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The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees

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Molecular Plant 2024年第5期17卷 725-746页

作者： Tingting Shi Xinxin Zhang Yukang Hou Changfu Jia Xuming Dan Yulin Zhang Yuanzhong Jiang Qiang Lai Jiajun Feng Jianju Feng Tao Ma Jiali Wu Shuyu Liu Lei Zhang Zhiqin Long Liyang Chen Nathaniel R.Street Par K.Ingvarsson Jianquan Liu Tongming Yin Jing Wang Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education College of Life SciencesSichuan UniversityChengduSichuanChina College of Horticulture and Forestry Tarim UniversityAlar 843300China Umea Plant Science Centre Department of Plant PhysiologyUmea UniversityUmeaVasterbottenSweden Linnean Centre for Plant Biology Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural SciencesUppsalaSweden The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China Nanjing Forestry UniversityNanjingJiangsuChina

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies.Poplars,among the world’s most widely distributed and cultivated trees,exhibit extensive phenotypic diversity and environmental adaptability.In this study,we present a genus-level super-pangenome comprising 19 Populus genomes,revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation.Through the integration of pangenomes with transcriptomes,methylomes,and chromatin accessibility mapping,we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures,notably CG methylation in gene-body regions.Further comparative genomic analyses have enabled the identification of 142202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence.We have experimentally validated a∼180-bp presence/absence variant affecting the expression of the CUC2 gene,crucial for leaf serration formation.Finally,we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome(http://***).Together,the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.

关键词： Populus pangenomes whole-genome duplication structural variation genome evolution

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Modifying current thin-film microextraction(TFME)solutions for analyzing prohibited substances:Evaluating new coatings using liquid chromatography

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Journal of Pharmaceutical Analysis 2022年第3期12卷 470-480页

作者： Łukasz Sobczak Dominika Kołodziej Krzysztof Gorynski Bioanalysis Scientific Group Faculty of PharmacyCollegium Medicum in Bydgoszcz at Nicolaus Copernicus University in Torun85-089BydgoszczPoland

For identifying and quantifying prohibited substances,solid-phase microextraction(SPME)continues to arouse interest as a sample preparation method.However,the practical implementation of this method in routine laboratory testing is currently hindered by the limited number of coatings compatible with the ubiquitous high-performance liquid chromatography(HPLC)systems.Only octadecyl(C18)and polydimethylsiloxane/divinylbenzene ligands are currently marketed for this purpose.To address this situation,the present study evaluated 12 HPLC-compatible coatings,including several chemistries not currently used in this application.The stationary phases of SPME devices in the geometry of thin filmcoated blades were prepared by applying silica particles bonded with various functional ligands(C18,octyl,phenyl-hexyl,3-cyanopropyl,benzenesulfonic acid,and selected combinations of these),as well as unbonded silica,to a metal support.Most of these chemistries have not been previously used as microextraction coatings.The 48 most commonly misused substances were selected to assess the extraction efficacy of each coating,and eight desorption solvent compositions were used to optimize the desorption conditions.All samples were analyzed using an HPLC system coupled with triple quadrupole tandem mass spectrometry.This evaluation enables selection of the best-performing coatings for quantifying prohibited substances and investigates the relationship between extraction efficacy and the physicochemical characteristics of the analytes.Ultimately,using the most suitable coatings is essential for trace-level analysis of chemically diverse prohibited substances.

关键词： Sample preparation Solid-phase microextraction Thin-film microextraction Prohibited substances Drugs of abuse High-performance liquid chromatography

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Evaluation of in vitro digestibility of Aspergillus oryzae fungal biomass grown on organic residue derived‑VFAs as a promising ruminant feed supplement

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Journal of Animal Science and Biotechnology 2023年第6期14卷 2614-2629页

作者： Clarisse Uwineza Mohammadali Bouzarjomehr Milad Parchami Taner Sar Mohammad J.Taherzadeh Amir Mahboubi swedish Centre for Resource Recovery University of Boras50190 BorasSweden

Background As demand for high quality animal feed continues to raise,it becomes increasingly important to mini-mize the environmental impact of feed production.An appealing sustainable approach to provide feed fractions is to use organic residues from agro-food industry.In this regard,volatile fatty acids(VFAs)such as acetic,propionic and butyric acids,derived from bioconversion of organic residues can be used as precursors for production of micro-bial protein with ruminant feed inclusion potential.This study aims to investigate the in vitro digestibility of the Asper-gillus oryzae edible fungal biomass cultivated on VFAs-derived from anaerobic digestion of residues.The produced fungal protein biomass,along with hay clover silage and rapeseed meal were subjected to various in vitro assays using two-stage Tilley and Terry(TT),gas,and bag methods to evaluate and compare its digestibility for application in ruminant feed.Results The produced fungal biomass contained a higher crude protein(CP)(41%–49%)and rather similar neutral detergent fiber(NDF)(41%–56%)compared to rapeseed meal.The rumen in vitro dry matter digestibility(IVDMD)of the fungal biomass in the TT method ranged from 82%to 88%(statistically similar to that of the gas method(72%to 85%)).The IVDMD of fungal biomass were up to 26%and 40%greater than that of hay clover silage and rapeseed meal,respectively.The type of substrate and bag method had pronounced effect on the fermentation products(ammonium-N(NH4+-N),total gas and VFAs).Fungal biomass digestion resulted in the highest release of NH4+-N(340–540 mg/L)and the ratio of acetate to propionate ratio(3.5)among subjected substrates.Conclusion The results indicate that gas method can be used as a reliable predictor for IVDMD as well as fermenta-tion products.Furthermore,the high IVDMD and fermentation product observed for Aspergillus oryzae fungal biomass digestion,suggest that the supplementation of fungal biomass will contribute to improving the rumen digestion by providing necessary nitrogen and energy

关键词： Aspergillus oryzae Fungal biomass In vitro dry matter digestibility Ruminant feed Volatile fatty acids

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Recent weakening of seasonal temperature difference in East Asia beyond the historical range of variability since the 14th century

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Science China Earth Sciences 2023年第5期66卷 1133-1146页

作者： Jianglin WANG Bao YANG Zhiyuan WANG Jürg LUTERBACHER Fredrik Charpentier LJUNGQVIST Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands Northwest Institute of Eco-Environment and ResourcesChinese Academy of SciencesLanzhou730000China Key Laboratory of Desert and Desertification Northwest Institute of Eco-Environment and ResourcesChinese Academy of SciencesLanzhou730000China School of Geography and Ocean Science Nanjing UniversityNanjing210023China College of Geography and Environmental Science Zhejiang Normal UniversityJinhua321004China Science and Innovation Department World Meteorological Organization(WMO)Geneva1211Switzerland Department of History Stockholm UniversityStockholm10691Sweden Bolin Centre for Climate Research Stockholm UniversityStockholm10691Sweden swedish collegium for advanced study LinneanumThunbergsvägen 2Uppsala75238Sweden

Seasonal differences of temperature are crucial components of the Earth's climate system.However,the relatively short observational record,especially for East Asia,has limited progress in understanding seasonal differences.In this study,we identify ten tree-ring chronologies separately correlated with local winter(December-February)temperatures and twelve different tree-ring chronologies separately correlated with summer(June-August)temperatures across East Asia.Using these discrete seasonal tree-ring chronologies,we develop two independent winter and summer temperature reconstructions covering the period 1376-1995 CE for East Asia,and compare them with model simulations.Our reconstructions show a more significant volcanic cooling and earlier onset of modern warming in summer than in winter.The reconstructed summer-minus-winter temperature decreased since as early as the late 19th century,which has driven the current state of seasonal temperature difference to out of the natural variability since the 1370s.Climate models could generally reproduce the variability and trends in seasonal reconstructions,but might largely underestimate seasonal differences due to the fact that seasonal expressions on external forcing and modes of internal variability are too small.Our study highlights the importance of using proxy-based seasonal reconstructions to evaluate the performance of climate models,and implies a substantial weakening of seasonal temperature differences in the future.

关键词： Seasonal temperature differences Temperature reconstruction East Asia Tree rings Recent warming

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Maximizing recovery time between knock-out races improves sprint cross-country skiing performance

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Journal of Sport and Health Science 2022年第1期11卷 21-29页

作者： Kerry McGawley Coline Van Waerbeke Karl-Johan Westberg Erik P.Andersson swedish Winter Sports Research Centre Department of Health SciencesMid Sweden UniversityOstersund 83125Sweden

Background:In a sprint cross-country(XC)ski competition,the difference in recovery times separating the first and the second semi-final(SF)heats from the final(F)may affect performance.The aim of the current study was to compare the effects of longer vs.shorter recovery periods prescribed between the 3 knock-out races of a simulated sprint XC ski competition involving a prologue(P),quarter-final(QF),SF,and F.Methods:Eleven well-trained XC ski athletes completed 2 simulated sprint XC ski competitions on a treadmill involving 4×883-m roller-ski bouts at a 4°incline using the gear 3 ski-skating sub-technique.The first 3 bouts were completed at a fixed speed(PFIX,QFFIX,and SFFIX)corresponding to~96%of each individual’s previously determined maximal effort.The final bout was performed as a self-paced sprint time trial(FSTT).Test conditions differed by the time durations prescribed between the QFFIX,SFFIX,and FSTT,which simulated real-world XC ski competition conditions using maximum(MAX-REC)or minimum(MIN-REC)recovery periods.Results:The FSTT was completed 5.4±5.5 s faster(p=0.009)during MAX-REC(179.2±18.1 s)compared to MIN-REC(184.6±20.0 s),and this was linked to a significantly higher power output(p=0.010)and total metabolic rate(p=0.009).The pre FSTT blood lactate(BLa)concentration was significantly lower during MAX-REC compared to MIN-REC(2.5±0.8 mmol/L vs.3.6±1.6 mmol/L,respectively;p=0.027),and the pre-to-post FSTT increase in BLa was greater(8.8±2.1 mmol/L vs.7.1±2.3 mmol/L,respectively;p=0.024).No other differences for MAX-REC vs.MIN-REC reached significance(p>0.05).Conclusion:Performance in a group of well-trained XC skiers is negatively affected when recovery times between sprint heats are minimized which,in competition conditions,would occur when selecting the last QF heat.This result is combined with a higher pre-race BLa concentration and a reduced rise in BLa concentration under shorter recovery conditions.These findings may help inform decision making when XC skiers are faced with selecting a QF heat wi

关键词： Energetics Repeated sprints Roller skiing Simulated competition Tactics

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Direct GHG emissions from a pilot scale MBR-process treating municipal wastewater

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Advances in Climate Change Research 2022年第1期13卷 138-145页

作者： Christian BARESEL Jingjing YANG Niclas BORNOLD Kare TJUS Linda KANDERS Klara WESTLING IVL swedish Environmental Research Institute AB Valhallavagen 81Stockholm 10031Sweden

To evaluate direct greenhouse gas emissions from Membrane Biological Reactor(MBR),measurements of nitrous oxide(N_(2)O)and methane(CH_(4))were made at a pilot-scale MBR treating municipal wastewater Measurements were conducted during two campaigns with some changes in processes,i.***.introducing a pre-aeration tank in the second measurement,different distributions of aeration in the treatment line,not the same wastewater inflow rate,two types of ultrafiltration membrane.It was found that about 0.004% and 0.07% of the total ammonium loads were emitted as N_(2)O,CH_(4) emissions were 0.026% and 0.12% of incoming TOC(0.008% and 0.04% of incoming COD)in 2014 and 2018.The obtained N_(2)O emission values were relatively low.The study suggested that a high aeration at the beginning of the treatment line may result in significantly high emissions of both N_(2)O and CH_(4).A significant change in aeration in the membrane ultrafiltration tank did not have the same impact.The MBR process is known for high quality effluent but have been questioned due to its higher carbon footprint due to energy consumption.This study gave a reference case about direct GHG emissions from MBR process and provide information for the further evaluation of MBR processes.

关键词： Greenhouse gases(GHGs) Nitrous oxide(N_(2)O) Methane(CH_(4)) Membrane biological reactor(MBR)

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Risk of venous thromboembolic disease in postmenopausal women taking oral or transdermal hormone replacement therapy

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2011年第1期12卷 12-17页

作者： Barbara RUSZKOWSKA GraZyna GADOMSKA Liliana BIELIS Marzena GRUSZKA Barbara GóRALCZYK Danuta RO GraZyna ODROWAZ-SYPNIEWSKA Department of Pathophysiology Collegium Medicum in BydgoszczNicolaus Copernicus University in Toruń Department of Laboratory Medicine Collegium Medicum in BydgoszczNicolaus Copernicus University in Toruń Department of Laboratory Medicine Collegium Medicum in BydgoszczNicolaus Copernicus University in Toruń

Objective: The influence of hormone replacement therapy (HRT) on hemostasis processes depends on the type of hormone,the combination of doses,the time of taking HRT,and the route of administration (oral,transdermal,implanted).The aim of the current study was to assess some parameters of coagulation,especially tissue factor pathway inhibitor (TFPI) and tissue factor (TF) in postmenopausal women using oral or transdermal HRT.Methods: The study was conducted on 76 healthy women,including 46 women aged 44–58 years who were taking oral (26) or transdermal (20) HRT,and 30 women aged 44–54 years who did not take HRT as the control group.Plasma concentrations of TF,TFPI,thrombin-antithrombin complex (TAT),and D-dimer were performed by enzyme-linked immunosorbent assay (ELISA).Moreover,the concentration of fibrinogen and activity of protein C were measured by chromogenic and chronometric methods.Results: We observed a significantly higher concentration of TF and a significantly lower concentration of TFPI in women taking oral and transdermal HRT in comparison with the control group.We also found a significantly lower concentration of fibrinogen in women taking oral HRT vs.the control group.Moreover,no statistically significant changes in concentrations of TAT and D-dimer,or activity of protein C were noted.Conclusions: In this study,the occurrence of an increased TF concentration simultaneously with a decreased concentration of TFPI in women taking HRT indicates hypercoagulability.No significant modification of TAT or D-dimer occurred,and thus there may not be increased risk of thrombosis.

关键词： Menopause Coagulation Hormone replacement therapy

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Assessment of ghrelin and leptin receptor levels in postmenopausal women who received oral or transdermal menopausal hormonal therapy

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2012年第1期13卷 35-42页

作者： Barbara RUSZKOWSKA Alina SOKUP Arleta KULWAS Maciej W.SOCHA Krzysztof GóRALCZYK Barbara GóRALCZYK Danuta ROS Department of Pathophysiology Collegium Medicum in BydgoszczNicolaus Copernicus University in Toruń Department of Gastroenterology Angiology and Internal DiseasesCollegium Medicum in BydgoszczNicolaus Copernicus University in Toruń Department of Obstetrics Gynecology and Oncological GynecologyCollegium Medicum in BydgoszczNicolaus Copernicus University in Toruń

Objective:In postmenopausal women,an increased leptin concentration and reduced levels of ghrelin and adiponectin were observed.The aim of this study was to evaluate the concentrations of the active form of ghrelin,total ghrelin,leptin receptor,lipoprotein(a)(Lp(a)),and plasminogen activator inhibitor type 1(PAI-1) in postmenopausal women who received oral or transdermal menopausal hormonal therapy(MHT).Methods:The study involved 76 healthy women:46 women aged from 44 to 58 years who received oral(26) or transdermal(20) MHT;the control group consisted of 30 women aged from 44 to 54 years who did not receive MHT.The plasma concentrations of total ghrelin,the active form of ghrelin,Lp(a),and PAI-1:Ag were measured by enzyme-linked immunosorbent assay(ELISA).The concentration of the leptin receptor was measured by enzyme immunometric assay(EIA).Results:We observed a significantly higher concentration of total ghrelin and the active form of ghrelin in women who received transdermal MHT in comparison with those who took oral MHT.We also found a significantly lower concentration of total ghrelin in women who received oral MHT compared with the control group.A higher concentration of PAI-1:Ag was found in the group of women who took transdermal MHT in comparison with those who took oral MHT and with the control group.The differences were statistically significant.Additionally,we found a significant negative correlation between the concentrations of total ghrelin and PAI-1:Ag and a positive correlation between the concentrations of total ghrelin and leptin receptor in women who received transdermal MHT.Conclusions:The study showed that women who used transdermal MHT had higher levels of total ghrelin than women who took oral MHT.This indicates a beneficial effect of the transdermal route of MHT.However,transdermal therapy was associated with adverse effects with regard to the observed higher levels of PAI-1:Ag,which in turn,can lead to a reduction in fibrinolytic activity.

关键词： ghrelin 瘦素受体激素治疗绝经后妇女纤溶酶原激活物抑制物高水口服

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Re-imagining the Pastoral:Anonymity and the Late-Sixteenth-Century Reader in Fray Luis de León's First Ode

比较文学与世界文学

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比较文学与世界文学 2015年第2期 156-181页

作者： Anthony John Lappin Maynooth University Ireland swedish collegium

Pseudo-anonymity is used as a means of understanding this late Renaissance inflexion ofthe pastoral genre,in that it permits the author to occupy an ideal space of achieved(yet still humble)virtue and to further express the neo-Stoic ideal of retreat from the socio-political demands of the world into an environment which is characterized by a harmonious experience of nature within a garden setting,geared not for economic or material production but whose purpose is to foment cultural and intellectual fecundity.Moreover,by the dislocation of the author-figure from a historical individual to an ideal type,the poem may itself offer this transformative process to the well-informed reader,providing them with a means of partaking through imaginative participation in the creativity of this Edenic locus amoenus,and thus leading them on,by its function as an access to the following works of poetry within the collection,to other poems that express the neo-Stoic pursuit,attainment and exhortation,of and to virtue.

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Solid-phase microextraction of endogenous metabolites from intact tissue validated using a Biocrates standard reference method kit

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Journal of Pharmaceutical Analysis 2023年第1期13卷 55-62页

作者： Runshan Will Jiang Karol Jaroch Janusz Pawliszyn Department of Chemistry University of WaterlooWaterlooN2L 3G1Canada Department of Pharmacodynamics and Molecular Pharmacology Faculty of PharmacyCollegium Medicum in BydgoszczNicolaus Copernicus University in TorunBydgoszcz85-089Poland

Improved analytical methods for the metabolomic profiling of tissue samples are constantly needed.Currently,conventional sample preparation methods often involve tissue biopsy and/or homogenization,which disrupts the endogenous metabolome.In this study,solid-phase microextraction(SPME)fibers were used to monitor changes in endogenous compounds in homogenized and intact ovine lung tissue.Following SPME,a Biocrates AbsoluteIDQ assay was applied to make a downstream targeted metabolomics analysis and confirm the advantages of in vivo SPME metabolomics.The AbsoluteIDQ kit enabled the targeted analysis of over 100 metabolites via solid-liquid extraction and SPME.Statistical analysis revealed significant differences between conventional liquid extractions from homogenized tissue and SPME results for both homogenized and intact tissue samples.In addition,principal component analysis revealed separated clustering among all the three sample groups,indicating changes in the metabolome due to tissue homogenization and the chosen sample preparation method.Furthermore,clear differences in free metabolites were observed when extractions were performed on the intact and homogenized tissue using identical SPME procedures.Specifically,a direct comparison showed that 47 statistically distinct metabolites were detected between the homogenized and intact lung tissue samples(Pstudy's findings highlight both the importance of sample preparation in tissue-based metabolomics studies and SPME's unique ability to perform minimally invasive extractions without tissue biopsy or homogenization while providing broad metabolite coverage.

关键词： Solid-phase microextraction Solvent extraction Metabolomics Sample preparation In vivo sampling

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