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.

Detecting Glacial Refugia in the Southern Ocean

Throughout the Plio-Pleistocene glacial cycles, the Antarctic ice sheets expanded and contracted repeatedly, which led to the repeated erosion of the Antarctic continental shelf throughout glacial maxima. Even though molecular and paleontological evidence suggests most extant Antarctic benthos persisted in situ in the Southern Ocean during Plio-Pleistocene, where and how they survived remain mostly hypothesised.

Our paper recently published in Ecography synthesises current geological and ecological evidence to understand where and how benthos might have survived glacial cycles and how this challenging period might have impacted past species demography. We also examined current molecular evidence of glacial refugia in the Southern Ocean, as well as discussed future directions for employing testable frameworks and genomic methods in Southern Ocean molecular studies.

Jesus clouds

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).

Jesus clouds
Whale spotting made easy when you’re staring into the “Jesus clouds”.

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!

Patiently waiting for the rock dredge to come up on deck. Photo credit: Adrian Koolhof.

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.

First animal collected on this voyage – a crowd favourite after speaking about brittle star genomics during transit!
A rare calm day in the Southern Ocean.

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

Abalone sampling at Southern Ocean Mariculture

Jan and Phoebe visited Southern Ocean Mariculture (SOM) in Port Fairy, Victoria at the start of July to collect samples for Phoebe’s honours project. Phoebes project, supported by the Fisheries Research and Development Corporation and the Australian Abalone Growers Association, seeks to test established methods of early prediction of genetic merit in abalone broodstock. It was freezing in Port Fairy in comparison to sunny Townsville, but great to see the abalone growth and the impressive technology and set up at SOM! Thanks for hosting us!

Abalone = Yum!

8th International Barcode of Life Conference

Jan gave a plenary lecture at the 8th International Barcode of Life Conference in Trondheim, Norway on June 19. Jan spoke about “Dating the West Antarctic ice sheet collapse using molecular sequence data.” The conference was great – loads of metabarcoding presentations including monitoring freshwater and marine environments and also using barcoding to ascertain the ingredients in foods. Great to catch up with old friends and make new ones and see a little bit of beautiful Norway!

Jan delivering her lecture in Trondheim