In vitro culture of the strobilar stage of Echinococcus granulosus from protoscoleces of human, camel, cattle, sheep and goat origin from Kenya and buffalo origin from India

Protoscoleces from human, camel, cattle, sheep, goat (all from Kenya) and buffalo (from India) hydatid cysts were cultured under identical conditions in vitro using the diphasic culture system of Smyth (1979b). Organisms from all sources grew and segmented in culture. Genital anlagen developed in all cultured worms but further genital differentiation occurred only in cultures of cattle (testes) and camel (testes and genital pore) material. The possible significance of these results is discussed in relation to the general epidemiology of hydatid disease and the potential infectivity of the different strains to man.     

Canine reproduction: I. Reaction of animals to collection of semen and insemination procedures

Two methods of semen collection were attempted on ten untrained dogs of several breeds. Manual manipulation as described proved most reliable for untrained dogs. Electro-ejaculation was attempted unsucessfully with twelve additional dogs.Two methods of insemination were compared. Equipment found most satisfactory is described and a modification suggested.     

Helping decision making for reliable and cost‐effective 2b‐RAD sequencing and genotyping analyses in non‐model species

High‐throughput sequencing has revolutionized population and conservation genetics. RAD sequencing methods, such as 2b‐RAD, can be used on species lacking a reference genome. However, transferring protocols across taxa can potentially lead to poor results. We tested two different IIB enzymes (AlfI and CspCI) on two species with different genome sizes (the loggerhead turtle Caretta caretta and the sharpsnout seabream Diplodus puntazzo) to build a set of guidelines to improve 2b‐RAD protocols on non‐model organisms while optimising costs. Good results were obtained even with degraded samples, showing the value of 2b‐RAD in studies with poor DNA quality. However, library quality was found to be a critical parameter on the number of reads and loci obtained for genotyping. Resampling analyses with different number of reads per individual showed a trade‐off between number of loci and number of reads per sample. The resulting accumulation curves can be used as a tool to calculate the number of sequences per individual needed to reach a mean depth ≥20 reads to acquire good genotyping results. Finally, we demonstrated that selective‐base ligation does not affect genomic differentiation between individuals, indicating that this technique can be used in species with large genome sizes to adjust the number of loci to the study scope, to reduce sequencing costs and to maintain suitable sequencing depth for a reliable genotyping without compromising the results. Here, we provide a set of guidelines to improve 2b‐RAD protocols on non‐model organisms with different genome sizes, helping decision‐making for a reliable and cost‐effective genotyping.     

Generation of initial molecular dynamics configurations in arbitrary geometries and in parallel

A computational pre-processing tool for generating initial configurations of molecules for molecular dynamics simulations in geometries described by a mesh of unstructured arbitrary polyhedra is described. The mesh is divided into separate zones and each can be filled with a single crystal lattice of atoms. Each zone is filled by creating an expanding cube of crystal unit cells, initiated from an anchor point for the lattice. Each unit cell places the appropriate atoms for the user-specified crystal structure and orientation. The cube expands until the entire zone is filled with the lattice; zones with concave and disconnected volumes may be filled. When the mesh is spatially decomposed into portions for distributed parallel processing, each portion may be filled independently, meaning that the entire molecular system never needs to fit onto a single processor, allowing very large systems to be created. The computational time required to fill a zone with molecules scales linearly with the number of cells in the zone for a fixed number of molecules, and better than linearly with the number of molecules for a fixed number of mesh cells. Our tool, molConfig, has been implemented in the open source C++ code OpenFOAM.