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Mutation signatures inform the natural host of SARS-CoV-2

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National Science Review 2022年第2期9卷 9-12页

作者： Shanjun Deng Ke Xing Xionglei He State Key Laboratory of Biocontrol School of Life Sciences Sun Yat-Sen University school of life sciences Guangzhou University

The origin of SARS-CoV-2,the causative virus of COVID-19,has been a mystery since the beginning of the outbreak and has been heavily debated lately.One of the main reasons for this is that RaTG13,the closest relative found to date [1](in the horseshoe bat Rhinolophus affinis),has only 96.1% nucleotide similarity to SARS-CoV-2 (with～1200 nucleotide differences).

关键词： CORONAVIRUS

Impact of tourism on the vigilance behavior of the Cyprus rock agama(Laudakia cypriaca)

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Integrative Zoology 2024年第3期19卷 577-583页

作者： Artur GOLAWSKI Iris CHARALAMBIDOU Sylwia GOLAWSKA Faculty of sciences Siedlce University of Natural Sciences and HumanitiesSiedlcePolandand Department of life sciences School of Life and Health SciencesUniversity of NicosiaNicosiaCyprus

Escape behavior is a common antipredator strategy among wild animals.Here,we investigated the effect of four factors on the vigilance behavior of the endemic Cyprus rock agama(Laudakia cypriaca).Flight initiation distance(FID,the minimum distance to which an observer can approach a lizard before it flees)was measured in relation to the type of location(tourist vs.nontourist area),the observer’s starting distance,air temperature,and substrate temperature.We collected data for 39 agamas in tourist areas and 34 of these lizards in nontourist areas.As a whole,the mean starting distance was 10.5 m and the FID was 3.6 m.The average substrate temperature was 34.0℃ and the average air temperature 29.6℃.Only the type of area affected the agamas’escape decisions with FID being 1.8 m shorter in tourist areas than in nontourist areas(2.7 m vs.4.5 m).This is probably due to the habituation of lizards to the presence of humans in the former areas.This study shows that tourism strongly affects the behavior of lizards,which may have consequences for the functioning of the population.Tourists can increase the safety of lizards by creating a human shield to deter predators.Once the tourist season is over,lizards may become more vulnerable to predators.

关键词： anthropogenic disturbance flight initiation distance lizards tourism vigilance behavior

Plant pan-genomics:recent advances,new challenges,and roads ahead

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Journal of Genetics and Genomics 2022年第9期49卷 833-846页

作者： Wei Li Jianan Liu Hongyu Zhang Ze Liu Yu Wang Longsheng Xing Qiang He Huilong Du school of life sciences Institute of Life Sciences and Green DevelopmentHebei UniversityBaodingHebei 071000China

Pan-genomics can encompass most of the genetic diversity of a species or population and has proved to be a powerful tool for studying genomic evolution and the origin and domestication of species,and for providing information for plant improvement.Plant genomics has greatly progressed because of improvements in sequencing technologies and the rapid reduction of sequencing costs.Nevertheless,pangenomics still presents many challenges,including computationally intensive assembly methods,high costs with large numbers of samples,ineffective integration of big data,and difficulty in applying it to downstream multi-omics analysis and breeding research.In this review,we summarize the definition and recent achievements of plant pan-genomics,computational technologies used for pan-genome construction,and the applications of pan-genomes in plant genomics and molecular breeding.We also discuss challenges and perspectives for future pan-genomics studies and provide a detailed pipeline for sample selection,genome assembly and annotation,structural variation identification,and construction and application of graph-based pan-genomes.The aim is to provide important guidance for plant pan-genome research and a better understanding of the genetic basis of genome evolution,crop domestication,and phenotypic diversity for future studies.

关键词： Plant pan-genome Genomic evolution Crop domestication Graph-based genome

PRRSV degrades MDA5 via dual autophagy receptors P62 and CCT2 to evade antiviral innate immunity

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Virologica Sinica 2024年第2期39卷 264-276页

作者： Ruiqi Sun Yanyu Guo Lilin Zhang Huixia Zhang Boxuan Yin Xiaoyang Li Changyan Li Liu Yang Lei Zhang Zexing Li Jinhai Huang school of life sciences Tianjin UniversityTianjin300072China

Porcine reproductive and respiratory syndrome virus(PRRSV)is a major economically devastating pathogen that has evolved various strategies to evade innate immunity.Downregulation of antiviral interferon largely promotes PRRSV immunoevasion by utilizing cytoplasmic melanoma differentiation-associated gene 5(MDA5),a receptor that senses viral RNA.In this study,the downregulated transcription and expression levels of porcine MDA5 in PRRSV infection were observed,and the detailed mechanisms were explored.We found that the interaction between P62 and MDA5 is enhanced due to two factors:the phosphorylation modification of the autophagic receptor P62 by the upregulated kinase CK2αand the K63 ubiquitination of porcine MDA5 catalyzed by the E3 ubiquitinase TRIM21 in PRRSV-infected cells.As a result of these modifications,the classic P62-mediated autophagy is triggered.Additionally,porcine MDA5 interacts with the chaperonin containing TCP1 subunit 2(CCT2),which is enhanced by PRRSV nsp3.This interaction promotes the aggregate formation and autophagic clearance of MDA5-CCT2-nsp3 independently of ubiquitination.In summary,enhanced MDA5 degradation occurs in PRRSV infection via two autophagic pathways:the binding of MDA5 with the autophagy receptor P62 and the aggrephagy receptor CCT2,leading to intense innate immune suppression.The research reveals a novel mechanism of immune evasion in PRRSV infection and provides fundamental insights for the development of new vaccines or therapeutic strategies.

关键词： Porcine reproductive and respiratory syndrome virus(PRRSV) nsp3 Autophagy MDA5

DNA methylation profiling reveals new potential subtype-specific gene markers for early-stage renal cell carcinoma in Caucasian population

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Quantitative Biology 2022年第1期10卷 79-93页

作者： Alvaro Filbert Liko Edward Ciputra Nathaniel Alvin Sanjaya Priskila Cherisca Then aka David Agustriawan Department of Biomedicine School of Life SciencesIndonesia International Institute for Life SciencesJakarta 13210Indonesia Department of Bioinformatics School of Life SciencesIndonesia International Institute for Life SciencesJakarta 13210Indonesia

Background:Renal cell carcinoma(RCC)is among the top adult cancers worldwide,with a challenging management due to lack of early diagnosis,therapy resistance,and diverse molecular background.Aberrant DNA methylation has been associated with RCC development due to transcription deregulation.We discovered potential DNA methylation-based biomarkers for stage I RCC in Caucasian population from The Cancer Genome Atlas(TCGA)database.Methods:Patients’clinical,methylation beta-value,and mRNA expression data were retrieved.Differential methylation and expression analysis were conducted to obtain differentially methylated CpG-gene pairs.Inversely correlated CpG-gene pairs between their expression and methylation levels were selected using Pearson’s correlation test and then screened for any recorded somatic mutations.Their biomarker capacities were analyzed’using the Kaplan-Meier and receiver operating characteristic analysis,followed by protein network and functional enrichment analysis.Results:We obtained differentially methylated CpGs in clear cell(KIRC)and papillary RCC(KIRP)but not chromophobe RCC(KICH).Six inversely correlated CpG-gene pairs with no reported cancer-associated mutations were selected.Prognostic values were found in ATXN1 and RFTN1 for KIRC,along with GRAMD1B and TM4SF19 for KIRP,while diagnostic values were found in VIM and RFTN1 for KIRC,along with TNFAIP6 and TM4SF19 for KIRP.Both subtypes showed enrichment of immune and metabolism-related pathways.Conclusion:We discovered novel potential DNA methylation-based prognostic and diagnostic markers for early-stage RCC in Caucasian population.Validation by wet laboratory analysis and adjustments for confounding variables might be needed,considering our study limitation to specific race.

关键词： biomarker chromophobe renal cell carcinoma clear cell renal cell carcinoma DNA methylation papillary renal cell carcinoma TCGA

Evolution of lmiRNAs and their targets from MITEs for rice adaptation

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Journal of Integrative Plant Biology 2022年第12期64卷 2411-2424页

作者： Tianxiao Huang Yan Li Wei Wang Le Xu Jingrui Li Yijun Qi Center for Plant Biology School of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua University.Peking University Joint Center for life sciences School of Life SciencesTsinghua UniversityBeijing 100084China

Twenty-four nucleotide long microRNAs(ImiRNAs)direct DNA methylation at target genes and regulate their transcription.The evolutionary origin of ImiRNAs and the range of ImiRNA-mediated regulation remain obscure.Here,we reannotated ImiRNAs and their targets in rice by applying stringent criteria.We found that the majority of ImiRNAs are derived from Miniature Inverted-repeat Transposable Elements(MITEs)and most sites targeted by MITE-derived ImiRNAs reside within MITEs,suggesting co-evolution of ImiRNAs and their targets through MITE amplification.ImiRNAs undergo dynamically changes under stress conditions and the genes targeted by ImiRNAs show an enrichment for stress-responsive genes,suggesting that ImiRNAs are widely involved in plant responses to stresses.We constructed the evolutionary histories of ImiRNAs and their targets.Nearly half of ImiRNAs emerged before or when the AA genome was diverged,while the emergence of ImiRNA targets coincided with or followed the emergence of ImiRNAs.Furthermore,we found that the sequences of a ImiRNA target site underwent variations,coincident with the divergence of rice accessions and the distribution of rice accessions in different geographical locations and climatic conditions.Our findings highlight MITEs as an important origin of ImiRNAs and suggest that the evolution of ImiRNA-target regulatory modules may contribute to rice adaptation to environmental changes.

关键词： DNA methylation evolution miRNA stress

Arabidopsis mitochondrial single-stranded DNA-binding proteins SSB1 and SSB2 are essential regulators of mtDNA replication and homologous recombination

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Journal of Integrative Plant Biology 2022年第10期64卷 1952-1965页

作者： Jie Qian Min Zheng Lingyu Wang Yu Song Jiawen Yan Yi‐Feng Hsu school of life sciences Southwest UniversityChongqing 400715China

Faithful DNA replication is one of the most essential processes in almost all living organisms.However,the proteins responsible for organellar DNA replication are still largely unknown in plants.Here,we show that the two mitochondriontargeted single-stranded DNA-binding(SSB)proteins SSB1 and SSB2 directly interact with each other and act as key factors for mitochondrial DNA(mt DNA)maintenance,as their single or double loss-of-function mutants exhibit severe germination delay and growth retardation.The mt DNA levels in mutants lacking SSB1 and/or SSB2 function were two-to four-fold higher than in the wild-type(WT),revealing a negative role for SSB1/2 in regulating mt DNA replication.Genetic analysis indicated that SSB1 functions upstream of mitochondrial DNA POLYMERASE IA(POLIA)or POLIB in mt DNA replication,as mutation in either gene restored the high mt DNA copy number of the ssb1-1 mutant back to WT levels.In addition,SSB1 and SSB2 also participate in mitochondrial genome maintenance by influencing mt DNA homologous recombination(HR).Additional genetic analysis suggested that SSB1 functions upstream of ORGANELLAR SINGLE-STRANDED DNABINDING PROTEIN1(OSB1)during mt DNA replication,while SSB1 may act downstream of OSB1and MUTS HOMOLOG1 for mt DNA HR.Overall,our results yield new insights into the roles of the plant mitochondrion-targeted SSB proteins and OSB1 in maintaining mt DNA stability via affecting DNA replication and DNA HR.

关键词： Arabidopsis mitochondria mtDNA replication mtDNA recombination SSB

Are microbes and metabolites influencing the parental consumption of nestlings’feces in gray-backed shrikes?

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Current Zoology 2022年第6期68卷 667-678页

作者： Jie HU Jingyuan ZENG Yurou SHI Sen SONG school of life sciences Lanzhou UniversityLanzhou730000China

The behavioral video recordings of the gray-backed shrike Lanius tephronotus revealed that parent birds eat the feces produced by their nestlings.“Parental nutrition hypothesis”attributes the origin of this behavior to nutrition-recovery and cost-saving,respectively.However,the presence of usable nutrients in the nestlings’feces is unknown because of traditional technology.In this study,we analyzed all the metabolites and the variations in the diversity and content of microbes in the feces of gray-backed shrike nestlings.We aimed to report the changes in microbes and metabolites with the age of nestlings and point out that the parent birds that eat the feces may gain potential nutrition benefits.The results showed that the relative abundances of Proteobacteria,Firmicutes,and Bacteroidota,changed significantly when the nestlings were 6 days old.The relative abundances of 6 probiotics,which are involved in digestion,metabolism,and immunity-related physiological functions,decreased in the nestlings’feces gradually with age;therefore,these probiotics may be obtained by parent birds upon ingestion of the feces of young nestlings.Among the metabolites that were detected,20 were lipids and some had a role in anti-parasitic functions and wound healing;however,their relative contents decreased with age.These beneficial substances in the nestlings’feces may stimulate the parents to swallow the feces.Moreover,there were many aromatic metabolites in the newly hatched nestlings’feces,but the content of bitter metabolites increased as they grew up.Therefore,our results are in accordance with the nutritional hypothesis.

关键词： feces disposal metabolite microbiota nestlings probiotics

Base flow separation for soil erosion simulation in a granitic forested headwater catchment using a process-based model, GeoWEPP

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International Journal of Sediment Research 2023年第4期38卷 494-502页

作者： Takuhei Yamasaki Shoichiro Hamamoto Taku Nishimura The Graduate school of Agricultural and life sciences The University of Tokyo

Distributed erosion models, which simulate the physical processes of water flow and soil erosion, are effective for predicting soil erosion in forested catchments. Although subsurface flow through multiple pathways is dominant for runoff generation in forested headwater catchments, the process-based erosion model, Geo-spatial interface for Water Erosion Prediction Project(Geo WEPP), does not have an adequate subsurface component for the simulation of hillslope water flow. In the current study, the quick flow related to soil erosion during rainfall events is separated from the total hydrograph using base flow separation for Geo WEPP to use direct runoff to predict sediment discharge from a granitic-forested catchment in Japan. Water runoff and sediment discharge also are simulated using the conventional method that reproduces the total hydrograph, and the accuracy of the calculation and estimated erodibility parameters are evaluated. The proposed procedure reproduced the quick-flow runoff during rainfall and the cumulative sediment discharge from the catchment. Simultaneously, the proposed procedure overestimates water runoff during extreme weather events, such as typhoons. The estimated erodibility parameters for the hillslope soil were comparable to those of the surface soil in Japan using both the proposed procedure and the conventional one. Conversely, the channel erodibility obtained from the proposed procedure matched the observed sediment characteristics in the granitic forested catchment. The proposed procedure is a promising method to predict sediment discharge from forested catchments based on the geological features of the catchment.

关键词： Soil erosion Base flow separation GeoWEPP Headwater catchment Forest