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Bubble coalescence in interacting system of DNA molecules

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International Journal of Biomathematics 2024年第4期17卷 195-216页

作者： U.A.Rozikov V.I.Romanouskiy Institute of Mathematics 9 Universitet Street100174 Tashkent Uzbekistan AKFA University National Park StreetBarkamol MFY Mirzo-Ulugbek District111221 Tashkent Uzbekistan national University of Uzbekistan 4Universitet Street 100174 TashkentUzbekistan

We consider two models of interacting DNA molecules:First is(four parametric)bubble coalescence model in interacting DNAs(shortly:BCI-DNA).Second is(three parametric)bubble coalescence model in a condensed DNA molecules(shortly BCC-DNA).To study bubble coalescence thermodynamics of BCI-DNA and BCC-DNA models we use methods of statistical ***,we define Hamiltonian of each model and give their translation-invariant Gibbs measures(TIGMs).For the first model,we find parameters such that corresponding Hamiltonian has up to three TIGMs(three phases of system)biologically meaning existence of three states:“No bubble coalescence”,“Dominated soft zone”,“Bubble coalescence”.For the second model,we show that for any(admissible)parameters,this model has unique *** is a state where“No bubble coalescence”phasedominates.

关键词： DNA bubble configuration Cayley tree Gibbs measure Potts model

Optimized protoplast isolation and transfection with a breakpoint:accelerating Cas9/sgRNA cleavage efficiency validation in monocot and dicot

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aBIOTECH 2024年第2期5卷 151-168页

作者： Debasmita Panda Subhasis Karmakar Manaswini Dash Swagat Kumar Tripathy Priya Das Sagar Banerjee Yiping Qi Sanghamitra Samantaray Pradipta Kumar Mohapatra Mirza J.Baig Kutubuddin A.Molla ICAR national Rice Research Institute CuttackOdisha 753006India Department of Botany Ravenshaw UniversityCuttackOdisha 753003India Department of Plant Science and Landscape Architecture University of MarylandCollege ParkMD 20742USA

The CRISPR-Cas genome editing tools are revolutionizing agriculture and basic biology with their simplicity and precision ability to modify target genomic ***-predicted guide RNAs(gRNAs)often fail to induce efficient cleavage at target *** target loci are inaccessible due to complex chromatin ***,there is no suitable tool available to predict the architecture of genomic target sites and their ***,significant time and resources are spent on performing editing experiments with inefficient *** in vitro-cleavage assay could provide a rough assessment of gRNA efficiency,it largely excludes the interference of native genomic *** in-vivo testing gives a proper assessment of the cleavage ability of editing reagents in a native genomic ***,we developed a modified protocol that offers highly efficient protoplast isolation from rice,Arabidopsis,and chickpea,using a sucrose gradient,transfection using PEG(polyethylene glycol),and validation of single guide RNAs(sgRNAs)cleavage efficiency of *** have optimized various parameters for PEG-mediated protoplast transfection and achieved high transfection efficiency using our protocol in both monocots and *** introduced plasmid vectors containing Cas9 and sgRNAs targeting genes in rice,Arabidopsis,and chickpea *** dual sgRNAs,our CRISPRdeletion strategy offers straightforward detection of genome editing success by simple agarose gel *** sequencing of PCR products confirmed the editing efficiency of specific ***,we demonstrated that isolated protoplasts can be stored for up to 24/48 h with little loss of viability,allowing a pause between isolation and *** high-efficiency protocol for protoplast isolation and transfection enables rapid(less than 7 days)validation of sgRNA cleavage efficiency before proceeding with stable *** isolation and transfection method can als

关键词： Protoplast Genome editing Transgene-free edited plants Rice Chickpea

Synchronous deprotonation–protonation for mechanically robust chitin/aramid nanofibers conductive aerogel with excellent pressure sensing, thermal management, and electromagnetic interference shielding

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Nano Research 2024年第3期17卷 2038-2049页

作者： Xinxin Zhang Kunpeng Qian Jianhui Fang Sineenat Thaiboonrod Miao Miao Xin Feng Department of Chemistry College of SciencesShanghai UniversityShanghai 200444China Research Center of Nano Science and Technology College of SciencesShanghai UniversityShanghai 200444China School of Materials Sciences and Engineering Shanghai UniversityShanghai 200444China national Nanotechnology Center(NANOTEC) National Science and Technology Development Agency(NSTDA)Thailand Science ParkPathum Thani 12120Thailand

Aerogels with regularly porous structure and uniformly distributed conductive networks have received extensive attention in wearable electronic sensors,electromagnetic shielding,and so ***,the poor mechanical properties of the emerging nanofibers-based aerogels are limited in practical *** this work,we developed a synchronous deprotonation–protonation method in the KOH/dimethyl sulfoxide(DMSO)system at room temperature for achieving chitin cross-linked aramid nanofibers(CANFs)rather than chitin nanofibers(ChNFs)and aramid nanofibers(ANFs)separately by using chitin and aramid pulp as raw *** freeze-drying process,the cross-linked chitin/aramid nanofibers(CA)aerogel exhibited the synergetic properties of ChNF and ANF by the dual-nanofiber compensation *** mechanical stress of CA aerogel was 170 kPa at 80%compressive strain,increased by 750%compared with pure ChNF ***,the compressibility of CA aerogel was somewhat improved compared to ANF *** enhancement verified that the crosslinking reaction between ANF and ChNF during the synchronous deprotonation process was ***,the conductive aerogels with uniform porous structure(CA-M)were successfully obtained by vacuum impregnating CA aerogels in Ti_(3)C_(2)T_(x) MXene solution,displaying low thermal conductivity(0.01 W/(m·K)),high electromagnetic interference(EMI)shielding effectiveness(SE)(75 dB),flame retardant,and heat ***,the as-obtained CA-M aerogels were also applied as a pressure sensor with excellent compression cycle stability and superior human motion monitoring *** a result,the dual-nanofiber based conductive aerogels have great potentials in flexible/wearable electronics,EMI shielding,flame retardant,and heat insulation.

关键词： synchronous deprotonation–protonation electromagnetic interference(EMI)shielding flame retardant heat insulation pressure sensing

Bulked Segregant RNA-Seq Analysis of Pollinated Pistils Reveals Genes Influencing Spikelet Fertility in Rice

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Rice science 2024年第5期31卷 556-571,I0031-I0056页

作者： Kanokwan KAEWMUNGKUN Keasinee TONGMARK Sriprapai CHAKHONKAEN Numphet SANGARWUT Theerachai THANANANTA Amorntip MUANGPROM Department of Biotechnology Faculty of Science and TechnologyThammasat UniversityRangsit CentreKhlong LuangPathum Thani 12120Thailand national Center for Genetic Engineering and Biotechnology National Science and Technology Development AgencyThailand Science ParkKhlong LuangPathum Thani 12120Thailand

Prezygotic isolation is important for successful fertilization in rice, significantly affecting yield. This study focused on F_(5:6) generation plants derived from inter-subspecific crosses(Nipponbare × KDML105) with low(LS) and high seed-setting rates(HS), in which normal pollen fertility was observed. However, LS plants showed a reduced number of pollen grains adhering to the stigma and fewer pollen tubes reaching the ovules at 4-5 h post-pollination, compared with HS plants. Bulked segregant RNA-Seq analysis of pollinated pistils from the HS and LS groups revealed 249 and 473 differentially expressed genes(DEGs), respectively. Kyoto Encyclopedia of Genes and Genomes analysis of the HS and LS-specific DEGs indicated enrichment in metabolic pathways, pentose and glucuronate interconversions, and flavonoid biosynthesis. Several of these DEGs exhibited co-expression with pollen development genes and formed extensive clusters of co-expression networks. Compared with LS pistils, enzyme genes controlling pectin degradation, such as OsPME35 and OsPLL9, showed similar expression patterns, with higher levels in HS pistils pre-pollination. Os02g0467600, similar to cinnamate 4-hydroxylase gene(CYP73), involved in flavonoid biosynthesis, displayed higher expression in HS pistils post-pollination. Our findings suggest that OsPME35, OsPLL9, and Os02g0467600 contribute to prezygotic isolation by potentially modifying the stigma cell wall(OsPME35 and OsPLL9) and controlling later processes such as pollen-stigma adhesion(Os02g0467600) genes. Furthermore, several DEGs specific to HS and LS were co-localized with QTLs and functional genes associated with spikelet fertility. These findings provide valuable insights for further research on rice spikelet fertility, ultimately contributing to the development of high-yielding rice varieties.

关键词： bulked segregant RNA-Seq flavonoid inter-subspecific cross pectin pollinated pistil prezygotic barrier spikelet fertility

Effective roles of exercise and diet adherence in non-alcoholic fatty liver disease

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World Journal of Gastroenterology 2024年第29期30卷 3456-3460页

作者： Wei Zhu School of Life Sciences and Technology Tongji UniversityShanghai 200092China Shanghai Xirong Information Science and Technology Co. Ltd.National Science and Technology ParkTongji UniversityShanghai 200092China

Non-alcoholic fatty liver disease(NAFLD)is characterized by symptoms of excessive fat accumulation and steatosis in the liver without alcohol intake in *** associated pathogenic mechanism is not completely understood and there are no specific drugs for patients with *** and diet adherence are the best options for the management of NAFLD *** associated analysis models of adherence to these interventions are used to assess their effectiveness in the management of NAFLD patients using specificity,sensitivity,and so *** have indicated that the relative ratio of NAFLD can be reduced by physical activity with diet *** the future,the pathogenesis of NAFLD should be clarified with stratified efforts to develop appropriate drugs,and both exercise and diet adherence should be optimized using better questionnaire design and evaluation models for patients with NAFLD.

关键词： Exercise and diet adherence Non-alcoholic fatty liver disease Delphi Mediterranean diet Physical lifestyle

Anti-epileptic and Neuroprotective Effects of Ultra-low Dose NADPH Oxidase Inhibitor Dextromethorphan on Kainic Acid-induced Chronic Temporal Lobe Epilepsy in Rats

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Neuroscience Bulletin 2024年第5期40卷 577-593页

作者： Jing-Jing Yang Ying-Xin Liu Yan-Fang Wang Bi-Ying Ge Ying Wang Qing-Shan Wang Sheng Li Jian-Jie Zhang Ling-Ling Jin Jau-Shyong Hong Sheng-Ming Yin Jie Zhao College of Basic Medical Sciences Dalian Medical UniversityDalian116044China Department of Neurology The First Affiliated Hospital of Dalian Medical UniversityDalian116011China national and Local Joint Engineering Research Center for Drug Research and Development of Neurodegenerative Diseases Dalian116044China School of Public Health Dalian Medical UniversityDalian116044China Neurobiology Laboratory National Institute of Environmental Health SciencesNational Institutes of HealthResearch Triangle ParkDurhamNC27709USA

Neuroinflammation mediated by microglia and oxidative stress play pivotal roles in the development of chronic temporal lobe epilepsy(TLE).We postulated that kainic acid(KA)-Induced status epilepticus triggers microglia-dependent inflammation,leading to neuronal damage,a lowered seizure threshold,and the emergence of spontaneous recurrent seizures(SRS).Extensive evidence from our laboratory suggests that dextromethorphan(DM),even in ultra-low doses,has anti-inflammatory and neuroprotective effects in many animal models of neurodegenerative *** results showed that administration of DM(10 ng/kg per day;subcutaneously via osmotic minipump for 4 weeks)significantly mitigated the residual effects of KA,including the frequency of SRS and seizure *** addition,DM-treated rats showed improved cognitive function and reduced hippocampal neuronal *** found suppressed microglial activation-mediated neuroinflammation and decreased expression of hippocampal gp91^(phox) and p47^(phox) proteins in KA-induced chronic TLE ***,even after discontinuation of DM treatment,ultra-low doses of DM continued to confer long-term anti-seizure and neuroprotective effects,which were attributed to the inhibition of microglial NADPH oxidase 2 as revealed by mechanistic studies.

关键词： Temporal lobe epilepsy Dextromethorphan NADPH oxidase Ultra-low dose

Spatial-temporal shifting patterns and in situ conservation of spotted seal(Phoca largha)populations in the Yellow Sea ecoregion

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Integrative Zoology 2024年第2期19卷 307-318页

作者： Hongfei ZHUANG Fei SHAO Chao ZHANG Wancai XIA Shouqiang WANG Fangyuan QU Zongling WANG Zhichuang LU Linlin ZHAO Zhaohui ZHANG First Institute of Oceanography Ministry of Natural ResourcesQingdaoChina Department of Natural Resources of Shandong Province Shandong Forestry Protection and Development Service CenterJinanChina national park(Protected Areas)Development Center National Forestry and Grassland AdministrationBeijingChina College of Life Science China West Normal UniversityNanchongChina Liaoning Ocean and Fisheries Science Research Institute DalianChina

Understanding the habitat shifting pattern is a prerequisite for implementing in situ conservation of migratory *** seals(Phoca largha)inhabiting the Yellow Sea ecoregion(YSE)comprise a small population with independent genes and represent a charismatic flagship species in this ***,this population has declined by 80%since the 1940s,and increased support from the countries around the YSE is urgently needed to address the potential local extinction risk.A time-series niche model and life-history weighted systematic conservation planning were designed on the basis of a satellite beacon tracking survey(2010–2020)of the YSE *** results showed clustering and spreading shifting patterns during the breeding and migratory seasons,*** closed-loop migration route formed in the YSE indicated that this population might be geographically isolated from populations in other breeding areas around the *** conservation priority area(CPA),with an area of 19632 km^(2)(3.58%of the total YSE area),was the most effective response to the potential in situ ***,nearly 80%of the CPA was exposed outside the existing marine protected areas(MPAs).Future establishment of MPAs in China should strategically consider the conservation gap identified herein,and it is recommended for Korea’s closed fishing season to be spatially set in the western Korean Peninsula from May to *** study also exemplified that the lack of temporal information would lead to the dislocation of niche modeling for migratory species represented by spotted *** should be paid to protecting small and migratory populations in marine biodiversity conservation planning.

关键词： conservation priority area marine protected area migration seasonal management spotted seal

Enhanced performance of solution-processed carbon nanotube transparent electrodes in foldable perovskite solar cells through vertical separation of binders by using eco-friendly parylene substrate

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Carbon Energy 2024年第7期6卷 83-93页

作者： Unsoo Kim Jeong-Seok Nam Jungjin Yoon Jiye Han Mansoo Choi Il Jeon Department of Mechanical Engineering Seoul National UniversitySeoulRepublic of Korea Global Frontier Center for Multiscale Energy Systems Seoul National UniversitySeoulRepublic of Korea Frontier Energy Solution SeoulRepublic of Korea Department of Nano Engineering Department of Nano Science and TechnologySKKU Advanced Institute of Nanotechnology(SAINT)Sungkyunkwan University(SKKU)SuwonRepublic of Korea Department of Materials Science and Engineering Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA

The successful utilization of an eco-friendly and biocompatible parylene-C substrate for high-performance solution-processed double-walled carbon nanotube(CNT)electrode-based perovskite solar cells(PSCs)was *** the use of a novel inversion transfer technique,vertical separation of the binders from the CNTs was induced,rendering a stronger p-doping effect and thereby a higher conductivity of the *** resulting foldable devices exhibited a power conversion efficiency of 18.11%,which is the highest reported among CNT transparent electrode-based PSCs to date,and withstood more than 10,000 folding cycles at a radius of 0.5 mm,demonstrating unprecedented mechanical ***,solar modules were fabricated using entirely laser scribing processes to assess the potential of the solution-processable nanocarbon ***,this is the only one to be processed entirely by the laser scribing process and to be biocompatible as well as eco-friendly among the previously reported nonindium tin oxide-based perovskite solar modules.

关键词： double-walled carbon nanotubes parylene substrates perovskite modules perovskite solar cells solution-processable electrodes surfactant removal

Oryza CLIMtools:A genome–environment association resource reveals adaptive roles for heterotrimeric G proteins in the regulation of rice agronomic traits

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Plant Communications 2024年第4期5卷 145-165页

作者： Angel Ferrero-Serrano David Chakravorty Kobie J.Kirven Sarah M.Assmann Biology Department Pennsylvania State University208 Mueller LaboratoryUniversity ParkPA 16802USA Intercollege Graduate Degree Program in Bioinformatics and Genomics Pennsylvania State University208 Mueller LaboratoryUniversity ParkPA 16802USA

Modern crop varieties display a degree of mismatch between their current distributions and the suitability of the local climate for their *** address this issue,we present Oryza CLIMtools(https://***/CLIMtools/oryza_v1.0/),thefirst resource for pan-genome prediction of climate-associated genetic variants in a crop *** CLIMtools consists of interactive web-based databases that enable the user to(1)explore the local environments of traditional rice varieties(landraces)in South-East Asia and(2)investigate the environment by genome associations for 658 Indica and 283 Japonica rice landrace accessions collected from georeferenced local environments and included in the 3K Rice Ge-nomes *** demonstrate the value of these resources by identifying an interplay betweenflowering time and temperature in the local environment that is facilitated by adaptive natural variation in OsHD2 and disrupted by a natural variant in *** quantitative trait locus analysis has suggested the impor-tance of heterotrimeric G proteins in the control of agronomic ***,we analyzed the climate associations of natural variants in the different heterotrimeric G protein *** identified a coordi-nated role of G proteins in adaptation to the prevailing potential evapotranspiration gradient and revealed their regulation of key agronomic traits,including plant height and seed and panicle *** conclude by highlighting the prospect of targeting heterotrimeric G proteins to produce climate-resilient crops.

关键词： Oryza sativa rice G by E adaptation flowering time GWAS OsHD2 OsSOC1 heterotrimeric G pro-tein OsRGA1 d1 OsGS3 OsDEP1 OsGGC2