Local genetic adaptation to habitat in wild chimpanzees.

How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees.

Treponematosis in critically endangered Western chimpanzees (Pan troglodytes verus) in Senegal.

Treponematoses encompass a group of chronic and debilitating bacterial diseases transmitted sexually or by direct contact and attributed to Treponema pallidum. Despite being documented since as far back as 1963, the epidemiology of treponematoses in wild primates has remained an uninvestigated territory due to the inherent challenges associated with conducting examinations and obtaining invasive biological samples from wild animals. The primary aim of this study was to investigate the presence of treponemal infections in the critically endangered Western chimpanzees in Senegal, utilizing an innovative non-invasive stool serology method. We provide compelling evidence of the existence of anti-Treponema-specific antibodies in 13 out of 29 individual chimpanzees. Our study also underscores the significant potential of stool serology as a valuable non-invasive tool for monitoring and surveilling crucial emerging diseases in wild animals. We recognize two major implications: (1) the imperative need to assess the risks of treponematosis in Western chimpanzee populations and (2) the necessity to monitor and manage this disease following a holistic One Health approach.

n-Alkanes formed by methyl-methylene addition as a source of meteoritic aliphatics.

Aliphatics prevail in asteroids, comets, meteorites and other bodies in our solar system. They are also found in the interstellar and circumstellar media both in gas-phase and in dust grains. Among aliphatics, linear alkanes (n-CnH2n+2) are known to survive in carbonaceous chondrites in hundreds to thousands of parts per billion, encompassing sequences from CH4 to n-C31H64. Despite being systematically detected, the mechanism responsible for their formation in meteorites has yet to be identified. Based on advanced laboratory astrochemistry simulations, we propose a gas-phase synthesis mechanism for n-alkanes starting from carbon and hydrogen under conditions of temperature and pressure that mimic those found in carbon-rich circumstellar envelopes. We characterize the analogs generated in a customized sputter gas aggregation source using a combination of atomically precise scanning tunneling microscopy, non-contact atomic force microscopy and ex-situ gas chromatography-mass spectrometry. Within the formed carbon nanostructures, we identify the presence of n-alkanes with sizes ranging from n-C8H18 to n-C32H66. Ab-initio calculations of formation free energies, kinetic barriers, and kinetic chemical network modelling lead us to propose a gas-phase growth mechanism for the formation of large n-alkanes based on methyl-methylene addition (MMA). In this process, methylene serves as both a reagent and a catalyst for carbon chain growth. Our study provides evidence of an aliphatic gas-phase synthesis mechanism around evolved stars and provides a potential explanation for its presence in interstellar dust and meteorites.

Savanna chimpanzee (Pan troglodytes) crop feeding at Dindefelo, Senegal: challenges and implications for conservation.

Chimpanzees (Pan troglodytes) are categorized as Endangered by the International Union for Conservation of Nature, and habitat loss due to conversion of land for agriculture is one of the major threats to wild populations of this species. This challenging scenario can lead to negative human-chimpanzee interactions, including crop feeding. Chimpanzees consume crops across their geographical range, although little is known about this behavior in savanna habitats. Here we provide new evidence of crop feeding by savanna chimpanzees. We conducted our observations at Dindefelo, a community nature reserve in southeastern Senegal. The chimpanzees were observed to feed on mango (Mangifera indica) and also on baobab (Adansonia digitata), a wild species considered a crop by local people when found in and around villages. Although local people use the fruits of these species for food and income, they tolerated crop-feeding events until recently. In 2023, a case of harassment of a crop-feeding chimpanzee in a mango orchard was witnessed, and four days later a chimpanzee corpse was found at the same place. We conclude that habitat conversion into agricultural fields, uncontrolled bush fires and extraction of wild fruits are the important factors influencing crop-feeding events at Dindefelo. Our findings highlight the need to better understand human-chimpanzee interactions in the anthropogenic landscape of Dindefelo to help mitigate negative attitudes and behaviors towards chimpanzees.

Traditional potato tillage systems in the Peruvian Andes impact bacterial diversity, evenness, community composition, and functions in soil microbiomes.

The soil microbiome, a crucial component of agricultural ecosystems, plays a pivotal role in crop production and ecosystem functioning. However, its response to traditional tillage systems in potato cultivation in the Peruvian highlands is still far from understood. Here, ecological and functional aspects of the bacterial community were analyzed based on soil samples from two traditional tillage systems: 'chiwa' (minimal tillage) and 'barbecho' (full tillage), in the Huanuco region of the Peruvian central Andes. Similar soil bacterial community composition was shown for minimal tillage system, but it was heterogeneous for full tillage system. This soil bacterial community composition under full tillage system may be attributed to stochastic, and a more dynamic environment within this tillage system. 'Chiwa' and 'barbecho' soils harbored distinct bacterial genera into their communities, indicating their potential as bioindicators of traditional tillage effects. Functional analysis revealed common metabolic pathways in both tillage systems, with differences in anaerobic pathways in 'chiwa' and more diverse pathways in 'barbecho'. These findings open the possibilities to explore microbial bioindicators for minimal and full tillage systems, which are in relationship with healthy soil, and they can be used to propose adequate tillage systems for the sowing of potatoes in Peru.

Biomechanical Gait Effects of a Single Intervention with Wearable Closed Loop Control FES System in Chronic Stroke Patients. A Proof-of-Concept Pilot Study.

Foot drop is a gait disturbance characterized by difficulty in performing ankle dorsiflexion during the swing phase of the gait cycle. Current available evidence shows that functional electrical stimulation (FES) on the musculature responsible for dorsal ankle flexion during gait can have positive effects on walking ability. This study aims to present a proof of concept for a novel easy-to-use FES system and evaluates the biomechanical effects during gait in stroke patients, compared to unassisted walking. Gait was quantitatively evaluated in a movement analysis laboratory for five subjects with chronic stroke, in basal condition without assistance and in gait assisted with FES. Improvements were found in all temporospatial parameters during FES-assisted gait, evidenced by statistically significant differences only in gait speed (p=0.02). Joint kinematics showed positive changes in hip abduction and ankle dorsiflexion variables during the swing phase of the gait cycle. No significant differences were found in the Gait Deviation Index. In conclusion, the present pilot study demonstrates that the use of this FES system in the tibialis anterior muscle can cause gait functional improvements in subjects with foot drop due to chronic stroke.

Bone-related behaviours of captive chimpanzees (Pan troglodytes) during two excavating experiments.

After stone tools, bone tools are the most abundant artefact type in the Early Pleistocene archaeological record. That said, they are still relatively scarce, which limits our understanding of the behaviours that led to their production and use. Observations of extant primates constitute a unique source of behavioural data with which to construct hypotheses about the technological forms and repertoires exhibited by our hominin ancestors. We conducted two different experiments to investigate the behavioural responses of two groups of captive chimpanzees (Pan troglodytes; n = 33 and n = 9) to disarticulated, defleshed, ungulate bones while participating in a foraging task aimed at eliciting excavating behaviour. Each chimpanzee group was provided with bone specimens with different characteristics, and the two groups differed in their respective experience levels with excavating plant tools. We found that several individuals from the inexperienced group used the provided bones as tools during the task. In contrast, none of the individuals from the experienced group used bones as excavating tools, but instead continued using plant tools. These chimpanzees also performed non-excavating bone behaviours such as percussion and tool-assisted extraction of organic material from the medullary cavity. Our findings serve as a proof-of-concept that chimpanzees can be used to investigate spontaneous bone tool behaviours such as bone-assisted excavation. Furthermore, our results raise interesting questions regarding the role that bone characteristics, as well as previous tool-assisted excavating experience with other raw materials, might have in the expression of bone tool-assisted excavation.

Rational Continuous Neural Network Identifier for Singular Perturbed Systems With Uncertain Dynamical Models.

This study aims at designing a robust nonparametric identifier for a class of singular perturbed systems (SPSs) with uncertain mathematical models. The identifier structure uses a novel identifier based on a differential neural network (DNN) with rational form, which can take into account the multirate nature of SPS. The identifier uses a mixed learning law including a rational formulation of neural networks which is useful to solve the identification of the fast dynamics in the SPS dynamics. The rational form of the design is proposed in such a way that no-singularities (denominator part of the rational form never touches the origin) are allowed in the identifier dynamics. A proposed control Lyapunov function and a nonlinear parameter identification methodology yield to design the learning laws for the class of novel rational DNN which appears as the main contribution of this study. A complementary matrix inequality-based optimization method allows to get the smallest attainable convergence invariant region. A detailed implementation methodology is also given in the study with the aim of clarifying how the proposed identifier can be used in diverse SPSs. A numerical example considering the dynamics of the enzymatic-substrate-inhibitor system with uncertain dynamics is showing how to apply the DNN identifier using the multirate nature of the proposed DNN identifier for SPSs. The proposed identifier is compared to a classical identifier which is not taking into account the multirate nature of SPS. The benefits of using the rational form for the identifier are highlighted in the numerical performance comparison based on the mean square error (MSE). This example justifies the ability of the suggested identifier to reconstruct both the fast and slow dynamics of the SPS.

Population dynamics and genetic connectivity in recent chimpanzee history.

Knowledge on the population history of endangered species is critical for conservation, but whole-genome data on chimpanzees (Pan troglodytes) is geographically sparse. Here, we produced the first non-invasive geolocalized catalog of genomic diversity by capturing chromosome 21 from 828 non-invasive samples collected at 48 sampling sites across Africa. The four recognized subspecies show clear genetic differentiation correlating with known barriers, while previously undescribed genetic exchange suggests that these have been permeable on a local scale. We obtained a detailed reconstruction of population stratification and fine-scale patterns of isolation, migration, and connectivity, including a comprehensive picture of admixture with bonobos (Pan paniscus). Unlike humans, chimpanzees did not experience extended episodes of long-distance migrations, which might have limited cultural transmission. Finally, based on local rare variation, we implement a fine-grained geolocalization approach demonstrating improved precision in determining the origin of confiscated chimpanzees.

Population Diversity of Antibiotic Resistant Enterobacterales in Samples From Wildlife Origin in Senegal: Identification of a Multidrug Resistance Transposon Carrying bla CTX-M-15 in Escherichia coli.

Introduction: The role of wildlife in the transmission of antimicrobial resistant (AMR) is suspected but scarcely reported in current studies. Therefore, we studied the dynamics and prevalence of antibiotic-resistant Enterobacterales in antibiotic-limited areas of Senegal. Materials and Methods: We collected fecal samples from monkeys and apes (N = 226) and non-fecal environmental samples (N = 113) from Senegal in 2015 and 2019. We grew the samples on selective media, subsequently isolated AMR Enterobacterales, and then sequenced their genomes. Results: We isolated 72 different Enterobacterales among which we obtained a resistance rate of 65% for colistin (N = 47/72) and 29% for third generation-cephalosporin (C3G) (29%, N = 21/72). Interestingly, almost 46% of our isolates, among Enterobacter sp., Citrobacter cronae and Klebsiella aerogenes, belong to 34 new STs. Moreover, the genes bla CTX-M-15, bla TEM1B , sul2, dfrA14, qnrs, aph(3''), aph(6), tetA, and tetR harbored within a transposon on the IncY plasmid of ST224 Escherichia coli were transferred and inserted into a ST10 E. coli phage coding region. Conclusion: Wildlife constitutes a rich, unexplored reservoir of natural microbial diversity, AMR genes and international resistant clones pathogenic in humans. The presence of a transposon that carries AMR genes is intriguing since no antibiotics are used in the non-human primates we studied.

Experimental investigation of orangutans' lithic percussive and sharp stone tool behaviours.

Early stone tools, and in particular sharp stone tools, arguably represent one of the most important technological milestones in human evolution. The production and use of sharp stone tools significantly widened the ecological niche of our ancestors, allowing them to exploit novel food resources. However, despite their importance, it is still unclear how these early lithic technologies emerged and which behaviours served as stepping-stones for the development of systematic lithic production in our lineage. One approach to answer this question is to collect comparative data on the stone tool making and using abilities of our closest living relatives, the great apes, to reconstruct the potential stone-related behaviours of early hominins. To this end, we tested both the individual and the social learning abilities of five orangutans to make and use stone tools. Although the orangutans did not make sharp stone tools initially, three individuals spontaneously engaged in lithic percussion, and sharp stone pieces were produced under later experimental conditions. Furthermore, when provided with a human-made sharp stone, one orangutan spontaneously used it as a cutting tool. Contrary to previous experiments, social demonstrations did not considerably improve the stone tool making and using abilities of orangutans. Our study is the first to systematically investigate the stone tool making and using abilities of untrained, unenculturated orangutans showing that two proposed pre-requisites for the emergence of early lithic technologies-lithic percussion and the recognition of sharp-edged stones as cutting tools-are present in this species. We discuss the implications that ours and previous great ape stone tool experiments have for understanding the initial stages of lithic technologies in our lineage.

Chimpanzees (Pan troglodytes) in savanna landscapes.

Chimpanzees (Pan troglodytes) are the only great apes that inhabit hot, dry, and open savannas. We review the environmental pressures of savannas on chimpanzees, such as food and water scarcity, and the evidence for chimpanzees' behavioral responses to these landscapes. In our analysis, savannas were generally associated with low chimpanzee population densities and large home ranges. In addition, thermoregulatory behaviors that likely reduce hyperthermia risk, such as cave use, were frequently observed in the hottest and driest savanna landscapes. We hypothesize that such responses are evidence of a "savanna landscape effect" in chimpanzees and offer pathways for future research to understand its evolutionary processes and mechanisms. We conclude by discussing the significance of research on savanna chimpanzees to modeling the evolution of early hominin traits and informing conservation programs for these endangered apes.

A rationally designed self-immolative linker enhances the synergism between a polymer-rock inhibitor conjugate and neural progenitor cells in the treatment of spinal cord injury.

Rho/ROCK signaling induced after spinal cord injury (SCI) contributes to secondary damage by promoting apoptosis, inflammation, and axon growth inhibition. The specific Rho-kinase inhibitor fasudil can contribute to functional regeneration after SCI, although inherent low stability has hampered its use. To improve the therapeutic potential of fasudil, we now describe a family of rationally-designed bioresponsive polymer-fasudil conjugates based on an understanding of the conditions after SCI, such as low pH, enhanced expression of specific proteases, and a reductive environment. Fasudil conjugated to poly-l-glutamate via a self-immolative redox-sensitive linker (PGA-SS-F) displays optimal release kinetics and, consequently, treatment with PGA-SS-F significantly induces neurite elongation and axon growth in dorsal root ganglia explants, spinal cord organotypic cultures, and neural precursor cells (NPCs). The intrathecal administration of PGA-SS-F after SCI in a rat model prevents early apoptosis and induces the expression of axonal growth- and neuroplasticity-associated markers to a higher extent than the free form of fasudil. Moreover, a combination treatment comprising the acute transplantation of NPCs pre-treated with PGA-SS-F leads to enhanced cell engraftment and reduced cyst formation after SCI. In chronic SCI, combinatory treatment increases the preservation of neuronal fibers. Overall, this synergistic combinatorial strategy may represent a potentially efficient clinical approach to SCI treatment.

Bacterial Infections in Humans and Nonhuman Primates from Africa: Expanding the Knowledge.

The close phylogenetic relationship between humans and other primates creates exceptionally high potential for pathogen exchange. The surveillance of pathogens in primates plays an important role in anticipating possible outbreaks. In this study, we conducted a molecular investigation of pathogenic bacteria in feces from African nonhuman primates (NHPs). We also investigated the pathogens shared by the human population and gorillas living in the same territory in the Republic of Congo. In total, 93% of NHPs (n=176) and 95% (n=38) of humans were found to carry at least one bacterium. Non-pallidum Treponema spp. (including T. succinifaciens, T. berlinense, and several potential new species) were recovered from stools of 70% of great apes, 88% of monkeys, and 79% of humans. Non-tuberculosis Mycobacterium spp. were also common in almost all NHP species as well as in humans. In addition, Acinetobacter spp., members of the primate gut microbiota, were mainly prevalent in human and gorilla. Pathogenic Leptospira spp. were highly present in humans (82%) and gorillas (66%) stool samples in Congo, but were absent in the other NHPs, therefore suggesting a possible gorillas-humans exchange. Particular attention will be necessary for enteropathogenic bacteria detected in humans such as Helicobacter pylori, Salmonella spp. (including S. typhi/paratyphi), Staphyloccocus aureus, and Tropheryma whipplei, some of which were also present in gorillas in the same territory (S. aureus and T. whipplei). This study enhances our knowledge of pathogenic bacteria that threaten African NHPs and humans by using a non-invasive sampling technique. Contact between humans and NHPs results in an exchange of pathogens. Ongoing surveillance, prevention, and treatment strategies alone will limit the spread of these infectious agents.

Structure of Chimpanzee Gut Microbiomes across Tropical Africa.

Understanding variation in host-associated microbial communities is important given the relevance of microbiomes to host physiology and health. Using 560 fecal samples collected from wild chimpanzees (Pan troglodytes) across their range, we assessed how geography, genetics, climate, vegetation, and diet relate to gut microbial community structure (prokaryotes, eukaryotic parasites) at multiple spatial scales. We observed a high degree of regional specificity in the microbiome composition, which was associated with host genetics, available plant foods, and potentially with cultural differences in tool use, which affect diet. Genetic differences drove community composition at large scales, while vegetation and potentially tool use drove within-region differences, likely due to their influence on diet. Unlike industrialized human populations in the United States, where regional differences in the gut microbiome are undetectable, chimpanzee gut microbiomes are far more variable across space, suggesting that technological developments have decoupled humans from their local environments, obscuring regional differences that could have been important during human evolution. IMPORTANCE Gut microbial communities are drivers of primate physiology and health, but the factors that influence the gut microbiome in wild primate populations remain largely undetermined. We report data from a continent-wide survey of wild chimpanzee gut microbiota and highlight the effects of genetics, vegetation, and potentially even tool use at different spatial scales on the chimpanzee gut microbiome, including bacteria, archaea, and eukaryotic parasites. Microbial community dissimilarity was strongly correlated with chimpanzee population genetic dissimilarity, and vegetation composition and consumption of algae, honey, nuts, and termites were potentially associated with additional divergence in microbial communities between sampling sites. Our results suggest that host genetics, geography, and climate play a far stronger role in structuring the gut microbiome in chimpanzees than in humans.

Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal.

Antibiotic resistance genes exist naturally in various environments far from human usage. Here, we investigated multidrug-resistant Klebsiella pneumoniae, a common pathogen of chimpanzees and humans. We screened antibiotic-resistant K. pneumoniae from 48 chimpanzee stools and 38 termite mounds (n = 415 samples) collected in protected areas in Senegal. The microsatellite method was used to identify chimpanzee individuals (n = 13). Whole-genome sequencing was performed on K. pneumoniae complex isolates to identify antibiotic-resistant genes and characterize clones. We found a high prevalence of carbapenem-resistant K. pneumoniae among chimpanzee isolates (18/48 samples from 7/13 individuals) and ceftriaxone resistance among both chimpanzee individuals (19/48) and termite mounds (7/415 termites and 3/38 termite mounds). The blaOXA-48 and the blaKPC-2 genes were carried by international pOXA-48 and pKPC-2 plasmids, respectively. The ESBL plasmid carried blaCTX-M-15, blaTEM-1B, and blaOXA-1 genes. Genome sequencing of 56 isolates identified two major clones associated with hospital-acquired infections of K. pneumoniae (ST307 and ST147) in chimpanzees and termites, suggesting circulation of strains between the two species, as chimpanzees feed on termites. The source and selection pressure of these clones in this environment need to be explored.

Mapping the periapex anatomical pattern of teeth involved in sodium hypochlorite accidents: a cross-sectional quasi-experimental study.

AIM: To determine the anatomical reasons for sodium hypochlorite (NaOCl) accidents by testing whether this mishap is likely to occur in cases where the anatomical apex of the teeth fenestrates the overlying buccal cortical alveolar bone, allowing NaOCl to gain direct access to buccal soft tissues. METHODOLOGY: Following a cross-sectional, nonrandomized design, 13 patients who suffered unintentional NaOCl accidents whilst undergoing root canal treatment were included. After remission of symptoms, the root canals were fully irrigated with an innocuous radiopaque solution (saline diluted Claritrast 300) and subsequently CBCT scanned to create a 3D-map of the periapex and tracking of the irrigant pathway throughout the periapical tissues. An extra group of five control patients, who underwent root canal treatment with no NaOCl accident, was also CBCT-scanned after irrigation with the tracking radiopaque solution. The anatomical relationship of the cortical bone and the root apex, as well as the distribution of irrigation solution in the periapical tissue, was associated with patients undergoing a NaOCl accident or not, using a Fisher's exact test. RESULTS: The frequency of teeth with apical cortical fenestration was significantly higher in the NaOCl accident-positive group, compared to the negative (P < 0.001). All 13 accident-positive patients had an anatomical apex in direct contact with the buccal soft tissue via fenestration of the overlying cortical bone and direct contact of the foramen with the soft tissues. The radiopaque solution was distributed in the soft tissue in these cases. In contrast, accident-negative patients had no fenestration of the buccal cortical bone and the anatomical root apex was within the cancellous bone or within a bone-confined periapical lesion. The radiopaque solution was also found in the cancellous bone or the periapical lesion, but patients had no manifestations of a NaOCl accident. CONCLUSION: This quasi-experimental cross-sectional clinical study suggests that, in addition to the presence of the extruded NaOCl solution, a patent foramen that fenestrates the cortical bone merging into the mucosal tissue might constitute a risk for the clinical manifestation of a NaOCl accident. Preoperative 3D scans aid in anticipating when an accident is likely to occur.

Recent genetic connectivity and clinal variation in chimpanzees.

Much like humans, chimpanzees occupy diverse habitats and exhibit extensive behavioural variability. However, chimpanzees are recognized as a discontinuous species, with four subspecies separated by historical geographic barriers. Nevertheless, their range-wide degree of genetic connectivity remains poorly resolved, mainly due to sampling limitations. By analyzing a geographically comprehensive sample set amplified at microsatellite markers that inform recent population history, we found that isolation by distance explains most of the range-wide genetic structure of chimpanzees. Furthermore, we did not identify spatial discontinuities corresponding with the recognized subspecies, suggesting that some of the subspecies-delineating geographic barriers were recently permeable to gene flow. Substantial range-wide genetic connectivity is consistent with the hypothesis that behavioural flexibility is a salient driver of chimpanzee responses to changing environmental conditions. Finally, our observation of strong local differentiation associated with recent anthropogenic pressures portends future loss of critical genetic diversity if habitat fragmentation and population isolation continue unabated.

Genotype & phenotype in Lowe Syndrome: specific OCRL1 patient mutations differentially impact cellular phenotypes.

Lowe Syndrome (LS) is a lethal genetic disorder caused by mutations in the OCRL1 gene which encodes the lipid 5' phosphatase Ocrl1. Patients exhibit a characteristic triad of symptoms including eye, brain and kidney abnormalities with renal failure as the most common cause of premature death. Over 200 OCRL1 mutations have been identified in LS, but their specific impact on cellular processes is unknown. Despite observations of heterogeneity in patient symptom severity, there is little understanding of the correlation between genotype and its impact on phenotype. Here, we show that different mutations had diverse effects on protein localization and on triggering LS cellular phenotypes. In addition, some mutations affecting specific domains imparted unique characteristics to the resulting mutated protein. We also propose that certain mutations conformationally affect the 5'-phosphatase domain of the protein, resulting in loss of enzymatic activity and causing common and specific phenotypes (a conformational disease scenario). This study is the first to show the differential effect of patient 5'-phosphatase mutations on cellular phenotypes and introduces a conformational disease component in LS. This work provides a framework that explains symptom heterogeneity and can help stratify patients as well as to produce a more accurate prognosis depending on the nature and location of the mutation within the OCRL1 gene.