Genomics, public health and developing countries: the case of the Mexican National Institute of Genomic Medicine (INMEGEN)

In 2004, the government of Mexico established the National Institute of Genomic Medicine (INMEGEN), to carry out disease-related genomic studies that will address national health problems and stimulate scientific and technological development by generating new commercial products and services in genomic medicine. Towards this end, INMEGEN is carrying out a large-scale genotyping project to map genomic variation within its own population. The initiative is expected to generate a key resource for local researchers to understand disease susceptibility and variation in drug responses, which will contribute to Mexico's goal of developing public health genomics - a field in which Mexico is proving to be a leader amongst emerging economies.     

The next steps for genomic medicine: challenges and opportunities for the developing world

This is a historical moment on the path to genomic medicine - the point at which theory is about to be translated into practice. We have previously described human genome variation studies taking place in Mexico, India, Thailand, and South Africa. Such investments into science and technology will enable these countries to embark on the path to the medical and health applications of genomics, and to benefit economically. Here we provide a perspective on the challenges and opportunities facing these and other countries in the developing world as they begin to harness genomics for the benefit of their populations.     

Hippocrates revisited? Old ideals and new realities

Individual genomics has arrived, personal decisions to make use of it are a new reality. What are the implications for the patient-physician relationship? In this article we address three factors that call the traditional concept of confidentiality into question. First, the illusion of absolute data safety, as shown by medical informatics. Second, data sharing as a standard practice in genomics research. Comprehensive data sets are widely accessible. Third, genotyping has become a service that is directly available to consumers. The availability and accessibility of personal health data strongly suggest that the roles in the clinical encounter need to be remodeled. The old ideal of physicians as keepers of confidential information is outstripped by the reality of individuals who decide themselves about the way of using their data.     

The textures of globalization: biopolitics and the closure of xenotourism

In this paper, we explore the tensions around a recent controversial development in medical tourism: xenotourism in Mexico. We take this bioendeavor – now ceased – to be emblematic of the global character of contemporary biomedicine, providing insights into the production and operation of scientific knowledge. We explore this through what we call the “textures of globalization”: the anxiety regarding the extent to which Mexico was understood as an (in)appropriate venue for the generation of novel knowledge on xenotransplantation, and as a location for xenotourism. These tensions, which oscillated between calls for individual freedom (choice) and global regulation (standardization), ultimately led to the closure of xenotourism in Mexico.     

HIV and Latino migrant workers in the USA

Abstract

Migrant workers from Latin America are an essential source of economic development in the US agricultural industry. A majority of migrants are from Mexico and are undocumented and they represent a vulnerable and marginalized group in American society. There is a growing concern for HIV disease in the migrant community. The HIV prevalence rate among migrants is higher than the average rates in USA and in countries of Latin America. There are many behavioural, social, cultural, and health care risk factors and barriers that place migrants at increased risk for HIV infection. Many migrant workers contract HIV while working and living in the USA, which has contributed to rising HIV infection rates in Mexico. In order to prevent an increasing epidemic of HIV disease in Latino migrant workers, there is an urgent call for new and improved health care policies at the international, federal, state, and local levels.     

Widening the net on genome sequencing

GENOMES: With the DNA sequencing of most key model organisms finished or well on the way, one genomics institute is filling an important niche, using novel criteria to take on species from organisms that occupy a unique place in the evolutionary tree to others that have an ability to digest explosives.     

Functional differentiation of proteins: implications for structural genomics

Structural genomics is a broad initiative of various centers aiming to provide complete coverage of protein structure space. Because it is not feasible to experimentally determine the structures of all proteins, it is generally agreed that the only viable strategy to achieve such coverage is to carefully select specific proteins (targets), determine their structure experimentally, and then use comparative modeling techniques to model the rest. Here we suggest that structural genomics centers refine the structure-driven approach in target selection by adopting function-based criteria. We suggest targeting functionally divergent superfamilies within a given structural fold so that each function receives a structural characterization. We have developed a method to do so, and an itemized survey of several functionally rich folds shows that they are only partially functionally characterized. We call upon structural genomics centers to consider this approach and upon computational biologists to further develop function-based targeting methods.     

Genomics research in the UK--the social science agenda

We sketch the development of UK genetics and genomics research, and emphasize the UK's key role in the international genetics and genomics research community. We highlight in particular the part played by the UK's Research Councils and other funders. With the move from genomics to post-genomics research, the field is diversifying, and interdisciplinarity becomes increasingly important, as traditional disciplinary boundaries become blurred, or break down, in the face of newly emerging sciences. We consider the changing nature of health and ill health in the developed and developing world, and questions about the complex nature of the relationships between genes and the environment, and their future implications for human health and human populations. We describe the ESRC's activities, stressing the importance of both the social, ethical and legal issues raised by these emerging disciplines, and of public engagement. Finally, we link the data handling and analysis issues raised by these emerging sciences, with other new research areas, in particular the UK's e-Science programme.     

Biotechnology to improve health in developing countries -- a review

The growing health disparities between the developing and the developed world call for urgent action from the scientific community. Science and technology have in the past played a vital role in improving public health. Today, with the tremendous potential of genomics and other advances in the life sciences, the contribution of science to improve public health and reduce global health disparities is more pertinent than ever before. Yet the benefits of modern medicine still have not reached millions of people in developing countries. It is crucial to recognize that science and technology can be used very effectively in partnership with public health practices in developing countries and can enhance their efficacy. The fight to improve global health needs, in addition to effective public health measures, requires rapid and efficient diagnostic tools; new vaccines and drugs, efficient delivery methods and novel approaches to therapeutics; and low-cost restoration of water, soil and other natural resources. In 2002, the University of Toronto published a report on the "Top 10 Biotechnologies for Improving Health in Developing Countries". Here we review these new and emerging biotechnologies and explore how they can be used to support the goals of developing countries in improving health.     

It is time to end the patenting of software

One of the most significant outcomes of genomics has been arapid increase in the rate that we as a community can generatedata on interesting biological systems. Rapid improvements intechnologies such as DNA microarrays and proteomics applicationshave produced a climate where the challenge is no longer collectinghigh quality data but rather managing and analyzing it. As wein the bioinformatics community have addressed this challenge,we have had to carefully consider the way in which the resultsof our intellectual efforts—the software tools that wedevelop—are made available to the wider research community.Increasingly, bioinformatics scientists are coming to call fordevelopment in an open source environment in which softwareis distributed with its underlying source code     

AN ACOUSTIC LINK BETWEEN BLUE WHALES IN THE EASTERN TROPICAL PACIFIC AND THE NORTHEAST PACIFIC1

Blue whale calls in the eastern North Pacific Ocean consist of a two-part call often termed the A-B call. This call has been described for regions offshore of Oregon, Washington, and California, USA and the Sea of Cortez, Mexico (reviewed in Rivers 1997). Data collected from moored hydrophones in the eastern tropical Pacific (ETP) indicate that the A-B pattern is common in this region as well. There is consistency in this call type throughout the eastern North Pacific and throughout the year. This acoustic evidence indicates continuity between blue whales in the ETP and those found west of North America. The acoustic data suggest that the population of blue whales generally referred to as the “Californi/Mexico” stock might better be termed the “northeast Pacific” stock of blue whales.     

Ecology and Ethnobiology of the Slender-billed Grackle Quiscalus palustris

A renaissance-era encyclopedia compiled by Fray Bernardino de Sahagun and his research group of elite native scholars from the Royal College of the Holy Cross, Tlatelolco, Valley of Mexico, provides new information on the Slender-billed Grackle (Quiscalus palustris), a bird that disappeared before modern field studies of it could be made. In sixteenth-century Mexico, this grackle nested in emergent aquatic vegetation and in towns. It was abundant, went around in flocks, and did great damage in the maize crop. Although normally not eaten by humans, it was exploited for its feathers and sacrificed to the Aztec fire god. The Slender-billed Grackle inhabited both the Valley of Mexico and the Valley of Toluca. It was found in marshes, but the degree to which it was dependent on marsh habitats is unknown. Edward Alphonso Goldman, who saw living Slender-billed Grackles in the field, declined to call this bird a marsh specialist. Three records exist of Slender-billed Grackles and Great-tailed Grackles (Quiscalus mexicanus) inhabiting the same locality during the same time period. The author recommends that searches for this grackle be expanded to include non-marsh habitats and areas outside its known historical range.     

Structural Genomics of Eukaryotic Targets at a Laboratory Scale

Structural genomics programs are distributed worldwide and funded by large institutions such as the NIH in United-States, the RIKEN in Japan or the European Commission through the SPINE network in Europe. Such initiatives, essentially managed by large consortia, led to technology and method developments at the different steps required to produce biological samples compatible with structural studies. Besides specific applications, method developments resulted mainly upon miniaturization and parallelization. The challenge that academic laboratories faces to pursue structural genomics programs is to produce, at a higher rate, protein samples. The Structural Biology and Genomics Department (IGBMC – Illkirch – France) is implicated in a structural genomics program of high eukaryotes whose goal is solving crystal structures of proteins and their complexes (including large complexes) related to human health and biotechnology. To achieve such a challenging goal, the Department has established a medium-throughput pipeline for producing protein samples suitable for structural biology studies. Here, we describe the setting up of our initiative from cloning to crystallization and we demonstrate that structural genomics may be manageable by academic laboratories by strategic investments in robotic and by adapting classical bench protocols and new developments, in particular in the field of protein expression, to parallelization.     

Impact of insurance and supply of health professionals on coverage of treatment for hypertension in Mexico: population based study

Objective To examine the independent and combined contributions of insurance status and supply of health professionals on coverage of antihypertensive treatment among adults in Mexico.Design Population based study.Setting Mexico.Participants 4032 hypertensive adults (2967 uninsured and 1065 insured): 1065 uninsured adults matched with 1065 adults insured through Seguro Popular, a programme to expand health insurance coverage to uninsured people in Mexico.Main outcome measures Coverage of antihypertensive treatment and coverage of antihypertensive treatment with control of blood pressure.Results Rates of treatment for hypertension varied by insurance status and supply of health professionals. Hypertensive adults insured through Seguro Popular had a significantly higher probability of receiving antihypertensive treatment (odds ratio 1.50, 95% confidence interval 1.27 to 1.78) and receiving antihypertensive treatment with control of blood pressure (1.35, 1.00 to 1.82). Greater supply of health professionals in areas with coverage through Seguro Popular was a significant predictor of antihypertensive treatment after adjusting for covariates (1.49, 1.00 to 2.20).Conclusions Expansion of healthcare coverage to uninsured people in Mexico was associated with greater use of antihypertensive treatment and blood pressure control, particularly in areas with a greater supply of health professionals.     

The Past and Future of Tuberculosis Research

Renewed efforts in tuberculosis (TB) research have led to important new insights into the biology and epidemiology of this devastating disease. Yet, in the face of the modern epidemics of HIV/AIDS, diabetes, and multidrug resistance—all of which contribute to susceptibility to TB—global control of the disease will remain a formidable challenge for years to come. New high-throughput genomics technologies are already contributing to studies of TB''s epidemiology, comparative genomics, evolution, and host–pathogen interaction. We argue here, however, that new multidisciplinary approaches—especially the integration of epidemiology with systems biology in what we call “systems epidemiology”—will be required to eliminate TB.     

The epidemiology of coccidioidomycosis in Mexico

Coccidioidomycosis, also known as San Joaquin Valley Fever, is an endemic mycosis restricted to the American deserts, caused by the ascomycete Coccidioides spp. In 2000 it was estimated that more than 100,000 cases of the disease took place in the United States, and that these numbers have been rising over time. The current impact of this disease in Mexico is unknown, but the available data suggest that an increase of the incidence of this mycosis in California and Arizona might have the same impact in Mexican nearby States. These two USA States both have a bioclimatic pattern similar to the nearby Mexican States endemic for coccidioidomycosis. The main objective of this study was to collect the available information on the historical and epidemiological research done in Mexico to assess the impact of the disease and to evaluate whether the disease have a tendency to increase in the endemic areas and if this grow could represent a problem of public health in Mexico. We have conducted an extensive search on this topic in Health institutions and Academic facilities of California, Arizona and Mexico. After analyzing the scarce Mexican records we found that: 1) the main studies conducted in Mexico are limited to the northern desert areas of the country, mainly in the states of Sonora, Coahuila, Nuevo Leon and the Baja California peninsula; 2) until 1994 an increase of coccidioidomycosis in Mexico was noted; and 3) we found that Mexico shares a similar epidemiological data as that reported in the United States. For instance, the most affected groups in Mexico were children under 5 years-old and adults over 45 years-old. The collective information suggests the need to implement joined organized efforts and multi-institutional collaboration to clarify the current situation of this important endemic disease of North America to administer a viable early detection plan of this mycosis in Mexico.     

Discovery of an endemic area of Gnathostoma turgidum infection among opossums, Didelphis virginiana, in Mexico

Gnathostomosis, caused by Gnathostoma binucleatum, is a serious public health issue in Mexico. Although 2 other Gnathostoma spp., G. turgidum and G. lamothei, have been found in wild animals, their natural life cycle or their relation to human disease remains unclear. While we were conducting an epidemiological survey on Gnathostoma spp. in Sinaloa State, Mexico, we found an endemic area for G. turgidum in common opossums, Didelphis virginiana, located in Tecualilla, Sinaloa. The species identification was carried out by morphological and molecular biological methods. This is the first record of an endemic area for G. turgidum infection in opossums, D. virginiana, in the Americas.     

Functional genomics of lactic acid bacteria: from food to health

Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health.     

环境基因组学的研究进展

本文系统地介绍了环境基因组学的基本概念和主流技术平台,及其在环境污染控制、健康风险检测与评价等方面地应用．并阐释了环境基因组学与环境蛋白组学、生物信息学之间的关系。环境基因组学在生物基因组水平上揭示了环境污染物与生物之间的相互作用,为维护人体与环境健康,进行分子水平遗传物质的检测与调控。奠定了理论基础与技术支持,目前已经成为控制环境污染,提高人体与环境健康质量的重要议题。