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.

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

Distribution of Palinuridae and Scyllaridae phyllosoma larvae within the East Australian Current: a climate change hot spot

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

The evolution and origin of tetrodotoxin acquisition in the blue-ringed octopus (genus Hapalochlaena)

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.

Featured image is by Flickr user Rickard Ling (CC 2.0)

Comparative Proteomic Analysis of Slime from the Striped Pyjama Squid, Sepioloidea lineolata, and the Southern Bottletail Squid, Sepiadarium austrinum (Cephalopoda: Sepiadariidae)

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

Featured image is of Sepioloidea lineolata. Photograph by Richard Ling <wikipedia@rling.com> [CC BY-SA 3.0], via Wikimedia Commons

Shotgun Proteomics Analysis of Saliva and Salivary Gland Tissue from the Common Octopus Octopus vulgaris

Legana C. H. W. Fingerhut, Jan M. Strugnell, Pierre Faou, Álvaro Roura Labiaga, Jia Zhang, and Ira R. Cooke

Phylogenetic tree of molluscan serine proteases. Shaded clade is exclusive to Cephalopods and expressed in the venom gland

A wide variety of octopus and cuttlefish species use venom to disable and kill their prey.   Although this has been known for over a hundred years the molecules responsible for this toxicity remain relatively unknown.  In this paper we found that a particular family of proteins (serine proteases) are extremely diverse and abundant in the venom glands of octopus.  Although serine proteases are common in all animals (and not always toxins) we found that they are extraordinarily diverse in octopus and cuttlefish, and that this diversity is almost entirely due to molecules that are found in the venom glands.

Most of the work for this paper was done by Legana as part of her honours year. Well done Legana on your first paper.

Featured image is of Felicinda the octopus who was the mother of octopuses featured in this study. Photograph by Álvaro Roura

 Published in the Journal of Proteome Research