Claudio Slamovits
Author's posts
Feb 08
Evolution of amino acid propensities under stability-mediated epistasis
Mol Biol Evol. 2022 Feb 4:msac030. doi: 10.1093/molbev/msac030. Online ahead of print. ABSTRACT Site-specific amino acid preferences are influenced by the genetic background of the protein. The preferences for resident amino acids are expected to, on average, increase over time because of replacements at other sites – a nonadaptive phenomenon referred to as the ‘evolutionary …
Feb 04
Alexandriicola marinus gen. nov., sp. nov., a new member of the family Rhodobacteraceae isolated from marine phycosphere
Two yellow-pigmented bacterial strains, LZ-14 ^(T) and ABI-LZ29, were isolated from the cultivable phycosphere microbiota of the highly toxic marine dinoflagellate Alexandrium catenella LZT09 and demonstrated obvious microalgae growth-promoting potentials toward the algal host. To elucidate the taxonomic status of the two bioactive bacterial strains, they were subjected to a polyphasic taxonomic characterization. Both strains were found to be Gram-negative, aerobic, rod-shaped and motile; to…
Feb 04
Author Correction: Microbiome differential abundance methods produce different results across 38 datasets
Nat Commun. 2022 Feb 3;13(1):777. doi: 10.1038/s41467-022-28401-w. NO ABSTRACT PMID:35115546 | DOI:10.1038/s41467-022-28401-w
Feb 02
A robust approach to estimate relative phytoplankton cell abundances from metagenomes
Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of…
Jan 19
The Earth BioGenome Project 2020: Starting the clock
Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115635118. doi: 10.1073/pnas.2115635118. NO ABSTRACT PMID:35042800 | DOI:10.1073/pnas.2115635118
Jan 19
Why sequence all eukaryotes?
Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115636118. doi: 10.1073/pnas.2115636118. ABSTRACT Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there …
Jan 19
Standards recommendations for the Earth BioGenome Project
Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115639118. doi: 10.1073/pnas.2115639118. ABSTRACT A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer …
Jan 18
Microbiome differential abundance methods produce different results across 38 datasets
Nat Commun. 2022 Jan 17;13(1):342. doi: 10.1038/s41467-022-28034-z. ABSTRACT Identifying differentially abundant microbes is a common goal of microbiome studies. Multiple methods are used interchangeably for this purpose in the literature. Yet, there are few large-scale studies systematically exploring the appropriateness of using these tools interchangeably, and the scale and significance of the differences between them. …
Jan 17
First record of the spatial organization of the nucleosome-less chromatin of dinoflagellates: The nonrandom distribution of microsatellites and bipolar arrangement of telomeres in the nucleus of Gambierdiscus australes (Dinophyceae)
Dinoflagellates are a large group of protists whose exceptionally large genome is organized in permanently condensed nucleosome-less chromosomes. In this study, we examined the potential role of repetitive DNAs in both the structure of dinoflagellate chromosomes and the architecture of the dinoflagellate nucleus. Non-denaturing fluorescent in situ hybridization (ND-FSH) was used to determine the abundance and physical distribution of telomeric DNA and 16 microsatellites (1- to 4-bp repeats) in…
Jan 15
Unveiling the genomic structures and evolutionary events of the saxitoxin biosynthetic gene sxtA in the marine toxic dinoflagellate Alexandrium
Marine dinoflagellates Alexandriumare known to produce saxitoxin (STX) and cause paralytic shellfish poisoning (PSP) which can result in mortality in human. SxtA is considered a core gene for the biosynthesis of STX. However, its gene coding structure and evolutionary history have yet to be fully elucidated. Here, we determined the full-length sequences of sxtA cDNA and genomic coding regions from two toxic dinoflagellates, Alexandrium catenella (LIMS-PS-2645 and LIMS-PS-2647) andA. pacificum…