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Scientific Reports Oct 2023HLA and disease studies by using single allele statistics have been fruitless during the last 40 years for explaining association pathogenesis of the associated...
HLA and disease studies by using single allele statistics have been fruitless during the last 40 years for explaining association pathogenesis of the associated diseases.Other approaches are necessary to untangle this puzzle. We aim to revisit complement alleleism in humans and primates for both studying MHC and disease association to complotypes and extended MHC haplotypes in order to also explain the positive directional selection of maintaining immune response genes (complement, MHC adaptive and MHC non-specific genes) that keeps these three type of genes together in a short chromosome stretch (MHC) for million years. These genes may be linked to conjointly avoid microbes attack and autoimmunity. In the present paper, it is obtained a new Bf chimpanzee allele, provisionaly named Patr-Bf*A:01,that differs from other Bf alleles by having CTG at eleventh codon of exon 2 in order to start the newly suggested methodology and explain functional and evolutionary MHC obscure aspects. Exons 1 to 6 of Ba fragment of Bf gene were obtained from chimpanzee. This new chimpanzee Factor B allele (Patr-Bf*A:01) is to be identical to a infrequent human Bf allele (SNP rs641153); it stresses the strong evolutive pressure upon certain alleles that are trans specific. It also may apply to MHC extended haplotipes which may conjointly act to start an adequate immune response. It is the first time that a complement MHC class III allele is described to undergo trans species evolution,in contrast to class I and class II alleles which had already been reported . Allelism of complement factors are again proposed for studying MHC complement genes, complotypes, and extended MHC haplotypes which may be more informative that single MHC marker studies.
Topics: Male; Animals; Humans; Alleles; Pan troglodytes; Major Histocompatibility Complex; Hominidae; Histocompatibility Antigens; Complement Factor B; Chromosomes
PubMed: 37794053
DOI: 10.1038/s41598-023-42016-1 -
Scientific Reports Oct 2023Detailed observations of animal reactions to a collapsed individual in wild are rare but essential to debates about the perception of death by nonhuman animals,...
Detailed observations of animal reactions to a collapsed individual in wild are rare but essential to debates about the perception of death by nonhuman animals, including chimpanzees. A male juvenile chimpanzee named Volta, a member of the M group in the Mahale Mountains National Park, fell from a tall tree and was temporarily incapacitated, suffering a severe concussion and nasal bone fracture. However, Volta showed signs of gradual recovery. We compared the behavior of other chimpanzees towards Volta with the previous reports on the behavior towards collapsed or recently dead group members. We found that behaviors towards Volta were similar to those observed towards collapsed or dead members. These included other-regarding behaviors and aggressive behaviors, and notably, licking of Volta's blood, which has not been previously reported. Adult males tended to be in close proximity to Volta for longer periods than adult females. The social situation with adult males including alpha male, surrounding Volta likely influenced the behavior of other individuals. Exploring the state of recovery of the injured individual, by closely approaching, directing various behaviors, and observing the reactions of the victim, and demonstrate tolerance and consideration towards the victim.
Topics: Humans; Male; Animals; Female; Pan troglodytes; Behavior, Animal; Aggression; Accidents; Social Behavior; Tanzania
PubMed: 37794020
DOI: 10.1038/s41598-023-43229-0 -
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 -
NeuroImage Nov 2023Mapping the chimpanzee brain connectome and comparing it to that of humans is key to our understanding of similarities and differences in primate evolution that occurred...
Mapping the chimpanzee brain connectome and comparing it to that of humans is key to our understanding of similarities and differences in primate evolution that occurred after the split from their common ancestor around 6 million years ago. In contrast to studies on macaque species' brains, fewer studies have specifically addressed the structural connectivity of the chimpanzee brain and its comparison with the human brain. Most comparative studies in the literature focus on the anatomy of the cortex and deep nuclei to evaluate how their morphology and asymmetry differ from that of the human brain, and some studies have emerged concerning the study of brain connectivity among humans, monkeys, and apes. In this work, we established a new white matter atlas of the deep and superficial white matter structural connectivity in chimpanzees. In vivo anatomical and diffusion-weighted magnetic resonance imaging (MRI) data were collected on a 3-Tesla MRI system from 39 chimpanzees. These datasets were subsequently processed using a novel fiber clustering pipeline adapted to the chimpanzee brain, enabling us to create two novel deep and superficial white matter connectivity atlases representative of the chimpanzee brain. These atlases provide the scientific community with an important and novel set of reference data for understanding the commonalities and differences in structural connectivity between the human and chimpanzee brains. We believe this study to be innovative both in its novel approach and in mapping the superficial white matter bundles in the chimpanzee brain, which will contribute to a better understanding of hominin brain evolution.
Topics: Humans; Animals; White Matter; Pan troglodytes; Brain; Magnetic Resonance Imaging; Brain Mapping; Connectome; Macaca
PubMed: 37722605
DOI: 10.1016/j.neuroimage.2023.120362 -
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 -
Royal Society Open Science Sep 2023The forelimbs of hominoid primates (apes) are decidedly more flexible than those of monkeys, especially at the shoulder, elbow and wrist joints. It is tempting to link...
The forelimbs of hominoid primates (apes) are decidedly more flexible than those of monkeys, especially at the shoulder, elbow and wrist joints. It is tempting to link the greater mobility of these joints to the functional demands of vertical climbing and below-branch suspension, but field-based kinematic studies have found few differences between chimpanzees and monkeys when comparing forelimb excursion angles during vertical ascent (upclimbing). There is, however, a strong theoretical argument for focusing instead on vertical descent (downclimbing), which motivated us to quantify the effects of climbing directionality on the forelimb kinematics of wild chimpanzees () and sooty mangabeys (). We found that the shoulders and elbows of chimpanzees and sooty mangabeys subtended larger joint angles during bouts of downclimbing, and that the magnitude of this difference was greatest among chimpanzees. Our results cast new light on the functional importance of downclimbing, while also burnishing functional hypotheses that emphasize the role of vertical climbing during the evolution of apes, including the human lineage.
PubMed: 37680499
DOI: 10.1098/rsos.230145 -
PloS One 2023The Underwater Acoustic Sensor Network (UASN) is a large network in which the vicinity of a transmitting node is made up of numerous operational sensor nodes. The...
The Underwater Acoustic Sensor Network (UASN) is a large network in which the vicinity of a transmitting node is made up of numerous operational sensor nodes. The communication process may be substantially disrupted due to the underwater acoustic channel's time-varying and space-varying features. As a result, the underwater acoustic communication system faces the problems of reducing interference and enhancing communication effectiveness and quality through adaptive modulation. To overcome this issue, this paper intends to propose a model for optimal path selection and secured data transmission in UASN via Long Short-Term Memory (LSTM) based energy prediction. The proposed model of transmitting the secured data in UASN through the optimal path involves two major phases. Initially, the nodes are selected under the consideration of constraints like energy, distance and link quality in terms of throughput. Moreover, the energy is predicted with the aid of LSTM and the optimal path is selected with the proposed hybrid optimization algorithm termed as Pelican Updated Chimp Optimization Algorithm (PUCOA), which is the combination of two algorithms including the Pelican Optimization Algorithm (POA) and Chimp Optimization Algorithm (COA). Further, the data is transmitted via the optimal path securely by encrypting the data with the proposed improved blowfish algorithm (IBFA). At last, the developed LSTM+PUCOA model is validated with standard benchmark models and it proves that the performance of the proposed LSTM+PUCOA model attains 90.85% of accuracy, 92.78% of precision, 91.78% of specificity, 89.79% of sensitivity, 7.21% of FPR, 89.76% of F1 score, 89.77% of MCC, 10.20% of FNR, 92.45% of NPV, and 10.22% of FDR for Learning percentage 70.
Topics: Humans; Animals; Physical Phenomena; Acoustics; Algorithms; Benchmarking; Pan troglodytes
PubMed: 37669288
DOI: 10.1371/journal.pone.0289306 -
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 -
Scientific Reports Sep 2023It is known that the ~ 1.6 kb Neuroblastoma BreakPoint Family (NBPF) repeats are human specific and contributing to cognitive capabilities, with increasing...
It is known that the ~ 1.6 kb Neuroblastoma BreakPoint Family (NBPF) repeats are human specific and contributing to cognitive capabilities, with increasing frequency in higher order repeat 3mer HORs (Olduvai triplets). From chimpanzee to modern human there is a discontinuous jump from 0 to ~ 50 tandemly organized 3mer HORs. Here we investigate the structure of NBPF 3mer HORs in the Neanderthal genome assembly of Pääbo et al., comparing it to the results obtained for human hg38.p14 chromosome 1. Our findings reveal corresponding NBPF 3mer HOR arrays in Neanderthals with slightly different monomer structures and numbers of HOR copies compared to humans. Additionally, we compute the NBPF 3mer HOR pattern for the complete telomere-to-telomere human genome assembly (T2T-CHM13) by Miga et al., identifying two novel tandem arrays of NBPF 3mer HOR repeats with 5 and 9 NBPF 3mer HOR copies. We hypothesize that these arrays correspond to novel NBPF genes (here referred to as NBPFA1 and NBPFA2). Further improving the quality of the Neanderthal genome using T2T-CHM13 as a reference would be of great interest in determining the presence of such distant novel NBPF genes in the Neanderthal genome and enhancing our understanding of human evolution.
Topics: Humans; Animals; Neanderthals; Chromosomes, Human; Chromosomes, Human, Pair 1; Neuroblastoma; Family; Pan troglodytes
PubMed: 37660151
DOI: 10.1038/s41598-023-41517-3 -
PLoS Biology Sep 2023Human language is supported by a cortical network involving Broca's area, which comprises Brodmann Areas 44 and 45 (BA44 and BA45). While cytoarchitectonic homolog areas...
Human language is supported by a cortical network involving Broca's area, which comprises Brodmann Areas 44 and 45 (BA44 and BA45). While cytoarchitectonic homolog areas have been identified in nonhuman primates, it remains unknown how these regions evolved to support human language. Here, we use histological data and advanced cortical registration methods to precisely compare the morphology of BA44 and BA45 in humans and chimpanzees. We found a general expansion of Broca's areas in humans, with the left BA44 enlarging the most, growing anteriorly into a region known to process syntax. Together with recent functional and receptorarchitectural studies, our findings support the conclusion that BA44 evolved from an action-related region to a bipartite system, with a posterior portion supporting action and an anterior portion supporting syntactic processes. Our findings add novel insights to the longstanding debate on the relationship between language and action, and the evolution of Broca's area.
Topics: Humans; Animals; Brain; Language; Pan troglodytes
PubMed: 37656748
DOI: 10.1371/journal.pbio.3002266