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.     

Retinal microvasculature and vasoreactivity changes in hypertension using optical coherence tomography-angiography

Graefe's Archive for Clinical and Experimental Ophthalmology - To evaluate the retinal vasculature and vasoreactivity of patients with hypertension (HTN) using spectral domain optical coherence...     

Quantitative in vitro and in vivo pharmacological profile of CE-178253, a potent and selective cannabinoid type 1 (CB1) Receptor Antagonist

Background

Carbon tetra chloride (CCl₄), an industrial solvent, is a hepatotoxic agent and it is the well established animal model for free radical-induced liver injury. The present investigation was carried out to establish the protective effect of natansnin, a novel dibenzoyl glycoside from Salvinia natans against CCl₄ induced oxidative stress and cellular degeneration in rat liver.

Results

CCl₄ significantly increased the levels of lipid peroxides, oxidized glutathione and decreased the levels of reduced glutathione, SOD and CAT. CCl₄ induce marked histopathological changes and increase in the levels of apoptotic proteins. CCl₄ treatment significantly increased the levels of apoptotic proteins such as caspases-3, PARP, Bax, Bid and cytochrome C and also increased the levels of inflammatory mediators iNos and Cox-2. Natansnin treatment significantly decreased the levels of CCl₄ induced apoptotic proteins and inflammatory mediators. Further natansinin treatment significantly inhibited the CCl₄ induced apoptosis which was evident form the reduced TUNEL positive cells.

Conclusions

In conclusion, our study demonstrated the protective effect of natansnin against CCl₄ induced oxidative stress and cellular degeneration in rat liver tissue. This protective effect of natansnin can be correlated to its direct antioxidant effect.     

Structural diversity of streptokinase and activation of human plasminogen

The beta domain of streptokinase is required for plasminogen activation and contains a region of sequence diversity associated with infection and disease in group A streptococci. We report that mutagenesis of this polymorphic region does not alter plasminogen activation, which suggests an alternative function for this molecular motif in streptococcal disease.     

Human papilloma virus and esophageal carcinoma in a Latin-American region

AIM： To investigate the presence of high-risk human papilloma virus （HPV） in esophageal squamous cell carcinomas （ESCCs） in a non-selected Mexican population. METHODS： Cases with a pathological diagnosis of squamous cell carcinoma of the esophagus were obtained from Department of Pathology files, at the National Cancer Institute in Mexico City during the period between 2000 and 2008. Slides from each case were reviewed and cases with sufficient neoplastic tissue were selected for molecular analysis. DNA was extracted from paraffin-embedded tissue samples for polymerase chain reaction analysis to detect HPV DNA sequences. Demographic and clinical data of each patient were retrieved from corresponding clinical records. RESULTS： HPV was detected in 15 （25%） of ESCCs. HPV-16 was the most frequently observed genotype, followed by HPV-18; HPV-59 was also detected in one case. Unfortunately, HPV genotype could not be established in three cases due to lack of material for direct sequencing, although universal primers detected the presence of HPV generic sequences. No low-risk HPV genotypes were found nor was HPV-16/18 co- infection. HPV presence in ESCC was not significantly associated with gender, age, alcohol consumption, smoking, anatomic location, or histologic grade. All patients belonged to low and very low socioeconomic strata, and were diagnosed at advanced disease stage. Male patients were most commonly affected and the male：female ratio in HPV-positive ESCC increased two- fold in comparison with HPV-negative cases （6.5：1 vs 3/1：1）. CONCLUSION： High prevalence of high-risk HPV in ESCC in Mexico does not support the hypothesis that HPV-associated ESCC is more common in areas with higher ESCC incidence rates.     

Src kinase activation by direct interaction with the integrin beta cytoplasmic domain

Src tyrosine kinases transmit integrin-dependent signals pivotal for cell movement and proliferation. Here, we establish a mechanism for Src activation by integrins. c-Src is shown to bind constitutively and selectively to beta3 integrins through an interaction involving the c-Src SH3 domain and the carboxyl-terminal region of the beta3 cytoplasmic tail. Clustering of beta3 integrins in vivo activates c-Src and induces phosphorylation of Tyr-418 in the c-Src activation loop, a reaction essential for adhesion-dependent phosphorylation of Syk, a c-Src substrate. Unlike c-Src, Hck, Lyn, and c-Yes bind more generally to beta1A, beta2, and beta3 cytoplasmic tails. These results invoke a model whereby Src is primed for activation by direct interaction with an integrin beta tail, and integrin clustering stabilizes activated Src by inducing intermolecular autophosphorylation. The data provide a paradigm for integrin regulation of Src and a molecular basis for the similar functional defects of osteoclasts or platelets from mice lacking beta3 integrins or c-Src.