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.
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
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.
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.
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
Ira gave a talk on the genomics of non-model organisms at the UQ Winter School in Mathematical and Computational Biology. It was great to be given an opportunity to talk about some of my favourite topics and meet a bunch of talented bioinformaticians. Hats off to the organisers of this fantastic annual event including Nick Hamilton (Dr. Nick) who took this photo of me.
Special issue focusing on women in Marine Science in Australia featuring Jan Strugnell and Laura Woodings.
Laura Woodings, Nick Murphy, Andrew Jeffs, Iain Suthers, Geoff Liggins and Jan M. Strugnell
Laura sequenced the barcoding gene, Cytochrome oxidase I (COI), from palinurid and scyllarid lobster larvae (phyllosoma) caught off the east coast of Australia. She detected two tropical and one subtropical palinurid species ~75–1800 km to the south or southwest of their known species distribution. These results indicate tropical lobster species are reaching temperate regions, providing these species the opportunity to establish in temperate regions if or when environmental conditions become amenable to settlement.
Published in Marine and Freshwater Research
Featured image is a Phyllosoma by Ernst Haekel
Brooke L. Whitelaw, Ira R. Cooke, Julian Finn, Kyall Zenger, J.M. Strugnell
Blue ringed octopus make use of a deadly neurotoxin, TTX (tetrodotoxin) which is also found a wide variety of other animals. In order to do this they must be able to tolerate the toxin themselves, as well as acquire it from the environment or produce it. This paper reviews what we know about the evolution of ttx acquisition in blue ringed octopuses.
Nikeisha J. Caruana , Jan M. Strugnell, Pierre Faou, Julian Finn, and Ira R. Cooke
Nikeisha compared the slime from two bobtail squids and found that their proteomic composition was very similar. She also found several highly abundant, short secreted proteins in the slime, for which a function is unknown.
Published in the Journal of Proteome Research