The VIRCA Project: virus resistant cassava for Africa

The VIRCA (Virus Resistant Cassava for Africa) project is a collaborative program between the Donald Danforth Plant Science Center, USA the National Crops Resources Research Institute, Uganda and the Kenya Agricultural Research Institute, Kenya. VIRCA is structured to include all aspects of the intellectual property, technology, regulatory, biosafety, quality control, communication and distribution components required for a GM crop development and delivery process. VIRCA's goal is to improve cassava for resistance to the viral diseases cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) using pathogen-derived RNAi technology, and to field test, obtain regulatory approval for and deliver these products to small landholder farmers. During Phase I of the project, proof of concept was achieved by production and testing of virus resistant plants under greenhouse and confined field trials in East Africa. In VIRCA Phase II, two farmer-preferred varieties will be modified for resistance to CBSD and CMD, and lead events identified after molecular and field screening. In addition to delivery of royalty-free improved planting materials for farmers, VIRCA capacity building activities are enhancing indigenous capability for crop biotechnology in East Africa.     

Biochemical changes in cerebrospinal fluid of Chlorocebus aethiops naturally infected with zoonotic Meningonema peruzzii

BACKGROUND: Thirty-four wild Chlorocebus aethiops monkeys were trapped for research purposes. METHODS: During routine quarantine check-up, cerebrospinal fluid (CSF) and blood were microscopically examined for parasites. Estimations of CSF protein levels were made by the biuret method and the white cell counts by the hemocytometer. RESULTS: Seven monkeys demonstrated microfilariae in blood and CSF. This was accompanied by a two- and ninefold increase in CSF total protein and white cell counts, respectively. Necropsy of one of the blood and CSF microfilariae-positive animals revealed the presence of adult worms in the brain meninges. The parasites were identified as the zoonotic filaroid nematode Meningonema peruzii. CONCLUSIONS: Wild C. aethiops monkeys developed CSF changes resulting, most probably, from infection with M. peruzii. Moreover, the monkeys could be acting as an important reservoir. The study highlights the need for epidemiological and pathogenological studies of this parasite, which is of public health significance. Moreover, C. aethiops proved to be a useful primate model for the study of this zoonotic infection.     

The role of farm structure on bird assemblages around a Kenyan tropical rainforest

Although it is clear that the farmlands neighbouring fragmented forests are utilized by some forest birds, it is not clear how birds in general respond to farmland habitat mosaic. An effort was made to determine how bird density and foraging assemblages were influenced by farm structural characteristics and distance from forest edge. Thirty farms up to a distance of 12 km around Kakamega forest in western Kenya were studied. Farm structure entailed size, hedge volume, habitat heterogeneity, woody plant density, plant diversity and crop cover. Birds were surveyed using line transects and DISTANCE analyses and classified into six feeding guilds and three habitat associations. Size of farms increased away from the forest, as woody plant density, plant diversity, indigenous trees and subsistence crop cover declined. The most important farm structure variable was hedge volume, which enhanced bird species richness, richness of shrub‐land bird species and insectivorous bird density (R = 0.58, P < 0.01). Bird density increased with tree density while indigenous trees were suitable for insectivores and nectarivores. There were very few forest bird encounters. Agricultural practices incorporating maintenance of hedges and sound selection of agroforestry trees can enhance conservation of birds on farmland, though, not significantly for forest species.     

Distribution of Epilithic Diatoms in Response to Environmental Conditions in an Urban Tropical Stream, Central Kenya

Use of diatoms in monitoring water quality is well acknowledged in developed countries, but only recently has the assessment started gaining importance in developing countries. Diatoms can be obtained from natural and artificial substrates. Appreciating the differences and similarities of diatom assemblages on both substrates may contribute to a better understanding and standardization particularly during monitoring of water quality. During this study we assessed diatom assemblages, biodiversity and trophic indices in relation to water quality along the Nairobi River. Fifteen sites were sampled in September 2000 during the dry season. Diatoms were collected from natural substrates (stones, pebbles) and artificial substrates (100% acrylic wool). On artificial and natural substrates, a total of 190 and 151 taxa were found, respectively, the majority of these taxa (80%) have cosmopolitan distribution and are also widespread throughout tropical African. Species composition changed downstream, five taxa dominated upper and mid stream sites whereas lower stream sites were dominated by one or two taxa. Species richness, diversity, dominance and evenness were positively correlated with NO₃, O₂ and altitude but decreased markedly downstream with a simultaneous increase in total dissolved solids, alkalinity, chemical oxygen demand and PO₄. Ordination and classification (CANOCO and TWINSPAN) showed that diatom assemblages in the Nairobi River responded strongly to water quality changes with respect to concentrations of NO₃, NO₂, total dissolved solids and temperature. Taxa common at less impacted upstream sites included Gomphonema gracilis, Anomoeoneis brachysira and Fragilaria biceps; while common taxa at midstream sites with agricultural catchments were Gomphonema parvulum, Navicula cryptocephala, N. schroeteri, N. bryophila, N. halophila, Nitzschia linearis var. linearis and Cymbella silesica. Achnanthes minutissima var. saprophila, Gomphonema angustum, Navicula subminuscula, N. arvensis, Nitzschia palea and N. umbonata were most common at urban sites, which were polluted by residential and industrial effluents. Trophic diatom indices suggested that water quality was poor at most sites in the Nairobi River. Most sites along the river had low Generic Diatom Index values, GDI (<12) and high Trophic Diatom Index values, TDI 73–78 (median = 76) and 75–84 (median = 77) for artificial and natural substrates, respectively. This study showed that diatoms' response on natural and artificial substrates were similar and reflected environmental conditions correctly.     

Mobile microscopy and telemedicine platform assisted by deep learning for the quantification of Trichuris trichiura infection

Soil-transmitted helminths (STH) are the most prevalent pathogens among the group of neglected tropical diseases (NTDs). The Kato-Katz technique is the diagnosis method recommended by the World Health Organization (WHO) although it often presents a decreased sensitivity in low transmission settings and it is labour intensive. Visual reading of Kato-Katz preparations requires the samples to be analyzed in a short period of time since its preparation. Digitizing the samples could provide a solution which allows to store the samples in a digital database and perform remote analysis. Artificial intelligence (AI) methods based on digitized samples can support diagnosis by performing an objective and automatic quantification of disease infection. In this work, we propose an end-to-end pipeline for microscopy image digitization and automatic analysis of digitized images of STH. Our solution includes (a) a digitization system based on a mobile app that digitizes microscope samples using a 3D printed microscope adapter, (b) a telemedicine platform for remote analysis and labelling, and (c) novel deep learning algorithms for automatic assessment and quantification of parasitological infections by STH. The deep learning algorithm has been trained and tested on 51 slides of stool samples containing 949 Trichuris spp. eggs from 6 different subjects. The algorithm evaluation was performed using a cross-validation strategy, obtaining a mean precision of 98.44% and a mean recall of 80.94%. The results also proved the potential of generalization capability of the method at identifying different types of helminth eggs. Additionally, the AI-assisted quantification of STH based on digitized samples has been compared to the one performed using conventional microscopy, showing a good agreement between measurements. In conclusion, this work has presented a comprehensive pipeline using smartphone-assisted microscopy. It is integrated with a telemedicine platform for automatic image analysis and quantification of STH infection using AI models.     

Socio-economic values and traditional strategies of managing wetland resources in Lower Tana River, Kenya

Understanding local people's socio-economic values of wetlands and traditional mechanisms of managing natural resources forms the basis of conserving them. In order to sustainably manage wetland resources in Tana River National Primate Reserve (TRNPR) and its environs, a study was carried out to document values, threats and traditional strategies of managing natural resources. The target communities were the Pokomo and Wardei who inhabit the TRNPR. The study was carried out in different periods in the year 2000 and 2001 and entailed administration of questionnaires, interviews and focused group discussions. Thirty residents were interviewed from six villages in the west bank of Tana River. The study found that oxbow lakes and Tana River formed the main types of wetlands and provided multiple values such as farming, transportation, security and social-cultural values to the local people. These values formed an important premise for conservation. Farming and fishing were the main economic activities of the Pokomo people while Wardei combined livestock rearing with occasional shifting cultivation. The two communities used different traditional systems in managing resources that they needed for their livelihood. The study concludes that the local people can and indeed must play a central role in the conservation of threatened wildlife and habitats in the Lower Tana River.     

The use of stable carbon isotopes as tracers of ecosystem functioning in contrasting wetland ecosystems of Lake Victoria,Kenya

Aquatic macrophytes and sediments from two contrasting wetland ecosystems of Lake Victoria, Kenya (Lower Sondu Miriu and Kibos systems) were analyzed for their stable carbon isotopic composition in order to observe patterns in system functioning in these two ecosystems. The aquatic macrophytes had carbon isotope ratios ranging from –8.92 to –29.18 per mil (parts per thousand difference from the reference). For the dominant macrophytes, we observed most ¹³C enriched values for Cyperus papyrus and most ¹³C depleted values for Eichhornia crassipes. On transects from the river to the lake, Kibos sediments maintained lower carbon isotope signatures compared to the Lower Sondu Miriu sediments. The possible causes of the observed variation in the ¹³C signatures from sediments and aquatic macrophytes in the two-wetland ecosystems are outlined.     

Phytoplankton community structure and environment in the Kenyan waters of Lake Victoria

• 1 Phytoplankton species composition, numerical abundance, spatial distribution and total biomass measured as chlorophyll a concentration were studied in relation to environmental factors in September 1994 (dry season) and March 1995 (rainy season), respectively, in the Kenyan waters of Lake Victoria; 103 species were recorded.
• 2 Blue‐green algae (Cyanophyceae) were most diverse, followed by diatoms (Bacillariophyceae), green algae (Chlorophyceae) and dinoflagellates (Dinophyceae).
• 3 Twinspan separated the phytoplankton communities in the Nyanza Gulf and those in the open lake during both seasons. During the dry season, the Nyanza Gulf was strongly dominated by blue‐greens, while diatoms dominated in the open lake. During the rainy season, blue‐greens remained dominant in the Nyanza Gulf although the number of species found was lower than during the dry season; in the open lake, blue‐greens replaced diatoms as the dominant group and there were more species than in the dry season.
• 4 Canonical correspondence analysis indicated that the phytoplankton species distribution was significantly correlated with turbidity during the dry season and with SiO₂ during the rainy season. Chlorophyll a concentrations ranging from 2.0 to 71.5 mg m^‐3 in the dry season and 2.0–17.2 mg m^‐3 in the rainy season confirm earlier reports of increasing phytoplankton biomass in Lake Victoria since the 1960s.

     

Dietary preference of cheetahs (Acinonyx jubatus) in south‐eastern Kenya

The conversion of natural ecosystems due to anthropogenic activities has led to the destruction of natural habitats and to the deterioration of habitat quality. Top predators particularly respond sensitively to changes in habitat structures, including the availability of prey. The cheetah Acinonyx jubatus prefers small‐medium‐sized, wild ungulate prey due to the cheetah''s morphological adaptations. However, the majority of the species’ population is found beyond protected areas, where habitat structures, species abundances, and community composition are highly influenced by human activities. Only few studies have analyzed the diet preference of cheetahs in relation to prey availability and abundance for rangelands beyond protected areas in Eastern Africa. The study aimed to determine cheetah prey preference in the rangelands of south‐eastern Kenya based on scat analyses. We compared dietary preference of cheetah with prey availability. For this purpose, we conducted standardized game counts. We analyzed 27 cheetah scat samples collected across the same study area where we also conducted game counts. We found that Grant''s gazelle Gazella granti contributed the highest portion of cheetah''s diet, although Thomson''s gazelle Gazella thomsonii was the most abundant medium‐sized ungulate prey in the study areas. We also recorded two primate species, yellow baboon Papio cynocephalus and vervet monkey Chlorocebus pygerythrus, as well as the rock hyrax Procavia capensis in the cheetah diet. These species have never been documented as cheetah prey before. Furthermore, our results document livestock as potential prey for cheetahs. These observations underline that cheetah use diverse prey in rangelands outside protected areas, and that the abundance of specific prey does not influence cheetah prey preference.     

Effects of plant structure on butterfly diversity in Mt. Marsabit Forest – northern Kenya

Butterflies, like most forest dependent animals are good ecological indicators of the health of the forests they dwell. For example, butterfly species richness decreases after a forest disturbance and fragmentation but a few species may subsequently invade the forest fragment and boost the species richness. Studies were conducted to determine the effects of human activity and seasonal changes on butterfly species in the affected new habitats. Results showed that both seasonal and habitat changes significantly affect the butterfly abundance (P = 0.0001). Similarly, there was significant correlation between plant diversity and butterfly diversity in wet season (r = 0.854) and dry season (r = 0.855). The significance of these studies as a useful tool for sustainable forest use and conservation is discussed.