scholarly journals Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 60
Author(s):  
Fabrizio Menardo ◽  
Liliana K. Rutaihwa ◽  
Michaela Zwyer ◽  
Sonia Borrell ◽  
Iñaki Comas ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Indian Ocean ◽  
Positive Selection ◽  
South Asia ◽  
Local Adaptation ◽  
Endosomal Sorting ◽  
Gene Coding ◽  
History Of ◽  
The Indian Ocean ◽  
Historical Role

Background: Lineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC) causing tuberculosis (TB) in humans. L1 and L3 are prevalent around the rim of the Indian Ocean, the region that accounts for most of the world’s new TB cases. Despite their relevance for this region, L1 and L3 remain understudied. Methods: We analyzed 2,938 L1 and 2,030 L3 whole genome sequences originating from 69 countries. We reconstructed the evolutionary history of these two lineages and identified genes under positive selection. Results: We found a strongly asymmetric pattern of migration from South Asia toward neighboring regions, highlighting the historical role of South Asia in the dispersion of L1 and L3. Moreover, we found that several genes were under positive selection, including genes involved in virulence and resistance to antibiotics . For L1 we identified signatures of local adaptation at the esxH locus, a gene coding for a secreted effector that targets the human endosomal sorting complex, and is included in several vaccine candidates. Conclusions: Our study highlights the importance of genetic diversity in the MTBC, and sheds new light on two of the most important MTBC lineages affecting humans.

scholarly journals Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 60
Author(s):  
Fabrizio Menardo ◽  
Liliana K. Rutaihwa ◽  
Michaela Zwyer ◽  
Sonia Borrell ◽  
Iñaki Comas ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Indian Ocean ◽  
Positive Selection ◽  
South Asia ◽  
Local Adaptation ◽  
Endosomal Sorting ◽  
Gene Coding ◽  
History Of ◽  
The Indian Ocean ◽  
Historical Role

Background: Lineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC) causing tuberculosis (TB) in humans. L1 and L3 are prevalent around the rim of the Indian Ocean, the region that accounts for most of the world’s new TB cases. Despite their relevance for this region, L1 and L3 remain understudied. Methods: We analyzed 2,938 L1 and 2,030 L3 whole genome sequences originating from 69 countries. We reconstructed the evolutionary history of these two lineages and identified genes under positive selection. Results: We found a strongly asymmetric pattern of migration from South Asia toward neighboring regions, highlighting the historical role of South Asia in the dispersion of L1 and L3. Moreover, we found that several genes were under positive selection, including genes involved in virulence and resistance to antibiotics. For L1 we identified signatures of local adaptation at the esxH locus, a gene coding for a secreted effector that targets the human endosomal sorting complex, and is included in several vaccine candidates. Conclusions: Our study highlights the importance of genetic diversity in the MTBC, and sheds new light on two of the most important MTBC lineages affecting humans.

scholarly journals Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim

2020 ◽  
Author(s):  
Fabrizio Menardo ◽  
Liliana K. Rutaihwa ◽  
Michaela Zwyer ◽  
Sonia Borrell ◽  
Iñaki Comas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mycobacterium Tuberculosis ◽  
Indian Ocean ◽  
Local Adaptation ◽  
Whole Genome ◽  
Genome Sequences ◽  
Vaccine Candidates ◽  
Endosomal Sorting ◽  
Gene Coding ◽  
The Indian Ocean

AbstractLineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC), causing tuberculosis (TB) in humans. L1 and L3 are endemic to the Rim of the Indian Ocean, the region that accounts for most of the world’s new TB cases. Despite their relevance for this region, L1 and L3 remain understudied. Here we analyzed 2,938 L1 and 2,030 L3 whole genome sequences originating from 69 countries. We show that South Asia played a central role in the dispersion of these two lineages to neighboring regions. Moreover, we found that L1 exhibits signatures of local adaptation at the esxH locus, a gene coding for a secreted effector that targets the human endosomal sorting complex, and is included in several vaccine candidates. Our study highlights the importance of genetic diversity in the MTBC, and sheds new light on two of the most important MTBC lineages affecting humans.

scholarly journals Coffee: An Indian Ocean Perspective

2016 ◽  
Vol 11 (2) ◽  
pp. 61-81
Author(s):  
Shane J. Barter
Keyword(s):  
Indian Ocean ◽  
South Asia ◽  
Latin American ◽  
Eastern Africa ◽  
Coffee Production ◽  
Production And Consumption ◽  
History Of ◽  
Coffee Farmers ◽  
The Indian Ocean ◽  
Indian Ocean World

Abstract Studies of coffee production and consumption are dominated by emphases on Latin American production and American consumption. This paper challenges the Atlantic perspective, demanding an equal emphasis on the Indian Ocean world of Eastern Africa, the Middle East, South Asia, and Southeast Asia. A geographical approach to historical as well as contemporary patterns of coffee production and consumption provides an opportunity to rethink the nature of coffee as a global commodity. The Indian Ocean world has a much deeper history of coffee, and in recent decades, has witnessed a resurgence in production. The nature of this production is distinct, providing an opportunity to rethink dependency theories. Coffee in the Indian Ocean world is more likely to be produced by smallholders, countries are less likely to be economically dependent on coffee, farmers are more likely to harvest polycultures, and countries represent both consumers and producers. A balanced emphasis of Atlantic and Indian Ocean worlds allows us to better understand coffee production and consumption, together telling a more balanced, global story of this important commodity.

A Dissenting Voice: The Clash of Trade and Warfare in Giovanni da Empoli's Account of His Second Voyage to Portuguese Asia

Itinerario ◽  
2021 ◽  
pp. 1-19
Author(s):  
Matteo Salonia
Keyword(s):  
Indian Ocean ◽  
South Asia ◽  
International Markets ◽  
Empire Building ◽  
Portuguese Empire ◽  
History Of ◽  
The Indian Ocean ◽  
Early Phases

Abstract Giovanni da Empoli's second voyage to Asia (1510–1514) was eventful and violent, characterised by the emergence of conflicting agendas among different groups of Portuguese. The Florentine merchant's long letter about the voyage is an extraordinary document, and provides insights in three important areas. First, it allows us to fill some of the gaps in the history of the early phases of Portuguese empire building, questioning the extent to which the Crown was pursuing a clear and coherent strategy that included the conquest of Malacca. Second, it problematises further our conception of “the Portuguese” by reporting episodes of Portuguese-on-Portuguese violence and opposing views on the objectives of Portuguese fleets in the Indian Ocean. Finally, Giovanni unequivocally expresses admiration for the international markets of Eastern city-ports and openly criticises the militarist attitude and lawless tactics of the Portuguese viceroy, Alfonso de Albuquerque, thereby inviting us to reconsider the chronology of a “cosmopolitan reaction” among Italian writers visiting South Asia.

Editorial Introduction

2020 ◽  
Vol 4 (1) ◽  
pp. 1
Author(s):  
Editors of the JIOWS
Keyword(s):  
Nineteenth Century ◽  
Indian Ocean ◽  
Western Indian Ocean ◽  
Late Nineteenth Century ◽  
Fourth Volume ◽  
History Of ◽  
The Indian Ocean ◽  
Complex Relationships ◽  
Indian Ocean World ◽  
Shed Light

The editors are proud to present the first issue of the fourth volume of the Journal of Indian Ocean World Studies. This issue contains three articles, by James Francis Warren (Murdoch University), Kelsey McFaul (University of California, Santa Cruz), and Marek Pawelczak (University of Warsaw), respectively. Warren’s and McFaul’s articles take different approaches to the growing body of work that discusses pirates in the Indian Ocean World, past and present. Warren’s article is historical, exploring the life and times of Julano Taupan in the nineteenth-century Philippines. He invites us to question the meaning of the word ‘pirate’ and the several ways in which Taupan’s life has been interpreted by different European colonists and by anti-colonial movements from the mid-nineteenth century to the present day. McFaul’s article, meanwhile, takes a literary approach to discuss the much more recent phenomenon of Somali Piracy, which reached its apex in the last decade. Its contribution is to analyse the works of authors based in the region, challenging paradigms that have mostly been developed from analysis of works written in the West. Finally, Pawelczak’s article is a legal history of British jurisdiction in mid-late nineteenth-century Zanzibar. It examines one of the facets that underpinned European influence in the western Indian Ocean World before the establishment of colonial rule. In sum, this issue uses two key threads to shed light on the complex relationships between European and other Western powers and the Indian Ocean World.

Australianama

2019 ◽  
Author(s):  
Samia Khatun
Keyword(s):  
Indian Ocean ◽  
South Asian ◽  
South Asian Diaspora ◽  
Post Cold War ◽  
Asian Diaspora ◽  
Broken Hill ◽  
History Of ◽  
The Indian Ocean ◽  
Anglophone World ◽  
Indian Ocean World

Australian deserts remain dotted with the ruins of old mosques. Beginning with a Bengali poetry collection discovered in a nineteenth-century mosque in the town of Broken Hill, Samia Khatun weaves together the stories of various peoples colonized by the British Empire to chart a history of South Asian diaspora. Australia has long been an outpost of Anglo empires in the Indian Ocean world, today the site of military infrastructure central to the surveillance of 'Muslim-majority' countries across the region. Imperial knowledges from Australian territories contribute significantly to the Islamic-Western binary of the post- Cold War era. In narrating a history of Indian Ocean connections from the perspectives of those colonized by the British, Khatun highlights alternative contexts against which to consider accounts of non-white people. Australianama challenges a central idea that powerfully shapes history books across the Anglophone world: the colonial myth that European knowledge traditions are superior to the epistemologies of the colonized. Arguing that Aboriginal and South Asian language sources are keys to the vast, complex libraries that belie colonized geographies, Khatun shows that stories in colonized tongues can transform the very ground from which we view past, present and future.

The Paving Stone Theory of World Tectonics

2018 ◽  
Author(s):  
Roy Livermore
Keyword(s):  
Indian Ocean ◽  
Plate Tectonics ◽  
Earth Science ◽  
Transform Faults ◽  
Plate Motions ◽  
Euler’S Theorem ◽  
History Of ◽  
New Ideas ◽  
Entire History ◽  
The Indian Ocean

Tuzo Wilson introduces the concept of transform faults, which has the effect of transforming Earth Science forever. Resistance to the new ideas is finally overcome in the late 1960s, as the theory of moving plates is established. Two scientists play a major role in quantifying the embryonic theory that is eventually dubbed ‘plate tectonics’. Dan McKenzie applies Euler’s theorem, used previously by Teddy Bullard to reconstruct the continents around the Atlantic, to the problem of plate rotations on a sphere and uses it to unravel the entire history of the Indian Ocean. Jason Morgan also wraps plate tectonics around a sphere. Tuzo Wilson introduces the idea of a fixed hotspot beneath Hawaii, an idea taken up by Jason Morgan to create an absolute reference frame for plate motions.

Spatial and Temporal Continuities of Merchant Networks in South Asia and the Indian Ocean (1500-2000)

2007 ◽  
Vol 50 (2-3) ◽  
pp. 91-105 ◽  
Author(s):  
Gita Dharampal-Frick ◽  
Bhaswati Bhattacharya ◽  
Jos Gommans
Keyword(s):  
Indian Ocean ◽  
South Asia ◽  
The People ◽  
Merchant Networks ◽  
The Indian Ocean

AbstractWe believe ourselves to be the most astute men that one can encounter, and the people here surpass us in everything. And there are Moorish merchants worth 400,000 to 500,000 ducats. And they can do better calculations by memory than we can do with the pen. And they mock us, and it seems to me that they are superior to us in countless things, save with sword in hand, which they cannot resist.

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