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Two complete mitogenomes of Ocypodoidea(Decapoda: Brachyura), Cleistostoma dilatatum(Camptandriidae) and Euplax sp.(Macrophthalmidae) and its phylogenetic implications

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Acta Oceanologica Sinica 2023年第4期42卷 81-92页

作者： Ying Zhang liming Wei Bingjian liu liqin liu zhenming lü li Gong National Engineering laboratory of Marine Germplasm Resources Exploration and Utilization National Engineering Research Center for Facilitated Marine AquacultureZhoushan 316022China Marine Science and Technology College Zhejiang Ocean UniversityZhoushan 316022China

Complete mitochondrial genomes(mitogenomes) can provide useful information for phylogenetic relationships,gene rearrangement, and molecular evolution. In the present study, two newly sequenced mitogenomes of Ocypodoidea(Cleistostoma dilatatum and Euplax sp.) were reported for the first time, which are 15 444 bp and16 129 bp in length, respectively. Cleistostoma dilatatum is the first species in the family Camptandriidae whose complete mitogenome was sequenced. Each mitogenome contains an entire set of 37 genes and a putative control region, but their gene arrangements are largely different. Tandem duplication and random loss model is proposed to account for their gene arrangements. Comparative genomic analyses of 19 mitogenomes clustering in one branch reveal that 18 of them shared the same gene rearrangement, while that of C. dilatatum mitogenome was consistent with the ancestral gene arrangement of Brachyura. The dN/dS ratio analysis shows that all PCGs are evolving under purifying selection. Phylogenetic analyses show that all Macrophalmidae species cluster together as a group, and then form a sister clade with Camptandriidae. Moreover, the polyphyly of three superfamilies(Ocypodoidea, Eriphioidea, and Grapsoidea) is reconfirmed. These findings help to confirm the phylogenetic position of Camptandriidae, as well as provide new insights into the phylogeny of Brachyura.

关键词： Camptandriidae Macrophthalmidae mitogenome gene rearrangement phylogenetic analysis

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Comparative mitochondrial genome analysis of Sesarmidae and its phylogenetic implications

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Acta Oceanologica Sinica 2022年第8期41卷 62-73页

作者： Ying Zhang lei Meng liming Wei Bingjian liu liqin liu zhenming lü Yang Gao li Gong National Engineering laboratory of Marine Germplasm Resources Exploration and Utilization Zhejiang Ocean UniversityZhoushan 316022China Marine Science and Technology College Zhejiang Ocean UniversityZhoushan 316022China School of Fishery Zhejiang Ocean UniversityZhoushan 316022China

Here,we sequenced the complete mitogenome of Parasesarma eumolpe(Brachyura:Grapsoidea:Sesarmidae)for the first *** characteristics of this newly sequenced mitogenome were described and compared with other Sesarmidae *** 15646-bp mitogenome contains 13 protein-coding genes(PCGs),two ribosomal RNA genes(r RNAs),22 transfer RNA genes(t RNAs),and an A-T rich *** of the PCGs are initiated by the start codon ATN and terminated by the standard TAN codon or an incomplete *** pairwise Ka/Ks ratio analysis shows that all 13 PCGs are under purifying selection,whereas the ATP8 gene is an outlier,with pairwise comparison values ranging from neutral selection(0.000)to positive selection(1.039).The gene arrangement of *** compared with ancestral Decapoda shows the translocation of two t RNAs(t RNA-His and t RNA-Gln),which is identical to other Sesarmidae *** analyses show that all Sesarmidae species are placed into one group,and the polyphyly of Eriphioidea,Ocypodoidea,and Grapsoidea is well *** relationship between gaps in the QIM region and the phylogeny of Sesarmidae is *** is obvious that both the G5(the gap between Q and I)and G6(the gap between I and M)decrease progressively with the evolution *** results will help to better understand the genomic evolution within Sesarmidae and provide insights into the phylogeny of Brachyura.

关键词： sesarmid crab mitogenome gene rearrangement tandem duplication/random loss phylogenetic analysis

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Complete Mitochondrial Genome of Myra affinis(Decapoda:Brachyura:leucosiidae)and Its Phylogenetic Implications for Brachyura

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Journal of Ocean University of China 2022年第4期21卷 987-997页

作者： ZHANG Ying MENG lei MIAO Zengliang WEI liming lIU Bingjian lIU liqin GONG li lÜzhenming Engineering laboratory of Marine Germplasm Resources Exploration and Utilization National Engineering Research Center forFacilitated Marine AquacultureMarine Science and Technology CollegeZhejiang Ocean UniversityZhoushan 316022China School of Fishery Zhejiang Ocean UniversityZhoushan 316022China

Knowledge of complete mitochondrial genomes(mitogenomes)can help understand the molecular evolution and phylogenetic relationships of various *** date,the phylogenetic status of leucosiidae within Brachyura remains unresolved because of the limited number of mitogenomes *** the present study,the complete mitogenome of Myra affinis was sequenced using next-generation sequencing to supplement the limited mitogenome information of *** 15349 bp-long mitogenome includes 13 protein-coding genes(PCGs),22 transfer RNAs(tRNAs),2 ribosomal RNAs(rRNAs),and a putative control *** overall base composition is 34.5%A,36.1%T,11.5%G,and 17.9%C,with a high AT bias(70.6%).All 13 PCGs start with the standard ATN codon and stop with the TAN codon or incomplete *** for tRNA-Ser,all other tRNAs have a typical cloverleaf-like secondary *** analyses based on the maximum likelihood and Bayesian inference methods are employed to generate identical phylogenetic topologies,thereby supporting the sister relationship between leucosiidae and Matutidae for the first *** monophyly of Eubrachyura is well established,and its sister relationship with Raninoida is strongly *** results of this work will not only help achieve a better understanding of the characteristics of the *** mitogenome and the phylogenetic position of leucosiidae,but also provide relevant information for further studies on the phylogeny of Brachyura.

关键词： leucosiid crab mitogenome phylogenetic analysis Brachyura

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Complete Mitochondrial Genome Analysis of Daphniopsis tibetana(Branchiopoda:Diplostraca):New Insights into the Taxonomy of the Genus and Its Phylogenetic Implications for Branchiopoda

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Journal of Ocean University of China 2022年第6期21卷 1622-1632页

作者： lIU Bingjian PENG Ying lIU Yifan lI Jiasheng ZHANG Kun CHEN Jian GONG li lIU liqin lÜzhenming ZHANG Chi National Engineering laboratory of Marine Germplasm Resources Exploration and Utilization Zhejiang Ocean UniversityZhoushan 316022China Institute of Fisheries Science Tibet Academy of Agricultural and Animal Husbandry SciencesLhasa 850002China Key laboratory of Tropical Marine Bio-Resources and Ecology Chinese Academy of SciencesGuangzhou 510301China

Daphniopsis tibetana is widely distributed in Xinjiang,Qinghai,Tibet of China,as well as in Russia and India,which is the dominant zooplankton in many high-altitude(4000 m)salt *** can adapt to saline waters,whereas the other species of the superorder Cladocera can only inhabit in ***,the phylogenetic status of *** in Branchiopoda remains unclear primarily because of limited *** this study,complete mitochondrial genome sequences of *** were sequenced and annotated for the first time to obtain a comprehensive understanding of its phylogenetic *** complete mitogenome of *** is 16196 bp in *** contains 37 genes,including two ribosomal RNAs(12S and 16S rRNAs)genes,22 transfer RNA(tRNA)genes,13 protein-coding genes,and one non-coding *** overall base composition is 29.6%A,33.2%T,19.0%G,and 18.2%C with a high AT bias(62.8%).Except for trnS1(GCT),most tRNAs have a typical cloverleaf secondary *** analysis based on maximum likelihood and Bayesian inference generates identical phylogenetic topology and shows the phylogenetic status of ***,which reconfirm the distinction between the genera Daphniopsis and ***,the class Branchiopoda is clustered into three clades(Anostraca,Notostraca,and Diplostraca)with high support *** results provide not only a comprehensive understanding of the characteristics of *** mitogenome and its phylogenetic position in Diplostraca,but also information for future research on the phylogeny of Branchiopoda.

关键词： Daphniopsis tibetana mitogenome phylogenetic analysis Branchiopoda Diplostraca

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Comparative mitochondrial genome analysis of Varunidae and its phylogenetic implications

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Acta Oceanologica Sinica 2022年第6期41卷 119-131页

作者： Ying Zhang li Gong Xinting lu Zengliang Miao lihua Jiang Bingjian liu liqin liu Pengfei li Xu Zhang zhenming lü National Engineering laboratory of Marine Germplasm Resources Exploration and Utilization Zhejiang Ocean UniversityZhoushan 316022China Marine Science and Technology College Zhejiang Ocean UniversityZhoushan 316022China Guangxi Key laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry Guangxi Beibu Gulf Marine Research CenterGuangxi Academy of SciencesNanning 530007China Key laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of SciencesBeijing 100101China

Complete mitochondrial genomes(mitogenomes)can indicate phylogenetic relationships,as well as useful information for gene rearrangement mechanisms and molecular ***,the phylogenetic location of the genus Varuna(Brachyura:Varunidae)has not been well resolved mainly because of limited representatives(only two extant species).Here,we determined a new mitogenome of this genus(Varuna litterata)and added the published mitogenomes to reconstruct the phylogeny of *** 16368-bp mitogenome contains the entire set of 37 genes and a putative control *** characteristics of this newly sequenced mitogenome were described and compared with the other 15 Varunidae *** 16 analyzed mitogenomes have identical gene order and similar molecular *** sliding window and genetic distance analyses demonstrate highly variable nucleotide diversity,with comparatively low variability of COI and COII,and high variability of *** nonsynonymous/synonymous substitution rates(dN/dS ratio)analysis shows that all 13 PCGs are under purifying selection and ATP8 gene evolves under the least selective *** tRNA genes,two rRNAs,one PCG,and the putative control region are found to be rearranged with respect to the pancrustacean ground pattern gene *** duplication/random loss model is adopted to explain the large-scale gene rearrangement events occurring in Varunidae *** analyses show that all Varunidae species are placed into one group,and form a sister clade with ***,the phylogenetic relationships within Varunidae are not completely consistent based on the two different datasets used in this *** findings will contribute to a better understanding of gene rearrangement and molecular evolution in Varunidae mitogenomes,as well as provide insights into the phylogenetic studies of Brachyura.

关键词： varunid crab Varuna litterata mitogenome gene rearrangement tandem duplication/random loss phylogeny

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Comparative mitochondrial genome analysis of Cynoglossidae(Teleost:Pleuronectiformes)and phylogenetic implications

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Acta Oceanologica Sinica 2023年第11期42卷 69-80页

作者： Bilin Hu Tingqi Jiang liming Wei Nannan Zhang Kaixin Wang liqin liu Bingjian liu Jing liu zhenming lü li Gong National Engineering laboratory of Marine Germplasm Resources Exploration and Utilization Zhejiang Ocean UniversityZhoushan 316022China Marine Science and Technology College Zhejiang Ocean UniversityZhoushan 316022China

Generally,a teleostean group(e.g.,family or genus)owns one type or a set of similar mitochondrial gene *** is interesting,however,that four different types of gene arrangement have been found in the mitochondrial genome(mitogenome)of Cynoglossidae *** far,the possible mechanisms of mitogenomic gene rearrangement and its potential implications have aroused widespread attention and caused lots of ***,a total of 21 Cynoglossidae mitogenomes and a newly sequenced mitogenome of Cynoglossus puncticpes(Pleuronectiformes:Cynoglossidae)were *** length ranges from 16417 bp to 18369 bp,which is mainly caused by the length heteroplasmy of control region(CR).Further analysis reveals that the difference of tandem repeats acts as a determining factor resulting in the length *** most gene rearrangements of Cynoglossinae mitogenomes,tRNA-Gln gene encoded by the l-strand has translocated to the H-strand(Q inversion),accompanied by the translocation of CR in *** *** typical IQM order(tRNA-Ile-Gln-Met)changed to QIM *** duplication/random loss and mitochondrial recombination were accepted as the most possible models to account for the rearrangements in *** *** trees showed a strong correlation between the gap spacer in the rearranged QIM area and phylogeny,which provides a fresh idea for phylogenetic studies in future.

关键词： mitogenome gene rearrangement tandem duplication/random loss mitochondrial inversion control region phylogenetic study

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A modified smoothed particle hydrodynamics method considering residual stress for simulating failure and its application in layered rock mass

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Journal of Mountain Science 2024年第6期21卷 2091-2112页

作者： XIA Chengzhi SHI zhenming KOU Huanjia Department of Geotechnical Engineering College of Civil EngineeringTongji UniversityShanghai 200092China Key laboratory of Geotechnical and Underground Engineering of Ministry of Education Tongji UniversityShanghai 200092China

Residual strength is an indispensable factor in evaluating rock fracture,yet the current Smoothed Particle Hydrodynamics(SPH)framework rarely considers its influence when simulating *** improved cracking strategy considering residual stress in the base bond SPH method was proposed to simulate failures in layered rocks and slopes and verified by experimental results and other simulation methods(i.e.,the discrete element method).Modified Mohr–Coulomb failure criterion was applied to distinguish the mixed failure of tensile and *** fracture markψwas introduced to improve the kernel function after tensile damage,and the calculation of residual stress after the damage was derived after shear *** simulations were carried out to evaluate its performance under different stress and scale conditions and to verify its effectiveness in realistically reproducing crack initiation and propagation and coalescence,even fracture and *** results indicate that the improved cracking strategy precisely captures the fracture and failure pattern in layered rocks and rock *** residual stress of brittle tock is correctly captured by the improved SPH *** improved SPH method that considers residual strength shows an approximately 13%improvement in accuracy for the safety factor of anti-dip layered slopes compared to the method that does not consider residual strength,as validated against analytical *** infer that the improved SPH method is effective and shows promise for applications to continuous and discontinuous rock masses.

关键词： Smoothed particle hydrodynamics Cracking strategy Residual stress layered rock Crack propagation

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Multi-Component Resource Recycling from Waste light-Emitting Diode Under Hydrothermal Condition:Plastic Package Degradation,Speciation of Nano-TiO_(2),and Environmental Impact Assessment

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Engineering 2024年第8期39卷 253-261页

作者： Yongliang Zhang lu Zhan zhenming Xu School of Environmental Science and Engineering Shanghai Jiao Tong UniversityShanghai 200240China

light emitting diodes(lEDs)have accounted for most of the lighting market as the technology matures and costs continue to *** a new type of e-waste,lED is a double-edged sword,as it contains not only precious and rare metals but also organic packaging *** previous studies,lED recycling focused on recovering precious and strategic metals while ignoring harmful substances such as organic packaging *** crushing and other traditional methods,hydrothermal treatment can provide an environment-friendly process for decomposing packaging *** work developed a closed reaction vessel,where the degradation rate of plastic polyphthalamide(PPA)was close to 100%,with nano-TiO_(2)encapsulated in plastic PPA being efficiently recovered,while metals contained in lED were also recycled ***,the role of water in plastic PPA degradation that has been overlooked in current studies was explored and speculated in detail in this *** impact assessment revealed that the proposed recycling route for waste lED could significantly reduce the overall environmental impact compared to the currently published *** the developed method could reduce more than half the impact of global ***,this research provides a theoretical basis and a promising method for recycling other plastic-packaged e-waste devices,such as integrated circuits.

关键词： Waste lED Hydrothermal treatment Recycling Plastic PPA degradation Packaging materials

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low-resolution Kramers-Kronig detection system with error-feedback noise shaping

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Science China(Information Sciences) 2024年第5期67卷 259-269页

作者： Xiangyong DONG zhenming YU Hongyu HUANG Kaixuan SUN Kun XU State Key laboratory of Information Photonics and Optical Communications Beijing University of Posts and Telecommunications

In this paper, we investigated the effects of error-feedback noise shaping(EFNS) on a lowresolution Kramers-Kronig(KK) detection system for the first time. Both 16-ary quadrature amplitude modulation(16-QAM) and 64-ary quadrature amplitude modulation(64-QAM) were considered in the experiment. The carrier tone was added on the transmitter side using the virtual carrier-assisted single sideband(VCA-SSB) method to meet the minimum phase(MP) condition. Under the MP condition, KK detection only needs the intensity of the optical signal to be detected by one photodiode(PD) to retrieve the phase information. However, the virtual carrier tone increases the carrier-to-signal power ratio(CSPR), which results in a high peak-to-average power ratio(PAPR) at the transmitter, causing an increase in quantization noise. To mitigate quantization noise in the low-resolution KK detection system, EFNS was applied. The application of EFNS increased the optimal CSPR of the KK detection system and improved receiver sensitivity. Using a 4-bit DAC and the EFNS, 80 km transmission was achieved in the 60-Gbit/s 64-QAM KK detection system.

关键词： optical fiber communications Kramers-Kronig receiver error-feedback noise shaping quantization noise carrier-to-signal power ratio

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The molecular genetics of PI3K/PTEN/AKT/mTOR pathway in the malformations of cortical development

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Genes & Diseases 2024年第5期11卷 252-271页

作者： Qing Ma Guang Chen Ying li zhenming Guo Xue Zhang NHC and CAMS Key laboratory of Molecular Probe and Targeted Theranostics Harbin Medical UniversityHarbinHeilongjiang 150000China Department of Urology The Fourth Hospital of Harbin Medical UniversityHarbinHeilongjiang 150000China Department of Child and Adolescent Health School of Public HealthHarbin Medical UniversityHarbinHeilongjiang 150000China Institute for Regenerative Medicine Shanghai East HospitalFrontier Science Center for Stem Cell ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghai 200120China

Malformations of cortical development(MCD)are a group of developmental disorders characterized by abnormal cortical structures caused by genetic or harmful environmental *** kinds of MCD are caused by genetic *** is the common cause of intellectual disability and intractable *** rapid advances in imaging and sequencing technologies,the diagnostic rate of MCD has been increasing,and many potential genes causing MCD have been successively ***,the high genetic heterogeneity of MCD makes it challenging to understand the molecular pathogenesis of MCD and to identify effective targeted ***,in this review,we outline important events of cortical *** we illustrate the progress of molecular genetic studies about MCD focusing on the PI3K/PTEN/AKT/mTOR ***,we briefly discuss the diagnostic methods,disease models,and therapeutic strategies for *** information will facilitate further research on *** the role of the PI3K/PTEN/AKT/mTOR pathway in MCD could lead to a novel strategy for treating MCD-related diseases.

关键词： Epilepsy Gene mutation Genetics Malformations of cortical development PI3K/PTEN/AKT/mTOR pathway

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