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| 1 | Discovering the roles of subsurface microorganisms: Progress and future of deep biosphere investigation显示文摘The discovery of the marine 'deep biosphere'-microorganisms living deep below the seafloor-is one of the most significant and exciting discoveries since the ocean drilling program began more than 40 years ago. Study of the deep biosphere has become a research frontier and a hot spot both for geological and biological sciences. Here, we introduce the history of the discovery of the deep biosphere, and then we describe the types of environments for life below the seafloor, the energy sources for the living creatures, the diversity of organisms within the deep biosphere, and the new tools and technologies used in this research field. We will highlight several recently completed Integrated Ocean Drilling Program Expeditions, which targeted the subseafloor deep biosphere within the crust and sediments. Finally, future research directions and challenges of deep biosphere investigation towards uncovering the roles of subsurface microorganisms will be briefly addressed. | WANG FengPing LU ShuLin ORCUTT Beth N XIE Wei CHEN Ying XIAO Xiang EDWARDS Katrina J | 2013 | Chinese Science Bulletin2013，58，4： | 6 |
| 2 | Molecular diversity of Thermococcales isolated from Guaymas Basin hydrothermal vents显示文摘Members of Thermococcales are organoheterotrophic hyperthermophilic anaerobes consisting of three genera, Thermococcus, Pyrococcus, and Palaeococcus, among which Thermococcus are the most frequently isolated. In this study, a variety of Thermococcales strains were isolated from the Guaymas Basin hydrothermal vents under different temperatures and pressures. Based on their 16S rRNA gene sequences, all the strains isolated from 85 C or 95 C enrichment cultures at ambient pressure were classified as Thermococcus, while strains isolated from 108 C-30 MPa enrichment cultures belonged to Pyrococcus. The combination of high pressure and high temperature for enrichment was shown to be an efficient method for isolating Pyrococcus strains. Through selecting and analyzing with multiple molecular phylogenetic markers, the isolated Thermococcales strains were found quite diversified including several putative novel species. This demonstrates a vast genetic reservoir of Thermoccoccales in the deep-sea hydrothermal vents, and a fast evolving of the Thermococcales species adapting to the fast changing environment. | LIU Lupeng WANG Fengping XU Jun XIAO Xiang | 2013 | Acta Oceanologica Sinica2013，32，6： | 2 |
| 3 | Molecular Survey of Sulphate-Reducing Bacteria in the Deep-Sea Sediments of the West Pacific Warm Pool显示文摘The sulfate-reducing bacteria(SRB) community in the deep-sea sediments of the west Pacific Warm Pool(WP) was surveyed by molecular phylogenetic analyses using primers targeting the 16S rRNA gene fragments of SRB. Specific 16S rRNA gene libraries from five sediment layers(1-cm,3-cm,6-cm,10-cm and 12-cm layer) of the 12-cm core of WP-0 were constructed. The clones in the five libraries were differentiated by restriction fragment length polymorphism(RFLP) and representative clones were selected to sequence. It was found that the clones fell into four groups,which were closest related to Desulfotomaculum,Desul-facinum,Desulfomonile and Desulfanuticus. Desulfacinum-like clones were only detected in the upper layers of the sediment core,whereas Desulfomonile-like clones were only present in the deeper layers. Fluorescence in situ hybridization(FISH) was further carried out to visualize and count the SRB and bacteria in the five sediment layers. It was found that SRB constituted only a small proportion of the bacteria community(0.34%-1.95%) ,it had the highest content in the 3-cm layer(1.95%) and had a depth-related decreasing tendency along the 12-cm core. | WANG Peng XIAO Xiang ZHANG Haiyan WANG Fengping | 2008 | Journal of Ocean University of China2008，7，3： | 1 |
| 4 | Analysis of archaeal 16S rDNA from deep-sea sediments sam-ples显示文摘 | Xu Meixiang Wang fengping Xiao Xiang | | 0，，： | 1 |
| 5 | Phylogenetic analysis of Archaea in the deep-sea sediments of west Pacific Warm Pool显示文摘 | Peng Wang Xiang Xiao Fengping Wang | 2005 | Extremophiles2005，，3： | 1 |
| 6 | Phase diagram of the ternary system lauric acid-capric acid-naphthalene 显示文摘 | JIN Longfei XIAO Fengping | 2004 | Thermochimica Acta2004，424，12： | 1 |
| 7 | Response of bacteria in the deep-sea sediments and the Antarctic soils to carbohydrates: Effects on ectoenzyme activity and bacterial community显示文摘The response of bacteria to various carbohydrates in the deep-sea sediments and the Antarctic soils was investigated using cellulose, chitin, and olive oil. It was found that the carbohydrates significantly increased the corresponding specific ectoenzyme activity (β- glucosidase, β-N-acetylglucosaminidase, lipase) in the samples from deep-sea sediments. In the case of Antarctic soil samples, the cellulose or olive oil amendments had minor or no effect on β-glucosidase or lipase activity, except the chitin which stimulated β- N-acetylglucosaminidase production. The responses of the bacteria in the deep-sea sediment sample WP02-3 and the Antarctic soil sample CC-TY2 towards the chitin amendment were further analyzed. Chitin amendments were shown to stimulate the ectoenzyme activity in all the tested sediments and the soils. The bacterial response before and after the carbohydrates amendments were compared by denaturing gradient gel electrophoresis and quantitative competitive polymerase chain reaction. Significant changes were found in the structure and density of the bacterial community in the deep sea sediments as compared to the Antarctic soil sample, where the effects were relatively lower. There was no change in the bacterial population in both studied samples in response to carbohydrates amendments. These data indicate that the bacterial communities in the oligotrophic deep-sea sediments are more dynamic than that in the Antarctic soils as they respond to the nutrient sources efficiently by regulation of ectoenzyme activity and/or changing community structure. | Xiang Zeng | 2010 | Journal of Environmental Sciences2010，22，11： | 1 |
| 8 | Bacterial community along a historic lake sediment core of Ardley Island, west Antarctica显示文摘 | Shengkang Li Xiang Xiao Xuebin Yin Fengping Wang | 2006 | Extremophiles2006，，5： | 1 |
| 9 | Role of Filamentous Phage SW1 in Regulating the Lateral Flagella of Shewanella piezotolerans Strain WP3 at Low Temperatures显示文摘 | Huahua Jian Xiang Xiao Fengping Wang | 2013 | Applied and Environmental Microbiology2013，，22： | 1 |
| 10 | Distribution and Diversity of Bacteria and Archaea in Marine Sediments Affected by Gas Hydrates at Mississippi Canyon in the Gulf of Mexico显示文摘 | Guangbin Ye Shufang Wang Lijing Jiang Xiang Xiao Fengping Wang John Noakes Chuanlun Zhang | 2009 | Geomicrobiology Journal2009，，6： | 1 |
| 11 | Structures of the cloned chitinase and its truncant from A. caviae显示文摘Aeromonas caviae can secrete several chintinases with different molecular weights. One chitinase gene chi 1 has been cloned and sequenced. It encodes a protein of 865 amino acids with a signal peptide at the N-terminus, a polycystic kidney disease(PKD)-like domain, a triosephosphate isomerase(TIM) catalytic region, a receptor for egg jelly(REJ)-like domain and two tandem chitin binding domains (ChBDs). The entire chitinase degrades colloid chitin both endolytically and exolytically into N-acetylglucosamine, chitobiose and chitotriose. When removing the 302 amino acids at C-teminus its activity remains but the degraded products are chitobiose, chitotriose and chitotetraose. The study shows that for the full-length chitinase, its substrate with the shortest length is chitotriose while in its truncated form, it is chitotetraose. | ZHOU Ying, WANG Fengping and XIAO Xiang(1. School of Life Science, Xiamen University, Xiamen 361005, China 2. Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China) | 2002 | Progress in Natural Science:Materials International2002，12，8： | 0 |
| 12 | New approaches for archaeal genome-guided cultivation显示文摘Archaea,one of the three domains of life along with Bacteria and Eukarya,contains ancient life forms such as methanogen that are observed today on Earth,and one lineage Asgard archaea is also considered the closest ancestor of Eukarya.Recently,with the development of interdisciplinary studies from Earth and Life sciences,archaeal organisms are considered to play pivotal roles in geochemical cycling in nature.However,our understanding of the attributes,origin and evolution,geochemical and ecological functions of Archaea is hampered by the scarcity of archaeal isolates,which has represented a challenge to researchers for the last 40 years.Cultivation-independent sequencing and phylogenomic analyses have demonstrated a considerable diversity of Archaea with more than 20 novel phyla.However,only four archaeal phyla have cultured representatives,leaving large gaps in our knowledge of the metabolic capabilities and ecological functions of the majority of archaeal strains identified exclusively by DNA sequencing.In this review,we summarize the discovery and development of archaeal research,highlight the knowledge gap between uncultured and cultured archaeal microbes,and call on the importance of devoting greater research efforts to archaeal cultivation.Finally,we outlined new ideas and strategic approaches,namely,(1)genome-based methods,(2)microbial network information-based methods,(3)genome-scale model-guided methods,and(4)machine learning methods,to enable the cultivation of uncultivated archaeal microbes using accumulated high-throughput sequencing data. | Yinzhao WANG Yoichi KAMAGATA Meng LI Feifei HAN Fengping WANG Xiang XIAO | 2021 | Science China Earth Sciences2021，64，10： | 0 |
| 13 | Deep Learning‑Assisted Quantitative Susceptibility Mapping as a Tool for Grading and Molecular Subtyping of Gliomas显示文摘This study aimed to explore the value of deep learning(DL)-assisted quantitative susceptibility mapping(QSM)in glioma grading and molecular subtyping.Forty-two patients with gliomas,who underwent preoperative T2 fluid-attenuated inversion recovery(T2 FLAIR),contrast-enhanced T1-weighted imaging(T1WI+C),and QSM scanning at 3.0T magnetic resonance imaging(MRI)were included in this study.Histopathology and immunohistochemistry staining were used to determine glioma grades,and isocitrate dehydrogenase(IDH)1 and alpha thalassemia/mental retardation syndrome X-linked gene(ATRX)subtypes.Tumor segmentation was performed manually using Insight Toolkit-SNAP program(www.itksnap.org).An inception convolutional neural network(CNN)with a subsequent linear layer was employed as the training encoder to capture multi-scale features from MRI slices.Fivefold cross-validation was utilized as the training strategy(seven samples for each fold),and the ratio of sample size of the training,validation,and test dataset was 4:1:1.The performance was evalu-ated by the accuracy and area under the curve(AUC).With the inception CNN,single modal of QSM showed better perfor-mance in differentiating glioblastomas(GBM)and other grade gliomas(OGG,grade II–III),and predicting IDH1 mutation and ATRX loss(accuracy:0.80,0.77,0.60)than either T2 FLAIR(0.69,0.57,0.54)or T1WI+C(0.74,0.57,0.46).When combining three modalities,compared with any single modality,the best AUC/accuracy/F1-scores were reached in grading gliomas(OGG and GBM:0.91/0.89/0.87,low-grade and high-grade gliomas:0.83/0.86/0.81),predicting IDH1 mutation(0.88/0.89/0.85),and predicting ATRX loss(0.78/0.71/0.67).As a supplement to conventional MRI,DL-assisted QSM is a promising molecular imaging method to evaluate glioma grades,IDH1 mutation,and ATRX loss. | Wenting Rui Shengjie Zhang Huidong Shi Yaru Sheng Fengping Zhu YiDi Yao Xiang Chen Haixia Cheng Yong Zhang Ababikere Aili Zhenwei Yao Xiao‑Yong Zhang Yan Ren | 2023 | Phenomics2023，3，3： | 0 |
| 14 | Genome-wide identification and expression analysis of the GhIQD gene family in upland cotton(Gossypium hirsutum L.)显示文摘Background:Calmodulin(CaM)is one of the most important Ca^(2+)signaling receptors because it regulates diverse physiological and biochemical reactions in plants.CaM functions by interacting with CaM-binding proteins(CaMBPs)to modulate Ca^(2+)signaling.IQ domain(IQD)proteins are plant-specific CaMBPs that bind to CaM by their specific CaM binding sites.Results:In this study,we identified 102 GhIQD genes in the Gossypium hirsutum L.genome.The GhIQD gene family was classified into four clusters(Ⅰ,Ⅱ,Ⅲ,andⅣ),and we then mapped the GhIQD genes to the G.hirsutum L.chromosomes.Moreover,we found that 100 of the 102 GhIQD genes resulted from segmental duplication events,indicating that segmental duplication is the main force driving GhIQD gene expansion.Gene expression pattern analysis showed that a total of 89 GhIQD genes expressed in the elongation stage and second cell wall biosynthesis stage of the fiber cells,suggesting that GhIQD genes may contribute to fiber cell development in cotton.In addition,we found that 20 selected GhIQD genes were highly expressed in various tissues.Exogenous application of MeJA significantly enhanced the expression levels of GhIQD genes.Conclusions:Our study shows that GhIQD genes are involved in fiber cell development in cotton and are also widely induced by MeJA.Thw results provide bases to systematically characterize the evolution and biological functions of GhIQD genes,as well as clues to breed better cotton varieties in the future. | DOU Lingling LV Limin KANG Yangyang TIAN Ruijie HUANG Deqing LI Jiayin LI Siyi LIU Fengping CAO Lingyan JIN Yuhua LIU Yang LI Huaizhu WANG Wenbo PANG Chaoyou SHANG Haihong ZOU Changsong SONG Guoli XIAO Guanghui | 2021 | Journal of Cotton Research2021，4，1： | 0 |
| 15 | Metal-organic frameworks based single-atom catalysts for advanced fuel cells and rechargeable batteries显示文摘The next-generation energy storage systems such as fuel cells,metal-air batteries,and alkali metal(Li,Na)-chalcogen(S,Se)batteries have received increasing attention owing to their high energy density and low cost.However,one of the main obstacles of these systems is the poor reaction kinetics in the involved chemical reactions.Therefore,it is essential to incorporate suitable and efficient catalysts into the cell.These years,single-atom catalysts(SACs)are emerging as a frontier in catalysis due to their maximum atom efficiency and unique reaction selectivity.For SACs fabrication,metal-organic frameworks(MOFs)have been confirmed as promising templates or precursors due to their high metal loadings,structural adjustability,porosity,and tailorable catalytic site.In this review,we summarize effective strategies for fabricating SACs by MOFs with corresponding advanced characterization techniques and illustrate the key role of MOFs-based SACs in these batteries by explaining their reaction mechanisms and challenges.Finally,current applications,prospects,and opportunities for MOFs-based SACs in energy storage systems are discussed. | Yifei Wu Peng Hu Fengping Xiao Xiaoting Yu Wenqi Yang Minqi Liang Ziwei Liang Aixin Zhu | 2023 | Journal of Energy Chemistry2023，，5： | 0 |
| 16 | Correlation of PCSK1 with nonalcoholic fatty liver disease in a Han Chinese population:a case-control observational study显示文摘Objective: This study aimed to investigate the association between single-nucleotide polymorphisms (SNPs) ofPCSK1 (proprotein convertase subtilisin/kexin type 1) related to obesity and nonalcoholic fatty liver disease (NAFLD).Methods: In this case-control observational study, four candidate SNPs (rs6234, rs155971, rs6232, rs3811951) ofPCSK1 were genotyped in 732 NAFLD patients and 823 healthy control participants, all of whom were of ethnic Han Chinese descent. All participants came from Shanghai, China, and joined our study during 2015 to 2016. The frequencies of each allele and genotype, paired linkage disequilibrium, and haplotype were calculated on the SHEsis platform. In addition to SHEsis, five different genetic models (codominant, dominant, recessive, overdominant, and log-additive) were employed to identify the correlation between genotype frequency and NAFLD. This study was approved by the Medical Ethics Committee of Shanghai University of Traditional Chinese Medicine (approved No. 2017LCSY069).Results: In a comparison of NAFLD patients and healthy participants, none of the fourPCSK1 SNPs were significantly correlated with the occurrence of NAFLD (P>0.05), in either genotypic or allelic distribution. The recessive model of rs3811951 appeared to show a correlation (odds ratio=1.077;95% confidence interval=0.924-1.256;P=0.04), but there was no statistical significance after Bonferroni correction (Pcorr>0.0125).Conclusions: Four obesity-relatedPCSK1 SNPs (rs6234, rs155971, rs6232, rs3811951) showed no significant correlation with the development of NAFLD in a Han Chinese population. | Xiao Yang Fan Yuan Na Wu Decheng Ren Liangjie Liu Yan Bi Lei Ji Ke Han Mofan Feng Kai Su Fengping Yang Xi Wu Qing Lu Siran Yue Fengyan Jiang Ruirui Wang Guang He Baocheng Liu Xingwang Li Yi Shi | 2022 | Journal of Bio-X Research2022，5，3： | 0 |
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