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 14:9, s. 3415-3431
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- This paper summarizes the recent activities of the Chromosome-Centric Human Proteome Project (C-HPP) consortium, which develops new technologies to identify yet-to-be annotated proteins (termed "missing proteins") in biological samples that lack sufficient experimental evidence at the protein level for confident protein identification. The C-HPP also aims to identify new protein forms that may be caused by genetic variability, post-translational modifications, and alternative splicing. Proteogenomic data integration forms the basis of the C-HPP's activities; therefore, we have summarized some of the key approaches and their roles in the project. We present new analytical technologies that improve the chemical space and lower detection limits coupled to bioinformatics tools and some publicly available resources that can be used to improve data analysis or support the development of analytical assays. Most of this paper's content has been compiled from posters, slides, and discussions presented in the series of C-HPP workshops held during 2014. All data (posters, presentations) used are available at the C-HPP Wild (http://c-hpp.webhosting.rug.nl/) and in the Supporting Information.
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| 3. |
- Smith, LK, et al.
(författare)
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Adaptive translational reprogramming of metabolism limits the response to targeted therapy in BRAFV600 melanoma
- 2022
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1, s. 1100-
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Tidskriftsartikel (refereegranskat)abstract
- Despite the success of therapies targeting oncogenes in cancer, clinical outcomes are limited by residual disease that ultimately results in relapse. This residual disease is often characterized by non-genetic adaptive resistance, that in melanoma is characterised by altered metabolism. Here, we examine how targeted therapy reprograms metabolism in BRAF-mutant melanoma cells using a genome-wide RNA interference (RNAi) screen and global gene expression profiling. Using this systematic approach we demonstrate post-transcriptional regulation of metabolism following BRAF inhibition, involving selective mRNA transport and translation. As proof of concept we demonstrate the RNA processing kinase U2AF homology motif kinase 1 (UHMK1) associates with mRNAs encoding metabolism proteins and selectively controls their transport and translation during adaptation to BRAF-targeted therapy. UHMK1 inactivation induces cell death by disrupting therapy induced metabolic reprogramming, and importantly, delays resistance to BRAF and MEK combination therapy in multiple in vivo models. We propose selective mRNA processing and translation by UHMK1 constitutes a mechanism of non-genetic resistance to targeted therapy in melanoma by controlling metabolic plasticity induced by therapy.
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| 4. |
- Waller, Rhian, 1978, et al.
(författare)
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A review of current knowledge on reproductive and larval processes of deep-sea corals
- 2023
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Ingår i: Marine Biology. - 0025-3162. ; 170
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Forskningsöversikt (refereegranskat)abstract
- The presence of corals living in deep waters around the globe has been documented in various publications since the late 1800s, when the first research vessels set sail on multi-year voyages. Ecological research on these species, however, only truly began some 100 years later. We now know that many species of deep-sea coral provide ecosystem services by creating complex habitat for thousands of associated species, and thus are major contributors to global marine biodiversity. Among the many vital ecological processes, reproduction provides a fundamental link between individuals and populations of these sessile organisms that enables the maintenance of current populations and provides means for expansion to new areas. While research on reproduction of deep-sea corals has increased in pace over the last 20 years, the field is still vastly understudied, with less than 4% of all known species having any aspect of reproduction reported. This knowledge gap is significant, because information on reproduction is critical to our understanding of species-specific capacity to recover from disturbances (e.g., fishing impacts, ocean warming, and seafloor mining). It is important, therefore, to examine the current state of knowledge regarding deep-sea coral reproduction to identify recent advances and potential research priorities, which was the aim of the present study. Specifically, this review synthesizes the research carried out to date on reproduction in deep-living species of corals in the orders Alcyonacea, Scleractinia, Antipatharia, Pennatulacea (class Anthozoa), and family Stylasteridae (class Hydrozoa).
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