Publications by authors named "Yuchun Yang"

25 Publications

  • Page 1 of 1

Absolute Structure Determination and Kv1.5 Ion Channel Inhibition Activities of New Debromoaplysiatoxin Analogues.

Mar Drugs 2021 Nov 11;19(11). Epub 2021 Nov 11.

Department of Development Technology of Marine Resources, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.

Potassium channel Kv1.5 has been considered a key target for new treatments of atrial tachyarrhythmias, with few side effects. Four new debromoaplysiatoxin analogues with a 6/6/12 fused ring system were isolated from marine cyanobacterium sp. Their planar structures were elucidated by HRESIMS, 1D and 2D NMR. The absolute configuration of oscillatoxin J () was determined by single-crystal X-ray diffraction, and the absolute configurations of oscillatoxin K (), oscillatoxin L () and oscillatoxin M () were confirmed on the basis of GIAO NMR shift calculation followed by DP4 analysis. The current study confirmed the absolute configuration of the pivotal chiral positions (7S, 9S, 10S, 11R, 12S, 15S, 29R and 30R) at traditional ATXs with 6/12/6 tricyclic ring system. Compound , and exhibited blocking activities against Kv1.5 with IC values of 2.61 ± 0.91 µM, 3.86 ± 1.03 µM and 3.79 ± 1.01 µM, respectively. However, compound exhibited a minimum effect on Kv1.5 at 10 µM. Furthermore, all of these new debromoaplysiatoxin analogs displayed no apparent activity in a brine shrimp toxicity assay.
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http://dx.doi.org/10.3390/md19110630DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8622842PMC
November 2021

Salinity Drives Functional and Taxonomic Diversities in Global Water Metagenomes.

Front Microbiol 2021 1;12:719725. Epub 2021 Nov 1.

State Key Laboratory of Biocontrol, School of Life Sciences, School of Ecology, Sun Yat-sen University, Guangzhou, China.

A tight association between microbial function and taxonomy is the basis of functional prediction based on taxonomy, but such associations have been controversial in water biomes largely due to the probable prevalence of functional redundancy. However, previous studies on this topic used a relatively coarse resolution of ecosystem functioning, potentially inflating the estimated functional redundancy. Thus, a comprehensive evaluation of the association between high-resolution functional traits and taxonomic diversity obtained from fresh and saline water metagenomic data is urgently needed. Here, we examined 938 functionally and taxonomically annotated water metagenomes obtained worldwide to scrutinize the connection between function and taxonomy, and to identify the key driver of water metagenomes function or taxonomic composition at a global scale. We found that pairwise similarity of function was significantly associated with taxonomy, though taxonomy had higher global dissimilarity than function. Classification into six water biomes resulted in greater variation in taxonomic compositions than functional profiles, as the key regulating factor was salinity. Fresh water microbes harbored distinct functional and taxonomic structures from microbes in saline water biomes, despite that taxonomy was more susceptible to gradient of geography and climate than function. In summary, our results find a significant relationship between taxonomic diversity and microbial functioning in global water metagenomes, although microbial taxonomic compositions vary to a larger extent than functional profiles in aquatic ecosystems, suggesting the possibility and necessity for functional prediction of microorganisms based on taxonomy in global aquatic ecosystems.
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http://dx.doi.org/10.3389/fmicb.2021.719725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8591284PMC
November 2021

Activities and metabolic versatility of distinct anammox bacteria in a full-scale wastewater treatment system.

Water Res 2021 Nov 14;206:117763. Epub 2021 Oct 14.

Environmental Science and Engineering Research Group, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, The People's Republic of China; Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Zhuhai, Guangdong, The People's Republic of China. Electronic address:

Anaerobic ammonium oxidation (anammox) is a key N-producing process in the global nitrogen cycle. Major progress in understanding the core mechanism of anammox bacteria has been made, but our knowledge of the survival strategies of anammox bacteria in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Here, by combining metagenomics with in situ metatranscriptomics, complex anammox-driven nitrogen cycles in an anoxic tank and a granular activated carbon (GAC) biofilm module of a full-scale WWTP treating landfill leachate were constructed. Four distinct anammox metagenome-assembled genomes (MAGs), representing a new genus named Ca. Loosdrechtii, a new species in Ca. Kuenenia, a new species in Ca. Brocadia, and a new strain in "Ca. Kuenenia stuttgartiensis", were simultaneously retrieved from the GAC biofilm. Metabolic reconstruction revealed that all anammox organisms highly expressed the core metabolic enzymes and showed a high metabolic versatility. Pathways for dissimilatory nitrate reduction to ammonium (DNRA) coupled to volatile fatty acids (VFAs) oxidation likely assist anammox bacteria to survive unfavorable conditions and facilitate switches between lifestyles in oxygen fluctuating environments. The new Ca. Kuenenia species dominated the anammox community of the GAC biofilm, specifically may be enhanced by the uniquely encoded flexible ammonium and iron acquisition strategies. The new Ca. Brocadia species likely has an extensive niche distribution that is simultaneously established in the anoxic tank and the GAC biofilm, the two distinct niches. The highly diverse and impressive metabolic versatility of anammox bacteria revealed in this study advance our understanding of the survival and application of anammox bacteria in the full-scale wastewater treatment system.
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http://dx.doi.org/10.1016/j.watres.2021.117763DOI Listing
November 2021

Effect of pinolenic acid on oxidative stress injury in HepG2 cells induced by HO.

Food Sci Nutr 2021 Oct 25;9(10):5689-5697. Epub 2021 Aug 25.

Forestry Academy of Jilin Province Changchun China.

To investigate the effect and mechanism of pinolenic acid (PNA) on HO-induced oxidative stress injury in HepG2 cells. Methods: PNA was used to regulate oxidative stress injury of HepG2 cells induced by HO. Quantification of cell survival rate, accumulation of intracellular reactive oxygen species (ROS), and expression levels of anti-oxidation-related genes were determined using MTT, fluorescent probe technology (DCFH-DA), and real-time quantitative reverse transcription polymerase chain technology (qRT-PCR) method, respectively. Meanwhile, the activity of intracellular antioxidant enzymes was determined by biochemical methods. The results showed that PNA improved the survival rate of HepG2 cells induced by HO (29.59%, high-dose group), reduced the accumulation of intracellular ROS (65.52%, high-dose group), and reduced the level of intracellular malondialdehyde (MDA; 65.52%, high-dose group). All these results were dose-dependent, which indicated that PNA can improve oxidative stress damage of cells. Furthermore, the mechanism of PNA regulating oxidative stress was investigated from the gene level. Results showed that under supplementation of PNA, the activity of superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px) had been improved (39.74%, 17.58%, and 23.83%, high-dose group). Further studies on gene expression which controls the activity of antioxidant enzymes showed that under the regulation of PNA, the expression level of Keap1 gene was decreased, while Nrf2 gene was increased. The expression levels of HO-1 and NQO1 in the downstream of Nrf2 were increased. Results indicated that under the regulation of PNA, Nrf2 was separated from Keap1, entered the nucleus, bound to ARE, and up-regulated the expression levels of HO-1 and NQO1 genes. Conclusion: PNA has a conspicuous improvement effect on oxidative stress damage induced by HO in HepG2 cells. We also found the antioxidant mechanisms of PNA where it protected cells from oxidative stress damage by causing nuclear translocation of Nrf2 gene and up-regulated the expression levels of antioxidant enzymes in the downstream. This shows that PNA prevented oxidative stress by mediating the Keap1/Nrf2 transcriptional pathway and down-regulating enzyme activities.
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http://dx.doi.org/10.1002/fsn3.2534DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8498045PMC
October 2021

Analysis of risk factors for different subtypes of acute coronary syndrome.

J Int Med Res 2021 May;49(5):3000605211008326

Department of Comprehensive Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Province, China.

Aims: To investigate the different risk factors among different subtypes of patients with acute coronary syndrome (ACS).

Methods: A total of 296 patients who had ACS were retrospectively enrolled. Blood and echocardiographic indices were assessed within 24 hours after admission. Differences in risk factors and Gensini scores of coronary lesions among three groups were analyzed.

Results: Univariate analysis of risk factors for ACS subtypes showed that age, and levels of fasting plasma glucose, amino-terminal pro-brain natriuretic peptide, and creatine kinase isoenzyme were significantly higher in patients with non-ST-segment elevation myocardial infarction (NSTEMI) than in those with unstable angina pectoris (UAP). Logistic multivariate regression analysis showed that amino-terminal pro-brain natriuretic peptide and the left ventricular ejection fraction (LVEF) were related to ACS subtypes. The left ventricular end-diastolic diameter was an independent risk factor for UAP and ST-segment elevation myocardial infarction (STEMI) subtypes. The severity of coronary stenosis was significantly higher in NSTEMI and STEMI than in UAP. Gensini scores in the STEMI group were positively correlated with D-dimer levels (r = 0.429) and negatively correlated with the LVEF (r = -0.602).

Conclusion: Different subtypes of ACS have different risk factors. Our findings may have important guiding significance for ACS subtype risk assessment and clinical treatment.
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http://dx.doi.org/10.1177/03000605211008326DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8113931PMC
May 2021

Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration.

Water Res 2021 Mar 30;191:116798. Epub 2020 Dec 30.

Environmental Engineering, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China; Southern Laboratory of Ocean Science and Engineering, Zhuhai, Guangdong, China. Electronic address:

Recent studies indicate that ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal by wastewater treatment plants (WWTPs). However, our knowledge of the mechanisms employed by AOA for growth and survival in full-scale WWTPs is still limited. Here, metagenomic and metatranscriptomic analyses combined with a laboratory cultivation experiment revealed that three active AOAs (WS9, WS192, and WS208) belonging to family Nitrososphaeraceae were active in the deep oxidation ditch (DOD) of a full-scale WWTP treating landfill leachate, which is configured with three continuous aerobic-anoxic (OA) modules with low-intensity aeration (≤ 1.5 mg/L). AOA coexisted with AOB and complete ammonia oxidizers (Comammox), while the ammonia-oxidizing microbial (AOM) community was unexpectedly dominated by the novel AOA strain WS9. The low aeration, long retention time, and relatively high inputs of ammonium and copper might be responsible for the survival of AOA over AOB and Comammox, while the dominance of WS9, specifically may be enhanced by substrate preference and uniquely encoded retention strategies. The urease-negative WS9 is specifically adapted for ammonia acquisition as evidenced by the high expression of an ammonium transporter, whereas two metabolically versatile urease-positive AOA strains (WS192 and WS208) can likely supplement ammonia needs with urea. This study provides important information for the survival and application of the eutrophic Nitrososphaeraceae AOA and advances our understanding of archaea-dominated ammonia oxidation in a full-scale wastewater treatment system.
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http://dx.doi.org/10.1016/j.watres.2020.116798DOI Listing
March 2021

Diversity, abundance, and distribution of anammox bacteria in shipping channel sediment of Hong Kong by analysis of DNA and RNA.

Ecotoxicology 2021 Oct 12;30(8):1705-1718. Epub 2021 Jan 12.

Environmental Engineering, Guangdong Technion-Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, The People's Republic of China.

Anammox bacteria have been detected in various ecosystems, but their occurrence and community composition along the shipping channels have not been reported. In this study, anammox bacteria were recovered by PCR-amplified biomarker hzsB gene from the genomic DNA of the sediment samples. Phylogenetic tree revealed that Candidatus Scalindua and Ca. Brocadia dominated the anammox community of the Hong Kong channels; Ca. Scalindua spp. was present abundantly at the sites farther from the shore, whereas Ca. Jettenia and Ca. Kuenenia were detected as the minor members in the estuarine sediments near the shipping terminals. The highest values of Shannon-Wiener index and Chao1 were identified in the sediments along the Urmston road (UR), suggesting the highest α-diversity and species richness of anammox bacteria. PCoA analysis indicated that anammox bacterial communities along UR and Tai Hong (TH) channel were site-specific because these samples were grouped and clearly separated from the other samples. The maximum diversity of anammox bacteria was detected in UR samples, ranging from 6.28 × 10 to 1.28 × 10 gene copies per gram of dry sediment. A similar pattern of their transcriptional activities was also observed among these channels. Pearson's moment correlation and redundancy analysis indicated that NH-N was a strong factor shaping the community structure, which showed significant positive correlation with the anammox bacterial abundance and anammox transcriptional activities (p < 0.01, r > 0.8). Also, NH-N, (NO + NO)-N, and NH/NO were additional key environmental factors that influenced the anammox community diversity and distribution. This study yields a better understanding of the ecological distribution of anammox bacteria and the dominant genera in selective niche.
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http://dx.doi.org/10.1007/s10646-020-02332-yDOI Listing
October 2021

Ecological features and global distribution of Asgard archaea.

Sci Total Environ 2021 Mar 11;758:143581. Epub 2020 Nov 11.

Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China. Electronic address:

Asgard is a newly proposed archaeal superphylum, which has been suggested to hold the key to decipher the origin of Eukaryotes. However, their ecology remains largely unknown. Here, we conducted a meta-analysis of publicly available Asgard-associated 16S rRNA gene fragments, and found that just three previously proposed clades (Lokiarchaeota, Thorarchaeota, and Asgard clade 4) are widely distributed, whereas the other seven clades (phylum or class level) are restricted to the sediment biosphere. Asgard archaea, especially Loki- and Thorarchaeota, seem to adapt to marine sediments, and water depth (the depth of the sediment below water surface) and salinity might be crucial factors for the proportion of these microorganisms as revealed by multivariate regression analyses. However, the abundance of Asgard archaea exhibited distinct environmental drivers at the clade-level; for instance, the proportion of Asgard clade 4 was higher in less saline environments (salinity <6.35 psu), while higher for Heimdallarchaeota-AAG and Asgard clade 2 in more saline environment (salinity ≥35 psu). Furthermore, co-occurrence analysis allowed us to find a significant non-random association of different Asgard clades with other groups (e.g., Lokiarchaeota with Deltaproteobacteria and Anaerolineae; Odinarchaeota with Bathyarchaeota), suggesting different interaction potentials among these clades. Overall, these findings reveal Asgard archaea as a ubiquitous group worldwide and provide initial insights into their ecological features on a global scale.
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http://dx.doi.org/10.1016/j.scitotenv.2020.143581DOI Listing
March 2021

Subgroup level differences of physiological activities in marine Lokiarchaeota.

ISME J 2021 03 4;15(3):848-861. Epub 2020 Nov 4.

Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.

Asgard is a recently discovered archaeal superphylum, closely linked to the emergence of eukaryotes. Among Asgard archaea, Lokiarchaeota are abundant in marine sediments, but their in situ activities are largely unknown except for Candidatus 'Prometheoarchaeum syntrophicum'. Here, we tracked the activity of Lokiarchaeota in incubations with Helgoland mud area sediments (North Sea) by stable isotope probing (SIP) with organic polymers, C-labelled inorganic carbon, fermentation intermediates and proteins. Within the active archaea, we detected members of the Lokiarchaeota class Loki-3, which appeared to mixotrophically participate in the degradation of lignin and humic acids while assimilating CO, or heterotrophically used lactate. In contrast, members of the Lokiarchaeota class Loki-2 utilized protein and inorganic carbon, and degraded bacterial biomass formed in incubations. Metagenomic analysis revealed pathways for lactate degradation, and involvement in aromatic compound degradation in Loki-3, while the less globally distributed Loki-2 instead rely on protein degradation. We conclude that Lokiarchaeotal subgroups vary in their metabolic capabilities despite overlaps in their genomic equipment, and suggest that these subgroups occupy different ecologic niches in marine sediments.
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http://dx.doi.org/10.1038/s41396-020-00818-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8027215PMC
March 2021

Long-term effects of mixed planting on arbuscular mycorrhizal fungal communities in the roots and soils of Juglans mandshurica plantations.

BMC Microbiol 2020 10 12;20(1):304. Epub 2020 Oct 12.

Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin, 150040, P. R. China.

Background: Establishing mixed plantations is an effective way to improve soil fertility and increase forest productivity. Arbuscular mycorrhizal (AM) fungi are obligate symbiotic fungi that can promote mineral nutrient absorption and regulate intraspecific and interspecific competition in plants. However, the effects of mixed plantations on the community structure and abundance of AM fungi are still unclear. Illumina MiSeq sequencing was used to investigate the AM fungal community in the roots and soils of pure and mixed plantations (Juglans mandshurica × Larix gmelinii). The objective of this study is to compare the differential responses of the root and rhizosphere soil AM fungal communities of Juglans mandshurica to long-term mixed plantation management.

Results: Glomus and Paraglomus were the dominant genera in the root samples, accounting for more than 80% of the sequences. Compared with that in the pure plantation, the relative abundance of Glomus was higher in the mixed plantation. Glomus, Diversispora and Paraglomus accounted for more than 85% of the sequences in the soil samples. The relative abundances of Diversispora and an unidentified genus of Glomeromycetes were higher and lower in the pure plantation, respectively. The Root_P samples (the roots in the pure plantation) had the highest number of unique OTUs (operational taxonomic units), which belonged mainly to an unidentified genus of Glomeromycetes, Paraglomus, Glomus and Acaulospora. The number of unique OTUs detected in the soil was lower than that in the roots. In both the root and soil samples, the forest type did not have a significant effect on AM fungal diversity, but the Sobs value and the Shannon, Chao1 and Ace indices of AM fungi in the roots were significantly higher than those in the soil.

Conclusions: Mixed forest management had little effect on the AM fungal community of Juglans mandshurica roots and significantly changed the community composition of the soil AM fungi, but not the diversity.
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http://dx.doi.org/10.1186/s12866-020-01987-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7552469PMC
October 2020

Relationship between M235T and T174M polymorphisms in angiotensin gene and atrial fibrillation in Uyghur and Han populations of Xinjiang, China.

Int J Clin Exp Pathol 2020 1;13(8):2065-2074. Epub 2020 Aug 1.

Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University Urumqi, Xinjiang Uygur Autonomous Region, China.

Objective: To elucidate the association between angiotensin gene (AGT) M235T and T174M genetic polymorphisms in Han and Uyghur patients with atrial fibrillation (AF) in Xinjiang, China.

Methods: 100 cases of patients with AF of Han and 100 cases of patients with AF of Uyghur were selected as the experimental group, and 100 cases of patients with non-AF of Uyghur and non-AF of Han were selected as the control group. We amplified the AGT M235T site and AGT T174M site by PCR in 4 groups of patients, verified the polymorphism of the sites by gene sequencing, and compared their differences in each group.

Results: The high risk factors for AF such as sex, left atrial diameter (LAD), right atrial diameter (RAD), and coronary heart disease were significantly different between the Han case group and the control group ( < 0.05). There were significant differences in age, LAD, RAD, coronary heart disease and smoking as contributors to AF between Uyghur case group and control group ( < 0.05). The genotype frequency distribution of AGT M235T and AGT T174M loci in the AF group and control group of Han and Uyghur was in accordance with Hardy-Weinberg equilibrium law test. There was a significant difference in genotype frequency and allele frequency of AGT M235T locus between Han group, Uyghur AF group and control group ( < 0.05).

Conclusion: The AGT M235T and AGT T174M loci were associated with the occurrence of atrial fibrillation in the Han and Uyghur ethnic groups in Xinjiang.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7476944PMC
August 2020

Specific and effective detection of anammox bacteria using PCR primers targeting the 16S rRNA gene and functional genes.

Sci Total Environ 2020 Sep 15;734:139387. Epub 2020 May 15.

School of Food and Biotechnology, Guangdong Industry Polytechnic, Guangzhou, Guangdong 510300, People's Republic of China; Environmental Engineering, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People's Republic of China. Electronic address:

Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the nitrogen cycle by coupling ammonium and nitrite to produce dinitrogen gas (N). Polymerase chain reaction (PCR) is a fast, simple, and sensitive method that is widely used to assess the diversity, abundance, and activity of the slow-growing bacteria. In this review, we summarize and evaluate the wide variety of PCR primers targeting the 16S rRNA gene and functional genes (hzo, nir, and hzs) of anammox bacteria for their effectiveness and efficiencies in detecting this group of bacteria in different sample types. Furthermore, the efficiencies of different universal high-throughput sequencing 16S rRNA gene primers in anammox bacteria investigations were also evaluated to provide a reference for primer selection. Based on our in silico evaluation results, none of the 16S rRNA gene primers could recover all of the known anammox bacteria, but multiple hzo and hzs gene primers could accomplish this task. However, uncertain copies (1-3 copies) of hzo genes were identified in the genomes, and the hydrazine oxidation reaction catalyzed by hydrazine oxidoreductases (HZOs) can also be catalyzed by other hydroxylamine oxidoreductases (HAOs) in anammox bacteria, which can potentially result in large deviations in hzo-based qPCR and RT-qPCR analyses and results. Therefore, the use of optimal primers targeting unique hzs genes are recommended, although the efficiencies of these newly designed primers need further verification in practical applications. This article provides comprehensive information for the effective and specific detection of anammox bacteria using specific primers targeting the 16S rRNA gene and functional genes and serves as a basis for future high-quality primer design.
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http://dx.doi.org/10.1016/j.scitotenv.2020.139387DOI Listing
September 2020

Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota.

Microbiome 2020 03 31;8(1):43. Epub 2020 Mar 31.

Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.

Background: Bathyarchaeota, a newly proposed archaeal phylum, is considered as an important driver of the global carbon cycle. However, due to the great diversity of them, there is limited genomic information that accurately encompasses the metabolic potential of the entire archaeal phylum.

Results: In the current study, nine metagenome-assembled genomes of Bathyarchaeota from four subgroups were constructed from mangrove sediments, and metatranscriptomes were obtained for evaluating their in situ transcriptional activities. Comparative analyses with reference genomes and the transcripts of functional genes posit an expanded role for Bathyarchaeota in phototrophy, autotrophy, and nitrogen and sulfur cycles, respectively. Notably, the presence of genes for rhodopsins, cobalamin biosynthesis, and the oxygen-dependent metabolic pathways in some Bathyarchaeota subgroup 6 genomes suggest a light-sensing and microoxic lifestyle within this subgroup.

Conclusions: The results of this study expand our knowledge of metabolic abilities and diverse lifestyles of Bathyarchaeota, highlighting the crucial role of Bathyarchaeota in geochemical cycle. Video abstract.
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http://dx.doi.org/10.1186/s40168-020-00820-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7110647PMC
March 2020

Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation.

Sci China Life Sci 2020 Jun 16;63(6):886-897. Epub 2020 Mar 16.

Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.

Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the "Gerdarchaeota". Genomic analyses predict that Gerdarchaeota are facultative anaerobes in utilizing both organic and inorganic carbon. Unlike their closest relatives Heimdallarchaeota, Gerdarchaeota have genes encoding for cellulase and enzymes involved in the tetrahydromethanopterin-based Wood-Ljungdahl pathway. Transcriptomics showed that most of our identified Asgard archaea are capable of degrading organic matter, including peptides, amino acids and fatty acids, occupying ecological niches in different depths of layers of the sediments. Overall, this study broadens the diversity of the mysterious Asgard archaea and provides evidence for their ecological roles in coastal sediments.
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http://dx.doi.org/10.1007/s11427-020-1679-1DOI Listing
June 2020

Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems.

mBio 2020 03 17;11(2). Epub 2020 Mar 17.

Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, Hong Kong, People's Republic of China

The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different microorganisms. However, our knowledge of the survival strategies of comammox in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Analyses of genomes and transcriptomes of four comammox organisms from two full-scale WWTPs revealed that comammox were active and showed a surprisingly high metabolic versatility. A gene cluster for the utilization of urea and a gene encoding cyanase suggest that comammox may use diverse organic nitrogen compounds in addition to free ammonia as the substrates. The comammox organisms also encoded the genomic potential for multiple alternative energy metabolisms, including respiration with hydrogen, formate, and sulfite as electron donors. Pathways for the biosynthesis and degradation of polyphosphate, glycogen, and polyhydroxyalkanoates as intracellular storage compounds likely help comammox survive unfavorable conditions and facilitate switches between lifestyles in fluctuating environments. One of the comammox strains acquired from the anaerobic tank encoded and transcribed genes involved in homoacetate fermentation or in the utilization of exogenous acetate, both pathways being unexpected in a nitrifying bacterium. Surprisingly, this strain also encoded a respiratory nitrate reductase which has not yet been found in any other genome and might confer a selective advantage to this strain over other strains in anoxic conditions. The discovery of comammox in the genus changes our perception of nitrification. However, genomes of comammox organisms have not been acquired from full-scale WWTPs, and very little is known about their survival strategies and potential metabolisms in complex wastewater treatment systems. Here, four comammox metagenome-assembled genomes and metatranscriptomic data sets were retrieved from two full-scale WWTPs. Their impressive and-among nitrifiers-unsurpassed ecophysiological versatility could make comammox an interesting target for optimizing nitrification in current and future bioreactor configurations.
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http://dx.doi.org/10.1128/mBio.03175-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7078480PMC
March 2020

Complex microbial nitrogen-cycling networks in three distinct anammox-inoculated wastewater treatment systems.

Water Res 2020 Jan 30;168:115142. Epub 2019 Sep 30.

Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China. Electronic address:

Microbial nitrogen removal mediated by anaerobic ammonium oxidation (anammox) are cost-effective, yet it is time-consuming to accumulate the slow-growing anammox bacteria in conventional wastewater treatment plants (WWTPs). Inoculation of anammox enriched pellets is an effective way to establish anammox and achieve shortcut nitrogen removal in full-scale WWTPs. However, little is known about the complex microbial nitrogen-cycling networks in these anammox-inoculated WWTPs. Here, we applied metagenomic and metatranscriptomic tools to study the microbial nitrogen removal in three conventional WWTPs, which have been inoculated exogenous anammox pellets, representing partial-nitrification anammox (PNA) and nitrification-denitrification nitrogen removal processes. In the PNA system of Bali (BL), ammonia was partially oxidized by ammonia-oxidizing bacteria (AOB) Nitrosomonas and the oxidized nitrite and the remaining ammonium were directly converted to N by anammox bacteria Ca. Brocadia and Ca. Kuenenia. In the nitrification-denitrification system of Wenshan (WS), ammonia-oxidizing archaea (AOA) Thaumarchaeota unexpectedly dominated the nitrifying community in the presence of AOB Nitrosomonas. Meanwhile, the biomass yield of Ca. Brocadia was likely inhibited by the high biodegradable organic compound input and limited by substrate competitions from AOA, AOB, complete ammonia oxidizers (comammox) Nitrospira, nitrite-oxidizing bacteria (NOB) Nitrospira, and heterotrophic denitrifiers. Unexpectedly, comammox Nitrospira was the predominant nitrifier in the presence of AOB Nitrosomonas in the organic carbon-rich nitrification-denitrification system of Linkou (LK). These results clearly showed that distinct active groups were working in concert for an effective nitrogen removal in different WWTPs. This study confirmed the feasibility of anammox application in ammonium-rich systems by direct inoculation of the exogenous anammox pellets and improved our understanding of microbial nitrogen cycling in anammox-driven conventional WWTPs from both physiochemical and omics perspectives.
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http://dx.doi.org/10.1016/j.watres.2019.115142DOI Listing
January 2020

Metagenomic and metatranscriptomic analyses reveal activity and hosts of antibiotic resistance genes in activated sludge.

Environ Int 2019 08 23;129:208-220. Epub 2019 May 23.

Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China. Electronic address:

Wastewater treatment plants (WWTPs) are a source and reservoir for subsequent spread of various antibiotic resistance genes (ARGs). However, little is known about the activity and hosts of ARGs in WWTPs. Here, we utilized both metagenomic and metatranscriptomic approaches to comprehensively reveal the diversity, abundance, expression and hosts of ARGs in activated sludge (AS) from three conventional WWTPs in Taiwan. Based on deep sequencing data and a custom-made ARG database, a total of 360 ARGs associated with 24 classes of antibiotics were identified from the three AS metagenomes, with an abundance range of 7.06 × 10-1.20 × 10 copies of ARG/copy of 16S rRNA gene. Differential coverage binning analysis revealed that >22 bacterial phyla were the putative hosts of the identified ARGs. Surprisingly, genus Mycobacterium and family Burkholderiaceae were observed as multi-drug resistant harboring 14 and 50 ARGs. Metatranscriptome analysis showed 65.8% of the identified ARGs were being expressed, highlighting that ARGs were not only present, but also transcriptionally active in AS. Remarkably, 110 identified ARGs were annotated as plasmid-associated and displayed a close to two-fold increased likelihood of being transcriptionally expressed compared to those ARGs found exclusively within bacterial chromosomes. Further analysis showed the transcript abundance of aminoglycoside, sulfonamide, and tetracycline resistance genes was mainly contributed by plasmid-borne ARGs. Our approach allowed us to specifically link ARGs to their transcripts and genetic context, providing a comprehensive insight into the prevalence, expression and hosts of ARGs in AS. Overall, results of this study enhance our understanding of the distribution and dissemination of ARGs in WWTPs, which benefits environmental risk assessment and management of ARB and ARGs.
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http://dx.doi.org/10.1016/j.envint.2019.05.036DOI Listing
August 2019

Genomic and transcriptomic insights into the ecology and metabolism of benthic archaeal cosmopolitan, Thermoprofundales (MBG-D archaea).

ISME J 2019 04 4;13(4):885-901. Epub 2018 Dec 4.

Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, People's Republic of China.

Marine Benthic Group D (MBG-D) archaea, discovered by 16S rRNA gene survey decades ago, are ecologically important, yet understudied and uncultured sedimentary archaea. In this study, a comprehensive meta-analysis based on the 16S rRNA genes of MBG-D archaea showed that MBG-D archaea are one of the most frequently found archaeal lineages in global sediment with widespread distribution and high abundance, including 16 subgroups in total. Interestingly, some subgroups show significant segregations toward salinity and methane seeps. Co-occurrence analyses indicate significant non-random association of MBG-D archaea with Lokiarchaeota (in both saline and freshwater sediments) and Hadesarchaea, suggesting potential interactions among these archaeal groups. Meanwhile, based on four nearly complete metagenome-assembled genomes (MAGs) and corresponding metatranscriptomes reconstructed from mangrove and intertidal mudflat sediments, we provide insights on metabolic potentials and ecological functions of MBG-D archaea. MBG-D archaea appear to be capable of transporting and assimilating peptides and generating acetate and ethanol through fermentation. Metatranscriptomic analysis suggests high expression of genes for acetate and amino acid utilization and for peptidases, especially the M09B-type extracellular peptidase (collagenase) showing high expression levels in all four mangrove MAGs. Beyond heterotrophic central carbon metabolism, the MBG-D genomes include genes that might encode two autotrophic pathways: Wood-Ljundahl (WL) pathways using both HMPT and Hfolate as C carriers, and an incomplete dicarboxylate/4-hydroxybutyrate cycle with alternative bypasses from pyruvate to malate/oxaloacetate during dicarboxylation. These findings reveal MBG-D archaea as an important ubiquitous benthic sedimentary archaeal group with specific mixotrophic metabolisms, so we proposed the name Thermoprofundales as a new Order within the Class Thermoplasmata. Globally, Thermoprofundales and other benthic archaea might synergistically transform benthic organic matter, possibly playing a vital role in sedimentary carbon cycle.
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http://dx.doi.org/10.1038/s41396-018-0321-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6461988PMC
April 2019

Practical applications of PCR primers in detection of anammox bacteria effectively from different types of samples.

Appl Microbiol Biotechnol 2018 Jul 25;102(14):5859-5871. Epub 2018 May 25.

Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China.

Research on anammox (anaerobic ammonium oxidizing) bacteria is important due to their biogeochemical and industrial application significance since the first discovery made over two decades ago. By coupling NH and NO biochemically to form N gas, anammox bacteria contribute significantly to global marine and terrestrial nitrogen balance (responsible for 50, 9~40, and 4~37% of the nitrogen loss for marine, lakes, and paddy soil) and are also useful in energy-conserving nitrogen removal in wastewater treatment. PCR-based detection and quantification of anammox bacteria are an easy, essential, and widely accessible technique used ubiquitously for studying them in many environmental niches. In this article, we make a summary on practical applications of 16S rRNA and functional gene PCR primers, including hydrazine dehydrogenase (Hzo), nitrite reductase (NirS), hydrazine synthase (Hzs), and cytochrome c biogenesis proteins (Ccs) in detection of them. PCR primer performances in both practical applications and tests in silico are also presented for comparison. For detecting general and specific anammox bacterial groups, selection of appropriate PCR primers for different environmental samples and practical application guidance on choice of appropriate primer pairs for different purposes are also offered. This article provides practical information on selection and application of PCR technique in detection of anammox bacteria from the diverse environments to further promote convenient applications of this technique in research and other purposes.
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http://dx.doi.org/10.1007/s00253-018-9078-2DOI Listing
July 2018

Prognostic value of glucose metabolism for non-ST-segment elevation infarction patients with diabetes mellitus and single concomitant chronic total occlusion following primary percutaneous coronary intervention.

Medicine (Baltimore) 2017 Nov;96(45):e8362

NO 2 Cadre Wards Medicine Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, People's Republic of China.

Glucose metabolism status may play a predictive role in the severity of the complications among patients with type 2 diabetes mellitus (DM). However, few studies have focused on the prognostic value of glycosylated hemoglobin (HbA1c) and Homeostatic Model Assessment 2 for Insulin Resistance (HOMA2-IR) in patients with DM, non-ST-segment elevation infarction (NSTEMI), and single concomitant chronic total occlusion (CTO) following primary percutaneous coronary intervention (PCI). Short- and long-term prognostic value of HbA1c and HOMA2-IR in patients with DM with NSTEMI and single CTO who received primary percutaneous transluminal coronary intervention (pPCI).Data from 202 patients with NSTEMI and single CTO in nonculprit vessels were included. The incidence of revascularization, cardiogenic shock, ischemic stroke, major bleeding (ie, cerebral hemorrhage or massive hemorrhage of gastrointestinal tract), and cardiac death were combined as composite end points (CEPs). HbA1c was measured on admission and at 12 and 24 weeks after discharge. HOMA2-IR was measured on admission and at 6 and 12 weeks after discharge. The mean value of HbA1c and HOMA2-IR was calculated to determine the impact on 2.5-year CEPs. All patients were assessed during hospitalization and followed for up to 2.5 years after discharge.Mean age was 62.4 ± 11.8 years and 76% were male. Previous MI, lower left ventricular ejection fraction, and higher HbA1c (hazard ratio [HR] = 1.216; 95% confidence interval [CI] = 1.023-1.445; P = .023) were independently associated with a poor prognosis at 2.5 years. Higher HbA1c and HOMA2-IR on admission was associated with CEPs during hospitalization. Mean HOMA2-IR prior to pPCI was associated with revascularization (HR = 1.129; 95% CI = 1.008-1.265; P = .036) and ischemic stroke (HR = 1.276; 95% CI = 1.044-1.560; P = .017) during the 2.5 years follow-up period.Glucose metabolism status reflected by HbA1c and HOMA2-IR may provide prognostic value to patients with NSTEMI, type 2 DM, and single concomitant CTO following PCI. Therefore, patients with NSTEMI, CTO, and poor glycemic control should be carefully evaluated prior to PCI.
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http://dx.doi.org/10.1097/MD.0000000000008362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5690710PMC
November 2017

Analysis of the Global Warming Potential of Biogenic CO Emission in Life Cycle Assessments.

Sci Rep 2017 01 3;7:39857. Epub 2017 Jan 3.

Jilin Province Academy of Forestry Research, Changchun, 130033, China.

Biomass is generally believed to be carbon neutral. However, recent studies have challenged the carbon neutrality hypothesis by introducing metric indicators to assess the global warming potential of biogenic CO (GWP). In this study we calculated the GWP factors using a forest growth model and radiative forcing effects with a time horizon of 100 years and applied the factors to five life cycle assessment (LCA) case studies of bioproducts. The forest carbon change was also accounted for in the LCA studies. GWP factors ranged from 0.13-0.32, indicating that biomass could be an attractive energy resource when compared with fossil fuels. As expected, short rotation and fast-growing biomass plantations produced low GWP. Long-lived wood products also allowed more regrowth of biomass to be accounted as absorption of the CO emission from biomass combustion. The LCA case studies showed that the total life cycle GHG emissions were closely related to GWP and energy conversion efficiency. By considering the GWP factors and the forest carbon change, the production of ethanol and bio-power appeared to have higher GHG emissions than petroleum-derived diesel at the highest GWP.
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http://dx.doi.org/10.1038/srep39857DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5206676PMC
January 2017

Xanthone derivatives from the fermentation products of an endophytic fungus Phomopsis sp.

Nat Prod Commun 2015 Feb;10(2):305-8

Three new xanthones, 1-hydroxy-3-hydroxyethyl-5-methoxy-6-methoxycarbonylxanthone (1), 1,4-dihydroxy-3-hydroxyethyl-5-methoxy-6-methoxycarbonylxanthone (2), and 1-hydroxy-3-hydroxyethyl-4-methoxy-8-methoxycarbonylxanthone (3), together with five known xanthones (4-8) were isolated from the fermentation products of an endophytic fungus Phomopsis sp.. Their structures were elucidated by spectroscopic methods including extensive 1D- and 2D-NMR spectroscopic techniques. Compounds 1-3 and 7 were also tested for their cytotoxicity against five human tumor cell lines (NB4, A549, SHSY5Y, PC3, and MCF7) by the MTT method, with paclitaxel used as the positive control. Compound 1 showed cytotoxicity against A549 and PC3 cells with IC50 values of 3.2 and 2.5 μM, respectively, 2 showed potential cytotoxicity against NB4 cells, with an IC50 value of 3.6 μM, and 3 showed cytotoxicity against A549 cells with an IC50 value of 3.5 μM.
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February 2015

Utility of intra-aortic balloon pump support for multivessel coronary artery spasm and cardiac arrest.

Int J Cardiol 2014 Oct 4;176(3):e122-4. Epub 2014 Aug 4.

Cardiac Care Unit, Wuhan Asia Heart Hospital, Wuhan 430022, China.

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http://dx.doi.org/10.1016/j.ijcard.2014.07.231DOI Listing
October 2014

Association of PS gene polymorphism and soluble P-selectin levels in atrial fibrillation thromboembolism population in Xinjiang.

Biochem Biophys Res Commun 2014 Sep 1;452(3):303-7. Epub 2014 Aug 1.

Department of Cardiology, First Affiliated Hospital, Xinjiang Medical University, 137 Liyushan Road, Urumqi 830054, PR China. Electronic address:

Unlabelled: To investigate the association between the polymorphism of P choose element (p. selectin, PS) and soluble P-selectin levels in atrial fibrillation (AF) thromboembolism in Han and Uigur population of Xinjiang.

Method: Using ELISA method determination of plasma level of sPs. The frequency distributions of SNP sP-selectin gene promoter (-2123C/G) and SNP in exon region (Thr715Pro) were investigated by polymerase chain reaction (PCR)-restriction fragment length polymorphism and direct DNA sequence analysis among 302 Xinjiang Uigur and 340 age- and sex-matched Han people.

Results: Cases sPs exist significant difference serum level and the control group. The frequencies of the -2123C/G allele among the Uigur population had no significant differences from those of the Han population. Thr715Pro did not show any polymorphism in the two populations.

Conclusions: The sP-selectin gene polymorphisms are associated with serum sP-selectin levels or thromboembolic events, suggesting that the patients with nonvalvular AF and thromboembolic events may have genetic susceptibility.
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http://dx.doi.org/10.1016/j.bbrc.2014.07.120DOI Listing
September 2014

Effect of periodic pacemaker optimization on left atrial reverse remodeling in long-term cardiac resynchronization therapy.

J Interv Card Electrophysiol 2014 Jan 23;39(1):87-93. Epub 2013 Oct 23.

Department of Cardiology, First Affiliated Hospital, Xinjiang Medical University, 137 liyushan road, Urumqi, 830054, People's Republic of China.

Purpose: Few data exist about the effect of cardiac resynchronization therapy (CRT) on left atrial (LA) reverse remodeling and function, and whether echocardiographic (echo)-guide pacemaker optimization of atrioventricular and interventricular delays could beneficially affect LA reverse remodeling in long-term CRT therapy.

Methods: Effect of periodic pacemaker optimization on LA reverse remodeling induced by CRT was analyzed in 113 consecutive patients (mean age, 60 ± 11 years) and stratified according to periodic pacemaker optimization (group 1) and nonperiodic pacemaker optimization (group 2). Left atrial volumes index percent changes were assessed at every continuing 6-month follow-up visit. The primary endpoint was LA reverse remodeling. The secondary endpoint included left ventricular reverse remodeling and left ventricular ejection fraction.

Results: There is no significant difference of follow-up duration in subgroups (42.43 ± 18.94 months in group 1 vs 37.76 ± 20.24 months in group 2, p = 0.228). The responder's rate of subgroups showed similar after follow-up of 12 months (60.0 vs 53.2%, p = 0.483). After 24-month follow-up, the mean reduction of LAV index was similar in two groups (10.34 vs 7.53%, p = 0.257). The improvement effect of LA reverse remodeling induced by CRT was sustained during 24-month follow-up to the end of current study in periodic pacemaker optimization group. The degree of LAV index percent reduction was directly correlated to periodic pacemaker optimization at end of current analysis (17.13 vs 10.35%, p = 0.047).

Conclusions: Periodic echo-guide pacemaker optimization of atrioventricular and interventricular delays plays a positive role on LA reverse remodeling in long-term CRT therapy.
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http://dx.doi.org/10.1007/s10840-013-9833-3DOI Listing
January 2014
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