Accelerated evolution in the human lineage led to gain and loss of transcriptional enhancers in the RBFOX1 locus.

A long-standing goal of evolutionary biology is to decode how changes in gene regulatory networks contribute to human-specific traits. Human accelerated regions (HARs) are prime candidates for driving gene regulatory modifications in human development. The RBFOX1 locus is densely populated with HARs, providing a set of potential regulatory elements that could have changed its expression in the human lineage. Here, we examined the role of RBFOX1-HARs using transgenic zebrafish reporter assays and identified 15 transcriptional enhancers that are active in the developing nervous system, 9 of which displayed differential activity between the human and chimpanzee sequences. The engineered loss of two selected RBFOX1-HARs in knockout mouse models modified Rbfox1 expression at specific developmental stages and tissues in the brain, influencing the expression and splicing of a high number of Rbfox1 target genes. Our results provided insight into the spatial and temporal changes in gene expression driven by RBFOX1-HARs.

Granulomatous meningoencephalitis and blindness associated with Mycobacterium tuberculosis complex infection in a senile female chimpanzee (Pan troglodytes).

A 40-year old female chimpanzee (Pan troglodytes) developed hyporexia, weight loss, followed by progressive and complete blindness. Tomography demonstrated an intracranial mass in the rostroventral brain involving the optic chiasm, with a presumptive diagnosis of neoplasm. However, histopathology revealed a granulomatous meningoencephalitis, and tissue samples tested positive for Mycobacterium tuberculosis.

Caveats of chimpanzee ChAdOx1 adenovirus-vectored vaccines to boost anti-SARS-CoV-2 protective immunity in mice.

Several COVID-19 vaccines use adenovirus vectors to deliver the SARS-CoV-2 spike (S) protein. Immunization with these vaccines promotes immunity against the S protein, but against also the adenovirus itself. This could interfere with the entry of the vaccine into the cell, reducing its efficacy. Herein, we evaluate the efficiency of an adenovirus-vectored vaccine (chimpanzee ChAdOx1 adenovirus, AZD1222) in boosting the specific immunity compared to that induced by a recombinant receptor-binding domain (RBD)-based vaccine without viral vector. Mice immunized with the AZD1222 human vaccine were given a booster 6 months later, with either the homologous vaccine or a recombinant vaccine based on RBD of the delta variant, which was prevalent at the start of this study. A significant increase in anti-RBD antibody levels was observed in rRBD-boosted mice (31-61%) compared to those receiving two doses of AZD1222 (0%). Significantly higher rates of PepMix™- or RBD-elicited proliferation were also observed in IFNγ-producing CD4 and CD8 cells from mice boosted with one or two doses of RBD, respectively. The lower efficiency of the ChAdOx1-S vaccine in boosting specific immunity could be the result of a pre-existing anti-vector immunity, induced by increased levels of anti-adenovirus antibodies found both in mice and humans. Taken together, these results point to the importance of avoiding the recurrent use of the same adenovirus vector in individuals with immunity and memory against them. It also illustrates the disadvantages of ChAdOx1 adenovirus-vectored vaccine with respect to recombinant protein vaccines, which can be used without restriction in vaccine-booster programs. KEY POINTS: • ChAdOx1 adenovirus vaccine (AZD1222) may not be effective in boosting anti-SARS-CoV-2 immunity • A recombinant RBD protein vaccine is effective in boosting anti-SARS-CoV-2 immunity in mice • Antibodies elicited by the rRBD-delta vaccine persisted for up to 3 months in mice.

Vulvar squamous cell carcinoma in a captive female chimpanzee: A case report.

A necropsy was performed on a 43-year-old female zoo chimpanzee, with cancer in the vulvar and perivulvar region. She was diagnosed with squamous cell carcinoma, the presence of this tumor in domestic animals and non-human primates is very rare in the vulvar region and there were no previous reports found on it in chimpanzee, due to which this report contributes to the knowledge on chimpanzee pathologies.

Gene Content and Coding Diversity of the Growth Hormone Loci of Apes.

The growth hormone (GH) locus has experienced a dramatic evolution in primates, becoming multigenic and diverse in anthropoids. Despite sequence information from a vast number of primate species, it has remained unclear how the multigene family was favored. We compared the structure and composition of apes' GH loci as a prerequisite to understanding their origin and possible evolutionary role. These thorough analyses of the GH loci of the chimpanzee, gorilla, and orangutan were done by resorting to previously sequenced bacterial artificial chromosomes (BACs) harboring them, as well as to their respective genome projects data available in GenBank. The GH loci of modern man, Neanderthal, gibbon, and wild boar were retrieved from GenBank. Coding regions, regulatory elements, and repetitive sequences were identified and compared among species. The GH loci of all the analyzed species are flanked by the genes CD79B (5') and ICAM-1 (3'). In man, Neanderthal, and chimpanzee, the loci were integrated by five almost indistinguishable genes; however, in the former two, they rendered three different hormones, and in the latter, four different proteins were derived. Gorilla exhibited six genes, gibbon seven, and orangutan four. The sequences of the proximal promoters, enhancers, P-elements, and a locus control region (LCR) were highly conserved. The locus evolution might have implicated duplications of the ancestral pituitary gene (GH-N) and subsequent diversification of the copies, leading to the placental single GH-V gene and the multiple CSH genes.

Simia langobardorum: Were African apes traded in late medieval Lombardy?

Depictions of and references to apes (tailless hominoids) are very limited in early historical written accounts. The first known published representations of ape-like primates appear in Medieval European books during the first century following the invention of printing. Considering the current knowledge of ape iconography, this article examines an unusual image of a couple of ape-like creatures rendered in a European manuscript and explores the possible links of this challenging illustration with historical accounts and contexts during the late Middle Ages and early Renaissance. The studied manuscript is known as "BL Sloane MS 4016" and is a medieval herbal manuscript (Tratactus de Herbis) of Lombardian origin dated c. 1440. The illustration in question, which also appears in similar manuscripts, represents two primates. However, these representations differ significantly from those in the other manuscripts. The individuals have physical features that suggest attribution to chimpanzees. The location and the date of the manuscript in relation to the extended merchant and travel network between Europe and Africa during the late Medieval times and earlier Renaissance most likely indicate that free-living or traded chimpanzees or their images may have been the visual source for the illustration. The examination of early depictions and descriptions of apes helps us to understand how we, humans, have represented our own closest zoological relatives. In doing so, this study also provides a review of early ape iconography and historical accounts about African primates during the so-called Age of Discoveries.

Modularity of the wrist in extant hominines.

Wrist shape varies greatly across primates and previous studies indicate that the numerous morphological differences among them are related to a complex mixture of phylogeny and function. However, little is known about whether the variation in these various anatomical differences is linked and to what extent the wrist bones vary independently. Here, we used 3D geometric morphometrics on a sample of extant hominines (Homo sapiens, Pan troglodytes, Gorilla gorilla, and Gorilla beringei), to find the model that best describes the covariation patterns among four of the eight carpals (i.e., capitate, lunate, scaphoid, and trapezium). For this purpose, 15 modular hypotheses were tested using the Covariance Ratio. Results indicate that there is a covariation structure common to all hominines, which corresponds to stronger covariation within each carpal as compared to the covariation between carpals. However, the results also indicate that that there is a degree of codependence in the variation of some carpals, which is unique in humans, chimpanzees, and gorillas, respectively. In humans there is evidence of associated shape changes between the lunate and capitate, and between the scaphoid and trapezium. This covariation between lunate and capitate is also apparent in gorillas, while chimpanzees display the greatest disassociation among carpals, showing low covariation values in all pairwise comparisons. Our analyses indicate that carpals have an important level of variational independence which might suggest a high degree of independent evolvability in the wrists of hominines, and that although weak, the structure of associated changes of these four carpals varies across genera. To our knowledge this is the first report on the patterns of modularity between these four wrist bones in the Homininae and future studies might attempt to investigate whether the anatomical shape associations among carpals are functionally related to locomotion and manipulation.

Vitamin D status in chimpanzees in human care: a Europe wide study.

While vitamin D deficiency is a public health concern in humans, comparatively little is known about vitamin D levels in non-human primates. Vitamin D plays a crucial role in overall health and its deficiency is associated with a range of disorders, including cardiovascular disease, which is a leading cause of death in great apes. Serum samples (n = 245) from chimpanzees (Pan troglodytes) housed at 32 European zoos were measured for 25-hydroxyvitamin D2, 25-hydroxyvitamin D3 and total 25-hydroxyvitamin D (25-OHD) using liquid chromatography and tandem mass spectrometry. Of these samples, 33.1% indicated inadequate vitamin D status, using the human reference interval (25-OHD < 50 nmol/L). The season of the year, health status of the animal, and the provision of daily outdoor access had a significant effect on vitamin D status. This is the first large-scale study on vitamin D status of non-human great apes in human care. Inadequate 25-OHD serum concentrations are widespread in the chimpanzee population in Europe and could be a risk factor for the development of idiopathic myocardial fibrosis, a major cause of mortality in this species, as well as other diseases. A review of husbandry and nutrition practices is recommended to ensure optimal vitamin D supply for these endangered animals.

Integration between the cranial boundaries of the nasopharynx and the upper cervical vertebrae in Homo and Pan.

The nasopharynx is an important anatomical structure involved in respiration. Its bony boundaries, including the basicranium and upper cervical vertebrae, may be subject to selective pressures and constraints related to respiratory function. Here, we investigate phenotypic integration, or covariation, between the face, the basicranial boundaries of the nasopharynx, and the atlas and axis to understand constraints affecting these structures. We collected three-dimensional coordinate data from a sample of 80 humans and 44 chimpanzees, and used two-block partial least squares to assess RV (a multivariate generalization of Pearson's r2 ), rPLS , the covariance ratio, and effect size for integration among structures. We find that integration is significant among some of these structures, and that integration between the basicranial nasopharynx and vertebrae and between the face and vertebrae is likely independent. We also find divergences in the pattern of integration between humans and chimpanzees suggesting greater constraints among the human face and nasopharynx, which we suggest are linked to divergent developmental trajectories in the two taxa. Evolutionary changes in human basicranial anatomy, coupled with human-like developmental trajectories, may have required that the face grow to compensate any variation in nasopharyngeal structure. However, we were unable to determine whether the nasopharynx or the face is more strongly integrated with the vertebrae, and therefore whether respiration or biomechanical considerations related to positional behavior may be more strongly tied to vertebral evolution. Future work should focus on greater sample sizes, soft tissue structures, and more diverse taxa to further clarify these findings.

Evaluation of hydrogen peroxide efficacy against AZD1222 chimpanzee adenovirus strain in the recombinant COVID-19 vaccine for application in cleaning validation in a pharmaceutical manufacturing industry.

This study aimed to evaluate the performance of hydrogen peroxide vapour (HPV) to inactivate the chimpanzee adenovirus AZD1222 vaccine strain used in the production of recombinant COVID-19 vaccine for application in cleaning validation in pharmaceutical industries production areas. Two matrixes were tested: formulated recombinant COVID-19 vaccine (FCV) and active pharmaceutical ingredient (API). The samples were dried on stainless steel and exposed to HPV in an isolator. One biological indicator with population >106 Geobacillus stearothermophilus spores was used to validate the HPV decontamination cycle as standard. HPV exposure resulted in complete virus inactivation in FVC (≥5·03 log10 ) and API (≥6·40 log10 ), showing HPV efficacy for reducing chimpanzee adenovirus AZD1222 vaccine strain. However, the optimum concentration and contact time will vary depending on the type of application. Future decontamination studies scaling up the process to the recombinant COVID-19 vaccine manufacturing areas are necessary to evaluate if the HPV will have the same or better virucidal effectivity in each specific production area. In conclusion, HPV showed efficacy for reducing AZD1222 chimpanzee adenovirus strain and can be a good choice for pharmaceutical industries facilities disinfection during recombinant COVID-19 vaccine production.

ACUTE NECROTIZING AND EOSINOPHILIC MYOCARDITIS IN A CHIMPANZEE (PAN TROGLODYTES).

Cardiac disease is of importance in captive chimpanzee (Pan troglodytes) health. Here we report an eosinophilic and necrotizing myocarditis in a 17-y-old chimpanzee with no previous history of cardiac disease that progressed to death within 48 h. Toxic and infectious causes were ruled out. The chimpanzee had eosinophilia at different occasions in previous years. The animal had a severe, diffuse, and acute monophasic necrotizing myocarditis, with a moderate lymphoplasmacytic infiltrate that was rich in eosinophils. Ante- and postmortem investigations are compatible with an unusual eosinophilic myocarditis with clinical evolution and morphology comparable with human eosinophilic myocarditis secondary to hypereosinophilic syndrome.

Characterization and Application of Precore/Core-Related Antigens in Animal Models of Hepatitis B Virus Infection.

BACKGROUND AND AIMS: The hepatitis B core-related antigen (HBcrAg), a composite antigen of precore/core gene including classical hepatitis B core protein (HBc) and HBeAg and, additionally, the precore-related antigen PreC, retaining the N-terminal signal peptide, has emerged as a surrogate marker to monitor the intrahepatic HBV covalently closed circular DNA (cccDNA) and to define meaningful treatment endpoints. APPROACH AND RESULTS: Here, we found that the woodchuck hepatitis virus (WHV) precore/core gene products (i.e., WHV core-related antigen [WHcrAg]) include the WHV core protein and WHV e antigen (WHeAg) as well as the WHV PreC protein (WPreC) in infected woodchucks. Unlike in HBV infection, WHeAg and WPreC proteins were N-glycosylated, and no significant amounts of WHV empty virions were detected in WHV-infected woodchuck serum. WHeAg was the predominant form of WHcrAg, and a positive correlation was found between the serum WHeAg and intrahepatic cccDNA. Both WHeAg and WPreC antigens displayed heterogeneous proteolytic processing at their C-termini, resulting in multiple species. Analysis of the kinetics of each component of the precore/core-related antigen, along with serum viral DNA and surface antigens, in HBV-infected chimpanzees and WHV-infected woodchucks revealed multiple distinct phases of viral decline during natural resolution and in response to antiviral treatments. A positive correlation was found between HBc and intrahepatic cccDNA but not between HBeAg or HBcrAg and cccDNA in HBV-infected chimpanzees, suggesting that HBc can be a better marker for intrahepatic cccDNA. CONCLUSIONS: In conclusion, careful monitoring of each component of HBcrAg along with other classical markers will help understand intrahepatic viral activities to elucidate natural resolution mechanisms as well as guide antiviral development.

Differences among the forelimb arteries in groups of primates and a mathematical model explanation.

BACKGROUND: Recently, some studies about primates have claimed the importance of the vessels to maintain the muscles working; in fact, the arterial supply could suggest how strenuous the muscular performance is associated to locomotor behavior. The aim of this work was to study the anatomy of the arteries of the forelimbs of different groups of primates to evidence a general arterial model in comparative terms. METHODS: We propose a biophysical explanation for the arterial pattern of the forelimbs of primates' groups. RESULTS: Three pattern of the forelimb arteries in Primates were descript and the differences were explained using mathematical formulas. CONCLUSIONS: The anatomical study about the comparative anatomy of the arteries of the forelimbs of primates provided hypothesis about the three observed models, mainly in relation to brachial artery division and the number of the palmar arches, in mathematical models' terms.

Recommendations for improving photo quality in close range photogrammetry, exemplified in hand bones of chimpanzees and gorillas / Recomendaciones para mejorar la calidad de las fotos en fotogrametría de corto alcance, ejemplificado en huesos de las manos de chimpancés y gorillas

SUMMARY: Photogrammetry is becoming increasingly popular in morphological research and teaching due to its portability, ability to reliably render 3D models, and quality-to-price relationship relative to some popular surface scanners. Compared to surface scanners, however, the learning process in photogrammetry can be very time consuming. Here we describe common mistakes of photo capture in close-range photogrammetry that greatly affect 3D output and tips to improve them. Problems were identified after the 3D model construction of 780 hand bones of chimpanzees and gorillas from museum collections. Their hands are composed of 27 bones which vary in length and complexity. We show how lighting, object position and orientation, camera angle, and background affect the 3D output. By taking these factors into account, time and error rates for beginners can be greatly reduced and 3D model quality can be considerably improved.

RESUMEN: La fotogrametría está siendo cada vez más popular en la investigación y enseñanza morfológica. Esto debido a su portabilidad, confiabilidad de los modelos 3D y buena relación calidadprecio. Comparada con los escáneres de superficie, sin embargo, el proceso de aprendizaje de la fotogrametría puede llevar mucho tiempo. Aquí se describen errores comunes en la toma de fotos para fotogrametería que afectan de manera importante la creación de los modelos 3D, así como consejos para superarlos. Los problemas descritos fueron identificados luego de la construcción de 780 modelos 3D de huesos de la mano de chimpancés y gorillas depositados en distintas colecciones de museos. Las manos de estas especies están compuestas por 27 huesos que varían en tamaño y complejidad. En este artículo mostramos como la luz, la posición y orientación del objeto, el ángulo de la cámara y el fondo de la imagen afectan el resultado en 3D. Considerando estos factores, personas que están aprendiendo esta técnica pueden reducir de manera importante el tiempo y la probabilidad de error, y mejorar considerablemente la calidad de los modelos 3D.

NHP-immunome: A translational research-oriented database of non-human primate immune system proteins.

We are currently living the advent of a new age for medicine in which basic research is being quickly translated into marketable drugs, and the widespread access to genomics data is allowing the design and implementation of personalized solutions to medical conditions. Non-human primates (NHP) have gained an essential role in drug discovery and safety testing due to their close phylogenetic relationship to humans. In this study, a collection of well characterized genes of the human immune system was used to define the orthology-based immunome in four NHP species, with carefully curated annotations available based on multi-tissue RNA-seq datasets. A broad variation in the frequency of expressed protein isoforms was observed between species. Finally, this analysis also revealed the lack of expression of at least four different chemokines in new-world primates. In addition, transcripts corresponding to four genes including interleukin 12 subunit alpha were expressed in humans but no other primate species analyzed. Access to the non-human primate immunome is available in http://www.fidic.org.co:90/proyecto/.

Gain of transcription factor binding sites is associated to changes in the expression signature of human brain and testis and is correlated to genes with higher expression breadth.

The gain of transcription factor binding sites (TFBS) is believed to represent one of the major causes of biological innovation. Here we used strategies based on comparative genomics to identify 21,822 TFBS specific to the human lineage (TFBS-HS), when compared to chimpanzee and gorilla genomes. More than 40% (9,206) of these TFBS-HS are in the vicinity of 1,283 genes. A comparison of the expression pattern of these genes and the corresponding orthologs in chimpanzee and gorilla identified genes differentially expressed in human tissues. These genes show a more divergent expression pattern in the human testis and brain, suggesting a role for positive selection in the fixation of TFBS gains. Genes associated with TFBS-HS were enriched in gene ontology categories related to transcriptional regulation, signaling, differentiation/development and nervous system. Furthermore, genes associated with TFBS-HS present a higher expression breadth when compared to genes in general. This biased distribution is due to a preferential gain of TFBS in genes with higher expression breadth rather than a shift in the expression pattern after the gain of TFBS.

Experimental models used in evaluating anti-tuberculosis vaccines: the latest advances in the field.

INTRODUCTION: Tuberculosis is an infectious disease which is caused by bacilli from the M. tuberculosis complex. The Mycobacterium bovis Bacillus Calmette-Guérin vaccine is currently available as a prophylactic tool for preventing the disease; it has been shown to be efficient in preventing disseminated forms of tuberculosis during early ages; however, its efficiency is limited in areas where individuals have had prior exposure to environmental mycobacteria, and its efficacy decreases with a host's age. AREAS COVERED: Following a comprehensive search of the available literature, this review describes some of the most frequently used animal models, the most frequently used methods for evaluating efficacy in animal models and some in vitro strategies as alternatives for evaluating vaccines. EXPERT OPINION: Identifying the animal models used up to now for evaluating vaccines during their development stages, their characteristics and limitations, as well as knowledge regarding strategies for evaluating promising vaccine candidate efficacy, will ensure more efficient, reliable and reproducible pre-clinical trials. Although much of the knowledge accrued to date concerning vaccine effectiveness against tuberculosis has been based on animal models, it is clear that large questions still need to be resolved and that extrapolation of such efficacy to humans has yet to be achieved.

Detection of Shared Balancing Selection in the Absence of Trans-Species Polymorphism.

Trans-species polymorphism has been widely used as a key sign of long-term balancing selection across multiple species. However, such sites are often rare in the genome and could result from mutational processes or technical artifacts. Few methods are yet available to specifically detect footprints of trans-species balancing selection without using trans-species polymorphic sites. In this study, we develop summary- and model-based approaches that are each specifically tailored to uncover regions of long-term balancing selection shared by a set of species by using genomic patterns of intraspecific polymorphism and interspecific fixed differences. We demonstrate that our trans-species statistics have substantially higher power than single-species approaches to detect footprints of trans-species balancing selection, and are robust to those that do not affect all tested species. We further apply our model-based methods to human and chimpanzee whole-genome sequencing data. In addition to the previously established major histocompatibility complex and malaria resistance-associated FREM3/GYPE regions, we also find outstanding genomic regions involved in barrier integrity and innate immunity, such as the GRIK1/CLDN17 intergenic region, and the SLC35F1 and ABCA13 genes. Our findings not only echo the significance of pathogen defense but also reveal novel candidates in maintaining balanced polymorphisms across human and chimpanzee lineages. Finally, we show that these trans-species statistics can be applied to and work well for an arbitrary number of species, and integrate them into open-source software packages for ease of use by the scientific community.

Phylogeny Estimation by Integration over Isolation with Migration Models.

Phylogeny estimation is difficult for closely related populations and species, especially if they have been exchanging genes. We present a hierarchical Bayesian, Markov-chain Monte Carlo method with a state space that includes all possible phylogenies in a full Isolation-with-Migration model framework. The method is based on a new type of genealogy augmentation called a "hidden genealogy" that enables efficient updating of the phylogeny. This is the first likelihood-based method to fully incorporate directional gene flow and genetic drift for estimation of a species or population phylogeny. Application to human hunter-gatherer populations from Africa revealed a clear phylogenetic history, with strong support for gene exchange with an unsampled ghost population, and relatively ancient divergence between a ghost population and modern human populations, consistent with human/archaic divergence. In contrast, a study of five chimpanzee populations reveals a clear phylogeny with several pairs of populations having exchanged DNA, but does not support a history with an unsampled ghost population.

Quantifying uncertainty due to fission-fusion dynamics as a component of social complexity.

Groups of animals (including humans) may show flexible grouping patterns, in which temporary aggregations or subgroups come together and split, changing composition over short temporal scales, (i.e. fission and fusion). A high degree of fission-fusion dynamics may constrain the regulation of social relationships, introducing uncertainty in interactions between group members. Here we use Shannon's entropy to quantify the predictability of subgroup composition for three species known to differ in the way their subgroups come together and split over time: spider monkeys (Ateles geoffroyi), chimpanzees (Pan troglodytes) and geladas (Theropithecus gelada). We formulate a random expectation of entropy that considers subgroup size variation and sample size, against which the observed entropy in subgroup composition can be compared. Using the theory of set partitioning, we also develop a method to estimate the number of subgroups that the group is likely to be divided into, based on the composition and size of single focal subgroups. Our results indicate that Shannon's entropy and the estimated number of subgroups present at a given time provide quantitative metrics of uncertainty in the social environment (within which social relationships must be regulated) for groups with different degrees of fission-fusion dynamics. These metrics also represent an indirect quantification of the cognitive challenges posed by socially dynamic environments. Overall, our novel methodological approach provides new insight for understanding the evolution of social complexity and the mechanisms to cope with the uncertainty that results from fission-fusion dynamics.