Joe’s comprehensive review on ciguatera poisoning, just published in Harmful Algae, offers an in-depth examination of the ecological dynamics of the toxic dinoflagellates Gambierdiscus and Fukuyoa. The paper evaluates current detection methods and provides innovative solutions to enhance monitoring and reduce the risk of ciguatera poisoning. This review serves as a valuable resource for researchers and practitioners aiming to understand and mitigate the impact of the worlds most prevalent non-bacterial seafood illness.
Author: iracooke
In pursuit of the perfect abalone genome
Roy’s beautiful genome paper is published today in Nature Scientific Data. Using a combination of Hi-Fi sequencing and Omni-C scaffolding, Roy managed to obtain an extremely high quality genome for this species. Even, better, this genome includes gene models generated with PacBio Iso-Seq making it by far the best abalone genome resource to date. The paper is titled, Chromosome-scale genome assembly of the tropical abalone, (Halitosis asinina)
Chromosomal inversions harbour deleterious mutations in the coral, Acropora kenti
A new paper led by Jia shows that there are at least five large, highly polymorphic chromosomal inversions in Acropora kenti, a widespread coral on the Great Barrier Reef. This paper highlights the potential importance of structural variation in corals, and the need for new approaches to characterise it. Published in Molecular Ecology.
DNA reveals the past and future of coral reefs
A new paper by Jia in Molecular Biology and Evolution showcases the power of whole genome sequencing to understand adaptive evolution in corals. Thanks to our collaborators in Western Australia we were able to obtain samples for deep WGS on 75 corals, including samples from the inshore Kimberley reefs and two offshore atolls. The results revealed very recent divergence driven by founder effects and strong selection, especially in the inshore reefs.
Paper: https://doi.org/10.1093/molbev/msac201
Press Release: https://www.coralcoe.org.au/media-releases/dna-reveals-the-past-and-future-of-coral-reefs
Evolutionary innovations in Antarctic brittle stars linked to glacial refugia
New paper by Sally, Catarina and Jan in Ecology & Evolution, uses COI sequences to investigate the population genetic patterns of the Antarctic brittle stars Ophionotus victoriae and O. hexactis with contrasting life histories (broadcasting vs brooding) and morphology (5 vs 6 arms). They found that, throughout the Pleistocene glacial maxima, O. victoriae likely persisted in deep sea refugia; whereas O. hexactis likely persisted in Antarctic island refugia. This work proposes the evolutionary innovations in O. hexactis (increase in arm number and a switch from broadcast spawning to brooding) could be linked to survival within island refugia, which open up new avenues for future genomic research!
Reference Genome and Population Genomics of coral (Acropora tenuis) on the inshore Great Barrier Reef
New paper by Ira, Jan and Jia in Science Advances (full article here), uses shallow whole genome sequencing to look at demographic history and selection for Acropora tenuis. The main findings are outlined in this tweet thread. Maria Nayfa also made this nice video of Ira explaining why genomes are so useful for understanding the history of the GBR.
Australian Geographic interviews Jan on “My Octopus Teacher”
My Octopus Teacher is a new documentary about the relationship between a man and an octopus. Jan was interviewed for her thoughts by Australian Geographic
ampir a new R package from the group
Antimicrobial peptides are part of the innate immune system and help defend the host against pathogens and regulate the microbiome. Antimicrobial peptides occur in all life, are incredibly diverse, mostly quite small (< 200 amino acids), and only comprise of a small proportion in a genome (~ 1%). This makes them very difficult to find. We created a classification model implemented in an R package, ampir, to predict antimicrobial peptides from protein sequences on a genome-wide scale. ampir was tested on multiple test sets (including complete proteomes) and performed with high accuracy. ampir can be used to narrow down the search space for novel antimicrobial peptides in genomes.
ampir was recently published in Bioinformatics and is available on CRAN and github . Legana has also created a companion repository to accompany the paper and document the thinking behind ampir’s model building process.
Adventures in the Southern Ocean
By Sally Lau
On the 10th January I sailed on the RV Investigator from Perth, WA to the Southern Ocean and Southern Indian Ocean, and embarked a 57 days voyage alongside an IMAS-led research team. The main focus of the voyage was to examine Australia’s marine jurisdiction around William’s Ridge (Kerguelen Plateau), and the ancient rifting, break up and separation of tectonic plates that once connected William’s Ridge and Broken Ridge (Southern Indian Ocean). I volunteered as a molecular ecologist on this voyage to sample, identify and preserve any benthic biota that came up with deep sea rock dredges, as well as a Marine Mammal Observer (MMO) to ensure all underwater seismic operations were performed in the best interests of cetaceans (Thankfully we didn’t observe any marine mammals during our seismic days! Win-win for all mammals in the areas!).
A typical day of seismic science on the Investigator meant many happy faces in the mess during dinner time. But all would not be possible without team work between everyone on board – from the bottom deck (ship engineers who ensured ship mechanics ran right), to the operation room (where scientists and technical staff made sure the raw data were coming in as anticipated, and field operators checking all airguns were firing correctly), to all the way up the bridge (master and mates who steered the ship on the right course) and monkey island (MMOs and volunteers who made sure no cetaceans were in sight).
When seismic operation was over during each day, that’s when rock (and roll) night dredges began. In total we deployed 21 dredges and recovered benthic biota from more than half of the dredges – not a bad haul! Overall, we collected benthic fauna from depths between <1000 m and >4000 m, including animals from various taxa such as annelids, brachiopods, bryozoan, cnidarian, crustaceans, echinoderms and poriferans. We have now transported these specimens safely back to WA museum and hopefully they will be interesting assets to the collections!
Life on a ship can be a bit tough during rough weather (e.g. 10 m swell on valentine’s day) but the amount of interesting science and activities that were happening had made it very worthwhile to be on a research cruise in the Southern Ocean. Before this trip, I had never thought I could understand birds, geology and ship mechanics but here I am – a proud twitcher with a brain full of knowledge of rocks, seismic, mapping and ship science! I am very thankful to the science party (esp my awesome lab partner Paige Maroni), medical staff on board and the crew who made this such a rewarding experience.
Quantitative Proteomic Analysis of the Slime and Ventral Mantle Glands of the Striped Pyjama Squid (Sepioloidea lineolata)
New paper in Journal of Proteome Research by group alumnus, Nikeisha Caruana uses quantitative proteomics to understand slime secretions in striped pyjama squid. For this work Nikeisha used a multi-tissue comparison to hone in proteins unique to slime-producing glands. The work is also the first time these glands have been described in detail and their proteomic similarity to the slime and physical structure implicates them as likely secretion structures.
Publication Link: https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.9b00738
Nikeisha Caruana is now a research fellow at the Bio 21 institute in Melbourne