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International Journal For Parasitology.... Aug 2024Intestinal protozoa, which can be asymptomatic or cause diarrhea, dysentery and even death, are among the main agents that affect nonhuman primates (NHPs) kept under...
Intestinal protozoa, which can be asymptomatic or cause diarrhea, dysentery and even death, are among the main agents that affect nonhuman primates (NHPs) kept under human care. Nevertheless, information on the molecular and morphometric profiles of parabasilids in the Neotropics is still scarce. In this context, the objective of this study was to isolate the Parabasalia protozoa detected in the feces of NHPs and their keepers in Pavlova and TYSGM9 media and to characterize the isolates by molecular biology and morphometry. Fecal samples from NHPs from five Brazilian institutions were analyzed. Direct examination was performed immediately after obtaining the samples. A total of 511 fecal samples from NHPs were collected, and 10.6% contained parabasilids. Regarding the handlers, of the 74 samples analyzed, three were positive. In vitro-generated parabasilid isolates were successfully obtained from all positive samples, as identified via microscopy. Isolates of the parasite were obtained both from New World NHPs, including the genera , , , , , , and and from the Old World primate . Forty-nine NHP isolates were molecularly identified: (16), (14), (13) and (6). The human isolates were identified as sp. (2) and (1). Visualization and morphometric analysis revealed trophozoites with piriform or rounded shapes that presented variable measurements. The isolates previously characterized as had up to five free flagella, while and sp. had up to four free flagella, and had a maximum of three free flagella. These morphometric characteristics corroborated the molecular identification. In general, a variety of parabasilids were observed to infect NHPs, and was isolated from biological samples from both NHPs and their keepers, a finding that reinforces the susceptibility of these hosts to infections by parabasilids in Brazil.
PubMed: 38827824
DOI: 10.1016/j.ijppaw.2024.100946 -
Genome Biology Sep 2023Comparative gene expression studies in apes are fundamentally limited by the challenges associated with sampling across different tissues. Here, we used single-cell RNA...
BACKGROUND
Comparative gene expression studies in apes are fundamentally limited by the challenges associated with sampling across different tissues. Here, we used single-cell RNA sequencing of embryoid bodies to collect transcriptomic data from over 70 cell types in three humans and three chimpanzees.
RESULTS
We find hundreds of genes whose regulation is conserved across cell types, as well as genes whose regulation likely evolves under directional selection in one or a handful of cell types. Using embryoid bodies from a human-chimpanzee fused cell line, we also infer the proportion of inter-species regulatory differences due to changes in cis and trans elements between the species. Using the cis/trans inference and an analysis of transcription factor binding sites, we identify dozens of transcription factors whose inter-species differences in expression are affecting expression differences between humans and chimpanzees in hundreds of target genes.
CONCLUSIONS
Here, we present the most comprehensive dataset of comparative gene expression from humans and chimpanzees to date, including a catalog of regulatory mechanisms associated with inter-species differences.
Topics: Humans; Animals; Pan troglodytes; Cell Line; Embryoid Bodies; Gene Expression Profiling; Transcriptome
PubMed: 37697401
DOI: 10.1186/s13059-023-03019-3 -
Personality Neuroscience 2023Autism spectrum disorder (ASD) is a developmental disorder characterized by stereotypies or repetitive behaviors and impairments in social behavior and...
Autism spectrum disorder (ASD) is a developmental disorder characterized by stereotypies or repetitive behaviors and impairments in social behavior and socio-communicative skills. One hallmark phenotype of ASD is poor joint attention skills compared to neurotypical controls. In addition, individuals with ASD have lower scores on several of the Big 5 personality dimensions, including Extraversion. Here, we examine these traits in a nonhuman primate model (chimpanzees; ) to further understand the relationship between personality and joint attention skills, as well as the genetic and neural systems that contribute to these phenotypes. We used archival data including receptive joint attention (RJA) performance, personality based on caretaker ratings, and magnetic resonance images from 189 chimpanzees. We found that, like humans, chimpanzees who performed worse on the RJA task had lower Extraversion scores. We also found that joint attention skills and several personality dimensions, including Extraversion, were significantly heritable. There was also a borderline significant genetic correlation between RJA and Extraversion. A conjunction analysis examining gray matter volume showed that there were five main brain regions associated with both higher levels of Extraversion and social cognition. These regions included the right posterior middle and superior temporal gyrus, bilateral inferior frontal gyrus, left inferior frontal sulcus, and left superior frontal sulcus, all regions within the social brain network. Altogether, these findings provide further evidence that chimpanzees serve as an excellent model for understanding the mechanisms underlying social impairment related to ASD. Future research should further examine the relationship between social cognition, personality, genetics, and neuroanatomy and function in nonhuman primate models.
PubMed: 38107781
DOI: 10.1017/pen.2023.8 -
Nature Ecology & Evolution Nov 2023Enhanced cognitive function in humans is hypothesized to result from cortical expansion and increased cellular diversity. However, the mechanisms that drive these...
Enhanced cognitive function in humans is hypothesized to result from cortical expansion and increased cellular diversity. However, the mechanisms that drive these phenotypic innovations remain poorly understood, in part because of the lack of high-quality cellular resolution data in human and non-human primates. Here, we take advantage of single-cell expression data from the middle temporal gyrus of five primates (human, chimp, gorilla, macaque and marmoset) to identify 57 homologous cell types and generate cell type-specific gene co-expression networks for comparative analysis. Although orthologue expression patterns are generally well conserved, we find 24% of genes with extensive differences between human and non-human primates (3,383 out of 14,131), which are also associated with multiple brain disorders. To assess the functional significance of gene expression differences in an evolutionary context, we evaluate changes in network connectivity across meta-analytic co-expression networks from 19 animals. We find that a subset of these genes has deeply conserved co-expression across all non-human animals, and strongly divergent co-expression relationships in humans (139 out of 3,383, <1% of primate orthologues). Genes with human-specific cellular expression and co-expression profiles (such as NHEJ1, GTF2H2, C2 and BBS5) typically evolve under relaxed selective constraints and may drive rapid evolutionary change in brain function.
Topics: Animals; Humans; Transcriptome; Primates; Brain; Gene Regulatory Networks; Pan troglodytes; Cytoskeletal Proteins; Phosphate-Binding Proteins
PubMed: 37667001
DOI: 10.1038/s41559-023-02186-7 -
Communications Biology Jul 2023Identifying the evolutionary origins of human speech remains a topic of intense scientific interest. Here we describe a unique feature of adult human neuroanatomy...
Identifying the evolutionary origins of human speech remains a topic of intense scientific interest. Here we describe a unique feature of adult human neuroanatomy compared to chimpanzees and other primates that may provide an explanation of changes that occurred to enable the capacity for speech. That feature is the Prefrontal extent of the Frontal Operculum (PFOp) region, which is located in the ventrolateral prefrontal cortex, adjacent and ventromedial to the classical Broca's area. We also show that, in chimpanzees, individuals with the most human-like PFOp, particularly in the left hemisphere, have greater oro-facial and vocal motor control abilities. This critical discovery, when combined with recent paleontological evidence, suggests that the PFOp is a recently evolved feature of human cortical structure (perhaps limited to the genus Homo) that emerged in response to increasing selection for cognitive and motor functions evident in modern speech abilities.
Topics: Adult; Animals; Humans; Speech; Pan troglodytes; Frontal Lobe; Primates; Voice
PubMed: 37407769
DOI: 10.1038/s42003-023-05066-9 -
Animals : An Open Access Journal From... Aug 2023Chimp Haven is a sanctuary for chimpanzees retired from biomedical research, rescued from the pet trade, or re-homed after other organizations could no longer care for...
Chimp Haven is a sanctuary for chimpanzees retired from biomedical research, rescued from the pet trade, or re-homed after other organizations could no longer care for them. To provide optimal care for over 300 chimpanzees, Chimp Haven's animal care team includes experts in behavioral science, veterinary treatment, and husbandry practices. To aid these teams in making routine welfare management decisions, a system of behavioral metrics provides objective data to guide decisions and track outcomes. Chimp Haven has built and piloted seven behavioral metric protocols over the past 5 years to provide staff with an objective and comprehensive picture of the chimpanzees' behavioral welfare. The data from behavioral observations, staff surveys, and routine staff documentation are analyzed and processed through Google Forms, ZooMonitor, Microsoft Power Bi, Microsoft Excel, and R. Each metric assists staff in making data-based decisions regarding the management of captive chimpanzees related to abnormal behavior, hair loss, wounding, social relationships, positive reinforcement training and overall wellness. In this article, we explore examples of each metric and how they have been utilized to monitor and make decisions for both social groups of chimpanzees as well as individuals. These metrics can be collected and shared easily in an understandable format, which may provide an important framework for others to follow to enable the tracking of welfare for other sanctuaries, non-human primates, as well as other species.
PubMed: 37627388
DOI: 10.3390/ani13162595 -
PloS One 2023Pathogen surveillance for great ape health monitoring has typically been performed on non-invasive samples, primarily feces, in wild apes and blood in sanctuary-housed...
Pathogen surveillance for great ape health monitoring has typically been performed on non-invasive samples, primarily feces, in wild apes and blood in sanctuary-housed apes. However, many important primate pathogens, including known zoonoses, are shed in saliva and transmitted via oral fluids. Using metagenomic methods, we identified viruses in saliva samples from 46 wild-born, sanctuary-housed chimpanzees at two African sanctuaries in Republic of Congo and Uganda. In total, we identified 20 viruses. All but one, an unclassified CRESS DNA virus, are classified in five families: Circoviridae, Herpesviridae, Papillomaviridae, Picobirnaviridae, and Retroviridae. Overall, viral prevalence ranged from 4.2% to 87.5%. Many of these viruses are ubiquitous in primates and known to replicate in the oral cavity (simian foamy viruses, Retroviridae; a cytomegalovirus and lymphocryptovirus; Herpesviridae; and alpha and gamma papillomaviruses, Papillomaviridae). None of the viruses identified have been shown to cause disease in chimpanzees or, to our knowledge, in humans. These data suggest that the risk of zoonotic viral disease from chimpanzee oral fluids in sanctuaries may be lower than commonly assumed.
Topics: Animals; Humans; Pan troglodytes; Saliva; Congo; Uganda; Zoonoses; Retroviridae
PubMed: 37384730
DOI: 10.1371/journal.pone.0288007 -
PLoS Genetics Feb 2024Genome-wide genealogies of multiple species carry detailed information about demographic and selection processes on individual branches of the phylogeny. Here, we...
Genome-wide genealogies of multiple species carry detailed information about demographic and selection processes on individual branches of the phylogeny. Here, we introduce TRAILS, a hidden Markov model that accurately infers time-resolved population genetics parameters, such as ancestral effective population sizes and speciation times, for ancestral branches using a multi-species alignment of three species and an outgroup. TRAILS leverages the information contained in incomplete lineage sorting fragments by modelling genealogies along the genome as rooted three-leaved trees, each with a topology and two coalescent events happening in discretized time intervals within the phylogeny. Posterior decoding of the hidden Markov model can be used to infer the ancestral recombination graph for the alignment and details on demographic changes within a branch. Since TRAILS performs posterior decoding at the base-pair level, genome-wide scans based on the posterior probabilities can be devised to detect deviations from neutrality. Using TRAILS on a human-chimp-gorilla-orangutan alignment, we recover speciation parameters and extract information about the topology and coalescent times at high resolution.
Topics: Animals; Humans; Genetic Speciation; Hominidae; Pan troglodytes; Phylogeny; Genetics, Population; Models, Genetic
PubMed: 38330138
DOI: 10.1371/journal.pgen.1010836 -
Veterinary Medicine and Science Nov 2023Vitamin D is essential for skeletal health, calcium homeostasis and general health. The major and more stable form of vitamin D in circulation is 25-hydroxyvitamin D...
BACKGROUND
Vitamin D is essential for skeletal health, calcium homeostasis and general health. The major and more stable form of vitamin D in circulation is 25-hydroxyvitamin D (25-OH-D); this is the most valuable indicator of vitamin D status. There are studies on laboratory and zoo-housed chimpanzees; however, serum vitamin D status has not been documented in chimpanzees in range countries.
OBJECTIVES
(1) Determine the range of circulating 25-OH-D concentrations in chimpanzees in range countries. (2) Assess the influence of age, sex, and sun exposure on 25-OH-D serum concentrations.
METHODS
Opportunistic blood samples were obtained from 127 clinically healthy chimpanzees. Serum 25-OH-D concentration was measured with a commercially available competitive ELISA.
RESULTS
The median overall 25-OH-D concentration for chimpanzees in range countries was 46.24 nmol/L (range: 17.10-109.23 nmol/L). Males had a significantly lower concentration (40.15 nmol/L) than females (49.61 nmol/L), and infants (37.99 nmol/L) had a significantly lower concentration than adults (46.04 nmol/L). Concentrations of 25-OH-D in chimpanzees in sunnier habitats were significantly higher compared to thick tropical forest habitat.
CONCLUSION
The present constitutes a large dataset of serum 25-OH-D concentrations in range country sanctuary chimpanzees and contributes to document normal ranges. Age, sex, and sun exposure influenced serum concentrations of 25-OH-D in sanctuary chimpanzees.
Topics: Male; Female; Animals; Pan troglodytes; Pilot Projects; Vitamin D Deficiency; Vitamin D; Vitamins
PubMed: 37725364
DOI: 10.1002/vms3.1279 -
BioRxiv : the Preprint Server For... Aug 2023Many traits, intrinsic and extrinsic to an organism, contribute to interindividual variation in immunity in wild habitats. The vertebrate includes genes encoding...
Many traits, intrinsic and extrinsic to an organism, contribute to interindividual variation in immunity in wild habitats. The vertebrate includes genes encoding antigen-presenting molecules that are highly variable, and that variation often predicts susceptibility/resistance to and recovery from pathogen infection. I compare variation at two long-term chimpanzee research sites, Kibale National Park in Uganda and Gombe National Park in Tanzania. Using decades of respiratory health data available for these chimpanzees, I test hypotheses associated with maintenance of diversity at loci, including heterozygote, divergent allele, and rare allele advantage hypotheses, and predictions for unique function of in great apes. I found, despite confirmation of recent shared ancestry between Kibale and Gombe chimpanzees, including an overlapping allele repertoire and similar MHC-B phenotype compositions, chimpanzees from the two research sites experienced differences in the occurrence of respiratory signs and had different associations of diversity with signs of respiratory illness. Kibale chimpanzees with heterozygous genotypes and different peptide-binding supertypes were observed less often with respiratory signs than those homozygous or possessing the same supertypes, but this same association was not observed among Gombe chimpanzees. Gombe chimpanzees with specific MHC-B phenotypes that enable engagement of Natural Killer (NK) cells were observed more often with respiratory signs than chimpanzees with other phenotypes, but this was not observed at Kanyawara. This study emphasizes local adaptation in shaping genetic and phenotypic traits in different infectious disease contexts, even among close genetic relatives of the same subspecies, and highlights utility for continued and simultaneous tracking of host immune genes and specific pathogens in wild species.
PubMed: 37577711
DOI: 10.1101/2023.08.02.551731