Daily Archives for October 12, 2019

A virus is attacking koalas’ genes. But their DNA is fighting back


Keith Chappell, The University of Queensland

A virus that infects koalas is steadily integrating itself into their DNA, ensuring that it is passed down from generation to generation. But the koala genome is defending itself, revealing that DNA has its own immune system to shut down invaders.

The virus, called koala retrovirus (KoRV), is linked to weakened immunity, cancer, and chlamydia infection in koalas. All retroviruses hijack the DNA in some cells of their host’s body, but not all of them manage to be transmitted to the host’s offspring.

Your DNA is 8% virus

Over the millions of years of evolutionary history, retroviruses have at one time or another made their way into the genomes of all species of vertebrates that we have studied.

We know about these ancient infections because retroviruses sometimes infect the animal’s sperm or egg cells, which means the virus incorporates its own DNA sequences into the genome that is passed from generation to generation.



Read more:
An ancient retrovirus has been found in human DNA – and it might still be active

These viral sequences can contribute to disease, but have also been “co-opted” by the host animals for processes that are essential to normal development. As much as 8% of the human genome is made up of the remnants of infectious viruses.

While we know that retroviruses have frequently appeared during evolutionary history, we don’t know much about how retroviral sequences infiltrate sperm and egg cells, or how these cells react.

Catching a retrovirus in the act

Almost all known retrovirus genome invasions happened millions of years ago. However, KoRV is a recently identified exception. The virus spreads between individuals, but is also infecting sperm and egg cells, so many koalas are born with this pathogen as part of their genome.

My colleagues and I at the University of Queensland are collaborating with scientists from the University of Massachusetts Medical School to analyse how koala sperm and egg cells respond to KoRV-A infection.

Our findings, published today in Cell, suggest these cells mount a novel “innate genome immune response” to viral infection, which may help control the spread of infectious KoRV.

Within this project, the team analysed DNA and RNA from different tissue samples from deceased wild koalas from South East Queensland. (Like DNA, RNA also contains genetic information about the koalas – but it is also what KoRV’s own genome is made of.)

The team specifically looked for short sequences of RNA, between 23 and 35 nucleotides long, known as PIWI Interacting RNAs (piRNAs). Clusters of piRNA sequences are retained within the genome and serve as a kind of memory bank of undesirable sequences – signatures of invading viruses – to be targeted.

An immune system for the genome

Based on our new findings, we suggest that there is a specialised immune system to defend against retroviral genome invasion. Like the ordinary immune system, this one includes an innate response – a sort of general-purpose defence against attackers – and an adaptive response, which learns to recognise specific pathogens and take them down.

At the early stages of egg or sperm infection, the altered DNA sequence results in a “molecular pattern” that is recognised by an innate genome immune system, which stops the activity of the virus and starts producing signature piRNA sequences to recognise the invader.



Read more:
Koalas sniff out juicy leaves and break down eucalypt toxins – it’s in their genome

The innate immune response works until a memory of the genome invader is created and a sequence-specific adaptive response kicks in.

We propose a framework through which a sequence from an invading retrovirus can first have its genes “silenced”, and then through targeted processes it eventually becomes an integral part of the host genome.

This “genome immune system” changes our understanding of what shapes the genomes of all animals. No more can we view the genome as a defenceless entity governed purely by natural selection – it fights back.The Conversation

Keith Chappell, Senior Research Fellow, School of Chemistry and Molecular Biosciences, The University of Queensland

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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It’s only October, so what’s with all these bushfires? New research explains it



Firefighters battle bushfires in Angourie, northern New South Wales, on September 10 this year, marking another early start to the season.
Jason O’Brien/AAP

Chris Lucas, Australian Bureau of Meteorology and Sarah Harris

Summer might be more than six weeks away, but out-of-control bushfires have already torn across parts of eastern Australia in recent days, destroying homes and threatening lives.

As of Wednesday afternoon, up to 30 homes were feared lost or badly damaged by bushfires burning in northern New South Wales. About 40 fires burned across the state.

This did not come as a surprise to meteorologists and fire agencies. Record-breaking heat and windy conditions were forecast for parts of NSW and Queensland this week, prompting severe fire danger ratings.

We’re often told the Australian bushfire season is starting earlier. This year it began in September on the eastern seaboard. Last year and in 2013, significant spring fires hit NSW and in 2015 they affected much of the nation’s southeast.

But what lies behind this phenomenon? We examined seasonal fire weather history for 44 years at 39 weather stations to find the precise answer.

This analysis is the most comprehensive ever conducted in Australia. It confirms the strength of the relationship between climate drivers such as El Niño, climate change, and the Australian bushfire season. It also demonstrates that a few milder bushfire seasons do not mean climate change isn’t happening.

A house burnt by bushfires in Laidley, southeast Queensland, photographed on October 9 2019.
Scott Davis/AAP

Hot, dry, windy conditions spell fire trouble

The prerequisites for a severe bushfire season are high temperatures, low humidity, and strong winds that coincide with long periods of low rainfall.

These weather ingredients are used to calculate an area’s fire danger rating, using the Forest Fire Danger Index. The index produces a score reflecting the severity of fire weather on a given day, where zero represents minimal fire danger, 50 represents conditions where a fire ban may be issued, and 100 is considered potentially catastrophic.



Read more:
Climate change is bringing a new world of bushfires

Loss of human lives and property most often occurs on days when the index is high in a particular area. But strong seasonal fire weather doesn’t always translate to high-impact fires. Other factors in play include terrain, vegetation, ignition and the weather on the day.

In our research, we analysed the strength of the worst fire weather conditions to understand the relative severity of fire weather during different seasons and years, in relation to various climate drivers.

A Bureau of Meteorology video explaining bushfire weather.

Why is fire weather so different every year?

In Australia, the year-to-year changes in climatic conditions are largely driven by three factors: the El Niño Southern Oscillation, the Indian Ocean Dipole, and the Southern Annular Mode.

Each of these climate drivers involves either changes to sea surface temperatures, wind movements, or both. They can all can affect temperature and rainfall patterns across the Southern Hemisphere, including Australia.

Our research confirmed that across the continent over more than four decades, climate drivers have affected the variability of Australia’s fire weather.



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Of these drivers, the El Niño Southern Oscillation is the most influential. Weather during an El Niño phase is typically hot and dry, leading to worse seasonal bushfire conditions.

The positive phase of the Indian Ocean Dipole often coincides with El Niño and exacerbates its effects. This phase generally results in lower than average rainfall across southern Australia.

But when these two climate modes are in a negative phase, our research confirms that Australia often experiences more rain and milder bushfire conditions.

The modes evolve over many months and their effects on fire weather persist for several seasons. Their state during winter and spring is a strong indicator for the rest of the fire season for much of Australia.

The strength of the relationship between climate drivers and fire weather in spring. Purple squares show the strength of the relationship. Larger squares indicate a stronger relationship.
User provided

The Southern Annular Mode refers to the north-south movement of strong westerly winds in parts of the Southern Hemisphere. When the mode is in a prolonged negative phase, fire weather conditions in Australia are worse – particularly in NSW. This effect is pronounced in winter and spring and means less rainfall and strong westerly winds.

The 2019 winter saw a persistent negative Southern Annular Mode, as did the 2013 and 2018 winter and spring seasons. There was a strong El Niño event and positive Indian Ocean Dipole in 2015. Australia’s bushfire season started earlier than usual in each of these years.

The converse is also true. In 2011 a strong La Niña (the opposite of an El Niño) resulted in milder bushfire seasons, as did the negative Indian Ocean Dipole of 2016.

Climate change is a culprit too

Long-term climate change in Australia is an undeniable reality. The State of the Climate 2018 report for Australia notes strong land surface temperature increases and a 10-20% decline in cool season rainfall across southern Australia since the 1970s. These changes are closely associated with increasing human greenhouse gas emissions, as well as natural variability.

The changed conditions has led to an average increase in the severity of seasonal bushfire weather across Australia – especially in southern parts of the continent. The increased severity affects all seasons but in particular spring, which means that, on average, the bushfire season is starting earlier.

NSW Premier Gladys Berejiklian visits the control room at the NSW Rural Fire Service headquarters in Sydney on October 9, 2019.
AAP/James Gourley

Pulling it all together

Our research has made clear that climate modes bring large and rapid swings to the fire weather, while human-induced climate change gradually increases background fire weather conditions. The trend generally means an earlier start to the bushfire seasons than in the past.



Read more:
Grim fire season looms but many Australians remain unprepared

Climate change is definitely playing a role in producing the earlier start to bushfire seasons and overall more extreme seasons, particularly in southeastern Australia. However, the natural variations in climate modes continue to play a key role, meaning we should not expect every bushfire season to be worse than the last as a result of climate change.

Similarly, a few milder bushfire seasons among a string of record high seasons does not mean that climate change should be dismissed.The Conversation

Chris Lucas, Senior Research Scientist, Australian Bureau of Meteorology and Sarah Harris, Manager Research and Development, Country Fire Authority

This article is republished from The Conversation under a Creative Commons license. Read the original article.