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Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

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Horticulture Research 2023年第11期10卷 96-105页

作者： Alan E.Yocca adrian Platts Elizabeth Alger Scott Teresi Molla F.Mengist Juliana Benevenuto Luis Felipe V.Ferrão MacKenzie Jacobs Michal Babinski Maria Magallanes-Lundback Philipp Bayer Agnieszka Golicz Jodi L.Humann Dorrie Main Richard V.Espley David Chagné Nick w.Albert Sara Montanari Nicholi Vorsa James Polashock Luis Díaz-Garcia Juan Zalapa Nahla V.Bassil Patricio R.Munoz Massimo Iorizzo Patrick P.Edger Department of Horticulture Michigan State UniversityEast LansingMI48824United States Department of Plant Biology Michigan State UniversityEast LansingMI48824United States Genetics and Genome Sciences Michigan State UniversityEast LansingMI48824United States Plants for Human Health Institute North Carolina State UniversityKannapolisNC United States Horticultural Sciences Department University of FloridaGainesvilleFL 32611United States Department of Biochemistry and Molecular Biology Michigan State UniversityEast LansingMI48824United States University of western Australia Perth 6009 Australia Justus Liebig University Giessen35390 Germany Department of Horticulture Washington State UniversityPullmanWA99163United States The New Zealand Institute for Plant and Food Research Limited(PFR) AucklandNew Zealand The New Zealand Institute for Plant and Food Research Limited(PFR) PalmerstonNew Zealand The New Zealand Institute for Plant and Food Research Limited(PFR) MotuekaNew Zealand SEBS Plant BiologyRutgers UniversityNew Brunswick NJ 01019 United States Department of Viticulture and Enology University of CaliforniaDavisDavisCA 95616United States National Clonal Germplasm Repository USDA-ARSCorvallisOR 97333United States Department of Horticulture North Carolina State UniversityKannapolisNC United States MSU AgBioResearch Michigan State UniversityEast LansingMI48824United States

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s,respectively,and in part owing to their f lavors and health-promoting benefits are now cultivated and consumed *** industry continues to face a wide variety of production challenges(*** pressures),as well as a demand for higher-yielding cultivars with improved fruit quality ***,molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value ***,we describe the construction and analysis of the first pangenome for both blueberry and *** analysis of these pangenomes revealed both crops exhibit great genetic diversity,including the presence-absence variation of 48.4%genes in highbush blueberry and 47.0%genes in *** genes,those not shared by all cultivars,are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites,including compounds previously associated with improving fruit quality *** discovery of thousands of genes,not present in the previous reference genomes for blueberry and cranberry,will serve as the basis of future research and as potential targets for future breeding *** pangenome,as a multiple-sequence alignment,as well as individual annotated genomes,are publicly available for analysis on the Genome Database for Vaccinium-a curated and integrated web-based relational ***,the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

关键词： breeding cultivar crops

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成功控制禽球虫病的挑战

国外畜牧学（猪与禽） 2008年第4期28卷 13-17页

作者：文豪（译）缪德年（校） Martin w. Shirley adrian L. Smith Damer P. Blake 不详英国动物健康研究所分子寄生虫学研究室英国动物健康研究所肠道免疫学组

艾美尔球虫以宿主特异性的方式感染家畜,是引起球虫病的病原体。艾美尔球虫的控制是必要的。目前主要的控制方法是化学疗法,而用由活野毒株或弱毒虫株制成的疫苗进行免疫预防则呈流行趋势。新一代的亚单位疫苗、活载体疫苗和DNA疫苗正... 详细信息

艾美尔球虫以宿主特异性的方式感染家畜,是引起球虫病的病原体。艾美尔球虫的控制是必要的。目前主要的控制方法是化学疗法,而用由活野毒株或弱毒虫株制成的疫苗进行免疫预防则呈流行趋势。新一代的亚单位疫苗、活载体疫苗和DNA疫苗正在研究之中,而合适抗原的鉴定是仍需要解决的难题。本文简述了过去和当前控制球虫病的方法,及一种鉴定作为候选疫苗免疫保护性抗原的新方法。

关键词：艾美尔球虫控制疫苗遗传图谱抗原鉴定

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Author Correction: A machine learning enabled hybrid optimization framework for efficient coarse-graining of a model polymer

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npj Computational Materials 2023年第1期9卷 203-203页

作者： Zakiya Shireen Hansani weeratunge adrian Menzel Andrew w.Phillips Ronald G.Larson Kate Smith-Miles Elnaz Hajizadeh The University of Melbourne Department of Mechanical Engineering Faculty of Engineering and Information Technology Melbourne Australia (GRID:grid.1008.9) (ISNI:0000 0001 2179 088X) Defence Science and Technology Group Platforms Division Melbourne Australia (GRID:grid.431245.5) (ISNI:0000 0004 0385 5290) University of Michigan Department of Chemical Engineering Ann Arbor USA (GRID:grid.214458.e) (ISNI:0000 0004 1936 7347) The University of Melbourne School of Mathematics and Statistics Melbourne Australia (GRID:grid.1008.9) (ISNI:0000 0001 2179 088X)

Correction to:npj Computational Materials https://***/10.1038/s41524-022-00914-4,published online 04 November 2022 The original version of this Article omitted some contributions in the Author Contributions section and incorrectly read[H.w.:Formal analysis,data visualization,review and editing.]The correct Author Contributions should read:[H.w.:Conceptua-lisation,formal analysis,data visualisation,writing,review and editing;*** *** equally to the conduct of the research and preparation of the manuscript.]This has now been corrected in both the PDF and HTML versions of the Article.

关键词： optimization formal grain

Imaging of liver cancer

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world Journal of Gastroenterology 2009年第11期15卷 1289-1300页

作者： Ben Ariff Claire R Lloyd Sameer Khan Mohamed Shariff Andrew V Thillainayagam Devinder S Bansi Shahid A Khan Simon D Taylor-Robinson adrian KP Lim Department of Imaging Imperial College Healthcare NHS Trust Charing Cross Hospital Campus Fulham Palace Road London W6 8RF United Kingdom Department of Hepatology and Gastroenterology Division of Medicine Imperial College London St Mary's Hospital Campus South Wharf Road London W2 1NY United Kingdom

Improvements in imaging technology allow exploitation of the dual blood supply of the liver to aid in the identif ication and characterisation of both malignant and benign liver lesions. Imaging techniques available include contrast enhanced ultrasound, computed tomography and magnetic resonance imaging. This review discusses the application of several imaging techniques in the diagnosis and staging of both hepatocellular carcinoma and cholangiocarcinoma and outlines certain characteristics of benign liver lesions. The advantages of each imaging technique are highlighted, while underscoring the potential pitfalls and limitations of each imaging modality.

关键词： Hepatic cell carcinoma Cholangiocarcinoma Contrast enhanced ultrasound Computed tomography Magnetic resonance imaging

Application of single and combination therapy of clarithromycin and tamoxifen to suppress breast cancer cell proliferation and metabolism

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中华乳腺病杂志（电子版） 2012年第1期6卷 26-31页

作者： wings T.Y.Loo Louis w.C.Chow adrian Y.S Yip Mary N.B.Cheung UNIMED Medical Institute Organization for Oncology and Translational Research Hong Kong Organization for Oncology and Translational Research School of Chinese Medicine Li Ka Shing Faculty of MedicineUniversity of Hong Kong Clinical Trial Center Li Ka Shing Faculty of MedicineUniversity of Hong Kong

Objective This study compares the anti-tumor effects of single and combination use of clarithromycin and tamoxifen on estrogen receptor (ER) positive breast cancer cell lines,BT-483 and MCF-7 as well as triple negative cell line,MBA-MD-231,which acts as a negative *** effect of solid breast tumor inhibition by clarithromycin is also *** BT-483,MCF-7 and MBA-MD-231 were cultured in 6-well plates in a 37 ℃ humidified incubator without CO2 for 24 h prior to the addition of the test *** test groups were clarithromycin (Group 1),tamoxifen (Group 2),clarithromycin and tamoxifen (Group 3),and control (Group 4).Group 3 was prepared in 1 to 1 ratio at a concentration of 1.5 mmol/L clarithromycin and 25 μmol/L *** the other hand,1 mm3 solid breast tumors were submerged into various groups as above for 24 *** the harvest day,the proliferation of cancer cells and solid breast tumor samples were measured by wST-1 proliferation reagent while ATP bioluminescence assay was employed to measure the metabolic rate of the three cell *** The proliferation of BT-483 and MCF-7 was suppressed most by combination use of clarithromycin and tamoxifen with statistical *** two drugs did not have an inhibitory effect on the hormonal negative cancer *** solid breast tumor samples,all the test groups showed reduced metabolic rate as compared with the control group (Pwhile single use of clarithromycin effectively inhibits the proliferation of solid breast tumor.

关键词：摘要编辑部编辑工作读者

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Inhibition of N-Myc down regulated gene 1 in in vitro cultured human glioblastoma cells

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world Journal of Clinical Oncology 2012年第7期3卷 104-110页

作者： Harun M Said Buelent Polat Susanne Stein Mathias Guckenberger Carsten Hagemann adrian Staab Astrid Katzer Jelena Anacker Michael Flentje Dirk Vordermark Department of Radiation Oncology University of Wuerzburg 97080 Würzburg Germany Department of Hematology and Oncology Johannes Gutenberg University Ⅲ Medical School 55101 Mainz Germany Department of Neurosurgery Tumorbiology Laboratory University of Wuerzburg 97080 Würzburg Germany Department of Radiation Oncology Paul Scherer Institute CH-5100 Villingen Switzerland Department of Gynaecology and Obstetrics University of Wuerzburg 97080 Würzburg Germany Department of Radiation Oncology University-Halle-Wittenberg 06110 Halle Germany

AIM: To study short ds RNA oligonucleotides(si RNA)as a potent tool for artificially modulating gene expression of N-Myc down regulated gene 1(NDRG1) gene induced under different physiological conditions(Normoxia and hypoxia) modulating NDRG1 transcription, m RNA stability and translation. METHODS: A cell line established from a patient with glioblastoma multiforme. Plasmid DNA for transfections was prepared with the Endofree Plasmid Maxi kit. From plates containing 5 × 107 cells, nuclear extracts were prepared according to previous protocols. The p SUPERNDRG1 vectors were designed, two sequences were selected from the human NDRG1 c DNA(5'-GCATTATTGGCATGGGAAC-3' and 5'-ATGCAGAGTAACGTGGAAG-3'. reverse transcription polymerase chain reaction was performed using primers designed using published information on β-actin and hypoxia-inducible factor(HIF)-1α m RNA sequences in Gen Bank. NDRG1 m RNA and protein level expression results under different conditions of hypoxia or reoxygenation were compared to aerobic control conditions using the Mann-whitney U test. Reoxygenation values were also compared to the NDRG1 levels after 24 h of hypoxia(P was considered significant).RESULTS: si RNA- and iodoacetate(IAA)-mediated downregulation of NDRG1 m RNA and protein expression in vitro in human glioblastoma cell lines showed a nearly complete inhibition of NDRG1 expression when compared to the results obtained due to the inhibitory role of glycolysis inhibitor IAA. Hypoxia responsive elements bound by nuclear HIF-1 in human glioblastoma cells in vitro under different oxygenation conditions and the clearly enhanced binding of nuclear extracts from glioblastoma cell samples exposed to extreme hypoxic conditions confirmed the HIF-1 western blotting results. CONCLUSION: NDRG1 represents an additional diagnostic marker for brain tumor detection, due to the role of hypoxia in regulating this gene, and it canrepresent a potential target for tumor treatment in human glioblastoma. T

关键词： N-Myc down regulated gene 1 Short dsRNA oligonucleotides Human cancer diseases Brain cancer Radiotherapy

Disruption of splicing-regulatory elements using CRISPR/Cas9 to rescue spinal muscular atrophy in human iPSCs and mice

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National Science Review 2020年第1期7卷 92-101页

作者： Jin-Jing Li Xiang Lin Cheng Tang Ying-Qian Lu Xinde Hu Erwei Zuo He Li wenqin Ying Yidi Sun Lu-Lu Lai Hai-Zhu Chen Xin-Xin Guo Qi-Jie Zhang Shuang wu Changyang Zhou Xiaowen Shen Qifang wang Min-Ting Lin Li-Xiang Ma Ning wang adrian R.Krainer Linyu Shi Hui Yang wan-Jin Chen Department of Neurology and Institute of Neurology The First Affiliated Hospital of Fujian Medical University Fujian Key Laboratory of Molecular Neurology Fujian Medical University Institute of Neuroscience State Key Laboratory of Neuroscience Key Laboratory of Primate Neurobiology CAS Center for Excellence in Brain Science and Intelligence Technology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Key Lab of Computational Biology CAS-MPG Partner Institute for Computational Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Department of Anatomy Histology & Embryology Shanghai Medical College Fudan University Cold Spring Harbor Laboratory Cold Spring Harbor

we here report a genome-editing strategy to correct spinal muscular atrophy(SMA). Rather than directly targeting the pathogenic exonic mutations, our strategy employed Cas9 and guide-sg RNA for the targeted disruption of intronic splicing-regulatory elements. we disrupted intronic splicing silencers(ISSs, including ISS-N1 and ISS + 100) of survival motor neuron(SMN) 2, a key modifier gene of SMA, to enhance exon 7 inclusion and full-length SMN expression in SMA iPSCs. Survival of splicing-corrected iPSC-derived motor neurons was rescued with SMN restoration. Furthermore, co-injection of Cas9 mRNA from Streptococcus pyogenes(SpCas9) or Cas9 from Staphylococcus aureus(SaCas9) alongside their corresponding sgRNAs targeting ISS-N1 into zygotes rescued 56% and 100% of severe SMA transgenic mice(Smn-/-, SMN2tg/-).The median survival of the resulting mice was extended to >400 days. Collectively, our study provides proof-of-principle for a new strategy to therapeutically intervene in SMA and other RNA-splicing-related diseases.

关键词： spinal muscular atrophy SMN2 splicing-regulatory elements CRISPR/Cas9 germline correction

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分子育种提高甜菜抗病性(续完)

中国甜菜糖业 2008年第2期 23-26页

作者：张春来徐德昌姜孝成周岩张春香 Nigel w．Scott Malcolm C．Elliott adrian Slater Norman Borlaug Institute for Plant Science Research De Montfort University Leicester UK 哈尔滨工业大学糖业研究院黑龙江哈尔滨150090 中国农业科学院甜菜研究所、黑龙江大学农作物研究院黑龙江哈尔滨150080 河南科技学院生物工程系河南新乡453003

通过国内外在分子育种水平上对甜菜多种病害抗病性研究的分析和总结,综述了国内外分子育种方面提高甜菜抗病性的研究进展。

关键词：甜菜分子育种提高抗病性

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Disrupted Ca^(2+) h homeostasis and immunodeficiency in patients with functional IP_(3) receptor subtype 3 defects

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Cellular & Molecular Immunology 2023年第1期20卷 11-25页

作者： Julika Neumann Erika Van Nieuwenhove Lara E.Terry Frederik Staels Taylor R.Knebel Kirsten welkenhuyzen Kourosh Ahmadzadeh Mariah R.Baker Margaux Gerbaux Mathijs willemsen John S.Barber Irina I.Serysheva Liesbeth De waele François Vermeulen Susan Schlenner Isabelle Meyts David IYule Geert Bultynck Rik Schrijvers Stephanie Humblet-Baron adrian Liston VIB Center for Brain and Disease Research LeuvenBelgium Department of Microbiology and Immunology KU LeuvenLeuvenBelgium UZ Leuven LeuvenBelgium Department of Pharmacology and Physiology University of RochesterRochesterNY14526USA Laboratory of Molecular and Cellular Signaling Department of Cellular and Molecular MedicineLeuven KankerinstituutKU LeuvenLeuvenBelgium Laboratory of Immunobiology Department Microbiology and ImmunologyRega InstituteKU LeuvenLeuvenBelgium Department of Biochemistry and Molecular Biology Structural Biology Imaging CenterMcGovern Medical School at The University of Texas Health Science Center at HoustonHoustonTX77030USA Pediatric Department Academic Children Hospital Queen FabiolaUniversitéLibre de BruxellesBrusselsBelgium Department of Pediatric Neurology University Hospitals LeuvenLeuvenBelgium Department of Pulmonology University Hospitals LeuvenLeuvenBelgium Laboratory for Inborn Errors of Immunity Department of Immunology and MicrobiologyKU LeuvenLeuvenBelgium Laboratory for Allergy and Clinical Immunology and Immunogenetics Research Group Department of MicrobiologyImmunology and TransplantationKU LeuvenLeuvenBelgium Immunology Programme The Babraham InstituteBabraham Research CampusCambridgeCB223ATUK

Calcium signaling is essential for lymphocyte activation, with genetic disruptions of store-operated calcium (Ca^(2+)) entry resulting in severe immunodeficiency. The inositol 1,4,5-trisphosphate receptor (IP_(3)R), a homo- or heterotetramer of the IP_(3)R1-3 isoforms, amplifies lymphocyte signaling by releasing Ca^(2+) from endoplasmic reticulum stores following antigen stimulation. Although knockout of all IP_(3)R isoforms in mice causes immunodeficiency, the seeming redundancy of the isoforms is thought to explain the absence of variants in human immunodeficiency. In this study, we identified compound heterozygous variants of ITPR3 (a gene encoding IP_(3)R subtype 3) in two unrelated Caucasian patients presenting with immunodeficiency. To determine whether ITPR3 variants act in a nonredundant manner and disrupt human immune responses, we characterized the Ca^(2+) signaling capacity, the lymphocyte response, and the clinical phenotype of these patients. we observed disrupted Ca^(2+) signaling in patient-derived fibroblasts and immune cells, with abnormal proliferation and activation responses following T-cell receptor stimulation. Reconstitution of IP_(3)R3 in IP_(3)R knockout cell lines led to the identification of variants as functional hypomorphs that showed reduced ability to discriminate between homeostatic and induced states, validating a genotype–phenotype link. These results demonstrate a functional link between defective endoplasmic reticulum Ca^(2+) channels and immunodeficiency and identify IP_(3)Rs as diagnostic targets for patients with specific inborn errors of immunity. These results also extend the known cause of Ca^(2+)-associated immunodeficiency from store-operated entry to impaired Ca^(2+) mobilization from the endoplasmic reticulum, revealing a broad sensitivity of lymphocytes to genetic defects in Ca^(2+) signaling.

关键词： Primary immunodeficiency Calcium signalling whole exome sequencing