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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68卷 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

关键词： sexual reproduction transcriptomic proteomic genome rearrangement PIWI NHEJ

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New insight into the origin and evolution of the flora and fauna of Hainan Island, China

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Science China Earth Sciences 2025年第1期68卷 52-61页

作者： Hua ZHU center for Integrative Conservation Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Yunnan International Joint Laboratory of Southeast Asia Biodiversity Conservation Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants

The origin of the biota of Hainan Island, China, remains a fundamental scientific problem. Comparative studies on the biota, geological tectonics, and paleomagnetism proposed that during the Eocene, Hainan Island connected Vietnam and Guangxi, and then moved to the southeast to reach its present location. This review mainly discusses its biota origin from molecular phylogeny and palaeobotanical research. The formation and evolution of the biological groups of Hainan Island were identified via research on their genomes, phylogeny, and molecular biogeography. This research showed that the genera and species that appeared and diverged early in their evolution(i.e., before the Miocene) can be explained by the land connection between Hainan Island, Vietnam, and Guangxi during the Eocene-Oligocene. According to Southeast Asian tectonic theory, in the Middle Miocene(at about 15 million years ago), Hainan Island had moved to its present position. The population and genetic divergence of species with late divergence times(after 15 Ma) can be reasonably explained by the close proximity(or land connection) between Hainan Island and the Leizhou Peninsula, enabling genetic communication between Hainan Island and the Chinese mainland, but have exceptional cases. Conclusions have been obtained through palaeobotanical studies, showing that in the Eocene-Oligocene period, southwest China and Hainan Island had subtropical vegetation and flora. However, the fossil group in southeast China(in Maoming, near present-day Hainan Island) in the Late Eocene indicated a tropical rainforest vegetation and flora. This suggests that in the Paleogene, Hainan Island may have been located near or on the southwest border of Guangxi and northern Vietnam, rather than in its present location. The floristic division of the flora of Hainan Island basically presents a northeast-southwest inclined distribution pattern. This pattern can be explained by the counterclockwise rotation of Hainan Island during i

关键词： Molecular phylogeny Biogeography Paleobotany Origin of flora and fauna Hainan Island of China

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

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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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Speciesα-diversity promotes butβ-diversity restricts aboveground biomass in tropical forests,depending on stand structure and environmental factors

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Journal of Forestry Research 2023年第4期34卷 889-901页

作者： Umar Aftab Abbasi Eskil Mattsson Sarath Premalal Nissanka Arshad Ali Forest Ecology Research Group College of Life SciencesHebei UniversityBaoding 071002People’s Republic of China IVL Swedish Environmental Research Institute Aschebergsgatan 4441133 GothenburgSweden gothenburg global biodiversity Centre(GGBC) GothenburgSweden Department of Crop Science Faculty of AgricultureUniversity of PeradeniyaPeradeniyaSri Lanka

Forest plays a vital role in the global biogeochemical cycles through a high rate of carbon sequestration and harboring ***,local species diversity is declining while also becoming increasingly homogenized across *** eff ects of local biotic processes(e.g.,speciesα-diversity and stand structural heterogeneity)and environmental factors on aboveground biomass(AGB)have been widely tested,there is a huge knowledge gap for the eff ect of regional biotic processes(i.e.,taxonomic and functionalβ-diversity)in ***,we hypothesized that regional and local environmental factors along with biotic processes jointly regulate AGB through species shifts in tropical *** piecewise structural equation modeling(pSEM),we linked climatic water availability,soil fertility,stand structural heterogeneity(either tree DBH inequality,height inequality,or stand density),speciesα-diversity,taxonomic or functionalβ-diversity(and its two components;β-turnover andβ-richness),and AGB across 189 inventory plots in tropical forests of Sri *** fertility and climatic water availability shaped local and regional biotic *** structural heterogeneity promoted speciesα-diversity but declinedβ-diversity(but increasedβ-taxonomic turnover).Speciesα-diversity and stand structural heterogeneity promoted AGB whereas taxonomic and functionalβ-diversity declined(butβ-taxonomic turnover increased)*** relationships of AGB with speciesα-diversity andβ-diversity varied from signifi cant to nonsignifi cant positive depending on the specifi c combinations of stand structural heterogeneity metrics *** study shows that local biotic processes could increase AGB due to the local and regional niche complementarity eff ect whereas the regional biotic processes could restrict AGB due to the regional selection or functional redundancy eff ect under favorable environmental *** argue that biotic homogenization,as well as drought conditions,ma

关键词： biodiversity Biotic homogenization Climate Forest functioning Soil Tree size

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Parallel patterns and trends in functional structures in extinct island mammals

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Integrative Zoology 2014年第2期9卷 167-182页

作者： Alexandra A.E.VAN DER GEER Naturalis Netherlands biodiversity center LeidenNetherlands

Endemic mammalian species on islands are generally known to have followed a different evolutionary pathway than their mainland relatives. General patterns, such as body size trends, have been described regularly. How-ever, most island mammal species are unique and each of them is adapted to a specific local niche as part of an equally specific ecological assemblage. Therefore, comparing island species across taxa, islands and time is in-herently dangerous without understanding the adaptational value of the studied feature in the compared taxa and without taking the ecological setting of the taxa into account. In this contribution, general and recurring patterns are described per taxon. Some features, like body mass change and sturdy limbs, are relatively general, where-as most features, like bone fusions and change of orbital axis, occur only in a very few taxa. Some features are even contradictory, such as brain size and degree of hypsodonty, with each taxon having its own particular de-sign. In conclusion, general patterns are more often than not just trends and need to be applied with caution.

关键词： body proportions fossil record island rule paleo-insular mammals Pleistocene

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Recent Advances in Artificial Sensory Neurons:Biological Fundamentals,Devices,Applications,and Challenges

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Nano-Micro Letters 2025年第3期17卷 168-216页

作者： Shuai Zhong Lirou Su Mingkun Xu Desmond Loke Bin Yu Yishu Zhang Rong Zhao Guangdong Institute of Intelligence Science and Technology HengqinZhuhai 519031People’s Republic of China College of Integrated Circuits Zhejiang UniversityHangzhou 3112000People’s Republic of China ZJU-Hangzhou global Scientific and Technological Innovation center Hangzhou 310027People’s Republic of China Department of Science Mathematics and TechnologySingapore University of Technology and DesignSingapore 487372Singapore Department of Precision Instruments Tsinghua UniversityBeijing 100084People’s Republic of China center for Brain‑Inspired Computing Research Tsinghua UniversityBeijing 100084People’s Republic of China IDG/McGovern Institute for Brain Research Tsinghua UniversityBeijing 100084People’s Republic of China

Spike-based neural networks,which use spikes or action potentialsto represent information,have gained a lot of attention because of their high energyefficiency and low power *** fully leverage its advantages,convertingthe external analog signals to spikes is an essential *** including analog-to-digital converters or ring oscillators,and sensorssuffer from high power and area *** efforts are devoted to constructingartificial sensory neurons based on emerging devices inspired by the biologicalsensory *** can simultaneously perform sensing and spike conversion,overcoming the deficiencies of traditional sensory *** review summarizesand benchmarks the recent progress of artificial sensory *** starts with thepresentation of various mechanisms of biological signal transduction,followed bythe systematic introduction of the emerging devices employed for artificial ***,the implementations with different perceptual capabilitiesare briefly outlined and the key metrics and potential applications are also ***,we highlight the challenges and perspectives for the future development of artificial sensory neurons.

关键词： Artificial intelligence Emerging devices Artificial sensory neurons Spiking neural networks Neuromorphic sensing

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On the intraspecific variability in basal metabolism and the food habits hypothesis in birds

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Current Zoology 2010年第6期56卷 759-766页

作者： F. BOZINOVIC P. SABAT center for Advanced Studies in Ecology and biodiversity LINC-Globaland Departamento de EcologíaFacultad de Ciencias BiológicasPontificia Universidad Católica de Chile center for Advanced Studies in Ecology and biodiversity LINC-Globaland Departamento de EcologíaFacultad de Ciencias BiológicasPontificia Universidad Catolica de Chile Departamento de Ciencias Ecológicas Facultad de CienciasUniversidad de Chile

The food habits hypothesis （FHH） stands as one of the most striking and often-cited interspecific patterns to emerge from comparative studies of endothermic energetics. The FHH identifies three components of diet that potentially produce variability in mass-independent BMR, i.e. food quality, food availability, and food predictability or environmental productivity. The hypothesis predicts that species with diets of low energy content and/or low digestibility should evolve low mass-independent BMRs. The effects of food habits on BMR have been widely investigated at the interspecific level, but the variation between individuals and populations has been largely ignored. Our focus is to compare predictions derived from interspecific studies with data collected from within-species studies to explore the mechanisms and functional significance of adaptive responses predicted by the food-habits hypothesis among birds. We conclude that if BMR is correlated with daily energy expenditure, then organisms that can lower BMR will reduce daily energy expenditure and hence, food requirements. Birds that lower BMR in stressful environments may increase survival. Nevertheless, the mechanism （s） by which birds eating a low quality diet reduce BMR and whether lower BMR affects fitness remain to be determined [Current Zoology 56 （6）： 759-766, 2010].

关键词： Intraspecific comparisons Avian energetics Food habits hypothesis Diet Basal metabolic rate

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Solution‑Processed Thin Film Transparent Photovoltaics:Present Challenges and Future Development

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Nano-Micro Letters 2025年第2期17卷 566-600页

作者： Tianle Liu Munerah M.S.Almutairi Jie Ma Aisling Stewart Zhaohui Xing Mengxia Liu Bo Hou Yuljae Cho UM-SJTU Joint Institute Shanghai Jiao Tong UniversityShanghai 200240People’s Republic of China School of Physics and Astronomy Cardiff UniversityCardiff CF243AAWalesUK Department of Electrical and Computer Engineering Yale UniversityNew HavenCT 06511USA Energy Sciences Institute Yale UniversityWest HavenCT 06516USA Future Photovoltaics Research center Global Institute of Future TechnologyShanghai Jiao Tong UniversityShanghai 200240People’s Republic of China

Electrical energy is essential for modern society to sustain economic *** soaring demand for the electrical energy,together with an awareness of the environmental impact of fossil fuels,has been driving a shift towards the utilization of solar ***,traditional solar energy solutions often require extensive spaces for a panel installation,limiting their practicality in a dense urban *** overcome the spatial constraint,researchers have developed transparent photovoltaics(TPV),enabling windows and facades in vehicles and buildings to generate electric *** TPV advancements are focused on improving both transparency and power output to rival commercially available silicon solar *** this review,we first briefly introduce wavelength-and non-wavelengthselective strategies to achieve *** of merit and theoretical limits of TPVs are discussed to comprehensively understand the status of current TPV *** we highlight recent progress in different types of TPVs,with a particular focus on solution-processed thin-film photovoltaics(PVs),including colloidal quantum dot PVs,metal halide perovskite PVs and organic *** applications of TPVs are also reviewed,with emphasis on agrivoltaics,smart windows and ***,current challenges and future opportunities in TPV research are pointed out.

关键词： Transparent semiconductors Solution-processable transparent solar cell Emerging solar cell materials Buildingintegrated photovoltaics

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Temperature relations of aerial and aquatic physiological performance in a mid-intertidal limpet Cellana toreuma: Adaptation to rapid changes in thermal stress during emersion

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Integrative Zoology 2015年第1期10卷 159-170页

作者： Xiongwei HUANG Tifeng WANG Ziwen YE Guodong HAN Yunwei DONG State Key Laboratory of Marine Environmental Science College of Marine and Earth SciencesXiamen UniversityXiamenChina Marine biodiversity and global Change center Xiamen UniversityXiamenChina

The physiological performance of a mid-intertidal limpet Cellana toreuma was determined to study the physiological adaptation of intertidal animals to rapid changes and extreme temperatures during *** relationship between the Arrhenius breakpoint temperature(ABT)and in situ operative body temperature was studied to predict the possible impact of climate change on the *** temperature coefficient(Q10)of emersed animals was higher than that of submersed animals and the ratio of aerial:aquatic heart rate rose with increasing *** ABTs of submersed and emersed animals were 30.2 and 34.2°C,*** heart rate and levels of molecular biomarkers(hsps,ampkα,ampkβand sirt1 mRNA)were determined in 48 h simulated semi-diurnal *** were no obvious changes of heart rate and gene expression during the transition between emersion and submersion at room temperature,although expressions of hsp70 and hsp90 were induced significantly after thermal *** results indicate that *** can effectively utilize atmospheric oxygen,and the higher Q10 and ABT of emersed animals are adaptations to the rapid change and extreme thermal stress during ***,the in situ operative body temperature frequently exceeds the aerial ABT of ***,indicating the occurrence of large-scale mortality of *** in summer,and this species should be sensitive to increasing temperature in the scenario of climate change.

关键词： climate change intertidal limpet physiological adaptation temperature

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Mating system and genetic diversity of a rare desert legume Ammopiptanthus nanus (Leguminosae)

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Journal of Systematics and Evolution 2009年第1期47卷 57-66页

作者： Daniel J CRAWFORD Department of Ecology and Evolutionary Biology and the Natural History Museum and Biodiversity Research CenterThe University of Kansas

Ammopiptanthus nanus is an endangered evergreen shrub endemic to the deserts of central Asia and plays an important role in delaying further desertification. We examined allozyme variation and AFLP diversity in A. nanus populations and investigated the mating system of this species using progeny arrays assayed for poly-morphic allozyme loci. Mating system analysis in the Keyi’eryongke’er population showed low levels of out-crossing, and strong inbreeding depression. Low levels of genetic variation were detected at both population (allozyme, Pp=14.0%, A=1.14, He=0.031; AFLP, Pp=14.5%, Shannon’s information index I=0.063) and species (allozyme, Pp=21.1%, A=1.21, He=0.040; AFLP, Pp=20.9%, I=0.083) levels; while moderate genetic differentiation existed among populations, as indicated by allozymes (GST=0.081) and AFLP (GST=0.151-0.193). Founder effect, bottlenecks in evolutionary history, the mixed mating system and co-ancestry may have influenced the level of genetic diversity in A. nanus. Markers of both types provide new insights for conservation management, indicating that the Biao’ertuokuoyi and Keyi’eryongke’er populations should be given priority for in situ conservation and regarded as seed sources for ex situ conservation.

关键词： AFLP allozyme Ammopiptanthus conservation endangered plant genetic structure outcrossing rate

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