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Rational design of unrestricted pRN1 derivatives and their application in the construction of a dual plasmid vector system for Saccharolobus islandicus

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mLife 2024年第1期3卷 119-128页

作者： Pengpeng Zhao Xiaonan Bi Xiaoning Wang Xu Feng Yulong Shen Guanhua Yuan Qunxin She CRISPR and Archaea Biology Research Center State Key Laboratory of Microbial Technology and Microbial Technology InstituteShandong UniversityQingdaoChina

Saccharolobus islandicus REY15A represents one of the very few archaeal models with versatile genetic tools,which include efficient genome editing,gene silencing,and robust protein expression ***,plasmid vectors constructed for this crenarchaeon thus far are based solely on the pRN2 cryptic *** this plasmid coexists with pRN1 in its original host,early attempts to test pRN1-based vectors consistently failed to yield any stable host-vector system for *** hypothesized that this failure could be due to the occurrence of CRISPR immunity against pRN1 in this *** identified a putative target sequence in orf904 encoding a putative replicase on pRN1(target N1).Mutated targets(N1a,N1b,and N1c)were then designed and tested for their capability to escape the host CRISPR immunity by using a plasmid inter-ference *** results revealed that the original target triggered CRISPR immunity in this archaeon,whereas all three mutated targets did not,indicating that all the designed target mutations evaded host *** mutated targets were then incorporated into orf904 individually,yielding corresponding mutated pRN1 backbones with which shuttle plasmids were constructed(pN1aSD,pN1bSD,and pN1cSD).*** transformation revealed that pN1aSD and pN1bSD were functional shuttle vectors,but pN1cSD lost the capability for *** results indicate that the missense mutations in the conserved helicase domain in pN1c inactivated the *** further showed that pRN1-based and pRN2-based vectors were stably maintained in the archaeal cells either alone or in combination,and this yielded a dual plasmid system for genetic study with this important archaeal model.

关键词： archaeal genetics CRISPR-Cas CRISPR escape mutations dual plasmid vectors Saccharolobus-E.coli shuttle vectors

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Nuclear transport receptors underpin plastidial retrograde signaling

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Molecular Plant 2024年第7期17卷 993-995页

作者： Min Jia Yangnan Gu department of Plant and microbial Biology University of CaliforniaBerkeleyBerkeleyCAUSA

The nucleus integrates cytosolic and organellar signals to regulate gene expression during plant stress responses,and this process is highly dependent on shuttling of signaling molecules in and out of the *** nucleocytoplasmic transport of macromolecules is facilitated by nuclear transport receptors(NTRs).NTRs are broadly categorized into exportins,which mediate the export of cargo from the nucleus to the cytoplasm,and importins,which facilitate the import of cargo into the *** importin family comprises importin-α(IMPa)and importin-β(IMPp).IMPa proteins are adaptor proteins and composed of three functional domains:an N-terminal IMPβ-binding(IBB)domain,ten Armadillo(ARM)repeats responsible for recognizing and interacting with cargo,and an exportin-interacting domain crucial for recycling via nuclear export(Wing et al.,2022).During a nuclear transport event,*** cargo containing a classical nuclear localization signal(cNLS)through its ARM repeats and engages IMPβvia its IBB domain,forming the cargo-IMPa-IMPβternary ***βfacilitates translocation of this complex through the nuclear *** inside the nucleus,RanGTP competes with IMPa for binding to IMPβ,promoting disassembly of the transport complex and releaseofcargo.

关键词： complex. integrate ternary

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Nitrogen-based fertilizers differentially affect protist community composition in paddy field soils

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Soil Ecology Letters 2024年第3期6卷 35-44页

作者： Seda Ozer Bodur Solomon Oloruntoba Samuel Kazuki Suzuki Naoki Harada Rasit Asiloglu Graduate School of Science and technology Niigata UniversityNiigataJapan department of Plant and microbial Biology North Carolina State UniversityRaleighNCUSA Institute of Science and technology Niigata UniversityNiigataJapan

Protists are one of the most diverse and dominant microbial groups and they play critical roles in the soil *** nitrogen fertilizers have a profound impact on protist communities,still less is known about how different nitrogen fertilizer types affect protist community composition in different soil *** we investigated the effects of six inorganic nitrogen fertilizers(urea,ammonium nitrate,ammonium sulfate,potassium nitrate,ammonium chloride,and diammonium hydrogen phosphate)and an organic fertilizer(a mixture of rice husk and cow manure)on protist community composition in three paddy field soils using a high-throughput sequencing *** effect of the fertilizers on the functional groups of protists,namely consumers(predators and decomposers),photoautotrophs,and parasites(plant pathogens and animal parasites)was also *** results showed that nitrogen fertilizers had distinctive effects on the beta diversity of the protists,while we also observed that the same fertilizer had slightly different effects depending on the soil *** and Rhizaria were the most affected protist taxonomical groups,while predatory protists were the main functional groups that were affected by nitrogen *** forest analysis showed that most of the fertilizer-affected protists were predators,among which Cercozoa was the most affected *** conclusion,our results provide important insights into the impact of nitrogen fertilizers on soil protist communities.

关键词： nitrogen fertilizer bottom-up paddy field predatory protist soil protist community

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Gut microbial interactions based on network construction and bacterial pairwise cultivation

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Science China(Life Sciences) 2024年第8期67卷 1751-1762页

作者： Min-Zhi Jiang Chang Liu Chang Xu He Jiang Yulin Wang Shuang-Jiang Liu State Key Laboratory of microbial technology Shandong UniversityQingdao 266000China State Key Laboratory of microbial Resources and Environmental Microbiology Research Center(EMRC)Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Association networks are widely applied for the prediction of bacterial interactions in studies of human gut ***,the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated *** this study,we addressed this challenge by integrating in vitro time series network(TSN)associations and cocultivation of TSN taxon *** samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 *** cells were harvested for DNA extraction and metagenomic sequencing.A total of 198 metagenome-assembled genomes(MAGs)were *** dynamics of bacteria growing on the YCFA agar were used to infer microbial association *** experimentally validate the interactions of taxon pairs in networks,we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank,respectively,for pairwise *** co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism(51.67%),followed by commensalism(21.67%),amensalism(18.33%),competition(5%)and exploitation(3.33%).Genome-centric analysis further revealed that the commensal gut bacteria(helpers and beneficiaries)might interact with each other via the exchanges of amino acids with high biosynthetic costs,short-chain fatty acids,and/or *** also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7%of these strains was significantly *** approach provides new insights into the gut microbiome complexity and microbial interactions in association *** work highlights that the positive relationships in gut microbial communities tend to be overestimated,and that amino acids,short-chain fatty acids,and vitamins are contributed to the positive relationships.

关键词： human gut microbiome gut microbial pairwise interaction co-culture association network microbial community

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Two MADS-box proteins,AGL9 and AGL15,recruit the FIS-PRC2 complex to trigger the phase transition from endosperm proliferation to embryo development in Arabidopsis

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Molecular Plant 2024年第7期17卷 1110-1128页

作者： Shen Zhang Devasantosh Mohanty Adnan Muzaffar Min Ni department of Plant and microbial Biology University of Minnesota at Twin CitiesSaint PaulMinnesota MN 55108United States of AmericaUSA

Spatiotemporal regulation of gene expression by polycomb repressive complex 2(PRc2)is critical for animal and plant *** Arabidopsis fertilization independent seed(FIS)-PRC2 complex functions specifically during plant reproduction from gametogenesis to seed *** a double fertilization event,triploid endosperm proliferates early,followed by the growth of a diploid embryo,which replaces the endosperm in Arabidopsis and many *** genes critical for endosperm proliferation such as IKkU2 and MINI3 are activated after *** we report that two MADS-box AGAMOUS-LIKE(AGL)proteins associate with the key endosperm proliferation loci and recruit the FIS-PRC2 repressive complex at 4-5 days after pollination(DAP).Interestingly,AGL9 and AGL15 only accumulate toward the end of endosperm proliferation at 4-5 DAP and promote the deposition of H3K27me3 marks at key endosperm proliferation *** of AGL9 and AGL15 or overexpression of AGL9 or AGL15 significantly influence endosperm proliferation and ***-wide analysis with cleavage Under Targets and tagmentation(CUT&Tag)sequencing and RNA sequencing revealed the landscape of endosperm H3K27me3 marks and gene expression profiles in Col-0 and agl9 ***&Tag qPCR also demonstrated the occupancy of the two MADS-box proteins and FIS-PRC2 on a few representative target *** studies suggest that MADS-box proteins could potentially recruit PRc2 to regulate many other developmental processes in plants or even in fungi and animals.

关键词： AGL9 AGL15 embryo endosperm IKU2 MEDEA MINI3

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Rearranged 19-nor-7,8-seco-labdane diterpenoids and Diels-Alder cycloadducts from the Chinese liverwort Pallavicinia ambigua:Structural elucidation,photoinduced rearrangement,and cytotoxic activity

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Chinese Chemical Letters 2024年第3期35卷 415-418页

作者： Chunyang Zhang Yuelan Li Zhaojun Chu Shuangzhi Yuan Yanan Qiao Jiaozhen Zhang Lin Li Yueqing Zhang Ruifeng Tian Yajie Tang Hongxiang Lou department of Natural Products Chemistry Key Lab of Chemical Biology(MOE)School of Pharmaceutical SciencesShandong UniversityJi'nan 250012China State Key Laboratory of microbial technology Shandong UniversityQingdao 266237China

Two distinctive rearranged 19-nor-7,8-seco-labdane diterpenoids(1 and 2)with a novel tetracyclo[5.***.1.0^(2,5.)0^(4,10)]decane skeleton,a derivative of the open tetrahydrofuran ring(7),three dimeric compounds(8-10),and four revised homologs(3-6)were obtained from Chinese liverwort Pallavicinia *** structures were identified via combined analysis of their spectroscopic data,single-crystal X-ray diffraction patterns,and ECD *** light-driven conversion of compound 5 to compounds 1-4 demonstrated that photochemically induced postmodification involved in biosynthesis is an important way to diversify natural structures.A preliminary cytotoxicity assay revealed that compound 5 showed significant inhibition in the human prostate cancer(PC-3)cell line via an apoptotic pathway.

关键词： Liverwort Pallavicinia ambigua 19-nor-7 8-seco-Labdan diterpenoid Photoinduced rearrangement Cytotoxic activity

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Spontaneous mutations and mutational responses to penicillin treatment in the bacterial pathogen Streptococcus pneumoniae D39

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Marine Life Science & technology 2024年第3期6卷 198-211页

作者： Wanyue Jiang Tongtong Lin Jiao Pan Caitlyn ERivera Clayton Tincher Yaohai Wang Yu Zhang Xiang Gao Yan Wang Ho‑Ching T.Tsui Malcolm E.Winkler Michael Lynch Hongan Long Institute of Evolution and Marine Biodiversity KLMMEOcean University of ChinaQingdao 266003China Laboratory for Marine Biology and Biotechnology Laoshan LaboratoryQingdao 266237China department of Biology Indiana UniversityBloomingtonIN 47405USA School of Mathematics Science Ocean University of ChinaQingdao 266000China State Key Laboratory of microbial technology Microbial Technology InstituteSchool of Life ScienceShandong UniversityQingdao 266237China Biodesign Center for Mechanisms of Evolution Arizona State UniversityTempeAZ 85281USA

Bacteria with functional DNA repair systems are expected to have low mutation rates due to strong natural selection for genomic ***,our study of the wild-type Streptococcus pneumoniae D39,a pathogen responsible for many common diseases,revealed a high spontaneous mutation rate of 0.02 per genome per cell division in mutation-accumulation(MA)*** rate is orders of magnitude higher than that of other non-mutator bacteria and is characterized by a high mutation bias in the A/T *** high mutation rate may have resulted from a reduction in the overall efficiency of selection,conferred by the tiny effective population size in *** line with this,*** D39 also exhibited the lowest DNA mismatch-repair(MMR)efficiency among *** with the antibiotic penicillin did not elevate the mutation rate,as penicillin did not induce DNA damage and *** lacks a stress response *** findings suggested that the MA results are applicable to within-host scenarios and provide insights into pathogen evolution.

关键词： Neutral evolution Mutation spectrum Antibiotics DNA mismatch repair Oxidative damage repair

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A Hybrid Optimization Approach of Single Point Incremental Sheet Forming of AISI 316L Stainless Steel Using Grey Relation Analysis Coupled with Principal Component Analysiss

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Journal of Wuhan University of technology(Materials Science) 2024年第1期39卷 160-166页

作者： A Visagan P Ganesh department of Production technology Madras Institute of TechnologyChennai-600044India

We investigated the parametric optimization on incremental sheet forming of stainless steel using Grey Relational Analysis(GRA) coupled with Principal Component Analysis(PCA). AISI 316L stainless steel sheets were used to develop double wall angle pyramid with aid of tungsten carbide tool. GRA coupled with PCA was used to plan the experiment conditions. Control factors such as Tool Diameter(TD), Step Depth(SD), Bottom Wall Angle(BWA), Feed Rate(FR) and Spindle Speed(SS) on Top Wall Angle(TWA) and Top Wall Angle Surface Roughness(TWASR) have been studied. Wall angle increases with increasing tool diameter due to large contact area between tool and workpiece. As the step depth, feed rate and spindle speed increase,TWASR decreases with increasing tool diameter. As the step depth increasing, the hydrostatic stress is raised causing severe cracks in the deformed surface. Hence it was concluded that the proposed hybrid method was suitable for optimizing the factors and response.

关键词： single point incremental forming AISI 316L taguchi grey relation analysis principal component analysis surface roughness scanning electron microscopy

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Insertion sequence transposition activates antimycobacteriophage immunity through an Isr2-silenced lipid metabolism gene island

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mLife 2024年第1期3卷 87-100页

作者： Yakun Li Yuyun Wei Xiao Guo Xiaohui Li Lining Lu Lihua Hu Zheng-Guo He State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources Guangxi Research Center for Microbial and Enzyme Engineering TechnologyCollege of Life Scienceand TechnologyGuangxi UniversityNanningChina

Insertion sequences(ISs)exist widely in bacterial genomes,but their roles in the evolution of bacterial antiphage defense remain to be ***,we report that,under the pressure of phage infection,the IS1o96 transposition of Mycobacterium smegmatis into the Isr2 gene can occur at high frequencies,which endows the mutant mycobacterium with a broad-spectrum antiphage ***2 functions as a negative regulator and directly silences expression of a gene island composed of 11 lipid metabolism-related *** complete or partial loss of the gene island leads to a significant decrease of bacteriophage adsorption to the mycobacterium,thus defending against phage ***,a phage that has evolved mutations in two tail-filament genes can re-escape from the Isr2 inactivation-triggered host *** study uncovered a new signaling pathway for activating antimycobacteriophage immunity by Is transposition and provided insight into the natural evolution of bacterial antiphage defense.

关键词： antiphage defense bacteriophage gene island insertion sequence mycobacteria

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Effect of organic component(tartrate) addition on cerium nitrate's ability to inhibit corrosion of mild steel in NaCl solution

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Journal of Rare Earths 2024年第10期42卷 1995-2002页

作者： Minakshi Koundal Chhaya Sharma A.K.Singh department of Applied Science and Engineering Indian Institute of Technology RoorkeeSaharanpur Campus department of Pulp and Paper technology Indian Institute of technology Roorkee Saharanpur Campus

Cerium tartrate（CeTar）,produced in this study by precipitating cerium nitrate with potassium sodium tartrate（KNaTar）,was examined as a corrosion *** loss tests show inhibition efficiency of 71.7% with Ce（NO3）3and 88.7% with CeTar inhibitor for one-month exposure to mild steel in 7 g/L NaCl *** inhibition efficiency drops to 28.6% with the fo rmer and remains around 8 7% with the latter inhibitor after six months of *** results from electrochemical testing indicate that the inhibition efficiency decreases by adding cerium ***,the cerium tartrate inhibitor demonstrates a nearly constant inhibition efficiency for up to 30 d,i.e.,≈90%.Electrochemical impedance spectroscopy（EIS） performed in these cases shows the following results:（ⅰ） with cerium nitrate,a film of iron and cerium oxide,which on prolonged exposure diminishes,and（ⅱ） with cerium tartrate,the formation of a bimetallic film（Fe-tartrate-Ce） and a mixture of cerium hydroxide and iro n oxide that protects steel for a longer *** inferences are based on the analyses of scanning electron microscopy/energydispersive X-ray analysis（SEM/EDAX）,X-ray diffraction（XRD）,Fourier transform infrared spectroscopy（FTIR）,X-ray photoelectron（XPS）,and Raman spectroscopy results.

关键词： Cerium nitrate Cerium tartrate Corrosion inhibition Inhibitor film characterization Mild steel Rare earths

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