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2020 Vol. 41, No. 4

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Review
Understanding the genetic mechanisms underlying particular adaptations/phenotypes of organisms is one of the core issues of evolutionary biology. The use of genomic data has greatly advanced our understandings on this issue, as well as other aspects of evolutionary biology, including molecular adaptation, speciation, and even conservation of endangered species. Despite the well-recognized advantages, usages of genomic data are still limited to non-mammal vertebrate groups, partly due to the difficulties in assembling large or highly heterozygous genomes. Although this is particularly the case for amphibians, nonetheless, several comparative and population genomic analyses have shed lights into the speciation and adaptation processes of amphibians in a complex landscape, giving a promising hope for a wider application of genomics in the previously believed challenging groups of organisms. At the same time, these pioneer studies also allow us to realize numerous challenges in studying the molecular adaptations and/or phenotypic evolutionary mechanisms of amphibians. In this review, we first summarize the recent progresses in the study of adaptive evolution of amphibians based on genomic data, and then we give perspectives regarding how to effectively identify key pathways underlying the evolution of complex traits in the genomic era, as well as directions for future research.
Exosomes are small vesicles secreted by all cell types in the brain and play a role in cell-cell communication through the transfer of cargo or encapsulation. Exosomes in the brain have considerable impact on neuronal development, activation, and regeneration. In addition, exosomes are reported to be involved in the onset and propagation of various neurodegenerative diseases. In this review, we discuss the content of exosomes derived from major cell types in the brain, and their function under physiological and pathological conditions.
Articles
Studies on behavioral flexibility in response to habitat differences and degradation are crucial for developing conservation strategies for endangered species. Trachypithecus species inhabit various habitats and display different patterns of strata use; however, the effect of habitat structure on strata use remains poorly studied. Here, we investigated strata use patterns of Indo-Chinese gray langurs (Trachypithecus crepusculus) in a primary evergreen forest in Mt. Wuliang, southwest China, from June 2012 to January 2016. In addition, we compared T. crepusculus strata use and terrestriality with five other Trachypithecus species from previous studies. Unlike langurs living in karst forests, our study group was typically arboreal and spent only 2.9% of time on the ground. The group showed a preference for higher strata when resting and lower strata (<20 m) when moving. The langurs primarily used time on the ground for geophagy, but otherwise avoided the ground during feeding. These strata use patterns are similar to those of limestone langurs (T. francoisi) when using continuous forests. At the genus level (n=6 species), we found a negative relationship between habitat forest cover and terrestriality. This negative relationship was also true for the five limestone langur species, implying limestone langurs increase territoriality in response to decreased forest cover. Our results document behavioral flexibility in strata use of Trachypithecus langurs and highlight the importance of the protection of continuous forests to promote langur conservation.
Magnetic brain stimulation has greatly contributed to the advancement of neuroscience. However, challenges remain in the power of penetration and precision of magnetic stimulation, especially in small animals. Here, a novel combined magnetic stimulation system (c-MSS) was established for brain stimulation in mice. The c-MSS uses a mild magnetic pulse sequence and injection of superparamagnetic iron oxide (SPIO) nanodrugs to elevate local cortical susceptibility. After imaging of the SPIO nanoparticles in the left prelimbic (PrL) cortex in mice, we determined their safety and physical characteristics. Depressive-like behavior was established in mice using a chronic unpredictable mild stress (CUMS) model. SPIO nanodrugs were then delivered precisely to the left PrL cortex using in situ injection. A 0.1 T magnetic field (adjustable frequency) was used for magnetic stimulation (5 min/session, two sessions daily). Biomarkers representing therapeutic effects were measured before and after c-MSS intervention. Results showed that c-MSS rapidly improved depressive-like symptoms in CUMS mice after stimulation with a 10 Hz field for 5 d, combined with increased brain-derived neurotrophic factor (BDNF) and inactivation of hypothalamic-pituitary-adrenal (HPA) axis function, which enhanced neuronal activity due to SPIO nanoparticle-mediated effects. The c-MSS was safe and effective, representing a novel approach in the selective stimulation of arbitrary cortical targets in small animals, playing a bioelectric role in neural circuit regulation, including antidepressant effects in CUMS mice. This expands the potential applications of magnetic stimulation and progresses brain research towards clinical application.
Spring viremia of carp virus (SVCV) causes devastating losses in aquaculture. Coumarin has an advantageous structure for the design of novel antiviral agents with high affinity and specificity. In this study, we evaluated a hydroxycoumarin medicine, i.e., 7-(6-benzimidazole) coumarin (C10), regarding its anti-SVCV effects in vitro and in vivo. Results showed that up to 12.5 mg/L C10 significantly inhibited SVCV replication in the epithelioma papulosum cyprini (EPC) cell line, with a maximum inhibitory rate of >97%. Furthermore, C10 significantly reduced cell death and relieved cellular morphological damage in SVCV-infected cells. Decreased mitochondrial membrane potential (ΔΨm) also suggested that C10 not only protected mitochondria, but also reduced apoptosis in SVCV-infected cells. For in vivo studies, intraperitoneal injection of C10 resulted in an anti-SVCV effect and substantially enhanced the survival rate of virus-infected zebrafish. Furthermore, C10 significantly enhanced antioxidant enzyme activities and decreased reactive oxygen species (ROS) to maintain antioxidant-oxidant balance within the host, thereby contributing to inhibition of SVCV replication. The up-regulation of six interferon (IFN)-related genes also demonstrated that C10 indirectly activated IFNs for the clearance of SVCV in zebrafish. This was beneficial for the continuous maintenance of antiviral effects because of the low viral loads in fish. Thus, C10 is suggested as a therapeutic agent with great potential against SVCV infection in aquaculture.
Pseudomonas plecoglossicida is a rod-shaped, gram-negative bacterium with flagella. It causes visceral white spot disease and high mortality in Larimichthys crocea during culture, resulting in serious economic loss. Analysis of transcriptome and quantitative real-time polymerase chain reaction (PCR) data showed that dksA gene expression was significantly up-regulated after 48 h of infection with Epinephelus coioides (log2FC=3.12, P<0.001). RNAi of five shRNAs significantly reduced the expression of dksA in P. plecoglossicida, and the optimal silencing efficiency was 96.23%. Compared with wild-type strains, the symptoms of visceral white spot disease in L. crocea infected with RNAi strains were reduced, with time of death delayed by 48 h and mortality reduced by 25%. The dksA silencing led to a substantial down-regulation in cellular component-, flagellum-, and ribosome assembly-related genes in P. plecoglossicida, and the significant up-regulation of fliC may be a way in which virulence is maintained in P. plecoglossicida. The GO and KEGG results showed that RNAi strain infection in L. crocea led to the down-regulation of inflammatory factor genes in immune-related pathways, which were associated with multiple immune response processes. Results also showed that dksA was a virulence gene in P. plecoglossicida. Compared with the wild-type strains, RNAi strain infection induced a weaker immune response in L. crocea.
The Chinese sturgeon (Acipenser sinensis Gray, 1835) is a large anadromous fish species, which is under considerable threat due to dramatic declines in population numbers. In the current study, population genetic diversity and individual reproductive success were assessed using nuclear microsatellite markers (simple sequence repeat, SSR) and complete mitochondrial (mtDNA) genome analysis of juveniles born in 2014. Results showed the existence of size polymorphism in the mtDNA genome of Chinese sturgeon, which was caused by a repeat motif. Population genetic diversity was high based on both SSR (Ho: 0.728±0.211; He: 0.779±0.122) and mtDNA genome analyses (H: 0.876±0.0035; Pi: 0.0011±0.0010). A positive inbreeding coefficient (FIS: 0.066±0.143) was also found, indicating the occurrence of inbreeding. Reconstruction of sibling groups identified 11 mothers and 11 fathers involved in reproduction of Chinese sturgeons in 2014. Variance in individual reproductive success was not significant, with reproductive success of parent fish instead shown to be relatively even (P=0.997>0.05), thus suggesting the absence of sweepstakes reproductive success (SRS). These results indicate that, in regard to conservation, loss of genetic diversity due to the effects of SRS is not of particular concern. However, we must focus on having an adequate number of adults and suitable environmental conditions to ensure that fish can reproduce.
Letters to the editor
During the breast-feeding period, infants undergo remarkable changes, including rapid physiological and developmental growth. However, little is known about gene expression features and sex-specific gene expression in breast-feeding infants. In this study, we sequenced 32 blood transcriptomes from 16 breast-feeding rhesus macaque (Macaca mulatta) infants and their lactating mothers. We identified 218 differentially expressed genes (DEGs) between infants and mothers, including 91 up-regulated and 127 down-regulated DEGs in the infant group. Functional enrichment analysis of the up-regulated DEGs and unique hub genes in infants showed primary enrichment in immunity, growth, and development. Protein-protein interaction analysis also revealed that genes at key positions in infants were mainly related to development and immunity. However, we only detected 23 DEGs between female and male infants, including three DEGs located on chromosome X and 14 DEGs located on chromosome Y. Of these DEGs, TMF1 regulated nuclear protein 1 (Trnp1), which was highly expressed in female infants, is crucial for controlling the tangential and radial expansion of the cerebral cortex in mammals. Thus, our study provides novel insight into the gene expression features of breast-feeding infants in non-human primates (NHPs) and reveals sex-specific gene expression between these infants.
Sleep is indispensable for human health, with sleep disorders initiating a cascade of negative consequences. As our closest phylogenetic relatives, non-human primates (NHPs) are invaluable for comparative sleep studies and exhibit tremendous potential for improving our understanding of human sleep and related disorders. Previous work on measuring sleep in NHPs has mostly used electroencephalography or videography. In this study, simultaneous videography and actigraphy were applied to observe sleep patterns in 10 cynomolgus monkeys (Macaca fascicularis) over seven nights (12 h per night). The durations of wake, transitional sleep, and relaxed sleep were scored by analysis of animal behaviors from videography and actigraphy data, using the same behavioral criteria for each state, with findings then compared. Here, results indicated that actigraphy constituted a reliable approach for scoring the state of sleep in monkeys and showed a significant correlation with that scored by videography. Epoch-by-epoch analysis further indicated that actigraphy was more suitable for scoring the state of relaxed sleep, correctly identifying 97.57% of relaxed sleep in comparison with video analysis. Only 34 epochs (0.13%) and 611 epochs (2.30%) were differently interpreted as wake and transitional sleep compared with videography analysis. The present study validated the behavioral criteria and actigraphy methodology for scoring sleep, which can be considered as a useful and a complementary technique to electroencephalography and/or videography analysis for sleep studies in NHPs.
Rhesus monkeys (Macaca mulatta) are valuable experimental animals for studies on neurodegenerative diseases due to their evolutionarily close relationship to humans (Zhang et al., 2014). Rhesus monkeys also display similar hallmarks of aging and neurodegeneration as humans, including formation of senile plaques in the brain (Beckman et al., 2019; Paspalas et al., 2018). However, changes in formaldehyde (FA) levels in the cerebrospinal fluid (CSF) of rhesus monkeys with aging have not been reported. Additionally, whether changes in CSF FA are correlated with changes in amyloid-β (Aβ) concentrations have not yet been explored. Here, the CSF levels of Aβ40, Aβ42, and FA were measured in 56 rhesus monkeys of different ages, ranging from 4 to 26 years old. Results revealed significant declines in Aβ40 and Aβ42, and an increase in FA with age. Interestingly, the increase in FA levels was negatively correlated with Aβ40 and Aβ42 concentrations in aged rhesus monkeys but not in young and middle-aged monkeys. These results appear to parallel changes seen within human aging, i.e., decreased levels of CSF Aβ and increased levels of FA in normal aged adults and Alzheimer’s disease (AD) patients. These findings further indicate that rhesus monkeys are a reliable model for studying age-related neurological disorders such as AD and suggest that FA is an important factor in AD development and may be used as a diagnostic indicator of such disease.
Intestinal biopsy is a basic experimental method for studying pathological changes in the intestinal tract during human immunodeficiency virus (HIV) infection. In this study, jejunal resection and anastomosis were successfully performed in 12 Chinese rhesus macaques (Macaca mulatta). The sampled gut tissues were then examined by hematoxylin and eosin (H&E) staining, electron microscopy, flow cytometry, immunofluorescence detection, and RNA quality analysis to ensure suitability for histological, physiological, pathological, and immunological detection, as well as mechanistic analysis at the cellular and molecular level. Importantly, the surgery did not affect the ratio or number of immune cells in peripheral blood or the concentration of lipids, proteins, and vitamins in plasma, which are important indicators of nutritional status. Our results thus indicated that jejunal resection and anastomosis are feasible, and that immune homeostasis and intestinal barrier integrity are not altered by surgery. All macaques recovered well (except for one), with no postoperative complications. Therefore, this animal surgery may be applicable for longitudinal intestinal research related to diseases such as acquired immunodeficiency syndrome (AIDS).
Infanticide by unrelated individuals is widely reported in the animal kingdom; however, little is known about cases perpetrated by a parent, particularly the mother. This article reports on three cases of mother-initiated infanticide in Qinling golden takins (Budorcas taxicolor bedfordi) recorded from video and camera images. Based on previous reports in other animals, we propose that the infanticide events observed in golden takins were related to the parental manipulation mechanism – i.e., killing an unhealthy infant to allow the mother to invest more care in potentially healthy offspring, and gain more fruitful reproductive opportunities. This appears to be an evolutionary-based selection strategy, whereby a species can prosper and succeed under the challenges of natural selection. However, further studies on both captive and wild populations are required to answer the various questions raised from our observations.
The egg laying behavior of brood parasites is at the heart of studies on host co-evolution. Therefore, research on egg laying behavior can improve our understanding of brood parasitism and associated processes. Over a seven year study period, we monitored 455 oriental reed warbler (Acrocephalus orientalis) nests during the egg laying period, 250 of which were parasitized by common cuckoos (Cuculus canorus). We collected 53 clear videos of common cuckoo parasitism, analyzed all recorded parasitic behavior in detail, and summarized the process of brood parasitism. Furthermore, based on analyses of the field video recordings, we propose a new explanation for egg removal behavior, namely the delivery hypothesis, i.e., egg pecking and biting by cuckoos may facilitate fast egg-laying and parasitism by reducing host attention and attack, with egg removal a side effect of egg pecking and biting. We concluded that common cuckoos change their behavior when hosts are present at the nest, with a set of behaviors performed to deal with host attack and successfully complete parasitic egg-laying regardless of time of day.
A new species of Tibetan loach, Triplophysa weiheensis sp. nov., is described from the Weihe River in Gansu Province, China, based on morphological and molecular analyses. The new species can be distinguished from all known congeners by a unique combination of the following characters: scaleless; snout abruptly sloping downward, anterior to anterior nostril; lower jaw crescentic, not sharp; body without obvious mottling; lateral line interrupted on posterior trunk at pelvic-fin distal extremity; caudal-peduncle length 2.0–2.7 times its depth; branched rays of pectoral fin 10–11; branched rays of pelvic fin 5–6; inner gill rakers on 1st gill arch 14–16; vertebrae 4+34–36; intestine with 6–7 loops, length ca. 1.8 times SL (n=3); bony capsule of air bladder small and thin; posterior chamber of air bladder absent.
Cis-regulatory elements play an important role in the development of traits and disease in organisms (Ma et al., 2020; Woolfe et al., 2005) and their annotation could facilitate genetic studies. The Encyclopedia of DNA Elements (ENCODE) (Davis et al., 2018) and Functional Annotation of Animal Genomes (FAANG) (FAANG Consortium et al., 2015) offer pioneering data on regulatory elements in several species. Currently, however, regulatory element annotation data remain limited for most organisms. In this study, we developed a tool (OrthReg) for annotating conserved orthologous cis-regulatory elements in targeted genomes using an annotated reference genome. Cross-species validation of this annotation tool using human and mouse ENCODE data confirmed the robustness of this strategy. To explore the efficiency of the tool, we annotated the pig genome and identified more than 28 million regulatory annotation records using the reference human ENCODE data. With this regulatory annotation, some putative regulatory non-coding variants were identified within domestication sweeps in European and East Asian pigs. Thus, this tool can utilize data produced by ENCODE, FAANG, and similar projects, and can be easily extended to customized experimental data. The extensive application of this tool will help to identify informative single nucleotide polymorphisms (SNPs) in post-genome-wide association studies and resequencing analysis of organisms with limited regulatory annotation data.
Erratum