Publications by authors named "Xingyu Ma"

20 Publications

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Ubiquitin-specific peptidase 39 promotes human glioma cells migration and invasion by facilitating ADAM9 mRNA maturation.

Mol Oncol 2021 Apr 2. Epub 2021 Apr 2.

Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, School of Medicine, Shenzhen University, Shenzhen, 518055, China.

Glioma cells are characterized by high migration and invasion ability, however the molecular mechanism behind both processes still remain to be investigated. Several studies have demonstrated that ubiquitin specific protease 39 (USP39) plays an oncogenic role in various cancer types. Here, we investigated the expression and function of USP39 in patients with glioma. Oncomine database analysis revealed that high USP39 expression significantly correlated with poor overall survival in patients with glioma. Knockdown of USP39 in U251 and U87 cell lines significantly inhibited their migration and invasion in vitro. Gene expression profiling of glioma cells transduced with shRNA against USP39 revealed that ADAM9, a molecule previously related to tumor cell migration and invasion, was significantly downregulated. Further on, USP39 induced ADAM9 mRNA maturation and decreased the expression of integrin β1. Additionally, overexpression of ADAM9 inhibited the migration and invasion of glioma cells caused by USP39 depletion in vitro. USP39 promoted the invasion of glioma cells in vivo and reduced the overall survival of the mice. Altogether, our data shows that USP39 induces mRNA maturation and elevates the expression of ADAM9 in glioma cells and may thus be considered as potential target for treating patients with glioma.
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http://dx.doi.org/10.1002/1878-0261.12958DOI Listing
April 2021

Novel clerodane-type diterpenoid Cintelactone A suppresses lipopolysaccharide -induced inflammation by promoting ubiquitination, proteasomal degradation of TRAF6.

Pharmacol Res 2021 Feb 19;164:105386. Epub 2020 Dec 19.

Key Laboratory of Medicinal Chemistry for Natural Resource of Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China. Electronic address:

Cellular inflammation is the underlying cause of several diseases and development of a safe and effective anti-inflammatory drug is need-of-the hour for treatment of diseases like lung inflammation. Callicarpa integerrima Champ. is a well-known herbal medicine with hemostatic and anti-inflammatory functions. However, the exact ingredient exhibiting anti-inflammatory activity in C. integerrima Champ. is largely unknown. Here, we first isolated, purified and characterized a novel clerodane-type diterpenoid Cintelactone A (CA) from C. integerrima Champ. We demonstrated that CA could significantly inhibit lipopolysaccharide (LPS)-induced pro-inflammatory cytokines and mediators production both in mouse peritoneal macrophages and THP1 cells. Consistently, CA also relieved inflammation and reduced LPS-induced lung injury in mice. We systematically elucidated the mechanism of action as well. CA interacted with Arg78 of tumor necrosis factor receptor-associated factor 6 (TRAF6) by hydrogen bonding. It further promoted the K48-linked ubiquitination and proteasomal degradation of TRAF6, and suppressed the activation of NF-κB and MAPKs signaling pathways. Collectively, our study reveals that new clerodane-type diterpenoid CA suppresses LPS-induced inflammation by promoting TRAF6 degradation, suggesting that CA as the potential therapeutic candidate for the treatment of inflammation associated diseases.
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http://dx.doi.org/10.1016/j.phrs.2020.105386DOI Listing
February 2021

Transferrin Receptor-Targeted PEG-PLA Polymeric Micelles for Chemotherapy Against Glioblastoma Multiforme.

Int J Nanomedicine 2020 11;15:6673-6688. Epub 2020 Sep 11.

Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, Shenzhen University School of Medicine, Shenzhen 518060, People's Republic of China.

Background: The safe and efficient delivery of chemotherapeutic agents is critical to glioma therapy. However, chemotherapy for glioma is extremely challenging because the blood-brain barrier (BBB) rigorously prevents drugs from reaching the tumor region.

Materials And Methods: TfR-T12 peptide-modified PEG-PLA polymer was synthesized to deliver paclitaxel (PTX) for glioma therapy. TfR was significantly expressed on brain capillary endothelial cells and glioma cells; therefore, TfR-T12 peptide-modified micelles can cross the BBB system and target glioma cells.

Results: TfR-T12-PEG-PLA/PTX polymeric micelles (TfR-T12-PMs) could be absorbed rapidly by tumor cells, and traversed effectively the BBB monolayers. TfR-T12-PMs can effectively inhibit the proliferation of U87MG cells in vitro, and TfR-T12-PMs loaded with paclitaxel presented better antiglioma effect with prolonged median survival of nude mice-bearing glioma than the unmodified PMs.

Conclusion: The TfR-T12-PMs could effectively overcome the BBB barrier and accomplish glioma-targeted drug delivery, thus validating its potential in improving the therapeutic outcome in multiforme.
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http://dx.doi.org/10.2147/IJN.S257459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7494234PMC
November 2020

Common Species Maintain a Large Root Radial Extent and a Stable Resource Use Status in Soil-Limited Environments: A Case Study in Subtropical China.

Front Plant Sci 2020 21;11:1260. Epub 2020 Aug 21.

Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China.

Coarse root systems provide a framework for water and nutrient absorption from the soil and play an important role in plant survival in harsh environments. However, the adaptions of plant roots in soil-limited environments with low water storage capacity and nutrient content needs to be better understood. The adaptation strategies of two common plant species (a deciduous tree and an evergreen shrub ) from two contrasting habitats (a shallow rocky soil and a nearby deep soil) in a karst region of subtropical China were compared and analyzed. Foliar nutrient concentrations, stoichiometry, stable carbon, and oxygen isotopes were used to determine plant nutrient and water use status across these two habitats. Six indexes, including maximum root depth, maximum root radial extent, number of major roots and secondary roots, and tapering rate and curvature, were all investigated to characterize coarse root systems. Results show that both species exhibited similar nutrient and water use status in the two habitats that had contrasting water holding capacity and available nutrient content. On the other hand, although maximum root depths of the individual plants were not deeper than 33 cm, maximum radial extents were much larger when compared to rooting depths. Specifically, the ratio of radial extent to depth in the soil-limited habitat was approximately 6 and 1.5 times higher than that in the deep-soil habitat for the tree and shrub, respectively. Additionally, especially for the tree, a larger root radial extent was further accompanied by lower root tapering rate and bending levels. Our results provided evidence that plants growing in soil-limited environments maintain a stable resource use status along with large radially extended coarse root systems in humid karst regions like southwest China.
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http://dx.doi.org/10.3389/fpls.2020.01260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7472101PMC
August 2020

The natural compound Cirsitakaoside enhances antiviral innate responses against vesicular stomatitis virus in vitro and in vivo.

Int Immunopharmacol 2020 Sep 8;86:106783. Epub 2020 Jul 8.

Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, Shenzhen University School of Medicine, Shenzhen 518060, China. Electronic address:

Cirsitakaoside, isolated and purified from the stems and leaves of Premna szemaoensis and Macaranga denticulata, is a natural compound with potential anti-inflammatory effects. However, the role of Cirsitakaoside in antiviral activity and the underlying mechanism remains largely unknown. In this study, we aimed to identify whether Cirsitakaoside has antiviral activity and investigated the underlying mechanisms. Mouse peritoneal macrophages were pretreated with Cir or DMSO, and then infected by Vesicular Stomatitis Virus (VSV) for indicated hours, Q-PCR and ELISA were used to detect the expression of interferons and pro-inflammatory cytokines, immunoblot assay were employed to investigate the involved signaling pathway in the antiviral effects of Cirsitakaoside. Furthermore, mice infected with VSV were used to investigate the antiviral activities of Cirsitakaoside in vivo. Our study demonstrated that Cirsitakaoside could promote type I IFN expression and inhibit pro-inflammatory cytokines such as IL-6 and TNF-α production in mouse peritoneal macrophages infected by VSV. Suppressive viral replication effects of Cirsitakaoside were observed on VSV-infected mouse peritoneal macrophages as well. Furthermore, Cirsitakaoside significantly increased the VSV-triggered phosphorylation of TBK1, IRF3 and reduced the phosphorylation of IκBα and p65 in mouse peritoneal macrophages. in vivo, the results showed that Cirsitakaoside-treated mice were more resistant to VSV infection by producing more IFN-β and less pro-inflammatory cytokines. Our study indicates that Cirsitakaoside is a good candidate for the treatment of viral infection and inflammation-related diseases.
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http://dx.doi.org/10.1016/j.intimp.2020.106783DOI Listing
September 2020

Nonlinear hydrodynamic instability and turbulence in pulsatile flow.

Proc Natl Acad Sci U S A 2020 05 11;117(21):11233-11239. Epub 2020 May 11.

Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria;

Pulsating flows through tubular geometries are laminar provided that velocities are moderate. This in particular is also believed to apply to cardiovascular flows where inertial forces are typically too low to sustain turbulence. On the other hand, flow instabilities and fluctuating shear stresses are held responsible for a variety of cardiovascular diseases. Here we report a nonlinear instability mechanism for pulsating pipe flow that gives rise to bursts of turbulence at low flow rates. Geometrical distortions of small, yet finite, amplitude are found to excite a state consisting of helical vortices during flow deceleration. The resulting flow pattern grows rapidly in magnitude, breaks down into turbulence, and eventually returns to laminar when the flow accelerates. This scenario causes shear stress fluctuations and flow reversal during each pulsation cycle. Such unsteady conditions can adversely affect blood vessels and have been shown to promote inflammation and dysfunction of the shear stress-sensitive endothelial cell layer.
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http://dx.doi.org/10.1073/pnas.1913716117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7260989PMC
May 2020

Mechanisms of Berberine for the Treatment of Atherosclerosis Based on Network Pharmacology.

Evid Based Complement Alternat Med 2020 19;2020:3568756. Epub 2020 Mar 19.

College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha 410208, China.

Atherosclerosis is a common metabolic disease characterized by lipid metabolic disorder. The processes of atherosclerosis include endothelial dysfunction, new endothelial layer formation, lipid sediment, foam cell formation, plaque formation, and plaque burst. Owing to the adverse effects of first-line medications, it is urgent to discover new medications to deal with atherosclerosis. Berberine is one of the most promising natural products derived from traditional Chinese medicine. However, the panoramic mechanism of berberine against atherosclerosis has not been discovered clearly. In this study, we used network pharmacology to investigate the interaction between berberine and atherosclerosis. We identified potential targets related to berberine and atherosclerosis from several databases. A total of 31 and 331 putative targets for berberine and atherosclerosis were identified, respectively. Then, we constructed berberine and atherosclerosis targets with PPI data. Berberine targets network with PPI data had 3204 nodes and 79437 edges. Atherosclerosis targets network with PPI data had 5451 nodes and 130891 edges. Furthermore, we merged the two PPI networks and obtained the core PPI network from the merged PPI network. The core PPI network had 132 nodes and 3339 edges. At last, we performed functional enrichment analyses including GO and KEGG pathway analysis in David database. GO analysis indicated that the biological processes were correlated with G1/S transition of mitotic cells cycle. KEGG pathway analysis found that the pathways directly associated with berberine against atherosclerosis were cell cycle, ubiquitin mediated proteolysis, MAPK signaling pathway, and PI3K-Akt signaling pathway. After combining the results in context with the available treatments for atherosclerosis, we considered that berberine inhibited inflammation and cell proliferation in the treatment of atherosclerosis. Our study provided a valid theoretical foundation for future research.
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http://dx.doi.org/10.1155/2020/3568756DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7106879PMC
March 2020

Androgen aggravates liver fibrosis by activation of NLRP3 inflammasome in CCl-induced liver injury mouse model.

Am J Physiol Endocrinol Metab 2020 05 17;318(5):E817-E829. Epub 2020 Mar 17.

College of Animal Science, Southwest University, Chongqing, China.

Studies have shown that there are differences between the sexes regarding to the occurrence and development of liver diseases, which may be associated with sex hormones. However, the mechanisms behind it are largely unknown. In this study, we first investigated the differences of liver injury between male and female mice, using the CCl-induced liver injury mouse model. It showed that the liver damage of male mice was much more severe than that of female mice. Both the acute injury and fibrosis of the liver were reduced when androgens were depleted by castration of male mice. The vulnerability of male liver was associated with testis endocrine and excessive activation of inflammatory response in the liver. Castrated male mice with testosterone supplementation showed aggravated liver inflammatory response and fibrosis. The activity of NOD-like receptor protein 3 (NLRP3) inflammasome was increased when testosterone supplementation was provided. However, the enhanced inflammatory response and fibrosis due to testosterone supplementation were negated by inhibiting the activation of NLRP3 using the specific small molecule inhibitor MCC950. It suggests that testosterone is a key factor that influences liver injury by regulating the NLRP3 inflammasome activation-mediated inflammatory response.
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http://dx.doi.org/10.1152/ajpendo.00427.2019DOI Listing
May 2020

Developing Single Nucleotide Polymorphisms for Identification of Cod Products by RAD-Seq.

Animals (Basel) 2020 Mar 3;10(3). Epub 2020 Mar 3.

BGI Zhenjiang Detection Co., LTD, Zhenjiang 212132, China.

The increase in the rate of seafood fraud, particularly in the expensive fishes, forces us to verify the identity of marine products. Meanwhile, the definition of cod lacks consistency at the international level, as few standards and effective application methods are capable of accurately detecting cod species. Genetic fingerprinting is important for both certifying authenticity and traceability of fish species. In this study, we developed a method that combines DNA barcoding and the restriction-site associated DNA sequencing (RAD-Seq) approach for the identification of cod products. We first obtained 6941 high-quality single nucleotide polymorphism (SNP)s from 65.6 gigabases (Gb) of RAD-Seq raw data, and two sequences that contain SNPs were finally used to successfully identify three different cod product species, which are Atlantic cod (), Greenland turbot (), and Patagonian toothfish (). This SNP-based method will help us to identify the products, which are sold under the name of "Xue Yu" (Cod) in China, and works in parallel with existing fish identification techniques to establish an efficient framework to detect and prevent fraud at all points of the seafood supply chain.
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http://dx.doi.org/10.3390/ani10030423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142540PMC
March 2020

Fire affects the taxonomic and functional composition of soil microbial communities, with cascading effects on grassland ecosystem functioning.

Glob Chang Biol 2020 02 26;26(2):431-442. Epub 2019 Oct 26.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.

Fire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies have focused on how fire affects taxonomic and functional diversities of soil microbial communities, along with changes in plant communities and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects in a grassland ecosystem 9 months after an experimental fire at the Jasper Ridge Global Change Experiment site in California, USA. Fire altered soil microbial communities considerably, with community assembly process analysis showing that environmental selection pressure was higher in burned sites. However, a small subset of highly connected taxa was able to withstand the disturbance. In addition, fire decreased the relative abundances of most functional genes associated with C degradation and N cycling, implicating a slowdown of microbial processes linked to soil C and N dynamics. In contrast, fire stimulated above- and belowground plant growth, likely enhancing plant-microbe competition for soil inorganic N, which was reduced by a factor of about 2. To synthesize those findings, we performed structural equation modeling, which showed that plants but not microbial communities were responsible for significantly higher soil respiration rates in burned sites. Together, our results demonstrate that fire 'reboots' the grassland ecosystem by differentially regulating plant and soil microbial communities, leading to significant changes in soil C and N dynamics.
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http://dx.doi.org/10.1111/gcb.14852DOI Listing
February 2020

High variations of methanogenic microorganisms drive full-scale anaerobic digestion process.

Environ Int 2019 05 7;126:543-551. Epub 2019 Mar 7.

State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 10084, China. Electronic address:

Anaerobic digestion is one of the most successful waste management strategies worldwide, wherein microorganisms play an essential role in reducing organic pollutants and producing renewable energy. However, variations of microbial community in full-scale anaerobic digesters, particularly functional groups relevant to biogas production, remain elusive. Here, we examined microbial community in a year-long monthly time series of 3 full-scale anaerobic digesters. We observed substantial diversification in community composition, with only a few abundant OTUs (e.g. Clostridiales, Anaerolineaceae and Methanosaeta) persistently present across different samples. Similarly, there were high variations in relative abundance of methanogenic archaea and methanogenic genes, which were positively correlated (r = 0.530, P < 0.001). Variations of methanogens explained 55.7% of biogas producing rates, much higher than the explanatory percentage of environmental parameters (16.4%). Hydrogenotrophic methanogens, especially abundant Methanomicrobiales taxa, were correlated with biogas production performance (r = 0.665, P < 0.001) and nearly all methanogenic genes (0.430 < r < 0.735, P < 0.012). Given that methanogenic archaea or genes are well established for methanogenesis, we conclude that high variations in methanogenic traits (e.g. taxa or genes) are responsible for biogas production variations in full-scale anaerobic digesters.
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http://dx.doi.org/10.1016/j.envint.2019.03.005DOI Listing
May 2019

Cysteine Dioxygenase Regulates the Epithelial Morphogenesis of Mammary Gland via Cysteine Sulfinic Acid.

iScience 2019 Mar 18;13:173-189. Epub 2019 Feb 18.

College of Animal Science, Southwest University, Chongqing, China. Electronic address:

Epithelial morphogenesis is a common feature in various organs and contributes to functional formation. However, the molecular mechanisms behind epithelial morphogenesis remain largely unknown. Mammary gland is an excellent model system to investigate the molecular mechanisms of epithelial morphogenesis. In this study, we found that cysteine dioxygenase (CDO), a key enzyme in cysteine oxidative metabolism, was involved in mammary epithelial morphogenesis. CDO knockout (KO) females exhibited severe defects in mammary branching morphogenesis and ductal elongation, resulting in poor lactation. CDO contributes to the luminal epithelial cell differentiation, proliferation, and apoptosis mainly through its downstream product cysteine sulfinic acid (CSA). Exogenous supplementation of CSA not only rescued the defects in CDO KO mouse but also enhanced ductal growth in wild-type mouse. It suggests that CDO regulates luminal epithelial differentiation and regeneration via CSA and consequently contributes to mammary development, which raises important implications for epithelial morphogenesis and pathogenesis of breast cancer.
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http://dx.doi.org/10.1016/j.isci.2019.02.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6406049PMC
March 2019

Microbial functional traits are sensitive indicators of mild disturbance by lamb grazing.

ISME J 2019 05 30;13(5):1370-1373. Epub 2019 Jan 30.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.

Mild disturbances are prevalent in the environment, which may not be easily notable but could have considerable ecological consequences over prolonged periods. To evaluate this, a field study was designed to examine the effects of very light-intensity lamb grazing on grassland soil microbiomes with different soil backgrounds. No significant change (P > 0.05) was observed in any vegetation and soil variables. Nonetheless, hundreds of microbial functional gene families, but not bacterial taxonomy, were significantly (P < 0.05) shifted. The relative abundances of both taxonomic markers and functional genes related to nitrifying bacteria were also changed. The observation highlighted herein, showing a high level of sensitivity with respect to functional traits (functionally categorized taxa or genes) in differentiating mild environmental disturbance, suggests that the key level at which to address microbial responses may not be "species" (by means of rRNA taxonomy), but rather at the functional gene level.
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http://dx.doi.org/10.1038/s41396-019-0354-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6474220PMC
May 2019

Long-term elevated CO shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials.

Sci Total Environ 2019 Feb 28;652:1474-1481. Epub 2018 Oct 28.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China. Electronic address:

The continuously increasing concentration of atmospheric CO has considerably altered ecosystem functioning. However, few studies have examined the long-term (i.e. over a decade) effect of elevated CO on soil microbial communities. Using 16S rRNA gene amplicons and a GeoChip microarray, we investigated soil microbial communities from a Californian annual grassland after 14 years of experimentally elevated CO (275 ppm higher than ambient). Both taxonomic and functional gene compositions of the soil microbial community were modified by elevated CO. There was decrease in relative abundance for taxa with higher ribosomal RNA operon (rrn) copy number under elevated CO, which is a functional trait that responds positively to resource availability in culture. In contrast, taxa with lower rrn copy number were increased by elevated CO. As a consequence, the abundance-weighted average rrn copy number of significantly changed OTUs declined from 2.27 at ambient CO to 2.01 at elevated CO. The nitrogen (N) fixation gene nifH and the ammonium-oxidizing gene amoA significantly decreased under elevated CO by 12.6% and 6.1%, respectively. Concomitantly, nitrifying enzyme activity decreased by 48.3% under elevated CO, albeit this change was not significant. There was also a substantial but insignificant decrease in available soil N, with both nitrate (NO) (-27.4%) and ammonium (NH) (-15.4%) declining. Further, a large number of microbial genes related to carbon (C) degradation were also affected by elevated CO, whereas those related to C fixation remained largely unchanged. The overall changes in microbial communities and soil N pools induced by long-term elevated CO suggest constrained microbial N decomposition, thereby slowing the potential maximum growth rate of the microbial community.
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http://dx.doi.org/10.1016/j.scitotenv.2018.10.353DOI Listing
February 2019

The Biogeographic Pattern of Microbial Functional Genes along an Altitudinal Gradient of the Tibetan Pasture.

Front Microbiol 2017 13;8:976. Epub 2017 Jun 13.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China.

As the highest place of the world, the Tibetan plateau is a fragile ecosystem. Given the importance of microbial communities in driving soil nutrient cycling, it is of interest to document the microbial biogeographic pattern here. We adopted a microarray-based tool named GeoChip 4.0 to investigate grassland microbial functional genes along an elevation gradient from 3200 to 3800 m above sea level open to free grazing by local herdsmen and wild animals. Interestingly, microbial functional diversities increase with elevation, so does the relative abundances of genes associated with carbon degradation, nitrogen cycling, methane production, cold shock and oxygen limitation. The range of Shannon diversities (10.27-10.58) showed considerably smaller variation than what was previously observed at ungrazed sites nearby (9.95-10.65), suggesting the important role of livestock grazing on microbial diversities. Closer examination showed that the dissimilarity of microbial community at our study sites increased with elevations, revealing an elevation-decay relationship of microbial functional genes. Both microbial functional diversity and the number of unique genes increased with elevations. Furthermore, we detected a tight linkage of greenhouse gas (CO) and relative abundances of carbon cycling genes. Our biogeographic study provides insights on microbial functional diversity and soil biogeochemical cycling in Tibetan pastures.
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http://dx.doi.org/10.3389/fmicb.2017.00976DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5468456PMC
June 2017

Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition.

Mol Ecol 2017 Aug 14;26(16):4186-4196. Epub 2017 Jul 14.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.

Aeolian soil erosion and deposition have worldwide impacts on agriculture, air quality and public health. However, ecosystem responses to soil erosion and deposition remain largely unclear in regard to microorganisms, which are the crucial drivers of biogeochemical cycles. Using integrated metagenomics technologies, we analysed microbial communities subjected to simulated soil erosion and deposition in a semiarid grassland of Inner Mongolia, China. As expected, soil total organic carbon and plant coverage were decreased by soil erosion, and soil dissolved organic carbon (DOC) was increased by soil deposition, demonstrating that field simulation was reliable. Soil microbial communities were altered (p < .039) by both soil erosion and deposition, with dramatic increase in Cyanobacteria related to increased stability in soil aggregates. amyA genes encoding α-amylases were specifically increased (p = .01) by soil deposition and positively correlated (p = .02) to DOC, which likely explained changes in DOC. Surprisingly, most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or unaltered by both erosion and deposition, probably arising from acceleration of organic matter mineralization. These divergent responses support the necessity to include microbial components in evaluating ecological consequences. Furthermore, Mantel tests showed strong, significant correlations between soil nutrients and functional structure but not taxonomic structure, demonstrating close relevance of microbial function traits to nutrient cycling.
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http://dx.doi.org/10.1111/mec.14194DOI Listing
August 2017

The complete mitochondrial genome of Eastern paradise fish ().

Mitochondrial DNA B Resour 2016 Mar 28;1(1):132-133. Epub 2016 Mar 28.

Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, China.

Eastern paradise fish, (also called ), lives in rivers of the Southeastern Asia. Although its whole genome is not available, we first obtained its complete mitochondrial genome through next-generation sequencing. The length of its mitochondrial genome is 16 568 bp with 13 protein-coding genes, two rRNA genes, 22 tRNA genes and one control region. The distribution and arrangement of genes in the mitochondrial genome are similar to those of other vertebrates. The GC content is 43.08%, similar to the reported . A phylogenetic tree was constructed to compare with nine related species by using MEGA 6.0. Through phylogenetic analysis, the relationship of species within the genus is determined.
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http://dx.doi.org/10.1080/23802359.2016.1144094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7800923PMC
March 2016

The complete mitochondrial genome of Florida gar ().

Mitochondrial DNA B Resour 2016 Mar 28;1(1):128-129. Epub 2016 Mar 28.

Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, China.

is a member of the family Lepisosteidae living in the Western Hemisphere. It is a primitive air-breathing fish with the special intermediate position of phylogeny and between elasmobranchs and teleosts. Herein, we first sequenced and assembled the complete mitochondrial genome of . The total length of mitochondrion is 16 320 bp with GC content of 42.43%, containing 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and a 564 bp control region. The accuracy of the fresh sequences was verified by phylogenetic analysis. This mitochondrial genome provides potentially important resources for addressing taxonomic issues and studying molecular evolution.
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http://dx.doi.org/10.1080/23802359.2016.1144092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7799559PMC
March 2016

Draft genome of the Chinese mitten crab, Eriocheir sinensis.

Gigascience 2016 28;5. Epub 2016 Jan 28.

Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 China.

Background: The Chinese mitten crab, Eriocheir sinensis, is one of the most studied and economically important crustaceans in China. Its transition from a swimming to a crawling method of movement during early development, anadromous migration during growth, and catadromous migration during breeding have been attractive features for research. However, knowledge of the underlying molecular mechanisms that regulate these processes is still very limited.

Findings: A total of 258.8 gigabases (Gb) of raw reads from whole-genome sequencing of the crab were generated by the Illumina HiSeq2000 platform. The final genome assembly (1.12 Gb), about 67.5 % of the estimated genome size (1.66 Gb), is composed of 17,553 scaffolds (>2 kb) with an N50 of 224 kb. We identified 14,436 genes using AUGUSTUS, of which 7,549 were shown to have significant supporting evidence using the GLEAN pipeline. This gene number is much greater than that of the horseshoe crab, and the annotation completeness, as evaluated by CEGMA, reached 66.9 %.

Conclusions: We report the first genome sequencing, assembly, and annotation of the Chinese mitten crab. The assembled draft genome will provide a valuable resource for the study of essential developmental processes and genetic determination of important traits of the Chinese mitten crab, and also for investigating crustacean evolution.
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http://dx.doi.org/10.1186/s13742-016-0112-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4730596PMC
October 2016

The Sinocyclocheilus cavefish genome provides insights into cave adaptation.

BMC Biol 2016 Jan 4;14. Epub 2016 Jan 4.

BGI-Shenzhen, Shenzhen, 518083, China.

Background: An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively.

Results: The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes.

Conclusion: As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.
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http://dx.doi.org/10.1186/s12915-015-0223-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4698820PMC
January 2016