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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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Protein-activated atomic layer deposition for robust crude-oil-repellent hierarchical nano-armored membranes

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Science bulletin 2024年第2期69卷 218-226页

作者： Xiaobin Yang Pan Sun Yajie Wen Anil U.Mane jeffrey W.Elam Jun Ma Shaomin Liu Seth b.Darling Lu Shao MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage State Key Laboratory of Urban Water Resource and EnvironmentSchool of Chemistry and Chemical EngineeringHarbin Institute of TechnologyHarbin 150001China Chemical Sciences and Engineering Division Argonne National LaboratoryLemont IL 60439USA Applied Materials Division Argonne National LaboratoryLemont IL 60439USA Advanced Materials for Energy-Water Systems Energy Frontier Research Center Argonne National LaboratoryLemont IL 60439USA Pritzker School of Molecular Engineering University of ChicagoChicago IL 60637USA Department of Physics University of Ilinois at ChicagoChicago IL 60607USA School of Environment Harbin Institute of TechnologyHarbin 150090China WA School of Mines:Minerals Energy and Chemical EngineeringCurtin UniversityPerth WA 6845Australia

Atomic layer deposition(ALD)offers unique capabilities to fabricate atomically engineered porous materials with precise pore tuning and multi-functionalization for diverse applications like advanced membrane separations towards sustainable energy-water ***,current ALD technique is inhibited on most non-polar polymeric membranes due to lack of accessible nucleation ***,we report a facile method to efficiently promote ALD coating on hydrophobic surface of polymeric membranes via novel protein activation/*** a proof of concept,TiO2 ALD-coated membranes activated by bovine serum albumin exhibit remarkable superhydrophilicity,ultralow underwater crude oil adhesion,and robust tolerance to rigorous environments including acid,alkali,saline,and *** importantly,excellent cyclable crude oil-in-water emulsion separation performance can be *** mechanism for activation/sensitization is rooted in reactivity for a particular set of amino ***,the universality of protein-sensitized ALD is demonstrated using common egg white,promising numerous potential usages in biomedical engineering,environmental remediation,lowcarbon manufacturing,catalysis,and beyond.

关键词： Membrane separation Atomic layer deposition Water treatment Antifouling

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Storylines of family medicine Ⅰ:framing family medicine–history,values and perspectives

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Family Medicine and Community Health 2024年第S3期12卷 2-11页

作者： William b Ventres Leslie A Stone Kathleen T Rowland Richard H Streiffer Michael D Macechko Julia A Roulier jeffrey M borkan Larry A Green Family and Preventive Medicine University of Arkansas for Medical Sciences College of MedicineLittle RockArkansasUSA Family and Preventive Medicine Rush Medical College of Rush UniversityChicagoIllinoisUSA College of Community Health Sciences University of AlabamaTuscaloosaAlabamaUSA UAMS Northwest Regional Campus Family Medicine Residency Program FayettevilleArkansasUSA UAMS North Central Regional Campus Family Medicine Residency Program BatesvilleArkansasUSA Family Medicine Brown University Warren Alpert Medical SchoolProvidenceRhode IslandUSA University of Colorado School of Medicine AuroraColoradoUSA

Storylines of Family Medicine is a 12-part series of thematically linked mini-essays with accompanying illustrations that explore the many dimensions of family medicine,as interpreted by individual family physicians and medical educators in the USA and elsewhere around the ***‘Ⅰ:framing family medicine—history,values,and perspectives’,the authors address the following themes:‘Notes on Storylines of Family Medicine’,‘Family medicine—the generalist specialty’,‘Family medicine’s achievements—a glass half full assessment’,‘Family medicine’s next 50 years—toward filling our glasses’,‘Four enduring truths of family medicine’,‘Names matter’,‘Family medicine at its core’and‘The ecology of medical care.’May readers find much food for thought in these essays.

关键词： glasses illustration Notes

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Promoting the production of challenging proteins via induced expression in CHO cells and modified cell-free lysates harboring T7 RNA polymerase and mutant eIF2α

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Synthetic and Systems biotechnology 2024年第3期9卷 416-424页

作者： jeffrey L.Schloßhauer Lena Tholen Alexander Korner Stefan Kubick Sofia Chatzopoulou Anja Honow Anne Zemella Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology-IZI Branch Bioanalytics and Bioprocesses-IZI-BBAm MühlenbergPotsdamGermany Fraunhofer Institute for Cell Therapy and Immunology-IZI Branch Bioanalytics and Bioprocesses-IZI-BBAm MühlenbergPotsdamGermany Faculty of Health Sciences Joint Faculty of the Brandenburg University of Technology Cottbus-SenftenbergThe Brandenburg Medical School Theodor FontaneUniversity of PotsdamPotsdamGermany Institute for Chemistry and biochemistry Laboratory of Protein BiochemistryFreie Universitat BerlinThielallee 6314195BerlinGermany Institute of biotechnology Technische Universit¨at BerlinStraße des 17.Juni 13510623BerlinGermany New/era/mabs GmbH August-Bebel-Str.8914482PotsdamGermany

Chinese hamster ovary(CHO)cells are crucial in biopharmaceutical production due to their scalability and capacity for human-like post-translational ***,toxic proteins and membrane proteins are often difficult-to-express in living ***,cell-free protein synthesis can be *** study explores innovative strategies for enhancing the production of challenging proteins through the modification of CHO cells by investigating both,cell-based and cell-free approaches.A major result in our study involves the integration of a mutant eIF2 translation initiation factor and T7 RNA polymerase into CHO cell lysates for cell-free protein *** resulted in elevated yields,while eliminating the necessity for exogenous additions during cell-free production,thereby substantially enhancing ***,we explore the potential of the Rosa26 genomic site for the integration of T7 RNA polymerase and cell-based tetracycline-controlled protein *** findings provide promising advancements in bioproduction technologies,offering flexibility to switch between cell-free and cell-based protein production as needed.

关键词： Inducible expression CHO cells Cell-free protein synthesis CRISPR T7 RNA polymerase eIF2 Rosa26

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Storylines of family medicine Ⅺ:professional identity formation—nurturing one’s own story

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Family Medicine and Community Health 2024年第S3期12卷 99-108页

作者： William b Ventres Leslie A Stone Hamish J Wilson Sumi M Sexton David J Doukas Jessica P Cerdena David M Kelley Michael D Fetters jeffrey J Haney John J Frey III Family and Preventive Medicine University of Arkansas for Medical Sciences College of MedicineLittle RockArkansasUSA General Practice and Rural Health University of Otago Dunedin School of MedicineDunedinNew Zealand Family Medicine Georgetown University School of MedicineWashingtonDistrict of ColumbiaUSA Family and Community Medicine Tulane University School of MedicineNew OrleansLouisianaUSA Family Medicine Residency Program Middlesex HealthMiddletownConnecticutUSA Family Medicine University of Michigan Medical SchoolAnn ArborMichiganUSA Medical Education and Clinical Sciences Washington State UniversitySpokaneWashingtonUSA Family Medicine and Community Health University of Wisconsin-Madison School of Medicine and Public HealthMadisonWisconsinUSA

Storylines of Family Medicine is a 12-part series of thematically linked mini-essays with accompanying illustrations that explore the many dimensions of family medicine,as interpreted by individual family physicians and medical educators in the USA and elsewhere around the ***‘Ⅺ:professional identity formation—nurturing one’s own story’,authors address the following themes:‘The social construction of professional identity’,‘On becoming a family physician’,‘What’s on the test?—professionalism for family physicians’,‘The ugly doc-ling’,‘Teachers—the essence of who we are’,‘Family medicine research—it starts in the clinic’,‘Socially accountability in medical education’,‘Personal philosophy and how to find it’and‘Teaching and learning with Storylines of Family Medicine’.May these essays encourage readers to find their own creative spark in medicine.

关键词： own becoming professional

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The proximity between hydroxyl and single atom determines the catalytic reactivity of Rh1/CeO_(2) single-atom catalysts

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Nano Research 2024年第1期17卷 397-406页

作者： Danfeng Wu Shuyun Zhou Congcong Du Juan Li Jianyu Huang Hong-xia Shen Abhaya K.Datye Shan Jiang jeffrey T.Miller Sen Lin Haifeng Xiong State Key Laboratory of Physical Chemistry of Solid Surfaces College of Chemistry and Chemical EngineeringXiamen UniversityXiamen 361005China State Key Laboratory of Photocatalysis on Energy and Environment College of ChemistryFuzhou UniversityFuzhou 350002China Clean Nano Energy Center State Key Laboratory of Metastable Materials Science and TechnologyYanshan UniversityQinhuangdao 066004China College of biology and Chemical Engineering Jiaxing UniversityJiaxing 314000China Department of Chemical&biological Engineering University of New MexicoAlbuquerqueNM 8731-0001USA Davidson School of Chemical Engineering Purdue UniversityWest LafayetteIN 47907-2100USA Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province(IKKEM) Xiamen 361102China Fujian Key Laboratory of Rare-earth Functional Materials Fujian Shanhai Collaborative Innovation Center of Rare-earth Functional MaterialsLongyan 366300China

The local structure of the metal single-atom site is closely related to the catalytic activity of metal single-atom catalysts(SACs).However,constructing SACs with homogeneous metal active sites is a challenge due to the surface heterogeneity of the conventional ***,we prepared two Rh1/CeO_(2)SACs(0.5Rh1/r-CeO_(2)and 0.5Rh1/c-CeO_(2),respectively)using two shaped CeO_(2)(rod and cube)exposing different facets,i.e.,CeO_(2)(111)and CeO_(2)(100).In CO oxidation reaction,the T100 of 0.5Rh1/r-CeO_(2)SACs is 120°C,while the T100 of 0.5Rh1/c-CeO_(2)SACs is as high as 200°*** in-situ CO diffuse reflectance infrared Fourier transform spectroscopy(CO-DRIFTS),we found that the proximity between OH group and Rh single atom on the plane surface plays an important role in the catalytic activity of Rh1/CeO_(2)SAC system in CO *** Rh single atom trapped at the CeO_(2)(111)crystal surface forms the Rh1(OH)adjacent species,which is not found on the CeO_(2)(100)crystal surface at room ***,during CO oxidation,the OH group far from Rh single atom on the 0.5Rh1/c-CeO_(2)disappears and forms Rh1(OH)adjacent species when the temperature is above 150°*** formation of Rh1(OH)adjacentCO intermediate in the reaction is pivotal for the excellent catalytic activity,which explains the difference in the catalytic activity of Rh single atoms on two different CeO_(2)*** formed Rh1(OH)adjacent-O-Ce structure exhibits good stability in the reducing atmosphere,maintaining the Rh atomic dispersion after CO oxidation even when pre-reduced at high temperature of 500°*** functional theory(DFT)calculations validate the unique activity and reaction path of the intermediate Rh1(OH)adjacentCO species *** work demonstrates that the proximity between metal single atom and hydroxyl can determine the formation of active intermediates to affect the catalytic performances in catalysis.

关键词： crystal plane Rh1/CeO_(2)single-atom catalyst proximity of Rh and hydroxyl coordination structure CO oxidation

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A medium chain fatty acid, 6-hydroxyhexanoic acid (6-HHA), protects against obesity and insulin resistance

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Acta Pharmaceutica Sinica b 2024年第4期14卷 1892-1894页

作者： Sara C.Sebag Meihua Hao Qingwen Qian Chawin Upara Qiong Ding Min Zhu jeffrey A.banas Huojun Cao Liu Hong Ling Yang Department of Anatomy and Cell biology University of Iowa Carver College of MedicineIowa CityIA 52242USA Fraternal Order of Eagles Diabetes Research Center University of Iowa Carver College of MedicineIowa CityIA 52242USA Pappajohn biomedical Institute University of Iowa Carver College of MedicineIowa CityIA 52242USA Iowa Institute for Oral Health Research University of Iowa College of DentistryIowa CityIA 52242USA

To the Editor,Obesity,one of the most serious health concerns worldwide,exacerbates periodontitis pathogenesis and reduces the effectiveness of ***,periodontitis-associated inflammation disrupts systemic lipid and glucose homeostasis,the major risk factors for developing obesity-associated *** studies have demonstrated that certain supplemental dietary lipids such as dietary polyunsaturated fatty acids,have beneficial outcomes for diabetic and obese *** addition to dietary lipid supply,the oral and gut microbiota produce fatty acids(FAs)which provide the host with essential nutrients and aid in defense against *** medium chain FAs(MCFAs;6–12 carbons)are bacterial-derived lipids shown to have anti-inflammatory and insulin sensitization effects in diverse cell types such as ***,whether and to what extent oral microbiota-produced MCFAs may ameliorate obesity-associated metabolic dysfunction are largely unknown.

关键词： obesity dietary lipids

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Storylines of family medicine Ⅳ:perspectives on practice—lenses of appreciation

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Family Medicine and Community Health 2024年第S3期12卷 33-42页

作者： William b Ventres Leslie A Stone Radeeb Akhtar jeffrey M Ring Lucy M Candib Erick Messias Ronald M Epstein Marc Tunzi Amy L Lee Christopher P Morley Carina M brown David Slawson Jill Konkin David G Campbell Ian Couper Susan Williams Robert brooks Lucie Walters Family and Preventive Medicine University of Arkansas for Medical Sciences College of MedicineLittle RockArkansasUSA Family Medicine and Community Health Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA Independent Health Psychologist Los AngelesCaliforniaUSA Family Medicine and Community Health UMass Chan Medical SchoolWorcesterMassachusettsUSA Psychiatry and behavioral Neurosciences Saint Louis University School of MedicineSaint LouisMissouriUSA Family Medicine University of Rochester Medical CenterRochesterNew YorkUSA Family Medicine Residency Program Natividad Medical CenterSalinasCaliforniaUSA Family Medicine Tufts University School of MedicineBostonMassachusettsUSA Public Health and Preventive Medicine SUNY Upstate Medical UniversitySyracuseNew YorkUSA Cone Health Family Medicine Residency The University of North Carolina School of MedicineGreensboroNorth CarolinaUSA Family Medicine Atrium HealthCharlotteNorth CarolinaUSA Family Medicine University of Alberta Faculty of Medicine&DentistryEdmontonAlbertaCanada Cunninghame Arm Medical Centre Australian College of Rural and Remote MedicineLakes EntranceQueenslandAustralia Ukwanda Centre for Rural Health Stellenbosch University Faculty of Medicine and Health SciencesCape TownWestern CapeSouth Africa Adelaide Rural Clinical School The University of AdelaideAdelaideSouth AustraliaAustralia Department of Rural Health Broken Hill UniversityBroken HillNew South WalesAustralia Adelaide Rural Clinical School The University of Adelaide Faculty of Health and Medical SciencesMount GambierSouth AustraliaAustralia

Storylines of Family Medicine is a 12-part series of thematically linked mini-essays with accompanying illustrations that explore the many dimensions of family medicine,as interpreted by individual family physicians and medical educators in the USA and elsewhere around the ***‘Ⅳ:perspectives on practice—lenses of appreciation’,authors address the following themes:‘Relational connections in the doctor–patient partnership’,‘Feminism and family medicine’,‘Positive family medicine’,‘Mindful practice’,‘The new,old ethics of family medicine’,‘Public health,prevention and populations’,‘Information mastery in family medicine’and‘Clinical courage.’May readers nurture their curiosity through these essays.

关键词： thematic illustration doctor

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蛋白活化原子层沉积用于超强原油排斥的层级纳米装甲膜（英文）

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Science bulletin 2024年第2期 218-226页

作者：杨晓彬孙盼温雅洁 Anil U.Mane jeffrey W.Elam 马军刘少敏 Seth b.Darling 邵路 MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage State Key Laboratory of Urban Water Resource and Environment School of Chemistry and Chemical Engineering Harbin Institute of Technology Chemical Sciences and Engineering Division Argonne National Laboratory Advanced Materials for Energy-Water Systems Energy Frontier Research Center Argonne National Laboratory School of Environment Harbin Institute of Technology Pritzker School of Molecular Engineering University of Chicago Department of Physics University of Illinois at Chicago Applied Materials Division Argonne National Laboratory WA School of Mines: Minerals Energy and Chemical Engineering Curtin University

Atomic layer deposition(ALD) offers unique capabilities to fabricate atomically engineered porous materials with precise pore tuning and multi-functionalization for diverse applications like advanced membrane separations towards sustainable energy-water systems. However, current ALD technique is inhibited on most non-polar polymeric membranes due to lack of accessible nucleation sites. Here, we report a facile method to efficiently promote ALD coating on hydrophobic surface of polymeric membranes via novel protein activation/sensitization. As a proof of concept, TiO2ALD-coated membranes activated by bovine serum albumin exhibit remarkable superhydrophilicity, ultralow underwater crude oil adhesion, and robust tolerance to rigorous environments including acid, alkali, saline, and *** importantly, excellent cyclable crude oil-in-water emulsion separation performance can be achieved. The mechanism for activation/sensitization is rooted in reactivity for a particular set of amino acids. Furthermore, the universality of protein-sensitized ALD is demonstrated using common egg white,promising numerous potential usages in biomedical engineering, environmental remediation, lowcarbon manufacturing, catalysis, and beyond.

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4-1bb transcriptomic expression patterns across malignancies:Implications for clinical trials of 4-1bb agonists

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Cancer Communications 2024年第10期44卷 1168-1172页

作者： Yuji Uehara Shumei Kato Daisuke Nishizaki Hirotaka Miyashita Suzanna Lee Mary K.Nesline Sarabjot Pabla jeffrey M.Conroy Paul DePietro Heidi Ko Jason K.Sicklick Razelle Kurzrock Department of Thoracic Oncology and Respiratory Medicine Tokyo Metropolitan Cancer and Infectious Diseases CenterKomagome HospitalTokyoJapan Department of Precision Cancer Medicine Center for Innovative Cancer TreatmentTokyo Medical and Dental UniversityTokyoJapan Center for Personalized Cancer Therapy and Division of Hematology and Oncology Department of MedicineUniversity of California San DiegoMoores Cancer CenterLa JollaCaliforniaUnited States Dartmouth Cancer Center Hematology and Medical OncologyLebanonNew HampshireUnited States Labcorp Oncology DurhamNorth CarolinaUnited States OmniSeq Incorporation BuffaloNew YorkUnited States Division of Surgical Oncology Department of SurgeryCenter for Personalized Cancer TherapyUniversity of California San DiegoLa JollaCaliforniaUnited States Medical College of Wisconsin Cancer Center and Genomic Sciences and Precision Medicine Center Medical College of WisconsinMilwaukeeWisconsinUnited States Department of Oncology Medical College of Wisconsin Cancer CenterMilwaukeeWisconsinUnited States Department of Oncology University of NebraskaOmahaNebraskaUnited States

4-1bb,a member of the tumor necrosis factor receptor superfamily,is an important co-stimulatory molecule regulating the activity of immune cells across a range of physiological and pathological processes,which culminates in a potent immune response(Figure 1A and b)[1,2].Numerous clinical trials have been conducted utilizing 4–1bb agonists(Supplemental Table S1);however,previous and ongoing 4-1bb agonist trials are being conducted without biomarker selection,which potentially explains their modest ***,several studies suggest the potential value of utilizing transcriptomics in addition to genomics to identify the unique immunologic signature of individual tumors[3–7].

关键词： clinical utilizing Figure

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