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Genome-wide CRISPR screening reveals key genes and pathways associated with 20-hydroxyecdysone signal transduction in the silkworm(Bombyx mori)

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Insect science 2024年第1期31卷 47-58页

作者： Hao Sun Jingya Chen Ruolin Wang Dan Liu Na Zhang Tong Zhang Ling Jia Sanyuan Ma Qingyou Xia State Key Laboratory of Silkworm Genome Biology Southwest UniversityChongqingChina biological science research center Southwest UniversityChongqingChina

Metamorphosis is a complex developmental process involving multiple pathways and a large number of genes that are regulated by juvenile hormone(JH)and 20-hydroxyecdysone(20E).Despite important progress in understanding various aspects of silkworm biology,the hormone signaling pathway in the silkworm remains poorly understood.Genome-wide screening using clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)-based libraries has recently emerged as a novel method for analyzing genome function,enabling further research into essential genes,drug targets,and virus-host interaction.Previously,we constructed a genome-wide CRISPR/Cas9-based library of the silkworm(Bombyx mori)and successfully revealed the genes involved in biotic or abiotic stress factor responses.In this study,we used our silkworm CRISPR library and large-scale genome-wide screening to analyze the key genes in the silkworm 20E signaling pathway and their mechanisms of action.Functional annotation showed that 20E regulates key proteins in processes that mainly occur in the cytoplasm and nucleus.Pathway enrichment analysis showed that 20E can activate phosphorylation and may affect innate immunity,interfere with intracellular nutrition and energy metabolism,and eventually cause cell apoptosis.The screening results were experimentally validated by generating cells with knockout alleles of the relevant genes,which had increased tolerance to 20E.Our findings provide a panoramic overview of signaling in response to 20E in the silkworm,underscoring the utility of genome-wide CRISPR mutant libraries in deciphering hormone signaling pathways and the mechanisms that regulate metamorphosis in insects.

关键词： CRISPR/Cas9 CRISPR library screening ecdysone 20E signal transduction silkworm whole genome editing

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How variable progenitor clones construct a largely invariant neocortex

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National science Review 2024年第1期11卷 129-144页

作者： Zhongfu Shen Jiajun Yang Qiangqiang Zhang Kuiyu Wang Xiaohui Lv Xiaolin Hu Jian Ma Song-Hai Shi New Cornerstone science Laboratory IDG/McG overn Institute for Brain Research Tsinghua-Peking Center for Life Sciences Beijing Frontier Research Center for Biological Structure School of Life Sciences Tsinghua University Department of Computer sciences Tsinghua University College of Life sciences Nankai University Chinese Institute for Brain research

The neocortex contains a vast collection of diverse neurons organized into distinct layers. While nearly all neocortical neurons are generated by radial glial progenitors(RGPs), it remains largely unclear how a complex yet organized neocortex is constructed reliably and robustly. Here, we show that the division behavior and neuronal output of RGPs are highly constrained with patterned variabilities to support the reliable and robust construction of the mouse neocortex. The neurogenic process of RGPs can be well-approximated by a consistent Poisson-like process unfolding over time, producing deep to superficial layer neurons progressively. The exact neuronal outputs regarding layer occupation are variable; yet, this variability is constrained systematically to support all layer formation, largely reflecting the variable intermediate progenitor generation and RGP neurogenic entry and exit timing differences. Together, these results define the fundamental features of neocortical neurogenesis with a balanced reliability and variability for the construction of the complex neocortex.

关键词： neocortex radial glial progenitor intermediate progenitor neurogenesis clonal variability layer formation

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Identification of overlay differentially expressed genes in both rats and goats with blast lung injury through comparative transcriptomics

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Chinese Journal of Traumatology 2024年第1期27卷 34-41页

作者： Hong Wang Jun-Hong Gao Xiao-Lin Fan Qing Lu Liang Li Ning Ma Qi Wang Yu-Hao Zhang Xi'an Key Laboratory of Toxicology and biological Effects Research Center for Toxicological and Biological EffectsInstitute for Hygiene of Ordnance IndustryXi'an710065China

Purpose:To identify the potential target genes of blast lung injury(BLI)for the diagnosis and treatment.Methods:This is an experimental study.The BLI models in rats and goats were established by conducting a fuel-air explosive power test in an unobstructed environment,which was subsequently validated through hematoxylin-eosin staining.Transcriptome sequencing was performed on lung tissues from both goats and rats.Differentially expressed genes were identified using the criteria ofq≤0.05 and|log2 fold change|≥1.Following that,enrichment analyses were conducted for gene ontology and the Kyoto Encyclopedia of Genes and Genomes pathways.The potential target genes were further confirmed through quantitative real-time polymerase chain reaction and enzyme linked immunosorbent assay.Results:Observations through microscopy unveiled the presence of reddish edema fluid,erythrocytes,and instances of focal or patchy bleeding within the alveolar cavity.Transcriptome sequencing analysis identified a total of 83 differentially expressed genes in both rats and goats.Notably,49 genes exhibited a consistent expression pattern,with 38 genes displaying up-regulation and 11 genes demonstrating down-regulation.Enrichment analysis highlighted the potential involvement of the interleukin-17 signaling pathway and vascular smooth muscle contraction pathway in the underlying mechanism of BLI.Furthermore,the experimental findings in both goats and rats demonstrated a strong association between BLI and several key genes,including anterior gradient 2,ankyrin repeat domain 65,bactericidal/permeability-increasing fold containing family A member 1,bactericidal/permeability-increasing fold containing family B member 1,and keratin 4,which exhibited up-regulation.Conclusions:Anterior gradient 2,ankyrin repeat domain 65,bactericidal/permeability-increasing fold containing family A member 1,bactericidal/permeability-increasing fold containing family B member 1,and keratin 4 hold potential as target genes for the prognosis,diagnosis,and treatment of BL

关键词： Blast lung injury Transcriptomic Target genes Differentially expressed genes

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On-surface synthesis and characterization of polyynic carbon chains

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National science Review 2024年第3期11卷 192-199页

作者： Wenze Gao Wei Zheng Luye Sun Faming Kang Zheng Zhou Wei Xu Interdisciplinary Materials research center School of Materials Science and Engineering Tongji University

Carbyne, an elusive sp-hybridized linear carbon allotrope, has fascinated chemists and physicists for decades. Due to its high chemical reactivity and extreme instability, carbyne was much less explored in contrast to the sp2-hybridized carbon allotropes such as graphene. Herein, we report the on-surface synthesis of polyynic carbon chains by demetallization of organometallic polyynes on the Au（111） surface;the longest one observed consists of ～60 alkyne units（120 carbon atoms）. The polyynic structure of carbon chains with alternating triple and single bonds was unambiguously revealed by bond-resolved atomic force microscopy. Moreover, an atomically precise polyyne, C14, was successfully produced via tip-induced dehalogenation and ring-opening of the decachloroanthracene molecule(C14Cl10) on a bilayer NaCl/Au（111） surface at 4.7 K, and a band gap of 5.8 eV was measured by scanning tunnelling spectroscopy,in a good agreement with the theoretical HOMO–LUMO gap（5.48 eV）.

关键词： polyyne scanning probe microscopy carbon allotrope on-surface synthesis organometallic polyyne

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Targeted DNA N^(6)-methyladenine editing by dCas9 fused to METTL4 in the lepidopteran model insect Bombyx mori

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Insect science 2024年第2期31卷 646-650页

作者： Feng Chen Hao Guo Weiqun Lan Mingyi Zhou Wenjng Geng Guanwang Shen Ping Lin Qingyou Xia Ping Zhao Zhiqing Li Integrative science center of Germplasm Creation in Western China(CHONGQING)science City Biological Science Research CenterSouthwest UniversityChongqingChina Chongqing Key Laboratory of Sericultural science Chongqing Engineering and Technology Research Center for Novel Silk MaterialsSouthwest UniversityChongqingChina

Dear Editor,N^(6)-Methyladenine(6mA)DNA modification is an important epigenetic mechanism with roles in regulating gene expression,nucleosome positioning,DNA damage repair,and cell cycle progression(Heyn&Esteller,2015;Luo et al.,2015;Boulias&Greer,2022).Despite progress in understanding the biological functions of 6mA,the contribution of individual 6mA installations on site-specific target genes is largely unknown,and therefore deciphering the molecular mechanism of 6mA in target gene expression has been difficult.

关键词： adenine fused Bombyx

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Chromosomal-level genome and metabolome analyses of highly heterozygous allohexaploid Dendrocalamus brandisii elucidate shoot quality and developmental characteristics

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Journal of Integrative Plant Biology 2024年第6期66卷 1087-1105页

作者： Jutang Jiang Zeyu Zhang Yucong Bai Xiaojing Wang Yuping Dou Ruiman Geng Chongyang Wu Hangxiao Zhang Cunfu Lu Lianfeng Gu Jian Gao Key Laboratory of National Forestry and Grassland Administration Beijing for Bamboo & Rattan Science and Technology Institute of Gene Science and Industrialization for Bamboo and Rattan Resources International Center for Bamboo and Rattan College of Forestry Basic Forestry and Proteomics Research Center Fujian Agriculture and Forestry University School of Life science Peking University College of biological sciences and Biotechnology Beijing Forestry University

Dendrocalamus brandisii(Munro) Kurz is a sympodial bamboo species with inimitable taste and flavorful shoots. Its rapid growth and use as high-quality material make this bamboo species highly valued for both food processing and wood applications. However, genome information for D. brandisii is lacking, primarily due to its polyploidy and large genome size.Here, we assembled a high-quality genome for hexaploid D. brandisii, which comprises 70chromosomes with a total size of 2,756 Mb,using long-read Hi Fi sequencing. Furthermore,we accurately separated the genome into its three constituent subgenomes. We used Oxford Nanopore Technologies long reads to construct a transcriptomic dataset covering 15 tissues for gene annotation to complement our genome assembly, revealing differential gene expression and post-transcriptional regulation. By integrating metabolome analysis, we unveiled that well-balanced lignin formation, as well as abundant flavonoid and fructose contents,contribute to the superior quality of D. brandisii shoots. Integrating genomic, transcriptomic,and metabolomic datasets provided a solid foundation for enhancing bamboo shoot quality and developing efficient gene-editing techniques. This study should facilitate research on D. brandisii and enhance its use as a food source and wood material by providing crucial genomic resources.

关键词： bamboo shoots Dendrocalamus brandisii (Munro) Kurz flavonoid genome lignin

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Cardiac energy metabolism disorder mediated by energy substrate imbalance and mitochondrial damage upon tebuconazole exposure

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Journal of Environmental sciences 2024年第2期136卷 270-278页

作者： Tingting Ku Jindong Hu Mengmeng Zhou Yuanyuan Xie Yutong Liu Xin Tan Lin Guo Guangke Li Nan Sang College of Environmental science and Resources Research Center of Environment and HealthShanxi UniversityTaiyuan 030006China

Tebuconazole exposure has been described as an increasing hazard to human health.An increasing number of recent studies have shown a positive association between tebuconazole exposure and cardiovascular disease risk,which is characterized by the reduction of adenosine triphosphate(ATP)synthesis.However,researches on the damage of tebuconazole exposure to energy metabolism and the related molecular mechanisms are limited.In the present study,male C57BL/6 mice were treated with tebuconazole at different low concentrations for 4 weeks.The results indicated that tebuconazole could accumulate in the heart and further induce the decrease of ATP content in the mouse heart.Importantly,tebuconazole induced an obvious shift in substrate utilization of fatty acid and glucose by disrupting their corresponding transporters(GLUT1,GLUT4,CD36,FABP3 and FATP1)expression,and significantly repressed the expression of mitochondrial biogenesis(Gabpa and Tfam)and oxidative phosphorylation(CS,Ndufa4,Sdhb,Cox5a and Atp5b)related genes in a dosedependent manner.Further investigation revealed that these alterations were related to the IRS1/AKT and PPARγ/RXRαpathways.These findings contribute to a better understanding of triazole fungicide-induced cardiovascular disease by revealing the key indicators associated with this phenomenon.

关键词： Tebuconazole Cardiotoxicity Energy metabolic disorders Energy substrate Mitochondrial damage

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Safety assessment of a novel marine multi-stress-tolerant yeast Meyerozyma guilliermondii GXDK6 according to phenotype and whole genome-sequencing analysis

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Food science and Human Wellness 2024年第4期13卷 2048-2059页

作者： Xueyan Mo Mengcheng Zhou Yanmei Li Lili Yu Huashang Bai Peihong Shen Xing Zhou Haojun Zhu Huijie Sun Ru Bu Chengjian Jiang State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources Guangxi Research Center for Microbial and Enzyme Engineering TechnologyCollege of Life Science and TechnologyGuangxi UniversityNanning 530004China National Engineering research center for Non-Food Biorefinery State Key Laboratory of Non-Food Biomass and Enzyme TechnologyGuangxi Research Center for Biological Science and TechnologyGuangxi Academy of SciencesNanning 530007China Guangxi Key Laboratory for Green Processing of Sugar Resources College of Biological and Chemical EngineeringGuangxi University of Science and TechnologyLiuzhou 545006China

The application of microorganisms as probiotics is limited due to lack of safety evaluation.Here,a novel multi-stress-tolerant yeast Meyerozyma guilliermondii GXDK6 with aroma-producing properties was identified from marine mangrove microorganisms.Its safety and probiotic properties were assessed in accordance with phenotype and whole-genome sequencing analysis.Results showed that the genes and phenotypic expression of related virulence,antibiotic resistance and retroelement were rarely found.Hyphal morphogenesis genes(SIT4,HOG1,SPA2,ERK1,ICL1,CST20,HSP104,TPS1,and RHO1)and phospholipase secretion gene(VPS4)were annotated.True hyphae and phospholipase were absent.Only one retroelement(Tad1-65_BG)was found.Major biogenic amines(BAs)encoding genes were absent,except for spermidine synthase(JA9_002594),spermine synthase(JA9_004690),and tyrosine decarboxylase(inx).The production of single BAs and total BAs was far below the food-defined thresholds.GXDK6 had no resistance to common antifungal drugs.Virulence enzymes,such as gelatinase,DNase,hemolytic,lecithinase,and thrombin were absent.Acute toxicity test with mice demonstrated that GXDK6 is safe.GXDK6 has a good reproduction ability in the simulation gastrointestinal tract.GXDK6 also has a strong antioxidant ability,β-glucosidase,and inulinase activity.To sum up,GXDK6 is considered as a safe probiotic for human consumption and food fermentation.

关键词： Meyerozyma guilliermondii Safety assessment Probiotics Marine mangrove microorganisms Whole-genome sequencing analysis

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The application of protease in aquaculture: Prospects for enhancing the aquafeed industry

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Animal Nutrition 2024年第1期16卷 105-121页

作者： Shiyou Chen Sahya Maulu Jie Wang Xiaoze Xie Xiaofang Liang Hao Wang Junjun Wang Min Xue National Aquafeed Safety Assessment center Institute of Feed Research Chinese Academy of Agricultural Sciences State Key Laboratory of Animal Nutrition College of Animal Science and Technology China Agricultural University School of biological and Marine sciences Faculty of Science and Engineering University of Plymouth Centre for Innovative Approach Zambia (CIAZ)

Low-fishmeal and protein-saving diets are two prominent nutritional strategies utilized to address challenges related to the scarcity and sustainability of protein sources in aquaculture. However, these diets have been associated with adverse effects on the growth performance, feed utilization, and disease resistance of aquatic animals. To mitigate these challenges, exogenous protease has been applied to enhance the quality of diets with lower protein contents or fishmeal alternatives, thereby improving the bioavailability of nutritional ingredients. Additionally, protease preparations were also used to enzymatically hydrolyze fishmeal alternatives, thus enhancing their nutritional utilization. The present review aims to consolidate recent research progress on the use of protease in aquaculture and conclude the benefits and limitations of its application, thereby providing a comprehensive understanding of the subject and identifying opportunities for future research.

关键词： Protease Low-fishmeal diet Protein-saving diets Exogenous digestive enzyme Aquafeed

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Structural insights into the Oryza sativa cation transporters HKTs in salt tolerance

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Journal of Integrative Plant Biology 2024年第4期66卷 700-708页

作者： Ran Gao Yutian Jia Xia Xu Peng Fu Jiaqi Zhou Guanghui Yang State Key Laboratory of Plant Environmental Resilience Frontiers Science Center for Molecular Design BreedingCollege of Biological SciencesChina Agricultural UniversityBeijing 100193China

The high-affinity potassium transporters(HKTs),selectively permeable to either Na^(+)alone or Na^(+)/K^(+),play pivotal roles in maintaining plant Na^(+)/K^(+)homeostasis.Although their involvement in salt tolerance is widely reported,the molecular underpinnings of Oryza sativa HKTs remain elusive.In this study,we elucidate the structures of OsHKT1;1 and OsHKT2;1,representing two distinct classes of rice HKTs.The dimeric assembled OsHKTs can be structurally divided into four domains.At the dimer interface,a half-helix or a loop in the third domain is coordinated by the C-terminal region of the opposite subunit.Additionally,we present the structures of OsHKT1;5 salt-tolerant and salt-sensitive variants,a key quantitative trait locus associated with salt tolerance.The salt-tolerant variant of OsHKT1;5 exhibits enhanced Na^(+)transport capability and displays a more flexible conformation.These findings shed light on the molecular basis of rice HKTs and provide insights into their role in salt tolerance.

关键词： HKT salt-tolerant structure

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