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Phased,chromosome-scale genome assemblies of tetraploid potato reveal a complex genome,transcriptome,and predicted proteome landscape underpinning genetic diversity

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Molecular Plant 2022年第3期15卷 520-536页

作者： Genevieve Hoopes Xiaoxi Meng John P.Hamilton Sai Reddy Achakkagari fernanda de alves freitas guesdes Marie E.Bolger Joseph J.Coombs Danny Esselink Natalie R.Kaiser Linda Kodde Maria Kyriakidou Brian Lavrijssen Natascha van Lieshout Rachel Shereda Heather K.Tuttle Brieanne Vaillancourt Joshua C.Wood Jan Mde Boer Nolan Bornowski Peter Bourke David Douches Herman Jvan Eck Dave Ellis Max J.Feldman Kyle M.Gardner Johannes C.P.Hopman Jiming Jiang Walter S.de Jong Joseph C.Kuhl Richard G.Novy Stan Oome Vidyasagar Sathuvalli Ek Han Tan Remco A.Ursum M.Isabel Vales Kelly Vining Richard G.F.Visser Jack Vossen G.Craig Yencho Noelle L.Anglin Christian W.B.Bachem Jeffrey B.Endelman Laura M.Shannon Martina V.Stromvik Helen H.Tai Bjorn Usadel C.Robin Buell Richard Finkers department of Plant Biology Michigan State UniversityEast LansingMI 48824USA department of Horticultural Science University of MinnesotaSt.PaulMN 55108USA department of Plant Science McGill UniversitySainte-Anne-de-BellevueQC H9X 3V9Canada Plant Breeding Wageningen University&ResearchPlant Breeding6708 PB Wageningenthe Netherlands IBG-4 Bioinformatics Forschungszentrum JülichWilhelm Johnen Str52428 JülichGermany department of Plant Soiland Microbial SciencesMichigan State UniversityEast LansingMI 48824USA Bayer Crop Science WoodlandCA 95695USA Averis Seeds B.V. 9640 AA Veendamthe Netherlands International Potato Center 1895 Avenida La MolinaLimaPeru USDA-ARS ProsserWA 99350USA Agriculture and Agri-Food Canada Fredericton Research and development Centre FrederictonNB E3B 4Z7Canada School of Integrative Plant Science Cornell UniversityIthacaNY 14853-1901USA department of Plant Sciences University of IdahoMoscowID 83844USA USDA-ARS Small Grains and Potato Germplasm ResearchAberdeenID 83210USA HZPC Research B.V. Edisonweg 58501 XG Jourethe Netherlands department of Crop and Soil Science Oregon State UniversityHermistonOR 97838USA School of Biology and Ecology University of Maine5735 Hitchner Hall OronoME 04469USA department of Horticultural Sciences Texas A&M UniversityCollege StationTX 77843-2133USA department of Horticulture Oregon State UniversityCorvallisOR 97331USA department of Horticultural Science North Carolina State UniversityRaleighNC 27695-7609USA department of Horticulture University of Wisconsin-MadisonMadisonWI 53706USA department of Horticulture Michigan State UniversityEast LansingMI 48824USA Institute for Biological Data Science Heinrich Heine UniversityDusseldorf40225 DusseldorfGermany Plant Resilience Institute Michigan State UniversityEast LansingMI 48824USA Present address:GenNovation B.V. Wageningenthe Netherlands

Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous *** assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity,including altered coding and transcript sequences,preferential allele expression,and structural variation that collectively result in a highly complex transcriptome and predicted proteome,which are distributed across the homologous *** species contribute to the extensive allelic diversity in tetraploid cultivars,demonstrating ancestral introgressions predating modern breeding *** a clonally propagated autotetraploid that undergoes limited meiosis,dysfunctional and deleterious alleles are not purged in tetraploid *** a quarter of the loci bore mutations are predicted to have a high negative impact on protein function,complicating breeder’s efforts to reduce genetic *** StCDF1 locus controls maturity,and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent *** of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous,diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.

关键词： potato allele diversity phased assembly polyploid pan-genome wild introgressions

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Variations in Atmospheric Electromagnetism and Their Impacts on Mortality Rates in the Southern and Northeastern Regions of Brazil

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Atmospheric and Climate Sciences 2025年第1期15卷 248-274页

作者： Rose Ane Pereira de freitas Julio Renato Quevedo Marques Reynerth Pereira da Costa Júlia alves Menezes Isabela de Brito Ferreira Rhavena Barbosa dos Santos Ulisses Eugenio Cavalcanti Confalonieri department of Meteorology Federal University of Pelotas (UFPel) Pelotas Brazil National Observatory (ON) Ministry of Science Rio de Janeiro Brazil Laboratory of Analysis and development of Indicators for Sustainability (LADIS) Division of Impacts Adaptation and Vulnerability (DIIAV) National Institute for Space Research (INPE) So Jos dos Campos Brazil department of Parasitology Institute of Biological Sciences Federal University of Minas Gerais (UFMG) Belo Horizonte Brazil department of Nursing and Medicine Federal University of Viosa (UFV) Viosa Brazil department of Food Technology Federal Fluminense University (UFF) and Rene Rachou Institute Fiocruz Belo Horizonte Brazil

This study examines the relationship between geomagnetic indices and mortality rates from specific diseases in the Northeast (NE) and Southern (S) regions of Brazil from 1996 to 2020. Solar activity data, including the Ap and Sudden Ionospheric Disturbance (SID) indices, were sourced from the World Data Center, while mortality data were obtained from the Mortality Information System (SIM-DATASUS). Acute Myocardial Infarction (AMI) emerged as the leading cause of mortality, with average death rates of 60.4, 56.8, and 58.3 deaths per 100,000 inhabitants in Pernambuco (PE), Rio Grande do Sul (RS), and Paraná (PR), respectively. Temporal analysis revealed a consistent upward trend in AMI mortality across most states, except for Santa Catarina (SC). Seasonal patterns identified through Principal Component Analysis (PCA) demonstrated that geomagnetic and climatic indices influenced mortality differently across regions and seasons. The Ap geomagnetic index was strongly correlated with higher AMI mortality rates during summer, while the SID index showed greater relevance during winter. A dipole phenomenon was observed, with AMI deaths increasing alongside geomagnetic activity in the S region but showing an inverse relationship in the NE region. These findings highlight the significant influence of geomagnetic variations on public health, particularly cardiovascular mortality. The study underscores the need for further research into the biological mechanisms underlying these associations and recommends the development of early warning systems and targeted preventive measures to mitigate the potential health impacts of geomagnetic disturbances, especially for vulnerable populations.

关键词： Solar Activity Cardiovascular Mortality Geomagnetic Disturbances

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Is there a window of opportunity for the therapeutic use of vitamin D in multiple sclerosis?

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Neural Regeneration Research 2022年第9期17卷 1945-1954页

作者： Sofia fernanda Gonçalves Zorzella-Pezavento Luiza Ayumi Nishiyama Mimura Marina Bonifácio denadai William Danilo Fernandes de Souza Thais fernanda de Campos Fraga-Silva Alexandrina Sartori department of Chemical and Biological Sciences Institute of BiosciencesSão Paulo State University(UNESP)BotucatuSão PauloBrazil

Multiple sclerosis is an autoimmune treatable but not curable *** are a multiplicity of medications for multiple sclerosis therapy,including a class entitled disease-modifying drugs that are mainly indicated to reduce the number and severity of disease *** all patients respond well to these therapies,and minor to severe adverse effects have been *** D,called sunshine vitamin,is being studied as a possible light at the end of the *** this review,we recapitulated the similar immunopathogenesis of multiple sclerosis and experimental autoimmune encephalomyelitis,the immunomodulatory and neuroprotective potential of vitamin D and the state-of-art concerning its supplementation to multiple sclerosis ***,based on our and other groups’experimental findings,we analyzed the need to consider the relevance of the route and the different time-point administration aspects for a more rational indication of this vitamin to multiple sclerosis patients.

关键词： central nervous system cytokines experimental autoimmune encephalomyelitis immunomodulation immunopathogenesis inflammation multiple sclerosis neuroprotection regulatory T cells vitamin D

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Genotype-environment interaction in Cordia trichotoma(Vell.)Arrá*** *** in two different soil conditions

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Journal of Forestry Research 2022年第1期33卷 309-319页

作者： Wanderley dos Santos Bruno Marchetti de Souza Daniele fernanda Zulian Gilberto Terra Ribeiro alves João Bosco Vasconcellos Gomes Mário Luiz Teixeira de Moraes Valderês Aparecida de Sousa Ananda Virginia de Aguiar Faculdade de Engenharia de Ilha Solteira Universidade Estadual Paulista“Júlio Mesquita Filho”Ilha Solteira 15385-000Brazil Sucupira Agroflorestas Fazenda SucupiraValença 45400-000Brazil EMBRAPA Florestas Empresa Brasileira de Pesquisa AgropecuáriaColombo 83411-000Brazil

Investment in silvicultural techniques is noticeably lacking,especially in breeding programs for non-conventional wood *** genotype×environment interaction(G×E)is essential to the development of breeding ***,this study aimed to estimate genetic diversity of and the effects of G×E interaction on two progeny tests of Cordia trichotoma,including the estimation of genetic gain and genetic diversity after *** the experiment,30 progenies of *** were tested at two sites with differing soil *** at breast height(1.30 m above soil surface,dbh-cm),total height,diameter at 30 cm from the soil,first branch height,and survival were all monitored for four *** deviance,best linear unbiased estimator,and harmonic mean of relative performance of genetic values(MHPRVG)were all calculated to predict breeding values,estimate genetic parameters,and analyze *** quantified traits varied significantly among progenies by soil type,with greatest variation recorded for genetic *** of the progenies led to predictions of genetic gain,ranging from 7.73 to 15.45%,for dbh at four years of *** calculated decrease in genetic diversity after selection showed that this parameter should be monitored in subsequent breeding cycles.G×E was low for all *** best-performing progenies proved most stable and best adapted to the different environmental conditions tested.

关键词： Effective population number Native species Productivity Stability and adaptability Tree improvement

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Red deer as a disperser of native,but not invasive plants’seeds

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Integrative Zoology 2023年第5期18卷 859-866页

作者： fernanda GARCIA António alves DA SILVA Ruben HELENO JoséPaulo SOUSA Joana alves Centre for Functional Ecology(CFE) TERRA Associate LaboratoryDepartment of Life SciencesUniversity of CoimbraCoimbraPortugal

INTRODUCTION Seed dispersal is a key process in the life cycle of most plants,with ecological and evolutionary consequences that go beyond vegetation dynamics and cascade to entire ecosystem functioning and stability(Traveset et al.2014).Seed dispersal largely constrains plant recruitment and the distribution of future plant cohorts,thus playing a critical role in the restoration of disturbed sites(Cain et al.2000;Higgins et al.2003).It can also threaten plant diversity by facilitating plant invasions(Vavra et al.2007;Heleno 2020).

关键词： consequences disperse disturbed

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Mesenchymal stem cell-and extracellular vesicle-based therapies for Alzheimer's disease:progress,advantages,and challenges

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Neural Regeneration Research 2023年第8期18卷 1645-1651页

作者： Renata Guedes de Jesus Gonçalves Juliana Ferreira Vasques Almir Jordão da Silva-Junior fernanda Gubert Rosalia Mendez-Otero Instituto de Biofísica Carlos Chagas Filho Universidade Federal do Rio de JaneiroRio de JaneiroBrazil Instituto Nacional de Ciência e Tecnologia em Medicina Regenerativa Rio de JaneiroBrazil Plataformas Inovadoras em Terapias Avançadas Departamento de Ciência e Tecnologia-Ministério da Saúde(DECIT-MS)Conselho Nacional de Desenvolvimento Científico e Tecnológico(CNPq)Brazil Programa Redes de Pesquisa em Saúde no Estado do Rio de Janeiro Rio de JaneiroBrazil Instituto de Ciências Biomédicas Universidade Federal do Rio de JaneiroRio de JaneiroBrazil Programa Redes de Pesquisa em Nanotecnologia no Estado do Rio de Janeiro Rio de JaneiroBrazil

Alzheimer's disease is a severe, highly disabling neurodegenerative disease, clinically characterized by a progressive decline in cognitive functions, and is the most common form of dementia in the elderly. For decades, the search for disease-modifying therapies has focused on the two main Alzheimer's disease histopathological hallmarks, seeking to prevent, mitigate, or clear the formation of extracellular aggregates of β-amyloid peptide and intracellular neurofibrillary tangles of tau protein, although without clinical success. Mesenchymal stem cell-based therapy has emerged as a promising alternative for the treatment of Alzheimer's disease, especially because it also targets other crucial players in the pathogenesis of the disease, such as neuroinflammation, synaptic dysfunction/loss, oxidative stress, and impaired neurogenesis. Herein, we review current knowledge of the therapeutic potential of mesenchymal stem cells and their extracellular vesicles for Alzheimer's disease, discussing the most recent findings in both preclinical and clinical trials as well as how advanced technologies have helped to overcome some limitations and contributed to stimulate the development of more effective treatments.

关键词： Alzheimer's disease amyloid-β cell therapy cell transplantation exosomes extracellular vesicles mesenchymal stem cell micro vesicles neuroinflammation tau protein

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Incidence of hepatocellular carcinoma in outpatients with cirrhosis in Brazil: A 10-year retrospective cohort study

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World Journal of Gastroenterology 2016年第46期22卷 10219-10225页

作者： Marcelo Campos Appel-da-Silva Suelen Aparecida da Silva Miozzo Isabella de Azevedo Dossin Cristiane Valle Tovo fernanda Branco Angelo alves de Mattos Graduate Program:Hepatology Universidade Federal de Ciências da Saúde de Porto Alegre(UFCSPA)Porto AlegreRS 900150-170Brazil Ultrasound Imaging Servince Hospital Santa Casa de Porto AlegrePorto AlegreRS 90050-170Brazil

AIM To determine the incidence of hepatocellular carcinoma(HCC) and the impact of HCC surveillance on early diagnosis and survival of cirrhotic outpatients. METHODS In this retrospective cohort study, cirrhotic outpatients undergoing HCC surveillance between March 2005 and March 2014 were analyzed. Exclusion criteria were HIV coinfection; previous organ transplantation; diagnosis of HCC at first consultation; missing data in the medical chart; and less than 1 year of follow-up. Surveillance was carried out every six months using ultrasound and serum alpha-fetoprotein determination. Ten-year cumulative incidence and survival were estimated through Kaplan-Meier analysis. RESULTS Four hundred and fifty-three patients were enrolled, of which 57.6% were male. Mean age was 55 years. Hepatitis C virus and heavy use of alcohol were the main etiologic agents of cirrhosis. HCC was diagnosed in 75 patients(16.6%), with an estimated cumulative incidence of 2.6% in the 1st year, 15.4% in the 5th year, and 28.8% in the 10 th year. Median survival was estimated at 17.6 mo in HCC patients compared to 234 mo in non-HCC patients(P detected in patients who underwent surveillance every 6 mo or less(P = 0.05). However, survival was not different between patients with early stage vs non-early stage tumors [HR = 0.54(0.15-1.89), P = 0.33].CONCLUSION HCC is a frequent complication in patients with cirrhosis and adherence to surveillance programs favors early diagnosis.

关键词： Liver cirrhosis Hepatocellular carcinoma Epidemiology Surveillance Survival

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Diversity of the endophytic filamentous fungal leaf community at different development stages of eucalyptus

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Journal of Forestry Research 2019年第3期30卷 1093-1103页

作者： Paulo Sergio Balbino Miguel Fabio Balbino Miguel Bruno Coutinho Moreira Marcelo Nagem Valerio de Oliveira Julio Cesar delvaux fernanda de Souza freitas Arnaldo Chaer Borges Maurcio Dutra Costa departamento de Medicina e Enfermagem Universidade Federal de VicosaVicosaMinas Gerais 36570-000Brazil departamento de Quimica Universidade Federal de Juiz de ForaJuiz de ForaMinas Gerais 36036-300Brazil Colegiado de Engenharia Agronomica Universidade Federal do Vale do Sao FranciscoPetrolinaPernambuco 56300-990 Brazil departamento de Ciencias Basicas da Vida Campus Governador Valadares Universidade Federal de Juiz de Fora Governador ValadaresMinas Gerais 35012-140Brazil Coordenacao Geral de Ensino Pesquisa e Extensao Instituto Federal do Triangulo MineiroItuiutabaMinas Gerais 38035-200Brazil departamento de Microbiologia Instituto de Biotecnologia Aplicada aAgropecuariaUniversidade Federal de Vicosa VicosaMinas Gerais 36570-000Brazil

Fungal endophytic species inhabiting the leaves of eucalypts are capable of utilising leaf sugars and can influence both plant growth and health. Endophytic fungal symbionts can use simple soluble sugars in leaves as their main carbon source. This study set out to determine the diversity and distribution of the endophytic filamentous fungal leaf community in the hybrid Eucalyptus urograndis due to its economic importance. The fungal leaf community was characterised using denaturing gradient electrophoresis (DGGE) and correlated with levels of leaf nutrients and sugars throughout plant development. Sequencing of DGGE bands revealed the presence of Basidiomycota and Ascomycota phyla. Fourteen species and three genera of filamentous fungi were identified, and the population structure was affected by the plant developmental stage. Levels of K, Cu, N and Mn influenced communities from the clonal garden, whereas leaves in the field had higher glucose, fructose and sucrose. Many fungi were found to be specific to a certain development stages: Diplomitoporus crustulinus, Podosphaera tridactyla and Aspergillus restrictus to the clonal garden stage;Chaetomella acutiseta and Ascotricha chartarum to the shading stage;Erratomyces patelii and Saxomyces sp. to the shading output stage;Lepidostroma sp. and Saxomyces sp. to the dispatch stage;and Mycosphaerella populicola to the field stage. Teratosphaeria toledana and Teratosphaeria acidotherma were found at more than one developmental stage. Cladosporium sp. and Rhodosporidium fluviale colonized and persisted in plants at the dispatch and field stages. This is the first report of P. tridactyla, A. restrictus, E. patelii, Saxomyces and Lepidostroma sp. as endophytes in eucalipt.

关键词： Diversity 18S rRNA denaturing gradient electrophoresis(DGGE) Sequencing

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Effect of resistance training volume on body adiposity,metabolic risk,and inflammation in postmenopausal and older females:Systematic review and meta-analysis of randomized controlled trials

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Journal of Sport and Health Science 2024年第2期13卷 145-159页

作者： Paulo Ricardo Prado Nunes Pamela Castro-e-Souza Anselmo alves de Oliveira Bruno de freitas Camilo Gislaine Cristina-Souza Lucio Marques Vieira-Souza Marcelo Augusto da Silva Carneiro department of Body and Human Movement Minas Gerais State University(UEMG)37902-092 PassosMGBrazil University Center of Planalto de Araxa(UNIARAXA) 38180-129 AraxaMGBrazil Physical Activity Health and Ageing Research Group(GPASE)Minas Gerais State University(UEMG)37902-092 PassosMGBrazil Exercise and Nutrition Research Group(GPEN) Minas Gerais State University(UEMG)37902-092 PassosMGBrazil Sport Sciences and Physical Exercise Study and Research Group(GEPCEEX) Minas Gerais State University(UEMG)37902-092 PassosMGBrazil Metabolism Nutrition and Exercise LaboratoryPhysical Education and Sport CenterLondrina State University(UEL)86050-070 LondrinaPRBrazil Postgraduate Program in Physical Education Federal University of Sergipe(UFS)49107-230 Sao CristovaoSEBrazil

Purpose:This meta-analytical study aimed to explore the effects of resistance training(RT) volume on body adiposity,metabolic risk,and inflammation in postmenopausal and older ***:A systematic search was performed for randomized controlled trials in PubMed,Scopus,Web of Science,and *** controlled trials with postmenopausal and older females that compared RT effects on body adiposity,metabolic risk,and inflammation with a control group(CG) were *** reviewers selected the studies,extracted the data,and performed the risk of bias and certainty of the evidence(Grading of Recommendations,Assessment,development,and Evaluation(GRAde)) *** body and abdominal adiposity,blood lipids,glucose,and C-reactive protein were included for meta-analysis.A random-effects model,standardized mean difference(Hedges’ g),and 95% confidence interval(95%CI) were used for ***:Twenty randomized controlled trials(overall risk of bias:some concerns;GRAde:low to very low) with overweight/obese postmenopausal and older females were *** groups were divided into low-volume RT(LVRT,~44 sets/week) and high-volume RT(HVRT,~77 sets/week).Both RT groups presented improved body adiposity,metabolic risk,and inflammation when compared to ***,HVRT demonstrated higher effect sizes than LVRT for glucose(HVRT=-1.19;95%CI:-1.63 to-0.74;LVRT=-0.78;95%CI:-1.15 to-0.41) and C-reactive protein(HVRT=-1.00;95%CI:-1.32 to-0.67;LVRT=-0.34;95%CI,-0.63 to-0.04)) when compared to ***:Compared to CG,HVRT protocols elicit greater improvements in metabolic risk and inflammation outcomes than LVRT in overweight/obese postmenopausal and older females.

关键词： C-reactive protein Fat mass Lipid profile Menopause Strength training

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Gangliosides in nervous system development,regeneration,and pathologies

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Neural Regeneration Research 2023年第1期18卷 81-86页

作者： Juliana F.Vasques Renata Guedes de Jesus Gonçalves Almir Jordão da Silva-Junior Robertta Silva Martins fernanda Gubert Rosalia Mendez-Otero Instituto de Ciências Biomédicas Universidade Federal do Rio de JaneiroRio de JaneiroBrazil Instituto de Biofísica Carlos Chagas Filho Universidade Federal do Rio de JaneiroRio de JaneiroBrazil Programa Redes de Pesquisa em Saúde no Estado do Rio de Janeiro Rio de JaneiroBrazil Programa Rede NanoSaúde do Estado do Rio de Janeiro Rio de JaneiroBrazil Instituto Nacional de Ciência e Tecnologia em Medicina Regenerativa Rio de JaneiroBrazil

Gangliosides,sialic acid-containing sphingolipids,are major constituents of neuronal *** to the number of sialic acids and the structure of the oligosaccharide chain,gangliosides can be classified as simple or complex and grouped in different *** of gangliosides have been identified in vertebrate cells,with different expression patterns during development and related to several physiological processes,especially in the nervous *** GD3 and its O-acetylated form,9acGD3,are highly expressed in early developmental stages,GM1,GD1a,GD1b,and GT1b are the most abundant ganglioside species in the mature nervous *** in enzymes involved in ganglioside metabolism can lead to the accumulation of specific species,a condition termed gangliosidosis and usually marked by severe neurological *** in ganglioside levels have also been described in several neurodegenerative diseases,such as Alzheimer’s and Parkinson’*** this review,we summarized recent information about the roles of GD3,9acGD3,GM1,GD1a,GD1b,GT1b,and other ganglioside species in nervous system development and regeneration,as well as clinical trials evaluating possible therapeutic applications of these molecules.

关键词： 9acGD3 gangliosides GD1a GD1b GD3 glycolipids GM1 GM2 GM3 GM4 GT1b

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