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1.
  • Aagaard Hagemann, Frederik, et al. (författare)
  • Challenges to Implementing the Urban Ecosystem Service Concept in Green Infrastructure Planning: A View from Practitioners in Swedish Municipalities
  • 2020
  • Ingår i: Socio-Ecological Practice Research. - : Springer Science and Business Media LLC. - 2524-5279 .- 2524-5287. ; 2, s. 283-296
  • Tidskriftsartikel (refereegranskat)abstract
    • In building a sustainable society, numerous ecosystem services have shown to play important roles for the benefit of urban residents. The distinct concept of Urban Ecosystem Services (UES) to accentuate and enhance the value of urban ecosystems has been proposed, primarily in research, with implementation in practice still at an early stage. This study examined challenges to future implementation of the UES concept in municipal planning and management of urban green spaces. Based on interviews in six Swedish municipalities, we identified four overall discourses challenging implementation of UES in municipal practice. These included (i) a need to prioritize UES in municipal planning in order to address the contemporary challenges of e.g., urbanization and biodiversity loss. This in turn creates (ii) a need for increased holistic thinking within the municipal organization, based on (iii) further documentation and standards, which should help (iv) initiate organizational transition and cross-sectorial approaches. These discourses provide interrelated challenges that could also act as opportunities for scientists and practitioners collaborations to advance integration of UES into planning and management, thereby increasing the sustainability of urban environments. This work provides a starting point for introduction of the UES concept into municipal planning.
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2.
  • Aagaard Hagemann, Frederik (författare)
  • From place to emplacement: the scalar politics of sustainability
  • 2020
  • Ingår i: Local Environment. - : Informa UK Limited. - 1354-9839 .- 1469-6711. ; 25, s. 447-462
  • Tidskriftsartikel (refereegranskat)abstract
    • Sustainability has emerged as a central concept for discussing the current state of the human-environment system and planning for its future. To delve into the depths of sustainability means to talk about ecology, economy, and equity as fundamentally interconnected. However, each continues to be colonised by normative epistemologies of ecological sciences, neoclassical economics, and development, suggesting that with enough science and development, a more equitable sustainability is achievable. In our analysis, place emerges as an alternative epistemology through which to analyze sustainability. Place exists at multiple spatial and temporal scales, understood through direct observation of boundaries, processes and patterns, phenomenologically through individual experience, and as a complex hybrid: always emerging through interactions among individuals and institutions. Despite the ubiquity of place in the socio-ecological literature, the complexity of place in relation to sustainability is under-theorised, and in as much as sustainability happens or does not happen in real places rather than in policies and models, a place-based sustainability framework is necessary to move forward. To address this gap, we developed the emplacement framework, consisting of four domains: displacement, misplacement, replacement, and emplacement. Each domain is dynamic, constructing place as praxis, and reframing sustainability as a site of collective inquiry and choices. Our goal is to facilitate the active and on-going practices of place-based research and engagement among scholars, activists, and other community members by providing a structure for transdisciplinary dialogue and the application of transdisciplinary research to enable better decision-making.
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3.
  • Aballay, Erwin (författare)
  • Rhizobacteria associated to Vitis vinifera and their effect on the control of Xiphinema index, Meloidogyne ethiopica and Vitis growth
  • 2012
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Plant-parasitic nematodes are one of the most important pests affecting the growth of vineyards due to the destruction of new roots. Several species are associated with this problem, the most important being the ectoparasite Xiphinema index and the endoparasite Meloidogyne ethiopica. The search for new pest and disease control methods based on bioantagonist microorganisms is an important aspect of modern agriculture and the development of tools based on the use of rhizobacteria is becoming a widely evaluated alternative. The present study on suppressive soils started with a survey undertaken in productive Chilean vineyards to explore the younger roots of grapevines and identify the presence of rhizobacteria. More than 1800 soils were surveyed and a set of 11 vineyards were selected and considered suitable for bacteria isolation, as they showed low densities of plant-parasitic nematodes. A total of 400 bacterial isolates in 25 genera were obtained using tryptic soy broth agar and identified with fatty acid profiling. Two of the most frequently isolated species were Pseudomonas putida (35.1%) and P. fluorescens (6.1%). The effect of these isolates on the parasitism and reproduction of X. index was assessed through assays using potted vine plants (cv. Thompson Seedless) and a bacterial suspension containing 1×106 CFU/mL. Some isolates from Bacillus megaterium, B. brevis, B. mycoides, B. sphaericus, B. thuringiensis, Pseudomonas corrugata, P. putida, P. alcaligenes, P. savastanoi, P. fluorescens, P. pseudoalcaligenes, P. viridiflava, Stenotrophomonas maltophilia, Serratia plymuthica, Cytophaga johnsonae, Rahnella aquatilis, Stenotrophomonas sp., Variovorax paradoxus and Curtobacterium flaccumfaciens reduced root damage and suppressed populations. Isolates of B. brevis, Comamonas acidovorans, B. megaterium, Pantoea agglomerans and P. savastanoi increased plant growth or root weight, but did not control nematodes. Most of the culture filtrates obtained from isolates from four vineyards were effective in killing X. index and decreasing egg hatching, which was not related to damage or population control. It was estimated that 89, 32 and 16% of the isolates were effective against X. index under supernatant conditions, in potted plants growing in sterile substrate and in potted plants growing in field soil, respectively. Sixteen bacterial isolates previously assessed were also evaluated on M. ethiopica in vine cv. Chardonnay. Seven isolates (Serratia marcescens, C. acidovorans, P. agglomerans, Sphingobacterium spiritivorum, B. mycoides, Alcaligenes piechaudii and S. plymuthica) decreased damage or reproduction, showing that different species of nematodes can respond differently to a particular isolate.
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4.
  • Abarenkov, Kessy, et al. (författare)
  • The curse of the uncultured fungus
  • 2022
  • Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :86, s. 177-194
  • Tidskriftsartikel (refereegranskat)abstract
    • The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as "uncultured fungus". These sequences beget lowresolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length that represent truly unidentifiable fungal taxa - and what proportion of them that would have deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers' perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.
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5.
  • Abarenkov, Kessy, et al. (författare)
  • The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered
  • 2024
  • Ingår i: Nucleic Acids Research. - 0305-1048 .- 1362-4962. ; 52:D1, s. D791-D797
  • Tidskriftsartikel (refereegranskat)abstract
    • UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into similar to 2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms. Graphical Abstract
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6.
  • Abbasi, Alireza, et al. (författare)
  • Ambidentate coordination of dimethyl sulfoxide in rhodium(III) complexes
  • 2011
  • Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 40:5, s. 1111-1118
  • Tidskriftsartikel (refereegranskat)abstract
    • The two dimethyl sulfoxide solvated rhodium(III) compounds, [Rh(dmso-kappa O)(5)(dmso-kappa S)](CF(3)SO(3))(3) (1 & 1* at 298 K and 100 K, respectively) and [Rh(dmso-kappa O)(3)(dmso-kappa S)(2)Cl](CF(3)SO(3))(2) (2), crystallize with orthorhombic unit cells in the space group Pna2(1) (No. 33), Z = 4. In the [Rh(dmso)(6)](3+) complex with slightly distorted octahedral coordination geometry, the Rh-O bond distance is significantly longer with O trans to S, 2.143(6) angstrom (1) and 2.100(6) angstrom (1*), than the mean Rh-O bond distance with O trans to O, 2.019 angstrom (1) and 2.043 angstrom (1*). In the [RhCl(dmso)(5)](3+) complex, the mean Rh-O bond distance with O trans to S, 2.083 angstrom, is slightly longer than that for O trans to Cl, 2.067(4) angstrom, which is consistent with the trans influence DMSO-kappa S > Cl > DMSO-kappa O of the opposite ligands. Raman and IR absorption spectra were recorded and analyzed and a complete assignment of the vibrational bands was achieved with support by force field calculations. An increase in the Rh-O stretching vibrational frequency corresponded to a decreasing trans-influence from the opposite ligand. The Rh-O force constants obtained were correlated with the Rh-O bond lengths, also including previously obtained values for other M(dmso)(6)(3+) complexes with trivalent metal ions. An almost linear correlation was obtained for the MO stretching force constants vs. the reciprocal square of the MO bond lengths. The results show that the metal ion-oxygen bonding of dimethyl sulfoxide ligands is electrostatically dominated in those complexes and that the stretching force constants provide a useful measure of the relative trans-influence of the opposite ligands in hexa-coordinated Rh(III)-complexes.
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7.
  • Abbott, Benjamin W., et al. (författare)
  • Biomass offsets little or none of permafrost carbon release from soils, streams, and wildfire : an expert assessment
  • 2016
  • Ingår i: Environmental Research Letters. - : IOP Publishing. - 1748-9326. ; 11:3
  • Tidskriftsartikel (refereegranskat)abstract
    • As the permafrost region warms, its large organic carbon pool will be increasingly vulnerable to decomposition, combustion, and hydrologic export. Models predict that some portion of this release will be offset by increased production of Arctic and boreal biomass; however, the lack of robust estimates of net carbon balance increases the risk of further overshooting international emissions targets. Precise empirical or model-based assessments of the critical factors driving carbon balance are unlikely in the near future, so to address this gap, we present estimates from 98 permafrost-region experts of the response of biomass, wildfire, and hydrologic carbon flux to climate change. Results suggest that contrary to model projections, total permafrost-region biomass could decrease due to water stress and disturbance, factors that are not adequately incorporated in current models. Assessments indicate that end-of-the-century organic carbon release from Arctic rivers and collapsing coastlines could increase by 75% while carbon loss via burning could increase four-fold. Experts identified water balance, shifts in vegetation community, and permafrost degradation as the key sources of uncertainty in predicting future system response. In combination with previous findings, results suggest the permafrost region will become a carbon source to the atmosphere by 2100 regardless of warming scenario but that 65%-85% of permafrost carbon release can still be avoided if human emissions are actively reduced.
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8.
  • Abbott, D. Wade, et al. (författare)
  • Seaweed and Seaweed Bioactives for Mitigation of Enteric Methane : Challenges and Opportunities
  • 2020
  • Ingår i: Animals. - : MDPI AG. - 2076-2615. ; 10:12
  • Forskningsöversikt (refereegranskat)abstract
    • Simple Summary The need to become more efficient in agriculture and the food industry exists parallel to the challenge of climate change. Meat and dairy production is the target of much scrutiny due to methane (CH4) emissions and global warming. On the other hand, it should be noted that two-thirds of the world's agricultural land consists of pastures and permanent grasslands and is used for livestock grazing. This land is predominantly unsuitable for arable purposes but facilitates the production of high-quality human-edible protein in the form of ruminant animal-derived meat and milk. This makes a significant contribution to feeding the world's population. There is a need to reduce CH4 emissions, however, and several approaches are being researched currently. Seaweeds are diverse plants containing bioactives that differ from their terrestrial counterparts and they are increasingly under investigation as a feed supplement for the mitigation of enteric CH4. Seaweeds are rich in bioactives including proteins, carbohydrates and to a lesser extent lipids, saponins, alkaloids and peptides. These bioactives could also play a role as feed ingredients to reduce enteric CH4. This review collates information on seaweeds and seaweed bioactives and their potential to impact on enteric CH4 emissions. Seaweeds contain a myriad of nutrients and bioactives including proteins, carbohydrates and to a lesser extent lipids as well as small molecules including peptides, saponins, alkaloids and pigments. The bioactive bromoform found in the red seaweed Asparagopsis taxiformis has been identified as an agent that can reduce enteric CH4 production from livestock significantly. However, sustainable supply of this seaweed is a problem and there are some concerns over its sustainable production and potential negative environmental impacts on the ozone layer and the health impacts of bromoform. This review collates information on seaweeds and seaweed bioactives and the documented impact on CH4 emissions in vitro and in vivo as well as associated environmental, economic and health impacts.
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9.
  • Abd El-Daim, Islam Ahmed Moustafa, et al. (författare)
  • Bacillus velezensis 5113 Induced Metabolic and Molecular Reprogramming during Abiotic Stress Tolerance in Wheat
  • 2019
  • Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9
  • Tidskriftsartikel (refereegranskat)abstract
    • Abiotic stresses are main limiting factors for agricultural production around the world. Plant growth promoting rhizobacteria (PGPR) have been shown to improve abiotic stress tolerance in several plants. However, the molecular and physiological changes connected with PGPR priming of stress management are poorly understood. The present investigation aimed to explore major metabolic and molecular changes connected with the ability of Bacillus velezensis 5113 to mediate abiotic stress tolerance in wheat. Seedlings treated with Bacillus were exposed to heat, cold/freezing or drought stress. Bacillus improved wheat survival in all stress conditions. SPAD readings showed higher chlorophyll content in 5113-treated stressed seedlings. Metabolite profiling using NMR and ESI-MS provided evidences for metabolic reprograming in 5113-treated seedlings and showed that several common stress metabolites were significantly accumulated in stressed wheat. Two-dimensional gel electrophoresis of wheat leaves resolved more than 300 proteins of which several were differentially expressed between different treatments and that cold stress had a stronger impact on the protein pattern compared to heat and drought. Peptides maps or sequences were used for database searches which identified several homologs. The present study suggests that 5113 treatment provides systemic effects that involve metabolic and regulatory functions supporting both growth and stress management.
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10.
  • Abd El-Daim, Islam Ahmed Moustafa, et al. (författare)
  • Identifying potential molecular factors involved in Bacillus amyloliquefaciens 5113 mediated abiotic stress tolerance in wheat
  • 2018
  • Ingår i: Plant Biology. - : Wiley. - 1435-8603 .- 1438-8677. ; 20, s. 271-279
  • Tidskriftsartikel (refereegranskat)abstract
    • Abiotic stressors are main limiting factors for agricultural production around the world. Plant growth-promoting bacteria have been successfully used to improve abiotic stress tolerance in several crops including wheat. However, the molecular changes involved in the improvement of stress management are poorly understood. The present investigation addressed some molecular factors involved in bacterially induced plant abiotic stress responses by identifying differentially expressed genes in wheat (Triticum aestivum) seedlings treated with the beneficial bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5113 prior to challenge with abiotic stress conditions such as heat, cold or drought. cDNA-AFLP analysis revealed differential expression of more than 200 transcript-derived fragments (TDFs) in wheat leaves. Expression of selected TDFs was confirmed using RT-PCR. DNA sequencing of 31 differentially expressed TDFs revealed significant homology with both known and unknown genes in database searches. Virus-induced gene silencing of two abscisic acid-related TDFs showed different effects upon heat and drought stress. We conclude that treatment with B.amyloliquefaciens 5113 caused molecular modifications in wheat in order to induce tolerance against heat, cold and drought stress. Bacillus treatment provides systemic effects that involve metabolic and regulatory functions supporting both growth and stress management.
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11.
  • Abd El-Daim, Islam Ahmed Moustafa, et al. (författare)
  • Impact of bacterial priming on some stress tolerance mechanisms and growth of cold stressed wheat seedlings
  • 2013
  • Ingår i: International Journal of Plant Biology. - : MDPI AG. - 2037-0156 .- 2037-0164. ; 4, s. 29-33
  • Tidskriftsartikel (refereegranskat)abstract
    • The potential to enhance growth of cold stressed wheat by seed treatment (priming) with the beneficial bacteria Bacillus amyloliquefaciens 5113 and Azospirillum brasilense NO40 were tested. Results showed an improved ability of bacteria-treated seedlings to survive at −5°C up to 12 h. Cold stress increased transcript levels of three stress marker genes and increased activity for the ascorbate-glutathione redox enzymes. However, primed and stressed seedlings generally showed smaller effects on the stress markers correlating with better growth and improved stress tolerance. Bacterial priming to improve crop plant performance at low temperature seems a useful strategy to explore further.
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12.
  • Abd El-Daim, Islam Ahmed Moustafa, et al. (författare)
  • Improved heat stress tolerance of wheat seedlings by bacterial seed treatment
  • 2014
  • Ingår i: Plant and Soil. - : Springer Science and Business Media LLC. - 0032-079X .- 1573-5036. ; 379, s. 337-350
  • Tidskriftsartikel (refereegranskat)abstract
    • Aim: To investigate if rhizosphere bacteria can improve heat tolerance of wheat. MethodsWheat (Triticum aestivum) seeds of the cultivars Olivin and Sids1 were treated with Bacillus amyloliquefaciens UCMB5113 or Azospirillum brasilense NO40 and young seedlings tested for management of short term heat stress. ResultsBacterial treatment improved heat stress management of wheat. Olivin showed higher heat tolerance than Sids1 both with non-inoculated and inoculated seeds. Heat increased transcript levels of several stress related genes in the leaves, while expression was lower in inoculated plants but elevated compared with the control. Enzymes of the ascorbate-glutathione redox cycle were activated in leaves after heat challenge but showed a lower response in inoculated plants. Metabolite profiling distinguished different treatments dependent on analysis technique with respect to primary and secondary metabolites. Analysis of some plant stress regulatory genes showed that bacterial treatment increased transcript levels while effects of heat treatment varied. Conclusions: The improvement of heat tolerance by bacteria seems associated with reduced generation of reactive oxygen species (and consequently less cell damage), small changes in the metabolome while preactivation of certain heat shock transcription factors seems important. Seed inoculation with beneficial bacteria seems a promising strategy to improve heat tolerance of wheat.
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13.
  • Abd El-Daim, Islam Ahmed Moustafa, et al. (författare)
  • Paenibacillus polymyxa A26 Sfp-type PPTase inactivation limits bacterial antagonism against Fusarium graminearum but not of F. culmorum in kernel assay
  • 2015
  • Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 6
  • Tidskriftsartikel (refereegranskat)abstract
    • Fusarium graminearum and F. culmorum are the causing agents of a destructive disease known as Fusarium head blight (FHB). FHB is a re-emerging disease in small grain cereals which impairs both the grain yield and the quality. Most serious consequence is the contamination of grain with Fusarium mycotoxins that are severe threat to humans and animals. Biological control has been suggested as one of the integrated management strategies to control FHB. Paenibacillus polymyxa is considered as a promising biocontrol agent due to its unique antibiotic spectrum. P. polymyxa A26 is an efficient antagonistic agent against Fusarium spp. In order to optimize strain A26 production, formulation and application strategies traits important for its compatibility need to be revealed. Here we developed a toolbox, comprising of dual culture plate assays and wheat kernel assays, including simultaneous monitoring of FHB causing pathogens, A26, and mycotoxin production. Using this system we show that, besides generally known lipopeptide antibiotic production by P. polymyxa, biofilm formation ability may play a crucial role in the case of stain A26 F. culmorum antagonism. Application of the system for effective strain selection and maintenance is discussed.
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14.
  • Abd El-Daim, Islam Ahmed Moustafa (författare)
  • Use of rhizobacteria for the alleviation of plant stress
  • 2015
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Plant growth promoting rhizobacteria are beneficial microbes able to induce plant stress tolerance and antagonise plant pathogens. The present study showed that wheat seedlings pre-treated with Bacillus thuringiensis AZP2 had better tolerance to severe drought stress and showed 78% greater plant biomass and five-fold higher survivorship compared to wheat seedlings not treated with the bacterium. The effect of B. thuringiensis AZP2 also resulted in improved net assimilation and reduced emission of stress volatiles. The study investigated the effect of the inactivation of sfp-type phosphopantetheinyl transferase in plant growth promoting bacterium Paenibacillus polymyxa A26. The inactivation of the sfp gene resulted in loss of NRP/PK production such fusaricidins and polymyxins. In contrast to the former Bacillus spp. model the mutant strain compared to wild type showed greatly enhanced biofilm formation ability. Its biofilm promotion is directly mediated by NRP/PK, as exogenous addition of the wild type metabolite extracts restores its biofilm formation level. Further, increased biofilm formation was connected with enhanced ability of the sfp inactivated strain to remarkably protect wheat seedlings by improving its survival and biomass under severe drought stress conditions compared to wild type. Fusarium graminearum and F. culmorum are the causing agents of a destructive disease known as Fusarium head blight (FHB). The disease is the leading cause of contamination of grain with Fusarium mycotoxins that are severe threat to humans and animals. Biological control has been suggested as one of the integrated management strategies to control FHB causing agents. The present study showed that P. polymyxa A26 is a potent antagonistic agent against F. graminearum and F. culmorum. In order to optimize strain A26 production, formulation and application strategies traits important for its compatibility need to be revealed. Hence, a toolbox comprising of dual culture plate assays and wheat kernel assays including simultaneous monitoring of the FHB causing pathogens, A26 and mycotoxins produced was developed in the present study. Using this system results showed that, besides the involvement of lipopeptide antibiotic production by P. polymyxa in the antagonism process, biofilm formation ability may play a crucial role in the case of A26 F. culmorum antagonism.
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15.
  • Abdalla, M., et al. (författare)
  • Simulation of CO2 and Attribution Analysis at Six European Peatland Sites Using the ECOSSE Model
  • 2014
  • Ingår i: Water, Air and Soil Pollution. - : Springer Science and Business Media LLC. - 1573-2932 .- 0049-6979. ; 225:11, s. 2182-2182
  • Tidskriftsartikel (refereegranskat)abstract
    • In this study, we simulated heterotrophic CO2 (Rh) fluxes at six European peatland sites using the ECOSSE model and compared them to estimates of Rh made from eddy covariance (EC) measurements. The sites are spread over four countries with different climates, vegetation and management. Annual Rh from the different sites ranged from 110 to 540 g C m(-2). The maximum annual Rh occurred when the water table (WT) level was between -10 and -25 cm and the air temperature was above 6.2 degrees C. The model successfully simulated seasonal trends for the majority of the sites. Regression relationships (r(2)) between the EC-derived and simulated Rh ranged from 0.28 to 0.76, and the root mean square error and relative error were small, revealing an acceptable fit. The overall relative deviation value between annual EC-derived and simulated Rh was small (-1 %) and model efficiency ranges across sites from -0.25 to +0.41. Sensitivity analysis highlighted that increasing temperature, decreasing precipitation and lowering WT depth could significantly increase Rh from soils. Thus, management which lowers the WT could significantly increase anthropogenic CO2, so from a carbon emissions perspective, it should be avoided. The results presented here demonstrate a robust basis for further application of the ECOSSE model to assess the impacts of future land management interventions on peatland carbon emissions and to help guide best practice land management decisions.
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16.
  • Abdel-Fattah, Wael R., et al. (författare)
  • Growth-regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes
  • 2024
  • Ingår i: Nucleic Acids Research. - : Oxford University Press. - 0305-1048 .- 1362-4962. ; 52:11, s. 6220-6233
  • Tidskriftsartikel (refereegranskat)abstract
    • Mediator is a well-known transcriptional co-regulator and serves as an adaptor between gene-specific regulatory proteins and RNA polymerase II. Studies on the chromatin-bound form of Mediator revealed interactions with additional protein complexes involved in various transcription-related processes, such as the Lsm2–8 complex that is part of the spliceosomal U6 small nuclear ribonucleoprotein complex. Here, we employ Chromatin Immunoprecipitation sequencing (ChIP-seq) of chromatin associated with the Lsm3 protein and the Med1 or Med15 Mediator subunits. We identify 86 genes co-occupied by both Lsm3 and Mediator, of which 73 were intron-containing ribosomal protein genes. In logarithmically growing cells, Mediator primarily binds to their promoter regions but also shows a second, less pronounced occupancy at their 3́-exons. During the late exponential phase, we observe a near-complete transition of Mediator from these promoters to a position in their 3́-ends, overlapping the Lsm3 binding sites ∼250 bp downstream of their last intron–exon boundaries. Using an unbiased RNA sequencing approach, we show that transition of Mediator from promoters to the last exon of these genes correlates to reduction of both their messenger RNA levels and splicing ratios, indicating that the Mediator and Lsm complexes cooperate to control growth-regulated expression of intron-containing ribosomal protein genes at the levels of transcription and splicing.
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17.
  • Abdellah, Tebani, et al. (författare)
  • Integration of molecular profiles in a longitudinal wellness profiling cohort.
  • 2020
  • Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
  • Tidskriftsartikel (refereegranskat)abstract
    • An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies andimmune cell profiling, complementedwith gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine.
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18.
  • Abdollahi, Mehdi, 1985, et al. (författare)
  • Tuning the pH-shift protein-isolation method for maximum hemoglobin-removal from blood rich fish muscle
  • 2016
  • Ingår i: Food Chemistry. - : Elsevier BV. - 0308-8146 .- 1873-7072. ; 212, s. 213-224
  • Tidskriftsartikel (refereegranskat)abstract
    • A main challenge preventing optimal use of protein isolated from unconventional raw materials (e.g., small pelagic fish and fish by-products) using the pH-shift method is the difficulty to remove enough heme-pigments. Here, the distribution of hemoglobin (Hb) in the different fractions formed during pH-shift processing was studied using Hb-fortified cod mince. Process modifications, additives and prewashing were then investigated to further facilitate Hb-removal. The alkaline pH-shift process version could remove considerably more Hb (77%) compared to the acidic version (37%) when proteins were precipitated at pH 5.5; most Hb was removed during dewatering. Protein precipitation at pH 6.5 improved total Hb removal up to 91% and 74% during alkaline and acid processing, respectively. Adding phytic acid to the first supernatant of the alkaline process version yielded 93% Hb removal. Combining one prewash with phytic acid at pH 5.5 followed by alkaline/acid pH-shift processing increased Hb removal up to 96/92%.
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19.
  • Abebe, Admas Alemu, et al. (författare)
  • Developing genomic tools to assist turnip rape [Brassica rapa (L.) subsp.oleifera (DC.) Metzg.] breeding
  • 2024
  • Ingår i: Frontiers in Genetics. - 1664-8021. ; 15
  • Tidskriftsartikel (refereegranskat)abstract
    • Introduction: Turnip rape is recognized as an oilseed crop contributing to environmentally sustainable agriculture via integration into crop rotation systems. Despite its various advantages, the crop’s cultivation has declined globally due to a relatively low productivity, giving way to other crops. The use of genomic tools could enhance the breeding process and accelerate genetic gains. Therefore, the present research investigated 170 turnip rape accessions representing its global gene pool to identify SNP markers associated nine phenological and agro-morphological traits and estimate the genomic breeding values (GEBVs) of the germplasm through GWAS and genomic prediction analyses, respectively.Methods: Field trials were conducted at two sites in northern and southern Sweden to obtain the phenotypic data while genotyping was conducted via the genotyping-by-sequencing (GBS) method. The traits studied include days to flowering (DTF) and maturity (DTM), plant height (PH), seed yield (YLD), thousand seed weight (TSW), silique length (SL), number of siliques (NS), number of seeds per silique (SS), and pod shattering resistance (PSHR).Results and conclusion: Analysis of variance revealed substantial variation among accessions, with significant genotype-by-environment interaction for most traits. A total of 25, 17, 16, 14, 7, 5, 3, and 3 MTAs were identified for TSW, DTF, PH, PSHR, SL, YLD, SS and DTM, respectively. An 80%–20% training-test set genomic prediction analysis was conducted using the ridge regression – BLUP (RR-BLUP) model. The accuracy of genomic prediction for most traits was high, indicating that these tools may assist turnip rape breeders in accelerating genetic gains. The study highlights the potential of genomic tools to significantly advance breeding programs for turnip rape by identifying pivotal SNP markers and effectively estimating genomic breeding values. Future breeding perspectives should focus on leveraging these genomic insights to enhance agronomic traits and productivity, thereby reinstating turnip rape as a competitive and sustainable crop in Sweden and broader global agriculture.
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20.
  • Abebe, Admas Alemu, et al. (författare)
  • Genome-Wide Association Analysis and Genomic Prediction for Adult-Plant Resistance to Septoria Tritici Blotch and Powdery Mildew in Winter Wheat
  • 2021
  • Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 12
  • Tidskriftsartikel (refereegranskat)abstract
    • Septoria tritici blotch (STB) caused by the fungal pathogen Zymoseptoria tritici and powdery mildew (PM) caused by Blumeria graminis f.sp tritici (Bgt) are among the forefront foliar diseases of wheat that lead to a significant loss of grain yield and quality. Resistance breeding aimed at developing varieties with inherent resistance to STB and PM diseases has been the most sustainable and environment-friendly approach. In this study, 175 winter wheat landraces and historical cultivars originated from the Nordic region were evaluated for adult-plant resistance (APR) to STB and PM in Denmark, Estonia, Lithuania, and Sweden. Genome-wide association study (GWAS) and genomic prediction (GP) were performed based on the adult-plant response to STB and PM in field conditions using 7,401 single-nucleotide polymorphism (SNP) markers generated by 20K SNP chip. Genotype-by-environment interaction was significant for both disease scores. GWAS detected stable and environment-specific quantitative trait locis (QTLs) on chromosomes 1A, 1B, 1D, 2B, 3B, 4A, 5A, 6A, and 6B for STB and 2A, 2D, 3A, 4B, 5A, 6B, 7A, and 7B for PM adult-plant disease resistance. GP accuracy was improved when assisted with QTL from GWAS as a fixed effect. The GWAS-assisted GP accuracy ranged within 0.53-0.75 and 0.36-0.83 for STB and PM, respectively, across the tested environments. This study highlights that landraces and historical cultivars are a valuable source of APR to STB and PM. Such germplasm could be used to identify and introgress novel resistance genes to modern breeding lines.
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21.
  • Abebe, Admas Alemu (författare)
  • Genome-wide association study for yield-related traits in sesame (Sesamum Indicum)
  • 2022
  • Ingår i: Plant Breeding. - : Wiley. - 0179-9541 .- 1439-0523. ; 141, s. 246-256
  • Tidskriftsartikel (refereegranskat)abstract
    • Sesame is an important oil crop in Ethiopia and other regions in terms of both area coverage and production. However, productivity is low due to biotic and abiotic stresses. Therefore, dissecting the genetic basis of quantitatively inherited yield-related traits is instrumental to developing stable and high-yielding varieties. A genome-wide association study (GWAS) was performed with a diverse set of 300 sesame accessions tested in two environments and 2997 SNP markers. In total, 21 significant marker-trait associations (MTAs) were detected for seven yield-related traits, including days to flower initiation (DFI), days to 50% flowering (DF), days to physiological maturity (DM), capsule length (CAPL), seeds per capsule (SPC), 1000-seed weight (TSW) and bacterial blight (BBL). The majority of MTAs detected on LG 3, 7 and 8 were associated with traits related to physiological periods. Dissecting genetic control of flowering time and maturity has a pivotal contribution to fostering sesame breeding and developing new varieties adaptable to changing climatic conditions. Our GWAS results will assist in incorporating alleles into the elite sesame germplasm through marker-assisted selection.
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22.
  • Abebe, Admas Alemu, et al. (författare)
  • Genomic selection in plant breeding: key factors shaping two decades of progress
  • 2024
  • Ingår i: Molecular Plant. - 1674-2052 .- 1752-9867. ; 17, s. 552-578
  • Forskningsöversikt (refereegranskat)abstract
    • Genomic selection, the application of genomic prediction (GP) models to select candidate individuals, has significantly advanced in the past two decades, effectively accelerating genetic gains in plant breeding. This article provides a holistic overview of key factors that have influenced GP in plant breeding during this period. We delved into the pivotal roles of training population size and genetic diversity, and their relationship with the breeding population, in determining GP accuracy. Special emphasis was placed on optimizing training population size. We explored its benefits and the associated diminishing returns beyond an optimum size. This was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization algorithms. The density and distribution of single-nucleotide polymorphisms, level of linkage disequilibrium, genetic complexity, trait heritability, statistical machine-learning methods, and non-additive effects are the other vital factors. Using wheat, maize, and potato as examples, we summarize the effect of these factors on the accuracy of GP for various traits. The search for high accuracy in GP—theoretically reaching one when using the Pearson’s correlation as a metric—is an active research area as yet far from optimal for various traits. We hypothesize that with ultra-high sizes of genotypic and phenotypic datasets, effective training population optimization methods and support from other omics approaches (transcriptomics, metabolomics and proteomics) coupled with deep-learning algorithms could overcome the boundaries of current limitations to achieve the highest possible prediction accuracy, making genomic selection an effective tool in plant breeding.
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23.
  • Abebe, Admas Alemu, et al. (författare)
  • Haplotype-tagged SNPs improve genomic prediction accuracy for Fusarium head blight resistance and yield-related traits in wheat
  • 2023
  • Ingår i: TAG Theoretical and Applied Genetics. - 0040-5752 .- 1432-2242. ; 136
  • Tidskriftsartikel (refereegranskat)abstract
    • Genomic prediction is a powerful tool to enhance genetic gain in plant breeding. However, the method is accompanied by various complications leading to low prediction accuracy. One of the major challenges arises from the complex dimensionality of marker data. To overcome this issue, we applied two pre-selection methods for SNP markers viz. LD-based haplotype-tagging and GWAS-based trait-linked marker identification. Six different models were tested with preselected SNPs to predict the genomic estimated breeding values (GEBVs) of four traits measured in 419 winter wheat genotypes. Ten different sets of haplotype-tagged SNPs were selected by adjusting the level of LD thresholds. In addition, various sets of trait-linked SNPs were identified with different scenarios from the training-test combined and only from the training populations. The BRR and RR-BLUP models developed from haplotype-tagged SNPs had a higher prediction accuracy for FHB and SPW by 0.07 and 0.092, respectively, compared to the corresponding models developed without marker pre-selection. The highest prediction accuracy for SPW and FHB was achieved with tagged SNPs pruned at weak LD thresholds (r2 < 0.5), while stringent LD was required for spike length (SPL) and flag leaf area (FLA). Trait-linked SNPs identified only from training populations failed to improve the prediction accuracy of the four studied traits. Pre-selection of SNPs via LD-based haplotype-tagging could play a vital role in optimizing genomic selection and reducing genotyping costs. Furthermore, the method could pave the way for developing low-cost genotyping methods through customized genotyping platforms targeting key SNP markers tagged to essential haplotype blocks.
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24.
  • Abebe, Admas Alemu (författare)
  • Multi-model genome-wide association and genomic prediction analysis of 16 agronomic, physiological and quality related traits in ICARDA spring wheat
  • 2021
  • Ingår i: Euphytica. - : Springer Science and Business Media LLC. - 0014-2336 .- 1573-5060. ; 217
  • Tidskriftsartikel (refereegranskat)abstract
    • Identification and exploration of the genetic architecture of traits related to yield, quality, and drought and heat tolerance is important for yield and quality improvement of wheat through marker-assisted selection. One hundred and ninety-two spring wheat genotypes were tested at two heat-stress locations in Sudan (Wad Medani and Dongula), a drought stress site in Morocco (Marchouch) and a site with high yield potential in Egypt (Sids) in replicated trials during the 2015-2016 and 2016-2017 cropping seasons. A total of 10,577 single nucleotide polymorphism markers identified from the 15 K wheat SNP assay were used in a genome-wide association (GWA) study and genomic prediction for 16 phenotypic traits related to yield, quality and drought and heat tolerance. Significant marker-trait associations were detected across GWAS models for all traits. Most detected marker-trait associations (MTAs) were environment-specific, signifying the presence of high quantitative trait loci-by-environment (QTL x E) interaction. Chromosome arm 5AL had significant multi-model MTAs for grain yield and yield-related traits at the heat-stress locations. Highly significant QTLs were detected on chromosome 2D for waxiness. Homoeologous group 2 and 6 chromosomes were with significant MTAs for grain protein content, gluten content, alveograph strength and Zeleny sedimentation test while chromosome arm 3BL was significant for both Z and W traits. Genomic prediction analysis with ridge regression-best linear unbiased prediction model estimated the breeding values of the studied traits with prediction accuracies ranging from 0.16 for leaf rolling to 0.72 for peduncle length. The identified QTLs could be targeted for marker-assisted selection or further studies aimed at fine mapping and cloning the causative genes and detecting favorable haplotypes with positive effects for agronomic, physiological or quality-related traits.
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25.
  • Abebe, Admas Alemu (författare)
  • Single- and multi-trait genomic prediction and genome-wide association analysis of grain yield and micronutrient-related traits in ICARDA wheat under drought environment
  • 2023
  • Ingår i: Molecular Genetics and Genomics. - 1617-4615 .- 1617-4623. ; 298, s. 12-
  • Tidskriftsartikel (refereegranskat)abstract
    • Globally, over 2 billion people suffer from malnutrition due to inadequate intake of micronutrients. Genomic-assisted breeding is identified as a valuable method to facilitate developing new improved plant varieties targeting grain yield and micronutrient-related traits. In this study, a genome-wide association study (GWAS) and single- and multi-trait-based genomic prediction (GP) analysis was conducted using a set of 252 elite wheat genotypes from the International Center for Agricultural Research in Dry Areas (ICARDA). The objective was to identify linked SNP markers, putative candidate genes and to evaluate the genomic estimated breeding values (GEBVs) of grain yield and micronutrient-related traits.. For this purpose, a field trial was conducted at a drought-prone station, Merchouch, Morocco for 2 consecutive years (2018 and 2019) followed by GWAS and genomic prediction analysis with 10,173 quality SNP markers. The studied genotypes exhibited a significant genotypic variation in grain yield and micronutrient-related traits. The GWAS analysis identified highly significantly associated markers and linked putative genes on chromosomes 1B and 2B for zinc (Zn) and iron (Fe) contents, respectively. The genomic predictive ability of selenium (Se) and Fe traits with the multi-trait-based GP GBLUP model was 0.161 and 0.259 improving by 6.62 and 4.44%, respectively, compared to the corresponding single-trait-based models. The identified significantly linked SNP markers, associated putative genes, and developed GP models could potentially facilitate breeding programs targeting to improve the overall genetic gain of wheat breeding for grain yield and biofortification of micronutrients via marker-assisted (MAS) and genomic selection (GS) methods.
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26.
  • Abebe, Admas Alemu, et al. (författare)
  • Unraveling the Genetic Basis of Key Agronomic Traits of Wrinkled Vining Pea (Pisum sativum L.) for Sustainable Production
  • 2022
  • Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
  • Tidskriftsartikel (refereegranskat)abstract
    • Estimating the allelic variation and exploring the genetic basis of quantitatively inherited complex traits are the two foremost breeding scenarios for sustainable crop production. The current study utilized 188 wrinkled vining pea genotypes comprising historical varieties and breeding lines to evaluate the existing genetic diversity and to detect molecular markers associated with traits relevant to vining pea production, such as wrinkled vining pea yield (YTM100), plant height (PH), earliness (ERL), adult plant resistance to downy mildew (DM), pod length (PDL), numbers of pods per plant (PDP), number of peas per pod (PPD), and percent of small wrinkled vining peas (PSP). Marker-trait associations (MTAs) were conducted using 6902 quality single nucleotide polymorphism (SNP) markers generated from the diversity arrays technology sequencing (DArTseq) and Genotyping-by-sequencing (GBS) sequencing methods. The best linear unbiased prediction (BLUP) values were estimated from the two-decades-long (1999-2020) unbalanced phenotypic data sets recorded from two private breeding programs, the Findus and the Birds eye, now owned by Nomad Foods. Analysis of variance revealed a highly significant variation between genotypes and genotype-by-environment interactions for the ten traits. The genetic diversity and population structure analyses estimated an intermediate level of genetic variation with two optimal sub-groups within the current panel. A total of 48 significant (P < 0.0001) MTAs were identified for eight different traits, including five for wrinkled vining pea yield on chr2LG1, chr4LG4, chr7LG7, and scaffolds (two), and six for adult plant resistance to downy mildew on chr1LG6, chr3LG5 (two), chr6LG2, and chr7LG7 (two). We reported several novel MTAs for different crucial traits with agronomic importance in wrinkled vining pea production for the first time, and these candidate markers could be easily validated and integrated into the active breeding programs for marker-assisted selection.
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27.
  • Abebe Abiye, Shenkut, et al. (författare)
  • Genetic diversity of five local Swedish chicken breeds detected by microsatellite markers
  • 2015
  • Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10
  • Tidskriftsartikel (refereegranskat)abstract
    • This study aimed at investigating the genetic diversity, relationship and population structure of 110 local Swedish chickens derived from five breeds (Gotlandshona, Hedemorahona, Olandsk dvarghona, Skansk blommehona, and Bohuslan-Dals svarthona, in the rest of the paper the shorter name Svarthona is used) using 24 microsatellite markers. In total, one hundred thirteen alleles were detected in all populations, with a mean of 4.7 alleles per locus. For the five chicken breeds, the observed and expected heterozygosity ranged from 0.225 to 0.408 and from 0.231 to 0.515, with the lowest scores for the Svarthona and the highest scores for the Skansk blommehona breeds, respectively. Similarly, the average within breed molecular kinship varied from 0.496 to 0.745, showing high coancestry, with Skansk blommehona having the lowest and Svarthona the highest coancestry. Furthermore, all breeds showed significant deviations from Hardy-Weinberg expectations. Across the five breeds, the global heterozygosity deficit (FIT) was 0.545, population differentiation index (F-ST) was 0.440, and the global inbreeding of individuals within breed (F-IS) was 0.187. The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed two main clusters, with Hedemorahona and Olandsk dvarghona breeds in one cluster, and Gotlandshona and Svarthona breeds in the second cluster leaving the Skansk blommehona in the middle. Based on the results of the STRUCTURE analysis, the most likely number of clustering of the five breeds was at K = 4, with Hedemorahona, Gotlandshona and Svarthona breeds forming their own distinct clusters, while Olandsk dvarghona and Skansk blommehona breeds clustered together. Losses in the overall genetic diversity of local Swedish chickens due to breeds extinction varied from -1.46% to -6.723%. The results of the current study can be used as baseline genetic information for genetic conservation program, for instance, to control inbreeding and to implement further genetic studies in local Swedish chickens.
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28.
  • Abedi, Tayebeh (författare)
  • Arsenic Uptake and Accumulation Mechanisms in Rice Species
  • 2020
  • Ingår i: Plants. - : MDPI AG. - 2223-7747. ; 9
  • Forskningsöversikt (refereegranskat)abstract
    • Rice consumption is a source of arsenic (As) exposure, which poses serious health risks. In this study, the accumulation of As in rice was studied. Research shows that As accumulation in rice in Taiwan and Bangladesh is higher than that in other countries. In addition, the critical factors influencing the uptake of As into rice crops are defined. Furthermore, determining the feasibility of using effective ways to reduce the accumulation of As in rice was studied. AsV and AsIII are transported to the root through phosphate transporters and nodulin 26-like intrinsic channels. The silicic acid transporter may have a vital role in the entry of methylated As, dimethylarsinic acid (DMA) and monomethylarsonic acid (MMA), into the root. Amongst As species, DMA(V) is particularly mobile in plants and can easily transfer from root to shoot. The OsPTR7 gene has a key role in moving DMA in the xylem or phloem. Soil properties can affect the uptake of As by plants. An increase in organic matter and in the concentrations of sulphur, iron, and manganese reduces the uptake of As by plants. Amongst the agronomic strategies in diminishing the uptake and accumulation of As in rice, using microalgae and bacteria is the most efficient.
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29.
  • Abedi, Tayebeh (författare)
  • Cadmium Uptake by Wheat (Triticum aestivum L.): An Overview
  • 2020
  • Ingår i: Plants. - : MDPI AG. - 2223-7747. ; 9
  • Forskningsöversikt (refereegranskat)abstract
    • Cadmium is a toxic heavy metal that may be detected in soils and plants. Wheat, as a food consumed by 60% of the world's population, may uptake a high quantity of Cd through its roots and translocate Cd to the shoots and grains thus posing risks to human health. Therefore, we tried to explore the journey of Cd in wheat via a review of several papers. Cadmium may reach the root cells by some transporters (such as zinc-regulated transporter/iron-regulated transporter-like protein, low-a ffinity calcium transporters, and natural resistance-associated macrophages), and some cation channels or Cd chelates via yellow stripe 1-like proteins. In addition, some of the effective factors regarding Cd uptake into wheat, such as pH, organic matter, cation exchange capacity (CEC), Fe and Mn oxide content, and soil texture (clay content), were investigated in this paper. Increasing Fe and Mn oxide content and clay minerals may decrease the Cd uptake by plants, whereas reducing pH and CEC may increase it. In addition, the feasibility of methods to diminish Cd accumulation in wheat was studied. Amongst agronomic approaches for decreasing the uptake of Cd by wheat, using organic amendments is most effective. Using biochar might reduce the Cd accumulation in wheat grains by up to 97.8%.
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30.
  • Abedi, Tayebeh (författare)
  • Constructed wetland modified by biochar/zeolite addition for enhanced wastewater treatment
  • 2019
  • Ingår i: Environmental technology & innovation. - : Elsevier BV. - 2352-1864. ; 16
  • Tidskriftsartikel (refereegranskat)abstract
    • Wastewater treatment for water reuse has received considerable attention owing to water resource shortage. One of the most effective wastewater treatment methods involves the use of constructed wetlands (CWs). In this study, synthetic wastewater was treated by using a biochar/zeolite CW. Phragmites australis (common reed) was translocated into two cylinders (lysimeters) that serve as vertical subsurface flow CWs. One CW (CW1) contained gravels as substrate layer, whereas the other CW (CW2) contained three substrate layers, namely, biochar, zeolite, and gravel layers. Response surface methodology was used for statistical analysis. In this study, CW2 performed better in removing pollutants from wastewater than CW1. At optimum pH (6.3) and retention time (57.4 h), 99.9% (1000 mg/L) COD, 99.9% (1000 mg/L) ammonia, 99.9% (50 mg/L) phenols, 99.9% (50 mg/L) Pb, and 99.9% (50 mg/L) Mn were removed by CW2. During this research, nitrous oxide emission was lower in CW2 than in CW1. (C) 2019 Elsevier B.V. All rights reserved.
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31.
  • Abedi, Tayebeh, et al. (författare)
  • The Spatio-Temporal Distribution of Cell Wall-Associated Glycoproteins During Wood Formation in Populus
  • 2020
  • Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 11
  • Tidskriftsartikel (refereegranskat)abstract
    • Plant cell wall associated hydroxyproline-rich glycoproteins (HRGPs) are involved in several aspects of plant growth and development, including wood formation in trees. HRGPs such as arabinogalactan-proteins (AGPs), extensins (EXTs), and proline rich proteins (PRPs) are important for the development and architecture of plant cell walls. Analysis of publicly available gene expression data revealed that many HRGP encoding genes show tight spatio-temporal expression patterns in the developing wood of Populus that are indicative of specific functions during wood formation. Similar results were obtained for the expression of glycosyl transferases putatively involved in HRGP glycosylation. In situ immunolabelling of transverse wood sections using AGP and EXT antibodies revealed the cell type specificity of different epitopes. In mature wood AGP epitopes were located in xylem ray cell walls, whereas EXT epitopes were specifically observed between neighboring xylem vessels, and on the ray cell side of the vessel walls, likely in association with pits. Molecular mass and glycan analysis of AGPs and EXTs in phloem/cambium, developing xylem, and mature xylem revealed clear differences in glycan structures and size between the tissues. Separation of AGPs by agarose gel electrophoresis and staining with beta-D-glucosyl Yariv confirmed the presence of different AGP populations in phloem/cambium and xylem. These results reveal the diverse changes in HRGP-related processes that occur during wood formation at the gene expression and HRGP glycan biosynthesis levels, and relate HRGPs and glycosylation processes to the developmental processes of wood formation.
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32.
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33.
  • Abelein, A, et al. (författare)
  • High-yield Production of Amyloid-β Peptide Enabled by a Customized Spider Silk Domain
  • 2020
  • Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1, s. 235-
  • Tidskriftsartikel (refereegranskat)abstract
    • During storage in the silk gland, the N-terminal domain (NT) of spider silk proteins (spidroins) keeps the aggregation-prone repetitive region in solution at extreme concentrations. We observe that NTs from different spidroins have co-evolved with their respective repeat region, and now use an NT that is distantly related to previously used NTs, for efficient recombinant production of the amyloid-β peptide (Aβ) implicated in Alzheimer’s disease. A designed variant of NT from Nephila clavipes flagelliform spidroin, which in nature allows production and storage of β-hairpin repeat segments, gives exceptionally high yields of different human Aβ variants as a solubility tag. This tool enables efficient production of target peptides also in minimal medium and gives up to 10 times more isotope-labeled monomeric Aβ peptides per liter bacterial culture than previously reported.
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34.
  • Abelein, Axel, et al. (författare)
  • Hydrophobicity and conformational change as mechanistic determinants for nonspecific modulators of amyloid β self-assembly
  • 2012
  • Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 51:1, s. 126-137
  • Tidskriftsartikel (refereegranskat)abstract
    • The link between many neurodegenerative disorders, including Alzheimer's and Parkinson's diseases, and the aberrant folding and aggregation of proteins has prompted a comprehensive search for small organic molecules that have the potential to inhibit such processes. Although many compounds have been reported to affect the formation of amyloid fibrils and/or other types of protein aggregates, the mechanisms by which they act are not well understood. A large number of compounds appear to act in a nonspecific way affecting several different amyloidogenic proteins. We describe here a detailed study of the mechanism of action of one representative compound, lacmoid, in the context of the inhibition of the aggregation of the amyloid β-peptide (Aβ) associated with Alzheimer's disease. We show that lacmoid binds Aβ(1-40) in a surfactant-like manner and counteracts the formation of all types of Aβ(1-40) and Aβ(1-42) aggregates. On the basis of these and previous findings, we are able to rationalize the molecular mechanisms of action of nonspecific modulators of protein self-assembly in terms of hydrophobic attraction and the conformational preferences of the polypeptide.
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35.
  • Abelein, Axel, et al. (författare)
  • Transient small molecule interactions kinetically modulate amyloid beta peptide self-assembly
  • 2012
  • Ingår i: FEBS Letters. - : Wiley. - 0014-5793 .- 1873-3468. ; 586:22, s. 3991-3995
  • Tidskriftsartikel (refereegranskat)abstract
    • Small organic molecules, like Congo red and lacmoid, have been shown to modulate the self-assembly of the amyloid beta peptide (A beta). Here, we show that A beta forms NMR invisible non-toxic co-aggregates together with lacmoid as well as Congo red. We find that the interaction involves two distinct kinetic processes and at every given time point only a small fraction of A beta is in the co-aggregate. These weak transient interactions kinetically redirect the aggregation prone A beta from self-assembling into amyloid fibrils. These findings suggest that even such weak binders might be effective as therapeutics against pathogenic protein aggregation.
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36.
  • Abeysinghe, Kasun S., et al. (författare)
  • Mercury flow through an Asian rice-based food web
  • 2017
  • Ingår i: Environmental Pollution. - : ELSEVIER SCI LTD. - 0269-7491 .- 1873-6424. ; 229, s. 219-228
  • Tidskriftsartikel (refereegranskat)abstract
    • Mercury (Hg) is a globally-distributed pollutant, toxic to humans and animals. Emissions are particularly high in Asia, and the source of exposure for humans there may also be different from other regions, including rice as well as fish consumption, particularly in contaminated areas. Yet the threats Asian wildlife face in rice-based ecosystems are as yet unclear. We sought to understand how Hg flows through rice-based food webs in historic mining and non-mining regions of Guizhou, China. We measured total Hg (THg) and methylmercury (MeHg) in soil, rice, 38 animal species (27 for MeHg) spanning multiple trophic levels, and examined the relationship between stable isotopes and Hg concentrations. Our results confirm biomagnification of THg/MeHg, with a high trophic magnification slope. Invertivorous songbirds had concentrations of THg in their feathers that were 15x and 3x the concentration reported to significantly impair reproduction, at mining and non-mining sites, respectively. High concentrations in specialist rice consumers and in granivorous birds, the later as high as in piscivorous birds,, suggest rice is a primary source of exposure. Spiders had the highest THg concentrations among invertebrates and may represent a vector through which Hg is passed to vertebrates, especially songbirds. Our findings suggest there could be significant population level health effects and consequent biodiversity loss in sensitive ecosystems, like agricultural wetlands, across Asia, and invertivorous songbirds would be good subjects for further studies investigating this possibility.
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37.
  • Abeysinghe, Kasun S., et al. (författare)
  • Total mercury and methylmercury concentrations over a gradient of contamination in earthworms living in rice paddy soil
  • 2017
  • Ingår i: Environmental Toxicology and Chemistry. - : Wiley. - 0730-7268 .- 1552-8618. ; 36:5, s. 1202-1210
  • Tidskriftsartikel (refereegranskat)abstract
    • Mercury (Hg) deposited from emissions or from local contamination, can have serious health effects on humans and wildlife. Traditionally, Hg has been seen as a threat to aquatic wildlife, because of its conversion in suboxic conditions into bioavailable methylmercury (MeHg), but it can also threaten contaminated terrestrial ecosystems. In Asia, rice paddies in particular may be sensitive ecosystems. Earthworms are soil-dwelling organisms that have been used as indicators of Hg bioavailability; however, the MeHg concentrations they accumulate in rice paddy environments are not well known. Earthworm and soil samples were collected from rice paddies at progressive distances from abandoned mercury mines in Guizhou, China, and at control sites without a history of Hg mining. Total Hg (THg) and MeHg concentrations declined in soil and earthworms as distance increased from the mines, but the percentage of THg that was MeHg, and the bioaccumulation factors in earthworms, increased over this gradient. This escalation in methylation and the incursion of MeHg into earthworms may be influenced by more acidic soil conditions and higher organic content further from the mines. In areas where the source of Hg is deposition, especially in water-logged and acidic rice paddy soil, earthworms may biomagnify MeHg more than was previously reported. It is emphasized that rice paddy environments affected by acidifying deposition may be widely dispersed throughout Asia.
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38.
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39.
  • Ablondi, Michela, et al. (författare)
  • Performance of Swedish Warmblood fragile foal syndrome carriers and breeding prospects
  • 2022
  • Ingår i: Genetics Selection Evolution. - : Springer Science and Business Media LLC. - 0999-193X .- 1297-9686. ; 54
  • Tidskriftsartikel (refereegranskat)abstract
    • Background Warmblood fragile foal syndrome (WFFS) is a monogenetic defect caused by a recessive lethal missense point mutation in the procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 gene (PLOD1, c.2032G>A). The majority of homozygous WFFS horses are aborted during gestation. Clinical signs of affected horses include fragile skin, skin and mucosa lacerations, hyperextension of the articulations, and hematomas. In spite of its harmful effect, a relatively high frequency of WFFS carriers has been found in Warmblood horses, suggesting a heterozygote advantage. Thus, in this study our aims were to: (1) estimate the frequency of WFFS carriers in the Swedish Warmblood breed (SWB), (2) estimate the effect of WFFS carrier genotype on performance traits in two SWB subpopulations bred for different disciplines, and (3) simulate the potential effects of balancing selection and different selection strategies on the frequency of carriers. Methods In total, 2288 SWB sport horses born between 1971 and 2020 were tested for the WFFS mutation and had estimated breeding values (EBV) for ten traditional evaluating and 50 linear descriptive traits. Results The frequency of WFFS carriers calculated from a pool of 511 randomly selected SWB horses born in 2017 was equal to 7.4% and ranged from 0.0 to 12.0% among the whole set of tested SWB horses, starting from 1971 till 2020. The effect of the WFFS carrier genotype was significant for several EBV mainly related to movements and dressage traits and especially for horses not bred for the show jumping discipline. Using simulation, we showed that balancing selection can maintain a recessive lethal allele in populations such as the SWB breed over generations and that the frequency is expected to slowly decrease in absence of balancing selection. Finally, we showed that selection against carrier sires can result in a more rapid decrease of the frequency of the mutant allele over time. Conclusion Further research is needed to confirm the apparent association between equine performance and the WFFS carrier genotype. Identification of such associations or new causative mutations for horse performance traits can serve as new tools in horse breeding to select for healthy, sustainable, and better performing horses.
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40.
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41.
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42.
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43.
  • Ablondi, Michela, et al. (författare)
  • Signatures of selection in the genome of Swedish warmblood horses selected for sport performance
  • 2019
  • Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 20
  • Tidskriftsartikel (refereegranskat)abstract
    • Background A growing demand for improved physical skills and mental attitude in modern sport horses has led to strong selection for performance in many warmblood studbooks. The aim of this study was to detect genomic regions with low diversity, and therefore potentially under selection, in Swedish Warmblood horses (SWB) by analysing high-density SNP data. To investigate if such signatures could be the result of selection for equestrian sport performance, we compared our SWB SNP data with those from Exmoor ponies, a horse breed not selected for sport performance traits. Results The genomic scan for homozygous regions identified long runs of homozygosity (ROH) shared by more than 85% of the genotyped SWB individuals. Such ROH were located on ECA4, ECA6, ECA7, ECA10 and ECA17. Long ROH were instead distributed evenly across the genome of Exmoor ponies in 77% of the chromosomes. Two population differentiation tests (F-ST and XP-EHH) revealed signatures of selection on ECA1, ECA4, and ECA6 in SWB horses. Conclusions Genes related to behaviour, physical abilities and fertility, appear to be targets of selection in the SWB breed. This study provides a genome-wide map of selection signatures in SWB horses, and ground for further functional studies to unravel the biological mechanisms behind complex traits in horses.
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44.
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45.
  • Aboshady, Hadeer Moursy, et al. (författare)
  • Dynamic transcriptomic changes of goat abomasal mucosa in response to Haemonchus contortus infection
  • 2020
  • Ingår i: Veterinary Research. - : Springer Science and Business Media LLC. - 0928-4249 .- 1297-9716. ; 51
  • Tidskriftsartikel (refereegranskat)abstract
    • Gastrointestinal nematode (GIN) infections are one of the major constraints for grazing sheep and goat production worldwide. Genetic selection for resistant animals is a promising control strategy. Whole-transcriptome analysis via RNA-sequencing (RNA-seq) provides knowledge of the mechanisms responsible for complex traits such as resistance to GIN infections. In this study, we used RNA-seq to monitor the dynamics of the response of the abomasal mucosa of Creole goat kids infected with Haemonchus contortus by comparing resistant and susceptible genotypes. A total of 8 cannulated kids, 4 susceptible and 4 resistant to GIN, were infected twice with 10 000 L3 H. contortus. During the second infection, abomasal mucosal biopsies were collected at 0, 8, 15 and 35 days post-infection (dpi) from all kids for RNA-seq analysis. The resistant animals showed early activation of biological processes related to the immune response. The top 20 canonical pathways of differentially expressed genes for different comparison showed activation of the immune response through many relevant pathways including the Th1 response. Interestingly, our results showed a simultaneous time series activation of Th2 related genes in resistant compared to susceptible kids.
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46.
  • Aboshady, Hadeer Moursy, et al. (författare)
  • Genomic variants from RNA-seq for goats resistant or susceptible to gastrointestinal nematode infection
  • 2021
  • Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 16
  • Tidskriftsartikel (refereegranskat)abstract
    • Gastrointestinal nematodes (GIN) are an important constraint in small ruminant production. Genetic selection for resistant animals is a potential sustainable control strategy. Advances in molecular genetics have led to the identification of several molecular genetic markers associated with genes affecting economic relevant traits. In this study, the variants in the genome of Creole goats resistant or susceptible to GIN were discovered from RNA-sequencing. We identified SNPs, insertions and deletions that distinguish the two genotypes, resistant and susceptible and we characterized these variants through functional analysis. The T cell receptor signalling pathway was one of the top significant pathways that distinguish the resistant from the susceptible genotype with 78% of the genes involved in this pathway showing genomic variants. These genomic variants are expected to provide useful resources especially for molecular breeding for GIN resistance in goats.
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47.
  • Aboshady, Hadeer Moursy (författare)
  • Genomic variation and molecular mechanisms of the host response to gastrointestinal nematodes in small ruminants
  • 2020
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Gastrointestinal nematode (GIN) infections are one of the major constrains for sheep and goat production worldwide. One of the promising control strategies is the genetic selection for resistant animals as there are no issues due to anthelmintic resistance and it aligns to demands for chemical-free food. Exploring possible phenotypic and genomic markers that could be used in breeding scheme besides understanding the mechanisms responsible for resistance were the main goals of this thesis. Thesis consists of General introduction, a brief description of GIN biology and methods to control GIN with focus on phenotypic and genomic markers, four papers and General discussion. In paper Ⅰ, a systematic review and meta-analysis were conducted to re-analyse and summarize the findings on immunoglobulins response to GIN in the literature and discuss the potential to use immunoglobulins as biomarkers of the host resistance. A conceptual model summarizing the role of immunoglobulins in resistance to GIN is proposed. In paper Ⅱ, transcriptome profiling of the abomasal mucosa and lymph node tissues were compared between non-infected, resistant and susceptible Creole goats experimentally infected with Haemonchus contortus. Results indicated that the maintenance of the integrity of the mucosa has probably the priority for the host at late infection stage. In paper Ⅲ, the dynamics of the response of the abomasal mucosa of resistant and susceptible Creole goats experimentally infected with H. contortus were compared. The immune response was activated through many relevant pathways including the Th1 immune response at different time post-infection. Interestingly, the results showed a simultaneous time series activation of Th2 related genes in resistant compared to susceptible kids. In paper Ⅳ, the genomic variants of Creole goats resistant and susceptible to H. contortus were discovered from RNAsequencing data at four different times post-infection. Single nucleotide polymorphisms, insertions and deletions that distinguish the resistant and the susceptible groups were identified and characterized through functional analysis. The T cell receptor signalling pathway was one of the top significant pathways that distinguish the resistant from the susceptible group with genomic variants in 78% of genes in this pathway.
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48.
  • Aboshady, Hadeer Moursy, et al. (författare)
  • Immunoglobulins as Biomarkers for Gastrointestinal Nematodes Resistance in Small Ruminants: A systematic review
  • 2020
  • Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10
  • Forskningsöversikt (refereegranskat)abstract
    • The rise of anthelmintic resistance worldwide has led to the development of alternative control strategies for gastrointestinal nematodes (GIN) infections, which are one of the main constraints on the health of grazing small ruminants. Presently, breeding schemes rely mainly on fecal egg count (FEC) measurements on infected animals which are time-consuming and requires expertise in parasitology. Identifying and understanding the role of immunoglobulins in the mechanisms of resistance could provide a more efficient and sustainable method of identifying nematode-resistant animals for selection. In this study we review the findings on immunoglobulin response to GIN in the literature published to date (june 2019) and discuss the potential to use immunoglobulins as biomarkers. The literature review revealed 41 studies which measured at least one immunoglobulin: 35 focused on lamb immune response (18 used non-naive lambs) and 7 on yearlings. In this review we propose a conceptual model summarizing the role of immunoglobulins in resistance to GIN. We highlight the need for more carefully designed and documented studies to allow comparisons across different populations on the immunoglobulin response to GIN infection.
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49.
  •  
50.
  • Aboshady, Hadeer Moursy, et al. (författare)
  • Transcriptome variation in response to gastrointestinal nematode infection in goats
  • 2019
  • Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 14, s. 20-
  • Tidskriftsartikel (refereegranskat)abstract
    • Gastrointestinal nematodes (GIN) are a major constraint for small ruminant production. Due to the rise of anthelmintic resistance throughout the world, alternative control strategies are needed. The development of GIN resistance breeding programs is a promising strategy. However, a better understanding of the mechanisms underlying genetic resistance might lead to more effective breeding programmes. In this study, we compare transcriptome profiling of abomasal mucosa and lymph node tissues from non-infected, resistant and susceptible infected Creole goats using RNA-sequencing. A total of 24 kids, 12 susceptible and 12 GIN resistant based on the estimated breeding value, were infected twice with 10,000 L3 Haemonchus contortus. Physiological and parasitological parameters were monitored during infection. Seven weeks after the second infection, extreme kids (n = 6 resistant and 6 susceptible), chosen on the basis of the fecal egg counts (FEC), and 3 uninfected control animals were slaughtered. Susceptible kids had significantly higher FEC compared with resistant kids during the second infection with no differences in worm burden, male and female worm count or establishment rate. A higher number of differentially expressed genes (DEG) were identified in infected compared with non-infected animals in both abomasal mucosa (792 DEG) and lymph nodes (1726 DEG). There were fewer DEG in resistant versus susceptible groups (342 and 450 DEG, in abomasal mucosa and lymph nodes respectively). 'Cell cycle' and 'cell death and survival' were the main identified networks in mucosal tissue when comparing infected versus non-infected kids. Antigen processing and presentation of peptide antigen via major histocompatibility complex class I were in the top biological functions for the DEG identified in lymph nodes. The TGF beta 1 gene was one of the top 5 upstream DEG in mucosal tissue. Our results are one of the fist investigating differences in the expression profile induced by GIN infection in goats.
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