Genomics of Loa loa, a Wolbachia-free filarial parasite of humans.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Nature Genetics (Impact Factor: 29.65). 03/2013; DOI: 10.1038/ng.2585
Source: PubMed

ABSTRACT Loa loa, the African eyeworm, is a major filarial pathogen of humans. Unlike most filariae, L. loa does not contain the obligate intracellular Wolbachia endosymbiont. We describe the 91.4-Mb genome of L. loa and that of the related filarial parasite Wuchereria bancrofti and predict 14,907 L. loa genes on the basis of microfilarial RNA sequencing. By comparing these genomes to that of another filarial parasite, Brugia malayi, and to those of several other nematodes, we demonstrate synteny among filariae but not with nonparasitic nematodes. The L. loa genome encodes many immunologically relevant genes, as well as protein kinases targeted by drugs currently approved for use in humans. Despite lacking Wolbachia, L. loa shows no new metabolic synthesis or transport capabilities compared to other filariae. These results suggest that the role of Wolbachia in filarial biology is more subtle than previously thought and reveal marked differences between parasitic and nonparasitic nematodes.

1 Bookmark
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Lateral gene transfer (LGT) from bacterial Wolbachia endosymbionts has been detected in ~20% of arthropod and nematode genome sequencing projects. Many of these transfers are large and contain a substantial part of the Wolbachia genome. Here, we re-sequenced three D. ananassae genomes from Asia and the Pacific that contain large LGTs from Wolbachia.We find that multiple copies of the Wolbachia genome are transferred to the Drosophila nuclear genome in all three lines. In the D. ananassae line from Indonesia, the copies of Wolbachia DNA in the nuclear genome are nearly identical in size and sequence yielding an even coverage of mapped reads over the Wolbachia genome. In contrast, the D. ananassae lines from Hawaii and India show an uneven coverage of mapped reads over the Wolbachia genome suggesting that different parts of these LGTs are present in different copy numbers. In the Hawaii line, we find that this LGT is underrepresented in third instar larvae indicative of being heterochromatic. Fluorescence in situ hybridization of mitotic chromosomes confirms that the LGT in the Hawaii line is heterochromatic and represents ~20% of the sequence on chromosome 4 (dot chromosome, Muller element F). This collection of related lines contain large lateral gene transfers composed of multiple Wolbachia genomes that constitute >2% of the D. ananassae genome (~5 Mbp) and partially explain the abnormally large size of chromosome 4 in D. ananassae.
    BMC genomics. 12/2014; 15(1):1097.
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: SUMMARY The genomes of more than 20 helminths have now been sequenced. Here we perform a meta-analysis of all sequenced genomes of nematodes and Platyhelminthes, and attempt to address the question of what are the defining characteristics of helminth genomes. We find that parasitic worms lack systems for surface antigenic variation, instead maintaining infections using their surfaces as the first line of defence against the host immune system, with several expanded gene families of genes associated with the surface and tegument. Parasite excretory/secretory products evolve rapidly, and proteases even more so, with each parasite exhibiting unique modifications of its protease repertoire. Endoparasitic flatworms show striking losses of metabolic capabilities, not matched by nematodes. All helminths do however exhibit an overall reduction in auxiliary metabolism (biogenesis of co-factors and vitamins). Overall, the prevailing pattern is that there are few commonalities between the genomes of independently evolved parasitic worms, with each parasite having undergone specific adaptations for their particular niche.
    Parasitology 12/2014; · 2.35 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Remote speaker verification services typically rely on the system having access to the users recordings, or features derived from them, and/or a model for the users voice. This conventional approach raises several privacy concerns. In this work, we address this privacy problem in the context of a speaker verification system using a factor analysis based front-end extractor, the so-called i-vectors. Preserving privacy in our context means that neither the system observes voice samples or speech models from the user, nor the user observes the universal model owned by the system. This is achieved by transforming speaker i-vectors to bit strings in a way that allows for the computation of approximate distances, instead of exact ones. The key to the transformation uses a hashing scheme known as secure binary embeddings. Then, an SVM classifier with a modified kernel operates on the hashes. Experiments showed that the secure system yielded similar results as its non-private counterpart. The approach may be extended to other types of biometric authentication.
    BiForD MIPRO 2014 - Biometrics & Forensics & De-Identification and Privacy Protection Special Session at the 37th International Convention on Information and Communication Technology, Electronics and Microelectronics, Opatija, Croatia; 05/2014

Full-text (2 Sources)

Available from
Jun 1, 2014