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Unveiling an ancient whole-genome duplication event in Stentor,the model unicellular eukaryotes

Science China Life Sciences 2025年

作者： Weibo Zheng Chao Li Zhaorui Zhou Xiao Chen Michael Lynch Ying Yan School of Life Sciences Ludong University Key Laboratory of evolution & marine biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity Ocean University of China Biodesign Center for Mechanisms of evolution Arizona State University marine College Shandong University

Whole-genome duplication(WGD) events are widespread across eukaryotes and have played a significant role in moulding the genetic architectures of diverse organisms. In the present study, the newly sequenced genome of a giant ciliated protist, Stentor roeselii, provides an opportunity for the analysis of the collinearity and retention of reciprocal best-hit genes between two Stentor species. As a main result, we have unveiled a previously undetected ancient WGD event shaping the genome of its congener, Stentor coeruleus, a model protist used in cytological and evolutionary studies. Genomes of two congeners, S. coeruleus and S. roeselii, are compared and analyzed, revealing that:(i)the former exhibits a much higher retention rate of colinear-gene pairs(28%) than does S. roeselii, and in S. coeruleus, 75% of genes that have a RBH hit in S. roeselii, have paralogs with high amino-acid identity, consistent with a WGD event in the lineage leading to S. coeruleus;(ii) the S. roeselii genome possesses extremely short intergenic regions, implying that the lengths of intergenic regions are under strong selection;(iii) the unique characteristics of introns may have been shaped in the common ancestor of heterotrichs;(iv) gene families that play a role in activities of multiple protein kinases and voltage-gated ion channels expanded rapidly in the ancestor of both taxa, possibly relating to the remarkable regenerative ability in Stentor. This study offers new insights into the evolutionary dynamics of ciliate genomes,with implications for understanding of the processes underlying the evolution of genomic complexity.

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Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

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Science China Life Sciences 2025年第1期 232-248页

作者： Yaohan Jiang Xiao Chen Chundi Wang Liping Lyu Saleh A.Al-Farraj Naomi A.Stover Feng Gao Key Laboratory of evolution & marine biodiversity (Ministry of Education) and institute of evolution & marine biodiversity Ocean University of China marine College Shandong University Zoology Department College of ScienceKing Saud University Department of Biology Bradley University Laboratory for marine Biology and Biotechnology Qingdao Marine Science and Technology Center

Sexual reproduction first appeared in unicellular protists and has continued to be an essential biological process in almost all *** protists, which contain both germline and somatic genomes within a single cell, have evolved a special form of sexual reproduction called conjugation that involves mitosis, meiosis, fertilization, nuclear differentiation, genome rearrangement, and the development of unique cellular structures. The molecular basis and mechanisms of conjugation vary dramatically among ciliates, and many details of the process and its regulation are still largely unknown. In order to better comprehend these processes and mechanisms from an evolutionary perspective, this study provides the first comprehensive overview of the transcriptome and proteome profiles during the entire life cycle of the newly-established marine model ciliate Euplotes vannus. Transcriptome analyses from 14 life cycle stages(three vegetative stages and 11 sexual stages) revealed over 26,000 genes that are specifically expressed at different stages, many of which are related to DNA replication,transcription, translation, mitosis, meiosis, nuclear differentiation, and/or genome rearrangement. Quantitative proteomic analyses identified 338 proteins with homologs associated with conjugation and/or somatic nuclear development in other ciliates, including dicer-like proteins, Hsp90 proteins, RNA polymerase Ⅱ and transcription elongation factors, ribosomal-associated proteins, and ubiquitin-related proteins. Four of these homologs belong to the PIWI family, each with different expression patterns identified and confirmed by RT-qPCR,which may function in small RNA-mediated genome rearrangement. Proteins involved in the nonhomologous end-joining pathway are induced early during meiosis and accumulate in the developing new somatic nucleus, where more than 80% of the germline sequences are eliminated from the somatic genome. A number of new candidate genes and proteins likely t

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Effect of temperature and photoperiod on maturation of Cephalothrix hongkongiensis(Nemertea: Palaeonemertea)

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Chinese Journal of Oceanology and Limnology 2014年第4期32卷 764-772页

作者：李应东宋肖跃张珊珊朱林孙世春 institute of evolution and marine biodiversity Ocean University of China

The limited knowledge about the relationships between environmental factors and the maturation and reproductive seasonality of nemerteans is mostly obtained from field studies, and in many cases is conjectural. Few species have been studied under well-controlled laboratory conditions. In this work, the effects of temperature and photoperiod on gonad development and spawning of Cephalothrix hongkongiensis were observed by rearing worms under different temperatures and photoperiods. Worms reared at 4~C and 6~C showed no growth or gonadal development, and all died within 109 days. At 8~C and 12~C, gonads could be seen from 90 days to the termination of the 360-day experiment, but no spawning was observed. Worms maintained at 16, 24, and 28~C showed both gonadal development and spawning, and matured faster at higher temperatures. Under a fixed temperature （16℃）, photoperiod did not have any significant impact on maturation and spawning. It is likely that temperature plays a major role in regulating the maturation and reproductive cycle of C. hongkongiensis.

关键词： temperature photoperiod gonad development reproduction Cephalothrix hongkongiensis Nemertea

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Colonization dynamics of periphytic diatoms in coastal waters of the Yellow Sea, northern China

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Acta Oceanologica Sinica 2014年第9期33卷 160-165页

作者： Liu Yuanyuan Zhang Wei Xu henglong institute of evolution and marine biodiversity Ocean university of China

The colonization features of periphytic diatoms were studied in coastal waters of the Yellow Sea, northern China from May to June 2010, using glass slides as an artificial substratum. Samples were collected at a time interval of 1, 3, 7, 10, 14, 21 and 28 d from two depths of 1 and 3 m. The dynamics of diatom colonization process had a similar pattern in community structure and fitted the logistic model in growth curve at both depths. The maximum abundance and the time for reaching 50% maximum abundance （10 d） showed no significant differences （P〉0.05） between two depths 1 and 3 m. Although the diatom communities repre- sented similar taxonomic composition, they differed in the temporal pattern of structural parameters and in succession dynamics of dominant species between the two layers. The species richness showed significantly higher values during the colonization period more than 14 d, while the species diversity and evenness rep- resented a higher variability with significantly different values （P〈0.05） at a depth of 1 m than at a deeper layer. The results suggest that the diatom colonization follows the logistic model growth curve and differs in colonization features between different depths in the coastal waters, and that the sampling strategy at i m is more effective to detect the ecological features for bioassessment in marine ecosystems.

关键词： bioassessment biofilm coastal waters colonization dynamics periphytic diatom

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Functional characterization of an orexin neuropeptide in amphioxus reveals an ancient origin of orexin/orexin receptor system in chordate

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Science China(Life Sciences) 2019年第12期62卷 1655-1669页

作者： Peng Wang Meng Wang Liping Zhang Shenjie Zhong Wanyue Jiang Ziyue Wang Chen Sun Shicui Zhang Zhenhui Liu institute of evolution & marine biodiversity College of Marine Life Science Ocean University of China

Amphioxus belongs to the subphylum cephalochordata, an extant representative of the most basal chordates, whose regulation of endocrine system remains ambiguous. Here we clearly demonstrated the existence of a functional orexin neuropeptide in amphioxus, which is able to interact with orexin receptor, activate both PKC and PKA pathways, decrease leptin expression, and stimulate lipogenesis. We also showed the transcription level of amphioxus orexin was affected by fasting or temperature,indicating a role of this gene in the regulation of energy balance. In addition, the expression of the amphioxus orexin was detected at cerebral vesicle, which has been proposed to be a homolog of the vertebrate brain. These data collectively suggest that a functional orexin neuropeptide has already emerged in amphioxus, which provide insights into the evolutionary origin of orexin in chordate and the functional homology between the cerebral vesicle and vertebrate brain.

关键词： amphioxus orexin neuropeptide evolution

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Near-perfect replication on amorphous alloys through active force modulation based on machine learning/neural network parameter prediction

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 181-191页

作者： Senkuan Meng Zheng Wang Ruisong Zhu Ruijie Liu Jiang Ma Lina Hu Weihua Wang Key Laboratory for Liquid-Solid Structural evolution and Processing of Materials (Ministry of Education) School of Materials Science and Engineering Shandong University College of Mechatronics and Control Engineering Shenzhen University Songshan Lake Materials Laboratory institute of Physics Chinese Academy of Sciences

As a microforming technique, micro/nano-structural replication possesses advantages of high precision and efficiency. With the remarkable superplasticity in the supercooled liquid region, amorphous alloys or metallic glasses(MGs) are regarded as ideal materials for miniature fabrication. However, due to the intrinsic metastable nature of supercooled liquids, the design of imprinting processes for MGs poses a challenge. In the past, process parameters have largely relied on trial-and-error *** this work, a low-frequency active force modulation system is employed to apply a stable, precise, and real-time feedback stress field for imprinting of MG samples. Low-frequency vibrations can facilitate the filling of microstructures on the template surface by reducing the effective viscosity of the supercooled liquid. With the dataset composed of orthogonal experiments, a machine learning strategy based on back-propagation(BP) neural networks was utilized to construct a 3D parameter space for temperature, stress, and time, and to predict the corresponding filling ratio. Furthermore, the optimal combination of imprinting process parameters was identified, and its filling ratio was experimentally validated to reach as high as 0.94. The near-perfect replication of microstructures confirms the superiority of the active force modulation system and the data-driven strategy of machine learning-assisted parameter design. At the same time, this one-step microforming process provides a new approach to addressing the accuracy-cost trade-off dilemma in precision manufacturing.

关键词： metallic glass amorphous alloy microforming imprinting machine learning

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Special topic on EvoDevo:emerging models and perspectives

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marine Life Science & Technology 2023年第4期5卷 431-434页

作者： Hongan Long Bo Dong MoE Key Laboratory of evolution and marine biodiversity Institute of Evolution and Marine BiodiversityOcean University of ChinaQingdao 266003China

Communication between developmental and evolutionary scientists has historically been a challenge,with their respective foci being molecular mechanisms during the development of an individual and long-term shifts in allele frequency in ***,uniting these perspectives provides a better understanding of biological *** Haeckel’s biogenetic argument that,“ontogeny recapitulates phylogeny,”offers us with an early glimpse at how useful such a synthesis of evolution and development(EvoDevo)can be.

关键词： functions. argument synthesis

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Robust interface and excellent as-built mechanical properties of Ti–6Al–4V fabricated through laser-aided additive manufacturing with powder and wire

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International Journal of Minerals,Metallurgy and Materials 2025年第1期32卷 154-168页

作者： Fei Weng Guijun Bi Youxiang Chew Shang Sui Chaolin Tan Zhenglin Du Jinlong Su Fern Lan Ng Key Laboratory for Liquid-Solid Structural evolution and Processing of Materials Ministry of EducationShandong Engineering&Technology Research Center for Superhard MaterialSchool of Materials Science and EngineeringShandong UniversityJinan 250061China institute of Intelligent Manufacturing Guangdong Academy of SciencesGuangzhou 510095China Singapore institute of Manufacturing Technology 5 Cleantech Loop636732Singapore

The feasibility of manufacturing Ti-6Al-4V samples through a combination of laser-aided additive manufacturing with powder(LAAM_(p))and wire(LAAM_(w))was explored.A process study was first conducted to successfully circumvent defects in Ti-6Al-4V deposits for LAAM_(p) and LAAM_(w),*** the optimized process parameters,robust interfaces were achieved between powder/wire deposits and the forged substrate,as well as between powder and wire *** characterization results revealed the epitaxial prior β grains in the deposited Ti-6Al-4V,wherein the powder deposit was dominated by a finerα′microstructure and the wire deposit was characterized by lamellar α *** mechanisms of microstructure formation and correlation with mechanical behavior were analyzed and *** mechanical properties of the interfacial samples can meet the requirements of the relevant Aerospace Material Specifications(AMS 6932)even without post heat *** fracture occurred within the interfacial area,further suggesting the robust *** findings of this study highlighted the feasibility of combining LAAM_(p) and LAAM_(w) in the direct manufacturing of Ti-6Al-4V parts in accordance with the required dimensional resolution and deposition rate,together with sound strength and ductility balance in the as-built condition.

关键词： laser-aided additive manufacturing powder deposition wire deposition interfacial characteristic mechanical behavior

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Morphology and Molecular Phylogeny of Two Little-Known Species of Loxodes, L. kahli Dragesco & Njiné, 1971 and L. rostrum Müller, 1786(Protist, Ciliophora, Karyorelictea)

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Journal of Ocean University of China 2019年第3期18卷 643-653页

作者： WANG Lun QU Zhishuai LI Song HU Xiaozhong institute of evolution and marine biodiversity Key Laboratory of Mariculture Ministry of Education Ocean University of China

The morphology and phylogeny of two little-known species, Loxodes kahli Dragesco & Njiné, 1971 and L. rostrum Müller, 1786, isolated from freshwater muddy sediments in China, were investigated based on live features, infraciliature, and small subunit ribosomal DNA(SSU rD NA) sequence data. Loxodes kahli is distinguished from its congeners mainly by the number and arrangement of macronuclei(6-17 in one row) and the number of right somatic ciliary rows(11-26). The Chinese populations of L. kahli also exhibit differences with other populations in terms of the body size and the number of right ciliary rows. The characteristics of L. rostrum are consistent with those of previous studies except for the number of right ciliary rows(9-10). The studied species were redefined based on the new information and previous descriptions. This study also gave a brief morphological summary of the species in the genus Loxodes by an identification key. SSU rDNA sequence-based phylogenetic analyses revealed that both species are grouped with their congeners, supporting the monophyly of the genus Loxodes.

关键词： anaerobe benthic ciliate ciliature Loxodida SSU rDNA

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Invasion by exogenous RNA:cellular defense strategies and implications for RNA inference

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marine Life Science & Technology 2023年第4期5卷 573-584页

作者： Danxu Tang Yan Liu Chundi Wang Lifang Li Saleh AAl‑Farraj Xiao Chen Ying Yan Laboratory of marine Protozoan biodiversity and evolution Marine CollegeShandong UniversityWeihai 264209China Key Laboratory of evolution and marine biodiversity(Ministry of Education)and institute of evolution and marine biodiversity Ocean University of ChinaQingdao 266003China Zoology Department College of ScienceKing Saud University11451 RiyadhSaudi Arabia Suzhou Research institute Shandong UniversitySuzhou 215123China

Exogenous RNA poses a continuous threat to genome stability and integrity across various *** evidence reveals complex mechanisms underlying the cellular response to exogenous RNA,including endo-lysosomal degradation,RNA-dependent repression and innate immune *** a variety of mechanisms,the natural anti-sense RNAdependent defensive strategy has been utilized both as a powerful gene manipulation tool and gene therapy strategy named RNA-interference(RNAi).To optimize the efficiency of RNAi silencing,a comprehensive understanding of the whole life cycle of exogenous RNA,from cellular entry to its decay,is *** this paper,we review recent progress in comprehending the recognition and elimination of foreign RNA by cells,focusing on cellular entrance,intracellular transportation,and immune-inflammatory *** leveraging these insights,we highlight the potential implications of these insights for advancing RNA interference efficiency,underscore the need for future studies to elucidate the pathways and fates of various exogenous RNA forms,and provide foundational information for more efficient RNA delivery methods in both genetic manipulation and therapy in different organisms.

关键词： Endocytosis Exogenous RNA Innate immune response RNA inference

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