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| 1 | A Chromosome-Level Genome Assembly of Garlic (Allium sativum) Provides Insights into Genome Evolution and Allicin Biosynthesis显示文摘Garlic,an economically important vegetable,spice,and medicinal crop,produces highly enlarged bulbs and unique organosulfur compounds.Here,we report a chromosome-level genome assembly for garlic,with a total size of approximately 16.24 Gb,as well as the annotation of 57561 predicted protein-coding genes,making garlic the first Allium species with a sequenced genome.Analysis of this garlic genome assembly reveals a recent burst of transposable elements,explaining the substantial expansion of the garlic genome.We examined the evolution of certain genes associated with the biosynthesis of allicin and inulin neoseries-type fructans,and provided new insights into the biosynthesis of these two compounds.Furthermore,a large-scale transcriptome was produced to characterize the expression patterns of garlic genes in different tissues and at various growth stages of enlarged bulbs.The reference genome and large-scale transcriptome data generated in this study provide valuable new resources for research on garlic biology and breeding. | Xiudong Sun Siyuan Zhu Ningyang Li Yi Cheng Jing Zhao Xuguang Qiao Li Lu Shiqi Liu Yanzhou Wang Chan Liu Benping Li Wu Guo Shuang Gao Zemao Yang Fu Li Zheng Zeng Qing Tang Yupeng Pan Mengjiao Guan Jian Zhao Xiaomi ng Lu Huanwe n Meng Zhenlin Han Chun she ng Gao Wenkai Jiang Xing Zhao Shilin Tian Jianguang Su Zhihui Cheng Touming Liu | 2020 | Molecular Plant2020，13，9： | 14 |
| 2 | Metabolic engineering of Bacillus amyloliquefaciens for efficient production ofα-glucosidase inhibitor1-deoxynojirimycin显示文摘Owing to the feature of strongα-glucosidase inhibitory activity,1-deoxynojirimycin(1-DNJ)has broad application prospects in areas of functional food,biomedicine,etc.,and this research wants to construct an efficient strain for 1-DNJ production,basing on Bacillus amyloliquefaciens HZ-12.Firstly,using the temperature-sensitive shuttle plasmid T2(2)-Ori,gene ptsG in phosphotransferase system(PTS)was weakened by homologous recombination,and non-PTS pathway was strengthened by deleting its repressor gene iolR,and 1-DNJ yield of resultant strain HZ-S2 was increased by 4.27-fold,reached 110.72 mg/L.Then,to increase precursor fructose-6-phosphate(F-6-P)supply,phosphofructokinase was weaken,fructose phosphatase GlpX and 6-phosphate glucose isomerase Pgi were strengthened by promoter replacement,moreover,regulator gene nanR was deleted,1-DNJ yield was further increased to 267.37 mg/L by 2.41-fold.Subsequently,promoter of 1-DNJ synthetase cluster was optimized,as well as 5′-UTRs of downstream genes in synthetase cluster,and 1-DNJ produced by the final strain reached 478.62 mg/L.Last but not the least,1-DNJ yield of 1632.50 mg/L was attained in 3 L fermenter,which was the highest yield of 1-DNJ reported to date.Taken together,our results demonstrated that metabolic engineering was an effective strategy for 1-DNJ synthesis,this research laid a foundation for industrialization of functional food and drugs based on 1-DNJ. | Xujie Li Meng Zhang Yu Lu Ningyang Wu Jian’gang Chen Zhixia Ji Yangyang Zhan Xin Ma Junyong Chen Dongbo Cai Shouwen Chen | 2023 | Synthetic and Systems Biotechnology2023，8，3： | 0 |
| 3 | A Noninvasive Approach to Evaluate Tumor Immune Microenvironment and Predict Outcomes in Hepatocellular Carcinoma显示文摘It is widely recognized that tumor immune microenvironment(TIME)plays a crucial role in tumor progression,metastasis,and therapeutic response.Despite several noninvasive strategies have emerged for cancer diagnosis and prognosis,there are still lack of efective radiomic-based model to evaluate TIME status,let alone predict clinical outcome and immune checkpoint inhibitor(ICIs)response for hepatocellular carcinoma(HCC).In this study,we developed a radiomic model to evaluate TIME status within the tumor and predict prognosis and immunotherapy response.A total of 301 patients who underwent magnetic resonance imaging(MRI)examinations were enrolled in our study.The intra-tumoral expression of 17 immune-related molecules were evaluated using co-detection by indexing(CODEX)technology,and we construct Immunoscore(IS)with the least absolute shrinkage and selection operator(LASSO)algorithm and Cox regression method to evaluate TIME.Of 6115 features extracted from MRI,fve core features were fltered out,and the Radiomic Immunoscore(RIS)showed high accuracy in predicting TIME status in testing cohort(area under the curve=0.753).More importantly,RIS model showed the capability of predicting therapeutic response to anti-programmed cell death 1(PD-1)immunotherapy in an independent cohort with advanced HCC patients(area under the curve=0.731).In comparison with previously radiomicbased models,our integrated RIS model exhibits not only higher accuracy in predicting prognosis but also the potential guiding signifcance to HCC immunotherapy. | Jianmin Wu Wanmin Liu Xinyao Qiu Jing Li Kairong Song Siyun Shen Lei Huo Lu Chen Mingshuang Xu Hongyang Wang Ningyang Jia Lei Chen | 2023 | Phenomics2023，3，6： | 0 |
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