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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 ***,among the world’s most widely distributed and cultivated trees,exhibit extensive phenotypic diversity and environmental *** 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 *** 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 *** 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 *** have experimentally validated a∼180-bp presence/absence variant affecting the expression of the CUC2 gene,crucial for leaf serration ***,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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Adsorption of yttrium(Y^(3+)) and concentration of rare earth elements from phosphogypsum using chitin and chitin aerogel

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Journal of Rare Earths 2024年第4期42卷 775-782页

作者： Glaydson S.dos Reis Diana Pinto Sabrina F.Lütke Eder C.Lima Luis F.O.Silva Irineu A.S.De Brum Guilherme L.Dotto Department of Forest Biomaterials and Technology Biomass Technology Centre Swedish University of Agricultural SciencesUmeaE13Swedn Universidad De La Costa Calle 58#55-66080002BarranquillaAtlanticoColombia Research Group on Adsorptive and Catalytic Process Engineering(ENGEPAC) Federal University of Santa MariaAv.Roraima100079705900Santa MariaRSBrazil Institute of Chemistry Federal University of Rio Grande do Sul90040060Porto AlegreBrazil

Chitin powder and chitin-aerogel were prepared from shrimp wastes and used to uptake Y^(3+)from aqueous solutions and concentrate this rare earth element from phosphogypsum(PG).Chitin aerogel displays a specific surface area of 945 m^(2)/g,while chitin powder is 3.6 m^(2)/g,which largely influences its adsorption *** the adsorption in synthetic solutions,the effect of pH on Y^(3+)removal is strong for chitin powder *** contrast,no big pH influence was detected for chitin *** interactions and chelation can highlight the proposed mechanism of Y^(3+)on chitin adsorbents for the powder and ***,in addition to these interactions,pore filling/pore diffusion is the main mechanism of Y^(3+)removal in the chitin *** aerogel is efficient in concentrating 8 times the Y^(3+)from PG,a very complex *** complex chitin aerogel-Y^(3+)can be a secondary source of rare earth elements for other applications.

关键词： Rare earths Sustainable material Chitin powder Chitin porous aerogel Yttrium adsorption and recovery

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The effects of temperature and resource availability on denitrification and relative N_(2)O production in boreal lake sediments

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Journal of Environmental Sciences 2016年第9期28卷 82-90页

作者： Maria Myrstener Anders Jonsson Ann-Kristin Bergstrom Department of Ecology and Environmental Science Umea University90187 UmeaSweden

Anthropogenic environmental stressors（like atmospheric deposition,land use change,and climate warming） are predicted to increase inorganic nitrogen and organic carbon loading to northern boreal lakes,with potential consequences for denitrification in ***,our ability to predict effects of these changes is currently limited as northern boreal lakes have been largely neglected in denitrification *** aim of this study was therefore to assess how maximum potential denitrification and N_2O production rates,and the relationship between the two（relative N_2O production）,is controlled by availability of nitrate（NO_3^-）,carbon（C）,phosphorus（P）,and *** were performed using the acetylene inhibition technique on sediments from a small,nutrient poor boreal lake in northern Sweden in *** potential denitrification and N_2O production rates at 4°C were reached already at NO_3^-additions of 106–120 μg NO_3^-–N/L,and remained unchanged with higher NO_3 *** incubation temperatures increased maximum potential denitrification and N_2O production rates,and Q10 was somewhat higher for N_2O production（1.77） than for denitrification（1.69）.The relative N_2O production ranged between 13% and 64%,and was not related to NO_3^-concentration,but the ratio increased when incubations were amended with C and P（from a median of 16% to 27%）.Combined,our results suggests that unproductive northern boreal lakes currently have low potential for denitrification but are susceptible to small changes in NO_3 loading especially if these are accompanied by enhanced C and P availability,likely promoting higher N_2O production relative to N_2.

关键词： Acetylene NO3 Carbon DOC Nitrous oxide ratio Sediment

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Mitigating the Prevalence of Diabetic Retinopathy in the United States: Utilization of the Chronic Care Model as a Public Health Framework

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Open Journal of Ophthalmology 2024年第2期14卷 103-116页

作者： Anthony Obiyom Kamalu Austin Ebhodaghe Ekeoba Emeka Canice Uzor Christian Chukwuka Duru Obinna Princewill Anyatonwu Ogemdi Emmanuel Adiele Chibuike Reginald Amuzie Chima Lawrence Odoemenam Public Health Department Louisiana State University Shreveport Shreveport USA College of Optometry State University of New York New York USA Faculty of Medicine and Health Sciences Department of Optometry Imo State University Owerri Nigeria Epidemiology and Global Health Unit Department of Public Health and Clinical Medicine Umea University Umea Sweden College of Medicine Georgetown University Washington DC USA Public Health Department School of Allied Health Professionals Louisiana State University Health Shreveport Shreveport USA

As the prevalence of diabetic retinopathy continues to be on the rise, the Chronic Care Model (CCM) offers a transformative, patient-focused approach for efficient diabetic retinopathy care, emphasizing the need for urgent and innovative strategies in the United States. The model integrates community resources, healthcare organizations, self-management support, delivery system design, decision support, and clinical information systems. Addressing challenges and solutions, the model emphasizes proactive and preventive measures, collaborative multidisciplinary care, technological integration, and overcoming resistance to change. This paper proposes the utilization of the Chronic Care Model (CCM) as a possible public health framework for comprehensive management of diabetic retinopathy in the United States. Implementing the CCM offers a comprehensive approach to diabetic retinopathy care, addressing both individual and systemic factors, essential for improving public health outcomes.

关键词： Chronic Care Model Diabetes Diabetic Retinopathy Model Implementation Vision Care

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Interplay between HEAT SHOCK PROTEIN 90 and HY5 Controls PhANG Expression in Response to the GUN5 Plastid Signal

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Molecular Plant 2012年第4期5卷 901-913页

作者： Peter Kindgren Louise Noren Juan de Dios Barajas Lopez Jehad Shaikhali Asa Strand umea Plant Science Centre Department of Plant Physiology Umea University S-901 87 Umea Sweden

The presence of genes encoding organellar proteins in different cellular compartments necessitates a tight coordination of expression by the different genomes of the eukaryotic cell. This coordination of gene expression is achieved by organelle-to-nucleus or retrograde communication. Stress-induced perturbations of the tetrapyrrole pathway trigger large changes in nuclear gene expression in plants. Recently, we identified HSP90 proteins as ligands of the pu- tative plastid signal Mg-ProtolX. In order to investigate whether the interaction between HSP90 and Mg-ProtolX is bio- logically relevant, we produced transgenic lines with reduced levels of cytosolic HSP90 in wild-type and gun5 backgrounds. Our work reveals that HSP90 proteins respond to the tetrapyrrole-mediated plastid signal to control expres- sion of photosynthesis-associated nuclear genes （PhANG） during the response to oxidative stress. We also show that the hy5 mutant is insensitive to tetrapyrrole accumulation and that Mg-ProtolX, cytosolic HSP90, and HY5 are all part of the same signaling pathway. These findings suggest that a regulatory complex controlling gene expression that includes HSP90 proteins and a transcription factor that is modified by tetrapyrroles in response to changes in the environment is evolutionarily conserved between yeast and plants.

关键词： abiotic/environmental stress cell signaling organelle biogenesis/function.

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AN EXTENDED BLOCK RESTRICTED ISOMETRY PROPERTY FOR SPARSE RECOVERY WITH NON-GAUSSIAN NOISE

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Journal of Computational Mathematics 2020年第6期38卷 827-838页

作者： Klara Leffler Zhiyong Zhou Jun Yu Department of Mathematics and Mathematical Statistics Umea UniversityUmeaSweden. Department of Statistics Zhejiang University City CollegeHangzhou 310015China Department of Mathematics and Mathematical Statistics Umea UniversityUmeaSweden

We study the recovery conditions of weighted mixedl2/lp minimization for block sparse signal reconstruction from compressed measurements when partial block support information is *** show theoretically that the extended block restricted isometry property can ensure robust recovery when the data fidelity constraint is expressed in terms of anlq norm of the residual error,thus establishing a setting wherein we are not restricted to Gaussian measurement *** illustrate the results with a series of numerical experiments.

关键词： Compressed sensing Block sparsity Partial support information Signal reconstruction Convex optimization

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Balancing past and present： how experience influences boldness over time in Eurasian perch

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Current Zoology 2017年第2期63卷 159-164页

作者： Gustav HELLSTROM Carin MAGNHAGEN Department of Ecology and Environmental Science Umea University SE-901 87 Umea Sweden Department of Wildlife Fish and Environmental Studies Swedish University of Agricultural Sciences 901 83 Umea Sweden.

Adapting to fluctuating predation conditions is a challenge for prey. By learning through experi- ence, animals may adjust their anti-predator behavior to better reflect current predation risk. Although many studies show experience of predation to alter prey behavior, little is known about how prey rely on such experience over time. By comparing boldness over different temporal scales between individuals of Eurasian perch, either experienced or naive of predators, we examine how risk is traded based on past and present experience. Differences in predator exposure during the first year of life were found to lead to differences in risk-taking behavior, even after the perch been kept in a predator-free environment for 9 months. However, the response to a potential predator was quickly readjusted after increased experience of current conditions. The results highlight how prey have to balance past experiences of predators against current threat levels.

关键词： behavior fish learning personality predation risk-taking.

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Metabolic changes in an animal model of amyotrophic lateral sclerosis evaluated by[^(18)F]-FDG positron emission tomography

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Translational Neurodegeneration 2021年第2期10卷 272-274页

作者： Bruno Lima Giacobbo Tomas Mediavilla Daniel JMarcellino Fahad Sultan Department of Integrative Medical Biology Umea UniversityUmeaSweden

Main text Energy metabolism has been proposed to be affected in amyotrophic lateral sclerosis(ALS),due to its relationship with SOD1^(G93A)-dependent mitochondrial loss-offunction[1,2].Although the metabolic state and the use of its dysfunction as an early diagnostic criterion have been evaluated in ALS patients by positron emission tomography(PET),preclinical research in animal models is *** this study,we imaged glucose metabolism using[^(18)F]-fluorodeoxyglucose(FDG)(NanoScan PET/CT,Mediso Medical Imaging Systems,Hungary)in both male and female mice expressing a mutated human SOD1 variant(hSOD1^(G93A))with ALS-like symptoms,and compared these animals to age-and sex-matched littermate controls(SOD1WT).

关键词： metabolism amyotrophic sclerosis

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Impacts of Norwegian large carnivore management strategy on national grazing sector

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Journal of Mountain Science 2019年第11期16卷 2470-2483页

作者： Inger HANSEN Geir-Harald STRAND Auvikki de BOON Camilla SANDSTROM Norwegian Institute of Bioeconomy Research Box 115N-1431 AsNorway Department of Political Science Umea University90187 UmeaSweden

Increasing populations of large carnivores are leading to tension and conflicts with livestock production,a situation that potentially might *** Norway the objective of the large carnivore policy is two-folded:to ensure viable carnivore populations and to secure a sustainable grazing *** main instrument is zonation,with carnivore management zones(CMZs)prioritized for reproduction of the large carnivore species separated from other areas prioritized for grazing *** objective of this paper is to describe current knowledge about the impact of the zoning management strategy on the grazing *** is done by documenting status and changes in sheep production,losses of livestock to predating carnivores,and the use of grazing areas inside and outside the *** protection for lynx,wolverine,bear and wolf cover 55%of the Norwegian mainland.30%of the sheep and 50%of the Sami reindeer grazing areas are found inside the ***(semi-domestic reindeer excluded)is using 59%of the available natural pasture areas outside the CMZs,but only 26%inside the *** lowest use of available grazing areas was found inside zones for wolves(12%)and brown bears(6%).Livestock in these zones are confined to fenced enclosures,mostly on the farm itself,or moved to pastures outside the management zone for summer *** losses increased in the affected regions during the period when carnivores were ***,losses declined when CMZs were established and mitigation efforts were implemented in these *** bulk of sheep and reindeer killed by carnivores are now found in boundary areas within 50 km off the CMZs,where sheep are still grazing on open mountain and forest ***,instruments to protect livestock in areas close to the CMZs are also *** number of sheep declined inside the CMZs from 1999 to 2014,but increased outside the *** reduction in the absolute number of sheep in the CMZs is balanced by

关键词： Carnivore management Depredation Management zones Rangeland Sheep Large carnivore policy

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Association between gastrointestinal symptoms and affectivity in patients with bipolar disorder

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World Journal of Gastroenterology 2016年第38期22卷 8540-8548页

作者： Pontus Karling Martin Maripuu Mikael Wikgren Rolf Adolfsson Karl-Fredrik Norrback Department of Public Health and Clinical Medicine Umea University Department of Clinical Sciences Division of PsychiatryUmea University

AIM To study if anxiety, depression and experience of stress are associated with gastrointestinal(GI) symptoms in patients with bipolar *** A total of 136 patients with bipolar disorder(mean age 49.9 years; 61% women) and 136 controls from the general population(mean age 51.0 years; 60% women) were included in the study. GI symptoms were assessed with The Gastrointestinal Symptom Rating Scale-irritable bowel syndrome(GSRS-IBS), level of anxiety and depression with The Hospital Anxiety and Depression Scale(HADS) and stress-proneness with Perceived Stress Questionnaire. Over a ten year period, all visits in primary care were retrospectively recorded in order to identify functional GI *** In subjects with low total HADS-score, there were no significant differences in GI-symptoms between patients and controls(GSRS-IBS 7.0 vs 6.5, P = 0.513). In the patients with bipolar disorder there were significant correlations between all GSRS and HADS subscores for all symptom clusters except for "constipation" and "reflux". Factors associated to GI symptoms in the patient group were female sex(adjusted OR = 2.37, 95%CI: 1.07-5.24) and high HADS-Depression score(adjusted OR = 3.64, 95%CI: 1.07-12.4). These patients had also significantly more visits for IBS than patients with low HADS-Depression scores(29% vs 8%, P = 0.008). However, there was no significant differences in consulting behaviour for functional GI disorders between patients and controls(25% vs 17%, P = 0.108).CONCLUSION Female patients and patients with high HADS depression score reported significantly more GI symptoms, whereas patients with low HADS scores did not differ from control subjects.

关键词： Anxiety Bipolar disorder Brain-Gut axis Depression Dyspepsia Functional gastrointestinal disorder Gastrointestinal Symptom Rating Scale-irritable bowel syndrome Irritable bowel syndrome Hospital Anxiety and Depression Scale Stress

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