Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these ‘source’ populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from a large population-based sample of infected individuals in Rakai District, Uganda, reconstruct partial transmission networks, and infer the direction of transmission within them at an estimated error rate of 16.3% [8.8–28.3%]. With this error rate, deep-sequence phylogenetics cannot be used against individuals in legal contexts, but is sufficiently low for population-level inferences into the sources of epidemic spread. The technique presents new opportunities for characterizing source populations and for targeting of HIV-1 prevention interventions in Africa

Differential Requirement for the Nonhelical Tailpiece and the C Terminus of the Myosin Rod in Caenorhabditis elegans Muscle

Myosin heavy chain (MHC) is a large, multidomain protein important for both cellular structure and contraction. To examine the functional role of two C-terminal domains, the end of the coiled-coil rod and the nonhelical tailpiece, we have generated constructs in which residues within these domains are removed or mutated, and examined their behavior in Caenorhabditis elegans striated muscle. Genetic tests demonstrate that MHC lacking only tailpiece residues is competent to support the timely onset of embryonic contractions, and therefore viability, in animals lacking full-length MHC. Antibody staining experiments show that this truncated molecule localizes as wild type in early stages of development, but may be defective in processes important for thick filament organization later in embryogenesis. Ultrastructural analysis reveals thick filaments of normal morphology in disorganized arrangement, as well as occasional abnormal assemblages. In contrast, molecules in which the four terminal residues of the coiled coil are absent or mutated fail to rescue animals lacking endogenous MHC. Loss of these four residues is associated with delayed protein localization and delayed contractile function during early embryogenesis. Our results suggest that these two MHC domains, the rod and the tailpiece, are required for distinct steps during muscle development

Habitat preferences of the secretive forest buffalo (Syncerus caffer nanus) in Central Africa

The forest buffalo Syncerus caffer nanus is one of the three subspecies of African buffalo inhabiting the rainforests of Western and Central Africa. Because of its secretive behaviour and main habitat (dense rainforests), there is little quantitative information on the habitat preferences of this buffalo. We present here the first data on the frequencies of this species along a habitat gradient ranging from clearings and rivers to forests, as well as the characteristics of the buffalo's resting places. We recorded information from a buffalo herd during the period January 2002-January 2004 in the Bai-Hokou area (Dzanga-Ndoki National Park, Central African Republic). Resting places were firstly compared with available habitat (i.e. resting vs. random sites) and, successively, comparisons were made between diurnal versus nocturnal and wet versus dry season resting places. Forest buffalos were found to be highly dependent on clearings, as well as on the more open forest stands, characterized by large trees and open canopy. Such preferences could be due to the tendency of the buffalos to rest all together; open patches are likely to facilitate social interactions between the members of the herd