The genomics of ecological flexibility,large brains,and long lives in capuchin monkeys revealed with fecalFACS

Ecological flexibility, extended lifespans, and large brains have long intrigued evolutionary biologists, and comparative genomics offers an efficient and effective tool for generating new insights into the evolution of such traits. Studies of capuchin monkeys are particularly well situated to shed light on the selective pressures and genetic underpinnings of local adaptation to diverse habitats, longevity, and brain development. Distributed widely across Central and South America, they are inventive and extractive foragers, known for their sensorimotor intelligence. Capuchins have among the largest relative brain size of any monkey and a lifespan that exceeds 50 y, despite their small (3 to 5 kg) body size. We assemble and annotate a de novo reference genome for Cebus imitator. Through high-depth sequencing of DNA derived from blood, various tissues, and feces via fluorescence-activated cell sorting (fecalFACS) to isolate monkey epithelial cells, we compared genomes of capuchin populations from tropical dry forests and lowland rainforests and identified population divergence in genes involved in water balance, kidney function, and metabolism. Through a comparative genomics approach spanning a wide diversity of mammals, we identified genes under positive selection associated with longevity and brain development. Additionally, we provide a technological advancement in the use of noninvasive genomics for studies of free-ranging mammals. Our intra- and interspecific comparative study of capuchin genomics provides insights into processes underlying local adaptation to diverse and physiologically challenging environments, as well as the molecular basis of brain evolution and longevity.

Large brains, long lifespans, extended juvenescence, tool use, and problem solving are hallmark characteristics of great apes, and are of enduring interest in studies of human evolution (1–4). Similar suites of traits have arisen in other lineages, including some cetaceans, corvids and, independently, in another radiation of primates, the capuchin monkeys. Like great apes, they have diverse diets, consume and seek out high-energy resources, engage in complex extractive foraging techniques (5, 6) to consume difficult-to-access invertebrates and nuts (6), and have an extended lifespan, presently recorded up to 54 y in captivity (7, 8). While they do not show evidence of some traits linked with large brain size in humans (e.g., human-like social networks and cultural and technological transmission from older to younger groupmates), their propensity for tool use and their ecological flexibility may have contributed to their convergence with the great apes (9), offering opportunities for understanding the evolution of key traits via the comparative method (10–12). Similar approaches have revealed positive selection on genes related to brain size and long lives in great apes and other mammals (13, 14), but our understanding of the genetic underpinnings of these traits remains far from complete.Capuchins also offer excellent opportunities to study local adaptation to challenging seasonal biomes. They occupy diverse habitats, including rainforests and, in the northern extent of their range, tropical dry forests. Particular challenges of the tropical dry forest are staying hydrated during the seasonally prominent droughts, high temperatures in the absence of foliage, and coping metabolically with periods of fruit dearth (Fig. 1). The long-term study of white-faced capuchins (Cebus imitator) occupying these seasonal forests has demonstrated that high infant mortality rates accompany periods of intense drought, illustrating the strength of this selective pressure (15). Furthermore, the seasonally low abundance of fruit is associated with muscular wasting and low circulating levels of urinary creatinine among these capuchins (16). Additionally, the sensory challenges of food search in dry versus humid biomes are also distinct. Odor detection and propagation is affected by temperature and humidity (17), and color vision is hypothesized to be adaptive in the search for ripe fruits and young reddish leaves against a background of thick, mature foliage (18), which is absent for long stretches in dry deciduous forests. The behavioral plasticity of capuchins is widely acknowledged as a source of their ability to adapt to these dramatically different habitats (19–21). However, physiological processes, including water balance and metabolic adaptations to low caloric intake, and sensory adaptations to food search, are also anticipated to be targets of natural selection, as seen in other mammals (22–24). Understanding population-level differences between primates inhabiting different biomes, contextualized by their demographic history, genomic diversity, and historical patterns of migration, will generate new insights.Open in a separate windowFig. 1.SSR during wet (Left) and dry (Center) seasons. (Right) Map of sampling locations in Costa Rica. The two northern sites, SSR and Cañas, have tropical dry-forest biomes, whereas the two southern sites, Quepos and Manuel Antonio, are tropical wet forests. Photos courtesy of A.D.M. Drawing of white-faced capuchin monkey by Alejandra Tejada-Martinez; map courtesy of Eric Gaba–Wikimedia Commons user: Sting.Unfortunately, high-quality biological specimens from wild capuchins are not readily available. As is the case with most of the world’s primates, many of which are rare or threatened (25), this has limited the scope of questions about their biology that can be answered. Although recent advances in noninvasive genomics have allowed for the sequencing of partial genomes by enriching the proportion of endogenous DNA in feces (26–29), it has not yet been feasible to sequence whole genomes from noninvasive samples at high coverage; this has limited the extent to which noninvasive samples can be used to generate genomic resources for nonmodel organisms, such as capuchins.Toward identifying the genetic underpinnings of local adaptation to seasonally harsh environments, large brains, and long lifespans, we assembled and annotated a reference genome of C. imitator (SI Appendix, Table S1). Additionally, we sequenced the genomes of individuals inhabiting two distinct environments in Costa Rica: Lowland evergreen rainforest (southern population) and lowland tropical dry forest (northern population). We conducted high-coverage resequencing (10× to 47×) for 10 of these individuals, and sequenced an additional 13 at low-coverage (0.1× to 4.4×). Importantly, to facilitate the population-wide analyses without the need for potentially harmful invasive sampling of wild primates, we developed a method for minimally biased, whole-genome sequencing of fecal DNA using fluorescence-activated cell sorting (fecalFACS) that we used to generate both high- and low-coverage genomes (Fig. 2). With these genomes, we assess the genetic underpinnings of capuchin-specific biology and adaptation in a comparative framework. First, we scanned the high-coverage genomes (six from the northern dry forest and four from the southern rainforest) for regions exhibiting population specific divergence to assess the extent of local adaptation to dry forest and rainforest environments. We examine how genes related to water balance, metabolism, muscular wasting, and chemosensation have diverged between populations. Second, we conduct an analysis of positive selection on the white-faced capuchin genome through codon-based models of evolution and enrichment tests focusing on genes that may underlie brain development and lifespan. Third, we identify the population structure, genomic diversity, and demographic history of the species using a mixture of traditional and noninvasive fecalFACS genomes (n = 23).Open in a separate windowFig. 2.Mapping percentages of sequencing reads from RNAlater preserved fecal DNA libraries prepared with FACS for (A) all samples (box-plot elements: center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range; points, outliers), and (B) individual libraries. (C) Increase in mapping rate for RNAlater preserved samples. (D) Relationship between mapped read duplication and number of cells with LOESS smoothing. The duplication rate decreases sharply once a threshold of about 1,000 cells is reached.     

Gastric emptying before and after cholecystectomy in patients with cholecystolithiasis

BACKGROUND/AIMS: The objective of the present study was to measure gastric emptying time of solids and semisolids in dyspeptic individuals with cholecystolithiasis before and 6 months after cholecystectomy in order to determine whether cholecystectomy interferes with gastric emptying. METHODOLOGY: A prospective, self-pairing study was conducted on 29 patients selected according to appropriate inclusion and exclusion criteria. Gastric emptying time of solids and semisolids was determined before and six months after laparoscopic cholecystectomy by the 13C-octanoic acid and 13C-acetate breath tests, respectively. The samples were analyzed by infrared spectrometry. The gastric retention time (lag phase) and gastric emptying half-time of solid and semisolid were determined and the results obtained before and after surgery were compared in the same patient. In addition, the effects of surgery on dyspeptic symptoms were assessed. RESULTS: No significant differences (p>0.05) in gastric retention time and gastric emptying half-time of solid and semisolid test meals were observed before and after cholecystectomy. Dyspeptic symptoms (pain, upper abdominal gases, early satiety, nausea and vomiting) improved after surgery. CONCLUSIONS: Laparoscopic cholecystectomy does not interfere with the gastric emptying time of solids or semisolids in dyspeptic individuals with cholecystolithiasis.     

Rapid clearance of circulating Leishmania kinetoplast DNA after treatment of visceral leishmaniasis

With the aim of evaluating the utility of the detection of Leishmania kDNA in peripheral blood for the cure assessment of visceral leishmaniasis (VL), a PCR based method was performed in patients with confirmed VL at three follow-up periods after specific chemotherapy with pentavalent antimonial. In 16 out of 17 (94.1%) patients with pre-treatment detectable kDNA that were clinically cured, the PCR turned negative up to 37 days after the initiation of treatment, remaining negative over 90 days after treatment. The clearance of Leishmania kDNA from peripheral blood of patients with VL hints to occur during or shortly after treatment concurring or preceding clinical recovery.     

CNS cryptococcoma in an HIV-positive patient

This is the first case of brain cryptococcoma in an AIDS patient reported in Argentina. The patient was a 28-year-old white heterosexual man with AIDS who presented with altered mental status, seizures, visual hallucinations, headache, and fever without significant focal neurological deficit. He had a lumbar puncture, and was treated for cryptococcal meningitis. Subsequent brain CT scanning and MRI disclosed a mass lesion in the occipital lobe. Histopathological examination of biopsy was compatible with cryptococcoma, and tissue culture revealed Cryptococcus neoformans. Resolution of the mass and edema resulted after treatment with intravenous amphotericin B for six weeks, which was followed with maintenance oral fluconazole. Intracranial mass is an uncommon complication in AIDS patients with cryptococcosis, and cryptococcoma should be considered as differential diagnosis of brain mass lesion in these patients. The etiologic diagnosis is necessary because central nervous system (CNS) toxoplasmosis, lymphoma, and tuberculoma can produce similar clinical syndromes and MRI or CT findings to cryptococcoma. Also, these pathologies may coexist with meningeal cryptococcosis.     

Low bone mineral density is associated to poor glycemic control and increased OPG expression in children and adolescents with type 1 diabetes

Aims

To investigate early alterations on bone mineral density (BMD) and RANK, RANKL and OPG mRNA expression in peripheral blood leukocytes (PBL) in children and adolescents with type 1 diabetes (T1D) and the relationship with glycemic control and bone biomarkers.

Methods

This cross-sectional study included 75 children and adolescents with T1D and 100 individuals without diabetes (normoglycemic–NG) aged 6–20 years old. T1D individuals were considered to have good (T1DG) or poor (T1DP) glycemic control according to the values of HbA1c. Phosphorus, magnesium, total and ionized calcium, osteocalcin, alkaline phosphatase and tartaric-resistant acid phosphatase (TRAP) values were determined in blood samples. BMD was measured by DEXA. RANK, RANKL and OPG mRNA expression was measured in PBL by real-time PCR.

Results

Osteocalcin values were decreased in diabetic groups in comparison to NG group (p < 0.05), and a negative correlation with both serum glucose (r = −0.265, p < 0.01) and Hb1Ac (r = −0.252, p < 0.01) in T1D group was found. BMD was lower in diabetic groups in comparison with NG group (p < 0.05) and a negative correlation was observed between BMD and both serum glucose (r = −0.357, p < 0.01) and HbA1c (r = −0.351, p < 0.01) in T1D group. OPG mRNA expression was significantly increased in T1D and T1DP groups in comparison with NG group (p < 0.05). In conclusion, children and adolescents with early onset T1D presented low bone mineral density associated to unsatisfactory glycemic control, increased OPG mRNA expression and low osteocalcin concentration.     

Fish navigation of large dams emerges from their modulation of flow field experience

Navigating obstacles is innate to fish in rivers, but fragmentation of the world’s rivers by more than 50,000 large dams threatens many of the fish migrations these waterways support. One limitation to mitigating the impacts of dams on fish is that we have a poor understanding of why some fish enter routes engineered for their safe travel around the dam but others pass through more dangerous routes. To understand fish movement through hydropower dam environments, we combine a computational fluid dynamics model of the flow field at a dam and a behavioral model in which simulated fish adjust swim orientation and speed to modulate their experience to water acceleration and pressure (depth). We fit the model to data on the passage of juvenile Pacific salmonids (Oncorhynchus spp.) at seven dams in the Columbia/Snake River system. Our findings from reproducing observed fish movement and passage patterns across 47 flow field conditions sampled over 14 y emphasize the role of experience and perception in the decision making of animals that can inform opportunities and limitations in living resources management and engineering design.Understanding how the design and management of civil infrastructure modifies the outcome of naturally evolved behavior in animals is critical for sustainably using limited environmental resources to spur economic development and maintain native species. The issue is particularly relevant for rivers, which make up only 0.0002% of water on Earth (1) but support more than 40% of the world’s human population (2, 3). River regulation to meet society’s needs has accelerated in the past two centuries (4), leaving over half of the world’s major rivers now fragmented by >50,000 large dams providing water, energy, flood control, and transportation (3, 5, 6). The demand for large hydropower continues, spurred by the need for economic development while limiting carbon use (7). However, dams impede the dispersal and migration of fish, a problem that, along with other factors, has contributed to the loss of populations and entire species (5). These losses have cultural, economic, and geopolitical repercussions (3, 8), because more than 40% of the world’s human population lives in internationally shared river basins (9) and declines in fish populations jeopardize the food security of hundreds of millions worldwide (10–12).In North America, the tension between economic development and living resource conservation is evident in the Columbia River basin. Flowing from Canada to the United States, the river once supported one of the world’s largest salmon runs, with annual returns of 10–16 million fish (13) sustaining tribal nations and ecosystems far from the ocean (14). However, years of overharvesting, land-use changes, ocean conditions, and dams have contributed to a decline in the annual return of salmon (15). To reverse the decline, millions of dollars are spent each year seeking a durable hydroelectric strategy to improve annual returns (1–2 million fish). A major emphasis in restoration is ensuring that millions of downstream migrating juvenile salmon reach the ocean where they grow before returning to the river as adults.Hydropower dams on the river provide three general routes of passage for downstream migrating fish: powerhouse turbines, a spillway, and often a bypass specifically designed for fish. These routes differ in their mortality effects on fish, so an understanding of how fish behavior determines route selection is important for mitigating the impacts of dams on the populations. However, route selection behavior is poorly understood. Not only has it been difficult to explain route passage patterns at one dam, but it has been even more difficult to explain why the pattern may be different at another dam with similar routes.     

Association of Long-Term Exposure to Traffic-Related Air Pollution with Blood Pressure and Hypertension in an Adult Population–Based Cohort in Spain (the REGICOR Study)

Background: Long-term exposure to traffic-related air pollution may increase blood pressure (BP) and induce hypertension. However, evidence supporting these associations is limited, and they may be confounded by exposure to traffic noise and biased due to inappropriate control for use of BP-lowering medications.Objectives: We evaluated the associations of long-term traffic-related air pollution with BP and prevalent hypertension, adjusting for transportation noise and assessing different methodologies to control for BP-lowering medications.Methods: We measured systolic (SBP) and diastolic BP (DBP) at baseline (years 2003–2005) in 3,700 participants, 35–83 years of age, from a population-based cohort in Spain. We estimated home outdoor annual average concentrations of nitrogen dioxide (NO₂) with a land-use regression model. We used multivariate linear and logistic regression.Results: A 10-μg/m³ increase in NO₂ levels was associated with 1.34 mmHg (95% CI: 0.14, 2.55) higher SBP in nonmedicated individuals, after adjusting for transportation noise. Results were similar in the entire population after adjusting for medication, as commonly done, but weaker when other methods were used to account for medication use. For example, when 10 mmHg were added to the measured SBP levels of medicated participants, the association was β = 0.78 (95% CI: –0.43, 2.00). NO₂ was not associated with hypertension. Associations of NO₂ with SBP and DBP were stronger in participants with cardiovascular disease, and the association with SBP was stronger in those exposed to high traffic density and traffic noise levels ≥ 55 dB(A).Conclusions: We observed a positive association between long-term exposure to NO₂ and SBP, after adjustment for transportation noise, which was sensitive to the methodology used to account for medication.Citation: Foraster M, Basagaña X, Aguilera I, Rivera M, Agis D, Bouso L, Deltell A, Marrugat J, Ramos R, Sunyer J, Vila J, Elosua R, Künzli N. 2014. Association of long-term exposure to traffic-related air pollution with blood pressure and hypertension in an adult population–based cohort in Spain (the REGICOR study). Environ Health Perspect 122:404–411; http://dx.doi.org/10.1289/ehp.1306497