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Biology subjects

Deen, J.

Publications and source records attributed to Deen, J..

2 recordsLinked to original sources

Animal movement in pastoralist populations and implications for pathogen spread and control

Infectious diseases are one of the most important constraints to livestock agriculture, and hence food, nutritional and economic security in developing countries. In any livestock system, the movement of animals is key to production and sustainability. This is especially true in pastoralist systems where animal movement occurs for a myriad of social, ecological, economic and management reasons. Understanding the dynamics of livestock movement within an ecosystem is important for disease surveillance and control, yet there is limited data available on the dynamics of animal movement in such populations. The aim of this study was to investigate animal transfer networks in a pastoralist community in Kenya, and assess network-based strategies for disease control. We used network analysis to characterize five types of animal transfer networks and evaluated implications of these networks for disease control through quantifying topological changes in the network because of targeted or random removal of nodes. To construct these networks, data were collected using a standardized questionnaire (N=164 households) from communities living within the Maasai Mara Ecosystem in southwestern Kenya. The median livestock movement distance for agistment (dry season grazing) was 39.49 kilometers (22.03-63.49 km), while that for gift, bride price, buying and selling were 13.97 km (0-40.30 km), 30.75 km (10.02-66.03 km), 31.14 km (17.56-59.08 km), and 33.21 km (17.78-58.49 km), respectively. Our analyses show that the Maasai Mara National Reserve, a protected area, was critical for maintaining connectivity in the agistment network. In addition, villages closer to the Maasai Mara National Reserve were regularly used for dry season grazing. In terms of disease control, targeted removal of highly connected village nodes was more effective at fragmenting each network than random removal of nodes, indicating that network-based targeting of interventions such as vaccination could potentially disrupt transmission pathways and reduce pathogen circulation in the ecosystem. In conclusion, this work shows that animal movements have the potential to shape patterns of disease transmission and control in this ecosystem. Further, we show that targeted control is a more practical and efficient measure for disease control.

ecology↗

Identifying microbial species by single-molecule DNA optical mapping and resampling statistics

Single molecule DNA mapping has the potential to serve as a powerful complement to high-throughput sequencing in metagenomic analysis. Offering longer read lengths and forgoing the need for complex library preparation and amplification, mapping stands to provide an unbiased view into the composition of complex viromes and/or microbiomes. To fully enable mapping-based metagenomics, sensitivity and specificity of DNA map analysis and identification need to be improved. Using detailed simulations and experimental data, we first demonstrate how fluorescence imaging of surface stretched, sequence specifically labeled DNA fragments can yield highly sensitive identification of targets. Secondly, a new analysis technique is introduced to increase specificity of the analysis, allowing even closely related species to be resolved. Thirdly, we show how an increase in resolution improves sensitivity. Finally, we demonstrate that these methods are capable of identifying species with long genomes such as bacteria with high sensitivity.

genomics↗