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RAD-seq data reveals robust phylogeny and morphological evolutionary history of Rhododendron

Horticultural Plant Journal 2024年第3期10卷 866-878页

作者： Yuanting Shen Gang Yao Yunfei Li Xiaoling Tian Shiming Li Nian Wang Chengjun Zhang Fei Wang yongpeng ma Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China University of Chinese Academy of Sciences Beijing 100049China Beijing Genomics of Institute ShenzhenGuangdong 518120China Guiyang Institute of Humanities and Technology GuiyangGuizhou 550025China State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River College of ForestryShandong Agricultural UniversityTai'anShandong 271018China The Southwest China of Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China West China Subalpine Botanical Garden Institute of BotanyChinese Academy of SciencesChengduSichuan 611834China

Rhododendron is famous for its high ornamental value.However,the genus is taxonomically difficult and the relationships within Rhododendron remain unresolved.In addition,the origin of key morphological characters with high horticulture value need to be explored.Both problems largely hinder utilization of germplasm resources.Most studies attempted to disentangle the phylogeny of Rhododendron,but only used a few genomic markers and lacked large-scale sampling,resulting in low clade support and contradictory phylogenetic signals.Here,we used restriction-site associated DNA sequencing(RAD-seq)data and morphological traits for 144 species of Rhododendron,representing all subgenera and most sections and subsections of this species-rich genus,to decipher its intricate evolutionary history and reconstruct ancestral state.Our results revealed high resolutions at subgenera and section levels of Rhododendron based on RAD-seq data.Both optimal phylogenetic tree and split tree recovered five lineages among Rhododendron.Subg.Therorhodion(cladeⅠ)formed the basal lineage.Subg.Tsutsusi and Azaleastrum formed cladeⅡand had sister relationships.CladeⅢincluded all scaly rhododendron species.Subg.Pentanthera(cladeⅣ)formed a sister group to Subg.Hymenanthes(cladeⅤ).The results of ancestral state reconstruction showed that Rhododendron ancestor was a deciduous woody plant with terminal inflorescence,ten stamens,leaf blade without scales and broadly funnelform corolla with pink or purple color.This study shows significant distinguishability to resolve the evolutionary history of Rhododendron based on high clade support of phylogenetic tree constructed by RAD-seq data.It also provides an example to resolve discordant signals in phylogenetic trees and demonstrates the application feasibility of RAD-seq with large amounts of missing data in deciphering intricate evolutionary relationships.Additionally,the reconstructed ancestral state of six important characters provides insights into the innovation of key characters in Rhododendron.

关键词： Rhododendron RAD-seq Missing data Quartet sampling(QS) Ancestral state reconstruction

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A VNS-NPGA Approach to Multi-Objective Optimization of Hub-and-spoke Logistics Network

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Journal of Traffic and Transportation Engineering(English Edition) 2024年

作者： Changxi ma Chuwei Shi Yun Yang yongpeng Zhao Zhuye Xu Bo Du School of Traffic and Transportation Lanzhou Jiaotong University Key Laboratory of Railway lndustry on Plateau Railway Transportation Intelligent management and Control Lanzhou Jiaotong University School of Tourism and management Yangling Vocational and Technical College School of New Energy and Power Engineering Lanzhou Jiaotong University National Engineering Research Center of Highway maintenance Technology Changsha University of Science & Technology SmaRT Infrastructure Facility University of Wollongong

To realize low-cost freight transport in the logistics network and improve the network operation efficiency， a multi-objective optimization model and the corresponding algorithm for a hub-and-spoke logistics network are proposed based on the multi-level location of hub points and channels layout. By considering the structure of the multi-level hub-and-spoke logistics network and the features of the connectivity between the hub and spoke points， the multi-objective optimization model is constructed with two objectives of minimizing the total network operation costs and the total network service time. By considering the characteristics of decision variables and models， a Variable Neighborhood Search (VNS)-Niched Pareto Genetic Algorithm (NPGA) approach with a three-stage encoding structure chromosome is proposed， where the VNS algorithm nested in NPGA is used for individual variable neighborhood search to optimize individual channel level genes， and NPGA is adopted to solve the multi-objective optimization model. To evaluate the performance of the proposed VNS-NPGA approach， a real-life case study based on a small-scale Australia Post data set was conducted， and 25 nodes of the Australia Post and 14 nodes of the Gansu Province 3-level hub-and-spoke logistics networks were established， respectively. The analysis results indicated that the network structure of multi-level hub points could avoid the detour problem existing in the traditional hub-and-spoke network， and showed better applicability in the narrow geographical structure. Compared to the traditional multi-objective evolutionary algorithms， VNS-NPGA can obtain better solutions through the distributed optimization of channel levels， avoiding the problem that a single algorithm cannot effectively deal with coupling relationships in genes.

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Two-photon live imaging of direct glia-to-neuron conversion in the mouse cortex

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Neural Regeneration Research 2024年第8期19卷 1781-1788页

作者： Zongqin Xiang Shu He Rongjie Chen Shanggong Liu Minhui Liu Liang Xu Jiajun Zheng Zhouquan Jiang Long ma Ying Sun yongpeng Qin Yi Chen Wen Li Xiangyu Wang Gong Chen Wenliang Lei Guangdong-Hong Kong-macao Institute of CNS Regeneration(GHMICR) Jinan UniversityGuangzhouGuangdong ProvinceChina Department of Neurosurgery The First Affiliated HospitalJinan UniversityGuangzhouGuangdong ProvinceChina Laboratory for Neuroimmunology in Health and Diseases Guangzhou First People’s HospitalSchool of MedicineSouth China University of TechnologyGuangzhouGuangdong ProvinceChina VIB-KU Leuven Center for Brain&Disease Research LeuvenFlemish RegionBelgium

Over the past decade,a growing number of studies have reported transcription factor-based in situ reprogramming that can directly conve rt endogenous glial cells into functional neurons as an alternative approach for n euro regeneration in the adult mammalian central ne rvous system.Howeve r,many questions remain regarding how a terminally differentiated glial cell can transform into a delicate neuron that forms part of the intricate brain circuitry.In addition,concerns have recently been raised around the absence of astrocyte-to-neuron conversion in astrocytic lineage-tra cing mice.In this study,we employed repetitive two-photon imaging to continuously capture the in situ astrocyte-to-neuron conversion process following ecto pic expression of the neural transcription factor NeuroD1 in both prolife rating reactive astrocytes and lineage-tra ced astrocytes in the mouse cortex.Time-lapse imaging over several wee ks revealed the ste p-by-step transition from a typical astrocyte with numero us short,tapered branches to a typical neuro n with a few long neurites and dynamic growth cones that actively explored the local environment.In addition,these lineage-converting cells were able to migrate ra dially or to ngentially to relocate to suitable positions.Furthermore,two-photon Ca2+imaging and patch-clamp recordings confirmed that the newly generated neuro ns exhibited synchronous calcium signals,repetitive action potentials,and spontaneous synaptic responses,suggesting that they had made functional synaptic connections within local neural circuits.In conclusion,we directly visualized the step-by-step lineage conversion process from astrocytes to functional neurons in vivo and unambiguously demonstrated that adult mammalian brains are highly plastic with respect to their potential for neuro regeneration and neural circuit reconstruction.

关键词： astrocyte-to-neuron conversion Ca2+imaging direct lineage conversion glia astrocyte in vivo reprogramming lineage-tracing mice NeuroD1 neuron two-photon imaging

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VOC emitted by biopharmaceutical industries:Source profiles,health risks,and secondary pollution

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Journal of Environmental Sciences 2024年第1期135卷 570-584页

作者： Jiawei ma Lin Li State Key Laboratory of Environmental Aquatic Chemistry Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China University of Chinese Academy of Sciences Beijing 100049China National Engineering Laboratory for VOCs Pollution Control material&Technology University of Chinese Academy of SciencesBeijing 101408China

The biopharmaceutical industry contributes substantially to volatile organic compounds(VOCs)emissions,causing growing concerns and social developmental conflicts.This study conducted an on-site investigation of the process-based emission of VOCs from three biopharmaceutical enterprises.In the workshops of the three enterprises,26 VOCs were detected,which could be sorted into 4 classes:hydrocarbons,aromatic hydrocarbons,oxygen-containing compounds,and nitrogen-containing compounds.Ketones were the main components of waste gases,accounting for 44.13%-77.85%of the overall VOCs.Process-based source profiles were compiled for each process unit,with the fermentation and extraction units of tiamulin fumarate being the main source of VOC emissions.Dimethyl heptanone,vinyl acetate,diethylamine,propylene glycol methyl ether(PGME),and benzene were screened as priority pollutants through a fuzzy comprehensive evaluation system.Ground level concentration simulation results of the Gauss plume diffusion model demonstrated that the diffusivity of VOCs in the atmosphere was relatively high,indicating potential non-carcinogenic and carcinogenic risks 1.5-2 km downwind.Furthermore,the process-based formation potentials of ozone and secondary organic aerosols(SOAs)were determined and indicated that N-methyl-2-pyrrolidone,dimethyl heptanone,and PGME should be preferentially controlled to reduce the ozone formation potential,whereas the control of benzene and chlorobenzene should be prioritized to reduce the generation of SOAs.Our results provide a basis for understanding the characteristics of VOC emission by biopharmaceutical industries and their diffusion,potentially allowing the development of measures to reduce health risks and secondary pollution.

关键词： Biopharmaceutical Volatile organic compound Priority pollutant Exposure risk Secondary pollution

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Absorption characteristics of elemental mercury in mercury chloride solutions

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Journal of Environmental Sciences 2014年第11期26卷 2257-2265页

作者： yongpeng ma Haomiao Xu Zan Qu Naiqiang Yan Wenhua Wang School of Environmental Science and Engineering Shanghai Jiao Tong University

Elemental mercury （Hg^0） in flue gases can be efficiently captured by mercury chloride （HgCl2） solution. However, the absorption behaviors and the influencing effects are still poorly understood. The mechanism of Hg^0 absorption by HgCl2 and the factors that control the removal were studied in this paper. It was found that when the mole ratio of Cl^- to HgCl2 is 10：1, the Hg^0 removal efficiency is the highest. Among the main mercury chloride species, HgCl3^- is the most efficient ion for Hg^0 removal in the HgCl2 absorption system when moderate concentrations of chloride ions exist. The Hg^0 absorption reactions in the aqueous phase were investigated computationaIIy using Moller-Plesset perturbation theory. The calculated Gibbs free energies and energy barriers are in excellent agreement with the results obtained from experiments. In the presence of SO3^2- and SO2, Hg^2＋ reduction occurred and Hg^0 removal efficiency decreased. The reduced Hg^0 removal can be controlled through increased chloride concentration to some degree. Low pH value in HgCla solution enhanced the Hg^0 removal efficiency, and the effect was more significant in dilute HgCl2 solutions. The presence of SO4^2- and NO3^- did not affect Hg^0 removal by HgCl2.

关键词： Nonferrous metal Smelting flue gas Elemental mercury Mercury chloride

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Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

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Journal of Integrative Plant Biology 2024年第3期66卷 546-578页

作者： Guojin Zhang Hong ma College of Life Sciences Hunan Normal UniversityChangsha 410081China Department of Biology 510 Mueller LaboratoryHuck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPA 16802USA

Angiosperms(flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the “abominable mystery,”hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological,and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences,dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families,and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella,Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families.Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore,we discuss the implications of nuclear phylogenomic analyses on ancestral

关键词： angiosperms evolution flowering plants nuclear gene phylogenomics phylogeny

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Comparative population genetic analyses suggest hybrid origin of Rhododendron pubicostatum,an endangered plant species with extremely small populations endemic to Yunnan,China

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Plant Diversity 2020年第4期42卷 312-318页

作者： Xuemei Zhang Hantao Qin Weijia Xie yongpeng ma Weibang Sun Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations Kunming Institute of BotanyChinese Academy of Sciences(CAS)Kunming650201YunnanChina Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of Sciences(CAS)Kunming650201China University of Chinese Academy of Sciences 100049BeijingChina Flower Research Institute Yunnan Academy of Agriculture SciencesKunming650201China

Gene flow between sympatric congeneric plants is thought to be very common and may pose serious threats to endangered species.In the present study,we evaluate the genetic diversity and divergence of three sympatric Rhododendron species in Jiaozi Mountain using newly developed microsatellites through the Illumina MiSeq sequencing approach.Genetic diversity of all three Rhododendron species studied was moderate in comparison to genetic parameters previously reported from species of this genus.Interestingly,genetic structure analysis of the three species identified a possible hybrid origin of the threatened Rh.pubicostatum.This sympatry should be considered a unimodal hybrid zone,since Rh.pubicostatum is predominant here.Unimodal hybrid zones are uncommon in Rhododendron,despite the fact that hybridization frequently occurs in the genus.Issues pertaining to the conservation of Rh.pubicostatum resulting from admixture of genetic material from its parental species are discussed.

关键词： Rhododendron pubicostatum Plant Species with Extremely Small Populations(PSESP) Microsatellite markers Illumina MiSeq sequencing Conservation management

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Dispersal and germination of winged seeds of Brandisia hancei,a shrub in karst regions of China

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Plant Diversity 2021年第3期43卷 234-238页

作者： Yongquan Ren Chengling Huang Jiaming Zhang yongpeng ma Xiaoling Tian College of Eco-Environmental Engineering Guizhou Minzu UniversityGuiyang 550025China Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations Kunming Institute of BotanyKunming 650201China The College of Humanities and Science of Guizhou Minzu University Guiyang 550025China

Brandisia hancei(Paulowniaceae)is a widely distributed shrub in karst regions in southwestern China.Its seeds have a membranous wing,and they mature just before the rainy season begins.To assess the effect of the wing on seed dispersal and germination of B.hancei,we measured the dispersal distance at varying wind speeds and release heights,falling duration from different release heights,floating duration on still water,rates of imbibition of water,and drying and soil adherence to seeds.Germination experiments were conducted on intact and de-winged seeds immediately after harvest.The wing increased the falling duration in still air and the floating ability on water.Dispersal distance of winged and de-winged seeds did not differ at a wind speed of 2.8 m s1,but at 3.6 and 4.0 m s1 dispersal distances were greater for de-winged than for winged seeds.Seed wing had little effect of absorption and retention of water,but significantly increased soil adherence to the seeds.mature seeds were non-dormant and germinated to over 90%with a mean germination time of about 10 days.By combining the environmental conditions in karst habitat with the seed traits of B.hancei,we conclude that dispersal and germination of winged seeds are adapted to the precipitation seasonality in heterogeneous habitats absence of soil.

关键词： Anemochory Hydrochory Membranous wing Seed dispersal Winged seed

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Uniform decomposition of velocity gradient tensor

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Journal of Hydrodynamics 2024年第1期36卷 24-34页

作者： Chenxi ma Chaoqun Liu Department of mathematics University of Texas at ArlingtonArlingtonTXUSA

In this paper,the principal decomposition of the velocity gradient tensor[∇v]is discussed in 3 cases based on the discriminant∆:∆0 with 3 distinct real eigen values,and∆=0 with 1 or 2 distinct real eigen values.The velocity gradient tensor can also be classified as rotation point,which can be decomposed into three parts,i.e.,rotation[R],shear[S]and stretching/compression[SC],and non-rotation point,we defined a new resistance term[L],and the tensor can be decomposed into three parts,i.e.,resistance[L],shear[S]and stretching/compression[SC].Example matric are also displayed to demonstrate the new decomposition.Connections of principal decomposition between 3 different cases,and between Resistance and Liutex will also be discussed.

关键词： Velocity gradient Liutex resistance fluid kinematics

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Copper slag assisted coke reduction of phosphogypsum for sulphur dioxide preparation

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Chinese Journal of Chemical Engineering 2024年第1期65卷 43-53页

作者： Dong ma Qinhui Wang State Key Laboratory of Clean Energy Utilization Institute for Thermal Power EngineeringZhejiang UniversityHangzhou 310027China

The reduction of phosphogypsum(PG)to lime slag and SO_(2)using coke can effectively alleviate the environmental problems caused by PG.However,the PG decomposition temperature remains high and the product yield remains poor.By adding additives,the decomposition temperature can be further reduced and PG decomposition rate and product yield can be improved.However,the use of current additives such as Fe_(2)O_(3)and SiO_(2)brings the problem of increasing economic cost.Therefore,it is proposed to use solid waste copper slag(CS)as a new additive to reduce PG to prepare SO2,which can reduce the cost and meet the environmental benefits at the same time.The effects of proportion,temperature and thermostatic time on PG decomposition are investigated by experimental and kinetic analysis combined with FactSage thermodynamic calculations to optimize the roasting conditions.Finally,the reaction mechanism is proposed.It is found that adding CS to the coke and PG system can increase the rate of PG decomposition and SO_(2)yield while lowering the PG decomposition temperature.For example,when the CS/PG mass ratio increases from 0 to 1,PG decomposition rate increases from 83.38%to 99.35%,SO_(2)yield increases from 78.62%to 96.81%,and PG decomposition temperature decreases from 992.4℃to 949.6℃.The optimal reaction parameters are CS/PG mass ratio of 1,Coke/PG mass ratio of 0.06 at 1100℃for 20 min with 99.35%PG decomposition rate and 96.81%SO_(2) yield.The process proceeds according to the following reactions:2CaSO_(4)+ 0.7C + 0.8Fe_(2)SiO_(4)→0.8Ca_(2)SiO_(4)+ 0.2Ca_(2)Fe_(2)O_(5)+ 0.4Fe_(3)O_(4)+2SO_(2)+ 0.7CO_(2)Finally,a process for decomposing PG with coke and CS is proposed.

关键词： Phosphogypsum Sulfur dioxide Copper slag Fluidized-bed Reduction Waste treatment

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