In order to shed light on the nature of the persistent reservoir of human immunodeficiency virus type 1 (HIV-1), we investigated signs of recent evolution in the pool of proviral DNA in patients on successful HAART. Pro-viral DNA, corresponding to the C2-V3-C3 region of the HIV-1 env gene, was collected from PBMCs isolated from 57 patients. Both "consensus" (57 patients) and clonal (7 patients) sequences were obtained from five time points spanning a 24-month period. The main computational strategy was to use maximum likelihood to fit a set of alternative phylogenetic models to the clonal data, and then determine the support for models that imply evolution between time points. Model fit and model-selection uncertainty was assessed using the Akaike information criterion (AIC) and Akaike weights. The consensus sequence data was also analyzed using a range of phylogenetic techniques to determine whether there were temporal trends indicating ongoing replication and evolution. In summary, it was not possible to detect definitive signs of ongoing evolution in either the bulk-sequenced or the clonal data with the methods employed here, but our results could be consistent with localized expression of archival HIV genomes in some patients. Interestingly, stop-codons were present at the same two positions in several independent clones and across patients. Simulation studies indicated that this phenomenon could be explained as the result of parallel evolution and that some sites were inherently more likely to evolve into stop codons.
Articles you may be interested in DMTB: A comprehensive online resource of 16S rRNA genes, ecological metadata, oligonucleotides, and magnetic properties of magnetotactic bacteria Chinese Science Bulletin 56, 476 (2011); Distribution of magnetotactic bacteria in China and characterization of magnetosomes Chinese Science Bulletin 41, 944 (1996); Characteristics of magnetotactic bacteria in Duanjiapo loess section, Shaanxi Province and their environment significance Science in China Series D-Earth Sciences 39, 478 (1996); Paleo-environmental study on the growth of magnetotactic bacteria and precipitation of magnetosomes in Chinese loess-paleosol sequences Chinese Science Bulletin 45, 21 (2000); An initial study of the influences of oxygen conditions on wild-type magnetotactic bacteria in sediment
Inferring evolutionary history of parasitism genes is important to understand how evolutionary mechanisms affect the occurrences of parasitism genes. In this study, we constructed multiple domain trees for parasitism genes and genes under free-living conditions. Further analyses of horizontal gene transfer (HGT)-like phylogenetic incongruences, duplications, and speciations were performed based on these trees. By comparing these analyses, the contributions of pre-adaptations were found to be more important to the evolution of parasitism genes than those of duplications, and pre-adaptations are as crucial as previously reported HGTs to parasitism. Furthermore, speciation may also affect the evolution of parasitism genes. In addition, Pristionchus pacificus was suggested to be a common model organism for studies of parasitic nematodes, including root-knot species. These analyses provided information regarding mechanisms that may have contributed to the evolution of parasitism genes.
Magnetotactic bacteria (MTB) are worth studying because of magnetosome biomineralization. Magnetosome biogenesis in MTB is controlled by multiple genes known as magnetosome-related genes. Recent advances in microarray bioinformatics provide a unique opportunity for studying functions of magnetosome-related genes and networks that they are involved in. Furthermore, microarray analysis can also help identify genes potentially associated with magnetosome biogenesis. To find more magnetosome-related genes in the CtrA regulon, we analyzed expression data of 8 samples of Magnetospirillum magneticum AMB-1 in the GSE35625 dataset in NCBI GEO. We identified 10 potential magnetosome-related genes using a nearest neighbor search strategy on both protein-protein interaction and gene co-expression networks. We also discovered and compared two co-expression modules which most known magnetosome-related genes belong to. These analyses provided several clues for the importance of energy on regulating co-expression module structures. In addition, we hypothesized that many magnetosome-related genes may develop new abilities to interact with other biomolecules including their functions in magnetosome biogenesis during evolution, since they are not hub genes in networks. Overall, our study provides useful information for researches on magnetotactic bacteria and magnetosome.
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