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Amino acids TORC(talk)to anabolism through uncharged tRNA

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Science China(Life Sciences) 2024年第8期67卷 1775-1776页

作者： Zhen-Zhen Ma Shi-Min Zhao The Obstetrics&Gynecology Hospital of Fudan University State Key Laboratory of Genetic EngineeringShanghai Key Laboratory of Metabolic Remodelling and HealthFudan UniversityShanghai 200090China

Anabolism is essential for proliferation as well as to replenish dysfunctional macromolecules in *** to that both substantial building blocks and energy are required for anabolism,cells must double check whether these prerequisites are met before deciding to start *** acids are building blocks of protein synthesis,their sufficiency in cells is closely monitored by several mechanisms,which all are linked to protein synthesis.

关键词： synthesis. synthesis deciding

Transfer of disulfide bond formation modules via yeast artificial chromosomes promotes the expression of heterologous proteins in Kluyveromyces marxianus

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mLife 2024年第1期3卷 129-142页

作者： Pingping Wu Wenjuan Mo Tian Tian Kunfeng Song Yilin Lyu Haiyan Ren Jungang Zhou Yao Yu Hong Lu state key Laboratory of genetic engineering School of Life SciencesFudan UniversityShanghaiChina Shanghai engineering Research Center of Industrial Microorganisms ShanghaiChina

Kluyveromyces marxianus is a food-safe yeast with great potential for producing heterologous *** the yield in *** remains a challenge and incorporating large-scale functional modules poses a technical obstacle in *** address these issues,linear and circular yeast artificial chromosomes of ***(KmYACs)were constructed and loaded with disulfide bond formation modules from Pichia pastoris or *** modules contained up to seven genes with a maximum size of 15 *** carried telomeres either from *** or *** were transferred successfully into *** and stably propagated without affecting the normal growth of the host,regardless of the type of telomeres and configurations of *** increased the overall expression levels of disulfide bond formation genes and significantly enhanced the yield of various heterologous *** high-density fermentation,the use of KmYACs resulted in a glucoamylase yield of 16.8 g/l,the highest reported level to date in *** and metabolomic analysis of cells containing KmYACs suggested increased flavin adenine dinucleotide biosynthesis,enhanced flux entering the tricarboxylic acid cycle,and a preferred demand for lysine and arginine as features of cells overexpressing heterologous ***,supplementing lysine or arginine further improved the ***,KmYAC provides a powerful platform for manipulating large modules with enormous potential for industrial applications and fundamental *** the disulfide bond formation module via YACs proves to be an efficient strategy for improving the yield of heterologous proteins,and this strategy may be applied to optimize other microbial cell factories.

关键词： disulfide bond formation expression of heterologous proteins Kluyveromyces marxianus telomere yeast artificial chromosome

Research on Bast Fiber Extracted from the White Bark of Three Species in the Genus Broussonetia

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Chinese Journal of Polymer Science 2024年第6期42卷 729-738页

作者： Shan-Shan Jin Si-Nong Wang Yan-Yan Huang Jing-Yu Zhang Peng Liu Hui Yu Hong-Dong Zhang Yu-Liang Yang Institute for Preservation and Conservation of Chinese Ancient Books Fudan University LibraryFudan UniversityShanghai200433China state key laboratory of Molecular engineering of polymers Department of Macromolecular ScienceFudan UniversityShanghai200433China

Against the backdrop of a global paper resource shortage,there is a growing need to identify fast-growing tree species capable of producing long-lasting *** plant species namely Broussonetia kazinoki,Broussonetia papyrifera and hybrid paper mulberry,belong to the Broussonetia genus,were collected from China to study their white bark suitability for pulp and *** chemical composition revealed that the holocellulose content in Broussonetia kazinoki and Broussonetia papyrifera was more than 80%.The molecular weight distribution of several holocellulose/α-cellulose is observed by GPC,which allows us to better observe the changes of various components on the molecular *** yield,lignin,whiteness,and molecular weight of the pulps obtained by NaOH treatment were *** microscope was used to characterize the fiber length-width ratio and ***,the improvement of the fiber rigidity method based on the Kratky-Porod chain model makes it more theoretical and further reveals the influencing factors of fiber *** study demonstrates the high potentiality of these three species for papermaking applications.

关键词： Broussonetia genus Cellulose Alkaline pulping Kratky-Porod chain model Fiber rigidity

Post-transcriptional regulation of grain weight and shape by the RBP-A-J-K complex in rice

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Journal of Integrative Plant Biology 2024年第1期66卷 66-85页

作者： Ding Ren Hui Liu Xuejun Sun Fan Zhang Ling Jiang Ying Wang Ning Jiang Peiwen Yan Jinhao Cui Jinshui Yang Zhikang Li Pingli Lu Xiaojin Luo state key Laboratory of genetic engineering and MOE engineering Research Center of Gene Technology School of Life SciencesFudan UniversityShanghai 200438China state key Laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475004China MOE key Laboratory of Crop Physiology Ecology and Genetic Breeding College of AgronomyJiangxi Agricultural UniversityNanchang 330045China state key Laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural Sciences(CAAS)Beijing 100081China College of Agronomy Anhui Agricultural UniversityHefei 230036China

RNA-binding proteins(RBPs)are components of the post-transcriptional regulatory system,but their regulatory effects on complex traits remain *** an integrated strategy involving map-based cloning,functional characterizations,and transcriptomic and population genomic analyses,we revealed that RBP-K(LOC_Os08g23120),RBP-A(LOC_Os11g41890),and RBP-J(LOC_Os10g33230)encode proteins that form an RBP-A-J-K complex that negatively regulates rice yield-related *** of the RBP-A-J-K complex indicated RBP-K functions as a relatively non-specific RBP chaperone that enables RBP-A and RBP-J to function ***,RBP-J most likely affects GA pathways,resulting in considerable increases in grain and panicle lengths,but decreases in grain width and *** contrast,RBP-A negatively regulates the expression of genes most likely involved in auxin-regulated pathways controlling cell wall elongation and carbohydrate transport,with substantial effects on the rice grain filling process as well as grain length and ***,RBP-K is relatively ancient and highly conserved,whereas RBP-J and RBP-A are more ***,the RBP-A-J-K complex may represent a typical functional model for many RBPs and protein complexes that function at transcriptional and post-transcriptional levels in plants and animals for increased functional consistency,efficiency,and versatility,as well as increased evolutionary *** results clearly demonstrate the importance of RBP-mediated post-transcriptional regulation for the diversity of complex ***,rice grain yield and quality may be enhanced by introducing various complete or partial loss-of-function mutations to specific RBP genes using clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein 9 technology and by exploiting desirable natural tri-genic allelic combinations at the loci encoding the components of the RBP-A-J-K complex through marker-assisted select

关键词： GL11 grain weight and shape post-transcriptional regulation RNA-binding proteins

A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants

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Science China(Life Sciences) 2024年第6期67卷 1280-1291页

作者： Yong Zhang Xiaotuo Zhang Qi Tang Lei Li Ting Jiang Yixiao Fang Hong Zhang Jixian Zhai Guodong Ren Binglian Zheng state key Laboratory of genetic engineering Institute of Plant BiologySchool of Life SciencesFudan UniversityShanghai 200438China Department of Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China

Lariat RNA is concomitantly produced by excised intron during RNA splicing,which is usually debranched by DBR1,an RNA debranching ***,increasing evidence showed that some lariat RNA could escape *** is known about how and why these lariat RNAs could be *** comparing the atlas of lariat RNAs between the non-dividing cell(mature pollen)and three actively dividing tissues(young shoot apex,young seeds,and young roots),we identified hundreds to thousands of lariat RNA naturally retained in each tissue,and the incidence of lariat RNA retention is much less in shoot apex while much more in *** lariat RNAs derived from the same intron or different lariat RNAs from the same pre-m RNA could be retained in one tissue while degraded in the other *** deciphering lariat RNA sequences,we identified an AG-rich(RAAAAVAAAR)motif and a UC-rich(UCUCUYUCUC)motif for pollen-specific and the other three tissues-retained lariat RNAs,*** of the pollen-specific AG-rich motif indeed enhanced lariat RNA retention in ***,hundreds of lariat RNAs harbored mi RNA binding sites,and dual-luciferase reporter assay showed that these natural lariat RNAs had the potential to protect expression of mi RNA target ***,our results uncover that selective retention of lariat RNA is an actively regulatory process,and provide new insights into understanding how lariat RNA metabolism may impact mi RNA activity.

关键词： intron turnover lariat RNA miRNA RNA splicing DBR1

Software Vulnerability Mining and Analysis Based on Deep Learning

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Computers, Materials & Continua 2024年第8期80卷 3263-3287页

作者： Shibin Zhao Junhu Zhu Jianshan Peng state key Laboratory of Mathematical engineering and Advanced Computing Zhengzhou450001China

In recent years,the rapid development of computer software has led to numerous security problems,particularly software *** flaws can cause significant harm to users’privacy and *** security defect detection technology relies on manual or professional reasoning,leading to missed detection and high false detection *** intelligence technology has led to the development of neural network models based on machine learning or deep learning to intelligently mine holes,reducing missed alarms and false ***,this project aims to study Java source code defect detection methods for defects like null pointer reference exception,XSS(Transform),and Structured Query Language(SQL)***,the project uses open-source Javalang to translate the Java source code,conducts a deep search on the AST to obtain the empty syntax feature library,and converts the Java source code into a dependency *** feature vector is then used as the learning target for the neural *** types of Convolutional Neural Networks(CNN),Long Short-Term Memory(LSTM),Bi-directional Long Short-Term Memory(BiLSTM),and Attention Mechanism+Bidirectional LSTM,are used to investigate various code defects,including blank pointer reference exception,XSS,and SQL injection *** results show that the attention mechanism in two-dimensional BLSTM is the most effective for object recognition,verifying the correctness of the method.

关键词： Vulnerability mining software security deep learning static analysis

Unlocking the secrets of TGR5: a new dawn in treating diabetic cardiomyopathy

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Biophysics Reports 2024年第4期10卷 254-256页

作者： Jin Li He Huang Institute of Metabolism and Integrative Biology State Key Laboratory of Genetic Engineering School of Life Sciences and Zhongshan Hospital Fudan University

Diabetic cardiomyopathy, marked by dysregulation of lipid metabolism leading to cardiac remodeling and dysfunction, highlights the critical need for balancing fatty acid transport(Karwi et al. 2022; van de Weijer et al. 2011). CD36 stands as the predominant fatty acid transporter within cardiomyocytes, and its function is intricately tied to its expression and localization(Glatz and Luiken 2018; Shu et al. 2022). Despite recent progress in elucidating the mechanisms behind CD36's hyperactivity, strategies to manage its localization are still emerging.

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Rare variants in FANCJ induce premature ovarian insufficiency in humans and mice

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Journal of genetics and Genomics 2024年第2期51卷 252-255页

作者： Xi Yang Shuting Ren Jialin Yang Yuncheng Pan Zixue Zhou Qing Chen Yunzheng Fang Lingyue Shang Feng Zhang Xiaojin Zhang Yanhua Wu state key Laboratory of genetic engineering at School of Life Sciences Human Phenome InstituteObstetrics and Gynecology HospitalFudan UniversityShanghai 200438China Obstetrics and Gynecology Hospital Institute of Reproduction and DevelopmentState Key Laboratory of Genetic Engineering at School of Life SciencesFudan UniversityShanghai 200011China Human Phenome Institute Zhangjiang Fudan International Innovation CenterFudan UniversityShanghai 201203China Obstetrics and Gynecology Hospital Institute of Reproduction and DevelopmentFudan UniversityShanghai 200011China state key Laboratory of genetic engineering at School of Life Sciences Obstetrics and Gynecology HospitalFudan UniversityShanghai 200438China National Demonstration Center for Experimental Biology Education School of Life SciencesFudan UniversityShanghai 200433China

Premature ovarian insufficiency(POI)is a severe female reproductive disorder that affects 1%of women in general populations(European Society for Human Reproduction and Embryology[ESHRE]Guideline Group on POI et al.,2016).An increasing prevalence up to 3.7%has been reported in a recent meta-analysis(Golezar et al.,2019).POl can lead to infertility or subfertility,as well as a range of complex complications suffering multi-organ systems,seriously threatening women's health and reducing the life *** contrast,POl is a representative heterogeneous disease with multiple *** more than 70 causative POI genes have been identified,the etiology of more than half of the POI patients is still ambiguous(Jiao et al.,2018).Unreported POI causative genes,therefore,remain to be identified.

关键词： insufficiency fertility

Revealing the role of CCoAOMT1: fine-tuning bHLH transcription factors for optimal anther development

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Science China(Life Sciences) 2024年第3期67卷 565-578页

作者： Zesen Lai Jianzheng Wang Ying Fu Menghan Wang Hong Ma Shiqing Peng Fang Chang state key Laboratory of genetic engineering Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity SciencesInstitute of Plant BiologySchool of Life SciencesFudan UniversityShanghai 200438China School of Tropical Agriculture and Forestry Agriculture-Rural Affairs and Rural RevitalizationHainan UniversityHaikou 570228China key Laboratory of Biology and genetic Resources of Tropical Crops Ministry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikou 571101China Department of Biology Huck Institutes of the Life SciencesPennsylvania State UniversityUniversity ParkPA 16802USA

The tapetum,a crucial innermost layer encompassing male reproductive cells within the anther wall,plays a pivotal role in normal pollen *** transcription factors (TFs) bHLH010/089/091 redundantly facilitate the rapid nuclear accumulation of DYSFUNCTIONAL TAPETUM 1,a gatekeeper TF in the ***,the regulatory mechanisms governing the activity of bHLH010/089/091 remain *** this study,we reveal that caffeoyl coenzyme A O-methyltransferase 1 (CCoAOMT1) is a negative regulator affecting the nuclear localization and function of bHLH010 and bHLH089,probably through their K259 *** findings underscore that CCoAOMT1 promotes the nuclear export and degradation of bHLH010 and ***,elevated CCoAOMT1 expression resulted in defective pollen development,mirroring the phenotype observed in bhlh010 bhlh089 ***,our investigation revealed that the K259A mutation in the bHLH089 protein disrupted its translocation from the nucleus to the cytosol and impeded its degradation induced by ***,transgenic plants with the probHLH089::bHLH089^(K259A)construct failed to rescue proper pollen development or gene expression in bhlh010 bhlh089 ***,these findings emphasize the need to maintain balanced TF homeostasis for male *** firmly establish CCoAOMT1 as a pivotal regulator that is instrumental in achieving equilibrium between the induction of the tapetum transcriptional network and ensuring appropriate anther development.

关键词： anther development nuclear localization bHLH O-methyltransferase transcription factor homeostasis