Development of a recombinase polymerase amplification lateral flow assay for the detection of active Trypanosoma evansi infections

Author summary Neglected tropical diseases (NTDs) affecting humans and/or domestic animals severely impair the socio-economic development of endemic areas. One of these diseases, animal trypanosomosis, affects livestock and is caused by the parasites of the Trypanosoma genus. The most widespread causative agent of animal trypanosomosis is T. evansi, which is found in large parts of the world (Africa, Asia, South America, Middle East, and the Mediterranean). Proper control and treatment of the disease requires the availability of reliable and sensitive diagnostic tools. DNA-based detection techniques are powerful and versatile in the sense that they can be tailored to achieve a high specificity and usually allow the reliable detection of low amounts of parasite genetic material. However, many DNA-based methodologies (such as PCR) require trained staff and well-equipped laboratories, which is why the research community has actively investigated in developing amplification strategies that are simple, fast, cost-effective and are suitable for use in minimally equipped laboratories and field settings. In this paper, we describe the development of a diagnostic test under a dipstick format for the specific detection of T. evansi, based on a DNA amplification principle (Recombinase Polymerase Amplification aka RPA) that meets the above-mentioned criteria. Background Animal trypanosomosis caused by Trypanosoma evansi is known as "surra" and is a widespread neglected tropical disease affecting wild and domestic animals mainly in South America, the Middle East, North Africa and Asia. An essential necessity for T. evansi infection control is the availability of reliable and sensitive diagnostic tools. While DNA-based PCR detection techniques meet these criteria, most of them require well-trained and experienced users as well as a laboratory environment allowing correct protocol execution. As an alternative, we developed a recombinase polymerase amplification (RPA) test for Type A T. evansi. The technology uses an isothermal nucleic acid amplification approach that is simple, fast, cost-effective and is suitable for use in minimally equipped laboratories and even field settings. Methodology/Principle findings An RPA assay targeting the T. evansi RoTat1.2 VSG gene was designed for the DNA-based detection of T. evansi. Comparing post-amplification visualization by agarose gel electrophoresis and a lateral flow (LF) format reveals that the latter displays a higher sensitivity. The RPA-LF assay is specific for RoTat1.2-expressing strains of T. evansi as it does not detect the genomic DNA of other trypanosomatids. Finally, experimental mouse infection trials demonstrate that the T. evansi specific RPA-LF can be employed as a test-of-cure tool

The first recorded activity pattern for the Sunda stink-badger Mydaus javanensis (Mammalia: Carnivora: Mephitidae) using camera traps

The Sunda stink-badger Mydaus javanensis is a small carnivore inhabiting the Southeast Asian islands of Borneo, Java, Sumatra, and the Natuna Archipelago. Documented sightings are relatively common, yet the species’ behavioural ecology remains poorly understood. Whilst the species is reported to be broadly nocturnal, its detailed activity pattern has never been quantified. This study analysed photographic events from a large scale, long-term camera trapping study to assess times of activity for the Sunda stink-badger. The study took place within the lowland riparian forest corridor of the Lower Kinabatangan Wildlife Sanctuary (LKWS) in the Northeast Bornean state of Sabah. Through 2010–2015, 24,506 potential trap nights collected 2,268 Sunda stink-badger images across 470 unique events. Sunda stink-badger activity pattern was modelled using kernel density estimation, and indicated a highly nocturnal activity pattern with no detected activity during the diurnal hours, consistent with previous records. All photographs were taken between 1839 hours and 0627 hours, and modelling indicated two clear peaks in nocturnal activity, the first at 2100 hours and the second at 0500 hours. Overlap in activity patterns was found to be high (≥ 80%) between wet and dry seasons, and also between moon phases, indicating a lack of seasonal or lunar effects on Sunda stink-badger activity. An encounter rate of 1.92 unique Sunda stink-badger events per 100 potential trap nights was recorded for the LKWS. This encounter rate was lower than those found in other regional studies with lower levels of anthropogenic disturbance, suggesting extensive anthropogenic disturbance may pose a potential negative impact to the species. Whilst activity patterns derived from camera trapping are restricted to movement through the environment, these results have established a baseline for Sunda stink-badger activity patterns within a fragmented habitat subjected to high levels of anthropogenic disturbance, and have improved the basic ecological understanding of the species

The influence of logging upon the foraging behaviour and diet of the endangered Bornean banteng

Logging causes soil compaction and alters the vegetation structure and plant diversity, and ungulates must adapt to modified conditions if they are to survive. We investigated the impact of logging upon the foraging ecology of the Bornean banteng using camera traps and botanical surveys. General linear models were used to explore the effects of site characteristics and plant diversity upon foraging duration, and plant specimens were identified to confirm dietary preferences. Foraging events were recorded over 40,168 nights in five forests. Foraging duration significantly decreased in open areas depauperate in species richness (F=7.82, p=<0.01); however, it increased with elevation (F=3.46, p=0.05). Their diet comprised eight invasive species (Mikania cordata and Chromolaena odorata, Cyperus difformis, Fimbristylis littoralis and Scleria sp., Desmodium triflorum, Eleusine indica and Selaginella sp.), which are characteristic of disturbed forest and fast to establish. Logging creates ideal conditions for these plants, which are preferentially selected by bantengs. Whilst logging may increase forage, the disturbances logging causes to the bantengs and the ensuing poaching may counteract any positive benefits. Developing forest management strategies that incorporate conservation of the bantengs may in turn encourage more favourable conditions for emergent timber species and also conserve this endangered wild cattle species

Bearded pig (Sus barbatus) utilisation of a fragmented forest-oil palm landscape in Sabah, Malaysian Borneo

Context: Oil palm plantations have become a dominant landscape in Southeast Asia, yet we still understand relatively little about the ways wildlife are adapting to fragmented mosaics of forest and oil palm. The bearded pig is of great ecological, social, and conservation importance in Borneo and is declining rapidly due to habitat loss and overhunting. Aims: We sought to assess how the bearded pig is adapting to oil palm expansion by investigating habitat utilisation, activity patterns, body condition, and minimum group size in a mosaic composed of forest fragments and surrounding oil palm. Methods: We conducted our study in Sabah, Malaysian Borneo, in and around the Lower Kinabatangan Wildlife Sanctuary, an area consisting of secondary forest fragments (ranging 1200-7400 ha) situated within an extensive oil palm matrix. We modelled bearded pig habitat use in forest fragments and oil palm plantations using survey data from line transects. Camera traps placed throughout the forest fragments were used to assess pig activity patterns, body condition, and minimum group size. Key results: All forest transects and 80% of plantation transects showed pig presence, but mean pig signs per transect were much more prevalent in forest (70.00 ± 13.00 SE) than in plantations (0.91 ± 0.42 SE). Pig tracks had a positive relationship with leaf cover and a negative relationship with grass cover; pig rooting sites had a positive relationship with wet and moderate soils as compared to drier soils. Pigs displayed very good body condition in forests across the study area, aggregated in small groups (mean = 2.7 ± 0.1 SE individuals), and showed diurnal activity patterns that were accentuated for groups with piglets and juveniles. Conclusions: Our findings suggest that bearded pigs in our study area regularly utilise oil palm as habitat, given their signs in most oil palm sites surveyed. However, secondary forest fragments adjacent to oil palm remain the most important habitat for the bearded pig, as well as many other species, and therefore must be conserved. Implications: Consistent bearded pig presence in oil palm is a potential indication of successful adaptation to agricultural expansion in the study area. However, the net effect of oil palm expansion in the region on bearded pig populations remains unknown

Low-Cost SMS Driven Location Tracking Platform Towards Anti-Poaching Efforts

Throughout the world, poaching has been an ever-present threat to a vast array of species for over many decades. Traditional anti-poaching initiatives target catching the poachers. However, the challenge is far more complicated than catching individual poachers. Poaching is an industry which needs to be fully investigated. Many stakeholders are directly and indirectly involved in poaching activities (e.g., some local restaurants illegally providing meat to tourists). Therefore, stopping or severely decapitating the poaching industry requires a unified understanding of all stakeholders. The best way to uncover these geographical and social relationships is to track the movements of poachers. However, location tracking is challenging in most rural areas where wildlife sanctuaries are typically located. Internet-connected communication (e.g. 3G) technologies typically used in urban cities are not feasible in these rural areas. Therefore, we decided to develop an SMS (short message service) base low-cost tracking system (SMS-TRACCAR) to track poachers. The proposed system was developed to be deployed in Kinabatangan Wildlife Sanctuary, Sabah, Malaysia and nearby villages and cities where poachers typically move around. Our evaluations demonstrated that SMS-based tracking could provide sufficient quality (granular) data (with minimum energy consumption) that enable us to monitor poacher vehicle movements within rural areas where no other modern communication technologies are feasible to use. However, it is important to note that our system can be used in any domain that requires SMS-based geo-location tracking. SMS-TRACCAR can be configured to track individuals as well as groups. Therefore, SMS-TRACCAR contributes not only to the wildlife domain but in the wider context as well.Comment: Technical Repor

Herd demography, sexual segregation and the effects of forest management on Bornean banteng Bos javanicus lowi in Sabah, Malaystian Borneo

Between 1973 and 2010, 39.5% of Sabah’s (Malaysian Borneo) natural forest cover was lost to deforestation and conversion to agriculture, therefore the remaining population of endangered Bornean banteng Bos javanicus lowi is being driven towards extinction. The Bornean banteng’s herd demography, sexual segregation and the effects of forest management were investigated at 393 camera locations in 6 forest reserves using generalised estimating equations (GEE) fitted via a generalised linear model (GLM). A total of 43344 camera trap nights and 832 independent banteng events were captured at 93 locations. The identification of 183 bantengs included 22 herds (>1 individual) and 12 solitary bulls, with a herd size range of 2 to 21. Significantly larger herds were observed in forest with <8 yr of post-logging regeneration (PLR), whereas herds were smaller in forest with <3, 4 and 16 yr of PLR. Within these forests, herds were significantly larger along logging roads than in open sites and on forest trails. Herds were significantly larger in upland compared to lowland dipterocarp forest, but significantly smaller when closer to the forest border. Bachelor herds were observed as frequently as mixed-sex herds, and there was a significantly higher capture frequency of female herds in the dry season, supporting the theory of sexual segregation. Frequency of calf births was highest in March and September, and calf captures peaked in June and July. This study contributes to a better understanding of banteng ecology, and will assist in the production of effective management strategies aimed at providing suitable habitat for re-population and enabling banteng population persistence

Protected area management priorities crucial for the future of Bornean elephants

Tropical protected area management strategies have traditionally been heavily skewed towards high carbon, primary forests. This focus can result in areas, such as heavily logged forests, being viewed as low quality and thus offered up for conversion. We assessed the importance of intact to heavily logged forests for the Bornean elephant in the Malaysian state of Sabah. By modelling distributions of elephants throughout Sabah based on GPS telemetry tracking of 29 individuals and airborne three-dimensional forest mapping, we present the most wide-scale analysis of forest use by Bornean elephants to date. Forests of 13 m in stature were found to be of highest suitability for elephants, especially when these areas were flat and low lying. Forest statures of this order are consistent with degraded landscapes, often viewed as suitable for oil palm conversion. Less than a quarter of fully-protected intact forests in Sabah were of suitable stature for elephants, whereas disturbed commercial forest reserves were found to be highly suitable. We suggest that the importance of degraded landscapes for the future of elephants is currently underestimated, and thus, the need for the preservation of such habitats is not seen as a priority. The loss of these landscapes to large-scale agriculture could prove detrimental to the longevity of the species in Borneo

Spatial and temporal behavioural responses of wild cattle to tropical forest degradation

<div><p>Identifying the consequences of tropical forest degradation is essential to mitigate its effects upon forest fauna. Large forest-dwelling mammals are often highly sensitive to environmental perturbation through processes such as fragmentation, simplification of habitat structure, and abiotic changes including increased temperatures where the canopy is cleared. Whilst previous work has focused upon species richness and rarity in logged forest, few look at spatial and temporal behavioural responses to forest degradation. Using camera traps, we explored the relationships between diel activity, behavioural expression, habitat use and ambient temperature to understand how the wild free-ranging Bornean banteng (<i>Bos javanicus lowi</i>) respond to logging and regeneration. Three secondary forests in Sabah, Malaysian Borneo were studied, varying in the time since last logging (6–23 years). A combination of generalised linear mixed models and generalised linear models were constructed using >36,000 trap-nights. Temperature had no significant effect on activity, however it varied markedly between forests, with the period of intense heat shortening as forest regeneration increased over the years. Bantengs regulated activity, with a reduction during the wet season in the most degraded forest (z = -2.6, Std. Error = 0.13, p = 0.01), and reductions during midday hours in forest with limited regeneration, however after >20 years of regrowth, activity was more consistent throughout the day. Foraging and use of open canopy areas dominated the activity budget when regeneration was limited. As regeneration advanced, this was replaced by greater investment in travelling and using a closed canopy. Forest degradation modifies the ambient temperature, and positively influences flooding and habitat availability during the wet season. Retention of a mosaic of mature forest patches within commercial forests could minimise these effects and also provide refuge, which is key to heat dissipation and the prevention of thermal stress, whilst retention of degraded forest could provide forage.</p></div

Use and selection of sleeping sites by proboscis monkeys, Nasalislarvatus, along the Kinabatangan River, Sabah, Malaysia

The choice of a sleeping site is crucial for primates and may influence their survival. In this study, we investigated several tree characteristics influencing the sleeping site selection by proboscis monkeys (Nasalis larvatus) along Kinabatangan River, in Sabah, Malaysia. We identified 81 sleeping trees used by one-male and all-male social groups from November 2011 to January 2012. We recorded 15 variables for each tree. Within sleeping sites, sleeping trees were taller, had a larger trunk, with larger and higher first branches than surrounding trees. The crown contained more mature leaves, ripe and unripe fruits but had vines less often than surrounding trees. In addition, in this study, we also focused on a larger scale, considering sleeping and non-sleeping sites. Multivariate analyses highlighted a combination of 6 variables that revealed the significance of sleeping trees as well as surrounding trees in the selection process. During our boat surveys, we observed that adult females and young individuals stayed higher in the canopy than adult males. This pattern may be driven by their increased vulnerability to predation. Finally, we suggest that the selection of particular sleeping tree features (i.e. tall, high first branch) by proboscis monkeys is mostly influenced by antipredation strategies