Biology subjects

Bunyan, M.

Publications and source records attributed to Bunyan, M..

5 recordsLinked to original sources

bioRxiv2021

Testing the efficacy of hyperspectral (AVIRIS-NG), multispectral (Sentinel-2) and radar (Sentinel-1) remote sensing images to detect native and invasive non-native trees

Invasive alien species (IAS) threaten tropical grasslands and native biodiversity and impact ecosystem service delivery, ecosystem function, and associated human livelihoods. Tropical grasslands have been dramatically and disproportionately lost to invasion by trees. The invasion continues to move rapidly into the remaining fragmented grasslands impacting various native grassland-dependent species and water streamflow in tropical montane habitats. The Shola Sky Islands of the Western Ghats host a mosaic of native grasslands and forests; of which the grasslands have been lost to exotic tree invasion (Acacias, Eucalyptus and Pines) since the 1950s. The invasion intensities, however, differ between these species wherein Acacia mearnsii and Pinus patula are highly invasive in contrast to Eucalyptus globulus. These disparities necessitate distinguishing these species for effective grassland restoration. Further, these invasive alien trees are highly intermixed with native species, thus requiring high discrimination abilities to native species apart from the non-native species. Here we assess the accuracy of various satellite and airborne remote sensing sensors and machine learning classification algorithms to identify the spatial extent of native habitats and invasive trees. Specifically, we test Sentinel-1 SAR and Sentinel-2 multispectral data and assess high spatial and spectral resolution AVIRIS-NG imagery identifying invasive species across this landscape. Sensor combinations thus include hyperspectral, multispectral and radar data and present tradeoffs in associated costs and ease of procurement. Classification methods tested include Support Vector Machine (SVM), Classification and Regression Trees (CART) and Random Forest (RF) algorithms implemented on the Google Earth Engine platform. Results indicate that AVIRIS-NG data in combination with SVM recover the highest classification skill (Overall -98%, Kappa-0.98); while CART and RF yielded < 90% accuracy. Fused Sentinel-1 and Sentinel-2 produce 91% accuracy, while Sentinel-2 alone yielded 91% accuracy with RF and SVM classification; but only with higher coverage of ground control points. AVIRIS-NG imagery was able to accurately (97%) demarcate the Acacia invasion front while Sentinel-1 and Sentinel-2 data failed. Our results suggest that Sentinel-2 images could be useful for detecting the native and non-native forests with more ground truth points, but hyperspectral data (AVIRIS-NG) permits distinguishing, native and non-native tree species and recent invasions with high precision using limited ground truth points. We suspect that large areas will have to be mapped and assessed in the coming years by conservation managers, NGOs to plan restoration, or to assess the success of restoration activities, and several data procurement and analysis steps may have to be simplified.

ecology↗

bioRxiv2020

Cellular barcoding of Toxoplasma reveals permissive host brain colonization

Molecular barcoding techniques have emerged as powerful tools to understand microbial pathogenesis. However, barcoding strategies have not been extended to protozoan parasites, which have unique genomic structures and virulence strategies compared to viral and bacterial pathogens. Here, we present a versatile CRISPR-based method to barcode protozoa, which we successfully apply to Toxoplasma gondii and Trypanosoma brucei. The murine brain is an important transmission niche for T. gondii, and brain persistence is a clinically untreatable feature of infection. The blood-brain barrier is expected to physically restrict parasite colonization of this niche, resulting in a selection bottleneck. Using libraries of barcoded T. gondii we evaluate shifts in the population structure from acute to chronic infection of mice. Contrary to expectation, most barcodes were present in the brain one-month post-intraperitoneal infection in both inbred CBA/J and outbred Swiss mice. Although parasite cyst number and barcode diversity declined over time, barcodes that represented a minor fraction of the inoculum could become a dominant population in the brain by three months post-infection. Together, these data establish the first, robust molecular barcoding approach for protozoa and evidence that the blood-brain barrier does not represent a major bottleneck to colonization by T. gondii.

microbiology↗

bioRxiv2020

Opportunities and challenges in using remote sensing for identifying grassland restoration sites and invasive tree species management in a global biodiversity hotspot

Tropical montane grasslands (TMG) support biodiverse and endemic taxa and provide vital ecosystems services to downstream communities. Yet invasive alien tree species across the world have threatened tropical grasslands and grassland endemic species. In India, TMG in the Shola Sky Islands of the Western Ghats have been reduced due to exotic tree invasions (acacias, pines, and eucalyptus species). The loss of grassland habitat has, in turn, reduced the range sizes of species endemic to grasslands (plants, birds, amphibians, and mammals), driving some populations to local extinction. Grassland conversion to exotic trees has also reduced the annual runoff in the Western Ghats. Conserving existing grassland and restoring invaded habitat is critical to reverse these losses. This research focused on identifying grassland restoration sites using satellite images with a high spatial resolution (RapidEye). We used an object-oriented Random Forest classification to map the area for grassland restoration. We have identified an area of 254 sq. km. as suitable for grassland restoration and an area of 362 sq. km. for grassland conservation and prevention from invasion by exotic tree species. For restoration, we recommend a cautious removal of young and isolated exotic trees at the invasion front and restoring grasslands, instead of removing dense stands of mature exotic trees. We find that areas with low fire frequency areas tend to be invaded, but areas invaded by exotic trees tend to burn hotter which may be harmful to grassland species and ecosystems. We assume that removing exotic tree species in the identified restoration sites and restoring the grassland will be helpful in recovering lost habitat and ensuring the viability of populations of indigenous and endemic species and increasing streamflow.

ecology↗

bioRxiv2018

An Artificial Intelligence Workflow for Defining Host-Pathogen Interactions

For image-based infection biology, accurate unbiased quantification of host-pathogen interactions is essential, yet often performed manually or using limited enumeration employing simple image analysis algorithms based on image segmentation. Host protein recruitment to pathogens is often refractory to accurate automated assessment due to its heterogeneous nature. An intuitive intelligent image analysis program to assess host protein recruitment within general cellular pathogen defense is lacking. We present HRMAn (Host Response to Microbe Analysis), an open-source image analysis platform based on machine learning algorithms and deep learning. We show that HRMAn has the capability to learn phenotypes from the data, without relying on researcher-based assumptions. Using Toxoplasma gondii and Salmonella typhimurium we demonstrate HRMAns capacity to recognize, classify and quantify pathogen killing, replication and cellular defense responses.

microbiology↗

bioRxiv2017

Free ISG15 as a dimer generates IL-1β-producing CD8α+ dendritic cells at the site of infection

ISG15 is strongly induced after type I IFN stimulation producing a protein comprised of two ubiquitin-like domains. Intracellularly, ISG15 can be covalently linked and modify the function of target proteins (ISGylation). In addition, free unconjugated ISG15 can be released from cells. We found that ISG15 is released in the serum of Toxoplasma gondii infected mice early after infection in a type-I IFN independent manner. Once in the extracellular space, free ISG15 forms dimers and enhances the release of key cytokines involved in the immune response to the parasite: IL-12, IFN-{gamma}, and IL-1{beta}. Its action is dependent on an actively invading and replicating live parasite. ISG15 induces an increase of IL-1{beta} later during infection by leading to increased IL-1{beta} producing CD8+ dendritic cells at the site of infection. Here, we define for the first time the molecular determinants of active free ISG15 and link ISG15 to IL-1{beta} production by CD8+ dendritic cells. Thus we define ISG15 as a novel secreted modulator of the cytokine response during Toxoplasma infection.

immunology↗