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transcriptomics and physiological analyses reveal that sulfur alleviates mercury toxicity in rice(Oryza sativa L.)

Journal of Environmental Sciences 2024年第1期135卷 10-25页

作者： Yingmei Huang Jicai Yi Xiaomin Li Fangbai Li National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and ManagementInstitute of Eco-Environmental and Soil SciencesGuangdong Academy of SciencesGuangzhou 510650China Guangzhou Institute of Geochemistry Chinese Academy of SciencesGuangzhou 510640China University of Chinese Academy of Sciences Beijing 100049China College of Life Sciences South China Agricultural UniversityGuangzhou 510642China SCNU Environmental Research Institute Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety&MOE Key Laboratory of Theoretical Chemistry of EnvironmentSouth China Normal UniversityGuangzhou 510006China

Mercury(Hg)is one of the most dangerous contaminants and has sparked global concern since it poses a health risk to humans when consumed through rice.Sulfur(S)is a crucial component for plant growth,and S may reduce Hg accumulation in rice grains.However,the detailed effects of S and the mechanisms underlying S-mediated responses in Hg-stressed rice plants remain unclear.Currently,to investigate the effects of S addition on rice growth,Hg accumulation,physiological indexes,and gene expression profiles,rice seedlings were hydroponically treated with Hg(20μmol/L Hg Cl_(2))and Hg plus elemental sulfur(100 mg/L).S application significantly reduced Hg accumulation in Hg-stressed rice roots and alleviated the inhibitory effects of Hg on rice growth.S addition significantly reduced Hg-induced reactive oxygen species generation,membrane lipid peroxidation levels,and activities of antioxidant enzymes while increasing glutathione content in leaves.Transcriptomic analysis of roots identified 3,411,2,730,and 581 differentially expressed genes in the control(CK)vs.Hg,CK vs.Hg+S,and Hg vs.Hg+S datasets,respectively.The pathway of S-mediated biological metabolism fell into six groups:biosynthesis and metabolism,expression regulation,transport,stimulus response,oxidation reduction,and cell wall biogenesis.The majority of biological process-related genes were upregulated under Hg stress compared with CK treatment,but downregulated in the Hg+S treatment.The results provide transcriptomic and physiological evidence that S may be critical for plant Hg stress resistance and will help to develop strategies for reduction or phytoremediation of Hg contamination.

关键词： Sulfur Mercury transcriptomics Detoxification

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transcriptomics integrated with metabolomics reveals the mechanism of CaCl_(2)-HCl electrolyzed water-induced glucosinolate biosynthesis in broccoli sprouts

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Food Science and Human Wellness 2024年第2期13卷 801-812页

作者： Cui Li Shuhui Song Yanan He Haijie Liu College of Food Science and Nutritional Engineering China Agricultural UniversityBeijing 100083China Institute of Agri-food Processing and Nutrition Beijing Academy of Agriculture and Forestry SciencesBeijing 100097China

Glucosinolates are important phytochemicals in Brassicaceae.We investigated the effect of CaCl_(2)-HCl electrolyzed water(CHEW)on glucosinolates biosynthesis in broccoli sprouts.The results showed that CHEW treatment significantly decreased reactive oxygen species(ROS)and malondialdeh yde(MDA)contents in broccoli sprouts.On the the 8^(th)day,compared to tap water treatment,the the total glucosinolate content of broccoli sprouts with CHEW treatment increased by 10.6%and calcium content was dramatically enhanced from 14.4 mg/g DW to 22.7 mg/g DW.Comparative transcriptome and metabolome analyses revealed that CHEW treatment activated ROS and calcium signaling transduction pathways in broccoli sprouts and they interacted through MAPK cascades.Besides,CHEW treatment not only promoted the biosynthesis of amino acids,but also enhanced the expression of structural genes in glucosinolate synthesis through transcription factors(MYBs,bHLHs,WRKYs,etc.).The results of this study provided new insights into the regulatory network of glucosinolates biosynthesis in broccoli sprouts under CHEW treatment.

关键词： Broccoli sprouts CaCl_(2)-HCl electrolyzed water Glucosinolates transcriptomics Metabolomics

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Impact of short-term ambient air pollution exposure on the risk of severe COVID-19

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Journal of Environmental Sciences 2024年第1期135卷 610-618页

作者： Baihuan Feng Jiangshan Lian Fei Yu Dan Zhang Weizhen Chen QiWang Yifei Shen Guoliang Xie Ruonan Wang Yun Teng Bin Lou Shufa Zheng Yida Yang Yu Chen Department of Laboratory Medicine The First Affiliated HospitalZhejiang University School of MedicineHangzhou 310000China Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province Hangzhou 310000China Institute of Laboratory Medicine Zhejiang UniversityHangzhou 310000China Department of Infectious Diseases The First Affiliated HospitalZhejiang University School of MedicineHangzhou 310000China State Key Laboratory for Diagnosis and Treatment of Infectious Diseases National Clinical Research Center for Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseasesthe First Affiliated HospitalZhejiang University School of MedicineHangzhou 310000China

Ecological studies suggested a link between air pollution and severe COVID-19 outcomes,while studies accounting for individual-level characteristics are limited.In the present study,we aimed to investigate the impact of short-term ambient air pollution exposure on disease severity among a cohort of 569 laboratory confirmed COVID-19 patients admitted to designated hospitals in Zhejiang province,China,from January 17 to March 3,2020,and elucidate the possible biological processes involved using transcriptomics.Compared with mild cases,severe cases had higher proportion of medical conditions as well as unfavorable results in most of the laboratory tests,and manifested higher air pollution exposure levels.Higher exposure to air pollutants was associated with increased risk of severe COVID-19 with odds ratio(OR)of 1.89(95%confidence interval(CI):1.01,3.53),2.35(95%CI:1.20,4.61),2.87(95%CI:1.68,4.91),and 2.01(95%CI:1.10,3.69)for PM_(2.5),PM_(10),NO_(2)and CO,respectively.OR for NO_(2)remained significant in two-pollutant models after adjusting for other pollutants.Transcriptional analysis showed 884 differentially expressed genes which mainly were enriched in virus clearance related biological processes between patients with high and low NO_(2)exposure levels,indicating that compromised immune response might be a potential underlying mechanistic pathway.These findings highlight the impact of shortterm air pollution exposure,particularly for NO_(2),on COVID-19 severity,and emphasize the significance in mitigating the COVID-19 burden of commitments to improve air quality.

关键词： Air pollution COVID-19 Severity transcriptomics Immune response

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Debaryomyces hansenii supplementation in low fish meal diets promotes growth,modulates microbiota and enhances intestinal condition in juvenile marine fish

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Journal of Animal Science and Biotechnology 2024年第1期15卷 253-276页

作者： Ignasi Sanahuja Alberto Ruiz Joana P.Firmino Felipe E.Reyes-López Juan B.Ortiz-Delgado Eva Vallejos-Vidal Lluis Tort Dariel Tovar-Ramírez Isabel M.Cerezo Miguel A.Moriñigo Carmen Sarasquete Enric Gisbert Aquaculture Program Institute of Agrifood Research and Technology(IRTA)La Rapita 43540Spain Centro de Biotecnologia Acuicola Universidad de Santiago de ChileSantiagoChile Instituto de Ciencias Marinas de Andalucia(ICMAN-CSIC) Avda.Republica Saharaui no 2Campus Universitario Rio San PedroPuerto RealCadiz 11510Spain Nucleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronomicas Facultad de Medicina Veterinaria y AgronomiaUniversidad de Las AmericasSantiagoChile Department of Cell Biology Physiologyand ImmunologyUniversitat Autonoma de BarcelonaBarcelonaSpain Centro de Investigaciones Biologicas del Noroeste SC CIBNORLa PazMexico Department of Microbiology Instituto de Biotecnologia Y Desarrollo Azul(IBYDA)Faculty of SciencesUniversity of Malaga29010 MalagaSpain SCBI Bioinformatic UnitUniversity of Malaga29590 MalagaSpain

Background The development of a sustainable business model with social acceptance,makes necessary to develop new strategies to guarantee the growth,health,and well-being of farmed animals.Debaryomyces hansenii is a yeast species that can be used as a probiotic in aquaculture due to its capacity to i)promote cell proliferation and differen-tiation,ii)have immunostimulatory effects,iii)modulate gut microbiota,and/or iv)enhance the digestive function.To provide inside into the effects of D.hansenii on juveniles of gilthead seabream(Sparus aurata)condition,we inte-grated the evaluation of the main key performance indicators coupled with the integrative analysis of the intestine condition,through histological and microbiota state,and its transcriptomic profiling.Results After 70 days of a nutritional trial in which a diet with low levels of fishmeal(7%)was supplemented with 1.1%of D.hansenii(17.2×10^(5) CFU),an increase of ca.12%in somatic growth was observed together with an improve-ment in feed conversion in fish fed a yeast-supplemented diet.In terms of intestinal condition,this probiotic modu-lated gut microbiota without affecting the intestine cell organization,whereas an increase in the staining intensity of mucins rich in carboxylated and weakly sulphated glycoconjugates coupled with changes in the affinity for certain lectins were noted in goblet cells.Changes in microbiota were characterized by the reduction in abundance of several groups of Proteobacteria,especially those characterized as opportunistic groups.The microarrays-based transcrip-tomic analysis found 232 differential expressed genes in the anterior-mid intestine of S.aurata,that were mostly related to metabolic,antioxidant,immune,and symbiotic processes.Conclusions Dietary administration of D.hansenii enhanced somatic growth and improved feed efficiency param-eters,results that were coupled to an improvement of intestinal condition as histochemical and transcriptomic tools indicated.This probiotic yeast stimulated host-microbiota interactions with

关键词： Debaryomyces hansenii Intestine condition Low fish meal diet Microbiota transcriptomics Yeast probiotic

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Patient-derived induced pluripotent stem cells with a MERTK mutation exhibit cell junction abnormalities and aberrant cellular differentiation potential

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World Journal of Stem Cells 2024年第5期16卷 512-524页

作者： Hang Zhang Ling-Zi Wu Zhen-Yu Liu Zi-Bing Jin Beijing Institute of Ophthalmology Beijing Tongren Eye CenterBeijing Tongren HospitalCapital Medical UniversityBeijing 100730China

BACKGROUND Human induced pluripotent stem cell(hiPSC)technology is a valuable tool for generating patient-specific stem cells,facilitating disease modeling,and invest-igating disease mechanisms.However,iPSCs carrying specific mutations may limit their clinical applications due to certain inherent characteristics.AIM To investigate the impact of MERTK mutations on hiPSCs and determine whether hiPSC-derived extracellular vesicles(EVs)influence anomalous cell junction and differentiation potential.METHODS We employed a non-integrating reprogramming technique to generate peripheral blood-derived hiPSCs with and hiPSCs without a MERTK mutation.Chromo-somal karyotype analysis,flow cytometry,and immunofluorescent staining were utilized for hiPSC identification.transcriptomics and proteomics were employed to elucidate the expression patterns associated with cell junction abnormalities and cellular differentiation potential.Additionally,EVs were isolated from the supernatant,and their RNA and protein cargos were examined to investigate the involvement of hiPSC-derived EVs in stem cell junction and differentiation.RESULTS The generated hiPSCs,both with and without a MERTK mutation,exhibited normal karyotype and expressed pluripotency markers;however,hiPSCs with a MERTK mutation demonstrated anomalous adhesion capability and differentiation potential,as confirmed by transcriptomic and proteomic profiling.Furthermore,hiPSC-derived EVs were involved in various biological processes,including cell junction and differentiation.CONCLUSION HiPSCs with a MERTK mutation displayed altered junction characteristics and aberrant differentiation potential.Furthermore,hiPSC-derived EVs played a regulatory role in various biological processes,including cell junction and differentiation.

关键词： Cell junction Cellular differentiation Extracellular vesicle Human induced pluripotent stem cells transcriptomics Proteomics

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Spi1 regulates the microglial/macrophage inflammatory response via the PI3K/AKT/mTOR signaling pathway after intracerebral hemorrhage

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Neural Regeneration Research 2024年第1期19卷 161-170页

作者： Guoqiang Zhang Jianan Lu Jingwei Zheng Shuhao Mei Huaming Li Xiaotao Zhang An Ping Shiqi Gao Yuanjian Fang Jun Yu Department of Neurosurgery The Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang ProvinceChina Department of Neurosurgery Huashan Hospital of Fudan University School of MedicineShanghaiChina Clinical Research Center for Neurological Diseases of Zhejiang Province HangzhouZhejiang ProvinceChina Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases HangzhouZhejiang ProvinceChina

Preclinical and clinical studies have shown that microglia and macrophages participate in a multiphasic brain damage repair process following intracerebral hemorrhage.The E26 transformation-specific sequence-related transcription factor Spi1 regulates microglial/macrophage commitment and maturation.However,the effect of Spi1 on intracerebral hemorrhage remains unclear.In this study,we found that Spi1 may regulate recovery from the neuroinflammation and neurofunctional damage caused by intracerebral hemorrhage by modulating the microglial/macrophage transcriptome.We showed that high Spi1expression in microglia/macrophages after intracerebral hemorrhage is associated with the activation of many pathways that promote phagocytosis,glycolysis,and autophagy,as well as debris clearance and sustained remyelination.Notably,microglia with higher levels of Soil expression were chara cterized by activation of pathways associated with a variety of hemorrhage-related cellular processes,such as complement activation,angiogenesis,and coagulation.In conclusion,our results suggest that Spi1 plays a vital role in the microglial/macrophage inflammatory response following intracerebral hemorrhage.This new insight into the regulation of Spi1 and its target genes may advance our understanding of neuroinflammation in intracerebral hemorrhage and provide therapeutic targets for patients with intracerebral hemorrhage.

关键词： intracerebral hemorrhage macrophage microglia neuroinflammation phagocytosis PI3K/AKT/mTOR signaling pathway Spi1 transcriptomics

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Transcriptomic and bioinformatics analysis of the mechanism by which erythropoietin promotes recovery from traumatic brain injury in mice

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Neural Regeneration Research 2024年第1期19卷 171-179页

作者： Weilin Tan Jun Ma Jiayuanyuan Fu Biying Wu Ziyu Zhu Xuekang Huang Mengran Du Chenrui Wu Ehab Balawi Qiang Zhou Jie Zhang Zhengbu Liao Department of Neurosurgery The First Affiliated Hospital of Chongqing Medical UniversityChongqingChina

Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate traumatic brain injury in mice by intrape ritoneal injection of erythro poietin for 3 consecutive days.RNA sequencing detected a total of 4065 differentially expressed RNAs,including 1059 mRNAs,92 microRNAs,799 long non-coding RNAs,and 2115circular RNAs.Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed that the coding and non-coding RNAs that were differentially expressed after traumatic brain injury and treatment with erythropoietin play roles in the axon guidance pathway,Wnt pathway,and MAPK pathway.Constructing competing endogenous RNA networks showed that regulatory relationship between the differentially expressed non-coding RNAs and mRNAs.Because the axon guidance pathway was repeatedly enriched,the expression of Wnt5a and Ephb6,key factors in the axonal guidance pathway,was assessed.Ephb6 expression decreased and Wnt5a expression increased after traumatic brain injury,and these effects were reversed by treatment with erythro poietin.These findings suggest that erythro poietin can promote recove ry of nerve function after traumatic brain injury through the axon guidance pathway.

关键词： axon guidance bioinformatics analysis competing endogenous RNA erythropoietin Gene Ontology Kyoto Encyclopedia of Genes and Genomes non-coding RNA RNA sequencing transcriptomics traumatic brain injury

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Endochondral ossification of hindlimbs in embryonic development of Japanese Quail(Coturnix japonica)

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Avian Research 2024年第1期15卷 123-132页

作者： Xuan Li Yuxin Zhang Hongfeng Zhao College of Life Sciences Shaanxi Normal UniversityXi’an710119China

The endochondral ossification of hindlimb is essential to a bird’s ability to stand,walk and fly.Most hindlimb is ossified in the embryos before hatching in precocial birds.However,the molecular mechanisms of hindlimb ossification in birds is still unclear.Therefore,we tried to examine the process of hindlimb ossification and its molecular regulation by using an animal model—Japanese Quail(Coturnix japonica).We selected four critical stages(Embryo Day:E6,E8,E12 and E16) of skeletal development of embryonic quails for hindlimb skeleton staining to show the process of endochondral ossification and to examine the molecular regulation of endochondral osteogenesis by RNA-Seq analysis.The results showed that ossification became increased with embryonic development and most hindlimb was ossified before hatching.RNA-Seq analysis revealed that various signaling pathways were involved with endochondral ossification with thyroid hormone signaling and WNT signaling pathway particularly enriched.Moreover,the expression levels of 42 genes were continuously upregulated and 14 genes were continuously downregulated from E6 to E16.The present study might provide new insights into complex molecular mechanisms in regulation of endochondral ossification.

关键词： Embryos Hindlimb Ossification Precocial transcriptomics

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4-Hydroxy-2-Oxoglutaric Acid,A KeyMetabolite Involved in Trypsin-Regulation of Arginine Metabolism in Hylocereus undatus during Storage

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Phyton-International Journal of Experimental Botany 2024年第5期93卷 885-900页

作者： Bairu Li Jingyu Jia Hemin Wang Jiaju Sun Enyan Chen Xin Li College of Food and Bioengineering Henan University of Science and TechnologyLuoyang471023China Henan Engineering Research Center of Food Microbiology Luoyang471023China National Demonstration Center for Experimental Food Processing and Safety Education Luoyang471000China

Trypsin,a novel superoxide scavenger,significantly enhances the storage quality of Hylocereus undatus(H.undatus).To elucidate the preservation mechanism of trypsin on H.undatus,a widely targeted metabolomic analysis,and transcriptomics analysis were conducted.Firstly,a total of 453 metabolites were identified,with organic acids and their derivatives constituting the largest proportion(25%).Amino acids and their metabolites,prominent among organic acids,were further analyzed.Among them,73 metabolites were associated with amino acids,and 37 exhibited significant differences.The most enriched Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway was arginine biosynthesis(map00220),with polyamine metabolites showing the most pronounced differences,particularly spermine(FC=1.7594).Compared with the control group,4-hydroxy-2-oxoglutaric acid was significantly upregulated(FC=2.117)in the process of spermine biosynthesis.Furthermore,the results of Gene Ontology(GO)and KEGG enrichment analysis of the H.undatus transcriptome profile revealed that trypsin treatment led to 187 differentially expressed genes associated with arginine.Both GO and KEGG analyses exhibited significant enrichment in the spermine biosynthetic process(GO:0006597)(map:00220)within the arginine biosynthesis pathway.Moreover,most enzymes and metabolites within the spermine biosynthesis pathway in H.undatus were upregulated.The results of the PPI network highlighted that ADC,SPDS,and SAMDC,among others,were pivotal proteins involved in trypsin-regulated arginine metabolism and spermine synthesis.This study revealed that trypsin could significantly delay postharvest senescence of H.undatus at room temperature.This effect might be attributed to trypsin triggering the synthesis of 4-hydroxy-2-oxoglutaric acid in the fruit peel,thereby promoting the biosynthesis of spermine and other polyamines.

关键词： Trypsin arginine transcriptomics widely targeted metabolomics

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transcriptomics and metabolomics analyses provide insights into postharvest ripening and senescence of tomato fruit under low temperature

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Horticultural Plant Journal 2023年第1期9卷 109-121页

作者： Chunmei Bai Caie Wu Lili Ma Anzhen Fu Yanyan Zheng Jiawei Han Changbao Li Shuzhi Yuan Shufang Zheng Lipu Gao Xinhua Zhang Qing Wang Demei Meng Jinhua Zuo State Key Laboratory of Food Nutrition and Safety College of Food Science and EngineeringTianjin University of Science&TechnologyTianjin 300457China College of Light Industry and Food Engineering Nanjing Forestry UniversityNanjingJiangsu 210037China Key laboratory of vegetable postharvest processing Ministry of AgricultureBeijing Key Laboratory of Fruit and Vegetable Storage and ProcessingKey Laboratory of Biology and Genetic Improvement of Horticultural Crops(North China)of Ministry of AgricultureKey Laboratory of Urban Agriculture(North)of Ministry of Agriculture and Rural AffairsInstitute of Agri-food Processing and NutritionBeijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry SciencesBeijing 100097China National Engineering Research Center for Information Technology in Agriculture Beijing 100097China School of Agricultural Engineering and Food Science Shandong University of TechnologyZiboShandong 255049China

Tomato is one of the most important vegetable crops in the world and is a model plant used to study the ripening of climacteric fleshy fruit.During the ripening process of tomato fruit,flavor and aroma metabolites,color,texture and plant hormones undergo significant changes.However,low temperatures delayed the ripening process of tomato fruit,inhibiting flavor compounds and ethylene production.Metabolomics and transcriptomics analyses of tomato fruit stored under low temperature(LT,5°C)and room temperature(RT,25°C)were carried out to investigate the effects of storage temperature on the physiological changes in tomato fruit after harvest.The results of transcriptomics changes revealed that the differentially expressed genes(DEGs)involved in tomato fruit ripening,including several kinds of transcription factors(TFs)(TCP,WRKY,MYB and bZIP),enzymes involved in cell wall metabolism[beta-galactosidase(β-GAL),pectinesterase(PE)and pectate lyase(PL),cellulose and cellulose synthase(CESA)],enzymes associated with fruit flavor and aroma[acetyltransferase(AT),malic enzyme(ME),lipoxygenase(LOX),aldehyde dehydrogenase(ALDH),alcohol dehydrogenase(ADH)and hexokinase(HK)],genes associated with heat stress protein 70 and genes involved in the production of plant hormones such as Ethylene responsive factor 1(ERF1),Auxin/indoleacetic acids protein(AUX/IAA),gibberellin regulated protein.Based on the above results,we constructed a regulatory network model of the effects of different temperatures during the fruit ripening process.According to the analysis of the metabolomics results,it was found that the contents of many metabolites in tomato fruit were greatly affected by storage temperature,including,organic acids(L-tartaric acid,a-hydroxyisobutyric acid and 4-acetamidobutyric acid),sugars(melezitose,beta-Dlactose,D-sedoheptulose 7-phosphate,2-deoxyribose 1-phosphate and raffinose)and phenols(coniferin,curcumin and feruloylputrescine).This study revealed the effects of storage temperature on postharvest tomato fruit and provided a

关键词： Metabolomics Tomato transcriptomics Temperature Fruit ripening

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