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opencc-by-4.0Aug 2023View details →

Decoding host-microbiome interactions through co-expression network analysis within the non-human primate intestine

Supplementary Table Captions: Supplementary Table S9. Evaluation and parameter determination of host and microbiome RNA read classification using simulation datasets Supplementary Table S10. 40 pathways significantly upregulated in the cecum as compared to the transverse colon Supplementary Table S11. Host-microbiome gene co-expression network edges Supplementary Table S12. Host-host gene co-expression network edges Supplementary Table S13. Microbiome-microbiome gene co-expression network edges Supplementary Table S14. List of genes included in each gene module identified from the gene co-expression network Supplementary Table S15. Results of enrichment analysis for each gene module identified from the gene co-expression network Supplementary Table S16. The top 32 bacterial species in terms of expression abundance based on metatranscriptome profiles Supplementary Table S17. Number of microbiome RNA reads annotated by the KEGG database Supplementary Table S18. Results of enrichment analysis of gene modules for each parameter Supplementary Table S19. Evaluation of modules in each parameter of Newman algorithm Supplementary Table S20. Evaluation of modules in each parameter of Louvain algorithm Supplementary Table S21. Evaluation of modules in each parameter of Leiden algorithm Supplementary Table S22. Evaluation of modules in each parameter of WGCNA

opencc-by-4.0Jul 2018View details →

Non-human primate anatomicals

Anatomical images (T1 weighted, 0.5mm isotropic voxels, 7T) of three healthy non-human primates. Images are not aligned to any template. mf = macaca fascicularis mm = macaca mulatta See ReadMe.md for info.

opencc-by-4.0Dec 2019View details →

Fig. 1 in Molecular characterization of Blastocystis sp. in captive wildlife in Bangladesh National Zoo: Non-human primates with high prevalence and zoonotic significance

Fig. 1. Phylogenetic tree of the Blastocystis sp. isolates and reference SSU rRNA gene sequences from GenBank based on maximum likelihood analysis. The tree was rooted on Karotomorpha sp. and Protoopalina intestinalis. Bootstrap values> 50% from 1,000 replicates are shown on the nodes. Reference sequences from GenBank have accession number and host designation. The isolates of seven subtypes, with their host designations, are indicated by triangle shape.

opencc-by-4.0Aug 2020View details →

Fig. 1 in Differentiation of Trichuris species eggs from non-human primates by geometric morphometric analysis

Fig. 1. Trichuris sp. eggs collected from the samples. A. Macaque (Macaca sylvanus) B. Colobus (Colobus guereza kikuyensis). C. Grivet (Chlorocebus aethiops. D. Brazza's monkey (Cercopithecus neglectus). The bar represents 20 μm.

opencc-by-4.0Aug 2020View details →

Fig. 2 in Differentiation of Trichuris species eggs from non-human primates by geometric morphometric analysis

Fig. 2. Trichuris sp. egg lineal measurements. L1: maximum width of polar opercula, L2: minimum width of polar opercula, L3: base width of polar opercula, L4: length of polar opercula, measured from exterior midpoint to the narrow midpoint, L5: total length of polar opercula, measured from the exterior midpoint to the base midpoint, L6: wall thickness at its midpoint, L7: wall thickness in contact with polar opercula, L8: interior length of the egg.

opencc-by-4.0Jun 2023View details →

GDNF gene therapy for alcohol use disorder in male non-human primates

These the minimal data sets that were utilized in analysis and interpretation for the manuscript "GDNF gene therapy treatment for alcohol use disorder" by Matthew Ford et al.  These data sets were collected during a study to evaluate the utility of viral-based GDNF expression in the ventral tegmental area to reduce alcohol intake and prevent relapse in a primate model of alcohol use disorder, and ultimately the feasibility of GDNF as a gene therapy for alcohol use disorder.  There are data sets on behavior, biochemical analyses, and cyclic voltammetry.

opencc-zeroJan 2024View details →

Data for: What you have, not who you know: food-enhanced social capital and changes in social behavioural relationships in a non-human primate

Social network position in non-human primates has far-reaching fitness consequences. Critically, social networks are both heterogenous and dynamic, meaning an individual's current network position is likely to change due to both intrinsic and extrinsic factors. However, our understanding of the drivers of changes in social network position is largely confined to opportunistic studies. Experimental research on the consequences of in situ, controlled network perturbations is limited. Here we conducted a food-based experiment in rhesus macaques to assess whether allowing an individual the ability to provide high-quality food to her group changed her social behavioural relationships. We considered both her social network position across five behavioural networks, as well as her dominance and kin interactions. We found that gaining control over a preferential food resource had far-reaching social consequences. There was an increase in both submission and aggression centrality and changes in the socio-demographic characteristics of her agonistic interaction partners. Further, we found that her grooming balance shifted in her favour as she received more grooming than she gave. Together, these results provide a novel, preliminary insight into how in situ, experimental manipulations can modify social network position and point to broader network-level shifts in both social capital and social power.

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The MOPEVAC multivalent vaccine induces sterile protection against New World Arenaviruses in non-human primates

Pathogenic New World arenaviruses (NWAs) cause hemorrhagic fevers and can have high mortality rates, as shown in recent outbreaks in South America. Neutralizing antibodies (Nabs) are critical for protection from NWAs. Having shown that the MOPEVAC vaccine, based on a hyper-attenuated arenavirus, induces NAbs against Lassa fever, we hypothesized that expression of NWA glycoproteins in this platform might protect against NWAs.   Cynomolgus monkeys immunized with MOPEVACMAC, targeting Machupo virus, prevented the lethality of this virus and induced partially NWA-cross-reactive Nabs. We then developed the pentavalent MOPEVACNEW vaccine, expressing glycoproteins from all pathogenic South American NWAs. Immunization of cynomolgus monkeys with MOPEVACNEW induced Nabs against five NWAs, strong innate followed by adaptive immune responses as detected by transcriptomics, and provided sterile protection against Machupo virus and the genetically distant Guanarito virus. MOPEVACNEW may thus be efficient to protect against existing and, potentially, emerging NWAs.

opencc-by-4.0Oct 2022View details →

zenodo36/100

emmetaobrien/nhpatlas: NIH Blueprint Non-Human Primate Atlas

The NIH Blueprint Non-Human Primate (NHP) Atlas consists of a suite of gene expression and neuroanatomical data for exploring the cellular and molecular architecture of the developing rhesus macaque brain. This dataset contains datalad links for downloading individual files from the NHP Atlas.

openother-openSep 2019View details →

publicAug 2024View details →

Multimodal mucosal and systemic immune characterization of a non-human primate trachoma model highlights the critical role of local immunity during acute phase disease

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publicNov 2024View details →

Electrophysiological recordings of prefrontal activity over learning in non-human primates

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publicJan 2024View details →

Data for: What you have, not who you know: food-enhanced social capital and changes in social behavioural relationships in a non-human primate

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publicJun 2025View details →

Prevalence of culicine salivary antibodies in non-human primates living in national parks in Thailand

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opencc-zeroDec 2015View details →

Data from: Patterns of MHC-dependent mate selection in humans and non-human primates: a meta-analysis

Genes of the major histocompatibility complex (MHC) in vertebrates are integral for effective adaptive immune response and are associated with sexual selection. Evidence from a range of vertebrates supports MHC-based preference for diverse and dissimilar mating partners, but evidence from human mate choice studies has been disparate and controversial. Methodologies and sampling peculiarities specific to human studies make it difficult to know whether wide discrepancies in results among human populations are real or artefact. To better understand what processes may affect MHC-mediated mate choice across humans and nonhuman primates, we performed phylogenetically controlled meta-analyses using 58 effect sizes from 30 studies across seven primate species. Primates showed a general trend favouring more MHC-diverse mates, which was statistically significant for humans. In contrast, there was no tendency for MHC-dissimilar mate choice, and for humans, we observed effect sizes indicating selection of both MHC-dissimilar and MHC-similar mates. Focusing on MHC-similar effect sizes only, we found evidence that preference for MHC similarity was an artefact of population ethnic heterogeneity in observational studies but not among experimental studies with more control over sociocultural biases. This suggests that human assortative mating biases may be responsible for some patterns of MHC-based mate choice. Additionally, the overall effect sizes of primate MHC-based mating preferences are relatively weak (Fisher's Z correlation coefficient for dissimilarity Zr = 0.044, diversity Zr = 0.153), calling for careful sampling design in future studies. Overall, our results indicate that preference for more MHC-diverse mates is significant for humans and likely conserved across primates.

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Neuronal data sample from PMd of non-human primates (Macaca Mulatta) performing a countermanding reaching task

Brief presentation of the subjects and task performed Two adult male rhesus macaque monkeys (Macaca mulatta; P, C) performed a countermanding reaching task. All experimental procedures, animal care, housing, and surgical procedures conformed with European (Directive 86/609/ECC and 2010/63/UE) and Italian (D.L. 116/92 and D.L. 26/2014) laws on the use of nonhuman primates in scientific research and were approved by the Italian Ministry of Health. In both monkeys a 96 channels Utah arrays (BlackRock Microsystem, USA) was employed to record neuronal activity from the dorsal premotor cortex (PMd) contralateral to the arm employed during the task. Behavioral task Monkeys performed a countermanding reaching task interacting with visual stimuli presented on a touch-screen. Each trial started with the presentation of a central stimulus (red dot) that they had touch with their finger and hold (400-900ms). Thereafter the central stimulus disappeared and, simultaneously, a target appeared (go signal) randomly at one of two opposite positions (left or right). In no-stop trials to perform a correct trial, monkeys had to move their hand form the central target, touch peripheral target and to maintain their fingers on it for a random time (400-800 ms). In stop trials at a variable delay (Stop signal delay, SSD) after the go signal was presented, the central stimulus reappeared (Stop signal) instructing the monkey to keep the hand on the starting position (additional holding time; 400-1000 ms) to perform a correct-stop trial. If the monkey moved the hand during stop trials, the trial was considered a wrong-stop trial. No-stop and stop trials were randomly intermingled in such a way that the no-stop trials were more frequent. Recordings The neuronal activity from each electrode was recorded by employing a Tucker Davies Technologies RZ2 system (sampling rate at 24.4 Khz). Single unit activity was then isolated by using Kilosort (Pachitariu, et al. in Advances in Neural information processing systems (2016) 4448-4456). Data and code reproduce and are linked the main figures and results of the paper "Neuronal population dynamics during motor plan cancellation in non-human primates" ,  Proceedings of the National Academy of Sciences (PNAS) For further inquiry please contact: stefano.ferraina@uniroma1.it or pierpaolo.pani@uniroma1.it

opencc-by-4.0Jun 2022View details →

opencc-zeroDec 2016View details →

Data from: Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier

Many genera of terrestrial vertebrates diversified exclusively on one or the other side of Wallace's Line, which lies between Borneo and Sulawesi islands in Southeast Asia, and demarcates one of the sharpest biogeographic transition zones in the world. Macaque monkeys are unusual among vertebrate genera in that they are distributed on both sides of Wallace's Line, raising the question of whether dispersal across this barrier was an evolutionary one-off or a more protracted exchange—and if the latter, what were the genomic consequences. To explore the nature of speciation over the edge of this biogeographic divide, we used genomic data to test for evidence of gene flow between macaque species across Wallace's Line after macaques colonized Sulawesi. We recovered evidence of post-colonization gene flow, most prominently on the X chromosome. These results are consistent with the proposal that gene flow is a pervasive component of speciation—even when barriers to gene flow seem almost insurmountable.

opencc-zeroSep 2021View details →

Micro-anatomic alterations of the placenta in a non-human primate model of gestational protein-restriction

Objectives: Maternal protein malnutrition is associated with impaired fetal growth, and lifetime consequences for the offspring. Our group has previously developed a model of protein-restriction in the non-human primate, which was associated with fetal growth restriction, stillbirth, decreased placental perfusion, and evidence of fetal hypoxia, suggesting perturbed vascular development. Previous assessments of placental vasculature have relied upon stereological or vascular casting methods, but these methods have limitations. Our objective was to histologically characterize the micro-anatomic alterations associated with adverse pregnancy outcomes using a newer method that permits investigation of the 3D vascular structure and surrounding histology. Methods: Rhesus macaques were assigned in the pre-gestational period to a control diet that contained 26% protein, or study diet containing 13% protein (50% PR diet). Placental tissue was collected at delivery and processed using a clarification, immunohistochemistry, and confocal microscopy protocol published previously by our group. 3-dimensional reconstructions and quantitative analysis of the vascular micro-anatomy was performed using analysis software (Imaris®) and statistical analysis incorporated maternal, pregnancy, and perinatal outcomes. Results: In unadjusted analysis, when comparing those pregnancies on a 50% PR diet (n=4) with those on a control diet (n=4), protein-restriction diet was associated with decreased maternal pre-pregnancy weight (difference of -1.975kg, 95% CI -3.267 to -0.6826). When controlling for maternal pre-pregnancy weight, fetal sex, and latency from tissue collection to imaging, a gestational protein-restriction diet was associated with decreases in total vascular length, total vascular surface area, total vascular volume, and vascular density. Conclusion: In this pilot study, a gestational protein-restriction diet was associated with changes in the placental micro-vasculature, which may be related to the observed adverse pregnancy outcomes and perturbed placental perfusion demonstrated in this model.

publicSep 2017View details →

Data from: Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier

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