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Extreme-phenotype GWAS unravels a complex nexus between apple(Malus domestica)red-flesh colour and internal flesh browning

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Fruit Research 2022年第1期2卷 110-123页

作者： Satish Kumar cecilia h.deng Claire Molloy Chris Kirk Blue Plunkett Kui Lin-Wang Andrew Allan Richard Espley The New Zealand Institute for Plant and Food Research Limited Hawke's Bay Research CentreHavelock North 4130New Zealand The New Zealand Institute for Plant and Food Research Limited Mount Albert Research CentreAuckland 1025New Zealand The New Zealand Institute for Plant and Food Research Limited Palmerston North Research CentrePalmerston North 4410New Zealand

The genetic link between apple red flesh(RF)coloration and the internal flesh browning disorder(FBD)is a major challenge when breeding high fruit quality RF apple cultivars.A genome-wide association study(GWAS)was conducted in a population of about 900 red-leaved seedlings to identify genomic regions and putative candidate genes using whole genome sequencing of the pools of extreme phenotypes(XP)for the RF colour coverage(using the weighted cortex index(WCI))and *** study identified novel genomic regions contributing to WCI and FBD variation in the red-leaved *** FBD-associated regions were enriched for genes regulating senescence,heat shock proteins,cytochrome P450,ascorbate metabolism and pectin methyl *** there were no significant regions in common for WCI and FBD,there were several genes(***85,MYB66,ethylene insensitive 3,DNAJ heat shock protein,WRKY7,and NAC42)enriched commonly between the genomic regions associated with these traits,potentially underpinning the genetic connection between WCI and *** of the differentially expressed genes between the R6:MdMYB10 and white-fleshed‘control’apples resided within the GWAS hotspot for WCI(*** synthase,UDP-Glycosyl transferase)and FBD(*** GTPase activating protein,lipoxygenase 1,phytoene synthase)–validating the XP-GWAS *** of several genes resided in the trait-associated genomic regions,suggesting that whole genome duplication plays an important role in the regulation of these *** genetic correlations between WCI and sensory traits were observed,and strategies to develop FBD-free high fruit quality RF cultivars are discussed.

关键词： cultivar breeding GWAS

The Gillenia trifoliata genome reveals dynamics correlated with growth and reproduction in Rosaceae

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horticulture Research 2021年第1期8卷 3144-3157页

作者： hilary S.Ireland Chen Wu cecilia h.deng Elena hilario Ali Saei Sylvia Erasmuson Ross N.Crowhurst Karine M.David Robert J.Schaffer David Chagn The New Zealand Institute for Plant and Food Research Ltd Private Bag 92196Auckland Mail CentreAuckland 1142New Zealand School of Biological Sciences The University of AucklandPrivate Bag 92019Auckland Mail CentreAuckland 1142New Zealand Genomics Aotearoa %Department of BiochemistryUniversity of OtagoPO Box 56Dunedin 9054New Zealand The New Zealand Institute for Plant and Food Research Ltd Private Bag 11600Palmerston North 4442New Zealand The New Zealand Institute for Plant and Food Research Ltd Private Bag 4704Christchurch Mail CentreChristchurch 8140New Zealand The New Zealand Institute for Plant and Food Research Ltd 55 Old Mill RoadRD 3Motueka 7198New Zealand

The Rosaceae family has striking phenotypic diversity and high syntenic *** trifoliata is sister species to the Maleae tribe of apple and~1000 other *** has many putative ancestral features,such as herb/sub-shrub habit,dry fruit-bearing and nine base *** coalescence of ancestral characters in a phylogenetically important species,positions Gillenia as a‘rosetta stone'for translational science within *** present genomic and phenological resources to facilitate the use of Gillenia for this *** Gillenia genome is the fi rst fully annotated chromosome-level assembly with an ancestral genome complement(x=9),and with it we developed an improved model of the Rosaceae ancestral *** and NAC gene family analyses revealed genome dynamics correlated with growth and reproduction and we demonstrate how Gillenia can be a negative control for studying fl eshy fruit development in Rosaceae.

关键词： Rosaceae dynamics striking

Unraveling a genetic roadmap for improved taste in the domesticated apple

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Molecular Plant 2021年第9期14卷 1454-1471页

作者： Liao Liao Weihan Zhang Bo Zhang Ting Fang Xiao-Fei Wang Yarning Cai Collins Ogutu Lei Gao Gang Chen Xiaoqing Nie Jinsheng Xu Quanyan Zhang Yiran Ren Jianqiang Yu Chukun Wang cecilia h.deng Baiquan Ma Beibei Zheng Chun-Xiang You Da-Gang hu Richard Espley Kui Lin-Wang Jia-Long Yao Andrew C.Allan Awais Khan Schuyler S.Korban Zhangjun Fei Ray Ming Yu-Jin hao Li Li Yuepeng han CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Hubei Hongshan LaboratoryWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhan 430074China Agricultural Bioinformatics Key Laboratory of hubei Province College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Center of Economic Botany Core Botanical GardensChinese Academy of SciencesWuhan 430074China University of Chinese Academy of Sciences 19A YuquanluBeijing 100049China College of horticulture Science and Engineering Shandong Agricultural UniversityTai-An 271018China Sino-African Joint Research Center Chinese Academy of SciencesWuhan 430074China The New Zealand Institute for Plant&Food Research Limited AucklandNew Zealand School of Biological Sciences University of AucklandPrivate Bag 92019Auckland 1142New Zealand Plant Pathology and Plant-Microbe Biology Section Cornell UniversityGenevaNY 14456USA Department of Natural Resources and Environmental Sciences University of Illinois at Urbana-ChampaignUrbanaIL 61801USA Boyce Thompson Institute Cornell UniversityIthacaNY 14853USA Department of Plant Biology University of Illinois at Urbana-ChampaignUrbanaIL 61801USA

Although taste is an important aspect of fruit quality, an understanding of its genetic control remains elusive in apple and other fruit crops. In this study, we conducted genomic sequence analysis of 497 Malus accessions and revealed erosion of genetic diversity caused by apple breeding and possible independent domestication events of dessert and cider apples. Signatures of selection for fruit acidity and size, but not for fruit sugar content, were detected during the processes of both domestication and improvement. Furthermore, we found that single mutations in major genes affecting fruit taste, including Ma1, MdTDT, and MdSOT2, dramatically decrease malate, citrate, and sorbitol accumulation, respectively, and correspond to important domestication events. Interestingly, Ma1 was identified to have pleiotropic effects on both organic acid content and sugar:acid ratio, suggesting that it plays a vital role in determining fruit taste. Fruit taste is unlikely to have been negatively affected by linkage drag associated with selection for larger fruit that resulted from the pyramiding of multiple genes with minor effects on fruit size. Collectively, our study provides new insights into the genetic basis of fruit quality and its evolutionary roadmap during apple domestication, pinpointing several candidate genes for genetic manipulation of fruit taste in apple.

关键词： apple fruit taste organic acids soluble sugars fruit size domestication

Identifying Malaria hotspots Regions in Ghana Using Bayesian Spatial and Spatiotemporal Models

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Infectious Diseases & Immunity 2024年第2期4卷 69-78页

作者： Abdul-Karim Iddrisu Dominic Otoo Gordon hinneh Yakubu Dekongmene Kanyiri Kanimam Yaaba Samuel cecilia Kubio Francis Balungnaa Dhari Veriegh Department of Mathematics and Statistics University of Energy and Natural ResourcesSunyani 233Ghana Department of Statistical Service Ghana Statistical ServiceBono RegionSunyani 233Ghana Department of Mathematics and ICT Gambaga College of EducationSunyani 233Ghana human Resources Division University of Energy and Natural ResourcesSunyani 233Ghana Department of Biological Science University of Energy and Natural ResourcesSunyani 233Ghana.

Background:Malaria remains a significant public health concern in Ghana,with varying risk levels across different geographical *** affects millions of people each year and imposes a substantial burden on the health care system and *** risk estimation and mapping are crucial for effectively allocating resources and implementing targeted interventions to identify regions with disease *** study aimed to identify regions exhibiting elevated malaria risk so that public health interventions can be implemented,and to identify malaria risk predictors that can be controlled as part of public health interventions for malaria ***:The data on laboratory-confirmed malaria cases from 2015 to 2021 were obtained from the Ghana health Service and Ghana Statistical *** studied the spatial and spatiotemporal patterns of the relative risk of malaria using Bayesian spatial and spatiotemporal *** malaria risk for each region was mapped to visually identify regions with malaria *** and heterogeneity of disease risks were established using correlated and uncorrelated structures via the conditional autoregressive and Gaussian models,*** estimates from the marginal posterior distribution were estimated within the Integrated Nested Laplace Approximation using the R ***:The spatial model indicated an increased risk of malaria in the North East,Bono East,Ahafo,Central,Upper West,Brong Ahafo,Ashanti,and Eastern *** spatiotemporal model results highlighted an elevated malaria risk in the North East,Upper West,Upper East,Savannah,Bono East,Central,Bono,and Ahafo *** spatial and spatiotemporal models identified the North East,Upper West,Bono East,Central,and Ahafo Regions as hotspots for malaria *** variations in risk were evident across regions(h=104.9,Phough climatic and economic factors influenced malaria infection,statistical significance was not

关键词： Malaria Disease hotspot Bayesian modeling Conditional auto-regressive Integrated Nested Laplace Approximation Spatial and spatiotemporal models

Macroalgal deep genomics illuminate multiple paths to aquatic,photosynthetic multicellularity

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Molecular Plant 2024年第5期17卷 747-771页

作者： David R.Nelson Alexandra Mystikou Ashish Jaiswal cecilia Rad-Menendez Michael J.Preston Frederik De Boever Diana C.El Assal Sarah Daakour Michael W.Lomas Jean-Claude Twizere David h.Green William C.Ratcliff Kourosh Salehi-Ashtiani Division of Science and Math New York University Abu DhabiAbu DhabiUAE Center for Genomics and Systems Biology(CGSB) New York University Abu DhabiAbu DhabiUAE Biotechnology Research Center Technology Innovation InstitutePO Box 9639Masdar CityAbu DhabiUAE Culture Collection of Algae and Protozoa Scottish Association for Marine ScienceObanScotlandUK National Center for Marine Algae and Microbiota Bigelow Laboratory for Ocean SciencesEast BoothbayMEUSA Laboratory of Viral Interactomes GIGA InstituteUniversity of LiegeLiegeBelgium School of Biological Sciences Georgia Institute of TechnologyAtlantaGAUSA

Macroalgae are multicellular,aquatic autotrophs that play vital roles in global climate maintenance and have diverse applications in biotechnology and eco-engineering,which are directly linked to their multicellularity ***,their genomic diversity and the evolutionary mechanisms underlying multicellularity in these organisms remain *** this study,we sequenced 110 macroalgal genomes from diverse climates and phyla,and identified key genomic features that distinguish them from their microalgal *** for cell adhesion,extracellular matrix formation,cell polarity,transport,and cell differentiation distinguish macroalgae from microalgae across all three major phyla,constituting conserved and unique gene sets supporting multicellular *** genes show phylum-and climate-specific expansions that may facilitate niche ***,our study reveals genetic determinants of convergent and divergent evolutionary trajectories that have shaped morphological diversity in macroalgae and provides genome-wide frameworks to understand photosynthetic multicellular evolution in aquatic environments.

关键词： macroalgae multicellularity comparative genomics evolution adhesome endogenous viral elements

Psychiatric comorbidities in epilepsy:population co-occurrence,genetic correlations and causal effects

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General Psychiatry 2024年第1期37卷 103-111页

作者： Viktor h Ahlqvist Christina Dardani Paul Madley-Dowd harriet Forbes Jessica Rast Caichen Zhong Renee M Gardner Christina Dalman Kristen Lyal cRAIG Newschaffer Torbjorn Tomson Michael Lundberg Daniel Berglind Neil M Davies Brian K Lee cecilia Magnusson Dheeraj Rai Department of Global Public health Karolinska InstitutetStockholmSweden Medical Research Council Integrative Epidemiology Unit Bristol Medical SchoolUniversity of BristolBristolUK Centre for Academic Mental health Population Health SciencesBristol Medical SchoolUniversity of BristolBristolUK Faculty of Epidemiology and Population health London School of Hygiene and Tropical MedicineLondonUK A.J.Drexel Autism Institute Drexel UniversityPhiladelphiaPAUSA Department of Epidemiology and Biostatistics School of Public HealthDrexel UniversityPhiladelphiaPAUSA College of health and human Development Pennsylvania State UniversityState CollegePAUSA Department of Clinical Neuroscience Karolinska InstitutetStockholmSweden Centre for Epidemiology and Community Medicine Region StockholmStockholmSweden K.G Jebsen Center for Genetic Epidemiology Department of Public Health and NursingNorwegian University of Science and TechnologyTrondheimNorway Division of Psychiatry University Collge LondonLondonUK Department of Statistical Sciences University Cllge LondonLondonK NIhR Biomedical Research Centre University of BristoBristolUK Avon and Wiltshire Partnership NHS Mental Health TrustBristolUK

Background Psychiatric comorbidities are common in patients with *** for the co-occurrence of psychiatric conditions and epilepsy remain poorly *** We aimed to triangulate the relationship between epilepsy and psychiatric conditions to determine the extent and possible origins of these *** Using nationwide Swedish health registries,we quantified the lifetime prevalence of psychiatric disorders in patients with *** then used summarydata from genome-wide association studies to investigate whether the identified observational associations could be attributed to a shared underlying genetic aetiology using cross-trait linkage disequilibrium score ***,we assessed the potential bidirectional relationships using two-sample Mendelian *** In a cohort of 7628495 individuals,we found that almost half of the 94435 individuals diagnosed with epilepsy were also diagnosed with a psychiatric condition in their lifetime(adjusted lifetime prevalence,44.09%;95%confidence interval(Cl)43.78%to 44.39%).We found evidence for a genetic correlation between epilepsy and some neurodevelopmental and psychiatric *** example,we observed a genetic correlation between epilepsy and attention-deficit/hyperactivity disorder(r,=0.18,95%Cl 0.09 to 0.27,phat was more pronounced in focal epilepsy(r=0.23,95%CI 0.09 to 0.36,phiatric *** Psychiatric comorbidities are common in patients with *** correlations may partially explain some comorbidities;however,there is little evidence of a bidirectional relationship between the genetic liability of epilepsy and psychiatric *** findings highlight the need to understand the role of environmental factors or rare genetic variations in the origins of psy

关键词： epilepsy Psychiat lifetime

histopathological Patterns and Early Postoperative Complications among Patients with Surgically Treated Thyroid Diseases at Bugando Medical Centre, Mwanza, Tanzania

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International Journal of Otolaryngology and head & Neck Surgery 2024年第2期13卷 103-119页

作者： Adam Sijaona Olivia M. Kimario Samson E. Kichiba Gustave Buname Fidelis Mbunda Rodrick h. Kabangira cecilia Protas Department of Otorhinolaryngology Head & Neck Surgery Catholic University of Health and Allied Sciences Mwanza Tanzania Department of Internal Medicine Kamanga Medics Zonal Referral Hospital Mwanza Tanzania Department of Otorhinolaryngology Head & Neck Surgery Bugando Medical Centre Mwanza Tanzania

Background: Thyroid diseases are among the leading endocrine disorders affecting a large proportion of people worldwide and show geographical variation in incidence and histopathological pattern related to age, sex, dietary and environmental factors. histopathological patterns of surgically treated thyroid diseases play an important role in early diagnosis and management of these diseases. There is, however, limited published data regarding histopathological reports on thyroid disease in our local setting. This study aimed to determine the histopathological patterns and highlight early postoperative complications among patients with surgically treated thyroid diseases at Bugando Medical Centre (BMC). Methods: This was a longitudinal study involving all patients with surgically treated thyroid diseases seen at BMC over a period of 6 months from October 2019 to March 2020. Results: A total of 84 patients were studied. Females outnumbered males by a female to male ratio of 11:1. The median age of patients was 44 [IQR, 35 - 54] years old, the youngest was 14 years old and the oldest was 76 years old. Colloid goiter was the most common non-neoplastic lesion accounting for 34 (44.7%) patients. Among the neoplastic lesions, follicular adenoma was the most commonly encountered benign pathologies (n = 16;21.1%), while papillary carcinoma was the most commonly encountered malignancy (n = 4;50%). Following thyroidectomy, 12 (14.3%) patients developed early complications, of which hemorrhage sometimes requiring blood transfusion was the leading intra/postoperative complications accounting for 4 (33.3%) patients. Other complications include temporary recurrent laryngeal nerve palsy 2 (16.7%), surgical site infection 2 (16.7%) and tracheomalacia, bronchospasm, thyroid abscess and respiratory obstruction in 1 (8.3%) patient each, respectively. In this study, malignant thyroid lesion (p Conclusion: This study demonstrated that colloid goiter was the most common non-neoplastic lesio

关键词： Thyroid Diseases histopathological Patterns Early Postoperative Complications Tanzania

Circulating extracellular vesicles:friends and foes in neurodegeneration

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Neural Regeneration Research 2022年第3期17卷 534-542页

作者： Anna Picca Flora Guerra Riccardo Calvani hélio JoséCoelho-Junior cecilia Bucci Emanuele Marzetti Fondazione Policlinico Universitario“Agostino Gemelli”IRCCS RomeItaly Aging Research Center Department of NeurobiologyCare Sciences and SocietyKarolinska Institutet and Stockholm UniversityStockholmSweden Department of Biological and Environmental Sciences and Technologies Universitàdel SalentoLecceItaly UniversitàCattolica del Sacro Cuore Institute of Internal Medicine and GeriatricsRomeItaly

Extracellular vesicles have been identified as pivotal mediators of intercellular communication with critical roles in physiological and pathological *** this route,several molecules(e.g.,nucleic acids,proteins,metabolites) can be transferred to proximal and distant targets to convey specific *** vesicle-associated cargo molecules have been proposed as markers of several disease conditions for their potential of tracking down the generating ***,circulating extracellular vesicles may represent biomarkers of dysfunctional cellular quality control systems especially in conditions characterized by the accrual of intracellular misfolded ***,the identification of extracellular vesicles as tools for the delivery of nucleic acids or other cargo molecules to diseased tissues makes these circulating shuttles possible targets for therapeutic *** increasing interest in the study of extracellular vesicles as biomarkers resides mainly in the fact that the identification of peripheral levels of extracellular vesicle-associated proteins might reflect molecular events occurring in hardly accessible tissues,such as the brain,thereby serving as a "brain liquid biopsy".The exploitation of extracellular vesicles for diagnostic and therapeutic purposed might offer unprecedented opportunities to develop personalized ***,we discuss the bright and dark sides of extracellular vesicles in the setting of two main neurodegenerative diseases(i.e.,Parkinson's and Alzheimer's diseases).A special focus will be placed on the possibility of using extracellular vesicles as biomarkers for the two conditions to enable disease tracking and treatment monitoring.

关键词： Alzheimer's disease amyloid protein exosomes misfolded proteins mitochondrial-derived vesicles neuroinflammation Parkinson's disease quality control Tau protein α-synuclein

Epidemiology and risk factors for mortality in critically ill patients with pancreatic infection

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Journal of Intensive Medicine 2024年第1期4卷 81-93页

作者： Marie Dejonckheere Massimo Antonelli Kostoula Arvaniti Koen Blot Ben CreaghBrown Dylan Wde Lange Jan De Waele Mieke Deschepper Yalim Dikmen George Dimopoulos Christian Eckmann Guy Francois Massimo Girardis Despoina Koulenti Sonia Labeau Jeffrey Lipman Fernando Lipovestky Emilio Maseda Philippe Montravers Adam Mikstacki JoseArtur Paiva cecilia Pereyra Jordi Rello JeanFrancois Timsit Dirk Vogelaers Stijn Blot the Abdominal Sepsis Study(AbSeS)group on behalf of the Trials Group of the European Society of Intensive Care Medicine Department of Internal Medicine and Pediatrics Faculty of Medicine and Health SciencesGhent UniversityGhentBelgium Department of Anesthesiology Intensive Care and Emergency MedicineFondazione Policlinico Universitario A.Gemelli IRCCSRomeItaly UniversitàCattolica del Sacro Cuore RomeItaly Intensive Care Unit Papageorgiou University Affiliated HospitalThessaloníkiGreece Department of Epidemiology and Public health SciensanoIxellesBelgium Surrey Perioperative Anaesthetic Critical Care Collaborative Research Group(SPACeR) Royal Surrey County HospitalGuildfordUK Department of Clinical and Experimental Medicine University of SurreyGuildfordUK Department of Intensive Care Medicine University Medical Center UtrechtUniversity UtrechtUtrechtthe Netherlands Department of Intensive Care Medicine Ghent University HospitalGhentBelgium Data Science Institute Ghent University HospitalGhentBelgium Department of Anesthesiology and Reanimation Cerrahpasa School of MedicineIstanbul University-CerrahpasaIstanbulTurkey rd Department of Critical Care “EVGENIDIO”HospitalNational and Kapodistrian University of AthensAthensGreece Department of General Visceral and Thoracic SurgeryKlinikum Hannoversch-MuendenGoettingen UniversityGöttingenGermany Division of Scientific Affairs-Research European Society of Intensive Care MedicineBrusselsBelgium Anesthesia and Intensive Care Department University Hospital of ModenaModenaItaly UQ Centre for Clinical Research Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia nd Critical Care Department Attikon University HospitalAthensGreece Department of Nursing Faculty of EducationHealth and Social WorkUniversity College GhentGhentBelgium Jamieson Trauma Institute The University of QueenslandBrisbaneQLDAustralia Nimes University hospital University of MontpellierNimesFrance Critical Care Department Hospital of the Interamerican Open University(UAI)Buenos AiresArgentina Surgical Critical Care Department of AnesthesiaHospital Universitario

Background:The AbSeS-classification defines specific phenotypes of patients with intra-abdominal infection based on the(1)setting of infection onset(community-acquired,early onset,or late-onset hospital-acquired),(2)presence or absence of either localized or diffuse peritonitis,and(3)severity of disease expression(infection,sepsis,or septic shock).This classification system demonstrated reliable risk stratification in intensive care unit(ICU)patients with intra-abdominal *** study aimed to describe the epidemiology of ICU patients with pancreatic infection and assess the relationship between the components of the AbSeS-classification and ***:This was a secondary analysis of an international observational study(“AbSeS”)investigating ICU patients with intra-abdominal *** patients with pancreatic infection were included in this analysis(n=165).Mortality was defined as ICU mortality within 28 days of observation for patients discharged earlier from the *** with mortality were assessed using logistic regression analysis and reported as odds ratio(OR)and 95%confidence interval(CI).Results:The overall mortality was 35.2%(n=58).The independent risk factors for mortality included older age(OR=1.03,95%CI:1.0 to 1.1 P=0.023),localized peritonitis(OR=4.4,95%CI:1.4 to 13.9 P=0.011),and persistent signs of inflammation at day 7(OR=9.5,95%CI:3.8 to 23.9,Phe implementation of additional source control interventions within the first week(OR=4.0,95%CI:1.3 to 12.2,P=0.013).Gramnegative bacteria were most frequently isolated(n=58,49.2%)without clinically relevant differences in microbial etiology between survivors and ***:In pancreatic infection,a challenging source/damage control and ongoing pancreatic inflammation appear to be the strongest contributors to an unfavorable short-term *** this limited series,essentials of the AbSeS-classification,such as the setting of infection onset,diffuse

关键词： Pancreatic infection Intensive care unit Mortality Intra-abdominal infection Sepsis