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Upgraded durian genome reveals the role of chromosome reshuffling during ancestral karyotype evolution,lignin biosynthesis regulation,and stress tolerance

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Science China(life Sciences) 2024年第6期67卷 1266-1279页

作者： Wanwan Li Xin Chen Jianing Yu Yuxian Zhu College of life Sciences Shaanxi Normal UniversityXi’an 710119China The State Key Laboratory of Protein and Gene Research College of Life SciencesPeking UniversityBeijing 100871China The Institute for Advanced studies Wuhan UniversityWuhan 430072China

Durian(Durio zibethinus)is a tropical fruit that has a unique flavor and aroma.It occupies a significant phylogenetic position within the Malvaceae family.Extant core-eudicot plants are reported to share seven ancestral karyotypes that have undergone reshuffling,resulting in an abundant genomic diversity.However,the ancestral karyotypes of the Malvaceae family,as well as the evolution trajectory leading to the28 chromosomes in durian,remain poorly understood.Here,we report the high-quality assembly of the durian genome with comprehensive comparative genomic analyses.By analyzing the collinear blocks between cacao and durian,we inferred 11 Malvaceae ancestral karyotypes.These blocks were present in a single-copy form in cacao and mainly in triplicates in durian,possibly resulting from a recent whole genome triplication(WGT)event that led to hexaploidization of the durian genome around 20(17–24)million years ago.A large proportion of the duplicated genes in durian,such as those involved in the lignin biosynthesis module for phenylpropane biosynthesis,are derived directly from whole genome duplication,which makes it an important force in reshaping its genomic architecture.Transcriptome studies have revealed that genes involved in feruloyl-Co A formations were highly preferentially expressed in fruit peels,indicating that the thorns produced on durian fruit may comprise guaiacyl and syringyl lignins.Among all the analyzed transcription factors(TFs),members of the heat shock factor family(HSF)were the most significantly upregulated under heat stress.All subfamilies of genes encoding heat shock proteins(HSPs)in the durian genome appear to have undergone expansion.The potential interactions between HSF Dzi05.397 and HSPs were examined and experimentally verified.Our study provides a high-quality durian genome and reveals the reshuffling mechanism of ancestral Malvaceae chromosomes to produce the durian genome.We also provide insights into the mechanism underlying lignin biosynthesis and heat stress tolerance.

关键词： Durio zibethinus whole genome duplication whole genome triplication Malvaceae ancestral karyotypes chromosome reshuffling lignin biosynthesis heat stress

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Intraspecific scaling and early life history determine the cost of free-flight in a large beetle(Batocera rufomaculata)

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Insect Science 2024年第2期31卷 524-532页

作者： Tomer Urcai Eran Levin Eran Gefen Gal Ribak Faculty of life Sciences School of ZoologyTel Aviv UniversityTel AvivIsrael Steinhardt Museum of Natural History Israel National Center for Biodiversity StudiesTel AvivIsrael department of Biology University of Haifa-OranimKiryat TivonIsrael

The scaling of the energetic cost of locomotion with body mass is well documented at the interspecific level.However,methodological restrictions limit our understanding of the scaling of flight metabolic rate(MR)in free-flying insects.This is particularly true at the intraspecific level,where variation in body mass and flight energetics may have direct consequences for the fitness of an individual.We applied a 13C stable isotope method to investigate the scaling of MR with body mass during free-flight in the beetle Batocera rufomaculata.This species exhibits large intraspecific variation in adult body mass as a consequence of the environmental conditions during larval growth.We show that the flight-MR scales with body mass to the power of 0.57,with smaller conspecifics possessing up to 2.3 fold higher mass-specific flight MR than larger ones.Whereas the scaling exponent of free-flight MR was found to be like that determined for tethered-flight,the energy expenditure during free-flight was more than 2.7 fold higher than for tethered-flight.The metabolic cost of flight should therefore be studied under free-flight conditions,a requirement now enabled by the 13C technique described herein for insect flight.

关键词： allometry body mass Coleoptera free-flight insect flight stable carbon isotope tethered-flight

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Therapeutic advances in neural regeneration for Huntington’s disease

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Neural Regeneration Research 2024年第9期19卷 1991-1997页

作者： Francesco D’Egidio Vanessa Castelli Giorgia Lombardozzi Fabrizio Ammannito Annamaria Cimini Michele d’Angelo department of life Health and Environmental SciencesUniversity of L’AquilaL’AquilaItaly

Huntington’s disease is a neurodegenerative disease caused by the expansion mutation of a cytosine-adenine-guanine triplet in the exon 1 of the HTT gene which is responsible for the production of the huntingtin (Htt) protein. In physiological conditions, Htt is involved in many cellular processes such as cell signaling, transcriptional regulation, energy metabolism regulation, DNA maintenance, axonal trafficking, and antiapoptotic activity. When the genetic alteration is present, the production of a mutant version of Htt (mHtt) occurs, which is characterized by a plethora of pathogenic activities that, finally, lead to cell death. Among all the cells in which mHtt exerts its dangerous activity, the GABAergic Medium Spiny Neurons seem to be the most affected by the mHtt-induced excitotoxicity both in the cortex and in the striatum. However, as the neurodegeneration proceeds ahead the neuronal loss grows also in other brain areas such as the cerebellum, hypothalamus, thalamus, subthalamic nucleus, globus pallidus, and substantia nigra, determining the variety of symptoms that characterize Huntington’s disease. From a clinical point of view, Huntington’s disease is characterized by a wide spectrum of symptoms spanning from motor impairment to cognitive disorders and dementia. Huntington’s disease shows a prevalence of around 3.92 cases every 100,000 worldwide and an incidence of 0.48 new cases every 100,000/year. To date, there is no available cure for Huntington’s disease. Several treatments have been developed so far, aiming to reduce the severity of one or more symptoms to slow down the inexorable decline caused by the disease. In this context, the search for reliable strategies to target the different aspects of Huntington’s disease become of the utmost interest. In recent years, a variety of studies demonstrated the detrimental role of neuronal loss in Huntington’s disease condition highlighting how the replacement of lost cells would be a reasonable strategy to overcome the neurodegeneration. In this view, num

关键词： cell therapy exosomes extracellular vesicles Huntingtin Huntington’s disease medium spiny neurons neurodegenerative disease neurogenesis neuronal loss stem cells

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Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

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Journal of Integrative Plant Biology 2024年第3期66卷 546-578页

作者： Guojin Zhang Hong Ma College of life Sciences Hunan Normal UniversityChangsha 410081China department of Biology 510 Mueller LaboratoryHuck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPA 16802USA

Angiosperms(flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the “abominable mystery,”hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological,and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences,dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families,and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella,Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families.Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore,we discuss the implications of nuclear phylogenomic analyses on ancestral

关键词： angiosperms evolution flowering plants nuclear gene phylogenomics phylogeny

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Remediation of amide pesticide-polluted soils by combined solarization and ozonation treatment

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Pedosphere 2024年第3期34卷 641-651页

作者： Isabel GARRIDO Carmen MMARTINEZ Pilar FLORES Pilar HELLIN Fulgencio CONTRERAS Jose FENOLL department of Sustainability and quality Group of Fruit and Vegetable Products Instituto Murciano de Investigacion y Desarrollo Agrario y MedioambientalLa Alberca 30150(Spain)

Agriculture has a close relationship with nature,but it can also be the source of negative and permanent environmental effects.The use of pesticides in modern agriculture is a common practice,but their side effects on the environment cannot be disregarded.In this study,we evaluated a combination of solarization and ozonation techniques for the elimination of six amide pesticides(boscalid,chlorantraniliprole,cyflufenamid,fluopyram,napropamide,and propyzamide)in soil.Initial experiments were performed with four different soils to assess the efficiency of this methodology at different soil temperatures and ozone dosages under laboratory conditions,and then a greenhouse pot experiment was conducted under controlled conditions during summer.Fifty days after the onset of the experiments,higher degradation percentages of amide pesticides were observed in ozonized soils than in other treated soils,particularly when ozone was applied at 10 cm soil depth.The results show that the utilization of ozonation,along with solarization,represents a valid method for degrading residues of the studied pesticides and suggest that this combined technology may be a promising tool for remediating pesticide-polluted soils.

关键词： intermediate ozone pesticide degradation pesticide residue polyethylene film remediation technique

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Enhancement of porcine in vitro embryonic development through luteolin‑mediated activation of the Nrf2/Keap1 signaling pathway

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Journal of Animal Science and Biotechnology 2024年第2期15卷 600-613页

作者： Se-Been Jeon Pil-Soo Jeong Min Ju Kim Hyo-Gu Kang Bong-Seok Song Sun-Uk Kim Seong-Keun Cho Bo-Woong Sim Futuristic Animal Resource&Research Center(FARRC) Korea Research Institute of Bioscience and Biotechnology(KRIBB)Cheongju 28116Republic of Korea department of Animal Science College of Natural Resources&Life SciencePusan National UniversityMiryang 50463Republic of Korea department of Animal Science and Biotechnology College of Agriculture and Life ScienceChungnam National UniversityDaejeon 34134Republic of Korea department of Functional Genomics University of Science and TechnologyDaejeon 34113Republic of Korea department of Animal Science Life and Industry Convergence Research Institute(RICRI)College of Natural Resources&Life SciencePusan National UniversityMiryang 50463Republic of Korea

Background Oxidative stress,caused by an imbalance in the production and elimination of intracellular reactive oxygen species(ROS),has been recognized for its detrimental effects on mammalian embryonic development.Luteolin(Lut)has been documented for its protective effects against oxidative stress in various studies.However,its specific role in embryonic development remains unexplored.This study aims to investigate the influence of Lut on porcine embryonic development and to elucidate the underlying mechanism.Results After undergoing parthenogenetic activation(PA)or in vitro fertilization,embryos supplemented with 0.5μmol/L Lut displayed a significant enhancement in cleavage and blastocyst formation rates,with an increase in total cell numbers and a decrease in the apoptosis rate compared to the control.Measurements on D2 and D6 revealed that embryos with Lut supplementation had lower ROS levels and higher glutathione levels compared to the control.Moreover,Lut supplementation significantly augmented mitochondrial content and membrane potential.Intriguingly,activation of the Nrf2/Keap1 signaling pathway was observed in embryos supplemented with Lut,leading to the upregulation of antioxidant-related gene transcription levels.To further validate the relationship between the Nrf2/Keap1 signaling pathway and effects of Lut in porcine embryonic development,we cultured PA embryos in a medium supplemented with brusatol,with or without the inclusion of Lut.The positive effects of Lut on developmental competence were negated by brusatol treatment.Conclusions Our findings indicate that Lut-mediated activation of the Nrf2/Keap1 signaling pathway contributes to the enhanced production of porcine embryos with high developmental competence,and offers insight into the mechanisms regulating early embryonic development.

关键词： Luteolin Mitochondrial function Nrf2/Keap1 signaling pathway Oxidative stress Porcine embryo development

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Dysregulation of RNA modification systems in clinical populations with neurocognitive disorders

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Neural Regeneration Research 2024年第6期19卷 1256-1261页

作者： Helen M.Knight Merve Demirbugen ?z Adriana PerezGrovas-Saltijeral Division of Cells Organisms and Molecular Genetics School of Life Sciences University of Notingham department of Pharmaceutical Toxicology Faculty of Pharmacy Ankara University

The study of modified RNA known as epitranscriptomics has become increasingly relevant in our understanding of disease-modifying mechanisms. Methylation of N6 adenosine(m6A) and C5 cytosine(m5C) bases occur on mRNAs, tRNA, mt-tRNA, and rRNA species as well as non-coding RNAs. With emerging knowledge of RNA binding proteins that act as writer, reader, and eraser effector proteins, comes a new understanding of physiological processes controlled by these systems. Such processes when spatiotemporally disrupted within cellular nanodomains in highly specialized tissues such as the brain, give rise to different forms of disease. In this review, we discuss accumulating evidence that changes in the m6A and m5C methylation systems contribute to neurocognitive disorders. Early studies first identified mutations within FMR1 to cause intellectual disability Fragile X syndromes several years before FMR1 was identified as an m6A RNA reader protein. Subsequently, familial mutations within the m6A writer gene METTL5, m5C writer genes NSUN2, NSUN3, NSUN5, and NSUN6, as well as THOC2 and THOC6 that form a protein complex with the m5C reader protein ALYREF, were recognized to cause intellectual development disorders. Similarly, differences in expression of the m5C writer and reader effector proteins, NSUN6, NSUN7, and ALYREF in brain tissue are indicated in individuals with Alzheimer’s disease, individuals with a high neuropathological load or have suffered traumatic brain injury. Likewise, an abundance of m6A reader and anti-reader proteins are reported to change across brain regions in Lewy bodies diseases, Alzheimer’s disease, and individuals with high cognitive reserve. m6A-modified RNAs are also reported significantly more abundant in dementia with Lewy bodies brain tissue but significantly reduced in Parkinson’s disease tissue, whilst modified RNAs are misplaced within diseased cells, particularly where synapses are located. In parahippocampal brain tissue, m6A modification is enriched in transcripts associated with psychiatri

关键词： 5-methylcytosine methylation Alzheimer’s disease cognitive diseases epitranscriptomics intellectual disability Lewy body diseases N6 adenosine RNA modification

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Recent progress and future directions of the research on nanoplastic-induced neurotoxicity

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Neural Regeneration Research 2024年第2期19卷 331-335页

作者： Seung-Woo Han Jinhee Choi Kwon-Yul Ryu department of life Science University of SeoulSeoulSouth Korea School of Environmental Engineering University of SeoulSeoulSouth Korea

Many types of plastic products,including polystyrene,have long been used in commercial and industrial applications.Microplastics and nanoplastics,plastic particles derived from these plastic products,are emerging as environmental pollutants that can pose health risks to a wide variety of living organisms,including humans.However,it is not well understood how microplastics and nanoplastics affect cellular functions and induce stress responses.Humans can be exposed to polystyrene-microplastics and polystyrene-nanoplastics through ingestion,inhalation,or skin contact.Most ingested plastics are excreted from the body,but inhaled plastics may accumulate in the lungs and can even reach the brain via the nose-to-brain route.Small-sized polystyrene-nanoplastics can enter cells by endocytosis,accumulate in the cytoplasm,and cause various cellular stresses,such as inflammation with increased pro-inflammatory cytokine production,oxidative stress with generation of reactive oxygen species,and mitochondrial dysfunction.They induce autophagy activation and autophagosome formation,but autophagic flux may be impaired due to lysosomal dysfunction.Unless permanently exposed to polystyrene-nanoplastics,they can be removed from cells by exocytosis and subsequently restore cellular function.However,neurons are very susceptible to this type of stress,thus even acute exposure can lead to neurodegeneration without recovery.This review focuses specifically on recent advances in research on polystyrene-nanoplastic-induced cytotoxicity and neurotoxicity.Furthermore,in this review,based on mechanistic studies of polystyrene-nanoplastics at the cellular level other than neurons,future directions for overcoming the negative effects of polystyrene-nanoplastics on neurons were suggested.

关键词： autophagy cellular stress cytotoxicity endocytosis exocytosis inflammation microplastics nanoplastics neurotoxicity oxidative stress polystyrene

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Effects of pyraclostrobin on growth,oxidative stress,and gene expression in relation to stress and ATP-binding cassette transporters in Tetrahymena thermophila

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Journal of Oceanology and Limnology 2024年第1期42卷 150-162页

作者： Yang LIU Jiale ZHANG Peng XIAO Xin LIU Yisifu MA Jing ZHANG Bangjun ZHANG Henan International Joint Laboratory of Aquatic Ecotoxicology and Health Protection Xinxiang 453007China College of life Sciences Henan Normal UniversityXinxiang 453007China Journal of Henan Normal University Xinxiang 453007China College of life and Environmental Science Wenzhou UniversityWenzhou 325035China department of Ecosystem studies School of Environmental ScienceUniversity of Shiga PrefectureShiga 522-8533Japan

Pyraclostrobin(PYR),a widely used fungicide,has negative effects on fish and algae,but its toxicity in protozoa remains unclear.In this study,the effects of PYR on the growth,oxidative stress,and gene expression related to stress and ATP-binding cassette(ABC)transporters in Tetrahymena thermophila were investigated.The result showed that the 96-h IC_(50)of PYR against T.thermophila was 17.2 mg/L.Moreover,PYR inhibited the growth of T.thermophila in concentration-or time-dependent manner.A morphological study revealed that the shape and size of T.thermophila changed,and damage of cell membrane surface was observed by scanning electron microscopy after 96 h of PYR exposure.The activities of superoxide dismutase(SOD)and catalase(CAT)increased throughout the experiment.In contrast,the glutathione(GSH)content was increased at 24 h and 48 h of exposure and decreased at 96 h.Moreover,a significant increase in malondialdehyde(MDA)level was observed in T.thermophila after96 h of exposure.Furthermore,PYR upregulated the HSP703,HSP705,GPx2,and ABAC15 gene expression in the 0.1–5-mg/L groups and downregulated the HSP704,HSP90,TGR,and ABCC52 mRNA levels at 96 h of exposure.These results suggest that PYR may exert adverse effects on T.thermophila by inducing oxidative stress and changing the gene expression related to ABC transporters and stress,which may enrich the understanding of the toxicity mechanism of PYR in aquatic organisms and provide reference data for aquatic ecological risk assessments.

关键词： pyraclostrobin Tetrahymena thermophila growth oxidative stress gene expression

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Impact of lifestyle interventions on pathogenesis of nonalcoholic fatty liver disease

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World Journal of Gastroenterology 2024年第20期30卷 2633-2637页

作者： Wafaa Mohamed Ezzat department of Internal Medicine Medical Research and Clinical Studies InstituteNational Research CenterGiza 12311Egypt

This editorial builds on the article titled“Establishment and validation of an adherence prediction system for lifestyle interventions in non-alcoholic fatty liver disease”by Zeng et al.We carried out a critical examination of nonalcoholic fatty liver disease(NAFLD)pathogenesis and how lifestyle interventions could facilitate disease resolution,particularly highlighting that non-alcoholic steatohepatitis(NASH)is a severe form of NAFLD.Our discussion details that weight loss is a pivotal factor in disease outcomes:A 3%-5%reduction is enough for resolution in 50%of non-obese individuals,while a 7%-10%reduction achieves similar benefits in obese individuals,as demonstrated by magnetic resonance spectroscopy.Additionally,the editorial underscores that such lifestyle changes are instrumental not only in resolving NAFLD but also in reversing hepatic steatosis and inflammation.These insights,derived from the research,emphasize the critical role of personalized lifestyle modifications in halting the progression of NAFLD to NASH and even reversing fibrosis,thus offering a template for effective patient management.

关键词： Nonalcoholic fatty liver disease Non-alcoholic steatohepatitis Diet Physical activity life style

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