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| 1 | Temperature and substrate availability regulate soil respiration in the tropical mountain rainforests,Hainan Island,China显示文摘Aims Tropical forest plays a key role in global C cycle;however,there are few studies on the C budget in the tropical rainforests in Asia.This study aims to(i)reveal the seasonal patterns of total soil respiration(R_(T)),litter respiration(R_(L))and soil respiration without surface organic litter(R_(NL))in the primary and secondary Asian tropical mountain rainforests and(ii)quantify the effects of soil temperature,soil moisture and substrate availability on soil respiration.Methods The seasonal dynamics of soil CO_(2) efflux was measured by an automatic chamber system(Li-8100),within the primary and secondary tropical mountain rainforests located at the Jianfengling National Reserve in Hainan Island,China.The litter removal treatment was used to assess the contribution of litter to belowground CO_(2) production.Important Findings The annual R_(T) was higher in the primary forest(16.73±0.87 Mg C ha−1)than in the secondary forest(15.10±0.26 Mg C ha−1).The rates of R_(T),R_(NL) and R_(L) were all significantly higher in the hot and wet season(May–October)than those in the cool and dry season(November–April).Soil temperature at 5cm depth could explain 55–61%of the seasonal variation in R_(T),and the temperature sensitivity index(Q_(10))ranked by R_(L)(Q_(10)=3.39)>R_(T)(2.17)>R_(NL)(1.76)in the primary forest and by R_(L)(4.31)>R_(T)(1.86)>R_(NL)(1.58)in the secondary forest.The contribution of R_(L) to R_(T) was 22–23%,while litter input and R_(T) had 1 month time lag.In addition,the seasonal variation of R_(T) was mainly determined by soil temperature and substrate availability.Our findings suggested that global warming and increased substrate availability are likely to cause considerable losses of soil C in the tropical forests. | Zhang Zhou Lai Jiang Enzai Du Huifeng Hu Yide Li Dexiang Chen Jingyun Fang | 2013 | Journal of Plant Ecology2013，6，5： | 8 |
| 2 | A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand显示文摘介绍研究的最近的抄写在真核细胞的染色体揭示了 antisense 抄本的一个出人意料地大的比例。这些 antisense 基因似乎由与感觉基因交往调整基因表示。以前的研究集中了于非编码的 antisense 基因,但是 antisense 蛋白质的可能的规章的角色糟糕被理解。在这研究,我们发现那基因 ADF1 作为抄写 suppressor 扮演的 antisense 编码的蛋白质,调整在 Saccharomyces cerevisiae 的感觉基因 MDF1 的表示。基于进化,基因, cytological 和生物化学的证据,我们证明编码蛋白质的感觉基因 MDF1 很可能发源从一个以前非编码的序列和罐头的 de novo 显著地在由有约束力的地席伪 2 并且这样中等的富人压制面包师的酵母的交配效率支持植物的生长。这些结果在几个重要问题上打开新灯,包括新 sense-antisense 相互作用机制,功能的基因的 de novo 起源,和交配小径的酵母的规定。 | Dan Li Yang Dong Yu Jiang Huifeng Jiang Jing Cai Wen Wang | 2010 | Cell Research2010，20，4： | 7 |
| 3 | Chromosome-level genome of Himalayan yew provides insights into the origin and evolution of the paclitaxel biosynthetic pathway显示文摘Taxus,commonly known as yew,is a well-known gymnosperm with great ornamental and medicinal value.In this study,by assembling a chromosome-level genome of the Himalayan yew(Taxus wallichiana)with 10.9 Gb in 12 chromosomes,we revealed that tandem duplication acts as the driving force of gene family evolution in the yew genome,resulting in the main genes for paclitaxel biosynthesis,i.e.those encoding the taxadiene synthase,P450s,and transferases,being clustered on the same chromosome.The tandem duplication may also provide genetic resources for the nature to sculpt the core structure of taxoids at different positions and subsequently establish the complex pathway of paclitaxel by neofunctionalization.Furthermore,we confirmed that there are two genes in the cluster encoding isoenzymes of a known enzyme in the paclitaxel biosynthetic pathway.The reference genome of the Himalayan yew will serve as a platform for decoding the complete biosynthetic pathway of paclitaxel and understanding the chemodi-versity of taxoids in gymnosperms. | Jian Cheng Xiao Wang Xiaonan Liu Xiaoxi Zhu Zihe Li Huanyu Chu Qian Wang QianQian Lou Bijun Cai Yiqun Yang Xiaoyun Lu Kai Peng Dingyu Liu Yuwan Liu Lina Lu Huan Liu Ting Yang Qijin Ge Chengcheng Shi Guichun Liu Zhiwei Dong Xun Xu Wen Wang Huifeng Jiang Yanhe Ma | 2021 | Molecular Plant2021，14，7： | 6 |
| 4 | Zanthoxylum-specific whole genome duplication and recent activity of transposable elements in the highly repetitive paleotetraploid Z.bungeanum genome显示文摘Zanthoxylum bungeanum is an important spice and medicinal plant that is unique for its accumulation of abundant secondary metabolites,which create a characteristic aroma and tingling sensation in the mouth.Owing to the high proportion of repetitive sequences,high heterozygosity,and increased chromosome number of Z.bungeanum,the assembly of its chromosomal pseudomolecules is extremely challenging.Here,we present a genome sequence for Z.bungeanum,with a dramatically expanded size of 4.23 Gb,assembled into 68 chromosomes.This genome is approximately tenfold larger than that of its close relative Citrus sinensis.After the divergence of Zanthoxylum and Citrus,the lineage-specific whole-genome duplication event q-WGD approximately 26.8 million years ago(MYA)and the recent transposable element(TE)burst~6.41 MYA account for the substantial genome expansion in Z.bungeanum.The independent Zanthoxylum-specific WGD event was followed by numerous fusion/fission events that shaped the genomic architecture.Integrative genomic and transcriptomic analyses suggested that prominent speciesspecific gene family expansions and changes in gene expression have shaped the biosynthesis of sanshools,terpenoids,and anthocyanins,which contribute to the special flavor and appearance of Z.bungeanum.In summary,the reference genome provides a valuable model for studying the impact of WGDs with recent TE activity on gene gain and loss and genome reconstruction and provides resources to accelerate Zanthoxylum improvement. | Shijing Feng Zhenshan Liu Jian Cheng Zihe Li Lu Tian Min Liu Tuxi Yang Yulin Liu Yonghong Liu He Dai Zujun Yang Qing Zhang Gang Wang Jisen Zhang Huifeng Jiang Anzhi Wei | 2021 | Horticulture Research2021，8，1： | 5 |
| 5 | Synthetic biology of plant natural products: From pathway elucidation to engineered biosynthesis in plant cells显示文摘Plant natural products(PNPs)are the main sources of drugs,food additives,and new biofuels and have become a hotspot in synthetic biology.In the past two decades,the engineered biosynthesis of many PNPs has been achieved through the construction of microbial cell factories.Alongside the rapid development of plant physiology,genetics,and plant genetic modification techniques,hosts have now expanded from single-celled microbes to complex plant systems.Plant synthetic biology is an emerging field that combines engineering principles with plant biology.In this review,we introduce recent advances in the biosynthetic pathway elucidation of PNPs and summarize the progress of engineered PNP biosynthesis in plant cells.Furthermore,a future vision of plant synthetic biology is proposed.Although we are still a long way from overcoming all the bottlenecks in plant synthetic biology,the ascent of this field is expected to provide a huge opportunity for future agriculture and industry. | Xiaoxi Zhu Xiaonan Liu Tian Liu Yina Wang Nida Ahmed Zhichao Li Huifeng Jiang | 2021 | Plant Communications2021，2，5： | 4 |
| 6 | Raising the production of phloretin by alleviation of by-product of chalcone synthase in the engineered yeast显示文摘Phloretin is an important skin-lightening and depigmenting agent from the peel of apples. Although de novo production of phloretin has been realized in microbes using the natural pathway from plants, the efficiency of phloretin production is still not enough for industrial application. Here, we established an artificial pathway in the yeast to produce phloretin via assembling two genes of p-coumaroyl-CoA ligase(4CL) and chalcone synthase(CHS). CHS is a key enzyme which conventionally condenses a CoA-tethered starter with three molecules of malonyl-CoA to form the backbone of flavonoids. However, there was 33% of byproduct generated via CHS by condensing two molecules of malonyl-CoA during the fermentation process. Hence, we introduced a more efficient CHS and improved the supply of malonyl-CoA through two pathways;the by-product ratio was decreased from 33% to 17% and the production of phloretin was improved from 48 to 83.2 mg L^(-1). Finally, a fed-batch fermentation process was optimized and the production of phloretin reached 619.5 mg L^(-1), which was 14-fold higher than that of the previous studies. Our work established a platform for the biosynthesis of phloretin from the low-cost raw material 3-(4-hydroxyphenyl) propanoic acid and also illustrated the potential for industrial scale bio-manufacturing of phloretin. | Chunmei Jiang Xiaonan Liu Xianqing Chen Yi Cai Yibin Zhuang Tian Liu Xiaoxi Zhu Hui Wang Yuwan Liu Huifeng Jiang Wen Wang | 2020 | Science China(Life Sciences)2020，63，11： | 3 |
| 7 | Discovery and modification of cytochrome P450 for plant natural products biosynthesis显示文摘Cytochrome P450s are widespread in nature and play key roles in the diversification and functional modification of plant natural products.Over the last few years,there has been remarkable progress in plant P450s identification with the rapid development of sequencing technology,“omics”analysis and synthetic biology.However,challenges still persist in respect of crystal structure,heterologous expression and enzyme engineering.Here,we reviewed several research hotspots of P450 enzymes involved in the biosynthesis of plant natural products,including P450 databases,gene mining,heterologous expression and protein engineering. | Xiaonan Liu Xiaoxi Zhu Hui Wang Tian Liu Jian Cheng Huifeng Jiang | 2020 | Synthetic and Systems Biotechnology2020，5，3： | 2 |
| 8 | The origin and evolution of the diosgenin biosynthetic pathway in yam显示文摘Diosgenin,mainly produced by Dioscorea species,is a traditional precursor of most hormonal drugs in the pharmaceutical industry.The mechanisms that underlie the origin and evolution of diosgenin biosynthesis in plants remain unclear.After sequencing the whole genome of Dioscorea zingiberensis,we revealed the evolutionary trajectory of the diosgenin biosynthetic pathway in Dioscorea and demonstrated the de novo biosynthesis of diosgenin in a yeast cell factory.First,we found that P450 gene duplication and neofunctionalization,driven by positive selection,played important roles in the origin of the diosgenin biosynthetic pathway.Subsequently,we found that the enrichment of diosgenin in the yam lineage was regulated by CpG islands,which evolved to regulate gene expression in the diosgenin pathway and balance the carbon flux between the biosynthesis of diosgenin and starch.Finally,by integrating genes fromplants,animals,and yeast,weheterologously synthesized diosgenin to 10mg/l in genetically-engineered yeast.Our study not only reveals the origin and evolutionary mechanisms of the diosgenin biosynthetic pathway in Dioscorea,but also introduces an alternative approach for the production of diosgenin through synthetic biology. | Jian Cheng Jing Chen Xiaonan Liu Xiangchen Li Weixiong Zhang Zhubo Dai Lina Lu Xiang Zhou Jing Cai Xueli Zhang Huifeng Jiang Yanhe Ma | 2021 | Plant Communications2021，2，1： | 2 |
| 9 | NUPR1 promotes the proliferation and metastasis of oral squamous cell carcinoma cells by activating TFE3-dependent autophagy显示文摘Oral squamous cell carcinoma(OSCC)is the most common type of oral malignancy,and metastasis accounts for the poor prognosis of OSCC.Autophagy is considered to facilitate OSCC development by mitigating various cellular stresses;nevertheless,the mechanisms of autophagy in OSCC cell proliferation and metastasis remain unknown.In our study,high-sensitivity label-free quantitative proteomics analysis revealed nuclear protein 1(NUPR1)as the most significantly upregulated protein in formalin-fixed paraffin-embedded tumour samples derived from OSCC patients with or without lymphatic metastasis. | Tengfei Fan Xiaoning Wang Sheng Zhang Ping Deng Yi Jiang Yidan Liang Sheng Jie Qing Wang Chuwen Li Guocai Tian Zhen Zhang Zhenhu Ren Bo Li Yanrong Chen Zhijing He Yan Luo Mingliang Chen Hanjiang Wu Zhengping Yu Huifeng Pi Zhou Zhou Zhiyuan Zhang | 2022 | Signal Transduction and Targeted Therapy2022，7，5： | 2 |
| 10 | Crystallization Kinetics of Lithium Aluminum Germanium Phosphate Glass by DSC Technique显示文摘The crystallization kinetics of Li2O-Al2O3-GeO2-P2O5 (LAGP) glass fabricated via the conventional melt-quenching method was studied by differential scanning calorimetry (DSC) under non-isothermal condition at different heating rates. The activation energy of glass transition Eg is 634.4 kJ/mol, indicating that LAGP glass is easy to crystallize at an elevated temperature. The activation energy of crystallization Ec and Avrami index n obtained from Matusita's model are 442.01 kJ/mol and 1.7, respectively. The value of n reveals that bulk crystallization predominates slightly over surface crystallization during crystallization process. LAGP glass-ceramics after different heat treatments have the same crystalline phases determined as major phase LiGe2(PO4)3, with AlPO4 and GeO2 as their impurity phases. | 何坤 WANG Yanhang 祖成奎 LIU Yonghua ZHAO Huifeng HAN Bin CHENG Jiang | 2012 | Journal of Wuhan University of Technology(Materials Science)2012，27，1： | 2 |
| 11 | pUGTdb:A comprehensive database of plant UDP-dependent glycosyltransferases显示文摘Dear Editor,Plant UDP-dependent glycosyltransferases(UGTs),belonging to the carbohydrate-active enzyme glycosyltransferase 1 family(Louveau and Osbourn,2019),not only play important roles in adaptation to various environments(Cai et al.,2020;Pastorczyk-Szlenkier and Bednarek,2021)but also endow plant natural products with great pharmaceutical and ecological significance(Margolin et al.,2020).In recent years,an increasing number of plant UGTs have been characterized to function in the biosynthesis of many bioactive compounds such as ginsenosides(Wei et al.,2015),breviscapine(Liu et al.,2018),and rubusoside(Xu et al.,2022). | Yuqian Liu Qian Wang Xiaonan Liu Jian Chengi Lei Zhang Huanyu Chu Ruoyu Wang Haoran Li Hong Chang Nida Ahmed Zhonghua Wang Xiaoping Liao Huifeng Jiang | 2023 | Molecular Plant2023，16，4： | 1 |
| 12 | Multi‑omics reveals that the host‑microbiome metabolism crosstalk of differential rumen bacterial enterotypes can regulate the milk protein synthesis of dairy cows显示文摘Background Dairy cows’lactation performance is the outcome of the crosstalk between ruminal microbial metabo-lism and host metabolism.However,it is still unclear to what extent the rumen microbiome and its metabolites,as well as the host metabolism,contribute to regulating the milk protein yield(MPY).Methods The rumen fluid,serum and milk of 12 Holstein cows with the same diet(45%coarseness ratio),parity(2–3 fetuses)and lactation days(120–150 d)were used for the microbiome and metabolome analysis.Rumen metabolism(rumen metabolome)and host metabolism(blood and milk metabolome)were connected using a weighted gene co-expression network(WGCNA)and the structural equation model(SEM)analyses.Results Two different ruminal enterotypes,with abundant Prevotella and Ruminococcus,were identified as type1 and type2.Of these,a higher MPY was found in cows with ruminal type2.Interestingly,[Ruminococcus]gauvreauii group and norank_f_Ruminococcaceae(the differential bacteria)were the hub genera of the network.In addition,differential ruminal,serum and milk metabolome between enterotypes were identified,where the cows with type2 had higher L-tyrosine of rumen,ornithine and L-tryptophan of serum,and tetrahydroneopterin,palmitoyl-L-carnitine,S-lactoylglutathione of milk,which could provide more energy and substrate for MPY.Further,based on the identi-fied modules of ruminal microbiome,as well as ruminal serum and milk metabolome using WGCNA,the SEM analysis indicated that the key ruminal microbial module1,which contains the hub genera of the network([Ruminococcus]gauvreauii group and norank_f_Ruminococcaceae)and high abundance of bacteria(Prevotella and Ruminococcus),could regulate the MPY by module7 of rumen,module2 of blood,and module7 of milk,which contained L-tyrosine and L-tryptophan.Therefore,in order to more clearly reveal the process of rumen bacterial regulation of MPY,we established the path of SEM based on the L-tyrosine,L-tryptophan and related components.The SEM based on the metabolites suggested that[Ruminococcus]gauvreauii group could inhibit the energy supply of serum tryptophan to MPY by milk S-lactoylglutathione,which could enhance pyruvate metabolism.Norank_f_Ruminococcaceae could increase the ruminal L-tyrosine,which could provide the substrate for MPY.Conclusion Our results indicated that the represented enterotype genera of Prevotella and Ruminococcus,and the hub genera of[Ruminococcus]gauvreauii group and norank_f_Ruminococcaceae could regulate milk protein synthesis by affecting the ruminal L-tyrosine and L-tryptophan.Moreover,the combined analysis of enterotype,WGCNA and SEM could be used to connect rumen microbial metabolism with host metabolism,which provides a fundamental understanding of the crosstalk between host and microorganisms in regulating the synthesis of milk composition. | Chenguang Zhang Mengya Wang Huifeng Liu Xingwei Jiang Xiaodong Chen Tao Liu Qingyan Yin Yue Wang Lu Deng Junhu Yao Shengru Wu | 2023 | Journal of Animal Science and Biotechnology2023，14，6： | 1 |
| 13 | The Relation Between Morphology of (Co) MoS2 Phases and Selective Hydrodesulfurization for CoMo Catalysts显示文摘 | Mingfeng Li Huifeng Li Feng Jiang | 2010 | Catal Today2010，149，12： | 1 |
| 14 | Metabolic engineering of Yarrowia lipolytica for scutellarin production显示文摘Scutellarin related drugs have superior therapeutic effects on cerebrovascular and cardiovascular diseases.Here,an optimal biosynthetic pathway for scutellarin was constructed in Yarrowia lipolytica platform due to its excellent metabolic potential.By integrating multi-copies of core genes from different species,the production of scutellarin was increased from 15.11 mg/L to 94.79 mg/L and the ratio of scutellarin to the main by-product was improved about 110-fold in flask condition.Finally,the production of scutellarin was improved 23-fold and reached to 346 mg/L in fed-batch bioreactor,which was the highest reported titer for de novo production of scutellarin in microbes.Our results represent a solid basis for further production of natural products on unconventional yeasts and have a potential of industrial implementation. | Yina Wang Xiaonan Liu Bihuan Chen Wei Liu Zhaokuan Guo Xiangyu Liu Xiaoxi Zhu Jiayu Liu Jin Zhang Jing Li Lei Zhang Yadi Gao Guanghui Zhang Yan Wang MIqbal Choudhary Shengchao Yang Huifeng Jiang | 2022 | Synthetic and Systems Biotechnology2022，7，3： | 1 |
| 15 | On the propagation and pulsation of Portevin-Le Chatelier deformation bands: An experimental study with digital speckle pattern metrology显示文摘 | Qingchuan Zhang Zhenyu Jiang Huifeng Jiang | 2005 | International Journal of Plasticity2005，21，： | 1 |
| 16 | Cloning and developmental expression of the Xenopus Nkx6 genes显示文摘 | Shuhua Zhao Huifeng Jiang Wen Wang Bingyu Mao | | 0，2007，： | 1 |
| 17 | PCPD:Plant cytochrome P450 database and web-based tools for structural construction and ligand docking显示文摘Plant cytochrome P450s play key roles in the diversification and functional modification of plant natural products.Although over 200,000 plant P450 gene sequences have been recorded,only seven crystalized P450 genes severely hampered the functional characterization,gene mining and engineering of important P450s.Here,we combined Rosetta homologous modeling and MD-based refinement to construct a high-resolution P450 structure prediction process(PCPCM),which was applied to 181 plant P450s with identified functions.Furthermore,we constructed a ligand docking process(PCPLD)that can be applied for plant P450s virtual screening.10 examples of virtual screening indicated the process can reduce about 80%screening space for next experimental verification.Finally,we constructed a plant P450 database(PCPD:http://gffzz90f9b80da1174166hu55uk6cqubwc6f9u.ffgz.tsg.suse.edu.cn/),which includes the sequences,structures and functions of the 181 plant P450s,and a web service based on PCPCM and PCPLD.Our study not only developed methods for the P450-specific structure analysis,but also introduced a universal approach that can assist the mining and functional analysis of P450 enzymes. | Hui Wang Qian Wang Yuqian Liu Xiaoping Liao Huanyu Chu Hong Chang Yang Cao Zhigang Li Tongcun Zhang Jian Cheng Huifeng Jiang | 2021 | Synthetic and Systems Biotechnology2021，6，2： | 1 |
| 18 | Identification and histopathological and pathogenicity analysis of Aeromonas salmonicida salmonicida from goldfish (Carassius auratus) in North China显示文摘In this study,bacterial pathogens were isolated from the liver,spleen,kidney,heart,and muscle of diseased goldfish(Carassius auratus)after a massive outbreak of disease in an aquaculture farm in Anshan,Liaoning Province,North China(N41°05′58.42″E122°53′31.89″).Based on physiological and biochemical characterization of the bacteria and 16S rDNA sequence analysis,the bacterial isolates were identified as Aeromonas salmonicida salmonicida.Virulence gene multilocus sequence typing analysis showed that the bacterial isolates from all the organs collected were of the same type,and clustered in the same phylogenetic group as A.salmonicida salmonicida.The pathogen,was named AS.17 and was resistant to rifampicin,bacitracin,vancomycin,penicillin and compound sulfamethoxazole,but was highly sensitive to nalidixic acid,lomefloxacin,spectinomycin,ofloxacin,and ciprofloxacin.Goldfish experimentally infected with AS.17 had similar symptoms to naturally infected fish,including gill filament anemia,intestinal bleeding,intra-abdominal fluid,and jaw bleeding.Histological analyses showed that the liver,the spleen,the kidney and the intestines of fish infected with AS.17 had severe pathological alterations.In summary,this study reports the isolation of A.salmonicida salmonicida from C.auratus in North China and provides a reference strain and a research foundation for further studies on A.salmonicida disease control and epidemiology. | Shibo Jin Songzhe Fu Ruijun Li Huifeng Dang Dongxu Gao Shigen Ye Zhiqiang Jiang | 2020 | Aquaculture and Fisheries2020，5，1： | 1 |
| 19 | Spatial characteristics of the Portevin-Le Chatelier deformationbands in Al-4 at % Cu polyerystals显示文摘 | Zhenyu Jiang Qingehuan Zhang Huifeng Jiang | 2005 | Materials Science and Engineering A2005，403，： | 1 |
| 20 | On the propagation and pulsation of Portevin-Le Chatelier deformation bands: An experimental study with digital speckle pattern metrology 显示文摘 | Qingchuan Zhang Zhenyu Jiang Huifeng Jiang | 2005 | International Journal ofPlasticity2005，21，： | 1 |
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