Category: Papers by CGEB labs

Description of the Marine Predator Sericomyxa perlucida gen. et sp. nov., a Cultivated Representative of the Deepest Branching Lineage of Vampyrellid Amoebae (Vampyrellida, Rhizaria)

J Eukaryot Microbiol. 2021 Jun 21:e12864. doi: 10.1111/jeu.12864. Online ahead of print. ABSTRACT The vampyrellids (Vampyrellida, Rhizaria) are an order of naked amoebae of considerable genetic diversity. Three families have been well defined (Vampyrellidae, Leptophryidae, Placopodidae), but most vampyrellid lineages detected by environmental sequencing are poorly known or completely uncharacterised. In the brackish sediment of …

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‘Species’ without species

Stud Hist Philos Sci. 2021 Apr 1;87:72-80. doi: 10.1016/j.shpsa.2021.03.006. Online ahead of print. ABSTRACT Biological science uses multiple species concepts. Order can be brought to this diversity if we recognize two key features. First, any given species concept is likely to have a patchwork structure, generated by repeated application of the concept to new domains. …

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The role of purifying selection in the origin and maintenance of complex function

Stud Hist Philos Sci. 2021 Apr 11;87:125-135. doi: 10.1016/j.shpsa.2021.03.005. Online ahead of print. ABSTRACT Fitness contribution alone should not be the criterion of ‘function’ in molecular biology and genomics. Disagreement over the use of ‘function’ in molecular biology and genomics is still with us, almost eight years after publicity surrounding the Encyclopedia of DNA Elements …

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Re-examination of two diatom reference genomes using long-read sequencing

BMC Genomics. 2021 May 24;22(1):379. doi: 10.1186/s12864-021-07666-3. ABSTRACT BACKGROUND: The marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity and ecology of this important algal group. Their reference genomes, published in 2004 and 2008, respectively, were the product of traditional Sanger sequencing. In the case of T. pseudonana, …

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Analysis of diverse eukaryotes suggests the existence of an ancestral mitochondrial apparatus derived from the bacterial type II secretion system

Nat Commun. 2021 May 19;12(1):2947. doi: 10.1038/s41467-021-23046-7. ABSTRACT The type 2 secretion system (T2SS) is present in some Gram-negative eubacteria and used to secrete proteins across the outer membrane. Here we report that certain representative heteroloboseans, jakobids, malawimonads and hemimastigotes unexpectedly possess homologues of core T2SS components. We show that at least some of them …

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Treasurer’s Report for Financial Year (FY) 2019

Mol Biol Evol. 2021 May 3:msab012. doi: 10.1093/molbev/msab012. Online ahead of print. NO ABSTRACT PMID:34009329 | DOI:10.1093/molbev/msab012

Identifying biases and their potential solutions in human microbiome studies

Microbiome. 2021 May 18;9(1):113. doi: 10.1186/s40168-021-01059-0. ABSTRACT Advances in DNA sequencing technology have vastly improved the ability of researchers to explore the microbial inhabitants of the human body. Unfortunately, while these studies have uncovered the importance of these microbial communities to our health, they often do not result in similar findings. One possible reason for …

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An in vivo genome-wide shRNA screen identifies BCL6 as a targetable biomarker of paclitaxel resistance in breast cancer

Mol Oncol. 2021 May 1. doi: 10.1002/1878-0261.12964. Online ahead of print. ABSTRACT Paclitaxel is a common breast cancer drug; however, some tumors are resistant. The identification of biomarkers for paclitaxel resistance or sensitivity would enable the development of strategies to improve treatment efficacy. A genome-wide in vivo shRNA screen was performed on paclitaxel-treated mice with …

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The past, present and future of the tree of life

Curr Biol. 2021 Apr 12;31(7):R314-R321. doi: 10.1016/j.cub.2021.02.052. ABSTRACT The advent of comparative genomics in the late 1990s led to the discovery of extensive lateral gene transfer in prokaryotes. The resulting debate over whether life as a whole is best represented as a tree or a network has since given way to a general consensus in …

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Mitochondrial Genome Evolution in Pelagophyte Algae

Genome Biol Evol. 2021 Mar 1;13(3):evab018. doi: 10.1093/gbe/evab018. ABSTRACT The Pelagophyceae are marine stramenopile algae that include Aureoumbra lagunensis and Aureococcus anophagefferens, two microbial species notorious for causing harmful algal blooms. Despite their ecological significance, relatively few genomic studies of pelagophytes have been carried out. To improve understanding of the biology and evolution of pelagophyte …

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