Browsing by Subject "Disease"
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Item Open Access A high-resolution map of human evolutionary constraint using 29 mammals.(Nature, 2011-10-12) Lindblad-Toh, Kerstin; Garber, Manuel; Zuk, Or; Lin, Michael F; Parker, Brian J; Washietl, Stefan; Kheradpour, Pouya; Ernst, Jason; Jordan, Gregory; Mauceli, Evan; Ward, Lucas D; Lowe, Craig B; Holloway, Alisha K; Clamp, Michele; Gnerre, Sante; Alföldi, Jessica; Beal, Kathryn; Chang, Jean; Clawson, Hiram; Cuff, James; Di Palma, Federica; Fitzgerald, Stephen; Flicek, Paul; Guttman, Mitchell; Hubisz, Melissa J; Jaffe, David B; Jungreis, Irwin; Kent, W James; Kostka, Dennis; Lara, Marcia; Martins, Andre L; Massingham, Tim; Moltke, Ida; Raney, Brian J; Rasmussen, Matthew D; Robinson, Jim; Stark, Alexander; Vilella, Albert J; Wen, Jiayu; Xie, Xiaohui; Zody, Michael C; Broad Institute Sequencing Platform and Whole Genome Assembly Team; Baldwin, Jen; Bloom, Toby; Chin, Chee Whye; Heiman, Dave; Nicol, Robert; Nusbaum, Chad; Young, Sarah; Wilkinson, Jane; Worley, Kim C; Kovar, Christie L; Muzny, Donna M; Gibbs, Richard A; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team; Cree, Andrew; Dihn, Huyen H; Fowler, Gerald; Jhangiani, Shalili; Joshi, Vandita; Lee, Sandra; Lewis, Lora R; Nazareth, Lynne V; Okwuonu, Geoffrey; Santibanez, Jireh; Warren, Wesley C; Mardis, Elaine R; Weinstock, George M; Wilson, Richard K; Genome Institute at Washington University; Delehaunty, Kim; Dooling, David; Fronik, Catrina; Fulton, Lucinda; Fulton, Bob; Graves, Tina; Minx, Patrick; Sodergren, Erica; Birney, Ewan; Margulies, Elliott H; Herrero, Javier; Green, Eric D; Haussler, David; Siepel, Adam; Goldman, Nick; Pollard, Katherine S; Pedersen, Jakob S; Lander, Eric S; Kellis, ManolisThe comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.Item Open Access Assessment of LD matrix measures for the analysis of biological pathway association.(Stat Appl Genet Mol Biol, 2010) Crosslin, David R; Qin, Xuejun; Hauser, Elizabeth RComplex diseases will have multiple functional sites, and it will be invaluable to understand the cross-locus interaction in terms of linkage disequilibrium (LD) between those sites (epistasis) in addition to the haplotype-LD effects. We investigated the statistical properties of a class of matrix-based statistics to assess this epistasis. These statistical methods include two LD contrast tests (Zaykin et al., 2006) and partial least squares regression (Wang et al., 2008). To estimate Type 1 error rates and power, we simulated multiple two-variant disease models using the SIMLA software package. SIMLA allows for the joint action of up to two disease genes in the simulated data with all possible multiplicative interaction effects between them. Our goal was to detect an interaction between multiple disease-causing variants by means of their linkage disequilibrium (LD) patterns with other markers. We measured the effects of marginal disease effect size, haplotype LD, disease prevalence and minor allele frequency have on cross-locus interaction (epistasis). In the setting of strong allele effects and strong interaction, the correlation between the two disease genes was weak (r=0.2). In a complex system with multiple correlations (both marginal and interaction), it was difficult to determine the source of a significant result. Despite these complications, the partial least squares and modified LD contrast methods maintained adequate power to detect the epistatic effects; however, for many of the analyses we often could not separate interaction from a strong marginal effect. While we did not exhaust the entire parameter space of possible models, we do provide guidance on the effects that population parameters have on cross-locus interaction.Item Open Access Biogenetic mechanisms predisposing to complex phenotypes in parents may function differently in their children.(J Gerontol A Biol Sci Med Sci, 2013-07) Kulminski, Alexander M; Arbeev, Konstantin G; Christensen, Kaare; Stallard, Eric; Miljkovic, Iva; Barmada, Michael; Yashin, Anatoliy IThis study focuses on the participants of the Long Life Family Study to elucidate whether biogenetic mechanisms underlying relationships among heritable complex phenotypes in parents function in the same way for the same phenotypes in their children. Our results reveal 3 characteristic groups of relationships among phenotypes in parents and children. One group composed of 3 pairs of phenotypes confirms that associations among some phenotypes can be explained by the same biogenetic mechanisms working in parents and children. Two other groups including 9 phenotype pairs show that this is not a common rule. Our findings suggest that biogenetic mechanisms underlying relationships among different phenotypes, even if they are causally related, can function differently in successive generations or in different age groups of biologically related individuals. The results suggest that the role of aging-related processes in changing environment may be conceptually underestimated in current genetic association studies using genome wide resources.Item Open Access Coral-associated Crabs and Macroalgae Alter Disease Spread in Branching Corals on the Great Barrier Reef(2020) Renzi, Julianna JollyDisease is an important driver of coral loss regionally and is projected to become more severe as temperatures increase around the world. Although there has been substantial research into the abiotic factors (e.g. temperature, nutrients) controlling coral diseases, we know significantly less about the biotic factors (i.e. species interactions) influencing disease dynamics. We examined how the species living on and within corals affect coral tissue loss from a white syndrome-like condition on Heron Island in the southern section of the Great Barrier Reef. We exposed Acropora aspera fragments in flow-through tanks to a fully crossed factorial experiment with three factors: the presence of a common symbiotic crab (Cyclodius ungulatus), contact with a common macroalgal complex, and simulated wounding mimicking fish predation. We found that crab presence increased coral survival from a white syndrome-type disease by over 25%, likely by removing macroalgae if present and by cleaning infected tissue. Conversely, contact with macroalgae dramatically increased coral mortality, with the chance of survival dropping to nearly 0 by the end of 25 days for corals that were in contact with algae. Wounding had no direct effect on coral health, but wounded corals with crabs did significantly better than corals with no wounding and crabs, which may be the result of coral-crab signaling. We suggest that A. aspera may produce nutrient-rich mucus when wounded, which attracts crab symbionts that help slow disease progression. These results suggest that incorporating biotic interactions into restoration designs may dramatically improve restoration outcomes and that adding beneficial symbionts may improve disease resilience at a local level.
Item Open Access Culture, Capture, and Disease: Shrimp Production in the Age of Industrial Aquaculture(2019) Dubik, Bradford AThis dissertation focuses on the relationship of industrial shrimp aquaculture and shrimp diseases, with an emphasis on the agency of disease in shaping the history of shrimp production. Shrimp aquaculture is concentrated in developing tropical economies, with the significant majority of shrimp exported to consumers in the Global North. The rise of shrimp aquaculture has been accompanied by the development of new technologies and practices, designed to facilitate and govern the growth of the industry. While successful in making aquaculture the single largest production method for shrimp, these innovations also created ideal environments for the emergence and spread of shrimp diseases, which have caused significant and persistent production losses. Disease has brought volatility and risk to producer livelihoods, while also necessitating further technological modernization and development interventions to curb disease outbreaks.
This research draws on qualitative interviews and contextual economic analyses to explore the role of disease at multiple scales. Chapter 2 examines how disease has shaped industry discourses and he practice of shrimp aquaculture across contexts. The role of the concept of biosecurity is examined to highlight the territorial nature of disease prevention. Chapter 3 explores the context of shrimp aquaculture development in Aceh, Indonesia. This chapter applies the general ideas explored in Chapter 2, to a real-world case, highlighting how the pairing of shrimp and disease is managed as a single commodity. Chapter 4 explores the reach of disease globally, and across methods of production. The economic effects of disease on U.S. wild shrimping are explored, along with the role of disease as a narrative element in resisting global aquaculture.
It is argued that shrimp disease shapes commodity relationships, influencing production decisions, and development priorities at multiple scales. The unsympathetic quality of disease makes disease prevention an ideal project for enrolling broad coalitions of human and non-human actors, and negating the politics embedded in the relationship of disease prevention with commodification more broadly.
Item Open Access Disease Risk in Wild Primate Populations: Host and Environmental Predictors, Immune Responses and Costs of Infection(2017) Akinyi, Mercy YvonneDisease risk in wild animal populations is driven by multiple factors, including host, parasite, and environmental traits, that facilitate the transmission of parasites and infection of hosts. Parasites inflict costs on their hosts that affect host fitness with downstream consequences on population structures and disease emergence patterns. Most disease risk-related studies are conducted in captive animals, while few have focused on free-ranging populations because of the logistical challenges associated with long-term monitoring of the hosts and sample collection. Hence, data regarding disease dynamics in natural populations are scarce, which limits our understanding of the ecological and evolutionary context of disease dynamics. In this thesis, we investigate the forces driving disease risk in wild primates and the possible consequences of infection on these hosts.
We used longitudinal and cross-sectional data sets from wild primate populations in Kenya, Eastern Africa, to examine the following aims: 1) the effect of host behavior on hormones associated with disease risk, 2) environmental and host factors that predispose individuals to helminth infections, and 3) the immune responses and fitness costs associated with helminth infections. First, we investigated how two maturational milestones in wild male baboons—natal dispersal and rank attainment—were associated with variation in fecal hormone metabolites (glucocorticoids and testosterone). These two hormones are generally considered to be immunosuppressive and are often associated with high parasite loads. Within this analysis, we also investigated whether changes in the frequencies of behaviors (mating and agonistic encounters) were associated with adult dominance rank attainment. Second, we investigated multiple sources of variance in helminth burdens in a well-studied population of wild female baboons, including factors that contribute to both exposure and susceptibility (group size, social status, rainfall, temperature, age, and reproductive status). Third, we investigated how hematological indices and body mass index were associated with helminth burden.
In the first study, our results revealed that rank attainment is associated with an increase in fecal glucocorticoids (fGC) levels but not fecal testosterone (fT) levels: males that have achieved an adult rank have higher fGC than males that have not yet attained an adult rank. We also found that males win more agonistic encounters and acquire more reproductive opportunities after they have attained adult rank than before they have done so. The second study revealed that female baboons in Amboseli were infected with diverse helminth taxa, including both directly transmitted and indirectly transmitted helminths. In general, high parasite risk was linked to large group sizes, low rainfall conditions, old age, and pregnancy, although these predictors varied somewhat across helminth species. Fecal GC levels were not associated with any measures of helminth burden. The third study found that helminth burdens were positively associated with circulating lymphocyte counts and negatively associated with neutrophil-lymphocyte ratios (NLR). We did not find any associations between helminth burdens and total WBC or eosinophil counts. Red blood cell indices were not predicted by our measures of helminth burden but instead varied with age class and sex. Helminth burdens were also negatively correlated with body mass index (BMI).
Overall, the findings of this thesis are consistent with the hypothesis that host and environmental traits are important predictors of disease risk and infection in wild primate populations. In addition, our results suggest that wild primates mount immune responses to helminth burden and that helminth infections may have detrimental consequences on host body condition. Our work enhances the limited data on sources of disease variation and associated costs in wild populations. It also emphasizes the continued need for disease surveillance and health monitoring in wild populations.
Item Open Access Do gender, disability, and morbidity affect aging rate in the LLFS? Application of indices of cumulative deficits.(Mech Ageing Dev, 2011-04) Kulminski, Alexander M; Arbeev, Konstantin G; Christensen, Kaare; Mayeux, Richard; Newman, Anne B; Province, Michael A; Hadley, Evan C; Rossi, Winifred; Perls, Thomas T; Elo, Irma T; Yashin, Anatoli IWe used an approach of cumulative deficits to evaluate the rate of aging in 4954 participants of the Long-Life Family Study (LLFS) recruited in the U.S. (Boston, New York, and Pittsburgh) and Denmark. We used an array of 85 health-related deficits covering major health dimensions including depression, cognition, morbidity, physical performance, and disability to construct several deficit indices (DIs) with overlapping and complementary sets of deficits to test robustness of the estimates. Our study shows that the DIs robustly characterize accelerated rates of aging irrespective of specific of deficits. When a wider spectrum of health dimensions is considered these rates are better approximated by quadratic law. Exponential rates are more characteristic for more severe health dimensions. The aging rates are the same for males and females. Individuals who contracted major diseases and those who were free of them exhibited the same aging rates as characterized by the DI constructed using mild deficits. Unlike health, disability can qualitatively alter the aging patterns of the LLFS participants. We report on systemic differences in health among the LLFS centenarians residing in New York and Boston. This study highlights importance of aggregated approaches to better understand systemic mechanisms of health deterioration in long-living individuals.Item Open Access Identification of cis-suppression of human disease mutations by comparative genomics.(Nature, 2015-08) Jordan, Daniel M; Frangakis, Stephan G; Golzio, Christelle; Cassa, Christopher A; Kurtzberg, Joanne; Task Force for Neonatal Genomics; Davis, Erica E; Sunyaev, Shamil R; Katsanis, NicholasPatterns of amino acid conservation have served as a tool for understanding protein evolution. The same principles have also found broad application in human genomics, driven by the need to interpret the pathogenic potential of variants in patients. Here we performed a systematic comparative genomics analysis of human disease-causing missense variants. We found that an appreciable fraction of disease-causing alleles are fixed in the genomes of other species, suggesting a role for genomic context. We developed a model of genetic interactions that predicts most of these to be simple pairwise compensations. Functional testing of this model on two known human disease genes revealed discrete cis amino acid residues that, although benign on their own, could rescue the human mutations in vivo. This approach was also applied to ab initio gene discovery to support the identification of a de novo disease driver in BTG2 that is subject to protective cis-modification in more than 50 species. Finally, on the basis of our data and models, we developed a computational tool to predict candidate residues subject to compensation. Taken together, our data highlight the importance of cis-genomic context as a contributor to protein evolution; they provide an insight into the complexity of allele effect on phenotype; and they are likely to assist methods for predicting allele pathogenicity.Item Open Access Impacts of disease in shrimp aquaculture on U.S. capture fishery prices(2017-04-28) Petesch, TessShrimp is one of the most traded seafood commodities in the world, and aquaculture now contributes more to global shrimp production than capture fishing. Since the 1970s, the shrimp culture industry has been simultaneously characterized by rapid growth due to falling production costs as well as severe losses from disease outbreaks. Previous research confirms that farmed and wild shrimp are substitutes and shrimp markets around the world are well integrated. We seek to determine if prices of wild shrimp in the U.S. Gulf of Mexico fishery reflect supply shocks in aquaculture attributed to acute disease epidemics. Analysis relies on U.S. farmed shrimp import data between 1990 and 2016 from three major producers: Ecuador, Thailand, and Indonesia. After testing country-level price indices for cointegration, we use structural break tests to determine if significant price changes coincide with anecdotal disease crises. We attempt to further characterize the shrimp market by testing if disease outbreaks correspond with changes in relative prices of larger, more valuable shrimp compared to smaller shrimp.Item Open Access Informing the 2011 UN Session on Noncommunicable Diseases: applying lessons from the AIDS response.(PLoS Med, 2011-09) Lamptey, Peter; Merson, Michael; Piot, Peter; Reddy, K Srinath; Dirks, RebeccaItem Open Access The Effects of Parasites on Coastal Marsh Ecosystem Structure and Functioning(2021) Morton, Joseph PhilipRecent experiments and comparative surveys in Southern US salt marshes revealed that a common larval trematode parasite, Parorchis acanthus, generated a trophic cascade that protected foundational marsh plants (Spartina alterniflora) from drought-associated overgrazing by suppressing the per capita grazing impacts of its host, the marsh periwinkle (Littoraria irrorata). While it is clear that parasites can play a positive role in mediating marsh ecosystem response to disturbance, there is still little known about the context dependency of this interaction, the role of definitive avian hosts in regulating parasite prevalence, and whether other commonly-occurring parasites may also modify processes that underpin ecosystem stability. The purpose of this project was to extend the current understanding of the roles played by parasites and their hosts in mediating marsh ecosystem stability. A field manipulation of Littoraria density in which infection prevalence with Parorchis acanthus was held at a constant value revealed that these parasites yielded positive impacts on Spartina aboveground biomass at middling densities of snails, but the positive effects of parasites were negligible at both low, and high snail densities. Surveys of drought-impacted marshes revealed that birds – the definitive hosts for trematode that infect Littoraria – congregated within die-off areas and that increased bird usage of die-off areas was associated with increased trematode parasitism in snails within grazer fronts, decreased per capita grazing rates of snails, and proportionate decreases in ecosystem die-off rate. Multi-site bird exclusion and mechanistic field studies experimentally confirmed that birds increased ecosystem resistance to drought-driven die-off by acting as the dispersive vectors for parasites that suppress Littoraria grazing. Finally, we explored how the trematode Cercaria opaca in ribbed mussels (Geukensia demissa) influenced the facultative mutualism between Guekensia and Spartina – an interaction that underlies marsh ecosystem resilience to drought-associated die-off. A field manipulation using experimentally infected mussels revealed that mutualistic benefits to Spartina decreased with increasing infection intensity in mussels. Subsequent mechanistic experiments demonstrated that increasing infection with C. opaca decreased mussel biodeposit production, the functional trait underlying mutualistic benefits to Spartina. Additionally, increasing parasite load was associated with decreased strength of both shells and byssal attachments, potentially explaining the relatively higher predation on heavily infected mussels in our field study. A survey of five North Carolina salt marshes revealed that infection intensity in mussels increased with proximity to die-off areas, indicating that C. opaca could influence marsh recovery following die-off events. Taken together, these results underscore the importance of parasitism’s influence on Southern salt marsh ecosystem stability and more generally show that parasites can be major arbiters of community structure and functioning.
Item Restricted Trade-offs between cancer and other diseases: do they exist and influence longevity?(Rejuvenation Res, 2010-08) Ukraintseva, Svetlana V; Arbeev, Konstantin G; Akushevich, Igor; Kulminski, Alexander; Arbeeva, Liubov; Culminskaya, Irina; Akushevich, Lucy; Yashin, Anatoli IRelationships between aging, disease risks, and longevity are not yet well understood. For example, joint increases in cancer risk and total survival observed in many human populations and some experimental aging studies may be linked to a trade-off between cancer and aging as well as to the trade-off(s) between cancer and other diseases, and their relative impact is not clear. While the former trade-off (between cancer and aging) received broad attention in aging research, the latter one lacks respective studies, although its understanding is important for developing optimal strategies of increasing both longevity and healthy life span. In this paper, we explore the possibility of trade-offs between risks of cancer and selected major disorders. First, we review current literature suggesting that the trade-offs between cancer and other diseases may exist and be linked to the differential intensity of apoptosis. Then we select relevant disorders for the analysis (acute coronary heart disease [ACHD], stroke, asthma, and Alzheimer disease [AD]) and calculate the risk of cancer among individuals with each of these disorders, and vice versa, using the Framingham Study (5209 individuals) and the National Long Term Care Survey (NLTCS) (38,214 individuals) data. We found a reduction in cancer risk among old (80+) men with stroke and in risk of ACHD among men (50+) with cancer in the Framingham Study. We also found an increase in ACHD and stroke among individuals with cancer, and a reduction in cancer risk among women with AD in the NLTCS. The manifestation of trade-offs between risks of cancer and other diseases thus depended on sex, age, and study population. We discuss factors modulating the potential trade-offs between major disorders in populations, e.g., disease treatments. Further study is needed to clarify possible impact of such trade-offs on longevity.