Category: Papers by CGEB labs

Shifts in amino acid preferences as proteins evolve: a synthesis of experimental and theoretical work

Protein Sci. 2021 Jul 28. doi: 10.1002/pro.4161. Online ahead of print. ABSTRACT Amino acid preferences vary across sites and time. While variation across sites is widely accepted, the extent and frequency of temporal shifts are contentious. Our understanding of the drivers of amino acid preference change is incomplete: To what extent are temporal shifts driven …

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Gut bacterial gene changes following pegaspargase treatment in pediatric patients with acute lymphoblastic leukemia

Leuk Lymphoma. 2021 Jul 19:1-12. doi: 10.1080/10428194.2021.1953006. Online ahead of print. ABSTRACT Treatment of pediatric acute lymphoblastic leukemia (ALL) with pegaspargase exploits ALL cells dependency on asparagine. Pegaspargase depletes asparagine, consequentially affecting aspartate, glutamine and glutamate. The gut as a confounding source of these amino acids (AAs) and the role of gut microbiome metabolism of …

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Correction to: A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere

Microbiome. 2021 Jul 6;9(1):155. doi: 10.1186/s40168-021-01120-y. NO ABSTRACT PMID:34229759 | DOI:10.1186/s40168-021-01120-y

A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere

Microbiome. 2021 Jun 21;9(1):141. doi: 10.1186/s40168-021-01054-5. ABSTRACT BACKGROUND: Plastics now pollute marine environments across the globe. On entering these environments, plastics are rapidly colonised by a diverse community of microorganisms termed the plastisphere. Members of the plastisphere have a myriad of diverse functions typically found in any biofilm but, additionally, a number of marine plastisphere …

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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