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Warmer temperature during asexual reproduction induce methylome, transcriptomic, and lasting phenotypic changes in Fragaria vesca ecotypes

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Horticulture research 2023年第9期10卷 121-135页

作者：张宇鹏 Guangxun Fan Tuomas Toivainen Torstein Tengs Igor Yakovlev Paal Krokene Timo Hytönen Carl Gunnar Fossdal Paul E.Grini EVOGENE Department of BiosciencesUniversity of Oslo0313 OsloNorway Department of Molecular Plant Biology Norwegian Institute of Bioeconomy Research1431ÅsNorway Department of Agricultural Sciences Viikki Plant Science CentreUniversity of Helsinki00014 HelsinkiFinland

Plants must adapt with increasing speed to global warming to maintain their *** rapid adaptation mechanism is epigenetic memory,which may provide organisms sufficient time to adapt to climate *** studied how the perennial Fragaria vesca adapted to warmer temperatures(28◦C vs.18◦C)over three asexual *** in flowering time,stolon number,and petiole length were induced by warmer temperature in one or more ecotypes after three asexual generations and persisted in a common garden *** methylome changes differed between the four ecotypes from Norway,Iceland,Italy,and Spain,but shared methylome responses were also *** differentially methylated regions(DMRs)occurred in the CHG context,and most CHG and CHH DMRs were hypermethylated at the warmer *** eight CHG DMR peaks,a highly similar methylation pattern could be observed between *** average,13%of the differentially methylated genes between ecotypes also showed a temperature-induced change in gene *** observed ecotype-specific methylation and expression patterns for genes related to gibberellin metabolism,flowering time,and epigenetic ***,we observed a negative correlation with gene expression when repetitive elements were found near(±2 kb)or inside *** conclusion,lasting phenotypic changes indicative of an epigenetic memory were induced by warmer temperature and were accompanied by changes in DNA methylation *** shared methylation patterns and transcriptome differences between *** accessions were observed,indicating that DNA methylation may be involved in both general and ecotype-specific phenotypic variation.

关键词： metabolism maintain adapted

Chromium adsorption on surface activated biochar made from tannery liming sludge:A waste-to-wealth approach

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Water Science and Engineering 2022年第4期15卷 328-336页

作者： Abul Hashem Sofia Payel Sadia Mim Anik Hasan Shahruk Nur-A-Tomal Aminur Rahman Majher I.Sarker Department of Leather Engineering Khulna University of Engineering&Technology(KUET)Khulna 9203Bangladesh Department of Public Health Engineering(DPHE) Zonal LaboratoryJashore 7400Bangladesh Global centre for Environmental Remediation(GCER) College of EngineeringScience and EnvironmentThe University of NewcastleCallaghanNSW 2308Australia Sustainable Biofuels and Co-Products research Unit Eastern Regional Research CenterAgricultural Research ServiceU.S.Department of AgricultureWyndmoorPA 19038USA

In a beamhouse,liming plays a key role in the removal of hair/wool and epidermis,but problems are created when waste liming sludge is discharged to the *** treatment of tannery wastewater is another major challenge to the *** this study,thermally-activated biochars derived from liming sludge were studied for their effective adsorption of chromium(Cr)from the tannery *** thermally activated biochars(B500,B550,B600,and B650)were prepared at different temperatures from the liming *** characteristics before and after the treatment were investigated using Fourier transform infrared spectroscopy,energy dispersive X-ray spectroscopy,Bru-nauer-Emmett-Teller,and scanning electron microscopy *** related functional groups(C-H,O-H,C-N,and=C-O)and chromium adsorption capacity were determined according to the surface morphology,element contents(C,O,Ca,Na,Al,Mg,and Si),surface area(5.8-9.2 m^(2)/g),pore size(5.22-5.53 nm),and particle size(652-1034 nm)of the experimental *** biochar originated at 600°C from the tannery liming sludge(B600)had a greater surface area with a chromium adsorption capacity of 99.8%in comparison to B500,B550,and B650 *** study developed an innovative way of utilizing liming sludge waste to minimize the pollution load and wastewater treatment cost in the tannery industry.

关键词： Adsorption Waste recycling Biochar application Thermal modification Tannery Solid waste

Identification of SUMO Targets by a Novel Proteomic Approach in Plants

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Journal of Integrative Plant Biology 2013年第1期55卷 96-107页

作者： Gema López-Torrejón Davide Guerra Rafael Catal Julio Salinas Juan C. del Pozo Centro de Biotecnología y Genómica de Plantas (INIA-UPM) Campus de Montegancedo CRA-Genomics research centre (GPG) Centro de Investigaciones Biológicas (CSIC) Campus de la Ciudad Universitaria de Madrid

Post-translational modifications （PTMs） chemically and physically alter the properties of proteins, including their folding, subcellular localization, stability, activity, and consequently their function. In spite of their relevance, studies on PTMs in plants are still limited. Small Ubiquitin-like Modifier （SUMO） modification regulates several biological processes by affecting protein-protein interactions, or changing the subcellular Iocalizations of the target proteins. Here, we describe a novel proteomic approach to identify SUMO targets that combines 2-D liquid chromatography, immunodetection, and mass spectrometry （MS） analyses. We have applied this approach to identify nuclear SUMO targets in response to heat shock. Using a bacterial SUMOylation system, we validated that some of the targets identified here are, in fact, labeled with SUMO1. Interestingly, we found that GIGANTEA （GI）, a photoperiodic-pathway protein, is modified with SUMO in response to heat shock both in vitro and in vivo.

关键词： Mass spectrometry plants post-translational modification proteomics SUMO.

An ultrafast reconfigurable nanophotonic switch using wavefront shaping of light in a nonlinear nanomaterial

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Light(Science & Applications) 2014年第1期3卷 78-84页

作者： Tom Strudley Roman Bruck Ben Mills Otto L Muskens Physics and Astronomy Faculty of Physical Sciences and EngineeringUniversity of SouthamptonHighfieldSouthampton SO171BJUK Optoelectronics research centre Faculty of Physical Sciences and EngineeringUniversity of SouthamptonHighfieldSouthampton SO171BJUK

We demonstrate a new concept for reconfigurable nanophotonic devices exploiting ultrafast nonlinear control of shaped wavefronts in a multimode nanomaterial consisting of semiconductor *** pulsed laser excitation of the nanowire mat is shown to provide an efficient nonlinear mechanism to control both destructive and constructive interference in a shaped *** of up to 63%are induced by optical pumping,due to a combination of multimode dephasing and induced transient *** show that part of the nonlinear phase dynamics can be inverted to provide a dynamical revival of the wavefront into an optimized spot with up to 18%increase of the peak to background ratio caused by pulsed laser *** concepts of multimode nonlinear switching demonstrated here are generally extendable to other photonic and plasmonic systems and enable new avenues for ultrafast and reconfigurable nanophotonic devices.

关键词： nanophotonics nanowires nonlinear optics reconfigurable ultrafast wavefront shaping

A dual positional specific lipoxygenase functions in the generation of flavor compounds during climacteric ripening of apple

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Horticulture research 2015年第1期2卷 280-292页

作者： Doreen Schiller Carolina Contreras Jörg Vogt Frank Dunemann Bruno G Defilippi Randolph Beaudry Wilfried Schwab Biotechnology of Natural Products Technische Universität MünchenLiesel-Beckmann-Str.1D-85354 FreisingGermany Department of Horticulture Michigan State University1066 Bogue StreetEast LansingMI 48824USA Julius Kühn-Institut(JKI)–Federal research centre for Cultivated Plants Institute for Breeding Research on Fruit CropsPillnitzer Platz 3aD-01326 DresdenGermany Julius Kühn-Institut(JKI)–Federal research centre for Cultivated Plants Institute for Breeding Research on Horticultural CropsErwin-Baur-Str.27D-06484 QuedlinburgGermany INIA La Platina PO Box 439-9SantiagoChile

Lipoxygenase(LOX)is an important contributor to the formation of aroma-active C6 aldehydes in apple(Malus×domestica)fruit upon tissue disruption but little is known about its role in autonomously produced aroma volatiles from intact *** explored the expression of 22 putative LOX genes in apple throughout ripening,but only six LOXs were expressed in a ripening-dependent *** LOX1:Md:1a,LOX1:Md:1c,LOX2:Md:2a and LOX2:Md:2b proteins showed 13/9-LOX,9-LOX,13/9-LOX and 13-LOX activity with linoleic acid,*** products of LOX1:Md:1c and LOX2:Md:2b were S-configured,LOX1:Md:1a and LOX2:Md:2a formed 13(R)-hydroperoxides as major ***-directed mutagenesis of Gly567 to an alanine converted the dual positional specific LOX1:Md:1a to an enzyme with a high specificity for 9(S)-hydroperoxide *** high expression level of the corresponding MdLOX1a gene in stored apple fruit,the genetic association with a quantitative trait locus for fruit ester and the remarkable agreement in regio-and stereoselectivity of the LOX1:Md:1a reaction with the overall LOX activity found in mature apple fruits,suggest a major physiological function of LOX1:Md:1a during climacteric ripening of *** LOX1:Md:1c,LOX2:Md:2a and LOX2:Md:2b may contribute to aldehyde production in immature fruit upon cell disruption our results furnish additional evidence that LOX1:Md:1a probably regulates the availability of precursors for ester production in intact fruit tissue.

关键词： specific autonomous probably

Pilot Study on the Intercalibration of a Categorisation System for FAlRer Digital Objects Related to Sensitive Data in the Life Sciences

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Data Intelligence 2022年第2期4卷 196-211页

作者： Christian Ohmann Romain David Monica Cano Abadia Florence Bietrix Jan-Willem Boiten Steve Canham Maria Luisa Chiusano Walter Dastru Arnaud Laroquette Dario Longo Michaela Theresia Mayrhofer Maria Panagiotopoulou Audrey Richard Pablo Emilio Verde European Clinical research Infrastructure Network(ECRIN) Paris 75013France European research Infrastructure on Highly Pathogenic Agents(ERINHA AISBL) Brussels 10ooBelgium Biobanking and Biomolecular Resources research Infrastructure(BBMRI) Graz 8010Austria European Infrastructure for Translational Medicine(EATRIS) Amsterdam 1081 HZThe Netherlands European Advanced Translational research Infrastructure(EATRIS)/Lygature Utrecht 3521 ALThe Netherlands European Marine Biological Resource centre(EMBRC)Department of Agricultural Sciences University Federico Il of Naples via UniversitaNaples 80138Italy Department of Molecular Biotechnology and Health Sciences Molecular Imaging CenterUniversity of TorinoTorino I-10125Italy European Marine Biological Resource centre(EMBRC) Paris 75252France European research Infrastructure for Biological and Biomedical Imaging(Euro-Biolmaging) Torino 10126Italy European research Infrastructure on Highly Pathogenic Agents(ERINHA AISBL) Brussels 1000Belgium Coordination centre for Clinical Trials Heinrich Heine University Dusseldorf Ringgold standard institutionNordrhein-Westfalen 40225Germany

Sharing sensitive data is a specific challenge for research infrastructures in the field of life *** that reason a toolbox has been developed,providing resources for researchers who wish to share and use sensitive data,to support the workflows for handling these kinds of digital *** and community approved annotations are required to be compliant with FAIR principles(Findability,Accessibility,Interoperability,Reusability).The toolbox makes use of a tagging(categorisation)system,allowing consistent labelling and categorisation of digital objects,in terms relevant to data sharing tasks and activities.A pilot study was performed within the Horizon 2020 project EOSC-Life,in which 2 experts from 6 life sciences research infrastructures were recruited to independently assign tags to the same set of 10 to 25 resources related to sensitive data management and data sharing(in total 110).Summary statistics of agreement and observer variation per research infrastructure are *** pilot study has shown that experts were able to attribute tags but in most cases with a considerable observer variation between *** the context of CWFR(Canonical Workflow Frameworks for research),this indicates the necessity for careful definition,evaluation and validation of parameters and processes related to workflow *** results from this pilot study were used to tackle this issue by revising the categorisation system and providing an updated version.

关键词： Sensitive data CWFR EOSC-Life Life sciences Toolbox Categorisation system Tagging FAIR

Traditional Chinese medicine targeting cancer stem cells as an alternative treatment for hepatocellular carcinoma

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Journal of Integrative Medicine 2020年第3期18卷 196-202页

作者： Kai-yue Tang Shi-lin Du Qian-lei Wang Yi-fan Zhang Hai-yan Song Institute of Digestive Diseases Longhua HospitalShanghai University of Traditional Chinese MedicineShanghai 200032China Department of Emergency Zhongshan HospitalFudan UniversityShanghai 200032China China-Canada centre of research for Digestive Diseases Shanghai 200032China

Hepatocellular carcinoma(HCC) is a prevalent and highly malignant cancer throughout the *** treatment of this disease is impeded by the high rate of metastasis, recurrence, and chemoresistance. Recent studies have revealed the close relationship between the malignant phenotype of HCC and cancer stem cells(CSCs). Therefore, CSC-targeted therapy is considered a promising strategy to eradicate HCC. Traditional Chinese medicine(TCM) can be effective in preventing recurrence and metastasis of some advanced HCC. A growing amount of literature has discovered that extracts or compounds derived from TCM exert an anti-CSC effect. This review introduces some formulas and chemical compounds derived from TCMs that have been reported to inhibit CSCs of HCC;these TCM-related drugs may help to provide an alternative approach to help manage cancers, especially for HCC which has a great potential of metastasis, recurrence, and chemoresistance.

关键词： Hepatocellular carcinoma Cancer stem cells Traditional Chinese medicine

Structure and floristic composition of tree stand in tropical forest in the Eastern Ghats of northern Andhra Pradesh, India

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Journal of Forestry research 2011年第4期22卷 491-500页

作者： C. Sudhakar Reddy Shilpa Babar Giriraj Amarnath Chiranjibi Pattanaik Forestry and Ecology Division National Remote Sensing Centre Indian Space Research Organization Hyderabad - 500 625 Andhra Pradesh India. MENRIS Division International Centre for Integrated Mountain Develop- ment Kathmandu Nepal Salim Ali centre for Ornithology & Natural History Deccan Regional Sta- tion 12-13-588/B Nagarjuna Nagar Colony Tarnaka Hyderabad-500 017Andhra Pradesh India.

The changes in species composition, abundance and forest stand structure were analyzed across altitudinal regimes in tropical forests of Eastern Ghats of northern Andhra Pradesh, India. Three 1-ha plots were established with one each in low, medium and high altitudes. A total of 153 species, 2129 stems （709 stems .ha^-1） of ≥10 cm girth were enumerated. Species richness and diversity pattern varied along altitudinal gradient and increased with the altitude. Species richness varied from 52 to 110 species-ha^-1 and stand density from 639 to 836 ***^-1 with average basal area of 34.39 m^***^-1. Shannon-Wiener index （H＇） ranged from 4.55 to 5.17. Low altitude （i.e., Site 1） is dominated byXylia xylocarpa （59.22） and Lagerstroemia parviflora （23.90）, medium altitude （i.e., Site 2） by Xylia xylocarpa （45;50） Bursera serrata （17.29）, and high altitude （i.e., Site 3） has Schleichera oleosa （28.25） Pterocarpus marsupium （26.55） as predominant species. Taxonomically, Rubiaceae （12 species）, Fabaceae （12）, Euphorbiaceae （11）, Rutaceae （7） and Lanraceae （7） were dominant families. Density-wise, Fabaceae, Combretaceae, Euphorbiaceae, Anacardiaceae and Myrtaceae were abundant. Thus, conservation assessment based on altitudinal regimes and the information on species structure and function can provide baseline information for monitoring and sustaining the biodiversity.

关键词： altitude conservation diversity Eastern Ghats speciescomposition

Paired Immunoglobulin-like Receptor B Inhibition in Müller Cells Promotes Neurite Regeneration After Retinal Ganglion Cell Injury in vitro

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Neuroscience Bulletin 2020年第9期36卷 972-984页

作者： Rongdi Yuan Mei Yang Wei Fan Jian Lan Yuan-Guo Zhou Department of Ophthalmology Xinqiao HospitalArmy Medical UniversityChongqing 400037China The Molecular Biology centre State Key Laboratory of TraumaBurn and Combined InjuryResearch Institute of Surgery and Daping HospitalArmy Medical UniversityChongqing 400042China

In the central nervous system(CNS),three types of myelin-associated inhibitors(MAIs) have major inhibitory effects on nerve *** include Nogo-A,myelin-associated glycoprotein,and oligodendrocyte-myelin *** possess two co-receptors,Nogo receptor(NgR) and paired immunoglobulin-like receptor B(PirB).Previous studies have confirmed that the inhibition of NgR only results in a modest increase in regeneration in the CNS;however,the inhibitory effects of PirB with regard to nerve regeneration after binding to MAIs remain *** this study,we demonstrated that PirB is expressed in primary cultures of retinal ganglion cells(RGCs),and the inhibitory effects of the three MAIs on the growth of RGC neurites are not significantly decreased after direct PirB knockdown using adenovirus PirB ***,we found that retinal Müller cells expressed PirB and that its knockdown enhanced the regeneration of co-cultured RGC *** knockdown also activated the JAK/Stat3 signaling pathway in Müller cells and upregulated ciliary neurotrophic factor *** findings indicate that PirB plays a novel role in retinal Müller cells and that its action in these cells may indirectly affect the growth of RGC *** results also reveal that PirB in Müller cells affects RGC neurite *** findings provide a novel basis for the use of PirB as a target molecule to promote nerve regeneration.

关键词： Neurite regeneration Müller cell Retina ganglion cell injury Ciliary neurotrophic factor