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Li S, Liao Y, Pang Y, Dong X, Strous M, Ji G. Denitrification and dissimilatory nitrate reduction to ammonia in long-term lake sediment microcosms with iron(II). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150835. [PMID: 34627917 DOI: 10.1016/j.scitotenv.2021.150835] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/19/2021] [Accepted: 10/02/2021] [Indexed: 06/13/2023]
Abstract
Nitrate is an abundant pollutant in aquatic environments. Competition between the nitrate reduction processes, denitrification, which converts nitrate into nitrogen gas, and dissimilatory nitrate reduction to ammonia (DNRA), which converts nitrate into ammonia, decides whether an ecosystem removes or retains nitrogen. The presence of iron was previously reported to stimulate DNRA while sometimes inhibiting denitrification in in-situ studies, but long-term effect of iron(II) inputs on the competition is unknown. Here we inoculated long-term microcosms with sediments from two freshwater lakes. During 540 days of incubations, the microcosms with nitrate and Fe(II) additions of both lakes were able to sustain high nitrate reduction rates. Lepidocrocite was produced as a product of iron oxidation. We found both denitrification and DNRA were stimulated by nitrate and iron in the absence of external organic carbon addition. Phylogenetic analysis of denitrification genes, nirK and nirS, and DNRA genes, nirB and nrfA, was performed with metagenomic sequencing results. Enrichment was shown for reported Fe(II)-dependent nitrate reducers associated with nirS and nirB. Most of these bacteria are affiliated with Betaproteobacteria. From 16S rRNA gene analysis, Betaproteobacteria was enriched as well. In parallel, heterotrophic denitrifiers and methanotrophic DNRA archaea increased in abundance. Our results suggested heterotrophic and Fe(II)-dependent nitrate reducers both contributed to denitrification and DNRA in long-term microcosm incubations provided with iron.
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Li S, Pang Y, Ji G. Increase of N 2O production during nitrate reduction after long-term sulfide addition in lake sediment microcosms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 291:118231. [PMID: 34571071 DOI: 10.1016/j.envpol.2021.118231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/19/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Microbial denitrification is a main source of nitrous oxide (N2O) emissions which have strong greenhouse effect and destroy stratospheric ozone. Though the importance of sulfide driven chemoautotrophic denitrification has been recognized, its contribution to N2O emissions in nature remains elusive. We built up long-term sulfide-added microcosms with sediments from two freshwater lakes. Chemistry analysis confirmed sulfide could drive nitrate respiration in long term. N2O accumulated to over 1.5% of nitrate load in both microcosms after long-term sulfide addition, which was up to 12.9 times higher than N2O accumulation without sulfide addition. Metagenomes were extracted and sequenced during microcosm incubations. 16 S rRNA genes of Thiobacillus and Defluviimonas were gradually enriched. The nitric oxide reductase with c-type cytochromes as electron donors (cNorB) increased in abundance, while the nitric oxide reductase receiving electrons from quinols (qNorB) decreased in abundance. cnorB genes similar to Thiobacillus were enriched in both microcosms. In parallel, enrichment was observed for enzymes involved in sulfur oxidation, which supplied electrons to nitrate respiration, and enzymes involved in Calvin Cycle, which sustained autotrophic cell growth, implying the coupling relationship between carbon, nitrogen and sulfur cycling processes. Our results suggested sulfur pollution considerably increased N2O emissions in natural environments.
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Dang Z, Zhu X, Wang L, Ji G. Titanium dioxide catalytic hydrothermal liquefaction to treat oily sludge: As hydrogen production catalyst. CHEMICAL ENGINEERING JOURNAL ADVANCES 2021. [DOI: 10.1016/j.ceja.2021.100139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Liao Y, Li S, Zhu X, Dang Z, Tang S, Ji G. The promotion and inhibition effect of graphene oxide on the process of microbial denitrification at low temperature. BIORESOURCE TECHNOLOGY 2021; 340:125636. [PMID: 34315127 DOI: 10.1016/j.biortech.2021.125636] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/15/2021] [Accepted: 07/18/2021] [Indexed: 06/13/2023]
Abstract
This study found that graphene oxide (GO) improved microbial denitrification at low temperatures (~12 °C), and the optimal concentration was 10 mg/L as the removal rate of NO3-N increased by 17%. At the optimal concentration, GO improved the electron transport system activity of the microbes and enhanced the activity of nitrate reductase and nitrite reductase while exhibited low microbial toxicity. The addition of GO increased the content of tightly bound extracellular polymeric substances (EPS). The results of fluorescence spectrometer indicated that GO accelerated the renewal of bound EPS (B-EPS). Fourier Transform infrared spectroscopy (FTIR) results showed that GO affected the secondary structure of the protein in B-EPS, making B-EPS more hydrophobic and promoting microbial aggregation. B-EPS affected by GO can promote the electron transfer process of microorganisms. However, high concentration (>25 mg/L) of GO may inhibit denitrification by competing for electrons, which was not conducive to denitrification thermodynamically.
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Xue QQ, Huang Y, Zuo SY, Zheng Q, Ji G, Zhou XY, Wu CY, Li Y. [Clinicopathological features and molecular genetic changes of lung salivary gland-type clear cell carcinoma]. ZHONGHUA BING LI XUE ZA ZHI = CHINESE JOURNAL OF PATHOLOGY 2021; 50:728-733. [PMID: 34405605 DOI: 10.3760/cma.j.cn112151-20210129-00129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the clinicopathological features, immunophenotype, differential diagnosis, molecular genetic changes and prognosis of salivary gland-type clear cell carcinoma (CCC) of the lung. Methods: Eight cases of salivary gland-type CCC of the lung diagnosed at Fudan University Shanghai Cancer Center and Shanghai Pulmonary Hospital, China from March 2017 to December 2020 were retrieved and analyzed. The pathological sections of these cases were studied using immunohistochemical staining, fluorescence in situ hybridization (FISH), and RNA-seq fusion gene detection based on next generation sequencing technique. The patients were followed up and the relevant literature was reviewed. Results: The 8 patients included 3 males and 5 females, with age ranging from 43 to 64 years (average, 58 years). All patients underwent radical lobectomy and lymph node dissection, while only one had lymph node metastases. The eight patients were followed up for 6 to 45 months, and were all recurrence-free. Histopathologically, the tumor was mainly composed of eosinophilic and clear cells arranged in trabecular, ribbon and nest patterns. Hyalinization was often observed in the stroma around the nest. Immunohistochemical staining showed that 8/8 cases were positive for EMA and CK7; 5/8 cases were positive for p63 and p40; 4/8 cases were positive for SOX10; and the cases were all negative for S-100, SMA and calponin. EWSR1 gene fusion was detected in all cases by FISH. RNA-seq fusion gene was detected in 6 cases based on next generation sequencing. The EWSR1-ATF1 gene fusion was detected in 5 cases, among which one case also had the ATF1-SPTLC2 gene fusion. All 5 cases with EWSR1-ATF1 gene fusion showed that EWSR1 exon 12/13 fused with ATF1 exon 3. And EWSR1-CREM gene fusion was detected in one case. Conclusions: Salivary gland-type CCC of the lung is an extremely rare primary lung tumor arising from the bronchial mucosa. The diagnosis and differential diagnosis of this tumor depend on classic histomorphology, especially the auxiliary detection of EWSR1 fusion gene. The primary treatment choice of this tumor is complete surgical resection. Lymph node metastases may occur, but the overall prognosis is good.
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Pang Y, Wang J, Li S, Ji G. Long-term sulfide input enhances chemoautotrophic denitrification rather than DNRA in freshwater lake sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 270:116201. [PMID: 33321438 DOI: 10.1016/j.envpol.2020.116201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/09/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
Partitioning between nitrate reduction pathways, denitrification and dissimilatory nitrate reduction to ammonium (DNRA) determines the fate of nitrate removal and thus it is of great ecological importance. Sulfide (S2-) is a potentially important factor that influences the role of denitrification and DNRA. However, information on the impact of microbial mechanisms for S2- on the partitioning of nitrate reduction pathways in freshwater environments is still lacking. This study investigated the effects of long-term (108 d) S2- addition on nitrate reduction pathways and microbial communities in the sediments of two different freshwater lakes. The results show that the increasing S2- addition enhanced the coupling of S2- oxidation with denitrification instead of DNRA. The sulfide-oxidizing denitrifier, Thiobacillus, was significantly enriched in the incubations of both lake samples with S2- addition, which indicates that it may be the key genus driving sulfide-oxidizing denitrification in the lake sediments. During S2- incubation of the Hongze Lake sample, which had lower inherent organic carbon (C) and sulfate (SO42-), Thiobacillus was more enriched and played a dominant role in the microbial community; while during that of the Nansi Lake sample, which had higher inherent organic C and SO42-, Thiobacillus was less enriched, but increasing abundances of sulfate reducing bacteria (Desulfomicrobium, Desulfatitalea and Geothermobacter) were observed. Moreover, sulfide-oxidizing denitrifiers and sulfate reducers were enriched in the Nansi Lake control treatment without external S2- input, which suggests that internal sulfate release may promote the cooperation between sulfide-oxidizing denitrifiers and sulfate reducers. This study highlights the importance of sulfide-driven denitrification and the close coupling between the N and S cycles in freshwater environments, which are factors that have often been overlooked.
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Tang S, Liao Y, Xu Y, Dang Z, Zhu X, Ji G. Microbial coupling mechanisms of nitrogen removal in constructed wetlands: A review. BIORESOURCE TECHNOLOGY 2020; 314:123759. [PMID: 32654809 DOI: 10.1016/j.biortech.2020.123759] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
Nitrogen removal through microorganisms is the most important pathway in constructed wetlands (CWs). In this review, we summarize the microbial coupling mechanisms of nitrogen removal, which are the common methods of nitrogen transformation. The electron pathways are shortened and consumption of oxygen and energy is reduced during the coupling of nitrogen transformation functional microorganisms. The highly efficient nitrogen removal mechanisms are cultivated from the design conditions in CWs, such as intermittent aeration and tidal flow. The coupling of microorganisms and substrates enhances nitrogen removal mainly by supplying electrons, and plants affect nitrogen transformation functional microorganisms by the release of oxygen and exudates from root systems as well as providing carriers for microbial attachment. In addition, inorganic elements such as Fe, S and H act as electron donors to drive the autotrophic denitrification process in CWs.
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He X, Ji G. Responses of AOA and AOB activity and DNA/cDNA community structure to allylthiourea exposure in the water level fluctuation zone soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:15233-15244. [PMID: 32072408 DOI: 10.1007/s11356-020-07952-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 01/30/2020] [Indexed: 06/10/2023]
Abstract
Ammonia oxidation is mainly performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Allylthiourea (ATU) has been found to specifically inhibit ammonia oxidation. However, the effect of ATU on AOA and AOB transcription has been infrequently studied. In the present study, we examined the responses of AOA and AOB activity and DNA/cDNA community structure to ATU exposure. The ammonia oxidation activity in the 100-mg/L ATU group was 4.3% of that in the control group after 7 days. When exposed to ATU, the gene abundance of AOA was favored compared with that of AOB, and there were no statistically significant differences in the abundance of AOB amoA in DNA and cDNA between the two groups. Compared with the control group, the gene abundance of AOA significantly increased by 5.23 times, while the transcription of AOA significantly decreased by 0.70 times. Moreover, the transcriptional ratio of AOA in the ATU group was only 0.05 times as high as that in the control group. ATU selectively affected AOB and completely inhibited Nitrosomonas europaea and Bacterium amoA.22.HaldeII.kultur at the genetic level. Under ATU exposure, all AOA clusters were transcribed, but three AOB clusters were not transcribed. Our results indicated that the ammonia oxidation potential of the soil of water level fluctuation areas, based on ATU inhibition, was associated mainly with AOA amoA gene abundance and AOB community shifts in DNA and cDNA.
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Wang C, Tang S, He X, Ji G. The abundance and community structure of active ammonia-oxidizing archaea and ammonia-oxidizing bacteria shape their activities and contributions in coastal wetlands. WATER RESEARCH 2020; 171:115464. [PMID: 31926374 DOI: 10.1016/j.watres.2019.115464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/19/2019] [Accepted: 12/31/2019] [Indexed: 06/10/2023]
Abstract
Aerobic ammonia oxidation, an important part of the global nitrogen cycle, is thought to be jointly driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in coastal wetlands. However, the activities and contributions of AOA and AOB in coastal wetlands have remained largely unknown. Here, we investigated the oxidation capability of AOA and AOB in four types of typical coastal wetlands (paddy, estuary, shallow and reed wetland) in the Bohai region in China using DNA-based stable-isotope probing (DNA-SIP), quantitative PCR and high-throughput sequencing techniques. We found that the community structure of AOB varied substantially, and the AOA structure was more stable across different coastal wetlands. The rate of AOA was 0.12, 0.84, 0.45 and 0.93 μg N g-1 soil d-1 in paddy, estuary, shallow and reed wetlands, and the rate of AOB was 5.61, 10.72, 0.74 and 1.16 μg N g-1 soil d-1, respectively. We found that the contribution of AOA gradually increased from paddy to estuary to shallow wetland and finally to reed wetland, with values of 2.03%, 7.25%, 37.53% and 44.51%, respectively. Our results provide new insight into the mechanisms of the differences in activities and the contributions of AOA and AOB in different coastal wetlands, and our findings may contribute to further understanding of the global nitrogen cycle.
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Zhang Y, Ji G, Wu T, Qiu J. Urbanization significantly impacts the connectivity of soil microbes involved in nitrogen dynamics at a watershed scale. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113708. [PMID: 31818616 DOI: 10.1016/j.envpol.2019.113708] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/23/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
As one of the most dominant ecosystems of urban green space, turfgrasses provide a wide range of ecosystem services. However, little is known about the interactions of microbial communities in turfgrass soils and how these interactions respond to expanding development of impervious surfaces during watershed urbanization. In this study, we analyzed bacterial communities and their co-occurrence patterns in turfgrass soils along an urbanization gradient as measured by the proportion of impervious surfaces in Jiulong River watershed in Fujian, China. Results show that the diversity and network size of bacterial communities negatively associated with impervious surfaces. The bacterial communities showed non-random co-occurrence patterns, with more intra-module connections observed for urbanized networks. The co-occurrence network with distinct modules of soil samples with contrasting land cover imperviousness suggested different functional organizations with altered microbial nitrogen processes. Structural equation modelling revealed that watershed impervious surfaces had indirect impacts on microbial connectivity by altering soil properties, including pH, temperature, moisture, C/N and nitrate (NO3-). Moreover, impervious surfaces affected microbial connectivity far more than human population density. Our study highlights the significance of human disturbances in affecting microbial interactions and assemblies in turfgrass ecosystems through impervious surfaces and provides benefits for sustainable urban planning and management at a watershed scale.
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Pang Y, Ji G. Biotic factors drive distinct DNRA potential rates and contributions in typical Chinese shallow lake sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:112903. [PMID: 31362259 DOI: 10.1016/j.envpol.2019.07.071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/27/2019] [Accepted: 07/13/2019] [Indexed: 06/10/2023]
Abstract
Dissimilatory nitrate reduction to ammonia (DNRA) is an important nitrate reduction pathway in lake sediments; however, little is known about the biotic factors driving the DNRA potential rates and contributions to the fate of nitrate. This study reports the first investigation of DNRA potential rates and contributions in lake sediments linked to DNRA community structures. The results of 15N isotope-tracing incubation experiments showed that 12 lakes had distinct DNRA potentials, which could be clustered into 2 groups, one with higher DNRA potentials (rates varied from 2.7 to 5.0 nmol N g-1 h-1 and contributions varied from 27.5% to 35.4%) and another with lower potentials (rates varied from 0.6 to 2.3 nmol N g-1 h-1 and contributions varied from 8.1% to 22.8%). Sediment C/N and the abundance of the nrfA gene were the key abiotic and biotic factors accounting for the distinct DNRA potential rates, respectively. A high-throughput sequencing analysis of the nrfA gene revealed that the sediment C/N could also affect the DNRA potential rates by altering the ecological patterns of the DNRA community composition. In addition, the interactions between the DNRA community and the denitrifying community were found to be obviously different in the two groups. In the higher DNRA potential group, the DNRA community mainly interacted with heterotrophic denitrifiers, while in the lower DNRA potential group, both heterotrophic and sulfur-driven autotrophic denitrifiers might cooperate with the DNRA community. The present study highlighted the role of the sulfur-driven nitrate reduction pathway in C-limited sediments, which has always been overlooked in freshwater environments, and gave new insights into the molecular mechanism influencing the fate of nitrate.
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Liu S, Li LZ, Chen CJ, Ji G, Luo BJ, Tian T, Sun C, Jiao HB. [Three patients with large area burns complicated by acute acalculous cholecystitis]. ZHONGHUA SHAO SHANG ZA ZHI = ZHONGHUA SHAOSHANG ZAZHI = CHINESE JOURNAL OF BURNS 2019; 35:543-545. [PMID: 31357827 DOI: 10.3760/cma.j.issn.1009-2587.2019.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
From April 2017 to April 2018, three male patients aged 46-71 years with large area burns were treated in our hospital. Acute acalculous cholecystitis (AAC) symptoms of the patients began to appear 15-81 days after injury. AAC was diagnosed 24-81 days after injury. Ultrasound-guided percutaneous transhepatic cholecystostomy was performed 26-82 days after injury. The symptoms subsided in 2 patients, and cholecystectomy was performed in 1 patient with gallbladder perforation 94 days after injury. The patients were cured and discharged 41-118 days after injury. No recurrence of cholecystitis occurred during 8-9 months of follow-up after discharge.
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Ji G, Xu R, Niu Y, Li N, Ivashkiv L, Bostrom MPG, Greenblatt MB, Yang X. Vascular endothelial growth factor pathway promotes osseointegration and CD31 hiEMCN hi endothelium expansion in a mouse tibial implant model: an animal study. Bone Joint J 2019; 101-B:108-114. [PMID: 31256654 DOI: 10.1302/0301-620x.101b7.bjj-2018-1473.r1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AIMS It is increasingly appreciated that coordinated regulation of angiogenesis and osteogenesis is needed for bone formation. How this regulation is achieved during peri-implant bone healing, such as osseointegration, is largely unclear. This study examined the relationship between angiogenesis and osteogenesis in a unique model of osseointegration of a mouse tibial implant by pharmacologically blocking the vascular endothelial growth factor (VEGF) pathway. MATERIALS AND METHODS An implant was inserted into the right tibia of 16-week-old female C57BL/6 mice (n = 38). Mice received anti-VEGF receptor-1 (VEGFR-1) antibody (25 mg/kg) and VEGF receptor-2 (VEGFR-2) antibody (25 mg/kg; n = 19) or an isotype control antibody (n = 19). Flow cytometric (n = 4/group) and immunofluorescent (n = 3/group) analyses were performed at two weeks post-implantation to detect the distribution and density of CD31hiEMCNhi endothelium. RNA sequencing analysis was performed using sorted CD31hiEMCNhi endothelial cells (n = 2/group). Osteoblast lineage cells expressing osterix (OSX) and osteopontin (OPN) were also detected with immunofluorescence. Mechanical pull-out testing (n = 12/group) was used at four weeks post-implantation to determine the strength of the bone-implant interface. After pull-out testing, the tissue attached to the implant surface was harvested. Whole mount immunofluorescent staining of OSX and OPN was performed to determine the amount of osteoblast lineage cells. RESULTS Flow cytometry revealed that anti-VEGFR treatment decreased CD31hiEMCNhi vascular endothelium in the peri-implant bone versus controls at two weeks post-implantation. This was confirmed by the decrease of CD31 and endomucin (EMCN) double-positive cells detected with immunofluorescence. In addition, treated mice had more OPN-positive cells in both peri-implant bone and tissue on the implant surface at two weeks and four weeks, respectively. More OSX-positive cells were present in peri-implant bone at two weeks. More importantly, anti-VEGFR treatment decreased the maximum load of pull-out testing compared with the control. CONCLUSION VEGF pathway controls the coupling of angiogenesis and osteogenesis in orthopaedic implant osseointegration by affecting the formation of CD31hiEMCNhi endothelium. Cite this article: Bone Joint J 2019;101-B(7 Supple C):108-114.
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Xu Y, Liu T, Zhu X, Ji G. Quantitative analysis of genetic associations in the biodegradative pathway of PAHs in wetland sediments of the Bohai coast region. CHEMOSPHERE 2019; 218:282-291. [PMID: 30472612 DOI: 10.1016/j.chemosphere.2018.11.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/08/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
The present study characterized the distribution and sources of polycyclic aromatic hydrocarbons (PAHs) in 57 sediment cores collected from estuary and tidal flat wetlands in the Bohai coast region and investigated the molecular degradation mechanism of PAHs. The results showed that the PAH concentrations in estuary sediments were significantly higher than in tidal flat sediments. PAH patterns and pollutant sources were more complicated in estuary sediments. Quantitative response relationships showed that in estuary sediments, the key factors affecting PAH degradation changed from initial dioxygenase genes and C23O to salicylate hydroxylase genes and C23O with an increase in the PAH ring number. In contrast, for tidal flat sediments, the initial dioxygenase genes remained the key factors (nidA and nahAc/nagAc, except only nidA for 5-ring PAHs) related to PAHs with different ring numbers. Non-metric multidimensional scaling (NMDS) analysis revealed that the lower catechol dioxygenase pathway coupled with the upper pyrene dioxygenase pathway. The total polycyclic aromatic hydrocarbon (TPAH) level across the Bohai coast region was most affected by catechol dioxygenation (catA + C23O). Catechol dioxygenation was directly affected by naphthalene dioxygenation/nahG ((nahAc + nagAc)/nahG), indicating that the interaction within the upper pathway coupled with the lower pathway. In addition, TOC had direct positive effects on catechol dioxygenation and nidA. This study improves our understanding of the biodegradative pathway of PAHs with different ring numbers and the response of PAHs to biotic and abiotic factors.
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Mazurenko A, Blatt S, Huber F, Parsons MF, Chiu CS, Ji G, Greif D, Greiner M. Implementation of a stable, high-power optical lattice for quantum gas microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:033101. [PMID: 30927819 DOI: 10.1063/1.5066623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 02/08/2019] [Indexed: 06/09/2023]
Abstract
We describe the design and implementation of a stable high-power 1064 nm laser system to generate optical lattices for experiments with ultracold quantum gases. The system is based on a low-noise laser amplified by an array of four heavily modified, high-power fiber amplifiers. The beam intensity is stabilized and controlled with a nonlinear feedback loop. Using real-time monitoring of the resulting optical lattice, we find the stability of the lattice site positions to be well below the lattice spacing over the course of hours. The position of the harmonic trap produced by the Gaussian envelope of the lattice beams is stable to about one lattice spacing and the long-term (six-month) relative root-mean-square stability of the lattice spacing itself is 0.5%.
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Wang L, Ji G, Huang S. Contribution of the Kodama and 4S pathways to the dibenzothiophene biodegradation in different coastal wetlands under different C/N ratios. J Environ Sci (China) 2019; 76:217-226. [PMID: 30528012 DOI: 10.1016/j.jes.2018.04.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/23/2018] [Accepted: 04/28/2018] [Indexed: 06/09/2023]
Abstract
Dibenzothiophene (DBT) degradation mechanisms and the transformation of pathways during the incubation of three types of coastal sediments with C/N ratios ranging from 1 to 9 were investigated. The DBT degradation efficiencies were clearly improved with increasing C/N ratio in reed wetland sediments, tidal wetlands sediments and estuary wetland sediments. The quantitative response relationships between DBT degradation rates and related functional genes demonstrate that the Kodama pathway-related gene groups were dominant factors at low C/N ratios, while the 4S-related gene groups mainly determined the degradation rate when the C/N ratio was up to 5. Network analysis also shows that the pathway shifts from the Kodama pathway to the 4S pathway occurred through changes in the connections between functional genomes and rates. Furthermore, there were competition and collaboration between the Kodama and 4S pathways. The 4S pathway-related bacteria were more active in estuary wetland sediments compared with reed wetland sediments and tidal wetland sediments. The higher degradation efficiency in estuary wetland sediments may indicate the greater participation of the 4S pathway in the DBT biodegradation reaction. And the effects of ring cleavage of Kodama pathway caused more complete metabolizing of DBT.
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Luo Z, Li S, Hou K, Ji G. Spatial and seasonal bacterioplankton community dynamics in the main channel of the Middle Route of South-to-North Water Diversion Project. Res Microbiol 2019; 170:24-34. [DOI: 10.1016/j.resmic.2018.08.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/30/2018] [Accepted: 08/22/2018] [Indexed: 12/01/2022]
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Zhang Y, Ji G, Wang C, Zhang X, Xu M. Importance of denitrification driven by the relative abundances of microbial communities in coastal wetlands. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 244:47-54. [PMID: 30321711 DOI: 10.1016/j.envpol.2018.10.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/16/2018] [Accepted: 10/02/2018] [Indexed: 06/08/2023]
Abstract
Excessive nitrogen (N) loadings from human activities have led to increased eutrophication and associated water quality impacts in China's coastal wetlands. Denitrification accounts for significant reduction of inorganic N to nitrous oxide (N2O) or dinitrogen gas (N2), and thereby curtails harmful effects of N pollution in coastal and marine ecosystems. However, the molecular drivers and limiting steps of denitrification in coastal wetlands are not well understood. Here, we quantified the abundances of functional genes involved in N cycling and determined denitrification rates using 15N paring technique in the coastal wetland sediments of Bohai Economic Rim in eastern China. Denitrification accounting for 80.7 ± 12.6% of N removal was the dominant pathway for N removal in the coastal wetlands. In comparison, anaerobic ammonium oxidation (ANAMMOX) removed up to 36.9 ± 7.3% of inorganic N. Structural equation modeling analysis indicated that the effects of ammonium on denitrification potential were mainly mediated by the relative abundances of nosZ/nirS, nirS/(narG + napA) and amoA/nirK. Denitrification was limited by the relative strength of two steps, namely N2O reduction to N2 and nitrite (NO2-) reduction to nitric oxide (NO). Our results suggest that the relative abundances of functional genes which are more stable than sediment chemical compounds in the context of environmental changes are indictive of denitrification potential in coastal wetlands.
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Zhang Y, Ji G. Quantitative responses of potential nitrification and denitrification rates to the size of microbial communities in rice paddy soils. CHEMOSPHERE 2018; 211:970-977. [PMID: 30119028 DOI: 10.1016/j.chemosphere.2018.08.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 06/08/2023]
Abstract
Nitrification and denitrification are important to nitrogen balance in agricultural ecosystems. However, the molecular drivers and limiting steps for these microbial processes in rice paddy soils are not well understood. Here, we assessed soil properties and abundances of functional genes affiliated with nitrification (amoA and nxrA), denitrification (nirS, nirK and nosZ), nitrate reduction (narG and napA) processes, and measured potential nitrification and denitrification rates (PNRs and PDRs) at 15 sites in Xiamen, China. The soil properties imposed indirect impacts on the potential rates by mediating the relative abundances of microbial communities. No significant relationships between the size of microbial communities and the potential rates were observed. Instead, we found the variables that best explained the variations in the PNRs and PDRs were AOB/nirS and (nirK + nirS)/nosZ, respectively. The PNRs were mainly limited by the relative strength of two steps, namely bacterial ammonium oxidation and nitrite into nitric oxide reduction, whereas the PDRs were mainly limited by the relative strength of the second and last denitrification steps. These results indicated that the dynamics of microbial communities based on the relative gene abundances are valuable in integrating fluctuations in soil physicochemical properties and are indictive of potential rates in paddy soils. Results of this study contribute to our quantitative understanding of the relative importance of soil physicochemical and biological factors in driving microbial potential in paddy soils.
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Ji G. A new novel gene ABCC5 promotes castration-resistant prostate cancer progression through ERK carcinogenic pathway. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy434.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Li S, Luo Z, Ji G. Seasonal function succession and biogeographic zonation of assimilatory and dissimilatory nitrate-reducing bacterioplankton. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:1518-1525. [PMID: 29801245 DOI: 10.1016/j.scitotenv.2018.05.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 06/08/2023]
Abstract
The dominance of different nitrate-reducing pathways determines nitrogen cycling patterns. Denitrification (DNF) has been widely studied, but assimilatory nitrate reduction (ANR) and dissimilatory nitrate reduction to ammonium (DNRA) have received much less attention. Their ecological patterns and responsible microbes are poorly understood. Here, we studied the structure and function succession of the three functional groups in the middle route of the South-to-North Water Diversion Project, which is a 1230 km canal spanning 8 degrees of latitude. The results reflected a nitrogen-removing pattern dominated by DNF in the summer and a nitrogen-retaining pattern dominated by ANR and DNRA in the winter. Stenotrophomonas, a typical denitrifier, was the keystone species in the summer and contributed to N2O production. Clostridium, a genus able to conduct ANR and DNRA, was the keystone species in the winter. Notably, a significant zonation pattern was discovered. According to the community structure, the system could be separated into two biogeographic zones, and the Yellow River (about latitude 35°N) is an important cut-off line. This bacterial biogeography followed different water characteristics and ecological processes. ANR was found to be an important process and seasonally transformed its habitat from the northern zone to the southern zone. DNRA bacteria were acclimated to the northern zone and favored at this region in both seasons. The generation of N2O, a strong greenhouse gas, also exhibited this zonation pattern. This is the first study to consider assimilatory and dissimilatory nitrate reducers together at a molecular level, and provides new insights into the underlying patterns of a nitrate-reducing bacterioplankton community.
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Li XQ, Wang X, Han YL, Ji G, Chen ZH, Zhang J, Zhu JP, Duan JX, He YJ, Yang XM, Liu WJ. [Effects of anteriolateral thigh perforator flap and fascia lata transplantation in combination with computed tomography angiography on repair of electrical burn wounds of head with skull exposure and necrosis]. ZHONGHUA SHAO SHANG ZA ZHI = ZHONGHUA SHAOSHANG ZAZHI = CHINESE JOURNAL OF BURNS 2018; 34:283-287. [PMID: 29804427 DOI: 10.3760/cma.j.issn.1009-2587.2018.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To explore the effects of anteriolateral thigh perforator flap and fascia lata transplantation in combination with computed tomography angiography (CTA) on repair of electrical burn wounds of head with skull exposure and necrosis. Methods: Seven patients with head electrical burns accompanied by skull exposure and necrosis were admitted to our burn center from March 2016 to December 2017. Head CTA was performed before the operation. The diameters of the facial artery and vein or the superficial temporal artery and vein were measured, and their locations were marked on the body surface. Preoperative CTA for flap donor sites in lower extremities were also performed to track the descending branch of the lateral circumflex femoral artery with the similar diameter as the recipient vessels on the head, and their locations were marked on the body surface. Routine wound debridement and skull drilling were performed successively. The size of the wounds after debridement ranged from 12 cm×8 cm to 20 cm×12 cm, and the areas of skull exposure ranged from 8 cm×6 cm to 15 cm×10 cm. Anteriolateral thigh perforator flaps with areas from 13 cm×9 cm to 21 cm×13 cm containing 5-10 cm long vascular pedicles were designed and dissected accordingly. The fascia lata under the flap with area from 5 cm×2 cm to 10 cm×3 cm was dissected according to the length of vascular pedicle. The fascia lata was transplanted to cover the exposed skull, and the anteriolateral thigh perforator flap was transplanted afterwards. The descending branch of the lateral circumflex femoral artery and its accompanying vein of the flap were anastomosed with superficial temporal artery and vein or facial artery and vein before the suture of flap. The flap donor sites were covered by intermediate split-thickness skin graft collected from contralateral thigh or abdomen. Results: The descending branch of the lateral circumflex femoral artery and its accompanying vein were anastomosed with superficial temporal artery and vein in six patients, while those with facial artery and vein in one patient. All the flaps survived after the operation, and no vascular crisis was observed. Wound healing was satisfactory. One patient was lost to follow up. Six patients were followed up for 6 to 10 months. The patients were bald in the head operation area with acceptable appearance. No psychiatric symptom such as headache or epileptic seizure was reported. The flap donor sites were normal in appearance. The muscle strength of the lower extremities all reached grade V. The sensation and movement of the lower extremities were normal. Conclusions: Anterolateral thigh perforator flap with fascia lata transplantation can effectively repair electrical burn wounds of head with skull exposure and necrosis. The fascia lata can be used to protect the vascular pedicle of flaps, which is beneficial to the survival of the flap. Preoperative head and lower extremities CTA can provide reference for intraoperative vascular exploration in donor site and recipient area, so as to shorten operation time.
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Ji G, Song G. Rapidly decreasing level of prostate-specific antigen during initial androgen deprivation therapy is a risk factor for early progression to castration-resistant prostate cancer. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx662.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Wang W, Ji G, Chen Y, Wang J, Sun J, Tang G, Xie Z, Zhao H, Liu G, Tan S, Chen G, Xue H. Changes in DNA Methylation of Glucocorticoid-Induced Tumor Necrosis Factor Receptor and Its Ligand in Liver Transplantation. Transplant Proc 2017; 49:1824-1833. [PMID: 28923633 DOI: 10.1016/j.transproceed.2017.06.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 05/31/2017] [Accepted: 06/16/2017] [Indexed: 10/18/2022]
Abstract
Liver transplantation (LT) is the criterion standard of care in patients with end-stage liver disease and those with tumors of hepatic origin in the setting of liver dysfunction. Chronic immune rejection of the liver transplant can lead to bad prognosis for patients. Glucocorticoid-induced tumor necrosis factor receptor (GITR) play a key role in dominant immunologic self-tolerance maintained by CD25+/CD4+ regulatory T cells. Here, we investigated the DNA methylation variations of GITR and GITR ligand (GITRL) using pyrosequencing by analyzing blood DNA samples of patients after LT. Our results showed that the methylation level of certain CpGs, such as CpG_13, in GITRL was significantly reduced after LT. Furthermore, we found that the GITRL methylation statuses of cohorts with no chronic immune rejection were significantly lower compared with cohorts with chronic immune rejection after LT treatment. However, the methylation statuses of GITR were less varied. Using linear regression analysis, we further found that factors such as upper gastrointestinal hemorrhage, splenectomy, and creatinine might affect DNA methylation patterns in chronic immune rejection cohorts. These findings provide novel insights into the pivotal role of GITRL as a potential molecular biomarker for the triage of liver transplantation.
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Zhao L, Ji G, Le X, Luo Z, Wang C, Feng M, Xu L, Zhang Y, Lau WB, Lau B, Yang Y, Lei L, Yang H, Xuan Y, Chen Y, Deng X, Yi T, Yao S, Zhao X, Wei Y, Zhou S. An integrated analysis identifies STAT4 as a key regulator of ovarian cancer metastasis. Oncogene 2017; 36:3384-3396. [PMID: 28114283 DOI: 10.1038/onc.2016.487] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 10/26/2016] [Accepted: 11/21/2016] [Indexed: 02/05/2023]
Abstract
Epithelial ovarian cancer (EOC) is one of the most common gynecological cancers, with diagnosis often at a late stage. Metastasis is a major cause of death in patients with EOC, but the underlying molecular mechanisms remain obscure. Here, we utilized an integrated approach to find potential key transcription factors involved in ovarian cancer metastasis and identified STAT4 as a critical player in ovarian cancer metastasis. We found that activated STAT4 was overexpressed in epithelial cells of ovarian cancer and STAT4 overexpression was associated with poor outcome of ovarian cancer patients, which promoted metastasis of ovarian cancer in both in vivo and in vitro. Although STAT4 mediated EOC metastasis via inducing epithelial-to-mesenchymal transition (EMT) of ovarian cancer cells in vivo, STAT4 failed to induce EMT directly in vitro, suggesting that STAT4 might mediate EMT process via cancer-stroma interactions. Further functional analysis revealed that STAT4 overexpression induced normal omental fibroblasts and adipose- and bone marrow-derived mesenchymal stem cells to obtain cancer-associated fibroblasts (CAF)-like features via induction of tumor-derived Wnt7a. Reciprocally, increased production of CAF-induced CXCL12, IL6 and VEGFA within tumor microenvironment could enable peritoneal metastasis of ovarian cancer via induction of EMT program. In summary, our study established a model that STAT4 promotes ovarian cancer metastasis via tumor-derived Wnt7a-induced activation of CAFs.
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