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Developing a CRISPR/FrCas9 system for core promoter editing in rice

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aBIOTECH 2024年第2期5卷 189-195页

作者： Hui Wang Jian Ding Jingyan Zhu Xiaoshuang Liu Rongfang Xu Ruiying Qin Dongfang Gu Min Li Pengcheng Wei Juan Li College of Agronomy Anhui Agricultural UniversityHefei 230036China Key Laboratory of Rice Genetic Breeding of Anhui Province Rice Research InstituteAnhui Academy of Agricultural SciencesHefei 230031China research centre for biological Breeding Technology Advance AcademyAnhui Agricultural UniversityHefei 230036China

Small mutations in the core promoter region of a gene may result in substantial changes in expression ***,targeting TA-rich sequences of core promoters may pose a challenge for Cas9 variants such as SpCas9 and other G-rich PAM-compatible *** this study,we engineered a unique FrCas9 system derived from Faecalibaculum rodentium for plant genome *** findings indicate that this system is efficient in rice when the TATA sequence is used as a *** addition,FrCas9 demonstrated activity against all 16 possible NNTA PAMs,achieving an efficiency of up to 35.3%in calli and generating homozygous or biallelic mutations in 31.3%of the T_(0)transgenic plants.A proof-ofconcept experiment to examine editing of the rice WX core promoter confirmed that FrCas9-induced mutations could modify gene expression and amylose *** mutations and deletions were produced by bidirectional editing,mediated by FrCas9,using a single palindromic TATA sequence as a ***,we developed FrCas9-derived base editors capable of programmable conversion between AT and GC pairs in *** study highlights a versatile FrCas9 toolset for plant core promoter editing,offering great potential for the fine-tuning of gene expression and creating of new germplasms.

关键词： Genome editing FrCas9 CRISPR Core promoter Base editing

Assessment of molecular markers and marker-assisted selection for drought tolerance in barley(Hordeum vulgare L.)

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Journal of Integrative Agriculture 2024年第1期23卷 20-38页

作者： Akmaral Baidyussen Gulmira Khassanova Maral Utebayev Satyvaldy Jatayev Rystay Kushanova Sholpan Khalbayeva Aigul Amangeldiyeva Raushan Yerzhebayeva KulpashBulatova Carly Schramm Peter Anderson Colin L.D.Jenkins Kathleen LSoole Yuri Shavrukov Faculty of Agronomy S.Seifullin Kazakh AgroTechnical Research UniversityAstana 010000Kazakhstan A.I.Barayev research and Production centre of Grain Farming Shortandy 021601Kazakhstan Kazakh research Institute of Agriculture and Plant Growing AlmalybakAlmaty District 040909Kazakhstan College of Science and Engineering Biological SciencesFlinders UniversityAdelaideSA 5042Australia

This review updates the present status of the field of molecular markers and marker-assisted selection(MAS),using the example of drought tolerance in *** accuracy of selected quantitative trait loci(QTLs),candidate genes and suggested markers was assessed in the barley genome *** common strategies are described for molecular marker development,candidate gene identification and verification,and their possible applications in MAS to improve the grain yield and yield components in barley under drought *** strategies are based on the following five principles:(1)Molecular markers are designated as genomic‘tags’,and their‘prediction’is strongly dependent on their distance from a candidate gene on genetic or physical maps;(2)plants react differently under favourable and stressful conditions or depending on their stage of development;(3)each candidate gene must be verified by confirming its expression in the relevant conditions,e.g.,drought;(4)the molecular marker identified must be validated for MAS for tolerance to drought stress and improved grain yield;and(5)the small number of molecular markers realized for MAS in breeding,from among the many studies targeting candidate genes,can be explained by the complex nature of drought stress,and multiple stress-responsive genes in each barley genotype that are expressed differentially depending on many other factors.

关键词： barley candidate genes drought tolerance gene verification via expression grain yield marker-assisted selection(MAS) molecular markers quantitative trait loci(QTLs) strategy for MAS

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 ***:This is an experimental *** 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 *** sequencing was performed on lung tissues from both goats and *** expressed genes were identified using the criteria ofq≤0.05 and|log2 fold change|≥*** that,enrichment analyses were conducted for gene ontology and the Kyoto Encyclopedia of Genes and Genomes *** potential target genes were further confirmed through quantitative real-time polymerase chain reaction and enzyme linked immunosorbent ***:Observations through microscopy unveiled the presence of reddish edema fluid,erythrocytes,and instances of focal or patchy bleeding within the alveolar *** sequencing analysis identified a total of 83 differentially expressed genes in both rats and ***,49 genes exhibited a consistent expression pattern,with 38 genes displaying up-regulation and 11 genes demonstrating *** analysis highlighted the potential involvement of the interleukin-17 signaling pathway and vascular smooth muscle contraction pathway in the underlying mechanism of ***,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 ***: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

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

Stability and transepithelial transport of oligopeptide(KRQKYD)with hepatocyte-protective activity from Jinhua ham in human intestinal Caco-2 monolayer cells

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Food Science and Human Wellness 2024年第3期13卷 1503-1512页

作者： Wen Nie Feiran Xu Kai Zhou Jieying Deng Ying Wang Baocai Xu Engineering research Center of Bio-process Ministry of EducationSchool of Food and Biological EngineeringHefei University of TechnologyHefei 230601China School of biological and Food Engineering Chuzhou UniversityChuzhou 239001China

The study evaluated the stability of an oligopeptide(Lys-Arg-Gln-Lys-Tyr-Asp,KRQKYD)and its transport mechanism by simulating gastrointestinal digestion and a model of human intestinal Caco-2 monolayer cells in *** this study,the effects of environmental factors(temperature,pH and NaCl concentration)and simulated gastrointestinal digestion on the stability of KRQKYD were evaluated by indicators of the levels of alanine transaminase(ALT),aspartate transaminase(AST)and malondialdehyde(MDA)in an alcoholinduced hepatocyte injury *** results showed that KRQKYD still maintained satisfactory hepatocyteprotective activity after treatment with different temperatures(20-80℃),pH(3.0-9.0),NaCl concentration(1%-7%)and simulated gastrointestinal digestion,which indicated that KRQKYD showed good stability to environmental factors and simulated gastrointestinal ***,the intact KRQKYD could be absorbed in a model of Caco-2 monolayer cells with a P_(app)value of(9.70±0.53)×10^(-7)cm/*** with an energy inhibitor(sodium azide),a competitive peptide transporter inhibitor(Gly-Pro)and a transcytosis inhibitor wortmannin did not decrease the level of transepithelial KRQKYD transport,indicating that the transport mechanism of KRQKYD was not associated with energy dependent,vector mediated and *** tight junction disruptor cytochalasin D significantly increased the level of transepithelial KRQKYD transport(P<0.05),suggesting that intact KRQKYD was absorbed by paracellular transport.

关键词： Jinhua ham KRQKYD(Lys-Arg-Gln-Lys-Tyr-Asp) Environmental stability Gastrointestinal digestive Transport mechanism

Study on the green extraction of corncob xylan by deep eutectic solvent

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Grain & Oil Science and Technology 2024年第1期7卷 50-59页

作者： Bingyu Jiao Le Wang Haitao Gui Zifu Ni Rong Du Yuansen Hu School of biological Engineering National Engineering Research Center of Wheat and Corn Further ProcessingZhengzhou 450001China

Corn as one of the world's major food crops,its by-product corn cob is also rich in ***,the unreasonable utilization of corn cob often causes the environmental pollution,waste of resources and other *** one of the most abundant polymers in nature,xylan is widely used in food,medicine,materials and other *** cob is rich in xylan,which is an ideal raw material for extracting ***,the intractable lignin is covalently linked to xylan,which increases the difficulty of xylan *** has been reported that the deep eutectic solvent(DES)could preferentially dissolve lignin in biomass,thereby dissolving the ***,the xylan in the extract was separated by ethanol precipitation *** xylan precipitate was obtained after centrifugation,while the supernatant was *** components of the supernatant after ethanol precipitation were separated by the rotary *** ethanol,water and DES were collected for the subsequent extraction of corn cob *** this study,a novel way was provided for the green production of corn cob *** DES was used to extract xylan from corn cob which was used as the raw *** effects of solid-liquid ratio,reaction time,reaction temperature and water content of DES on the extraction rate of corn cob xylan were investigated by the single factor ***,the orthogonal test was designed to optimize the xylan extraction *** structure of corn cob xylan was analyzed and *** results showed that the optimum extraction conditions of corn cob xylan were as follows:the ratio of corn cob to DES was 1:15(g:mL),the extraction time was 3 h,the extraction temperature was 60℃,and the water content of DES was 70%.Under these conditions,the extraction rate of xylan was 16.46%.The extracted corn cob xylan was distinctive triple helix of polysaccharide,which was similar to the structure of commercially available *** was effectively and workably extracted from corn

关键词： Corncob Deep eutectic solvent Xylan Process optimization Extraction

New insights into nitric oxide biosynthesis underpin lateral root development

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Molecular Plant 2024年第5期17卷 691-693页

作者： Kapuganti Jagadis Gupta Nidhi Yadav Aprajita Kumari Gary J.Loake National Institute for Plant Genome research Aruna Asaf Ali MargNew Delhi 110070India Institute of Molecular Plant Sciences School of Biological SciencesUniversity of EdinburghEH93BF EdinburghUK centre for Engineering Biology School of Biological SciencesUniversity of EdinburghEH93BF EdinburghUK

In recent years,nitric oxide(NO)has emerged as a key redox signaling molecule in plants functioning in the regulation of key developmental programs and the orchestration of responses to a plethora of environmental cues(Kolbert et al.,2019).The predominant route for the transfer of NO bioactivity is through S-nitrosylation,the addition of an NO moiety to a protein cysteine thiol to form an S-nitrosothiol(Yun et al.,2011).Specificity for this process is established by the structural constraints imposed by tertiary protein structure in gating access to given cysteine redox switches and associated proteins that can either facilitate the addition or removal of the NO moiety at these residues(Umbreen et al.,2018).

关键词： moiety addition redox

Physiological strategies in wild rodents:immune defenses of commensal rats

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Integrative Zoology 2024年第3期19卷 350-370页

作者： Ivana MIRKOV Dina TUCOVIC Jelena KULAS Anastasija MALESEVIC Dragan KATARANOVSKI Milena KATARANOVSKI Aleksandra POPOV ALEKSANDROV Immunotoxicology Group Department of EcologyInstitute for Biological Research“Sinisa Stankovic”—National Institute of Republic of SerbiaUniversity of BelgradeBelgradeSerbia

The importance of issues associated with urban/commensal rats and mice(property damage,management costs,and health risks)press upon research on these *** the demography of commensal rodents is mostly studied,the need for understanding factors influencing their natural morbidity/mortality is also *** this respect,more attention is expected to be paid to immunity,the physiological mechanism of defense against host survival threats(pathogens,parasites,diseases).Commensal rats and mice carry numerous pathogens that evoke diverse immune *** state of immunity in commensal house mice is studied in great detail,owing to the use of laboratory strains in biomedical *** commensal rats are,compared to mice,carriers of more zoonotic agents,rats’immunity is studied mainly in that *** of these zoonotic agents cause chronic,asymptomatic infections,which justified studies of immunological mechanisms of pathogen tolerance versus clearance regulation in *** of some infections in specific tissues/organs pressed upon analysis of local/regional immune responses and/or immunopathology.A survey of immunological activity/responses in commensal rats is given in this review,with mention of existing data in commensal *** should throw some light on the factors relevant to their morbidity and lifespan,supplementing the knowledge of commensal rodent ecology.

关键词： commensal rats and mice immunopathology infection inflammation tolerance

Brain Mechanisms Underlying Panic Attack and Panic Disorder

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Neuroscience Bulletin 2024年第6期40卷 795-814页

作者： Xuyan Guan Peng Cao Tsinghua Institute of Multidisciplinary Biomedical research Tsinghua UniversityBeijing102206China National Institute of biological Sciences(NIBS) Beijing102206China

Panic disorder is a psychiatric disorder characterized by recurrent panic attacks,with a prevalence of~4%in the general population,causing heavy personal and socioeconomic *** similarities of animal defense responses to clinical panic attack symptoms in humans make it possible to translate neuroanatomical pathways identified in animal studies to panic disorder in ***,in this review we first present a basic overview of panic disorder in humans including the main subtypes,models commonly used to trigger panic attacks,related hypotheses,the neurotransmitter systems that may be involved,and the current clinical treatments to give the reader a comprehensive understanding of panic *** animal section introduces the models that trigger panic-like behavior in animals and the brain regions that may be involved,providing insights for future elucidation of the neural circuit mechanisms behind panic attacks.

关键词： Panic disorder Panic attack Defense responses Animal studies Humans

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 ***-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 ***,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 *** 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 *** annotation showed that 20E regulates key proteins in processes that mainly occur in the cytoplasm and *** enrichment analysis showed that 20E can activate phosphorylation and may affect innate immunity,interfere with intracellular nutrition and energy metabolism,and eventually cause cell *** screening results were experimentally validated by generating cells with knockout alleles of the relevant genes,which had increased tolerance to *** 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