Human vertebrae showing characteristics signs of tuberculosis (Image source: Bos et al. 2014)
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The origins of New World tuberculosis: an ancient DNA approach
Skeletal evidence for tuberculosis (TB) in the archaeological record suggests that TB was present in the Americas long before the arrival of Europeans in the late fifteenth century. Previous research from the Stone Laboratory showed that about 1,000-1,200 years ago, seals transmitted TB to human populations living along the coast of Peru. We know that these people hunted seals for their food and fur. Handling and processing of TB-infected seals was likely the mode of transmission of TB from seals to humans. Did these seal-derived TB strains spread all over the Americas or were they restricted to the Peruvian coast? Did the strains spread via human-to-human transmission or was another animal host involved in this transmission? Were these the same strains that caused pre-contact era TB in n North America or were there other types of TB strains present as well? To answer these questions, I screen ancient human skeletal remains, showing signs of TB, for the presence of TB DNA. I use sophisticated ancient DNA extraction methods, target enrichment, and next-generation sequencing technology to reconstruct the genomes of ancient TB strains. By understanding the phylogenetic and evolutionary relationships among ancient and modern TB strains, we can answer questions about the origins and spread of this disease. This ongoing project formed the basis of my doctoral dissertation research conducted at ASU, under the supervision of Anne C. Stone, Jane E. Buikstra, and Michael S. Rosenberg, and in collaboration with Åshild Vågene, Kirsten Bos, Alexander Herbig, and Johannes Krause at the Max Planck Institute for the Science of Human History, Germany. |
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Leprosy in other animals
Leprosy is an age-old disease that remains highly endemic among the economically underprivileged countries of the world. Traditionally thought to be an exclusively human disease, isolated cases of naturally occurring leprosy have been observed in animals such as armadillos, red squirrels, and nonhuman primates. For my doctoral dissertation, I worked on two projects related to this topic - firstly, looking at the genomes of nonhuman primate M. leprae strains to help shed light on the potential for leprosy transmission between humans and other primates (Honap et al. 2018). Secondly, I sequenced the genome of the bacterium that causes leprosy in mice and cats, M. lepraemurium, to study its relationship to M. leprae (Benjak et al. 2017). |
Chimpanzee showing facial lesions of leprosy (Image source: Suzuki et al. 2010)
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Mycobacterial infections in wild animals
Research on TB and leprosy in nonhuman hosts suggests that these pathogens might be prevalent in other nonhuman primates. One of the projects I worked on during my Ph.D. aimed to assess whether we can screen non-invasive samples such as cheek swab samples for determining mycobacterial infection in nonhuman primates. We screened a population of wild tamarins from the Amazon region of Peru using quantitative PCR assays to test for the presence of TB and leprosy. These samples were collected by Dr. Mrinalini Erkenswick Watsa and Dr. Gideon Erkenswick Watsa (click here to learn about their work with primates in Peru).
Research on TB and leprosy in nonhuman hosts suggests that these pathogens might be prevalent in other nonhuman primates. One of the projects I worked on during my Ph.D. aimed to assess whether we can screen non-invasive samples such as cheek swab samples for determining mycobacterial infection in nonhuman primates. We screened a population of wild tamarins from the Amazon region of Peru using quantitative PCR assays to test for the presence of TB and leprosy. These samples were collected by Dr. Mrinalini Erkenswick Watsa and Dr. Gideon Erkenswick Watsa (click here to learn about their work with primates in Peru).
Other Research
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Recovering ancient human mitogenomes from dental calculus
The objective of this project was to reconstruct full human mitochondrial genomes from dental calculus samples acquired from human skeletal remains. This work was carried out in collaboration with LMAMR. We reconstructed complete mitogenomes for six individuals from the 700-year old Norris Farms #36 cemetery, using ancient DNA extracted from dental calculus, in conjunction with target enrichment and next-generation sequencing methods. Our results suggest that dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains, especially in cases where conventional samples, such as bone, are not available or are not sufficiently well-preserved for ancient DNA analyses. |
Dental calculus deposits on mandibular dentition (Image source: Ozga et al. 2016)
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Impact of host genetics on the outcome of Dengue virus infection
For my Masters thesis, I studied the influence of host (human) genetics on the outcome of Dengue virus infection. My advisor on this project was Dr. Kalichamy Alagarasu, National Institute of Virology, India. We studied single nucleotide polymorphisms in the vitamin D receptor gene and the oligoadenylate synthetase gene cluster, involved in the innate immune response. Our results suggest that polymorphisms in these genes are associated with differential outcomes of Dengue virus infection among Indian populations: certain haplotypes may confer protection whereas others may increase the risk of severe dengue disease.
For my Masters thesis, I studied the influence of host (human) genetics on the outcome of Dengue virus infection. My advisor on this project was Dr. Kalichamy Alagarasu, National Institute of Virology, India. We studied single nucleotide polymorphisms in the vitamin D receptor gene and the oligoadenylate synthetase gene cluster, involved in the innate immune response. Our results suggest that polymorphisms in these genes are associated with differential outcomes of Dengue virus infection among Indian populations: certain haplotypes may confer protection whereas others may increase the risk of severe dengue disease.