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  • 1.
    Ahad, Abdul
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Nick, Peter
    Actin is bundled in activation-tagged tobacco mutants that tolerate aluminum2007In: Planta, ISSN 0032-0935, E-ISSN 1432-2048, Vol. 225, no 2, p. 451-468Article in journal (Refereed)
    Abstract [en]

    A panel of aluminum-tolerant (AlRes) mutants was isolated by protoplast-based T-DNA activation tagging in the tobacco cultivar SR1. The mutants fell into two phenotypic classes: a minority of the mutants were fertile and developed similarly to the wild type (type I), the majority was male-sterile and grew as semi-dwarfs (type II). These traits, along with the aluminum tolerance, were inherited in a monogenic dominant manner. Both types of mutants were characterized by excessive bundling of actin microfilaments and by a strongly increased abundance of actin, a phenotype that could be partially phenocopied in the wild type by treatment with aluminum chloride. The actin bundles could be dissociated into finer strands by addition of exogenous auxin in both types of mutants. However, actin microfilaments and leaf expansion were sensitive to blockers of actin assembly in the wild type and in the mutants of type I, whereas they were more tolerant in the mutants of type II. The mutants of type II displayed a hypertrophic development of vasculature, manifest in form of supernumerary leaf veins and extended xylem layers in stems and petioles. Whereas mutants of type I were characterized by a normal, but aluminum-tolerant polar auxin-transport, auxin-transport was strongly promoted in the mutants of type II. The phenotype of these mutants is discussed in terms of reduced endocytosis leading, concomitantly with aluminum tolerance, to changes in polar auxin transport.

  • 2.
    Akhter, Shirin
    et al.
    Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Westrin, Karl Johan
    Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden.
    Zivi, Nathan
    Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden; Skogforsk, Uppsala Science Park, Uppsala, Sweden.
    Nordal, Veronika
    Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Kretzschmar, Warren W.
    Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden.
    Delhomme, Nicolas
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Street, Nathaniel R.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Nilsson, Ove
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Emanuelsson, Olof
    Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden.
    Sundström, Jens F.
    Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway2022In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 236, no 5, p. 1951-1963Article in journal (Refereed)
    Abstract [en]

    Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots.

    We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees.

    A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation.

    In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.

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  • 3.
    Akpinar, Ilgin
    et al.
    Istanbul University.
    Unal, Muammer
    Istanbul University.
    Sar, Taner
    University of Borås, Faculty of Textiles, Engineering and Business.
    Potential antifungal effects of silver nanoparticles (AgNPs) of different sizes against phytopathogenic Fusarium oxysporum f. sp. radicis-lycopersici (FORL) strains2021In: SN Applied Sciences, ISSN 2523-3963, E-ISSN 2523-3971, Vol. 3, no 4, p. 506-Article in journal (Refereed)
    Abstract [en]

    Fusarium species are the primary fungal pathogen affecting agricultural foodstuffs both in crop yield and economic loss. Due to these problems, control of phytopathogenic fungi has become one of the critical problems around the World. Nanotechnology is a new technology with potential in many fields, including agriculture. This study focused on determining potential effects of silver nanoparticles (AgNPs) with different nanosizes (3, 5, 8 and 10 nm) and at different concentrations (12.5–100 ppm) against phytopathogenic Fusarium oxysporum f. sp. radicis-lycopersici (FORL) strains. The maximum antifungal activity was achieved by decreasing nanosize and increasing concentration of AgNPs. Mycelium growth abilities were decreased about 50%, 75% and 90% by AgNPs treatment with 3 nm sizes at 25 ppm, 37.5 ppm and 50 ppm concentrations, respectively. The productivity of fungal biomass in the liquid growth media was found to be too limited at the 25–37.5 ppm of AgNPs concentrations with all sizes. In addition, both septation number and dimensions of micro- and macroconidia were found to be gradually decreased with the application of silver nanoparticles. This work showed that the low concentration of AgNPs could be used as potential antifungal agents and applied for control of phytopathogens.

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  • 4. Al Azzawi, Tiba Nazar Ibrahim
    et al.
    Khan, Murtaza
    Hussain, Adil
    Shahid, Muhammad
    Imran, Qari Muhammad
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics. School of Applied Biosciences, Kyungpook National University, Korea.
    Mun, Bong-Gyu
    Lee, Sang-Uk
    Yun, Byung-Wook
    Evaluation of Iraqi Rice Cultivars for Their Tolerance to Drought Stress2020In: Agronomy, E-ISSN 2073-4395, Vol. 10, no 11, article id 1782Article in journal (Refereed)
    Abstract [en]

    Drought stress is a serious problem around the globe and particularly in the Republic of Iraq. Rice is the third most consumed crop for the Iraqi people; however, its cultivation and production is very low due to several challenges including drought. The current study was performed to evaluate five Iraqi rice cultivars along with relevant (drought-tolerant and drought-susceptible) controls under drought stress, either by treatment with 10% PEG (polyethylene glycol) or through water withholding to induce natural drought stress. The phenotypes of all the cultivars were evaluated and the transcriptional responses of key drought-responsive candidate genes, identified through the EST-SSR marker-based approach, were studied. We also studied transcript accumulation of drought-related transcriptional factors, such as OsGRASS23, OsbZIP12, and OsDREB2A. Moreover, the reference cultivars also included a drought-tolerant inter-specific cultivar Nerica 7 (a cross between Oryza sativa ssp. indica X O. glaberrima). Among the cultivars, the more drought-tolerant phenotypic characteristics and higher transcript accumulation of drought-related marker genes OsE647 and OsE1899 and transcriptional factors OsGRASS23, OsbZIP12, and OsDREB2A were observed in four (out of five) significantly drought-tolerant Iraqi cultivars; Mashkab, followed by Furat, Yasmen, and Amber 33. On another note, Amber Barka was found to be significantly drought susceptible. Mashkab and Amber Barka were found to be the most drought-tolerant and-susceptible cultivars, respectively. The identified tolerant cultivars may potentially serve as a genetic source for the incorporation of drought-tolerant phenotypes in rice.

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  • 5. Ali, Muhammad Amjad
    et al.
    Azeem, Farrukh
    Nawaz, Muhammad Amjad
    Acet, Tuba
    Abbas, Amjad
    Imran, Qari Muhammad
    Laboratory of Plant Functional Genomics, College of Agriculture & Life Sciences, Kyngpook National University, Buk-gu Daegu, South Korea.
    Shah, Kausar Hussain
    Rehman, Hafiz Mamoon
    Chung, Gyuhwa
    Yang, Seung Hwan
    Transcription factors WRKY11 and WRKY17 are involved in abiotic stress responses in Arabidopsis2018In: Journal of plant physiology (Print), ISSN 0176-1617, E-ISSN 1618-1328, Vol. 226, p. 12-21Article in journal (Refereed)
    Abstract [en]

    Plant WRKY transcription factors play a vital role in abiotic stress tolerance and regulation of plant defense responses. This study examined AtWRKY11 and AtWRKY17 expression under ABA, salt, and osmotic stress at different developmental stages in Arabidopsis. We used reverse transcriptase PCR, quantitative real-time PCR, and promoter:GUS lines to analyze expression. Both genes were upregulated in response to abiotic stress. Next, we applied the same stressors to seedlings of T-DNA insertion wrky11 and 17 knock-out mutants (single and double). Under stress, the mutants exhibited slower germination and compromised root growth compared with the wild type. In most cases, double-mutant seedlings were more affected than single mutants. These results suggest that wrky11 and wrky17 are not strictly limited to plant defense responses but are also involved in conferring stress tolerance.

  • 6. Almeida, Pedro
    et al.
    Proux-Wera, Estelle
    Churcher, Allison M
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Soler, Lucile
    Dainat, Jacques
    Pucholt, Pascal
    Nordlund, Jessica
    Martin, Tom
    Ronnberg-Wastljung, Ann-Christin
    Nystedt, Bjorn
    Berlin, Sofia
    Mank, Judith E.
    Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion2020In: BMC Biology, E-ISSN 1741-7007, Vol. 18, no 1, article id 78Article in journal (Refereed)
    Abstract [en]

    Background: Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear.

    Results: Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes.

    Conclusions: Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.

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  • 7.
    Amith, Abraham
    et al.
    Rubber Research Institute of India, Kottayam, Kerala, India.
    Philip, Shaji
    Rubber Research Institute of India, Kottayam, Kerala, India.
    Joby, Joseph
    Rubber Research Institute of India, Kottayam, Kerala, India.
    Sivan, Pramod
    Rubber Research Institute of India, Kottayam, Kerala, India.
    Kuruvila, Jacob
    Rubber Research Institute of India, Kottayam, Kerala, India.
    Raveendran, Sindhu
    Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram-695 019, Kerala, India.
    Pandey, Ashok
    Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research (IITR), Lucknow-226 001, Uttar Pradesh, India.
    Byoung, Sang
    Kochupurackal, Jayachandran
    School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala, India.
    Growth promoting activities of antagonistic bacterial endophytes from Hevea brasiliensis (Willd. ex A.Juss.) Müll.Arg.2021In: Indian Journal of Experimental Biology, ISSN 0019-5189, Vol. 59, no 12, p. 827-833Article in journal (Refereed)
    Abstract [en]

    Rubber plantations are known to udergo various biotic and abiotic stresses. However, the symbiotic bacterial endophytes that inhabit them provide protection. Here, we isolated bacterial endophytes from the rubber tree, Hevea brasiliensis (Willd. ex A.Juss.) Müll.Arg. and studied their antagonistic activity against major pathogens such as Phytophthora meadii, Corynespora cassiicola and Corticium salmonicolar. The antifungal metabolites such as HCN, siderophores and salicylic acid were produced by the antagonistic endophytes under in vitro conditions. Bioassay showed the growth promotion by a consortium of selected antagonistic endophytes in H. brasiliensis seedlings. The photosynthetic efficiency of seedlings increased after endophyte inoculation. Endophyte-treated plants showed accumulation of starch granules in root tissues. The selected antagonistic isolates belong to Bacillus sp. and Pseudomonas sp. The study revealed the biocontrol and growth promoting potential of bacterial endophytes from H. brasiliensis.

  • 8.
    Andersson, Jessica
    et al.
    Halmstad University, School of Business, Innovation and Sustainability.
    Magnusson, Carl
    Halmstad University, School of Business, Innovation and Sustainability.
    Alternativa urbana odlingsmetodernas potential för självförsörjning i Sverige2024Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    During the COVID pandemic of 2019, Sweden saw a huge increase in food prices, as many of the country's grocery chains import a large amount of all foods. This research is motivated by the Swedish Parliament's motion "Self-Sufficiency of Food in Sweden" and the need for innovative solutions to enhance Sweden's food supply. This study focuses on alternative urban agriculture methods, with a focus on aeroponics, aquaponics, hydroponics, and vertical farming, and their potential for self-sufficiency in Sweden. This study aims to fill the gap in Swedish research on soilless urban farming methods and contribute to the understanding and acceptance of the alternative methods above. The study seeks to determine whether the yield of alternative cultivation methods is comparable to traditional methods, soil-based and greenhouse-based farming, in terms of resources invested and to identify the alternative method with the highest yield. Resources in this thesis will be defined as the amount of water that is used. Our thesis aims to support businesses and local governance in decision-making regarding implementation of alternative urban farming in Sweden. A literature search was conducted using keywords such as hydroponic, vertical farming and sustainability. Statistical analysis of collected data indicates significant differences in yield and water usage among the collected examples which resulted in vertical hydroponic farming offering the highest yield in terms of space utilization, with significant statistical significance (p < 0.05). Additionally, hydroponic farming requires the least amount of water compared to other methods although this is not a certainty as there was no significant statistical difference between the different methods. The study demonstrates that hydroponic farming can achieve higher yields compared to traditional soil-based farming and other alternative farming methods. The study emphasizes organizational and governmental solutions to improve self-sufficiency at the local and national levels. Alternative urban farming methods offer a sustainable contribution to increasing self-sufficiency while minimizing resource usage.

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  • 9.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci, Uppsala, Sweden;Texas A&M Univ, College Stn, TX 77843 USA.
    Fisher's quantitative genetic model and the molecular genetics of multifactorial traits2018In: Journal of Animal Breeding and Genetics, ISSN 0931-2668, E-ISSN 1439-0388, Vol. 135, no 6, p. 391-392Article in journal (Other academic)
  • 10.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX 77843 USA.;Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden..
    Mutations in Domestic Animals Disrupting or Creating Pigmentation Patterns2020In: Frontiers in Ecology and Evolution, E-ISSN 2296-701X, Vol. 8, article id 116Article, review/survey (Refereed)
    Abstract [en]

    The rich phenotypic diversity in coat and plumage color in domestic animals is primarily caused by direct selection on pigmentation phenotypes. Characteristic features are selection for viable alleles with no or only minor negative pleiotropic effects on other traits, and that alleles often evolve by accumulating several consecutive mutations in the same gene. This review provides examples of mutations that disrupt or create pigmentation patterns. White spotting patterns in domestic animals are often caused by mutations in KIT, microphthalmia transcription factor (MITF), or endothelin receptor B (EDNRB), impairing migration or survival of melanoblasts. Wild boar piglets are camouflage-colored and show a characteristic pattern of dark and light longitudinal stripes. This pattern is disrupted by mutations in Melanocortin 1 receptor (MC1R), implying that a functional MC1R receptor is required for wild-type camouflage color in pigs. The great majority of pig breeds carry MC1R mutations disrupting wild-type color and different mutations causing dominant black color were independently selected in European and Asian domestic pigs. The European allele evolved into a new allele creating a pigmentation pattern, black spotting, after acquiring a second mutation. This second mutation, an insertion of two C nucleotides in a stretch of 6 Cs, is somatically unstable and creates black spots after the open reading frame has been restored by somatic mutations. In the horse, mutations located in an enhancer downstream of TBX3 disrupt the Dun pigmentation pattern present in wild equids, a camouflage color where pigmentation on the flanks is diluted. A fascinating example of the creation of a pigmentation pattern is Sex-linked barring in chicken which is caused by the combined effect of both regulatory and coding mutations affecting the function of CDKN2A, a tumor suppressor gene associated with familial forms of melanoma in human. These examples illustrate how evolution of pigmentation patterns in domestic animals constitutes a model for evolutionary change in natural populations.

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  • 11.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Texas A&M Univ, Coll Vet Med & Biomed Sci, Dept Vet Integrat Biosci, College Stn, TX 77843 USA..
    White horses - non-coding sequences drive premature hair greying and predisposition to melanoma2024In: Upsala Journal of Medical Sciences, ISSN 0300-9734, E-ISSN 2000-1967, Vol. 129, no S1, article id e10626Article, review/survey (Refereed)
    Abstract [en]

    The Grey allele in horses is causing premature hair greying and susceptibility to melanoma. The causal mutation is a 4.6 kb tandem duplication in intron 6 of the Syntaxin 17 gene. A recent study demonstrated that the most common allele at the Grey locus (G3) involves three tandem copies of this sequence, whilst a more rare allele (G2) has two tandem copies and the wild-type allele (G1) only one copy. The G3 allele is causing fast greying and high incidence of skin melanoma, whereas the G2 allele is causing slow greying and no obvious increase in melanoma incidence. Further somatic copy number expansion has been documented in melanoma tissue from Grey horses. Functional studies showed that this intronic sequence acts as a weak melanocyte-specific enhancer that becomes substantially stronger by the copy number expansion. The Grey mutation is associated with upregulated expression of both Syntaxin 17 and the neighbouring NR4A3 gene in Grey horse melanomas. It is still an open question which of these genes is most important for the phenotypic effects or if causality is due to the combined effect of upregulation of both genes. Interestingly, RNAseq data in the Human Protein Atlas give support for a possible role of NR4A3 because it is particularly upregulated in human skin cancer, and it belongs to a cluster of genes associated with skin cancer and melanin biosynthesis. The Grey mutation and its association with melanoma provide a possibility to study the path to tumour development in numerous Grey horses carrying exactly the same predisposing mutation.

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  • 12. Andersson-Gunnerås, Sara
    et al.
    Mellerowicz, Ewa J
    Love, Jonathan
    Segerman, Bo
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ohmiya, Yasunori
    Coutinho, Pedro M
    Nilsson, Peter
    Henrissat, Bernard
    Moritz, Thomas
    Sundberg, Björn
    Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis2006In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 45, no 2, p. 144-165Article in journal (Refereed)
    Abstract [en]

    Stems and branches of angiosperm trees form tension wood (TW) when exposed to a gravitational stimulus. One of the main characteristics of TW, which distinguishes it from normal wood, is the formation of fibers with a thick inner gelatinous cell wall layer mainly composed of crystalline cellulose. Hence TW is enriched in cellulose, and deficient in lignin and hemicelluloses. An expressed sequence tag library made from TW-forming tissues in Populus tremula (L.) x tremuloides (Michx.) and data from transcript profiling using microarray and metabolite analysis were obtained during TW formation in Populus tremula (L.) in two growing seasons. The data were examined with the aim of identifying the genes responsible for the change in carbon (C) flow into various cell wall components, and the mechanisms important for the formation of the gelatinous cell wall layer (G-layer). A specific effort was made to identify carbohydrate-active enzymes with a putative function in cell wall biosynthesis. An increased C flux to cellulose was suggested by a higher abundance of sucrose synthase transcripts. However, genes related to the cellulose biosynthetic machinery were not generally affected, although the expression of secondary wall-specific CesA genes was modified in both directions. Other pathways for which the data suggested increased activity included lipid and glucosamine biosynthesis and the pectin degradation machinery. In addition, transcripts encoding fasciclin-like arabinogalactan proteins were particularly increased and found to lack true Arabidopsis orthologs. Major pathways for which the transcriptome and metabolome analysis suggested decreased activity were the pathway for C flux through guanosine 5'-diphosphate (GDP) sugars to mannans, the pentose phosphate pathway, lignin biosynthesis, and biosynthesis of cell wall matrix carbohydrates. Several differentially expressed auxin- and ethylene-related genes and transcription factors were also identified.

  • 13. Andreazza, N
    et al.
    Abreu, Ilka Nacif
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Sawaya, A
    Eberlin, M
    Mazzafera, P
    Production of imidazole alkaloids in cell cultures of jaborandi as affected by the medium pH2009In: Biotechnology letters, ISSN 0141-5492, E-ISSN 1573-6776, Vol. 31, no 4, p. 607-614Article in journal (Refereed)
    Abstract [en]

    The effect of pH (from 4.8 to 9.8) on the production of pilosine and pilocarpine and on their partition between cell and medium was studied in two lineages (P and PP) of Pilocarpus microphyllus cell suspension cultures. Highest mass accumulation was observed at high pHs and both lineages produced pilocarpine while only lineage PP produced pilosine. Both alkaloids were released in the medium but higher accumulation occurred in the cells. The highest production of pilocarpine was at pH 8.8-9.8 in both cell lineages. Other imidazole alkaloids were also identified in both lineages. At all pHs tested, the pH in the media cultures tended to stabilize around 6 after 10-15 days of cultivation. NO(3) (-) and NH(4) (+) variation in the media might partially explain the pH stabilization.

  • 14.
    Androsiuk, P.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. University of Warmia & Mazury, Poland.
    Shimono, A.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Westin, J.
    Lindgren, D.
    Fries, A.
    Wang, X. -R
    Genetic status of Norway spruce (Picea abies) breeding populations for northern Sweden2013In: Silvae Genetica, ISSN 0037-5349, Vol. 62, no 3, p. 127-136Article in journal (Refereed)
    Abstract [en]

    Efficient use of any breeding resources requires a good understanding of the genetic value of the founder breeding materials for predicting the gain and diversity in future generations. This study evaluates the distribution of genetic variation and level of relatedness among and within nine breeding populations of Norway spruce for Northern Sweden using nuclear microsatellite markers. A sample set of 456 individuals selected from 140 stands were genotyped with, 15 SSR loci. Over all loci each individual was identified with unique multilocus genotype. High genetic diversity (average H-e=0.820) and low population differentiation (F-ST = 0.0087) characterized this material. Although low in F-ST, the two northernmost populations were clustered as a distinct group diverged from the central populations. The population differentiation pattern corresponds well with the post glacial migration history of Norway spruce and the current gene flow and human activity in the region. The average inbreeding coefficient was 0.084 after removal loci with high frequency of null alleles. The estimated relatedness of the trees gathered in the breeding populations was very low (average kinship coefficient 0.0077) and not structured. The high genetic variation and low and not structured relatedness between individuals found in the breeding populations confirm that the Norway spruce breeding stock for northern Sweden represent valuable genetic resources for both long-term breeding and conservation programs.

  • 15.
    Aravind, Sanjukta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Optimization of Cultivation Strategies for Increased Isobutene Production in Cyanobacteria2023Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    The full text will be freely available from 2025-07-01 00:06
  • 16.
    Armada Moreira, Adam
    et al.
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Diacci, Chiara
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Manan Dar, Abdul Manan
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Berggren, Magnus
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Simon, Daniel
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Stavrinidou, Eleni
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering. Swedish Univ Agr Sci, Sweden.
    Benchmarking organic electrochemical transistors for plant electrophysiology2022In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 13, article id 916120Article in journal (Refereed)
    Abstract [en]

    Plants are able to sense and respond to a myriad of external stimuli, using different signal transduction pathways, including electrical signaling. The ability to monitor plant responses is essential not only for fundamental plant science, but also to gain knowledge on how to interface plants with technology. Still, the field of plant electrophysiology remains rather unexplored when compared to its animal counterpart. Indeed, most studies continue to rely on invasive techniques or on bulky inorganic electrodes that oftentimes are not ideal for stable integration with plant tissues. On the other hand, few studies have proposed novel approaches to monitor plant signals, based on non-invasive conformable electrodes or even organic transistors. Organic electrochemical transistors (OECTs) are particularly promising for electrophysiology as they are inherently amplification devices, they operate at low voltages, can be miniaturized, and be fabricated in flexible and conformable substrates. Thus, in this study, we characterize OECTs as viable tools to measure plant electrical signals, comparing them to the performance of the current standard, Ag/AgCl electrodes. For that, we focused on two widely studied plant signals: the Venus flytrap (VFT) action potentials elicited by mechanical stimulation of its sensitive trigger hairs, and the wound response of Arabidopsis thaliana. We found that OECTs are able to record these signals without distortion and with the same resolution as Ag/AgCl electrodes and that they offer a major advantage in terms of signal noise, which allow them to be used in field conditions. This work establishes these organic bioelectronic devices as non-invasive tools to monitor plant signaling that can provide insight into plant processes in their natural environment.

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  • 17.
    Arvidsson, Tommy
    The Nordic Africa Institute, Agrarian Change, Property and Resources.
    Food security now or wait for research to assess risks?: genetically modified crops and smallholder farmers in Africa2015Report (Other academic)
    Abstract [en]

    Genetically modified (GM) crops are by proponents considered as a possible solution to the food and nutrition problems in developing countries. However, there are also concerns of how side effects may affect environment and human health. These will probably still remain unknown for decades. But can Africa wait 30 years for research to give a definite answer about the risks connected with biotechnology?

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  • 18. Asadollahi, Mojtaba
    et al.
    Fekete, Éva
    Fekete, Erzsébet
    Karaffa, Levente
    Sándor, Erzsébet
    Pathogenicity differences between group I and group II of Botrytis cinerea2011In: Acta Agraria Debreceniensis, ISSN 1587-1282, no 43, p. 81-85Article in journal (Other academic)
  • 19. Asaf, Sajjad
    et al.
    Khan, Abdul Latif
    Aaqil Khan, Muhammad
    Imran, Qari Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.
    Kang, Sang-Mo
    Al-Hosni, Khdija
    Jeong, Eun Ju
    Lee, Ko Eun
    Lee, In-Jung
    Comparative analysis of complete plastid genomes from wild soybean (Glycine soja) and nine other Glycine species2017In: PLOS ONE, E-ISSN 1932-6203, Vol. 12, no 8Article in journal (Refereed)
    Abstract [en]

    The plastid genomes of different plant species exhibit significant variation, thereby providing valuable markers for exploring evolutionary relationships and population genetics. Glycine soja (wild soybean) is recognized as the wild ancestor of cultivated soybean (G. max), representing a valuable genetic resource for soybean breeding programmes. In the present study, the complete plastid genome of Gsoja was sequenced using Illumina paired-end sequencing and then compared it for the first time with previously reported plastid genome sequences from nine other Glycine species. The Gsoja plastid genome was 152,224 bp in length and possessed a typical quadripartite structure, consisting of a pair of inverted repeats (IRa/IRb; 25,574 bp) separated by small (178,963 bp) and large (83,181 bp) single-copy regions, with a 51-kb inversion in the large single-copy region. The genome encoded 134 genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 39 transfer RNA genes, and possessed 204 randomly distributed microsatellites, including 15 forward, 25 tandem, and 34 palindromic repeats. Whole-plastid genome comparisons revealed an overall high degree of sequence similarity between Gmax and Ggracilis and some divergence in the intergenic spacers of other species. Greater numbers of indels and SNP substitutions were observed compared with Gcyrtoloba. The sequence of the accD gene from Gsoja was highly divergent from those of the other species except for Gmax and Ggracilis. Phylogenomic analyses of the complete plastid genomes and 76 shared genes yielded an identical topology and indicated that Gsoja is closely related to Gmax and Ggracilis. The complete Gsoja genome sequenced in the present study is a valuable resource for investigating the population and evolutionary genetics of Glycine species and can be used to identify related species.

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  • 20. Asaf, Sajjad
    et al.
    Khan, Abdul Latif
    Khan, Muhammad Aaqil
    Imran, Qari Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea.
    Yun, Byung-Wook
    Lee, In-Jung
    Osmoprotective functions conferred to soybean plants via inoculation with Sphingomonas sp. LK11 and exogenous trehalose2017In: Microbiology Research, ISSN 0944-5013, E-ISSN 1618-0623, Vol. 205, p. 135-145Article in journal (Refereed)
    Abstract [en]

    Osmotic stress induced by drought can hinder the growth and yield of crop plants. To understand the eco-physiological role of osmoprotectants, the combined utilization of endophytes and osmolytes (trehalose) can be an ideal strategy used to overcome the adverse effects of drought. Hence, in the present study, we aimed to investigate the role of Sphingomonas sp. LK11, which produces phytohormones and synthesizes trehalose, in improving soybean plant growth under drought-induced osmotic stress (−0.4, −0.9, and −1.2 MPa). The results showed that the inoculation of soybean plants with Sphingomonas sp. LK11 significantly increased plant length, dry biomass, photosynthetic pigments, glutathione, amino acids (proline, glycine, and glutamate), and primary sugars as compared to control plants under varying drought stresses. Trehalose applied to the plant with or without endophyte-inoculation also showed similar plant growth-promoting attributes under stress. Stress exposure significantly enhanced endogenous jasmonic (JA) and abscisic (ABA) acid contents in control plants. In contrast, Sphingomonas sp. LK11-inoculation significantly lowered ABA and JA levels in soybean plants, but these phytohormones increased in response to combined treatments during stress. The drought-induced osmotic stress resistance associated with Sphingomonas sp. LK11 and trehalose was also evidenced by increased mRNA gene expression of soybean dehydration responsive element binding protein (DREB)-type transcription factors (GmDREBa and GmDREB2) and the MYB (myeloblastosis) transcription factor (GmMYBJ1) as compared to the control. In conclusion, our findings demonstrated that inoculation with this endophyte and trehalose improved the negative effects of drought-induced osmotic stress, and it enhanced soybean plant growth and tolerance.

  • 21. Asaf, Sajjad
    et al.
    Waqas, Muhammad
    Khan, Abdul L.
    Khan, Muhammad A.
    Kang, Sang-Mo
    Imran, Qari Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu, South Korea.
    Shahzad, Raheem
    Bilal, Saqib
    Yun, Byung-Wook
    Lee, In-Jung
    The complete chloroplast genome of wild rice (Oryza minuta) and its comparison to related species2017In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 8, article id 304Article in journal (Refereed)
    Abstract [en]

    Oryza minuta, a tetraploid wild relative of cultivated rice (family Poaceae), possesses a BBCC genome and contains genes that confer resistance to bacterial blight (BB) and white-backed (WBPH) and brown (BPH) plant hoppers. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of O. minuta with other Oryza species through an in-depth analysis of the composition and diversity of the chloroplast (cp) genome. The analysis revealed a cp genome size of 135,094 bp with a typical quadripartite structure and consisting of a pair of inverted repeats separated by small and large single copies, 139 representative genes, and 419 randomly distributed microsatellites. The genomic organization, gene order, GC content and codon usage are similar to those of typical angiosperm cp genomes. Approximately 30 forward, 28 tandem and 20 palindromic repeats were detected in the Ominuta cp genome. Comparison of the complete O. minuta cp genome with another eleven Oryza species showed a high degree of sequence similarity and relatively high divergence of intergenic spacers. Phylogenetic analyses were conducted based on the complete genome sequence, 65 shared genes and matK gene showed same topologies and O. minuta forms a single clade with parental O. punctata. Thus, the complete Ominuta cp genome provides interesting insights and valuable information that can be used to identify related species and reconstruct its phylogeny.

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  • 22.
    Asdal, Åsmund
    et al.
    Nordic Council of Ministers, The Nordic Genetic Resource Centre (NordGen).
    Brodal, Guro
    Norwegian Insititute of Bioeconomy Research, NIBIO.
    Solberg, Svein Øivind
    Inland Norway University of Applied Sciences.
    Yndgaard, Flemming
    von Bothmer, Roland
    Swedish University of Agricultural Sciences, SLU.
    Meen, Eivind
    Kimen Seed Laboratory.
    Seed Longevity and Survival of Seed Borne Diseases after 30 Years Conservation in Permafrost: Report from the 100 Year Storage experiment2019Report (Other academic)
    Abstract [en]

    The Nordic Gene bank established the 100 year seed storage experiment in Coal mine no. 3 outside Longyearbyen in 1986. Security duplicate samples of the Nordic seed collection had been deposited in permafrost in the coal mine since 1984. 

    The experiment was established with the aim to monitor the longevity of seeds in this Nordic back-up seed collection and to gain general knowledge about the longevity of seed stored under permafrost conditions, as well as studying the survival of seed borne plant pathogens.

    The experimental set up included in total 41 seed lots of 17 agricultural and horticultural crop species commonly grown in the Nordic countries. The seed germination experiment included two or three varieties of each crop. The experimental part dedicated to studies of pathogen survival included seeds from 11 crops naturally contaminated by pathogens.

    The test program comprises germination and pathogen survival tests every 2.5 years during the first 20 years and then every 5 years for the last 80 years. In total 25 identical sets of test seeds placed in sealed glass tubes were packed in wooden boxes, one box for each planned test year.

    The tests have been carried out according to schedule and this report sums up the results from the first 30 years of the experiment. All tests have been carried out in accordance with the same ISTA-protocols.

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  • 23.
    Aspeborg, Henrik
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Bhalerao, Rishikeshi
    Hertzberg, Magnus
    Johansson, Karin
    Johnsson, P.
    Karlsson, Ann
    Sandberg, Göran
    Schrader, Jarmo
    Sundberg, Björn
    Teeri, Tuula
    Trygg, Johan
    Wallbäcks, Lars
    Vegetabile material, plants and a method of producing a plant having altered lignin properties2008Patent (Other (popular science, discussion, etc.))
    Abstract [en]

    The present invention is related to a set of genes, which when modified in plants gives altered lignin properties. The invention provides DNA construct such as a vector useful in the method of the invention. Further, the invention relates to a plant cell or plant progeny of the plants and wood produced by the plants according to the invention Lower lignin levels will result in improved saccharification for bio-refining and ethanol production and improved pulp and paper. Increased lignin levels will utilise lignin properties for energy production. The genes and DNA constructs may be used for the identification of plants having altered lignin characteristics as compared to the wild-type. According to the invention genes and DNA constructs may also be used as candidate genes in marker assisted breeding.

  • 24.
    Aspeborg, Henrik
    et al.
    KTH, School of Biotechnology (BIO).
    Schrader, J.
    Coutinho, P. M.
    Stam, M.
    Kallas, A.
    Djerbi, S.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics.
    Denman, S.
    Amini, B.
    Sterky, Fredrik
    KTH, School of Biotechnology (BIO), Proteomics.
    Master, E.
    Sandberg, G.
    Mellerowicz, E.
    Sundberg, B.
    Henrissat, B.
    Teeri, Tuula T.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Carbohydrate-active enzymes involved in the secondary cell wall biogenesis in hybrid aspen2005In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 137, no 3, p. 983-997Article in journal (Refereed)
    Abstract [en]

    Wood formation is a fundamental biological process with significant economic interest. While lignin biosynthesis is currently relatively well understood, the pathways leading to the synthesis of the key structural carbohydrates in wood fibers remain obscure. We have used a functional genomics approach to identify enzymes involved in carbohydrate biosynthesis and remodeling during xylem development in the hybrid aspen Populus tremula x tremuloides. Microarrays containing cDNA clones from different tissue-specific libraries were hybridized with probes obtained from narrow tissue sections prepared by cryosectioning of the developing xylem. Bioinformatic analyses using the sensitive tools developed for carbohydrate-active enzymes allowed the identification of 25 xylem-specific glycosyltransferases belonging to the Carbohydrate-Active EnZYme families GT2, GT8, GT14, GT31, GT43, GT47, and GT61 and nine glycosidases (or transglycosidases) belonging to the Carbohydrate-Active EnZYme families GH9, GH10, GH16, GH17, GH19, GH28, GH35, and GH51. While no genes encoding either polysaccharide lyases or carbohydrate esterases were found among the secondary wall-specific genes, one putative O-acetyltransferase was identified. These wood-specific enzyme genes constitute a valuable resource for future development of engineered fibers with improved performance in different applications.

  • 25.
    Atikuzzaman, Mohammad
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Sanz, Libia
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Pla, Davinia
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Alvarez-Rodriguez, Manuel
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Rubér, Marie
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Calvete, Juan J.
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Rodriguez-Martinez, Heriberto
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Selection for higher fertility reflects in the seminal fluid proteome of modern domestic chicken2017In: Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics, ISSN 1744-117X, E-ISSN 1878-0407, Vol. 21, p. 27-40Article in journal (Refereed)
    Abstract [en]

    The high egg-laying capacity of the modern domestic chicken (i.e. White Leghorn, WL) has arisen from the low egg-laying ancestor Red Junglefowl (RJF) via continuous trait selection and breeding. To investigate whether this long-term selection impacted the seminal fluid (SF)-proteome, 2DE electrophoresis-based proteomic analyses and immunoassays were conducted to map SF-proteins/cytokines in RJF, WL and a 9th generation Advanced Intercross Line (AIL) of RJF/WL-L13, including individual SF (n = 4, from each RJF, WL and AIL groups) and pools of the SF from 15 males of each group, analyzed by 2DE to determine their degree of intra-group (AIL, WL, and RJF) variability using Principal Component Analysis (PCA); respectively an inter-breed comparative analysis of intergroup fold change of specific SF protein spots intensity between breeds. The PCA clearly highlighted a clear intra-group similarity among individual roosters as well as a clear inter-group variability (e.g. between RJF, WL and AIL) validating the use of pools to minimize confounding individual variation. Protein expression varied considerably for processes related to sperm motility, nutrition, transport and survival in the female, including signaling towards immunomodulation. The major conserved SF-proteins were serum albumin and ovotransferrin. Aspartate aminotransferase, annexin A5, arginosuccinate synthase, glutathione S-transferase 2 and l-lactate dehydrogenase-A were RJF-specific. Glyceraldehyde-3-phosphate dehydrogenase appeared specific to the WL-SF while angiotensin-converting enzyme, γ-enolase, coagulation factor IX, fibrinogen α-chain, hemoglobin subunit α-D, lysozyme C, phosphoglycerate kinase, Src-substrate protein p85, tubulins and thioredoxin were AIL-specific. The RJF-SF contained fewer immune system process proteins and lower amounts of the anti-inflammatory/immunomodulatory TGF-β2 compared to WL and AIL, which had low levels- or lacked pro-inflammatory CXCL10 compared to RJF. The seminal fluid proteome differs between ancestor and modern chicken, with a clear enrichment of proteins and peptides related to immune-modulation for sperm survival in the female and fertility.

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  • 26.
    Auffret, Alistair G
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Meineri, Eric
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Bruun, Hans Henrik
    Ejrnaes, Rasmus
    Graae, Bente J
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Ontogenetic niche shifts in three Vaccinium species on a sub-alpine mountain side2010In: Plant Ecology & Diversity, ISSN 1755-0874, E-ISSN 1755-1668, Vol. 3, no 2, p. 131-139Article in journal (Refereed)
    Abstract [en]

    Background: Climate warming in arctic and alpine regions is expected to result in the altitudinal migration of plant species, but current predictions neglect differences between species' regeneration niche and established niche.

    Aims: To examine potential recruitment of Vaccinium myrtillus, V. uliginosum and V. vitis-idaea on a mountain slope in northern Sweden in relation to current adult occurrence.

    Methods: We combined a seed-sowing experiment in seven community types with adult occurrence observations and species distribution mapping. Results: Emergence of V. myrtillus and V. vitis-idaea seedlings was significantly related to community type, while V. uliginosum was indifferent, but exhibited the highest average emergence. Adult occurrence was related to community, and ontogenetic niche shifts were observed for all three study species. V. myrtillus was shown to have the highest potential recruitment in habitats at altitudes above its current populations.

    Conclusions: The potential for migration exists, but incongruence between regenerative and established niches presents a challenge for colonisers, as well as for plant migration modelling.

  • 27.
    Axelsson, Erik
    et al.
    Uppsala University, Sweden.
    Ljungvall, Ingrid
    Swedish University of Agricultural Sciences, Sweden.
    Bhoumik, Priyasma
    Novartis Institutes for BioMedical Research, Switzerland.
    Bas Conn, Laura
    Uppsala University, Sweden.
    Muren, Eva
    Uppsala University, Sweden.
    Ohlsson, Åsa
    Swedish University of Agricultural Sciences, Sweden.
    Olsen, Lisbeth Høier
    University of Copenhagen, Denmark.
    Engdahl, Karolina
    Swedish University of Agricultural Sciences, Sweden.
    Hagman, Ragnvi
    Swedish University of Agricultural Sciences, Sweden.
    Hanson, Jeanette
    Swedish University of Agricultural Sciences, Sweden.
    Kryvokhyzha, Dmytro
    Uppsala University, Sweden.
    Pettersson, Mats
    Uppsala University, Sweden.
    Grenet, Olivier
    Novartis Institutes for BioMedical Research, Switzerland.
    Moggs, Jonathan
    Novartis Institutes for BioMedical Research, Switzerland.
    Del Rio-Espinola, Alberto
    Novartis Institutes for BioMedical Research, Switzerland.
    Epe, Christian
    Elanco Animal Health, USA.
    Taillon, Bruce
    Elanco Animal Health, USA.
    Tawari, Nilesh
    Elanco Animal Health, USA.
    Mane, Shrinivas
    Elanco Animal Health, USA.
    Hawkins, Troy
    Elanco Animal Health, USA.
    Hedhammar, Åke
    Swedish University of Agricultural Sciences, Sweden.
    Gruet, Philippe
    Novartis Animal Health, Switzerland.
    Häggström, Jens
    Swedish University of Agricultural Sciences, Sweden.
    Lindblad-Toh, Kerstin
    Uppsala University, Sweden.
    The genetic consequences of dog breed formation: Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels2021In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 17, no 9, article id e1009726Article in journal (Refereed)
    Abstract [en]

    Selective breeding for desirable traits in strictly controlled populations has generated an extraordinary diversity in canine morphology and behaviour, but has also led to loss of genetic variation and random entrapment of disease alleles. As a consequence, specific diseases are now prevalent in certain breeds, but whether the recent breeding practice led to an overall increase in genetic load remains unclear. Here we generate whole genome sequencing (WGS) data from 20 dogs per breed from eight breeds and document a ~10% rise in the number of derived alleles per genome at evolutionarily conserved sites in the heavily bottlenecked cavalier King Charles spaniel breed (cKCs) relative to in most breeds studied here. Our finding represents the first clear indication of a relative increase in levels of deleterious genetic variation in a specific breed, arguing that recent breeding practices probably were associated with an accumulation of genetic load in dogs. We then use the WGS data to identify candidate risk alleles for the most common cause for veterinary care in cKCs–the heart disease myxomatous mitral valve disease (MMVD). We verify a potential link to MMVD for candidate variants near the heart specific NEBL gene in a dachshund population and show that two of the NEBL candidate variants have regulatory potential in heart-derived cell lines and are associated with reduced NEBL isoform nebulette expression in papillary muscle (but not in mitral valve, nor in left ventricular wall). Alleles linked to reduced nebulette expression may hence predispose cKCs and other breeds to MMVD via loss of papillary muscle integrity.

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  • 28.
    Axelsson, Erik
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ljungvall, Ingrid
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Bhoumik, Priyasma
    Novartis Inst BioMed Res, Translat Med, Basel, Switzerland.;Swiss Fed Inst Technol, Sci & IT Serv, Basel Campus, Basel, Switzerland..
    Conn, Laura Bas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Murén, Eva
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ohlsson, Åsa
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden..
    Olsen, Lisbeth Hoier
    Univ Copenhagen, Dept Vet & Anim Sci, Copenhagen, Denmark..
    Engdahl, Karolina
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Hagman, Ragnvi
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Hanson, Jeanette
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Kryvokhyzha, Dmytro
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Pettersson, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Grenet, Olivier
    Novartis Inst BioMed Res, Translat Med, Basel, Switzerland..
    Moggs, Jonathan
    Novartis Inst BioMed Res, Translat Med, Basel, Switzerland..
    Del Rio-Espinola, Alberto
    Novartis Inst BioMed Res, Translat Med, Basel, Switzerland..
    Epe, Christian
    Elanco Anim Hlth, Greenfield, IN USA.;Boehringer Ingelheim Anim Hlth, Ingelheim, Germany..
    Taillon, Bruce
    Elanco Anim Hlth, Greenfield, IN USA..
    Tawari, Nilesh
    Elanco Anim Hlth, Greenfield, IN USA..
    Mane, Shrinivas
    Elanco Anim Hlth, Greenfield, IN USA..
    Hawkins, Troy
    Elanco Anim Hlth, Greenfield, IN USA..
    Hedhammar, Åke
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Gruet, Philippe
    Novartis Anim Hlth, St Aubin, Switzerland..
    Häggström, Jens
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Broad Inst MIT & Harvard, Cambridge, MA 02142 USA..
    The genetic consequences of dog breed formation-Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels2021In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 17, no 9, article id e1009726Article in journal (Refereed)
    Abstract [en]

    Selective breeding for desirable traits in strictly controlled populations has generated an extraordinary diversity in canine morphology and behaviour, but has also led to loss of genetic variation and random entrapment of disease alleles. As a consequence, specific diseases are now prevalent in certain breeds, but whether the recent breeding practice led to an overall increase in genetic load remains unclear. Here we generate whole genome sequencing (WGS) data from 20 dogs per breed from eight breeds and document a similar to 10% rise in the number of derived alleles per genome at evolutionarily conserved sites in the heavily bottlenecked cavalier King Charles spaniel breed (cKCs) relative to in most breeds studied here. Our finding represents the first clear indication of a relative increase in levels of deleterious genetic variation in a specific breed, arguing that recent breeding practices probably were associated with an accumulation of genetic load in dogs. We then use the WGS data to identify candidate risk alleles for the most common cause for veterinary care in cKCs-the heart disease myxomatous mitral valve disease (MMVD). We verify a potential link to MMVD for candidate variants near the heart specific NEBL gene in a dachshund population and show that two of the NEBL candidate variants have regulatory potential in heartderived cell lines and are associated with reduced NEBL isoform nebulette expression in papillary muscle (but not in mitral valve, nor in left ventricular wall). Alleles linked to reduced nebulette expression may hence predispose cKCs and other breeds to MMVD via loss of papillary muscle integrity.

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  • 29.
    Azeem, Muhammad
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Iqbal, Z.
    Emami, S. N.
    Nordlander, G.
    Nordenhem, H.
    Mozūratis, R.
    El-Seedi, Hesham
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Borg-Karlson, Anna-Karin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Chemical composition and antifeedant activity of some aromatic plants against pine weevil (Hylobius abietis)2020In: Annals of Applied Biology, ISSN 0003-4746, E-ISSN 1744-7348Article in journal (Refereed)
    Abstract [en]

    The pine weevil Hylobius abietis is an important pest causing severe damage to conifer seedlings in reforestation areas in Europe and Asia. Plants that have no evolutionary history with the pine weevil are of special interest in the search for compounds with a strong antifeedant activity. Thus, the essential oils of nine aromatic plants, viz Amomum subulatum, Cinnamomum tamala, Curcuma longa, Laurus nobilis, Ocimum basilicum, Origanum majorana, Origanum vulgare, Syzygium aromaticum and Trachyspermum ammi were extracted by hydrodistillation. The essential oil constituents were identified by gas chromatography–mass spectrometry, and antifeedant properties towards the pine weevil were assessed using choice feeding bioassay. The essential oils of C. longa, O. majorana, S. aromaticum and T. ammi showed an excellent antifeedant activity towards the pine weevil for 24 hr, whereas the essential oil of other plants showed the activity for 6 hr. There was a positive correlation between the amount of benzenoid compounds and the antifeedant activity of the essential oils. This study suggests that pine weevil non-host plant compounds have potential to be used for the protection of seedlings against pine weevil feeding. However, further study will be needed to explore the antifeedant activity of individual components and oils in the laboratory as well as in the field. 

  • 30.
    Bacete, Laura
    et al.
    Univ Politecn Madrid UPM, Ctr Biotecnol & Genom Plantas, Inst Nacl Invest & Tecnol Agr & Alimentaria INIA, Campus Montegancedo UPM, Pozuelo De Alarcon 28223, Madrid, Spain.;Univ Politecn Madrid, Dept Biotecnol Biol Vegetal, Escuela Tecn Super Ingn Agron Alimentaria & Biosi, Madrid 28040, Spain..
    Melida, Hugo
    Univ Politecn Madrid UPM, Ctr Biotecnol & Genom Plantas, Inst Nacl Invest & Tecnol Agr & Alimentaria INIA, Campus Montegancedo UPM, Pozuelo De Alarcon 28223, Madrid, Spain..
    Lopez, Gemma
    Univ Politecn Madrid UPM, Ctr Biotecnol & Genom Plantas, Inst Nacl Invest & Tecnol Agr & Alimentaria INIA, Campus Montegancedo UPM, Pozuelo De Alarcon 28223, Madrid, Spain..
    Dabos, Patrick
    Univ Toulouse, INRA, UPS, CNRS,LIPM, Castanet Tolosan, France..
    Tremousaygue, Dominique
    Univ Toulouse, INRA, UPS, CNRS,LIPM, Castanet Tolosan, France..
    Denance, Nicolas
    Univ Toulouse, INRA, UPS, CNRS,LIPM, Castanet Tolosan, France.;Univ Paul Sabatier, Lab Rech Sci Vegetales, CNRS, UMR 5546, Chemin Borde Rouge, F-31326 Castanet Tolosan, France..
    Miedes, Eva
    Univ Politecn Madrid UPM, Ctr Biotecnol & Genom Plantas, Inst Nacl Invest & Tecnol Agr & Alimentaria INIA, Campus Montegancedo UPM, Pozuelo De Alarcon 28223, Madrid, Spain.;Univ Politecn Madrid, Dept Biotecnol Biol Vegetal, Escuela Tecn Super Ingn Agron Alimentaria & Biosi, Madrid 28040, Spain..
    Bulone, Vincent
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. AlbaNova Univ Ctr, Sch Engn Sci Chem Biotechnol & Hlth, Royal IUniv Adelaide, RC Ctr Excellence Plant Cell Walls, Waite Campus, Urrbrae, SA 5064, Australia.;Univ Adelaide, Sch Agr Food & Wine, Waite Campus, Urrbrae, SA 5064, Australia..
    Goffner, Deborah
    Univ Paul Sabatier, Lab Rech Sci Vegetales, CNRS, UMR 5546, Chemin Borde Rouge, F-31326 Castanet Tolosan, France..
    Molina, Antonio
    Univ Politecn Madrid UPM, Ctr Biotecnol & Genom Plantas, Inst Nacl Invest & Tecnol Agr & Alimentaria INIA, Campus Montegancedo UPM, Pozuelo De Alarcon 28223, Madrid, Spain.;Univ Politecn Madrid, Dept Biotecnol Biol Vegetal, Escuela Tecn Super Ingn Agron Alimentaria & Biosi, Madrid 28040, Spain..
    Arabidopsis Response Regulator 6 (ARR6) Modulates Plant Cell-Wall Composition and Disease Resistance2020In: Molecular Plant-Microbe Interactions, ISSN 0894-0282, E-ISSN 1943-7706, Vol. 33, no 5, p. 767-780Article in journal (Refereed)
    Abstract [en]

    The cytokinin signaling pathway, which is mediated by Arabidopsis response regulator (ARR) proteins, has been involved in the modulation of some disease-resistance responses. Here, we describe novel functions of ARR6 in the control of plant disease-resistance and cell-wall composition. Plants impaired in ARR6 function (arr6) were more resistant and susceptible, respectively, to the necrotrophic fungus Plectosphaerella cucumerina and to the vascular bacterium Ralstonia solanacearum, whereas Arabidopsis plants that overexpress ARR6 showed the opposite phenotypes, which further support a role of ARR6 in the modulation of disease-resistance responses against these pathogens. Transcriptomics and metabolomics analyses revealed that, in arr6 plants, canonical disease-resistance pathways, like those activated by defensive phytohormones, were not altered, whereas immune responses triggered by microbe-associated molecular patterns were slightly enhanced. Cell-wall composition of arr6 plants was found to be severely altered compared with that of wild-type plants. Remarkably, pectin-enriched cell-wall fractions extracted from arr6 walls triggered more intense immune responses than those activated by similar wall fractions from wild-type plants, suggesting that an-6 pectin fraction is enriched in wall-related damage-associated molecular patterns, which trigger immune responses. This work supports a novel function of ARR6 in the control of cell-wall composition and disease resistance and reinforces the role of the plant cell wall in the modulation of specific immune responses.

  • 31.
    Barajas-Lopez, Juan de Dios
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Kremnev, Dmitry
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Shaikhali, Jehad
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Pinas-Fernandez, Aurora
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Strand, Åsa
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    PAPP5 is involved in the tetrapyrrole mediated plastid signalling during chloroplast development2013In: PLOS ONE, E-ISSN 1932-6203, Vol. 8, no 3, article id e60305Article in journal (Refereed)
    Abstract [en]

    The initiation of chloroplast development in the light is dependent on nuclear encoded components. The nuclear genes encoding key components in the photosynthetic machinery are regulated by signals originating in the plastids. These plastid signals play an essential role in the regulation of photosynthesis associated nuclear genes (PhANGs) when proplastids develop into chloroplasts. One of the plastid signals is linked to the tetrapyrrole biosynthesis and accumulation of the intermediates the Mg-ProtoIX and its methyl ester Mg-ProtoIX-ME. Phytochrome-Associated Protein Phosphatase 5 (PAPP5) was isolated in a previous study as a putative Mg-ProtoIX interacting protein. In order to elucidate if there is a biological link between PAPP5 and the tetrapyrrole mediated signal we generated double mutants between the Arabidopsis papp5 and the crd mutants. The crd mutant over-accumulates Mg-ProtoIX and Mg-ProtoIX-ME and the tetrapyrrole accumulation triggers retrograde signalling. The crd mutant exhibits repression of PhANG expression, altered chloroplast morphology and a pale phenotype. However, in the papp5crd double mutant, the crd phenotype is restored and papp5crd accumulated wild type levels of chlorophyll, developed proper chloroplasts and showed normal induction of PhANG expression in response to light. Tetrapyrrole feeding experiments showed that PAPP5 is required to respond correctly to accumulation of tetrapyrroles in the cell and that PAPP5 is most likely a component in the plastid signalling pathway down stream of the tetrapyrrole Mg-ProtoIX/Mg-ProtoIX-ME. Inhibition of phosphatase activity phenocopied the papp5crd phenotype in the crd single mutant demonstrating that PAPP5 phosphatase activity is essential to mediate the retrograde signal and to suppress PhANG expression in the crd mutant. Thus, our results suggest that PAPP5 receives an inbalance in the tetrapyrrole biosynthesis through the accumulation of Mg-ProtoIX and acts as a negative regulator of PhANG expression during chloroplast biogenesis and development.

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  • 32.
    Basso, Marcos Fernando
    et al.
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil.
    Lourenco-Tessutti, Isabela Tristan
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil.
    Moreira-Pinto, Clidia Eduarda
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil; Fed Univ Brasilia, Brazil.
    Mendes, Reneida Aparecida Godinho
    W5 Norte, Brazil; Fed Univ Brasilia, Brazil.
    Paes-de-Melo, Bruno
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil.
    das Neves, Maysa Rosa
    W5 Norte, Brazil.
    Macedo, Amanda Ferreira
    Univ Sao Paulo, Brazil.
    Figueiredo, Viviane
    Fed Univ Rio Janeiro, Brazil.
    Grandis, Adriana
    Univ Sao Paulo, Brazil.
    Macedo, Leonardo Lima Pepino
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil.
    Arraes, Fabricio Barbosa Monteiro
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil.
    Costa, Marcos Mota do Carmo
    W5 Norte, Brazil.
    Togawa, Roberto Coiti
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil.
    Enrich Prast, Alex
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. Linköping University, Biogas Research Center. Fed Univ Rio Janeiro, Brazil.
    Marcelino-Guimaraes, Francismar Correa
    Natl Inst Sci & Technol, Brazil; Embrapa Soybean, Brazil.
    Gomes, Ana Cristina Meneses Mendes
    W5 Norte, Brazil.
    Silva, Maria Cristina Mattar
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil.
    Floh, Eny Iochevet Segal
    Univ Sao Paulo, Brazil.
    Buckeridge, Marcos Silveira
    Univ Sao Paulo, Brazil.
    Engler, Janice de Almeida
    Natl Inst Sci & Technol, Brazil; Univ Cote dAzur, France.
    Grossi-de-Sa, Maria Fatima
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil; Univ Catolica Brasilia, Brazil.
    Overexpression of a soybean Globin (GmGlb1-1) gene reduces plant susceptibility to Meloidogyne incognita2022In: Planta, ISSN 0032-0935, E-ISSN 1432-2048, Vol. 256, no 4, article id 83Article in journal (Refereed)
    Abstract [en]

    Non-symbiotic globin class #1 (Glb1) genes are expressed in different plant organs, have a high affinity for oxygen, and are related to nitric oxide (NO) turnover. Previous studies showed that soybean Glb1 genes are upregulated in soybean plants under flooding conditions. Herein, the GmGlb1-1 gene was identified in soybean as being upregulated in the nematode-resistant genotype PI595099 compared to the nematode-susceptible cultivar BRS133 during plant parasitism by Meloidogyne incognita. The Arabidopsis thaliana and Nicotiana tabacum transgenic lines overexpressing the GmGlb1-1 gene showed reduced susceptibility to M. incognita. Consistently, gall morphology data indicated that pJ2 nematodes that infected the transgenic lines showed developmental alterations and delayed parasitism progress. Although no significant changes in biomass and seed yield were detected, the transgenic lines showed an elongated, etiolation-like growth under well-irrigation, and also developed more axillary roots under flooding conditions. In addition, transgenic lines showed upregulation of some important genes involved in plant defense response to oxidative stress. In agreement, higher hydrogen peroxide accumulation and reduced activity of reactive oxygen species (ROS) detoxification enzymes were also observed in these transgenic lines. Thus, based on our data and previous studies, it was hypothesized that constitutive overexpression of the GmGlb1-1 gene can interfere in the dynamics of ROS production and NO scavenging, enhancing the acquired systemic acclimation to biotic and abiotic stresses, and improving the cellular homeostasis. Therefore, these collective data suggest that ectopic or nematode-induced overexpression, or enhanced expression of the GmGlb1-1 gene using CRISPR/dCas9 offers great potential for application in commercial soybean cultivars aiming to reduce plant susceptibility to M. incognita.

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  • 33.
    Bautista, Rocí­o
    et al.
    University of Malaga.
    Villalobos, David, P.
    University of Malaga.
    Diaz-Moreno, Sara M
    University of Malaga.
    Cantón, Francisco, R.
    University of Malaga.
    Cánovas, Francisco, M.
    University of Malaga.
    Gonzalo Claros, M.
    University of Malaga.
    Toward a Pinus pinaster bacterial artificial chromosome library2007In: Annals of Forest Science, ISSN 1286-4560, E-ISSN 1297-966X, Vol. 64, no 8, p. 855-864Article in journal (Refereed)
    Abstract [en]

    Conifers are of great economic and ecological importance, but little is known concerning their genomic organization. This study is an attempt to obtain high-quality high-molecular-weight DNA from Pinus pinaster cotyledons and the construction of a pine BAC library. The preparation incorporates modifications like low centrifugation speeds, increase of EDTA concentration for plug maintenance, use of DNase inhibitors to reduce DNA degradation, use of polyvinylpyrrolidone and ascorbate to avoid secondary metabolites, and a brief electrophoresis of the plugs prior to their use. A total of 72 192 clones with an average insert size of 107 kb, which represents an equivalent of 11X pine haploid genomes, were obtained. The proportions of clones lacking inserts or containing chloroplast DNA are both approximately 1.6%. The library was screened with cDNA probes for seven genes, and two clones containing Fd-GOGAT sequences were found, one of them seemingly functional. Ongoing projects aimed at constructing a pinebacterial artificial chromosome library may benefit from the methods described here.

  • 34.
    Bellini, Catherine
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France.
    A synthetic auxin for cloning mature trees2024In: Nature Biotechnology, ISSN 1087-0156, E-ISSN 1546-1696Article in journal (Other academic)
  • 35. Benson, Samuel L
    et al.
    Maheswaran, Pratheesh
    Ware, Maxwell A
    Hunter, C Neil
    Horton, Peter
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ruban, Alexander V
    Johnson, Matthew P
    An intact light harvesting complex I antenna system is required for complete state transitions in Arabidopsis2015In: Nature plants, ISSN 2055-026X, Vol. 1, no 12, article id 15176Article in journal (Refereed)
    Abstract [en]

    Efficient photosynthesis depends on maintaining balance between the rate of light-driven electron transport occurring in photosystem I (PSI) and photosystem II (PSII), located in the chloroplast thylakoid membranes. Balance is achieved through a process of 'state transitions' that increases energy transfer towards PSI when PSII is overexcited (state II), and towards PSII when PSI is overexcited (state I). This is achieved through redox control of the phosphorylation state of light-harvesting antenna complex II (LHCII). PSI is served by both LHCII and four light-harvesting antenna complex I (LHCI) subunits, Lhca1, 2, 3 and 4. Here we demonstrate that despite unchanged levels of LHCII phosphorylation, absence of specific Lhca subunits reduces state transitions in Arabidopsis. The severest phenotype-observed in a mutant lacking Lhca4 (Delta Lhca4)-displayed a 69% reduction compared with the wild type. Yet, surprisingly, the amounts of the PSI-LHCI-LHCII supercomplex isolated by blue native polyacrylamide gel electrophoresis (BN-PAGE) from digitonin-solubilized thylakoids were similar in the wild type and Delta Lhca mutants. Fluorescence excitation spectroscopy revealed that in the wild type this PSI-LHCI-LHCII supercomplex is supplemented by energy transfer from additional LHCII trimers in state II, whose binding is sensitive to digitonin, and which are absent in Delta Lhca4. The grana margins of the thylakoid membrane were found to be the primary site of interaction between this 'extra' LHCII and the PSI-LHCI-LHCII supercomplex in state II. The results suggest that the LHCI complexes mediate energetic interactions between LHCII and PSI in the intact membrane.

  • 36.
    Berg, Håkan
    et al.
    Stockholm University, Stockholm Resilience Centre.
    Berg, Charlotte
    Nguyen, Thanh Tam
    Integrated Rice-Fish Farming: Safeguarding Biodiversity and Ecosystem Services for Sustainable Food Production in the Mekong Delta2012In: Journal of Sustainable Agriculture, ISSN 1044-0046, E-ISSN 1540-7578, Vol. 36, no 8, p. 859-872Article in journal (Refereed)
    Abstract [en]

    A comparison of agricultural practices, with a specific focus on pesticide use, between rice and rice-fish farmers in the Can Tho' and Tien Giang provinces of the Mekong Delta in 2007, shows that integrated rice-fish farming can provide a competitive alternative to intensive rice mono-cropping, if the farmer restricts the use of pesticides and takes full advantage of the ecosystem services provided by the rice-field ecosystem. In Can Tho', rice-fish farmers had significantly higher income (43.6 million dong ha(-1) year(-1)) than other farmer groups, while this was not seen among rice-fish famers in Tien Giang (32.4 million dong ha(-1) year(-1)), which partly could be due to a high use of insecticides (0.9 kg active ingredient ha(-1) crop(-1)) and comparatively low fish yield among these farmers. The study emphasizes the need to rethink current agricultural systems and to provide opportunities for more diverse systems that maintain and enhance a range of ecosystem services and protect human health. Future production systems should not be optimized to only provide a single ecosystem service, such as rice, but designed to deliver a variety of interlinked ecosystem service such as rice, fish, pest control, and nutrient recycling.

  • 37.
    Berglund, Jennie
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Wood Chemistry and Pulp Technology. Wallenberg Wood Science Center.
    Wood Hemicelluloses - Fundamental Insights on Biological and Technical Properties2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Hemicelluloses are a group of heterogeneous polysaccharides representing around 30 % of wood where the dominating types are xylans, glucomannans and xyloglucans. Hemicelluloses complex molecular structure makes it difficult to understand the relationship between structure and properties entirely, and their biological role is not yet fully verified. Additionally, hemicelluloses are sensitive to chemical processing and are not utilized to their full potentials for production of value-added products such as materials, additives to food and pharmaceutical products, etc. Increased knowledge regarding their functions is important for the development of both processes and products. The aim with this work has therefore been to increase the fundamental understanding about how the structure and properties of wood hemicelluloses are correlated, and properties such as flexibility, interaction with cellulose, solubility, resistance to chemical-, thermal-, and enzymatic degradation have been explored.

    Molecular dynamics (MD) simulations were used to, in detail, study the structures found in wood hemicelluloses. The flexibility was evaluated by comparing the impact of backbone sugars on the conformational space and also the impact of side groups was considered. Based on the conformational space of backbone glycosidic linkages the flexibility order of hemicelluloses in an aqueous environment was determined to be: xylan > glucomannan > xyloglucan. Additionally, the impact of xylan structure on cellulose interaction was evaluated by MD methods.

    Hemicelluloses were extracted from birch and spruce, and were used to fabricate different composite hydrogels with bacterial cellulose. These materials were studied with regards to mechanical properties, and it was shown that galactoglucomannans mainly contributed to an increased modulus in compression, whereas the most significant effect from xylan was increased strain under uniaxial tensile testing. Besides, other polysaccharides of similar structure as galactoglucomannans were modified and used as pure, well defined, models. Acetyl groups are naturally occurring decorations of wood hemicelluloses and can also be chemically introduced. Here, mannans with different degrees of acetylation were prepared and the influence of structure on solubility in water and the organic solvent DMSO were evaluated. Furthermore, the structure and water solubility influenced the interaction with cellulose. Acetylation also showed to increase the thermal and biological stability of mannans.

    With chemical pulping processes in mind, the degradability of spruce galactoglucomannans in alkaline solution were studied with regards to the structure, and the content of more or less stable structural regions were proposed.

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  • 38.
    Bergqvist, AS
    et al.
    Swedish University of Agriculture Science, Sweden.
    Yokoo, M
    Tohoku University , Japan; .
    Bage, R
    Swedish University of Agriculture Science, Sweden.
    Sato, E
    Tohoku University, Japan; .
    Rodriguez-Martinez, Heriberto
    Swedish University of Agriculture Science, Sweden.
    Detection of the hyaluronan receptor CD44 in the bovine oviductal epithelium2005In: Journal of reproduction and development, ISSN 0916-8818, E-ISSN 1348-4400, Vol. 51, no 4, p. 445-453Article in journal (Refereed)
    Abstract [en]

    Hyaluronan is involved in fundamental reproductive events such as sperm storage in the female reproductive tract, fertilization, and early embryo development, these functions are presumably mediated by its major cell surface receptor, CD44. The present study was conducted to investigate the presence and localization of CD44 in the bovine oviductal epithelium, using immunohistochemical and Western blot methods on tissue sections and epithelial cell extracts collected from the uterotubal junction (UTJ), isthmus, and ampulla of animals in the oestrus or luteal phase of the oestrous cycle. While positive immunolabelling for CD44 was found on the ad-luminal surface and supra-nuclear region of epithelial cells in all tubal segments investigated, in the UTJ, there were epithelial cells in which the entire cytoplasm positively stained. We found no differences in terms of CD44-positive staining between the different stages of the oestrous cycle. Presence of CD44 was detected by Western blotting in the tubal epithelium as a single band at 200 kDa. Although it appeared in all tubal segments, the expression of CD44 protein was more accentuated in the sperm reservoir (UTJ) than in the other segments. This is the first time CD44 has been detected in the epithelium of the tubal sperm reservoir in cattle, suggesting a pathway for the action of hyaluronan in this segment.

  • 39.
    Bianchi, Matteo
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Rafati, Nima
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Karlsson, Åsa
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Murén, Eva
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Rubin, Carl-Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sundberg, Katarina
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden..
    Andersson, Göran
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden..
    Kämpe, Olle
    Karolinska Inst, Dept Med Solna, Stockholm, Sweden..
    Hedhammar, Åke
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Broad Inst MIT & Harvard, Cambridge, MA 02142 USA..
    Rosengren Pielberg, Gerli
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs2020In: BMC Genomics, E-ISSN 1471-2164, Vol. 21, article id 307Article in journal (Refereed)
    Abstract [en]

    Background: Hypothyroidism is a common complex endocrinopathy that typically has an autoimmune etiology, and it affects both humans and dogs. Genetic and environmental factors are both known to play important roles in the disease development. In this study, we sought to identify the genetic risk factors potentially involved in the susceptibility to the disease in the high-risk Giant Schnauzer dog breed.

    Results: By employing genome-wide association followed by fine-mapping (top variant p-value=5.7x10(-6)), integrated with whole-genome resequencing and copy number variation analysis, we detected a similar to 8.9 kbp deletion strongly associated (p-value=0.0001) with protection against development of hypothyroidism. The deletion is located between two predicted Interferon alpha (IFNA) genes and it may eliminate functional elements potentially involved in the transcriptional regulation of these genes. Remarkably, type I IFNs have been extensively associated to human autoimmune hypothyroidism and general autoimmunity. Nonetheless, the extreme genomic complexity of the associated region on CFA11 warrants further long-read sequencing and annotation efforts in order to ascribe functions to the identified deletion and to characterize the canine IFNA gene cluster in more detail.

    Conclusions: Our results expand the current knowledge on genetic determinants of canine hypothyroidism by revealing a significant link with the human counterpart disease, potentially translating into better diagnostic tools across species, and may contribute to improved canine breeding strategies.

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  • 40.
    Biswas, M. K.
    et al.
    Huazhong Agricultural University, China.
    Ahmed, M. B.
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Mondal, M. A. A.
    University of Rajshahi, Bangladesh.
    Razvy, M. A.
    Huazhong Agricultural University, China.
    Hoque, A.
    University of Rajshahi, Bangladesh.
    Islam, R.
    University of Rajshahi, Bangladesh.
    Hossaina, M.
    University of Rajshahi, Bangladesh.
    Mandal, Abul
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    In exploitation of genetic diversity in potato breeding2010In: Agronomski Glasnik (Agronomy Journal), ISSN 1848-8900, Vol. 72, no 4-5, p. 261-276Article in journal (Refereed)
    Abstract [en]

    With a view to select divergent parents genetic diversity was estimated among twenty genotypes. Thirty F1 progenies developed by line-tester mating were studied from seedling generation to first clonal generation for five important agronomic traits. Cluster analysis reveals that the parents could be grouped into seven different clusters. Cluster means showed wide range of variation for several traits among singles as well as multi genotypic clusters. Considering diversity pattern, parents should select from cluster I, III, IV, and V for the improvement of potato. Analysis of variance revealed that all most all the sources of variation were highly significant for all the studied traits in both generations. Parents Challisha, Lalpakri, Patnai, Chamak, Sadagoti, TPS-67 and TPS-364 were found to be good general combiners for tuber yield and yield contribution traits due to their gca effects. The sca effects showed that out of 30 hybrids 12 were found to have specific combining ability for tuber yield and those hybrids also exhibited considerable heterosis for tuber yield and yield contributing traits.

  • 41. Bitocchi, Elena
    et al.
    Rau, Domenico
    Benazzo, Andrea
    Bellucci, Elisa
    Goretti, Daniela
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Biagetti, Eleonora
    Panziera, Alex
    Laido, Giovanni
    Rodriguez, Monica
    Gioia, Tania
    Attene, Giovanna
    McClean, Phillip
    Lee, Rian K.
    Jackson, Scott A.
    Bertorelle, Giorgio
    Papa, Roberto
    High Level of Nonsynonymous Changes in Common Bean Suggests That Selection under Domestication Increased Functional Diversity at Target Traits2017In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 7, article id 2005Article in journal (Refereed)
    Abstract [en]

    Crop species have been deeply affected by the domestication process, and there have been many efforts to identify selection signatures at the genome level. This knowledge will help geneticists to better understand the evolution of organisms, and at the same time, help breeders to implement successful breeding strategies. Here, we focused on domestication in the Mesoamerican gene pool of Phaseolus vulgaris by sequencing 49 gene fragments from a sample of 45 P. vulgaris wild and domesticated accessions, and as controls, two accessions each of the closely related species Phaseolus coccineus and Phaseolus dumosus. An excess of nonsynonymous mutations within the domesticated germplasm was found. Our data suggest that the cost of domestication alone cannot explain fully this finding. Indeed, the significantly higher frequency of polymorphisms in the coding regions observed only in the domesticated plants (compared to noncoding regions), the fact that these mutations were mostly nonsynonymous and appear to be recently derived mutations, and the investigations into the functions of their relative genes (responses to biotic and abiotic stresses), support a scenario that involves new functional mutations selected for adaptation during domestication. Moreover, consistent with this hypothesis, selection analysis and the possibility to compare data obtained for the same genes in different studies of varying sizes, data types, and methodologies allowed us to identify four genes that were strongly selected during domestication. Each selection candidate is involved in plant resistance/tolerance to abiotic stresses, such as heat, drought, and salinity. Overall, our study suggests that domestication acted to increase functional diversity at target loci, which probably controlled traits related to expansion and adaptation to new agro-ecological growing conditions.

  • 42. Bollhoner, Benjamin
    et al.
    Jokipii-Lukkari, Soile
    Bygdell, Joakim
    Stael, Simon
    Adriasola, Mathilda
    KTH, School of Biotechnology (BIO).
    Muniz, Luis
    Van Breusegem, Frank
    Ezcurra, Ines
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Wingsle, Gunnar
    Tuominen, Hannele
    The function of two type II metacaspases in woody tissues of Populus trees2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, no 4, p. 1551-1565Article in journal (Refereed)
    Abstract [en]

    Metacaspases (MCs) are cysteine proteases that are implicated in programmed cell death of plants. AtMC9 (Arabidopsis thaliana Metacaspase9) is a member of the Arabidopsis MC family that controls the rapid autolysis of the xylem vessel elements, but its downstream targets in xylem remain uncharacterized. PttMC13 and PttMC14 were identified as AtMC9 homologs in hybrid aspen (Populustremulaxtremuloides). A proteomic analysis was conducted in xylem tissues of transgenic hybrid aspen trees which carried either an overexpression or an RNA interference construct for PttMC13 and PttMC14. The proteomic analysis revealed modulation of levels of both previously known targets of metacaspases, such as Tudor staphylococcal nuclease, heat shock proteins and 14-3-3 proteins, as well as novel proteins, such as homologs of the PUTATIVE ASPARTIC PROTEASE3 (PASPA3) and the cysteine protease RD21 by PttMC13 and PttMC14. We identified here the pathways and processes that are modulated by PttMC13 and PttMC14 in xylem tissues. In particular, the results indicate involvement of PttMC13 and/or PttMC14 in downstream proteolytic processes and cell death of xylem elements. This work provides a valuable reference dataset on xylem-specific metacaspase functions for future functional and biochemical analyses.

  • 43.
    Bollhöner, Benjamin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jokipii-Lukkari, Soile
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Bygdell, Joakim
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Stael, Simon
    Adriasola, Mathilda
    Muñiz, Luis
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Van Breusegem, Frank
    Ezcurra, Inés
    Wingsle, Gunnar
    Tuominen, Hannele
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The function of two type II metacaspases in woody tissues of Populus trees2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, no 4, p. 1551-1565Article in journal (Refereed)
    Abstract [en]

    Metacaspases (MCs) are cysteine proteases that are implicated in programmed cell death of plants. AtMC9 (Arabidopsis thaliana Metacaspase9) is a member of the Arabidopsis MC family that controls the rapid autolysis of the xylem vessel elements, but its downstream targets in xylem remain uncharacterized. PttMC13 and PttMC14 were identified as AtMC9 homologs in hybrid aspen (Populustremulaxtremuloides). A proteomic analysis was conducted in xylem tissues of transgenic hybrid aspen trees which carried either an overexpression or an RNA interference construct for PttMC13 and PttMC14. The proteomic analysis revealed modulation of levels of both previously known targets of metacaspases, such as Tudor staphylococcal nuclease, heat shock proteins and 14-3-3 proteins, as well as novel proteins, such as homologs of the PUTATIVE ASPARTIC PROTEASE3 (PASPA3) and the cysteine protease RD21 by PttMC13 and PttMC14. We identified here the pathways and processes that are modulated by PttMC13 and PttMC14 in xylem tissues. In particular, the results indicate involvement of PttMC13 and/or PttMC14 in downstream proteolytic processes and cell death of xylem elements. This work provides a valuable reference dataset on xylem-specific metacaspase functions for future functional and biochemical analyses.

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    fulltext
  • 44. Bot, Phearom
    et al.
    Mun, Bong-Gyu
    Imran, Qari Muhammad
    Hussain, Adil
    Lee, Sang-Uk
    Loake, Gary
    Yun, Byung-Wook
    Differential expression of AtWAKL10 in response to nitric oxide suggests a putative role in biotic and abiotic stress responses2019In: PeerJ, Vol. 7Article in journal (Refereed)
  • 45. Botterweg-Paredes, Esther
    et al.
    Blaakmeer, Anko
    Hong, Shin-Young
    Sun, Bin
    Mineri, Lorenzo
    Kruusvee, Valdeko
    Xie, Yakun
    Straub, Daniel
    Ménard, Delphine
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Pesquet, Edouard
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Wenkel, Stephan
    Light affects tissue patterning of the hypocotyl in the shade-avoidance response2020In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 16, no 3, article id e1008678Article in journal (Refereed)
    Abstract [en]

    Plants have evolved strategies to avoid shade and optimize the capture of sunlight. While some species are tolerant to shade, plants such as Arabidopsis thaliana are shade-intolerant and induce elongation of their hypocotyl to outcompete neighboring plants. We report the identification of a developmental module acting downstream of shade perception controlling vascular patterning. We show that Arabidopsis plants react to shade by increasing the number and types of water-conducting tracheary elements in the vascular cylinder to maintain vascular density constant. Mutations in genes affecting vascular patterning impair the production of additional xylem and also show defects in the shade-induced hypocotyl elongation response. Comparative analysis of the shade-induced transcriptomes revealed differences between wild type and vascular patterning mutants and it appears that the latter mutants fail to induce sets of genes encoding biosynthetic and cell wall modifying enzymes. Our results thus set the stage for a deeper understanding of how growth and patterning are coordinated in a dynamic environment.

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    fulltext
  • 46.
    Bourdon, Matthieu
    et al.
    The Sainsbury Laboratory, University of Cambridge, Cambridge, UK; Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.
    Vilaplana, Francisco
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Bulone, Vincent
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia.
    Helariutta, Ykä
    The Sainsbury Laboratory, University of Cambridge, Cambridge, UK; Wood Development Group, University of Helsinki, Helsinki, Finland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
    et al.,
    Ectopic callose deposition into woody biomass modulates the nano-architecture of macrofibrils2023In: Nature Plants, E-ISSN 2055-0278, Vol. 9, no 9, p. 1530-1546Article in journal (Refereed)
    Abstract [en]

    Plant biomass plays an increasingly important role in the circular bioeconomy, replacing non-renewable fossil resources. Genetic engineering of this lignocellulosic biomass could benefit biorefinery transformation chains by lowering economic and technological barriers to industrial processing. However, previous efforts have mostly targeted the major constituents of woody biomass: cellulose, hemicellulose and lignin. Here we report the engineering of wood structure through the introduction of callose, a polysaccharide novel to most secondary cell walls. Our multiscale analysis of genetically engineered poplar trees shows that callose deposition modulates cell wall porosity, water and lignin contents and increases the lignin–cellulose distance, ultimately resulting in substantially decreased biomass recalcitrance. We provide a model of the wood cell wall nano-architecture engineered to accommodate the hydrated callose inclusions. Ectopic polymer introduction into biomass manifests in new physico-chemical properties and offers new avenues when considering lignocellulose engineering.

  • 47.
    Boutté, Yohann
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Frescatada-Rosa, Márcia
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Men, Shuzhen
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Chow, Cheung-Ming
    Ebine, Kazuo
    Gustavsson, Anna
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Johansson, Lenore
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ueda, Takashi
    Moore, Ian
    Jürgens, Gerd
    Grebe, Markus
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Endocytosis restricts Arabidopsis KNOLLE syntaxin to the cell division plane during late cytokinesis2010In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 29, no 3, p. 546-58Article in journal (Refereed)
    Abstract [en]

    Cytokinesis represents the final stage of eukaryotic cell division during which the cytoplasm becomes partitioned between daughter cells. The process differs to some extent between animal and plant cells, but proteins of the syntaxin family mediate membrane fusion in the plane of cell division in diverse organisms. How syntaxin localization is kept in check remains elusive. Here, we report that localization of the Arabidopsis KNOLLE syntaxin in the plane of cell division is maintained by sterol-dependent endocytosis involving a clathrin- and DYNAMIN-RELATED PROTEIN1A-dependent mechanism. On genetic or pharmacological interference with endocytosis, KNOLLE mis-localizes to lateral plasma membranes after cell-plate fusion. Fluorescence-loss-in-photo-bleaching and fluorescence-recovery-after-photo-bleaching experiments reveal lateral diffusion of GFP-KNOLLE from the plane of division to lateral membranes. In an endocytosis-defective sterol biosynthesis mutant displaying lateral KNOLLE diffusion, KNOLLE secretory trafficking remains unaffected. Thus, restriction of lateral diffusion by endocytosis may serve to maintain specificity of syntaxin localization during late cytokinesis.

  • 48.
    Braganca, F. M. Serra
    et al.
    Univ Utrecht, Fac Vet Med, Dept Clin Sci, NL-3584 CM Utrecht, Netherlands..
    Broomé, Michael
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Robotics, Perception and Learning, RPL.
    Rhodin, M.
    Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, Uppsala, Sweden..
    Bjornsdottir, S.
    Agr Univ Iceland, Hvanneyri, Borgarnes, Iceland..
    Gunnarsson, V
    Holar Univ Coll, Dept Equine Sci, Holar, Iceland..
    Voskamp, J. P.
    Univ Utrecht, Fac Vet Med, Dept Clin Sci, NL-3584 CM Utrecht, Netherlands..
    Persson-Sjödin, E.
    Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, Uppsala, Sweden..
    Back, W.
    Univ Utrecht, Fac Vet Med, Dept Clin Sci, NL-3584 CM Utrecht, Netherlands.;Univ Ghent, Fac Vet Med, Dept Surg & Anaesthesiol Domest Anim, B-9820 Merelbeke, Belgium..
    Lindgren, G.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden.;Katholieke Univ Leuven, Dept Biosyst, Livestock Genet, B-3001 Leuven, Belgium..
    Novoa-Bravo, M.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden.;Genet Anim Colombia Ltda, Bogota, Colombia..
    Roepstorff, C.
    Univ Zurich, Vetsuisse Fac, Equine Dept, Winterthurerstr 260, CH-8057 Zurich, Switzerland..
    van der Zwaag, B. J.
    Inertia Technol BV, Enschede, Netherlands..
    Van Weeren, P. R.
    Univ Utrecht, Fac Vet Med, Dept Clin Sci, NL-3584 CM Utrecht, Netherlands..
    Hernlund, E.
    Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, Uppsala, Sweden..
    Improving gait classification in horses by using inertial measurement unit (IMU) generated data and machine learning2020In: Scientific Reports, E-ISSN 2045-2322, Vol. 10, no 1, article id 17785Article in journal (Refereed)
    Abstract [en]

    For centuries humans have been fascinated by the natural beauty of horses in motion and their different gaits. Gait classification (GC) is commonly performed through visual assessment and reliable, automated methods for real-time objective GC in horses are warranted. In this study, we used a full body network of wireless, high sampling-rate sensors combined with machine learning to fully automatically classify gait. Using data from 120 horses of four different domestic breeds, equipped with seven motion sensors, we included 7576 strides from eight different gaits. GC was trained using several machine-learning approaches, both from feature-extracted data and from raw sensor data. Our best GC model achieved 97% accuracy. Our technique facilitated accurate, GC that enables in-depth biomechanical studies and allows for highly accurate phenotyping of gait for genetic research and breeding. Our approach lends itself for potential use in other quadrupedal species without the need for developing gait/animal specific algorithms.

  • 49.
    Buinovskaja, Greta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Identifying structural variants from plant short-read sequencing data2022Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
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    Master_Thesis_Greta_Buinovskaja
  • 50. Bygdell, Joakim
    et al.
    Srivastava, Vaibhav
    KTH, School of Biotechnology (BIO), Glycoscience.
    Obudulu, Ogonna
    Srivastava, Manoj K.
    Nilsson, Robert
    Sundberg, Bjorn
    Trygg, Johan
    Mellerowicz, Ewa J.
    Wingsle, Gunnar
    Protein expression in tension wood formation monitored at high tissue resolution in Populus2017In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 13, p. 3405-3417Article in journal (Refereed)
    Abstract [en]

    Tension wood (TW) is a specialized tissue with contractile properties that is formed by the vascular cambium in response to gravitational stimuli. We quantitatively analysed the proteomes of Populus tremula cambium and its xylem cell derivatives in stems forming normal wood (NW) and TW to reveal the mechanisms underlying TW formation. Phloem-, cambium-, and wood-forming tissues were sampled by tangential cryosectioning and pooled into nine independent samples. The proteomes of TW and NW samples were similar in the phloem and cambium samples, but diverged early during xylogenesis, demonstrating that reprogramming is an integral part of TW formation. For example, 14-3-3, reactive oxygen species, ribosomal and ATPase complex proteins were found to be up-regulated at early stages of xylem differentiation during TW formation. At later stages of xylem differentiation, proteins involved in the biosynthesis of cellulose and enzymes involved in the biosynthesis of rhamnogalacturonan-I, rhamnogalacturonan-II, arabinogalactan-II and fasciclin-like arabinogalactan proteins were up-regulated in TW. Surprisingly, two isoforms of exostosin family proteins with putative xylan xylosyl transferase function and several lignin biosynthesis proteins were also up-regulated, even though xylan and lignin are known to be less abundant in TW than in NW. These data provided new insight into the processes behind TW formation.

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