Academic Adventures to the Other Side of the Globe

Posted on 11 February 2025 by admin

by Luke Silver (Post-doc)

In August of 2024 I had the exciting opportunity to undertake a three-month research stay in the Institute of Evolutionary Ecology and Conservation Genomics at Ulm University. So how did this come about?

Professor Simone Sommer was one of my thesis reviewers and she reached out to Kathy and Carolyn with an opportunity to combine my skillset in genomes and MHC annotation with some newly generated bat sequences. So at the start of August, I departed Sydney for an almost 30 hour journey to the city of Ulm (about 1 hour west of Munich) in southern Germany. Upon arrival at Ulm train station, I was met by a postdoc Dr Dominik Melville who showed me to my accommodation for the next three months. With no German language knowledge, I headed to the supermarket and managed to annoy the person at the register by not pre-weighing my fruits and vegetables – just one of many times that having some German language skills would have come in handy.

The purpose of my visit was to manually annotate genes of a crucial immune gene family known as the major histocompatibility complex (MHC) in bats. These genes form molecules with are expressed on cell surfaces and are responsible for detecting self and non -self and presenting foreign pathogen derived peptides to other cells of the immune system. We were able to leverage the recently released data from phase 1 of the Bat1K project (a consortium that aims to sequence the genomes of all living bat species around the world).

I also managed to find time to sample plenty of the local delicacies of beer and pretzels and to travel in the local area including to the beautiful Lake Konstanz, Stuttgart, Nuremberg, Vienna, Salzburg and Prague. This is just a small example of how science can lead to new and exciting experiences and opportunities.

Dr Luke Silver’s research is focused on generating and using genomic and transcriptomic resources for threatened Australian species. He used these resources to investigate the evolution of the immune system and study how diversity within immune genes is linked to disease traits. He has experience in characterisation of complex immune gene families, in particular the major histocompatibility complex which is a key component of the adaptive immune system

@LukeSilver20

How to catch a koala

Posted on 6 June 2024 by admin

by Dr. Luke Silver

Until recently, the majority of research in the Australasian Wildlife Genomics Group occurred on the Tasmanian devil and trapping these marsupial carnivores is quite a straightforward process. Setting a trap overnight baited with a tasty piece of fresh meat to lure the devils inside. Recently, I was lucky enough to be invited to Kangaroo Island to help out on a koala field trip. It turns out trapping herbivorous marsupials is a far more demanding task as unfortunately you cannot lure a koala with a fresh branch of Eucalyptus leaves.

Firstly, you have to actually find the koala in their environment, which can range of extremely tall Eucalyptus trees to highly dense shrubbery regions of bush. Fortunately, n Kangaroo Island koalas are so numerous locating one is not as difficult a task in areas such as NSW and QLD where koala numbers a much lower. After finally locating a koala the real work begins, coaxing the individual out of its comfortable and safe perch within the tree. This is best achieved by using an extendable pole with a piece of fabric attached to the end and simply waving this in front of the koala, who in ideal circumstances slowly backs down the tree trunk to height where they can be captured. Often, this is not the case, with koalas using any avenue possible to escape, including jumping to another nearby branch or tree. Being able to go into the field and see the animals we work up close is just one of the perks of working in wildlife research.

Author

Luke Silver (PhD Student) is using genomic data to
investigate immune genes in Australian marsupials with a focus on koalas where he is using resequenced genomes to examine patterns of diversity in functional and neutral regions of the genome across the entire east coast of Australia. This work will be used to inform conservation and management decisions in the fight to save our threatened species.

LukeSilver20

Koalas and Chlamydia: How can genomics help?

Posted on 15 July 2023 by admin

by Luke Silver (PhD Student)

The mention of a koala infected with Chlamydia will often be met with rounds of laughter or even concern, “can I get Chlamydia from touching a koala?” For koalas, Chlamydia is no laughing matter with up to 100% of individuals in some populations infected with the bacteria. In many cases infection will lead to blindness, “wet bottom” as a result of bladder infection, infertility and eventually death. Unfortunately, unlike humans, koalas are unable to go to the doctor and receive treatment for the infection. Often koalas are taken to veterinary hospitals after a human interaction (such as vehicle strike or a dog attack) and it is there the infection is noticed and treatment can be administered.

Genomics is the study of the genes and nucleotides contained within an individual’s genome. By studying the genomics of koalas, we have been able to identify important genes which play a vital role in helping a koala clear a Chlamydia infection. One of these genes is a part of the major histocompatibility complex, or MHC, known for its vital role in recognition of pathogens. We are now using the whole genomes of over 400 koalas to investigate how diverse the MHC genes of koalas are across their entire range from northern Queensland to South Australia. A high level of genetic diversity in the MHC results in an individual or population being able to recognise a wider array of pathogens and may be linked to the health of this endangered marsupial. Scientists in other labs are attempting to develop a vaccine which can prevent koalas from contracting the infection in the first place which has shown promising results in early phase testing.

Finally, fortunately you are unable to catch Chlamydia from holding or touching a koala as the species which infects koalas is different from the species which infects humans.

Author

lukesilver20

Koala Genome Survey: an open data resource to improve conservation planning

Posted on 23 February 2023 by admin

Type: Journal Article

Reference: Hogg, C. J., Silver, L., McLennan, E. A., & Belov, K. (2023). Koala Genome Survey: An Open Data Resource to Improve Conservation Planning. Genes, 14(3), 546. doi: 10.3390/genes14030546

Summary

Genome sequencing is a powerful tool that can inform the management of threatened species. Koalas (Phascolarctos cinereus) are a globally recognized species that captured the hearts and minds of the world during the 2019/2020 Australian megafires. In 2022, koalas were listed as ‘Endangered’ in Queensland, New South Wales, and the Australian Capital Territory. Populations have declined because of various threats such as land clearing, habitat fragmentation, and disease, all of which are exacerbated by climate change. Here, we present the Koala Genome Survey, an open data resource that was developed after the Australian megafires. A systematic review conducted in 2020 demonstrated that our understanding of genomic diversity within koala populations was scant, with only a handful of SNP studies conducted. Interrogating data showed that only 6 of 49 New South Wales areas of regional koala significance had meaningful genome-wide data, with only 7 locations in Queensland with SNP data and 4 locations in Victoria. In 2021, we launched the Koala Genome Survey to generate resequenced genomes across the Australian east coast. We have publicly released 430 koala genomes (average coverage: 32.25X, range: 11.3–66.8X) on the Amazon Web Services Open Data platform to accelerate research that can inform current and future conservation planning.

See all our publications HERE!

Luke Silver

Posted on 1 January 2023 by admin

Silver, L. (2023). Birth, Death and Diversity: Using genomes and genomics to investigate evolution of the marsupial MHC. The University of Sydney.

The major histocompatibility complex (MHC) is an immune gene family involved in the vertebrate immune response. Class I and class II genes have roles in resistance to disease and show high levels of diversity. MHC genes evolve through a birth and death process with class I genes evolving faster than class II genes. Marsupials are an interesting study system as they give birth to highly altricial and immunologically naïve young. The number of reference genomes available for marsupials has increased and it is now possible to bioinformatically annotate and compare the repertoire of MHC genes and investigate functional diversity in a number of species. Koalas are an iconic Australian marsupial threatened by two pathogens, Chlamydia pecorum and koala retrovirus (KoRV) and are currently listed as ‘Endangered’, making research into their immune system imperative for conservation of the species. This thesis investigates the birth, death and diversity of MHC genes in marsupials. This thesis provides a workflow for investigating evolution and diversity of any gene family in any wildlife species. I was able to achieve this by: i) tracing patterns of gene gain and loss in class II MHC genes across the marsupial lineage (29 species), ii) determine the minimum sequence depth required to accurately genotype MHC genes, iii) identify associations between variation in immune genes, and disease progression using koalas and Chlamydia and iv) investigate variation in SNPs and copy number within MHC genes of koalas. Overall, my thesis demonstrates the power of genomic technologies to investigate the birth, death, and diversity of MHC genes. By leveraging existing genomic resources and investigating sequencing and analysis methods, I was able to identify patterns of gene gain and loss, investigate the role of MHC diversity in disease resistance, and measure diversity across the entire range of koalas.

https://sydney.primo.exlibrisgroup.com/permalink/61USYD_INST/1c0ug48/alma991031727098905106