‘InfraRivChange’: a web application to monitor river migration at sites of critical bridge infrastructure in the Philippines

Shifting rivers, particularly with high migration rates, represent a geomorphic hazard at sites of critical bridge infrastructure. Conventional attempts to map and measure shifts in the position of river channels usually requires the manual digitization of riverbanks from satellite imagery using Geographic Information Systems (GIS) – a time-consuming process only feasible at a limited number of bridge sites using a small selection of satellite images. As part of the CDRI Fellowship, the authors leveraged the cloud computing platform Google Earth Engine (GEE) to substantially upscale analyses using Earth observation (EO) data. Focusing on the Philippines, they designed a user-friendly web application for technical and non-technical users to monitor the relative risk of river migration at sites of critical bridge infrastructure by analysing thousands of satellite images. ‘InfraRivChange’ uses openly accessible satellite imagery from Landsat (30mspatial resolution) and Sentinel (10 m spatial resolution) to quantify river channel changes at bridge sites. The study demonstrates the web application at test sites and suggests use-cases relevant to disaster resilient infrastructure. As a low-cost approach for monitoring shifting large rivers in the vicinity of infrastructure, InfraRivChange can be incorporated into bridge monitoring systems (e.g., as a component of bridge stability assessments) and inform the design and placement of future infrastructure. They envision that InfraRivChange can be applied to additional forms transport infrastructure adjacent to rivers (e.g., road and rail) and extended to other dynamic riverine settings.CDRI Fellowship Application no. 201128342

Applications of Google Earth Engine in fluvial geomorphology for detecting river channel change

© 2020 The Authors. Cloud-based computing, access to big geospatial data, and virtualization, whereby users are freed from computational hardware and data management logistics, could revolutionize remote sensing applications in fluvial geomorphology. Analysis of multitemporal, multispectral satellite imagery has provided fundamental geomorphic insight into the planimetric form and dynamics of large river systems, but information derived from these applications has largely been used to test existing concepts in fluvial geomorphology, rather than for generating new concepts or theories. Traditional approaches (i.e., desktop computing) have restricted the spatial scales and temporal resolutions of planimetric river channel change analyses. Google Earth Engine (GEE), a cloud-based computing platform for planetary-scale geospatial analyses, offers the opportunity to relieve these spatiotemporal restrictions. We summarize the big geospatial data flows available to fluvial geomorphologists within the GEE data catalog, focus on approaches to look beyond mapping wet channel extents and instead map the wider riverscape (i.e., water, sediment, vegetation) and its dynamics, and explore the unprecedented spatiotemporal scales over which GEE analyses can be applied. We share a demonstration workflow to extract active river channel masks from a section of the Cagayan River (Luzon, Philippines) then quantify centerline migration rates from multitemporal data. By enabling fluvial geomorphologists to take their algorithms to petabytes worth of data, GEE is transformative in enabling deterministic science at scales defined by the user and determined by the phenomena of interest. Equally as important, GEE offers a mechanism for promoting a cultural shift toward open science, through the democratization of access and sharing of reproducible code.Natural Environment Research Council. Grant Number: NE/S00331

Detecting and quantifying morphological change in tropical rivers using Google Earth Engine and image analysis techniques

Copyright © 2020 The Author(s). Various tools have been demonstrated that are capable of delineating and characterizing river channels, but efforts to scale these analyses up to multi-temporal, catchment-scale applications are in their infancy. Here, we use Google Earth Engine (GEE) to extract the active channel (including the wetted channel and unvegetated, alluvial deposits) from the Bislak and Cagayan Rivers in the Philippines. Using temporal composites of Landsat 5, 7 and 8 satellite imagery over ~30 years, the active channel is resolved at annual intervals. The active channel occurrence frequency is mapped using image analysis techniques to detect large-scale planimetric change. Quantification of active channel centerline change is achieved using the RivMAP toolbox. Over a 135 km reach of the Cagayan River, the average migration rate was 17.5 m.a-1 ranging from 7.7 m.a-1 in 1988 to 37.0 m.a-1 in 2005. The findings quantify patterns of dynamism in tropical river systems and demonstrate the utility of GEE in fluvial geomorphology applications

River Styles and stream power analysis reveal the diversity of fluvial morphology in a Philippine tropical catchment

Availability of data and materials: Following review, all GIS datasets will be made available through the NERC data repository.Copyright © The Authors 2022. Characterisation of hydromorphological attributes is crucial for effective river management. Such information is often overlooked in tropical regions such as the Philippines where river management strategies mainly focus on issues around water quality and quantity. We address this knowledge gap using the River Styles Framework as a template to identify the diversity of river morphodynamics. We identify eight distinct River Styles (river types) in the Bislak catchment (586 km2) in the Philippines, showing considerable geomorphic diversity within a relatively small catchment area. Three River Styles in a Confined valley setting occupy 57% of the catchment area, another three in a partly confined valley setting occupy 37%, and two in the remaining 6% are found in a laterally unconfined valley setting. Five characteristic downstream patterns of River Styles were identified across the catchment. We observe that variation in channel slope for a given catchment area (i.e., total stream power) is insufficient to differentiate between river types. Hence, topographic analyses should be complemented with broader framed, catchment-specific approaches to river characterisation. The outputs and understandings from the geomorphic analysis of rivers undertaken in this study can support river management applications by explicitly incorporating understandings of river diversity and dynamics. This has the potential to reshape how river management is undertaken, to shift from reactive, engineering-based approaches that dominate in the Philippines, to more sustainable, ecosystem-based approaches to management.Department of Science and Technology—Philippine Council for Industry, Energy and Emerging Technology Research and Development (DOST-PCIEERD)—NERC Newton Fund grant (NE/S003312); Global Challenges Research Fund (SFC-GCRF) grant (2019)

National-scale geodatabase of catchment characteristics in the Philippines for river management applications

Data Availability: The ArcGIS web-application for interactively displaying the national-scale geodatabase is available here: https://glasgow-uni.maps.arcgis.com/apps/webappviewer/index.html?id=a88b9ca0919f4400881eab4a26370cee. Supporting datasets are available here: http://dx.doi.org/10.5525/gla.researchdata.1396. Supporting datasets include: (1) GIS shapefiles with river catchment properties; (2) GIS shapefiles with stream network properties; (3) spreadsheets containing the complete set of morphometric and topographic characteristics (n = 91); and, (4) example MATLAB code and topographic data to replicate the analysis for a selected catchment. The supporting datasets will also be uploaded to the Natural Environment Research Council (NERC) Environmental Information Data Centre.Copyright: © 2023 Boothroyd et al. Quantitative descriptions of stream network and river catchment characteristics provide valuable context for enabling geomorphologically-informed sustainable river management. For countries where high-quality topographic data are available, there are opportunities to enable open access availability of baseline products from systematic assessment of morphometric and topographic characteristics. In this study, we present a national-scale assessment of fundamental topographic characteristics of Philippine river systems. We applied a consistent workflow using TopoToolbox V2 to delineate stream networks and river catchments using a nationwide digital elevation model (DEM) acquired in 2013 and generated through airborne Interferometric Synthetic Aperture Radar (IfSAR). We assessed morphometric and topographic characteristics for 128 medium- to large-sized catchments (catchment area > 250 km2) and organised the results in a national-scale geodatabase. The dataset realises the potential of topographic data as part of river management applications, by enabling variations in hydromorphology to be characterised and contextualised. The dataset is used to reveal the diversity of stream networks and river catchments in the Philippines. Catchments have a continuum of shapes (Gravelius compactness coefficient ranges from 1.05 to 3.29) with drainage densities that range from 0.65 to 1.23 km/km2. Average catchment slope ranges from 3.1 to 28.1° and average stream slope varies by more than an order of magnitude from 0.004 to 0.107 m/m. Inter-catchment analyses show the distinctive topographic signatures of adjacent river catchments; examples from NW Luzon highlight topographic similarity between catchments whereas examples from Panay Island shown marked topographic differences. These contrasts underline the importance of using place-based analyses for sustainable river management applications. By designing an interactive ArcGIS web-application to display the national-scale geodatabase, we improve data accessibility and enable users to freely access, explore and download the data (https://glasgow-uni.maps.arcgis.com/apps/webappviewer/index.html?id=a88b9ca0919f4400881eab4a26370cee). The national-scale geodatabase provides a baseline understanding of fundamental topographic characteristics in support of varied geomorphological, hydrological and geohazard susceptibility applications.This research was undertaken as part of a Natural Environment Research Council (NERC) and Department of Science and Technology - Philippine Council for Industry, Energy and Emerging Technology Research and Development (DOST-PCIEERD) – Newton Fund grant NE/S003312. RDW and TBH are also grateful to NERC grant NE/W006871/1

Chronic Toxoplasma Infection Modifies the Structure and the Risk of Host Behavior

The intracellular parasite Toxoplasma has an indirect life cycle, in which felids are the definitive host. It has been suggested that this parasite developed mechanisms for enhancing its transmission rate to felids by inducing behavioral modifications in the intermediate rodent host. For example, Toxoplasma-infected rodents display a reduction in the innate fear of predator odor. However, animals with Toxoplasma infection acquired in the wild are more often caught in traps, suggesting that there are manipulations of intermediate host behavior beyond those that increase predation by felids. We investigated the behavioral modifications of Toxoplasma-infected mice in environments with exposed versus non-exposed areas, and found that chronically infected mice with brain cysts display a plethora of behavioral alterations. Using principal component analysis, we discovered that most of the behavioral differences observed in cyst-containing animals reflected changes in the microstructure of exploratory behavior and risk/unconditioned fear. We next examined whether these behavioral changes were related to the presence and distribution of parasitic cysts in the brain of chronically infected mice. We found no strong cyst tropism for any particular brain area but found that the distribution of Toxoplasma cysts in the brain of infected animals was not random, and that particular combinations of cyst localizations changed risk/unconditioned fear in the host. These results suggest that brain cysts in animals chronically infected with Toxoplasma alter the fine structure of exploratory behavior and risk/unconditioned fear, which may result in greater capture probability of infected rodents. These data also raise the possibility that selective pressures acted on Toxoplasma to broaden its transmission between intermediate predator hosts, in addition to felid definitive hosts

Adult Circadian Behavior in Drosophila Requires Developmental Expression of cycle, But Not period

Circadian clocks have evolved as internal time keeping mechanisms that allow anticipation of daily environmental changes and organization of a daily program of physiological and behavioral rhythms. To better examine the mechanisms underlying circadian clocks in animals and to ask whether clock gene expression and function during development affected subsequent daily time keeping in the adult, we used the genetic tools available in Drosophila to conditionally manipulate the function of the CYCLE component of the positive regulator CLOCK/CYCLE (CLK/CYC) or its negative feedback inhibitor PERIOD (PER). Differential manipulation of clock function during development and in adulthood indicated that there is no developmental requirement for either a running clock mechanism or expression of per. However, conditional suppression of CLK/CYC activity either via per over-expression or cyc depletion during metamorphosis resulted in persistent arrhythmic behavior in the adult. Two distinct mechanisms were identified that may contribute to this developmental function of CLK/CYC and both involve the ventral lateral clock neurons (LNvs) that are crucial to circadian control of locomotor behavior: (1) selective depletion of cyc expression in the LNvs resulted in abnormal peptidergic small-LNv dorsal projections, and (2) PER expression rhythms in the adult LNvs appeared to be affected by developmental inhibition of CLK/CYC activity. Given the conservation of clock genes and circuits among animals, this study provides a rationale for investigating a possible similar developmental role of the homologous mammalian CLOCK/BMAL1 complex

Adult Circadian Behavior in Drosophila Requires Developmental Expression of cycle, But Not period

Circadian clocks have evolved as internal time keeping mechanisms that allow anticipation of daily environmental changes and organization of a daily program of physiological and behavioral rhythms. To better examine the mechanisms underlying circadian clocks in animals and to ask whether clock gene expression and function during development affected subsequent daily time keeping in the adult, we used the genetic tools available in Drosophila to conditionally manipulate the function of the CYCLE component of the positive regulator CLOCK/CYCLE (CLK/CYC) or its negative feedback inhibitor PERIOD (PER). Differential manipulation of clock function during development and in adulthood indicated that there is no developmental requirement for either a running clock mechanism or expression of per. However, conditional suppression of CLK/CYC activity either via per over-expression or cyc depletion during metamorphosis resulted in persistent arrhythmic behavior in the adult. Two distinct mechanisms were identified that may contribute to this developmental function of CLK/CYC and both involve the ventral lateral clock neurons (LNvs) that are crucial to circadian control of locomotor behavior: (1) selective depletion of cyc expression in the LNvs resulted in abnormal peptidergic small-LNv dorsal projections, and (2) PER expression rhythms in the adult LNvs appeared to be affected by developmental inhibition of CLK/CYC activity. Given the conservation of clock genes and circuits among animals, this study provides a rationale for investigating a possible similar developmental role of the homologous mammalian CLOCK/BMAL1 complex

Ab Initio Identification of Novel Regulatory Elements in the Genome of Trypanosoma brucei by Bayesian Inference on Sequence Segmentation

Background: The rapid increase in the availability of genome information has created considerable demand for both comparative and ab initio predictive bioinformatic analyses. The biology laid bare in the genomes of many organisms is often novel, presenting new challenges for bioinformatic interrogation. A paradigm for this is the collected genomes of the kinetoplastid parasites, a group which includes Trypanosoma brucei the causative agent of human African trypanosomiasis. These genomes, though outwardly simple in organisation and gene content, have historically challenged many theories for gene expression regulation in eukaryotes. Methodology/Principle Findings: Here we utilise a Bayesian approach to identify local changes in nucleotide composition in the genome of T. brucei. We show that there are several elements which are found at the starts and ends of multicopy gene arrays and that there are compositional elements that are common to all intergenic regions. We also show that there is a composition-inversion element that occurs at the position of the trans-splice site. Conclusions/Significance: The nature of the elements discovered reinforces the hypothesis that context dependant RN

Transcriptomic Analysis of Toxoplasma Development Reveals Many Novel Functions and Structures Specific to Sporozoites and Oocysts

Sexual reproduction of Toxoplasma gondii occurs exclusively within enterocytes of the definitive felid host. The resulting immature oocysts are excreted into the environment during defecation, where in the days following, they undergo a complex developmental process. Within each oocyst, this culminates in the generation of two sporocysts, each containing 4 sporozoites. A single felid host is capable of shedding millions of oocysts, which can survive for years in the environment, are resistant to most methods of microbial inactivation during water-treatment and are capable of producing infection in warm-blooded hosts at doses as low as 1–10 ingested oocysts. Despite its extremely interesting developmental biology and crucial role in initiating an infection, almost nothing is known about the oocyst stage beyond morphological descriptions. Here, we present a complete transcriptomic analysis of the oocyst from beginning to end of its development. In addition, and to identify genes whose expression is unique to this developmental form, we compared the transcriptomes of developing oocysts with those of in vitro-derived tachyzoites and in vivo-derived bradyzoites. Our results reveal many genes whose expression is specifically up- or down-regulated in different developmental stages, including many genes that are likely critical to oocyst development, wall formation, resistance to environmental destruction and sporozoite infectivity. Of special note is the up-regulation of genes that appear “off” in tachyzoites and bradyzoites but that encode homologues of proteins known to serve key functions in those asexual stages, including a novel pairing of sporozoite-specific paralogues of AMA1 and RON2, two proteins that have recently been shown to form a crucial bridge during tachyzoite invasion of host cells. This work provides the first in-depth insight into the development and functioning of one of the most important but least studied stages in the Toxoplasma life cycle