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Temporal patterns of three sympatric pheasant species in the Nanling Mountains: N-mixture modeling applied to detect abundance

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Avian Research 2019年第4期10卷 405-414页

作者： Fasheng Zou Qiang Zhang Min Zhang Myung‑Bok Lee Xincai Wang Yuening Gong Changteng Yang Guangdong key laboratory of Animal conservation and Resource utilization Guangdong Public Laboratory of Wild Animal Conservation and UtilizationGuangdong Institute of Applied Biological ResourcesGuangzhou 510260China Guangdong Nanling National Nature Reserve Ruyuan 512727China

Background:The reliability of long-term population estimates is crucial for conservation and management *** previous studies assume that count indices are proportionally related to abundance;however,this assumption may not hold when detection varies spatially and *** examined seasonal variations in abundance of three bird species(Cabot’s Tragopan Tragopan caboti,Silver Pheasant Lophura nycthemera,and Whitenecklaced Partridge Arborophila gingica) along an elevational gradient,using N-mixture models that take into account imperfect detection in our bird ***:Camera-trapping was used to monitor temporal activity patterns of these species at Guangdong Nanling National Nature Reserve from December 2013 to November 2017(4 seasons per year).For abundance analysis(N-mixture modeling),we divided a year into 4 seasons,i.e.3 months per season,and performed the analysis by *** was incorporated into the N-mixture model as a covariate that may affect *** compared the N-mixture model with a null model(no covariate model) and selected the better model based on AIC values to make an ***:From 24 sampling sites,we obtained 6786 photographs of 8482 individuals of 44 bird species and 26 mammal *** Pheasant was photographed much more frequently and showed higher temporal activity frequency than White-necklaced Partridge or Cabot’s *** Pheasant was camera-captured most frequently in summer,and other two species in *** three species had two daytime activity peaks:between 6:00 *** 10:00 a.m.,and between 5:00 *** 7:00 p.m.,*** estimated abundance and detection probability from the N-mixture model were variable by *** particular,all three species showed greater abundance in summer than in winter,and estimated abundance patterns of all three species were more similar with observed cameratrapping counts in ***,in winter,elevation had a positive impact on abundan

关键词： Abundance estimation Camera-trapping Imperfect detectability Nanling Mountains Spatio-temporal distribution Sympatric distribution

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Ribosome profiling reveals the translational landscape and allele-specific translational efficiency in rice

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Plant Communications 2023年第2期4卷 119-135页

作者： Xi-Tong Zhu Run Zhou Jian Che Yu-Yu Zheng Muhammad Tahir ul Qamar Jia-Wu Feng Jianwei Zhang Junxiang Gao Ling-Ling Chen National key laboratory of Crop Genetic Improvement College of InformaticsHuazhong Agricultural UniversityWuhan 430070China State key laboratory for conservation and utilization of Subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanning 530004China

Translational regulation is a critical step in the process of gene expression and governs the synthesis of proteins from *** studies have revealed translational regulation in plants in response to various environmental ***,there have been no studies documenting the comprehensive landscape of translational regulation and allele-specific translational efficiency in multiple plant tissues,especially those of rice,a main staple crop that feeds nearly half of the world’s *** we used RNA sequencing and ribosome profiling data to analyze the transcriptome and translatome of an elite hybrid rice,Shanyou 63(SY63),and its parental varieties Zhenshan 97 and Minghui *** results revealed that gene expression patterns varied more among tissues than among varieties at the transcriptional and translational *** identified 3392 upstream open reading frames(uORFs),and the uORF-containing genes were enriched in transcription *** 668 of 13492 long non-coding RNAs could be translated into ***,we discovered numerous genes with allele-specific translational efficiency in SY63 and demonstrated that some cis-regulatory elements may contribute to allelic divergence in translational ***,these findings may improve our understanding of translational regulation in rice and provide information for molecular breeding research.

关键词： Ribo-seq translational landscape uORFs lncRNAs allele-specific translational efficiency rice Oryza sativa

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An Efficient Rice Mutagenesis System Based on Suspension-Cultured Cells

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Journal of Integrative Plant Biology 2013年第2期55卷 122-130页

作者： Yuan-Ling Chen Hui-Lin Liang Xing-Liang Ma Su-Lin Lou Yong-Yao Xie Zhen-Lan Liu Le-Tian Chen Yao-Guang Liu State key laboratory for conservation and utilization of Subtropical Agro-bioresources College of Life Sciences South China Agricultural University

Plant mutants are important bio-resources for crop breeding and gene functional studies. Conventional methods for generating mutant libraries by mutagenesis of seeds with physical or chemical agents are of low efficiency. Here, we developed a highly-efficient ethyl methanesulfonate （EMS） mutagenesis system based on suspension-cultured cells, with rice （Oryza sativa L.） as an example. We show that treatment of suspension-cultured tiny cell clusters with 0.4% EMS for 18-22 h followed by differentiation and regeneration produced as high as 29.4% independent mutant lines with visible phenotypic variations, including a number of important agronomic traits such as grain size, panicle size, grain or panicle shape, tiller number and angle, heading date, male sterility, and disease sensitivity. No mosaic mutant was observed in the mutant lines tested. In this mutant library, we obtained a mutant with an abnormally elongated uppermost internode. Sequencing and functional analysis revealed that this is a new allelic mutant of eui （elongated uppermost internode） caused by two point mutations in the first exon of the EUI gene, representing a successful example of this mutagenesis system.

关键词： Rice mutagenesis EMS suspension cell culture mutant.

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Effects of transgenic soybean on growth and phosphorus acquisition in mixed culture system

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Journal of Integrative Plant Biology 2015年第5期57卷 477-485页

作者： Jianna Xie Jia Zhou Xiurong Wang Hong Liao State key laboratory for conservation and utilization of Subtropical Agro-bioresources Root Biology CenterSouth China Agricultural University

Transgenic soybean plants overexpressing the Arabidopsis purple acid phosphatase gene AtPAP15 （OXp） or the soybean expansin gene GmEXPB2 （OXe） can improve phosphorous （P） efficiency in pure culture by increasing Apase secretion or changing root morphology. In this study, soybean‐soybean mixed cultures were employed to il uminate P acquisition among plants in mixed stands of transgenic and wild‐type soybean. Our results showed that transgenic soybean plants were much more competitive, and had greater growth and P uptake than wild‐type soybean in mixed culture in both low P calcareous and acid soils. Furthermore, OXe plants had an advantage in calcareous soils when mixed with OXp, whereas the latter performed much better in acid soils. In soybean‐maize mixed culture, transgenic soybean had no impact on maize growth compared to controls in both acid and calcareous soils with different P conditions. As for soybean in＆amp;nbsp;mixed culture, OXp plants had no significant advantages regardless of P availability or soil type, while P efficiency improved in OXe in calcareous soils compared to controls. These results imply that physiological traits could be easily affected by the mixed maize. Transgenic soybean plants with enhanced root traits had more competitive advantages than those with improved root physiology in mixed culture.

关键词： Soybean AtPAP15 GmEXPB2i phosphorus efficiency maize mixed culture

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Evolution and conservation genetics of pangolins

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Integrative Zoology 2024年第3期19卷 426-441页

作者： Tongtong GU Jingyang HU Li YU State key laboratory for conservation and utilization of Bio-Resource in Yunnan School of Life SciencesYunnan UniversityKunmingChina

Pangolins(Pholidota,Manidae)are classified as an evolutionarily distinct and globally endangered mammal due to their unique morphology(nail-like scales and a myrmecophagous diet)and being the victim of heavy poaching and worldwide *** such,pangolins serve as a textbook example for studying the special phenotypic evolutionary adaptations and conservation genetics of an endangered *** years have demonstrated significant advancements in the fields of molecular genetics and genomics,which have translated to a series of important research achievements and breakthroughs concerning the evolution and conservation genetics of *** review comprehensively presents the hitherto advances in phylogeny,adaptive evolution,conservation genetics,and conservation genomics that are related to pangolins,which will provide an ample understanding of their diversity,molecular adaptation mechanisms,and evolutionary *** addition,we highlight the priority of investigating species/population diversity among pangolins and suggest several avenues of research that are highly relevant for future pangolin conservation.

关键词： adaptive evolution conservation genetics conservation genomics pangolins phylogeny

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In-situ observation for formation and dissociation of carbon dioxide hydrate in porous media by magnetic resonance imaging

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Science China Earth Sciences 2013年第4期56卷 611-617页

作者： CHENG ChuanXiao ZHAO JiaFei SONG YongChen ZHU ZiHao LIU WeiGuo ZHANG Yi YANG MingJun YU XiChong key laboratory of Ocean Energy utilization and Energy conservation of Ministry of Education Dalian University of Technology CNOOC Research Center

The study of formation and dissociation of CO 2 hydrate in porous media was characterized by magnetic resonance imaging (MRI) system in in situ conditions. This work simulated porous media by using glass beads of uniform size. The growth and dissociation habit of CO2 hydrate was observed under different temperature and pressure conditions. The induction time and the hydrate saturation during the growth and dissociation process in different sizes of porous media were obtained by using the MRI signal intensity. The results indicate that hydrate growth rate and the induction time are affected by the size of porous media, pressure, and degree of supercooling. There are three hydrate growth stages, i.e., initial growth stage, rapid growth stage and steady stage. In this study,the CO2 hydrate forms preferentially at the surface of vessel and then gradually grows inward. The hydrate tends to cement the glass beads together and occupies the pore gradually. As the hydrate decomposes gradually, the dissociation rate increases to the maximum and then decreases to zero.

关键词： magnetic resonance imaging carbon dioxide hydrate porous media saturation induction time growth and dissocia- tion rate

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Molecular Control of Male Reproductive Development and Pollen Fertility in Rice

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Journal of Integrative Plant Biology 2012年第12期54卷 967-978页

作者： Jing-Xin Guo Yao-Guang Liu State key laboratory for conservation and utilization of Subtropical Agro-bioresources College of Life SciencesSouth China Agricultural University

Anther development and male fertility are essential biological pro- cesses for flowering plants and are important for crop seed produc- tion. Genetic manipulation of male fertility/sterility is critical for crop hybrid breeding. Rice （Oryza sativa L.） male sterility phenotypes, including genic male sterility, hybrid male sterility, and cytoplasmic male sterility, are generally caused by mutations of fertility-related genes, by incompatible interactions between divergent allelic or non-allelic genes, or by genetic incompatibilities between cytoplas-mic and nuclear genomes. Here, we review the recent advances in the molecular basis of anther development and male fertility-sterility conversion in specific genetic backgrounds, and the interactions with certain environmental factors. The highlighted findings in this review have significant implications in both basic studies and rice genetic improvement.

关键词： Anther development cytoplasmic male sterility hybrid sterility male fertility meiosis rice.

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Why is the beautyberry so colourful? Evolution,biogeography,and diversification of fruit colours in Callicarpa(Lamiaceae)

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Plant Diversity 2023年第1期45卷 6-19页

作者： Xing Liu Hui-Min Cai Wen-Qiao Wang Wei Lin Zhi-Wei Su Zhong-Hui Ma Department of Agricultural College State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresourcesGuangxi UniversityNonning 5300041GuangpaiPR China Institute of Marine Drugs Guangxi University of Chinese MedicineNoaning 530004.GuangciPR China

Fruit colour is essential to seed dispersal,speciation,and biological diversity in global *** relationship between fruit-colour variation and species diversification has long been of interest in evolutionary biology,but remains poorly understood at the genus ***,we used Callicarpa,a typical representative of pantropical angiosperm,to analyse whether fruit colours are correlated with biogeographic distribution,dispersal events,and diversification *** estimated a time-calibrated phylogeny for Callicarpa and reconstructed ancestral fruit *** phylogenetic methods,we estimated the major dispersal events across the phylogenetic tree and the most likely fruit colours related to each dispersal event,and tested whether the dispersal frequencies and distances of the four fruit colours between major biogeographical areas were *** then tested whether fruit colours are correlated with latitude,elevation,and diversification *** reconstructions showed that Callicarpa originated in the East Asia and Southeast Asia during the Eocene(-35.53 Ma) and diverse species diverged mainly in the Miocene and lasted into the ***-scale dispersal events were significantly associated with violet-fruited ***,different fruit colours were markedly correlated with different latitudes and elevations(e.g.,violet fruits were correlated with higher latitudes and elevations;red fruits and black fruits with lower latitudes;white fruits with higher elevations).Notably,violet fruits were statistically associated with highest diversification rates,driving fruit colour variation among different regions *** results contribute to further understanding why fruit colour is so variable at the genus level of angiosperms in different areas around the world.

关键词： Callicarpa Fruit colour Phylogeny Biogeography Dispersal Diversification

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Gene admixture in ethnic populations in upper part of Silk Road revealed by mtDNA polymorphism

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Science China(Life Sciences) 2008年第5期51卷 435-444页

作者： YANG LiuQi, TAN SiJie, YU HaiJing, ZHENG BingRong, QIAO EnFa, DONG YongLi, ZAN RuiGuang & XIAO ChunJie key laboratory of Bioresources conservation and utilization & Human Genetics Center, Yunnan University, Kunming 650091, China key laboratory of Bioresources conservation utilization & Human Genetics Center Yunnan University Kunming 650091 China

To evaluate the gene admixture on the current genetic landscape in Gansu Corridor (GC) in China, the upper part of the ancient Silk Road which connects the Eastern and Central Asia, we examined mitochondrial DNA (mtDNA) polymorphisms of five ethnic populations in this study. Using PCR-RFLP and sequencing, we analyzed mtDNA haplotypes in 242 unrelated samples in three ethnic populations from the GC region and two ethnic populations from the adjacent Xinjiang Uygur Autonomous Region of China. We analyzed the data in comparison with the previously reported data from Eastern, Central and Western Asia and Europe. We found that both European-specific haplogroups and Eastern Asian-specific haplogroups exist in the Gansu Corridor populations, while a modest matrilineal gene flow from Europeans to this region was revealed. The Gansu Corridor populations are genetically located between Eastern Asians and Central Asians, both of who contributed significantly to the maternal lineages of the GC populations. This study made the landscape of the gene flow and admixture along the Silk Road from Europe, through Central Asia, to the upper part of the Silk Road more complete.

关键词： polymorphism mtDNA gene admixture Gansu Corridor

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MpbR,an essential transcriptional factor for Mycobacterium tuberculosis survival in the host,modulates PIM biosynthesis and reduces innate immune responses

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Journal of Genetics and Genomics 2019年第12期46卷 575-589页

作者： Yugang Li Weihui Li Zhiwei Xie Hui Xu Zheng-Guo He National key laboratory of Agricultural Microbiology College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan430070China State key laboratory for conservation and utilization of Subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanning530004China

Mycobacterium tuberculosis possesses unique cellular envelope components that contribute to bacterial escape from host immune *** mannosides(PIMs)and their higher derivatives are important molecules implicated in host-pathogen interactions in the course of ***,the biosynthetic regulation of these specific lipids and its effect on the bacterial fate in the infected host remain ***,we show that a hypothetical *** transcriptional factor designated as MpbR negatively regulates two transporter genes and affects mycobacterial PIM biosynthesis and biofilm *** inhibits the accumulation of acylated PIM lipids and triggers the mycobacterium to reduce the production of reactive oxygen species and NO during infection,which enhances the survival of *** in *** deletion reduces *** lung burdens and inflammation of infected *** findings provide new insights into the regulation of mycobacterial lipid metabolism and its correlation with pathogenesis of ***.

关键词： Mycobacterium tuberculosis Transcriptional factor Lipid metabolism

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