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Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

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Science Bulletin 2016年第15期61卷 1176-1186页

作者： Yong Wang zhao-ming gao Jiang-Tao Li Salim Bougouffa Ren Mao Tian Vladimir B. Bajic Pei-Yuan Qian Sanya Institute of Deep Sea Science and Engineering ChineseAcademy of Sciences Sanya 572000 China Division of Life Science Hong Kong University of Science and Technology Clear Water Bay Hong Kong China State Key Laboratory of Marine Geology Tongji UniversityShanghai 200092 China Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal Jeddah 23955-6900 Saudi Arabia

Aerophobetes （or CD12） is a recently defined bacterial phylum, of which the metabolic processes and ecological importance remain unclear. In the present study, we obtained the draft genome of an Aerophobetes bac- terium TCSI from saline sediment near the Thuwal cold seep in the Red Sea using a genome binning method. Analysis of 16S rRNA genes of TCS1 and close relatives revealed wide distribution of Aerophobetes in deep-sea sediments. Phylogenetic relationships showed affinity between Aerophobetes TCS 1 and some thermophilic bac- terial phyla. The genome of TCS1 （at least 1.27 Mbp） contains a full set of genes encoding core metabolic path- ways, including glycolysis and pyruvate fermentation to produce acetyl-CoA and acetate. The identification of cross-membrane sugar transporter genes further indicates its potential ability to consume carbohydrates preserved inthe sediment under the microbial mat. Aerophobetes bac- terium TCS1 therefore probably carried out saccharolytic and fermentative metabolism. The genes responsible for autotrophic synthesis of acetyl-CoA via the Wood-Ljung- dahl pathway were also found in the genome. Phylogenetic study of the essential genes for the Wood-Ljungdahl pathway implied relative independence of Aerophobetes bacterium from the known acetogens and methanogens. Compared with genomes of acetogenic bacteria, Aero- phobetes bacterium TCS 1 genome lacks the genes involved in nitrogen metabolism, sulfur metabolism, signal trans- duction and cell motility. The metabolic activities of TCS 1 might depend on geochemical conditions such as supplies of CO2, hydrogen and sugars, and therefore the TCSI might be a facultative bacterium in anaerobic saline sedi- ments near cold seeps.

关键词： Deep-sea sediment Aerophobetes Metagenome Sugar fermentation Cold seep

Enrichment and characterization of ananaerobic cellulolytic microbial consortium SQD-1.1 from mangrove soil

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Enrichment and characterization of ananaerobic cellulolytic ...

Elevated progranulin contributes to synaptic and learning deficit due to loss of fragile X mental retardation protein

福建省海洋学会2014年学术年会暨福建省科协第十四届学术年会

作者： zhao-ming gao Ling-Wei Ruan Xun Xu State Key Laboratory of Marine Environmental Science College of Ocean & Earth Science Xiamen University Key Laboratory of Marine Biogenetic Resources Third Institute of OceanographyState Oceanic Administration (SOA)

Enrichment of microbial consortia provides an approach to simulate and investigate microbial communities in natural environments. In this study, a cellulolytic microbial consortium SQD-1.1 was enriched from mangrove soil of Qinglan port(Hainan, China) by 27-times continuous subcultivation under anaerobic static conditions. The consortium could completely degrade0.2%(w/v) filter paper within three days and utilized it as the sole carbon source. PCR-denaturing gradient gel electrophoresis(DGGE) analysis revealed a stable microbial community structure in the incubation process of 10 days and in the procedure of subcultivation. 24 OTUs belonging to seven phyla were obtained from the full-length 16 S rR NA gene library. Five clones, closest related to the genera Alkaliflexus, Clostridium, Alistipes, Spirochaeta and Trichococcus, were the predominant ones. Among them, M117, phylogeneticly showing high similarity(16S rR NA gene identity, 95.3%) with the cellulolytic anaerobic bacterium Clostridium straminisolvens CSK1 T, was the potential key cellulolytic bacterium. Using the plate cultivation method, twelve strains, including one potential new species and four potential new species of new genera, were isolated. The strainP 2, corresponding to the most frequently detected clone(M05) in the 16 S rR NA gene library, showed both CMCase and xylanase activity and may be another important cellulolytic bacterium. The findings of cellulase activity in cell pellet and cohesion and dockerin domains in metagenome data further suggested the potential of utilization of cellulosome by the consortium to degrade cellulose. Consortium SQD-1.1 provides a candidate for investigating the mechanism of cellulose degradation under anoxic conditions in natural environments.

关键词： microbial consortia cellulolytic bacterium mangrove cellulosome Cellulase

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中国药理学与毒理学杂志 2019年第10期 765-766页

作者： ZHANG Kun LI Yu-jiao GUO Yan-yan ZHENG Kai-yin YANG Qi YANG Le CHEN Tao ZHUO Min zhao ming-gao Department of Pharmacology School of PharmacyFourth Military Medical University Center for Neuron and Disease Frontier Institutes of Life Science and of Science and Technology Xi′an Jiaotong University Department of Anatomy Histology and Embryology and K.K.Leung Brain Research Center Fourth Military Medical University

OBJECTIVE Fragile X syndrome is an inheritable form of intellectual disability caused by loss of fragile X mental retardation protein(FMRP, encoded by the Fmr1 gene). METHODS Four protein level in brain homogenate were detected by ELISA. Morris water maze and novel object(location) were used to study changes of learning and memory. Golgi staining was used to study changes of dendritic spine density. Ed U staining was used to study number of neurogenesis in SGZ. Immunofluorescence staining was used to detect effects of exogenous protein on spine density and morphology. Patch clamp and Med64 electrophysiological technology were used to observe the effects of drugs on synaptic transmission and plasticity. Lentivirus expressing sh RNA was injected in medial prefrontal cortex(m PFC)to study gene function. RESULTS Absence of FMRP caused overexpression of progranulin(PGRN, encoded by Grn), a putative tumour necrosis factor receptor *** the present study, we found that PGRN m RNA and protein were upregulated in the of Fmr1 knock-out *** Fmr1 knock-out mice, elevated PGRN caused insufficient dendritic spine pruning and late-phase long-term potentiation in the m PFC of Fmr1 knock-out mice. Partial PGRN knock down restored spine morphology and reversed behavioural deficits, including impaired fear memory, hyperactivity, and motor inflexibility in Fmr1 knock-out mice. PGRN increased levels of phosphorylated glutamate ionotropic receptor Glu A1 and nuclear factor kappa B(NFκB) in cultured wild-type neurons. Tumour necrosis factor receptor 2(TNFR2) antibody perfusion blocked the effects of progranulin on Glu A1 phosphorylation; this result indicates that TNFR2 is required for PGRN mediated Glu A1 phosphorylation and late-phase long-term potentiation expression. However, high basal level of progranulin in Fmr1 knock-out mice prevented further facilitation of synaptic plasticity by exogenous PGRN. Partial downregulation of PGRN or TNFR2/NFκB signalling restored synaptic p

关键词： fragile X syndrome progranulin TNFR2 long-term potentiation synaptic plasticity

Investigation of bubbles escape behavior from low basicity mold flux for high-Mn high-Al steels using 3D X-ray microscope

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International Journal of Minerals,Metallurgy and Materials 2025年第1期32卷 102-110页

作者： Qiang Liu Xiang Li Shen Du ming gao Yanbin Yin Jiongming Zhang State Key Laboratory of Advanced Metallurgy University of Science and Technology BeijingBeijing 100083China

During the continuous casting process of high-Mn high-Al steels,various types of gases such as Ar need to escape through the top of the *** which,the behavior of bubbles traversing the liquid slag serves as a restrictive link,closely associated with viscosity and the thickness of liquid *** contrast to two-dimensional surface observation,three-dimensional(3D)analysis method can offer a more intuitive,accurate,and comprehensive ***,this study employs a 3D X-ray microscope(3D-XRM)to obtained spatial distribution and 3D morphological characteristics of residual bubbles in mold flux under different basicity of liquid slag,different temperatures,and different holding *** results indicate that as basicity of slag increases from 0.52 to 1.03,temperature increases from 1423 to 1573 K,the viscosity of slag decreases,the floating rate of bubbles *** addition,when holding time increases from 10 to 30 s,the bubbles floating distance increases,and the volume fraction and average equivalent sphere diameter of the bubbles solidified in the mold flux gradually *** one word,increasing the basicity,temperature,and holding time leading to an increase in the removal rate of bubbles especially for the *** findings of bubbles escape behavior provide valuable insights into optimizing low basicity mold flux for high-Mn high-Al steels.

关键词： mold flux low basicity bubbles three-dimensional X-ray microscope viscosity

Channel pruning on frequency response

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Science China(Information Sciences) 2025年第1期68卷 159-170页

作者： Hang LIN Yifan PENG Lin BIE Chenggang YAN Xibin zhao Yue gao School of Software Tsinghua University School of Automation Hangzhou Dianzi University

Network pruning has a significant role in reducing network parameters and accelerating the inference time of the network. Some existing methods prune the network based on the frequency of the data, and finally obtain a sub-network with high accuracy. However, according to our experimental analysis, different frequencies of information in the data contribute differently to the accuracy of the model, and using this information directly for pruning without making a selection will lead to incorrect results. We believe that pruning should retain the convolutional kernels in the network that process important information, while those kernels that process unimportant information should be removed. In this paper, we first investigate the meaning of each frequency band information in the spectrum and their contribution to the prediction accuracy of the network,and according to these results, we propose a new pruning method based on frequency response(PFR). Our PFR finds and removes the convolutional kernels in the network that specialize in processing unimportant information, resulting in a compact neural network model. PFR obtains significant experimental results on different datasets, for example, a 56.0% raduction of float points operations(FLOPs) on Res Net-50 and only 0.37% of Top-1 accuracy degradation on the Image Net dataset.

关键词： deep learning model compression filter pruning channel pruning frequency response

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Recent advances of metal vacancies in energy and environmental catalysis:Synthesis,characterization,and roles

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Green Energy & Environment 2025年第1期10卷 84-108页

作者： Long Sun Shunzheng zhao Sirui gao Ronghui Zhu Yiran Tan Xiaolong Tang Honghong Yi School of Energy and Environmental Engineering University of Science and Technology BeijingBeijing100083China Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants Beijing100083China

With the ongoing depletion of fossil fuels,energy and environmental issues have become increasingly critical,necessitating the search for effective ***,being one of the hallmarks of modern industry,offers a promising avenue for ***,the question of how to significantly enhance the performance of catalysts has gradually drawn the attention of *** engineering,a commonly employed and effective approach to improve catalyst activity,has become a significant research focus in the catalysis field in recent *** vacancies have received extensive attention due to their simple ***,exploration of metal vacancies has remained stagnant for a considerable period,resulting in a scarcity of comprehensive reviews on this ***,based on the latest research findings,this paper summarizes and consolidates the construction strategies for metal vacancies,characterization techniques,and their roles in typical energy and environmental catalytic ***,it outlines potential challenges in the future,aiming to provide valuable references for researchers interested in investigating metal vacancies.

关键词： Metal vacancies Catalysis Construction strategies Characterization techniques Roles

基于Fibonacci序列准周期结构的小角度低通空间滤波器

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光子学报 2017年第2期46卷 189-196页

作者：陈敏周宏敏罗朝明万婷高明盛湖南理工学院信息与通信工程学院湖南岳阳414000

利用常规材料构造了Fibonacci序列准周期结构,运用传输矩阵法研究了该结构的空间传输特性,并基于该结构优良的空间传输特性设计了小角度低通空间滤波器.数值模拟结果表明,该小角度空间滤波器的角域带宽可通过改变序列的结构类型和序列... 详细信息

利用常规材料构造了Fibonacci序列准周期结构,运用传输矩阵法研究了该结构的空间传输特性,并基于该结构优良的空间传输特性设计了小角度低通空间滤波器.数值模拟结果表明,该小角度空间滤波器的角域带宽可通过改变序列的结构类型和序列数来调谐,其调谐规律为:随着Fibonacci序列F(m,1)中m值的增加,对应空间滤波器的角域带宽减小;随着序列数的增大,对应角域带宽也减小.在调谐的基础上,还可通过改变构成准周期结构的介质折射率参量来精确调节其角域带宽.相比于基于超材料的小角度空间滤波器而言,基于Fibonacci序列的小角度空间滤波器制备更简单,且有望应用于新一代的高功率激光系统中.

关键词：信息光学空间滤波器传输矩阵法 Fibonacci序列准周期结构小角域带宽透射谱

Direct and rapid detection of serum amino acid and monoamine neurotransmitters to assist the diagnosis of panic disorder

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Science China Chemistry 2025年第1期68卷 377-384页

作者： Shiwen Liu Xuerui Wan Meng zhao Jiaqi Wang Weilan Wu Linlin You Yonggui Yuan Qian Xu Rong gao Key Laboratory of Environmental Medicine Engineering Ministry of Education School of Public Health Southeast University Key Laboratory of Modern Toxicology of Ministry of Education Department of Hygienic Analysis and Detection School of Public HealthNanjing Medical University Department of Psychosomatics and Psychiatry Zhongda Hospital School of Medicine Southeast University

The measurement of amino acid and monoamine neurotransmitters（NTs） in serum plays a central role in the identification and monitoring of clinical panic disorder（PD）. However, the strong polarity and chemical heterogeneity of NTs make direct extraction and rapid detection extremely challenging. Herein, we developed a strategy that integrated solid phase extraction based on magnetic Fe3O4coated with polydopamine（Fe3O4@PDA） and direct analysis of mass spectrometry in real time（DART-MS） for quantification of 10 NTs. We systematically investigated the optimal conditions of this strategy to achieve good accuracy and precision. Compared with existing magnetic solid phase extraction methods for NTs detection in biological samples, this strategy could adsorb more targets while having similar adsorption efficiencies, and the total process time was reduced by an average of 69.42%. We rapidly determined the metabolic abnormality of 6 types of NTs in the serum of PD patients and demonstrated their diagnostic accuracy. In addition, an outstanding feature of PD in which tryptophan was more metabolized by the KYN pathway and the 5-hydroxytryptamine pathway was inhibited could be elucidated by this strategy. Our results highlighted the potential ability of Fe3O4@PDA coupled with DART-MS to assist in the clinical diagnosis of PD.

关键词： neurotransmitters panic disorder magnetic solid phase extraction direct analysis of mass spectrometry in real time

Low-cost and fluoride-free synthesis of MFI zeolite nanosheets with enhanced stability for benzene alkylation with ethanol

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Journal of Energy Chemistry 2025年第1期100卷 458-468页

作者： Peng Zhu Cun Liu Yiren Yu Guoshu gao Yumeng zhao Xiongfu Zhang Guodong Liu Guohui Yang State Key Laboratory of Fine Chemicals School of Chemical Engineering Dalian University of Technology State Key Laboratory of Catalysis Dalian Institute of Chemical Physics Chinese Academy of Sciences

Zeolite nanosheets with a short b-axis thickness are highly desirable in lots of catalytic reactions due to their reduced diffusion resistance. Nevertheless, conventional synthesis methods usually require expensive structure-directing agents(SDAs), pricey raw materials, and eco-unfriendly fluorine-containing additives. Here, we contributed a cost-effective and fluoride-free synthesis method for synthesizing high-quality MFI zeolite nanosheets through a Silicalite-1(Sil-1) seed suspension and urea cooperative strategy, only with inexpensive colloidal silica as the Si source. Our approach was effective for synthesizing both Sil-1 and aluminum-containing ZSM-5 nanosheets. By optimizing key synthesis parameters,including seed aging time, seed quantity, and urea concentration, we achieved precise control over the crystal face aspect ratio and b-axis thickness. We also revealed a non-classical oriented nanosheet growth mechanism, where Sil-1 seeds induced the formation of quasi-ordered precursor particles, and the(010)crystal planes of these particles facilitated urea adsorption, thereby promoting c-axis-oriented *** obtained ZSM-5 nanosheets exhibited exceptional catalytic performance in the benzene alkylation with ethanol, maintaining stability for over 500 h, which is 5 times longer than traditional ZSM-5 catalysts. Furthermore, large-scale production of ZSM-5 nanosheets was successfully carried out in a 3 L highpressure autoclave, yielding samples consistent with those from laboratory-scale synthesis. This work marks a significant step forward in the sustainable and efficient production of MFI nanosheets using inexpensive and environmentally friendly raw materials, offering the broad applicability in catalysis.

关键词： Aspect ratio