2020, 41(3): 213-219. doi: 10.24272/j.issn.2095-8137.2020.031
The ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by infection with human coronavirus 2019 (HCoV-19 / SARS-CoV-2 / 2019-nCoV), is a global threat to the human population. Here, we briefly summarize the available data for the zoonotic origins of HCoV-19, with reference to the other two epidemics of highly virulent coronaviruses, SARS-CoV and MERS-CoV, which cause severe pneumonia in humans. We propose to intensify future efforts for tracing the origins of HCoV-19, which is a very important scientific question for the control and prevention of the pandemic.
Epidemiological survey of a captive Chinese rhesus macaque breeding colony in Yunnan for SRV, STLV and BV
2012, 33(1): 49-54. doi: 10.3724/SP.J.1141.2012.01049
Nonhuman primates are critical resources for biomedical research. Rhesus macaque is a popularly used laboratory nonhuman primate that share many characteristics with humans. However, rhesus macaques are the natural host of two exogenous retroviruses, SRV (simian type D retrovirus) and STLV (simian T lymphotropic virus). SRV and STLV may introduce potentially significant confounding factors into the study of AIDS model. Moreover, B virus (ceropithecine herpesvirus 1) is likely to harm not only rhesus macaque but also humans in experiments involving rhesus macaque. Yunnan province has large-scale breeding colonies of Chinese rhesus macaque. Therefore there is an urgent need for SPF Chinese rhesus macaque colonies. Here we investigated SRV, STLV and BV infections in 411 Chinese rhesus macaque by PCR technique. The results showed that the prevalence of SRV, STLV and BV among Chinese rhesus macaque breeding colony was 19.71% (81/411), 13.38% (55/411) and 23.11% (95/411), respectively. Comparison of viruses infection in different age-groups and male/female of Chinese rhesus macaque was also analyzed. This study will contribute to establishment of SPF Chinese rhesus macaque breeding colony.
Construction of a cDNA Library from the Testis and Sequence Analysis of the Ubiquitin Gene from Rana nigromaculata (in English)
2007, 28(1): 9-16.
A full-length cDNA library from the testis of dark-spotted frogs (Rana nigromaculata) was constructed with the SMART (switching mechanism at 5′ end of RNA transcript) technique. Total RNA was extracted from the testis and reverse transcripted into full-length cDNA using PowerScript reverse transcriptase. The first-strand cDNA was amplified using long-distance PCR (LD-PCR). After SfiⅠ digestion and fractionation, cDNA (>500 bp) was ligated to λ TriplEx2 vector and packaged with GigapackR Ⅲ Gold Packaging Extract. The titers of optimal primary libraries were 2.0×106 pfu/mL and 2.4×106 pfu/mL and the titers of the amplified libraries were 0.48×109 pfu/mL and 3.0×109 pfu/mL, respectively. The percentages of recombinant clones of primary libraries and amplified libraries were all over 90%. The libraries were converted into pTriplEx2 plasmids in E. coli BM 25.8 strain. The insert sizes were measured by PCR which showed most fragments were over 500 bp and the average length was 1.0?kb approximately. A positive clone of 1 171 bp was sequenced and named RnUb based on sequence similarity with the known ubiquitin genes in GenBank. This sequence was a full-length cDNA with complete coding sequences, which indicated that the library built a base for screening the full-length cDNA. These data showed that this library attained to the requirements of a standard cDNA library. This library provided a useful resource for the functional genomic research of Rana nigromaculata.
1998, 19(1): 59-61.
During February and March 1995,a Slovenian caving expedition led by Andrej Miheve in association with the Institute of Karst Geology from Guilin explored the karst region in Libo County,south of Guizhou,a province in China.During the expedition,3 blind loach specimens were collected by Gregor Aljancic,They have been recognized as a new species of the genus Paracobitis:P.longibarbatus sp.nov.The new species possesses the following characters:adipose keel is present along the dorsal and ventral edge of caudal peduncle,depth of adipose keel less than half of depth of caudal peduncle;nostrils are situated closely together,the anterior nostril formed into a tube with a long nostral barbel.These characters indicate that it belongs to the genus Paracobitis,regardless of the presence of a nostral barbel at the terminal of nostral tube.Similar nostral tube was observed also in P.variegatus longidorsalis Yang et al.The eyes and pigment are disappeared as the result of convergent evolution adapting to the lightless habitat.The same convergent phenomena are prevalent in the cavefishes of Cobitidae and Cyprinidae.This new species is the first blind loach in the genus Paracobitis,representing a specialized lineage of the genus.It is related to epigean P.variegatus longidorsalis which occurs in the same basin,Xijiang Basin.The new species can be easily distinguished from all congeneric species by the following characters:eyes and pigment disappeared,anterior nostril tube-like with a nostral barbel at the terminal;barbels,pectoral and pelvic fins well elongated;posterior margin of caudal fin strongly concave.
2020, 41(1): 3-19. doi: 10.24272/j.issn.2095-8137.2020.012
Hypobaric hypoxia (HH) exposure can cause serious brain injury as well as life-threatening cerebral edema in severe cases. Previous studies on the mechanisms of HH-induced brain injury have been conducted primarily using non-primate animal models that are genetically distant to humans, thus hindering the development of disease treatment. Here, we report that cynomolgus monkeys (Macaca fascicularis) exposed to acute HH developed human-like HH syndrome involving severe brain injury and abnormal behavior. Transcriptome profiling of white blood cells and brain tissue from monkeys exposed to increasing altitude revealed the central role of the HIF-1 and other novel signaling pathways, such as the vitamin D receptor (VDR) signaling pathway, in co-regulating HH-induced inflammation processes. We also observed profound transcriptomic alterations in brains after exposure to acute HH, including the activation of angiogenesis and impairment of aerobic respiration and protein folding processes, which likely underlie the pathological effects of HH-induced brain injury. Administration of progesterone (PROG) and steroid neuroprotectant 5α-androst-3β,5,6β-triol (TRIOL) significantly attenuated brain injuries and rescued the transcriptomic changes induced by acute HH. Functional investigation of the affected genes suggested that these two neuroprotectants protect the brain by targeting different pathways, with PROG enhancing erythropoiesis and TRIOL suppressing glutamate-induced excitotoxicity. Thus, this study advances our understanding of the pathology induced by acute HH and provides potential compounds for the development of neuroprotectant drugs for therapeutic treatment.
Mudskipper interleukin-34 modulates the functions of monocytes/macrophages via the colony-stimulating factor-1 receptor 1
2020, 41(2): 123-137. doi: 10.24272/j.issn.2095-8137.2020.026
Interleukin-34 (IL-34) is a novel cytokine that plays an important role in innate immunity and inflammatory processes by binding to the colony-stimulating factor-1 receptor (CSF-1R). However, information on the function of IL-34 in fish remains limited. In the present study, we identified an IL-34 homolog from mudskippers (Boleophthalmus pectinirostris). In silico analysis showed that the mudskipper IL-34 (BpIL-34) was similar to other known IL-34 variants in sequence and structure and was most closely related to an orange-spotted grouper (Epinephelus coioides) homolog. BpIL-34 transcripts were constitutively expressed in various tissues, with the highest level of expression found in the brain. Edwardsiella tarda infection significantly up-regulated the mRNA expression of BpIL-34 in the mudskipper tissues. The recombinant mature BpIL-34 peptide (rBpIL-34) was purified and used to produce anti-rBpIL-34 IgG. Western blot analysis combined with PNGase F digestion revealed that native BpIL-34 in monocytes/macrophages (MOs/MФs) was N-glycosylated. In vitro, rBpIL-34 treatment enhanced the phagocytotic and bactericidal activity of mudskipper MOs/MФs, as well as the mRNA expression of pro-inflammatory cytokines like tumor necrosis factor α (BpTNF-α) and BpIL-1β in these cells. Furthermore, the knockdown of mudskipper CSF-1R1 (BpCSF-1R1), but not mudskipper BpCSF-1R2, significantly inhibited the rBpIL-34-mediated enhanced effect on MO/MФ function. In conclusion, our results indicate that mudskipper BpIL-34 modulates the functions of MOs/MФs via BpCSF-1R1.
2012, 33(6): 574-585. doi: 10.3724/SP.J.1141.2012.06574
Metagenome, a term first dubbed by Handelsman in 1998 as “the genomes of the total microbiota found in nature”, refers to sequence data directly sampled from the environment (which may be any habitat in which microbes live, such as the guts of humans and animals, milk, soil, lakes, glaciers, and oceans). Metagenomic technologies originated from environmental microbiology studies and their wide application has been greatly facilitated by next-generation high throughput sequencing technologies. Like genomics studies, the bottle neck of metagenomic research is how to effectively and efficiently analyze the gigantic amount of metagenomic sequence data using the bioinformatics pipelines to obtain meaningful biological insights. In this article, we briefly review the state-of-the-art bioinformatics software tools in metagenomic research. Due to the differences between the metagenomic data obtained from whole genome sequencing (i.e., shotgun metagenomics) and amplicon sequencing (i.e., 16S-rRNA and gene-targeted metagenomics) methods, there are significant differences between the corresponding bioinformatics tools for these data; accordingly, we review the computational pipelines separately for these two types of data.
1999, 20(3): 189-195.
In the present paper,the origin of the family Perlidae and the distribution characters of the tribe and the subfamily were summarized and analyzed.Based on the distribution of the genera in the world,the eight distribution types of the genera were divided.In addition,the distribution characters of the Perlidae in China were also probed preliminarily.So far two subfamilies,four tribe and twenty genera have been found in China.Ten of them,of which three genera are endemic to China,are the Oriental genera;one Palaearctic genus;three OrientalPalaearctic genera;one Oriental-Nearctic genus;four OrientalPalaearctic-Nearctic genera and one OrientalPalaearctic-Nearctic-Afrotropical genus.Moreover,the main distribution character of Chinese Perlidae is that most of the species distribute Central China region,South China region and Southwest China region.The Central China region centralizes the distribution and the break of the perlid species,and made the dispersal for the others regions.
Review of the genus Brachytarsophrys (Anura: Megophryidae), with revalidation of Brachytarsophrys platyparietus and description of a new species from China
2020, 41(2): 105-122. doi: 10.24272/j.issn.2095-8137.2020.033
The genus-level recognition of monophyletic short-legged toads (Brachytarsophrys) has been recently implicated in the taxonomic debate of Megophrys sensu lato. In the present study, Brachytarsophrys is reasonably regarded as a distinct genus based on significant morphological differentiations and recent molecular analyses. Furthermore, a comprehensive review of this genus is performed, with two species groups proposed based on morphological differences and phylogenetic relationships. Particularly, Brachytarsophrys platyparietus is removed as a synonym of Brachytarsophrys carinense and considered a valid species due to significant genetic divergence and distinct morphological differences. In addition, a new species, Brachytarsophrys orientalis sp . nov ., is described based on a series of specimens collected from southeastern China. This work takes the member species of the genus Brachytarsophrys to seven, suggesting that the diversity of Brachytarsophrys is underestimated. In addition, the genus levels of other monophyletic groups within the subfamily Megophryinae are discussed.
Whole-genome sequencing of leopard coral grouper (Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution
2020, 41(3): 328-340. doi: 10.24272/j.issn.2095-8137.2020.038
Leopard coral groupers belong to the Plectropomus genus of the Epinephelidae family and are important fish for coral reef ecosystems and the marine aquaculture industry. To promote future research of this species, a high-quality chromosome-level genome was assembled using PacBio sequencing and Hi-C technology. A 787.06 Mb genome was assembled, with 99.7% (784.57 Mb) of bases anchored to 24 chromosomes. The leopard coral grouper genome size was smaller than that of other groupers, which may be related to its ancient status among grouper species. A total of 22 317 protein-coding genes were predicted. This high-quality genome of the leopard coral grouper is the first genomic resource for Plectropomus and should provide a pivotal genetic foundation for further research. Phylogenetic analysis of the leopard coral grouper and 12 other fish species showed that this fish is closely related to the brown-marbled grouper. Expanded genes in the leopard coral grouper genome were mainly associated with immune response and movement ability, which may be related to the adaptive evolution of this species to its habitat. In addition, we also identified differentially expressed genes (DEGs) associated with carotenoid metabolism between red and brown-colored leopard coral groupers. These genes may play roles in skin color decision by regulating carotenoid content in these groupers.
2008, 29(6): 674-678. doi: 10.3724/SP.J.1141.2008.06674
A new species of the genus Triplophysa was discovered in underground water of a cave near Nijiao Village, Qiubei County (24°05′N，104°01′E), Yunnan, China, in 2002 and 2006. The new species, Triplophysa qiubeiensis is similar to T. anterodorsalis Cao et Zhu (1989), and can be distinguished from all the cave-dwelling Triplophysa in China by the following characters: 1) eyes highly degenerated vs. eyes normal; 2) branched dorsal–fin ray 7 vs. 8－9; 3) caudal fin forked vs. emarginate. The new species is also similar to T. macromaculeta Yang (1990) from the same river system, Nanpan Jiang, but can be distinguished from the latter the following characters: 1) eyes highly degenerated vs. eyes normal; 2) without blotches vs. with blotches; 3) caudal fin forked vs. emarginate.
Analysis on Community Structure of Zooplankton in Zhoushan Fishing Ground and Its Adjacent Area in Summer
2010, 31(1): 99-107. doi: 10.3724/SP.J.1141.2010.01099
Based on the data acquired within the Zhoushan fishing ground and its adjacent area (29°30′ −31°30′ N, 121°30′ −124°30′ E), species composition, abundance, and species diversity of zooplankton were sampled by plankton net (50 cm mouth-diameter, 145 cm net length, 0.505 mm mesh-aperture) during August 2006. The results identified 93 species (exclude Larvae) from the samples, among which Copepods were the most diverse with 50 species. According to the standard of IRI (the species with IRI above 0.02 were regarded as dominant species in this paper), there were 12 dominant species: Euchaeta concinna, Dolioletta gegenbauri, Sagitta enflata, Sagitta bedoti, Calanus sinicus, Undinula vulgaris, Canthocalanus paupe, Macruran larvae, Diphyes chamissoni, Centropages dorsispinatus, Evadne tergestina, Acartia pacifica. The stations of high abundance were mainly in the southern part and oceanic sea, and low in the northern and near shore waters. Zooplankton in the Zhoushan fishing ground and its adjacent area exhibited high in evenness (0.70), high species number and high diversity indices (4.98). By hierarchical cluster analysis and non-metric multidimensional scaling (MDS) assisted analyzing, zooplankton in Zhoushan fishing ground and its adjacent area could be formed into three assemblages joining at a distance of 17.13%. The biota-environment matching (BIOENV) analysis showed that the abundance of zooplankton was correlated closely not only to salinity, nitrate, silicate, but also to the Cd and Pb.
2008, 29(2): 219-222. doi: 10.3724/SP.J.1141.2008.02219
A new horn toad Megophrys sangzhiensis sp. nov. (Holotype: CIB 200078, adult male, SVL 54.7 mm) has been recognized based on collections from Sangzhi County, Hunan Province in China. It was previously classified as M. caudoprocta Shen, in 1994 as both had a tail projecting above the vent. This new species can be distinguished from the latter by the following characteristics: Body is smaller in size, SVL 54.7 mm; a smaller tubercle is present on the outer edge of the upper eyelids; chest and belly is yellowish with dark brown or orange red spots; vomerine ridge is slender and not dilated at its posterior region, without vomerine teeth; larger and sparse black nuptial spinules are found on the first two fingers of males with vocal sac. The new species differs from M. spinata Liu Hu, in 1973 by having a tail projecting above the vent at the ventral view, smaller and denser black nuptial spinules are found on the first two fingers in males. The size and density of the nuptial spinules on the first two fingers of the new species presents at a middle degree between those of M. caudoprocta and M. spinata.
2011, 32(1): 70-80. doi: 10.3724/SP.J.1141.2011.01070
Cancer is the second leading disease causing human death. Pre-clinical in vivo studies are essential for translating in vitro laboratory research results into the clinic. Rodents, including the mouse and rat, have been widely used for pre-clinical studies due to their small size, clear genetic backgrounds, rapid propagation, and mature transgenic technologies. However, because rodents are evolutionarily distinct from humans, many pre-clinical research results using rodent models cannot be reproduced in the clinic. Non-human primates (NHPs) may be better animal models than rodents for human cancer research because NHPs and humans share greater similarity in regards to their genetic evolution, immune system, physiology and metabolism. This article reviews the latest progress of cancer research in NHPs by focusing on the carcinogenesis of different NHPs induced by chemical and biological carcinogens. Finally, future research directions for the use of NHPs in cancer research are discussed.
2007, 28(3): 265-270.
Pseudodendrothrips mori is a serious pest to mulberry trees and its infestation affects the qualitative and quantitative characteristics of mulberry leaves consumed by silkworm. The spatial distribution of mulberry thrips within plant and orchard was assessed using Taylor's power law and Morisita's index of dispersion. The results showed that P. mori populations were localized in certain parts of the trees and fields. Distribution of thrips within plant showed that the larval instars were located on lower canopy (leaves 5-10 from top) of trees but adults preferred the upper canopy (leaves 1-5 from top). The thrips density did not vary significantly among the leaf direction inside the trees. The thrips tended to be more accumulated on the trees located in East, South and North than in Center and West of orchard. The distributions of P. mori adults and larvae on the leaves were aggregated.
Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data
2020, 41(3): 247-257. doi: 10.24272/j.issn.2095-8137.2020.022
The outbreak of COVID-19 started in mid-December 2019 in Wuhan, China. Up to 29 February 2020, SARS-CoV-2 (HCoV-19 / 2019-nCoV) had infected more than 85 000 people in the world. In this study, we used 93 complete genomes of SARS-CoV-2 from the GISAID EpiFluTM database to investigate the evolution and human-to-human transmissions of SARS-CoV-2 in the first two months of the outbreak. We constructed haplotypes of the SARS-CoV-2 genomes, performed phylogenomic analyses and estimated the potential population size changes of the virus. The date of population expansion was calculated based on the expansion parameter tau (τ) using the formula t=τ/2u. A total of 120 substitution sites with 119 codons, including 79 non-synonymous and 40 synonymous substitutions, were found in eight coding-regions in the SARS-CoV-2 genomes. Forty non-synonymous substitutions are potentially associated with virus adaptation. No combinations were detected. The 58 haplotypes (31 found in samples from China and 31 from outside China) were identified in 93 viral genomes under study and could be classified into five groups. By applying the reported bat coronavirus genome (bat-RaTG13-CoV) as the outgroup, we found that haplotypes H13 and H38 might be considered as ancestral haplotypes, and later H1 was derived from the intermediate haplotype H3. The population size of the SARS-CoV-2 was estimated to have undergone a recent expansion on 06 January 2020, and an early expansion on 08 December 2019. Furthermore, phyloepidemiologic approaches have recovered specific directions of human-to-human transmissions and the potential sources for international infected cases.
2007, 28(4): 417-422.
Generation of germline chimera is the key step in ES cell-mediated transgenesis, whereas the production of chimera, especially germline competent, is the only way to prove whether such potency is maintained. In this experiment, an established ES cell line expressing strong green fluorescence was used to produce chimera mice. After cell passage, ES cells were microinjected into KM's blastocysts. Nine EGFP-expressing chimeric mice were produced including eight male and one female. They developed into healthy adults. Results of a flow cytometry test showed the existence of GFP in several mice tissues: heart (77.96±15.78)%, spleen (84.06±3.60)%, kidney (42.49±19.79)% and marrow (52.02±18.78)%. The ES cell line proved to be important for the germ-line in contributing to the coat-color analysis of offspring(F1), produced by the cross between a female KM mouse and a male chimeric mouse.
2008, 29(2): 203-211. doi: 10.3724/SP.J.1141.2008.02203
Bird diversity was surveyed in five urban parks of Guangzhou from January 1999 to April 2000, and from July 2006 to June 2007, using a transect line method. A total of sixty-four bird species were recorded. Japanese White-eye (Zosterops japonica), Chinese Bulbul (Pycnonotus sinensis), and Black-crowned Night Heron (Nycticorax nyctinorax) were dominant species. Residents, winter visitors and summer visitors accounted for 64.1%, 26.6% and 7.8% of recorded bird species, respectively. The greatest number of species was recorded in September (31), the least was recorded in July (20) and November (20). The mean encounter rates of birds was 65±;5 ind./h (±SE), with the highest in March (98±29 ind./h) and lowest in January (35±11 ind./h). There was fluctuation, but it did not differ significantly between months (F 11,48=1.35, P= 0.226). There were a greater number of migratory species in April, September and December. Encounter rates of migratory birds significantly differed between months (F 11，48=3.098，P=0.003). Bird richness differed among the five parks and significantly and positively correlated with the park area (R=0.905, P=0.035), with S=11.02 A0.28 (S：bird species richness, A：park area). This meant that a greater number of bird species occurred in larger parks. Parks with an area of about 65 hm2 were better for avian diversity conservation and land use in Guangzhou.
The Validity of Red Knobby Newt (Tylototriton shanjing) Species Status Based on Mitochondrial Cyt b Gene
2007, 28(4): 430-436.
The delimitation between Tylototriton shanjing and T. verrucosus was not clear. Forty individuals of T. verrucosus and T. shanjing were collected from fourteen localities in Southwest China and 753?bp of partial mitochondrial Cyt b gene sequence were sequenced. Molecular phylogenetic trees of T. verrucosus group were reconstructed using neighbor-joining, maximum parsimony and Bayesian inference methods. Pairwise sequence comparisons to determine the amount of variation were performed using MEGA 3.0 software. According to the results of phylogeny analysis and Kimura 2-parameter distance, the species validities were evaluated. The results showed that: (1) the T. shanjing did not form a monophyletic group; (2) the genetic distance was low between T. shanjing and T. verrucosus, it was only 1.2% on average. Therefore, T. shanjing as a valid species is not supported and can be argued to be a synonym of T. verrucosus. According to our phylogenetic tree, the genetic divergences and geographic distribution, T. verrucosus' distribution in the Yunnan Province can be divided into three geographic groups, i.e. the Pianma group, the Middle and West Yunnan group and the Southeast Yunnan group.