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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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Minimally invasive treatment of pancreatic necrosis

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World Journal of Gastroenterology 2012年第46期18卷 6829-6835页

作者： brian bello jeffrey b Matthews Department of Surgery School of Medicine University of Chicago

AIM: To systematically review these minimally invasive approaches to infected pancreatic necrosis. METHODS: We used the MEDLINE database to investigate studies between 1996 and 2010 with greater than 10 patients that examined these techniques. Using a combination of boolean operators, reports were retrieved addressing percutaneous therapy (341 studies), endoscopic necrosectomy (574 studies), laparoscopic necrosectomy via a transperitoneal approach (148 studies), and retroperitoneal necrosectomy (194 studies). Only cohorts with at least 10 or more patients were included. Non-English papers, letters, animal studies, duplicate series and reviews without original data were excluded, leaving a total of 27 studies for analysis. RESULTS: Twenty-seven studies with 947 patients total were examined (eight studies on percutaneous approach; ten studies on endoscopic necrosectomy; two studies on laparoscopic necrosectomy via a transperitoneal approach; five studies on retroperitoneal necrosectomy; and two studies on a combined percutaneous-retroperitoneal approach). Success rate, complications, mortality, and number of procedures were outcomes that were included in the review. We found that most published reports were retrospective in nature, and thus, susceptible to selection and publication bias. Few reports examined these techniques in a comparative, prospective manner. CONCLUSION: Each minimally invasive approach though was found to be safe and feasible in multiple reports. With these new techniques, treatment of infected pancreatic necrosis remains a challenge. We advocate a multidisciplinary approach to this complex problem with treatment individualized to each patient.

关键词： Acute pancreatitis Pancreatic abscess Pancreatic necrosis Necrosectomy Laparoscopic necrosectomy

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Recent advances in flexible and stretchable electronics, sensors and power sources

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Science China Chemistry 2012年第5期55卷 718-725页

作者： TOK jeffrey b.-H. Department of Chemical Engineering Stanford University Stanford CA 94305 USA

There has been ongoing keen interest to mold electronic devices into desired shapes and be laid on desired configurable surfaces. In specific, the ability to design materials that can bend, twist, compress and stretch repeatedly, while still able to maintain its full capability as conductors or electrodes, has led to numerous efforts to develop flexible and stretchable (bio)devices that are both technologically challenging and environmentally friendly (e.g. biodegradable). In this review, we highlight several recent significant results that have made impacts toward the field of flexible and stretchable electronics, sensors and power sources.

关键词： organic transistors flexible electronics stretchable electronics electronic skin sensor

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Volcano video data characterized and classified using computer vision and machine learning algorithms

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Geoscience Frontiers 2020年第5期11卷 1789-1803页

作者： Alex J.C.Witsil jeffrey b.Johnson Department of Geosciences Boise State UniversityBoiseIDUSA

Video cameras are common at volcano observatories,but their utility is often limited during periods of crisis due to the large data volume from continuous acquisition and time requirements for manual *** cameras to serve as effective monitoring tools,video frames must be synthesized into relevant time series signals and further analyzed to classify and characterize observable *** this study,we use computer vision and machine learning algorithms to identify periods of volcanic activity and quantify plume rise velocities from video *** were collected at Villarrica Volcano,Chile from two visible band cameras located^17 km from the vent that recorded at 0.1 and 30 frames per second between February and April *** these two months,Villarrica exhibited a diverse range of eruptive activity,including a paroxysmal eruption on 3 *** to and after the eruption,activity included nighttime incandescence,dark and light emissions,inactivity,and periods of cloud *** quantify the color and spatial extent of plume emissions using a blob detection algorithm,whose outputs are fed into a trained artificial neural network that categorizes the observable activity into five *** shifts from primarily nighttime incandescence to ash emissions following the 3 March paroxysm,which likely relates to the reemergence of the buried lava *** periods exhibiting plume emissions are further analyzed using a row and column projection algorithm that identifies plume onsets and calculates apparent plume horizontal and vertical rise *** onsets are episodic,occurring with an average period of^50 s and suggests a puffing style of degassing,which is commonly observed at ***,the lack of clear acoustic transients in the accompanying infrasound record suggests puffing may be controlled by atmospheric effects rather than a degassing regime at the *** presented here offer a generalized toolset for volcano monito

关键词： Volcano monitoring Plume exit velocity Volcano webcam Image processing Machine learning Villarrica

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Dynamic material performance of cold-formed steel hollow sections： a state-of-the-art review

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Frontiers of Structural and Civil Engineering 2017年第2期11卷 209-227页

作者： Cameron b. RITCHIE jeffrey A. PACKER Xiao-Ling ZHAO Amin HEIDARPOUR Yiyi CHEN Department of Civil Engineering University of Toronto Toronto Ontario MSS 1A4 Canada Department of Civil Engineering Monash University Victoria 3800 Australia College of Civil Engineering Tongji University Shanghai 200092 China

This paper presents a literature review focused on the material performance of cold-formed, carbon steel, hollow structural sections under impulsive （highly dynamic） loading. Impulsive loading, represented by impact and blast, is characterized by a very rapid, time-dependent loading regime in the affected members and materials. Thus, the effect of high-strain-rate loading is initially reviewed. Next the material toughness, an important energy-absorption property and one measure of a material＇s ability to arrest fracture, is considered by means of studying the Charpy V-notch behavior. The response of hollow sections under axial and lateral impact loading is then reviewed. Studies of blast on hollow sections, most of which fall under the categories of contact/near-field loading or far-field loading are presented. Under large-scale field blast experiments, cold-formed hollow sections have shown excellent behavior. Software for modeling blast loading and structural response, the latter including single degree of freedom analysis and explicit finite element analysis, is described and discussed.

关键词： cold-formed steel hollow structural sections composites impulsive loading impact blast experimentation analysis material properties

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THE MERGING OF TWO UNEQUAL AXISYMMETRIC PARALLEL TURbULENT JETS

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Journal of Hydrodynamics 2012年第2期24卷 257-262页

作者： bARATIAN-GHORGHI Zahra KAYE Nigel b. KHAN Abdul A. SMITH jeffrey R. Glenn Department of Civil Engineering Clemson University

Results of an experimental study of the merging of unequal parallel round turbulent jets are *** were conducted for a jet axial separation to nozzle diameter ratio of 3.0 and the Reynolds numbers ranging from 8 000 to 15 *** distance to the point where the jets are merged was measured for a range of jet source momentum flux *** different merger criteria were used based on the mean velocity profile,mean passive tracer concentration profile,and Reynolds stress *** results show that the concentration profile merges closest to the jet sources followed by the velocity profile with the Reynolds stress profile merging furthest from the *** all three profiles the merge distance is relatively insensitive to the momentum flux ratio,consistent with previous findings for slot jets and buoyant round *** measured merge distances are consistent with previously published results for equal round jets,though the poor spatial resolution of data in the literature means that limited comparison is *** are no studies of unequal jet merger currently in the literature that could be used for comparison.

关键词： turbulent jet merging jets unequal jets experiment

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A survey of FLS2 genes from multiple citrus species identifies candidates for enhancing disease resistance to Xanthomonas citri ssp. citri.

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Horticulture Research 2016年第1期3卷 208-218页

作者： Qingchun Shi Vicente J Febres jeffrey b Jones Gloria A Moore Horticultural Sciences Department University of FloridaGainesvilleFL 32611USA Plant Molecular and Cellular biology Program University of FloridaGainesvilleFL 32611USA Plant Pathology Department University of FloridaGainesvilleFL 32611USA

Pathogen-associated molecular patterns(PAMPs)-triggered immunity(PTI)is an important component of plant innate *** a previous study,we showed that the PAMP flg22 from Xanthomonas citri ***(Xflg22),the causal agent of citrus canker,induced PTI in citrus,which correlated with the observed levels of canker ***,we identified and sequenced two bacterial flagellin/flg22 receptors(FLS2-1 and FLS2-2)from‘Duncan’grapefruit(Citrus paradisi,CpFLS2-1 and CpFLS2-2)and‘Sun Chu Sha’mandarin(***,CrFLS2-1 and CrFLS2-2).We were able to isolate only one FLS2 from‘Nagami’kumquat(Fortunella margarita,FmFLS2-1)and gene flanking sequences suggest a rearrangement event that resulted in the deletion of FLS2-2 from the *** analysis,gene structure and presence of critical amino acid domains all indicate we identified the true FLS2 genes in ***2-2 was more transcriptionally responsive to Xflg22 than FLS2-1,with induced expression levels higher in canker-resistant citrus than in susceptible ***,‘Nagami’kumquat showed the highest FLS2-1 steady-state expression levels,although it was not induced by *** selected FmFLS2-1,CrFLS2-2 and CpFLS2-2 to further evaluate their capacity to enhance bacterial resistance using Agrobacterium-mediated transient expression *** FmFLS2-1 and CrFLS2-2,the two proteins from canker-resistant species,conferred stronger Xflg22 responses and reduced canker symptoms in leaves of the susceptible grapefruit *** two citrus genes will be useful resources to enhance PTI and achieve resistance against canker and possibly other bacterial pathogens in susceptible citrus types.

关键词： FLS2 citrus citri

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The Chapman-Richards Distribution and its Relationship to the Generalized beta

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Forest Ecosystems 2019年第3期6卷 219-235页

作者： jeffrey H.Gove Thomas b.Lynch Mark J.Ducey USDA Forest Service Northern Research Station271 Mast Road Durham 03824NHUSA Professor Emeritus Department of Natural Resource Ecology and ManagementOklahoma State UniversityAg Hall Room 008CStillwater 74078OKUSA Department of Natural Resources and the Environment University of New Hampshire114 James Hall Durham 03824NHUSA

background: The Chapman-Richards distribution is developed as a special case of the equilibrium solution to the McKendrick-Von Foerster equation. The Chapman-Richards distribution incorporates the vital rate assumptions of the Chapman-Richards growth function, constant mortality and recruitment into the mathematical form of the distribution. Therefore, unlike 'assumed' distribution models, it is intrinsically linked with the underlying vital rates for the forest area under consideration. Methods: It is shown that the Chapman-Richards distribution can be recast as a subset of the generalized beta distribution of the first kind, a rich family of assumed probability distribution models with known properties. These known properties for the generalized beta are then immediately available for the Chapman-Richards distribution, such as the form of the compatible basal area-size distribution. A simple two-stage procedure is proposed for the estimation of the model parameters and simulation experiments are conducted to validate the procedure for four different possible distribution shapes. Results: The simulations explore the efficacy of the two-stage estimation procedure;these cover the estimation of the growth equation and mortality-recruitment derives from the equilibrium assumption. The parameter estimates are shown to depend on both the sample size and the amount of noise imparted to the synthetic measurements. The results vary somewhat by distribution shape, with the smaller, noisier samples providing less reliable estimates of the vital rates and final distribution forms. Conclusions: The Chapman-Richards distribution in its original form, or recast as a generalized beta form, presents a potentially useful model integrating vital rates and stand diameters into a flexible family of resultant distributions shapes. The data requirements are modest, and parameter estimation is straightforward provided the minimal recommended sample sizes are obtained.

关键词： Diameter distributions Chapman-Richards growth Generalized beta distribution of the first kind Maximum likelihood McKendrick-Von Foerster equation Physiologically structured population model Size-structured distributions

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Parents' participation in physical activity predicts maintenance of some,but not all, types of physical activity in offspring during early adolescence:A prospective longitudinal study

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Journal of Sport and Health Science 2019年第3期8卷 273-279页

作者： Jennifer brunei jeffrey Gaudet Erin K.Wing Mathieu bélanger School of Human Kinetics University of Ottawa Institut du Savoir Montfort (ISM) H?pital Montfort Cancer Therapeutic Program Ottawa Hospital Research Institute (OHRI) Centre de formation medicale du Nouveau-brunswick Universite de Moncton Centre de formation médicale du Nouveau-brunswick Université de Moncton

Purpose: We aimed to examine the longitudinal associations between parents' and youth's participation in physical activity(PA).Methods-: One hundred and ninety youth cuompleted self-admitiistered questionnaires 3 times per year from 2011 to 2015, and their parents completed an interviewer-administered questionnaire during a telephone interview once in2011-2012. Data on youth's and parents' activities were classified as interdependent or coactive/***: Youth with one or both parents who participated in interdependent activities were more likely to maintain participation in interdependent activities(hazard ratio(HR) = 3.63: 95% confidence interval(CI) = 1.30-10.17). Youth's sustained participation in coactive/independent activities was not associated with parents' participation in coactive/independent activities(HR= 0.97; 95%CI=0.46-2.06).Conclusion: Longitudinal associations between parents' and youth's participation in PA differed across type of PA. Encouraging parents' participation in interdependent activities may promote sustained participation in interdependent activities in youth.

关键词： Longitudinal Maintenance Parental behavior Physical activity Sports Youth

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Stable isotope paleohydrology and chemostratigraphy of the Albian Wayan Formation from the wedge-top depozone,North American Western Interior basin

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Science China Earth Sciences 2017年第1期60卷 44-57页

作者： jeffrey b.ROSS Greg A.LUDVIGSON Andreas MOLLER Luis A.GONZALEZ J.D.WALKER Department of Geology University of Kansas Kansas Geological Survey University of Kansas

Understanding of the role of atmospheric moisture and heat transport in the climate system of the Cretaceous greenhouse world represents a major challenge in Earth system science. Stable isotopic paleohydrologic data from mid-Cretaceous paleosols in North America, from paleoequatorial to paleoArctic latitudes, have been used to constrain the oxygen isotope mass balance of the Albian hydrologic cycle. Over the range from 40°-50°N paleolatitude, sideritic paleosols predominate, indicating paleoenvironments with positive precipitation-evaporation （P-E） balances. Local exceptions occur on leeward side of the Sevier Orogen, where calcic paleosols in the wedge-top depozone record paleoenvironments with negative P-E balances in the orographic rain shadow. Stratigraphic sections in the Wayan Formation of Idaho （WF） were sampled from the wedge-top depozone. The units consist of stacked m-scale mudstone paleosols separated by m-scale sandstone-siltstone beds. Sections were sampled for organic carbon isotope profiles, and b-horizons from 6 well-developed paleosols were sampled for detrital zircons to determine maximum depositional ages. The first of these from the WF has produced a U-Pb concordia age of 101.0±1.1 Ma. This same WF section has produced a stratigraphic trend of upwardly decreasing δ18C values ranging from -24‰ upwards to -27‰ VPDb, suggesting correlation to the late Albian C15 C-isotope segment. Pedogenic carbonates from the WF principally consist of micritic calcite, with carbon-oxygen isotope values that array along meteoric calcite lines （MCLs） with δ18O values that range from -9.47‰ up to -8.39‰ VPDb. At approximately 42°N paleolatitude, these MCL values produce calculated paleoprecipitation values of-8.12‰ to -7.04‰ VSMOW, a range that is consistent with the estimates produced from other proxies at the same paleolatitudes across North America. These results indicate that despite the orographic rain shadow effect, the processes of meridional atmospheric moist

关键词： Cretaceous Paleoclimate Wayan Formation Pedogenic carbonates Geochronology

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