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Image credit: Researchers from the NUS Department of Biological Sciences extracted images of human activity in protected areas, such as hiking, from Flickr and tagged them to categorise the type of activity in the photo to analyse the global distribution of that activity across different protected areas.

Monitoring of nature reserves via social media and deep learning

By | News, Plant Science

Researchers have created a deep learning method to analyze social media images taken within protected green spaces to gain insights on human activity distribution as a way to monitor the ecological impacts of these activities.

Environmental biology researchers at the National University of Singapore (NUS) have developed an efficient method for rapidly identifying and classifying human activities within nature reserves at the global level, using social media and deep learning techniques.

Many people visit nature reserves for various reasons, such as hiking to keep fit. 

Despite these benefits, it is clear that having too many visitors could lead to overcrowding and negatively impact conservation efforts.

Consequently, to implement more effective land use management strategies for crowd control, governments need to gain insights into how these green spaces are used. 

However, as most of these nature reserves cover large land areas, using conventional field surveys to monitor human activities within them can be costly and time-consuming.

The research team, led by Associate Professor L Roman CARRASCO from the Department of Biological Sciences under the NUS Faculty of Science along with his PhD student, Mr Timothy Bing Lun YEE, has developed a technique to process social media images taken within protected areas (PAs) as a proxy for identifying human activities within them. 

By parsing these images through a deep learning image tagging model, the human activities depicted within them are automatically detected. 

These tagged images are then subsequently grouped into distinct categories of human activities. 

They analysed a total of 87,090 photos from 2,813 PAs in 207 countries for this study.

These findings have been published in Scientific Reports.

The researchers made some interesting observations. Most notably, distinct clusters of activity types across PAs aligned closely with expectations. 

For instance, there were many photographs of animals and plants in Southeast Asian PAs, while European PAs had numerous photographs of historic castles. 

Also, PAs within the same country showed similar activities, even if they had different physical environments.

In explaining the significance of this work, Mr YEE said, “While there have been similar studies, this is possibly the first study that tries to investigate human activities within PAs on a global scale. It demonstrates the utility of social media and deep learning in empowering researchers to investigate pressing environmental issues at a much larger scale.”

Prof CARRASCO added, “The team hopes that this technique can be adopted by nature organisations to monitor land use patterns in nature reserves efficiently and cost-effectively, enabling more targeted conservation efforts to protect ecosystems despite increasing visitor numbers.”


Read the paper: Scientific Reports

Article source: National University of Singapore

Image credit: Researchers from the NUS Department of Biological Sciences extracted images of human activity in protected areas, such as hiking, from Flickr and tagged them to categorise the type of activity in the photo to analyse the global distribution of that activity across different protected areas.


Image: Bristlecone Pine Great Basin National Park, Nevada--over 3,00 years old. Credit: George Longenecker/ Wikimedia Commons

Ancient pines could reveal the heat of thousands of past seasons

By | News, Plant Science

High in the arid White Mountains of eastern California stand the gnarled, twisted trunks of ancient bristlecone pines. These slow-growing trees quietly weather the ages; at more than 4,000 years old, some are more ancient than the Great Pyramid of Giza.Now, researchers present a novel approach that uses X-ray computed tomography (CT) to capture the wood density of bristlecone tree rings and generate annual resolution reconstructions of ancient temperatures.

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Image: A historic potato plant specimen collected by David Moore from the National Botanic Garden in Glasnevin, Ireland showing late-blight disease. Credit: Jean Ristaino, NC State University.

Study Analyzes Potato-Pathogen ‘Arms Race’ After Irish Famine

By | News

In an examination of the genetic material found in historic potato leaves, North Carolina State University researchers reveal more about the tit-for-tat evolutionary changes occurring in both potato plants and the pathogen that caused the 1840s Irish potato famine.

The study used a targeted enrichment sequencing approach to simultaneously examine both the plant’s resistance genes and the pathogen’s effector genes – genes that help it infect hosts – in a first-of-its-kind analysis.

“We use small pieces of historic leaves with the pathogen and other bacteria on them; the DNA is fragmented more than a normal tissue sample,” said Allison Coomber, an NC State former graduate student researcher and lead author of a paper in Nature Communications that describes the study. “We use small 80 base-pair chunks like a magnet to fish out similar pieces in this soup of DNA. These magnets are used to find resistance genes from the host and effector genes from the pathogen.”

“This is a first for looking at both potato and pathogen changes at the same time; usually researchers look at one or the other,” says Jean Ristaino, William Neal Reynolds Distinguished Professor of Plant Pathology at North Carolina State University and corresponding author of the paper. “The dual enrichment strategy employed here allowed us to capture targeted regions of genomes of both sides of the host-pathogen relationship, even when host and pathogen were present in unequal amounts. We couldn’t have done this work 15 years ago because the genomes weren’t sequenced.”

The study’s results show that the pathogen, Phytophthora infestans, is very adept at fighting off potato late blight disease resistance. For example, the study shows that the FAM-1 strain of the pathogen had the ability to defeat the resistance provided by the plant’s R1 resistance gene – even before plant breeders deployed it in potato.

“The pathogen would have been able to resist this R1 resistance gene even if it had been deployed years earlier, probably because it was exposed to a potato with that resistance gene in the wild,” Coomber said.

The study also shows that many of the pathogen’s effector genes have remained stable, although different mutations have occurred to increase its infection prowess as plant breeders attempted to breed resistance – specifically after 1937 when more structured potato breeding programs commenced in the United States and other parts of the globe.

The study also shows that the pathogen added a set of chromosomes between 1845 and 1954, the period of time in which the study’s plant samples were collected.

“We show in this work that after 100 years of human intervention, there are some genes that haven’t changed much in the pathogen,” Coomber said. “They are very stable potentially because they haven’t been selected on, or because they are really important to the pathogen. Targeting those genes would make it really hard for the pathogen to evolve an opposing response.”

“It’s hard to do effective plant breeding when we don’t know enough about the pathogen. Now that we know what effectors have changed over time, breeders may be able use resistance genes that are more stable or pyramid multiple resistance genes from different wild hosts,” Ristaino said.

“That’s where I see the future for this type of study – applying it to slow changes in pathogen virulence or other traits such as fungicide resistance.”

Amanda C. Saville, a research and laboratory specialist in Ristaino’s lab, also co-authored the paper. Funding was provided by a seed grant from the Triangle Center for Evolutionary Medicine, by National Science Foundation AgBioFews Training Grant Number 2018-1966 and by Grip4PSI Grant Number 557299.


Read the paper: Nature Communications

Article source: North Carolina State University

Author: Mick Kulikowski

Image: A historic potato plant specimen collected by David Moore from the National Botanic Garden in Glasnevin, Ireland showing late-blight disease. Credit: Jean Ristaino, NC State University.