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Influences of flexible defect on the interplay of supercoiling and knotting of circular DNA

Communications in Theoretical Physics 2021年第7期73卷 136-145页

作者： Caiyun Xiong Xiaolin Nie Yixue Peng Xun Zhou Yangtao Fan Hu Chen Yanhui Liu College of Physics Guizhou UniversityGuiyang 550025China School of Physics and Electronic Science Guizhou Normal UniversityGuiyang 550025China Collaborative Innovation Center for Optoelectronic Semiconductors and Efficient Devices PenTung Sah Institute of Micro-Nano Science and TechnologyXiamen UniversityXiamen361005China Research institute for Biomimetics and Soft Matter Fujian Provincial Key Lab for Soft Functional Materials ResearchDepartment of PhysicsXiamen UniversityXiamen361005China Breeding and Reproduction in The Plateau mountainous Region Ministry of Education(Guizhou University)Guizhou Guiyang550025China

Knots are discovered in biophysical systems,such as DNA and *** portions in knotted DNA are significantly bent and their corresponding bending angles are comparable with or larger than the sharp bending angle resulting in flexible *** role of flexible defects in the interplay of supercoiling and knotting of circular DNA were predicted by a Monte Carlo *** knotted DNA with a particular knot type,a flexible defect noticeably enhances the supercoiling of the knotted DNA and the decreasing excitation energy makes the knotted portion more compact.A reduction in twist rigidity and unwinding of flexible defects are incorporated into the numerical simulations,so that interplay of supercoiling and knotting of circular DNA is studied under torsional *** unwinding not only results in a wider linking number distribution,but also leads to a drift of the distribution to lower values.A flexible defect has obvious effects on knotting *** summation of equilibrium distribution probability for nontrivial knotted DNA with different contour length does not change with excitation energy monotonically and has a maximum at an intermediate value of excitation energy around 5 *** the phase space of knot length and gyration radius of knotted DNA,knot length does not anticorrelate with its gyration radius,which is attributed to the flexible defect in the knotted portion,which leads to the release of bending energy and inhibited the competition between entropy and bending energy.

关键词： knot flexible defect DNA topology knotted DNA Monte-Carlo simulation

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Species Diversity of Arbuscular Mycorrhizal Fungi in the Rhizosphere of Hevea brasiliensis in Hainan Island,China

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Phyton-International Journal of Experimental Botany 2021年第1期90卷 179-192页

作者： Xiubing Gao Jiejie Lv Can Guo Anlong Hu Xiaomao Wu Zengping Li guizhou Tea Research institute Guizhou Province Academy of Agricultural ScienceGuiyang550006China Agricultural Technology Research and Extension Center of Qiongzhong Li and Miao Autonomous County Qiongzhong572900China The Provincial Key Laboratory for Agricultural Pest Management in mountainous Region Institute of Plant ProtectionCollege of AgricultureGuizhou UniversityGuiyang550025China College of Environment and Plant Protection Hainan UniversityHaikou570228China

Hevea brasiliensis is one of the important economic trees with a great economic value for natural rubber *** between roots of *** and arbuscular mycorrhizal fungi(AMF)is widely recognized,and can provide a range of benefits for both of *** Island harbors is one of the largest plantations of *** in China,whereas the information regarding the diversity of AMF in the rhizosphere of *** on this island is *** diversity of AMF species in the rhizosphere of rubber tree plantations in Hainan was investigated in this study.A total of 72 soil samples from the rhizosphere of *** RY7-33-97 were *** included 48 samples from plantations in 11 cities or counties that had been planted for 15–25 years,and 24 samples from a demonstrating plantation site of the China National Rubber Tree Germplasm Repository representing plantations with tree plantation ages from one to 40 ***,a total of 68 morphotypes of AMF,belonging to the genera of Archaeospora(1),Glomus(43),Acaulospora(18),Entrophospora(3),Scutellospora(2),and Gigaspora(1)were isolated and identified,as per morphological characteristics of spores presented in the collected soil ***(Frequency,F=100%)and Acaulospora(F=100%)were the predominant genera,and ***(F=63.9%)and ***(F=63.9%)were the predominant *** species differed significantly among collected sites in spore density(SD,290.7–2,186.7 spores per 100 g dry soil),species richness(SR,4.3–12.3),and Shannon-Weiner index of diversity(H,1.24–2.24).SD was negatively correlated with available phosphorus level in the soil;SR was positively correlated with soil total phosphorus content;and H was positively correlated with levels of soil organic matter and total ***,SD,SR,and H were also correlated with *** plantation age,and an increasing trend was observed up to 40 *** results suggest that the AMF community was

关键词： Arbuscular mycorrhizal fungi rubber tree species diversity influence factors plantation age

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Optimal aspect ratio of endocytosed spherocylindrical nanoparticle

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Frontiers of physics 2015年第1期10卷 119-123页

作者： Ying-Bing Chen Yan-Hui Liu Yah Zeng Wei Mao Lin Hu Zong-Liang Mao Hou-Qiang Xu Key Laboratory of Animal Genetics Breeding and Reproduction in the Plateau Mountainous Region Ministry of Education College of Animal Science Guizhou University Guiyang 550025 China Soft Condensed Matter Laboratory College of Science Guizhou University Guiyang 550025 China State Key Laboratory of Theoretical Physics Institute of Theoretical Physics Chinese Academy of Sciences Beijing 100190 China College of Civil Engineering Guizhou University Guiyang 550025 China

Recent simulations have demonstrated that bioparticle size and shape modulate the process of endocytosis, and studies have provided more quantitative information that the endocytosis efficiency of spherocylindrical bioparticles is decided by its aspect ratio. At the same time, the dimensions of the receptor-ligand complex have strong effects on the size-dependent exclusion of proteins within the cellular environment. However, these earlier theoretical works including simulations did not consider the effects of ligand-receptor complex dimension on the endocytosis process. Thus, it is necessary to resolve the effects of ligand-receptor complex dimension and determine the optimal aspect ratio of spherocylindrical bioparticles in the process of endocytosis. Accordingly, we proposed a continuum elastic model, of which the results indicate that the aspect ratio depends on the ligand-receptor complex dimension and the radius of the spherocylindrical bioparticle. This model provides a phase diagram of the aspect ratio of endocytosed spherocylindrical bioparticles, the larger aspect ratio of which appears in the phase diagram with increasing ligand density, and highlights the bioparticle design.

关键词： cellular uptake depletion effects dimension of ligand-receptor complex elasticity theory

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Comparison in phytoplankton diversity-productivity-community stability between river-type reservoir and lake-type reservoir

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Journal of Oceanology and Limnology 2022年第4期40卷 1485-1507页

作者： Qiong WU Qiuhua LI Huan LUO Qian CHEN Huaxiang CHEN Yanjun DONG Shenghua LI College of Environment Hohai UniversityNanjing 210098China Pearl River Water resources Research institute Guangzhou 510611China Key Laboratory of the Pearl River Estuary Regulation and Protection of Ministry of Water resources Guangzhou 510611China Guangdong Provincial Engineering Technology Research Center for Life and Health of River&Lake Guangzhou 510611China Key Laboratory for Information System of mountainous Area and Protection of Ecological Environment of guizhou Province Guizhou Normal UniversityGuiyang 550001China Bureau of Ecological Environment of Xunwu County of Jiangxi Province Xunwu 342200China

Relationship between biodiversity and ecosystem function is one of the core issues in ecological ***,as the main producer of aquatic ecosystem,its diversity,productivity,and community stability are of great signifi cance to reveal ecosystem *** are signifi cant diff erences in hydrodynamics,water retention time,and phytoplankton community structure between river-type reservoir and newly built lake-type *** comparative analysis of phytoplankton community stability between the two types of reservoir has not been *** Reservoir(river-type)and Taihu Reservoir(lake-type),the two reservoirs in the Dongjiang River source area of Zhujiang(Pearl)River Basin,were selected for comparison in terms of multi-year operation *** impoundment,river-type ***-type,and shallow water ***-deep water *** were collected in dry season(December 2019),normal season(March 2020),and wet season(August 2020),on which the phytoplankton diversity and productivity of the two reservoirs,and the relationship and diff erence of community stability were *** show that(1)the number of phytoplankton species in Jiuquwan Reservoir decreased comparing that before algal bloom and the restoration treatment,while that in Taihu Reservoir increased compared with that before the impoundment of the *** was no signifi cant diff erence in functional groups and species number between the two reservoirs(P>0.05);(2)the biological stability,diversity,productivity,and resource utilization effi ciency of newly built lake-type reservoir were higher than those of multi-year river-type *** addition,the utilization effi ciency of phytoplankton resources was the highest in wet season in both *** increases in biodiversity,richness,and evenness promoted the stability of the community,while increases in productivity and resource utilization effi ciency weakened the stability of the community;(3)community stabili

关键词： community stability functional group stability phytoplankton diversity resource utilization effi ciency reservoir

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Large scale identification of SSR marker in perilla by next generation sequencing

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Oil Crop Science 2019年第2期4卷 100-109页

作者： Qi Shen He Wen Tianyuan Zhang Jing Xu Xianping Wang Shimei Yang Caifu Du Degang Zhao Rapeseed Research institute Guizhou Academy of Agricultural Sciences Guiyang China The Key Laboratory of Plant resources Conservation and Germplasm Innovation in mountainous Region (Ministry of Education) Guizhou University Guiyang China

Perilla frutescens (L.) is an edible, medicinal crop, and most popular in East Asia. Its molecular breeding and research are hampered by the paucity of molecular markers. Simple sequence repeat (SSR) markers are ubiquitous and widely used in eukaryotic genomes. EST-SSRs identification of perilla was performed in 116,387 reads generated by Illumina paired-end sequencing technology. In total 25,449 unigenes containing SSR and 33,867 SSR loci were identified, and 19,400 primer pairs were designed. Polymorphism of SSR primers was conducted by searching for insertions and deletions (INDELs), and 1,567 unique SSRs were predicted. Totally, 200 SSR primer pairs were selected for polymorphic validation among 23 perilla accessions. Results showed that 175 primer pairs produced amplicons, and 30 pairs exhibited polymorphism. Polymorphic ratio was higher by using INDEL method than using conventional primers. Phylogenetic analysis showed the 2 distinct groups: P. frutescens var. frutescens and P. frutescens var. crispa. Wrinkled leaf trait and seed trait were distinct between these 2 groups. However, no clear leaf color or geographic relationship was detected. The large scale development and identification of SSR marker in this research laid a foundation for genetic analysis and marker assisted breeding of cultivated perilla.

关键词： Perilla frutescens L. simple sequence repeats (SSR) next generation sequencing INDEL marker-assisted breeding

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Autotoxicity of Phthalate Esters in Tobacco Root Exudates:Effects on Seed Germination and Seedling Growth

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Pedosphere 2017年第6期27卷 1073-1082页

作者： DENG Jiajun ZHANG Yanling HU Jiwei JIAO Jiaguo HU Feng LI Huixin ZHANG Shixiang Soil Ecology Laboratory College of Resources and Environmental SciencesNanjing Agricultural UniversityNanjing 210095(China) ~hengzhou Tobacco Research institute of CNTC Zhengzhou 450001(China) guizhou Provincial Key Laboratory for Information System of mountainous Areas and Protection of Ecological Environment Guizhou Nounal UniversityGuiyang 550001(China) Testing Center of Agro-Product Quality and Safety of Jiangxi Province Nanchang 330046(China) Key Laboratory of Eco-Environmental and Tobacco Leaf Quality of CNTC Zhengzhou 450001(China)

Autotoxicity is one of the major factors that impede continuous *** is defined as the toxic influence of chemicals released from one plant species on the germination and growth of individuals of the same ***, in order to exam the autotoxicity of tobacco root exudates, root exudates were collected from tobacco plants grown both in cultural solution and on natural *** ultraperformance liquid chromatography coupled with triple-quadrupole tandem mass spectrometry, main autotoxic chemical substances in the root exudates were *** autotoxic effects of suspected autotoxins on seed germination(including germination rate,germination potential, germination index, and vigor index) and seedling growth were *** phthalate(or diisobutyl phthalate), dioctyl phthalate, and diisooctyl phthalate were identified in tobacco root *** was observed that high concentrations(greater than 0.5 mmol L^(-1)) of each identified phthalate ester caused significant(P < 0.05) inhibition of tobacco seed germination and seedling *** can be concluded that phthalate esters such as dibutyl phthalate, diisobutyl phthalate, and diisooctyl phthalate in tobacco root exudates may play an important role in tobacco autotoxicity.

关键词： autotoxins germination index germination potential germination rate vigor index

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Regulation of Calvin-Benson cycle enzymes under high temperature stress

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aBIOTECH 2022年第1期3卷 65-77页

作者： Juan-Hua Chen Ming Tang Xue-Qi Jin Han Li Li-Sha Chen Qing Long Wang Ai-Zhen Sun Yin Yi Fang-Qing Guo National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences Institute of Plant Physiology and EcologyChinese Academy of Sciences300 Fenglin RoadShanghai 200032China Key Laboratory of Plant Physiology and Developmental Regulation School of Life SciencesGuizhou Normal UniversityGuiyang 550001GuizhouChina Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst mountainous Areas of Southwestern China Guizhou Normal UniversityGuiyang 550001GuizhouChina University of Chinese Academy of Sciences Beijing 100049China

The Calvin Benson cycle(CBC)consists of three critical processes,including fixation of CO_(2) by Rubisco,reduction of 3-phosphoglycerate(3PGA)to triose phosphate(triose-P)with NADPH and ATP generated by the light reactions,and regeneration of ribulose 1,5-bisphosphate(RuBP)from *** activ-ities of photosynthesis-related proteins,mainly from the CBC,were found more significantly affected and regulated in plants challenged with high temperature stress,incuding Rubisco,Rubisco activase(RCA) and the enzymes involved in RuBP regeneration,such as sedoheptulose-1,7-bisphosphatase(SBPase).Over the past years,the regulatory mechanism of CBC,especially for redox-regulation,has attracted major interest,because balancing flux at the various enzymatic reactions and maintaining metabolite levels in a range are of critical importance for the optimal operation of CBC under high temperature stress,providing insights into the genetic manipulation of ***,we summarize recent progress regarding the identification of various layers of regulation point to the key enzymes of CBC for acclimation to environmental temperature changes along with open questions are also discussed.

关键词： Calvin-Benson cycle High temperature stress Redox regulation Rubisco Rubisco activase SBPase CO_(2)fixation

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Indoor Toxicity Determination of Several Pesticides to Ceratovacuna lanigera( Zehntner)

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Plant Diseases and Pests 2015年第1期6卷 19-21页

作者： Long Youhua Wang Weidong Yin Jianli College of Agriculture Guizhou University The Key Laboratory of Plant resources Conservation and Germplasm Innovation in mountainous Region ( Ministry of Education) Institute of Agro-Bioengineering and College of Life SciencesGuizhou University

Toxicity of 96% chlorpyrifos TC, 98% imidacloprid TC, 93% thiamethoxam TC and mixed pesticides of chlorpyrifos with other two agents （D ＋ B, D ＋ S） to C. lanigera （Zehntner） were determined under laboratory conditions by leaf dipping method. The results showed that all of the pesticides had high toxicity with the order of thiamethoxam TC 〉 imidacloprid TC 〉 D ＋ B 〉 chlorpyrifos TC 〉 D ＋ S. The results provided theoretic basis for selecting suitable insecti- cides to control the C. lanigera （Zehntner）.

关键词： Ceratovacuna lanigera (Zehntner) Toxicity determination Mixture

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Effects of Tsukamurella tyrosinosolvens P9 on growth,physiology and antioxdant enzyme of peanut under drought stress and after re-watering

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BIOCELL 2023年第6期47卷 1417-1430页

作者： CHANGMEI LONG TINGTING YANG YUJIE HAN LIZHEN HAN College of Life Sciences Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region(Ministry of Education)Collaborative Innovation Center for Mountain Ecology&Agro-Bioengineering(CICMEAB)Institute of Agro-BioengineeringGuizhou UniversityGuiyang550025China

Background:The plant-growth-promoting rhizobacterium Tsukamurella tyrosinosolvens is a rare strain of actinomycete,in order to recognize and expand the ecological functions of rare ***:In this experiment,we studied the effect of Tsukamurella tyrosinosolvens P9 on the drought resistance of peanut by inoculating peanut seedlings in pots and measuring the growth and physiological indicators of peanut under drought stress and re-watering ***:The results showed that during drought stress,the relative water content of the soil and leaves,chlorophyll content,and stomatal length,width,and aperture were significantly decreased while the levels of malondialdehyde(MDA),H_(2)O_(2) and stomatal density were significantly *** growth was also ***,inoculation with the P9 strain significantly promoted the growth of peanut under drought stress as plant height,fresh weight,root length and root weight were significantly higher compared with the uninoculated drought stress *** addition,in P9-inoculated plants,the water and chlorophyll contents were significantly higher and the activities of the antioxidant enzymes CAT and SOD were significantly increased(except during the six days of drought treatment).While the stomatal length,width,and aperture were improved,the levels of MDA and H2O2 were significantly *** staining showed that inoculation with P9 reduced O^(2−) accumulation under *** re-watering,the physiological indexes of inoculated plants recovered more quickly and grew ***:The results showed that *** P9 enhanced drought resistance and improves peanut growth by increasing leaf water content,increasing photosynthesis,regulating stomatal closure,and improving antioxidant enzyme activity.

关键词： PGPR Rare actinomycetes Drought resistance Biofertilizer

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Lake regime shift from submerged macrophyte to phytoplankton affected phosphorus speciation in sediment and eutrophic state in Caohai Lake,guizhou,China

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Journal of Oceanology and Limnology 2023年第6期41卷 2262-2275页

作者： Jixing DONG Yanmin GUO Pinhua XIA Yuanbin TIAN Feifei ZHENG Anyan LI Tao LIN Ruiwen LI guizhou Province Key Laboratory for Information System of mountainous Areas and Protection of Ecological Environment Guizhou Normal UniversityGuiyang 550001China Yangtze River Basin Ecological Environment Monitoring and Scientific Research Center Yangtze River Basin Ecological Environment Supervision and Administration BureauMinistry of Ecological EnvironmentWuhan 430010China

To understand the effect of regime shift in Caohai Lake in Yunnan-guizhou Plateau,SW China from submerged macrophyte dominance to phytoplankton dominance on the specification and distribution of phosphorus and on ecological and environmental states,changes in phosphorus specification in the sediments and water were *** form,composition,and distribution of phosphorus in sediment were sampled in July 2020(before regime shift)and July 2021(after regime shift)were *** reveal that phosphorus content in sediment was lower than that those of Erhai Lake and Dianchi Lake,Yunnan,SW China,on the same plateau,and was lower than those of Taihu Lake,Chaohu Lake,and Poyang Lake in the middle-lower Changjiang(Yangtze)River *** phosphorus(Or-P)was the main form(up to 60%),followed by inactive phosphorus(Ina-P),and the active phosphorus(Act-P),the least,which is opposite to those of Taihu Lake and Poyang Lake in the middle-lower Changjiang River Plain in the eastern ***-P content was high,indicating a high potential risk of phosphorous *** the regime shift,the total phosphorus in sediment decreased from 0.87±0.13 to 0.70±0.13 g/*** proportion of Or-P and Act-P decreased from 68.23% to 65.32% and from 5.35% to 4.69%,*** contrast,the proportion of Ina-P increased from 26.42% to 29.99%.The Moran’s I index revealed that the heterogeneity of the spatial distributions of the total phosphorus(S-TP)and Act-P in the sediments before regime shift was significant(P0.05).The regime shift aggravated the eutrophication of the lake,the trophic level index(TLI)increased from 48.42 to 54.49(P<0.01),and the previously mesotrophic lake became a mildly eutrophic *** results of this study revealed the impact of regime shift in the lake from submerged macrophyte dominance to phytoplankton dominanc

关键词： Caohai Lake sediment phosphorus specification regime shift

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