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As social animals, Indo-Pacific humpback dolphins have community differentiation, but the external-internal influencing factors and spatiotemporal dynamics are not well known. Thus, we monitored the social structure variation in an endangered Indo-Pacific humpback dolphin population in Xiamen Bay, China, during two periods, namely, 2007–2010 and 2017–2019, and analyzed the influence of habitat use and individual composition. In both periods, the population showed highly similar social differentiation, and the individuals were divided into two main clusters and a small cluster. The two main clusters occupied the east and west waters but the core distribution area of the east cluster moved further eastward during 2007–2010 and 2017–2019, and the distribution shift did not change the temporal stability of the social structure or inter-association of the east cluster. The 16 identical individuals in the two periods (accounting for 51.6% and 43.2%, respectively) seemed to constitute the basic framework of the social structure and could be the main reason for the stable social structure over the past decade. However, these individuals likely played a more critical role in maintaining the social network structure in 2007–2010 than that in 2017–2019. These results suggested that the internal factors of the dominant individuals’ composition contributed more to building the social network than the external factor of habitat use change. Based on the findings, different protective measures have been proposed for two main clusters respectively.
Molecular phylogenetic relationship based on mitochondrial genomes within novel deep-sea corals (Octocorallia: Alcyonacea) insights into the slow evolution and adaptation of the extreme deep-sea environment
, Available online , doi: 10.24272/j.issn.2095-8137.2023.039
A total of 10 Alcyonacea corals were collected at depths ranging from 900 m to 1640 m by the manned submersible Shenhai Yongshi during two cruises in the South China Sea (SCS). Phylogenetic distance and average nucleotide identity (ANI) analyses of mitochondrial genomes combined with morphology examination and sclerite scanning showed that the collected samples could be assigned to four suborders - Calcaxonia, Holaxonia, Scleraxonia, and Stolonifera - which might represent 10 novel deep-sea species. The analyses of the dissimilarity of GC skew, phylogenetic distance, and ANI indicated that the evolution of Octocorallia mitochondrial sequences was slow. The nonsynonymous (Ka) and synonymous (Ks) substitution (Ka/Ks) ratios indicated that 14 protein-coding genes (PCGs) were undergoing purifying selection and that the selection pressures might be from specific deep-sea environments. The correlation analysis of median values of Ka/Ks ratio of five gene families and environmental factors showed that the genes encoding cytochrome b (cob) and DNA mismatch repair protein (mutS) might be driven by environmental factors to format deep-sea species. This study highlighted the slow evolution and adaptative mechanism of deep-sea corals in the deep ocean.
Omega-3 polyunsaturated fatty acids (n-3 PUFAs), particularly docosahexaenoic acid (22:6n-3, DHA), have been shown to play a crucial role in reproduction and reproductive health of vertebrates, including humans. However, the underlying mechanism of this phenomenon remains largely unknown. In this study, we used two zebrafish genetic models, the elovl2-/- mutant as an endogenous DHA-deficient model and the fat1 (an omega-3 desaturase encoding gene) transgenic zebrafish as an endogenous DHA-rich model, to investigate the effects of DHA on oocyte maturation and oocyte quality. Our results show that the elovl2-/- mutant zebrafish had much lower fecundity and poorer oocyte quality than the wildtype controls, while the fat1 zebrafish had higher fecundity and better oocyte quality than wildtype controls. DHA deficiency in elovl2-/- embryos led to defects of egg activation, poor microtubule stability and reduced pregnenolone levels. Further study reveals that DHA promotes pregnenolone synthesis by promoting the transcription of cyp11a1, which encodes the cholesterol side-chain cleavage enzyme, thereby stabilizing microtubule assembly during oogenesis. In turn, the hypothalamic–pituitary–gonadal (HPG) axis is enhanced by DHA. In conclusion, using two unique genetic models, our study demonstrates the endogenously synthesized DHA promotes oocyte maturation and oocyte quality by promoting pregnenolone production via transcriptional regulation of cyp11a1.
Glycogen is the most effective energy reserve for metabolism in aquatic shellfish, and also contributes to the flavor and quality of oyster. Jinjiang oyster Crassostrea ariakensis is an economically and ecologically important species in China. In this study, RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) were performed respectively to explore the gene expression and dynamic changes of chromatin accessibility among the oysters with different glycogen contents. A total of 9483 differentially expressed genes (DEGs) and 7215 significantly differential chromatin accessibility genes (DCAGs) were obtained, with the intersection of DEGs and DCAGs reaching 2600. Many of those genes were enriched in the pathways related to glycogen metabolism such as "Glycogen metabolic process" and "Starch and sucrose metabolism". In addition, a total of 526 SNP loci associated with glycogen content obtained by the genome wide association study (GWAS) corresponded to 241 genes, 63 of which were also DEGs and DCAGs as revealed above. This study will enrich basic research data and provide insights into the molecular mechanisms underlying the regulation of glycogen metabolism in oyster.
, Available online , doi: 10.24272/j.issn.2095-8137.2023.012
Monitoring the prevalence of the antimicrobial resistance gene (ARG) is critical to address the global crisis of antibiotic resistant bacterial infections. However, the characterization of ARG and microbiome structure, as well as the indicators for routine ARG monitoring in pig farms, are still lacking under the variation in antimicrobial exposure between countries/regions. Hence, metagenomics and Random Forest machine learning algorithm were used to decipher the ARG profiles, microbiome, and ARG contamination indicators in pig manure under different antimicrobial pressures between China and Europe. The results showed that Chinese pigs exposed to high level antimicrobials had higher total and plasmid-mediated ARG abundances than European pigs (P < 0.05). ANT(6)-Ib, APH(3')-IIIa, and tet(40) were the shared core ARGs between Chinese and European pigs. The core ARG identified in pigs existed a linkage between corresponding country/regions pigs and humans. Moreover, Lactobacillus and Prevotella were the dominant phyla in the core microbiome of Chinese and European pigs, respectively. Forty ARG markers and 43 biomarkers were found to differentiate Chinese and European pig manure samples with 100% and 98.7% accuracy, respectively. We identified indicators to assess the ARG contamination in Chinese and European pigs with high accuracy (r = 0.72 ~ 0.88). Escherichia flexneri in Chinese and European pigs carried numerous ARGs, ranging from 21 to 37. This study emphasized the importance of global collaboration in reducing antimicrobial resistance (AMR) risk and provided indicators for evaluating the risk of ARG contamination in pig farms.
Geographical backgrounds and dispersal ability might have strong imprint on assemblage dissimilarity; however, these aspects have generally been overlooked in large-scale beta diversity studies. Here, we examined whether patterns and drivers of taxonomic beta diversity (TBD) and phylogenetic beta diversity (PBD) of breeding birds in China vary across 1) regions on both sides of the Hu Line, a line that demarcates China’s topographical, climatic, economic, and social patterns, and 2) species with different dispersal ability. TBD and PBD were calculated and partitioned into turnover and nestedness components using a moving window approach. Variables representing climate, habitat heterogeneity, and habitat quality were used to evaluate the effects of environmental filtering, whereas spatial distance was used to assess the influences of dispersal limitation. Variance partitioning analysis was used to assess the relative role of these variables. In general, TBD and PBD values were high in mountainous areas and environmental filtering largely determined TBD and PBD. However, different dominating environmental filters on both sides of the Hu Line led to divergent beta diversity patterns. Specifically, climate-driven species turnover and habitat heterogeneity-related species nestedness dominated the regions at east and west of the Hu Line, respectively. Additionally, bird species with stronger dispersal ability were more susceptible to environmental filtering resulting in more homogeneous assemblages. Our results indicated that regions with distinctive geographical backgrounds might present different ecological factors that lead to divergent assemblage dissimilarity patterns, and dispersal ability determines the response of assemblages to these ecological factors. Identifying a single universal explanation for the observed pattern without considering these aspects might lead to simplistic or incomplete conclusions. Therefore, it is essential to consider the combined effect of geographical background and dispersal ability for comprehensively understanding large-scale patterns of beta diversity and for planning conservation strategies.
Pig H3K4me3, H3K27ac and gene expression profiles reveal reproductive tissue-specific activity of transposable elements
, Available online , doi: 10.24272/j.issn.2095-8137.2023.060
Regulatory sequences and transposable elements (TEs) account for a large proportion of the genome sequences of species, while their roles in gene transcription, especially tissue-specific expression, remain largely unknown. Pigs are an excellent animal models for studying the biology of the genome sequences owing to their great diversity of wild and domesticated populations. Here, we integrated H3K27ac ChIP-seq, H3K4me3 ChIP-seq and RNA-seq data from 10 tissues of the same 7 fetuses and their consanguineously related 8 adult pigs to annotate the regulatory elements and TEs for their links with histone modifications and mRNA expression across varying tissues and development stages. The association analyses of mRNA expression with H3K27ac and H3K4me3 peak activity revealed that H3K27ac peaks showed stronger associations with gene expression than H3K4me3. We revealed that 1.45% of the TEs overlapped with H3K27ac or H3K4me3 peaks, of which the majority displayed tissue-specific activity. We identified a TE subfamily (LTR4C_SS) with binding motifs for SIX1 and SIX4 that showed specific enrichment in adult and fetal ovary H3K27ac peaks. We also revealed widespread expression of TEs as part of exons or promoters of genes from the RNA-seq data, including 4688 TE-containing transcripts that displayed development stage and tissue-specific expression. Notably, 1967 TE-containing transcripts were enriched in the testes. We highlighted that an LTR acting as a testis-specific alternative promoter in SRPK2 (a cell cycle-related protein kinase) in our pig data, MLT1F1, was also conserved in humans and mice, suggesting an ancient embedding of the TEs in testis-specific expressed genes or parallel evolution. Collectively, our work demonstrates that TEs are deeply embedded in the genome and exhibit important tissue-specific biological functions, particularly in the reproductive organs.
Parkinson’s disease (PD) is a neurodegenerative condition that results in dyskinesia, with oxidative stress playing a pivotal role in its progression. Antioxidant peptides may thus present therapeutic potential for PD. In this study, a novel cathelicidin peptide (Cath-KP; GCSGRFCNLFNNRRPGRLTLIHRPGGDKRTSTGLIYV) was identified from the skin of the Asiatic painted frog (Kaloula pulchra). Structural analysis using circular dichroism and homology modeling revealed a unique αββ conformation for Cath-KP. In vitro experiments, including free radical scavenging and ferric-reducing antioxidant analyses, confirmed its antioxidant properties. Using the 1-methyl-4-phenylpyridinium ion (MPP+)-induced dopamine cell line and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD mice, Cath-KP was found to penetrate cells and reach deep brain tissues, resulting in improved MPP+-induced cell viability and reduced oxidative stress-induced damage by promoting antioxidant enzyme expression and alleviating mitochondrial and intracellular reactive oxygen species accumulation through Sirtuin-1 (Sirt1)/Nuclear factor erythroid 2-related factor 2 (Nrf2) pathway activation. Both focal adhesion kinase (FAK) and p38 were also identified as regulatory elements. In the MPTP-induced PD mice, Cath-KP administration increased the number of tyrosine hydroxylase (TH)-positive neurons, restored TH content, and ameliorated dyskinesia. To the best of our knowledge, this study is the first to report on a cathelicidin peptide demonstrating potent antioxidant and neuroprotective properties in a PD model by targeting oxidative stress. These findings expand the known functions of cathelicidins, and hold promise for the development of therapeutic agents for PD.
Neural tube defects (NTDs) are severe congenital neurodevelopmental disorders arising from incomplete neural tube closure. Although folate supplementation has been shown to mitigate the incidence of NTDs, some cases, often attributable to genetic factors, remain unpreventable. The SHROOM3 gene has been implicated in NTD cases that are unresponsive to folate supplementation; at present, however, the underlying mechanism remains unclear. Neural tube morphogenesis is a complex process involving the folding of the planar epithelium of the neural plate. To determine the role of SHROOM3 in early developmental morphogenesis, we established a neuroepithelial organoid culture system derived from cynomolgus monkeys to closely mimic the in vivo neural plate phase. Loss of SHROOM3 resulted in shorter neuroepithelial cells and smaller nuclei. These morphological changes were attributed to the insufficient recruitment of cytoskeletal proteins, namely fibrous actin (F-actin), myosin II, and phospho-myosin light chain (PMLC), to the apical side of the neuroepithelial cells. Notably, these defects were not rescued by folate supplementation. RNA sequencing revealed that differentially expressed genes were enriched in biological processes associated with cellular and organ morphogenesis. In summary, we established an authentic in vitro system to study NTDs and identified a novel mechanism for NTDs that are unresponsive to folate supplementation.
PTEN-induced putative kinase 1 (PINK1), a mitochondrial kinase that phosphorylates Parkin and other proteins, plays a crucial role in mitophagy and protection against neurodegeneration. Mutations in PINK1 and Parkin can lead to loss of function and early onset Parkinson’s disease. However, there is a lack of strong in vivo evidence in rodent models to support the theory that loss of PINK1 affects mitophagy and induces neurodegeneration. Additionally, PINK1 knockout pigs (Sus scrofa) do not appear to exhibit neurodegeneration. In our recent work involving non-human primates, we found that PINK1 is selectively expressed in primate brains, while absent in rodent brains. To extend this to other species, we used multiple antibodies to examine the expression of PINK1 in pig tissues. In contrast to tissues from cynomolgus monkeys (Macaca fascicularis), our data did not convincingly demonstrate detectable PINK1 expression in pig tissues. Knockdown of PINK1 in cultured pig cells did not result in altered Parkin and BAD phosphorylation, as observed in cultured monkey cells. A comparison of monkey and pig striatum revealed more PINK1-phosphorylated substrates in the monkey brain. Consistently, PINK1 knockout in pigs did not lead to obvious changes in the phosphorylation of Parkin and BAD. These findings provide new evidence that PINK1 expression is specific to primates, underscoring the importance of non-human primates in investigating PINK1 function and pathology related to PINK1 deficiency.