Endre søk
Begrens søket
12 1 - 50 of 76
RefereraExporteraLink til resultatlisten
Permanent link
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
Treff pr side
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sortering
  • Standard (Relevans)
  • Forfatter A-Ø
  • Forfatter Ø-A
  • Tittel A-Ø
  • Tittel Ø-A
  • Type publikasjon A-Ø
  • Type publikasjon Ø-A
  • Eldste først
  • Nyeste først
  • Skapad (Eldste først)
  • Skapad (Nyeste først)
  • Senast uppdaterad (Eldste først)
  • Senast uppdaterad (Nyeste først)
  • Disputationsdatum (tidligste først)
  • Disputationsdatum (siste først)
  • Standard (Relevans)
  • Forfatter A-Ø
  • Forfatter Ø-A
  • Tittel A-Ø
  • Tittel Ø-A
  • Type publikasjon A-Ø
  • Type publikasjon Ø-A
  • Eldste først
  • Nyeste først
  • Skapad (Eldste først)
  • Skapad (Nyeste først)
  • Senast uppdaterad (Eldste først)
  • Senast uppdaterad (Nyeste først)
  • Disputationsdatum (tidligste først)
  • Disputationsdatum (siste først)
Merk
Maxantalet träffar du kan exportera från sökgränssnittet är 250. Vid större uttag använd dig av utsökningar.
  • 1.
    Abdelfattah, Ahmed
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Università Mediterranea di Reggio Calabria, Italy.
    Sanzani, Simona M.
    Wisniewski, Michael
    Berg, Gabriele
    Cacciola, Santa O.
    Schena, Leonardo
    Revealing Cues for Fungal Interplay in the Plant-Air Interface in Vineyards2019Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, artikkel-id 922Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Plant-associated microorganisms play a crucial role in plant health and productivity. Belowground microbial diversity is widely reported as a major factor in determining the composition of the plant microbiome. In contrast, much less is known about the role of the atmosphere in relation to the plant microbiome. The current study examined the hypothesis that the atmospheric microbiome influences the composition of fungal communities of the aboveground organs flowers, fruit, and leaves) of table grape and vice versa. The atmosphere surrounding grape plantings exhibited a significantly higher level of fungal diversity relative to the nearby plant organs and shared a higher number of phylotypes 5,536 OTUs, 40.3%) with the plant than between organs of the same plant. Using a Bayesian source tracking approach, plant organs were determined to be the major source of the atmospheric fungal community 92%). In contrast, airborne microbiota had only a minor contribution to the grape microbiome, representing the source of 15, 4, and 35% of the fungal communities of leaves, flowers, and fruits, respectively. Moreover, data indicate that plant organs and the surrounding atmosphere shared a fraction of each other's fungal communities, and this shared pool of fungal taxa serves as a two-way reservoir of microorganisms. Microbial association analysis highlighted more positive than negative interactions between fungal phylotypes. Positive interactions were more common within the same environment, while negative interactions appeared to occur more frequently between different environments, i. e., atmosphere, leaf, flower, and fruit. The current study revealed the interplay between the fungal communities of the grape phyllosphere with the surrounding air. Plants were identified as a major source of recruitment for the atmospheric microbiome, while the surrounding atmosphere contributed only a small fraction of the plant fungal community. The results of the study suggested that the plant-air interface modulates the plant recruitment of atmospheric fungi, taking a step forward in understanding the plant holobiont assembly and how the atmosphere surrounding plants plays a role in this process. The impact of plants on the atmospheric microbiota has several biological and epidemiological implications for plants and humans.

  • 2. Akhter, Shirin
    et al.
    Kretzschmar, Warren W.
    Nordal, Veronika
    Delhomme, Nicolas
    Street, Nathaniel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Nilsson, Ove
    Emanuelsson, Olof
    Sundström, Jens F.
    Integrative analysis of three RNA sequencing methods identifies mutually exclusive exons of MADS-box isoforms during early bud development in Picea abies2018Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 9, artikkel-id 1625Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Recent efforts to sequence the genomes and transcriptomes of several gymnosperm species have revealed an increased complexity in certain gene families in gymnosperms as compared to angiosperms. One example of this is the gymnosperm sister Glade to angiosperm TM3-like MADS-box genes, which at least in the conifer lineage has expanded in number of genes. We have previously identified a member of this subclade, the conifer gene DEFICIENS AGAMOUS LIKE 19 (DAL19), as being specifically upregulated in cone-setting shoots. Here, we show through Sanger sequencing of mRNA-derived cDNA and mapping to assembled conifer genomic sequences that DAL19 produces six mature mRNA splice variants in Picea abies. These splice variants use alternate first and last exons, while their four central exons constitute a core region present in all six transcripts. Thus, they are likely to be transcript isoforms. Quantitative Real-Time PCR revealed that two mutually exclusive first DAL19 exons are differentially expressed across meristems that will form either male or female cones, or vegetative shoots. Furthermore, mRNA in situ hybridization revealed that two mutually exclusive last DAL19 exons were expressed in a cell-specific pattern within bud meristems. Based on these findings in DAL19, we developed a sensitive approach to transcript isoform assembly from short-read sequencing of mRNA. We applied this method to 42 putative MADS-box core regions in P abies, from which we assembled 1084 putative transcripts. We manually curated these transcripts to arrive at 933 assembled transcript isoforms of 38 putative MADS-box genes. 152 of these isoforms, which we assign to 28 putative MADS-box genes, were differentially expressed across eight female, male, and vegetative buds. We further provide evidence of the expression of 16 out of the 38 putative MADS-box genes by mapping PacBio Iso-Seq circular consensus reads derived from pooled sample sequencing to assembled transcripts. In summary, our analyses reveal the use of mutually exclusive exons of MADS-box gene isoforms during early bud development in P. abies, and we find that the large number of identified MADS-box transcripts in P. abies results not only from expansion of the gene family through gene duplication events but also from the generation of numerous splice variants.

  • 3.
    Akhter, Shirin
    et al.
    Swedish Univ Agr Sci, Linnean Ctr Plant Biol, Uppsala Bioctr, Dept Plant Biol, Uppsala, Sweden..
    Kretzschmar, Warren W.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Nordal, Veronika
    Swedish Univ Agr Sci, Linnean Ctr Plant Biol, Uppsala Bioctr, Dept Plant Biol, Uppsala, Sweden..
    Delhomme, Nicolas
    Swedish Univ Agr Sci, Dept Forest Genet & Plant Physiol, Umea Plant Sci Ctr, Umea, Sweden..
    Street, Nathaniel R.
    Umea Sweden, Dept Plant Physiol, Umea Plant Sci Ctr, Umea, Sweden..
    Nilsson, Ove
    Swedish Univ Agr Sci, Dept Forest Genet & Plant Physiol, Umea Plant Sci Ctr, Umea, Sweden..
    Emanuelsson, Olof
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Sundström, Jens F.
    Swedish Univ Agr Sci, Linnean Ctr Plant Biol, Uppsala Bioctr, Dept Plant Biol, Uppsala, Sweden..
    Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies2018Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 9, artikkel-id 1625Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Recent efforts to sequence the genomes and transcriptomes of several gymnosperm species have revealed an increased complexity in certain gene families in gymnosperms as compared to angiosperms. One example of this is the gymnosperm sister Glade to angiosperm TM3-like MADS-box genes, which at least in the conifer lineage has expanded in number of genes. We have previously identified a member of this subclade, the conifer gene DEFICIENS AGAMOUS LIKE 19 (DAL19), as being specifically upregulated in cone-setting shoots. Here, we show through Sanger sequencing of mRNA-derived cDNA and mapping to assembled conifer genomic sequences that DAL19 produces six mature mRNA splice variants in Picea abies. These splice variants use alternate first and last exons, while their four central exons constitute a core region present in all six transcripts. Thus, they are likely to be transcript isoforms. Quantitative Real-Time PCR revealed that two mutually exclusive first DAL19 exons are differentially expressed across meristems that will form either male or female cones, or vegetative shoots. Furthermore, mRNA in situ hybridization revealed that two mutually exclusive last DAL19 exons were expressed in a cell-specific pattern within bud meristems. Based on these findings in DAL19, we developed a sensitive approach to transcript isoform assembly from short-read sequencing of mRNA. We applied this method to 42 putative MADS-box core regions in P abies, from which we assembled 1084 putative transcripts. We manually curated these transcripts to arrive at 933 assembled transcript isoforms of 38 putative MADS-box genes. 152 of these isoforms, which we assign to 28 putative MADS-box genes, were differentially expressed across eight female, male, and vegetative buds. We further provide evidence of the expression of 16 out of the 38 putative MADS-box genes by mapping PacBio Iso-Seq circular consensus reads derived from pooled sample sequencing to assembled transcripts. In summary, our analyses reveal the use of mutually exclusive exons of MADS-box gene isoforms during early bud development in P. abies, and we find that the large number of identified MADS-box transcripts in P. abies results not only from expansion of the gene family through gene duplication events but also from the generation of numerous splice variants.

  • 4. Alagna, F.
    et al.
    Caceres, M. E.
    Pandolfi, S.
    Collani, Silvio
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Mousavi, S.
    Mariotti, R.
    Cultrera, N. G. M.
    Baldoni, L.
    Barcaccia, G.
    The Paradox of Self-Fertile Varieties in the Context of Self-Incompatible Genotypes in Olive2019Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, artikkel-id 725Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Olive, representing one of the most important fruit crops of the Mediterranean area, is characterized by a general low fruit yield, due to numerous constraints, including alternate bearing, low flower viability, male-sterility, inter-incompatibility, and self-incompatibility (SI). Early efforts to clarify the genetic control of SI in olive gave conflicting results, and only recently, the genetic control of SI has been disclosed, revealing that olive possesses an unconventional homomorphic sporophytic diallelic system of SI, dissimilar from other described plants. This system, characterized by the presence of two SI groups, prevents self-fertilization and regulates inter-compatibility between cultivars, such that cultivars bearing the same incompatibility group are incompatible. Despite the presence of a functional SI, some varieties, in particular conditions, are able to set seeds following self-fertilization, a mechanism known as pseudo-self-compatibility (PSC), as widely reported in previous literature. Here, we summarize the results of previous works on SI in olive, particularly focusing on the occurrence of self-fertility, and offer a new perspective in view of the recent elucidation of the genetic architecture of the SI system in olive. Recent advances in research aimed at unraveling the molecular bases of SI and its breakdown in olive are also presented. The clarification of these mechanisms may have a huge impact on orchard management and will provide fundamental information for the future of olive breeding programs.

  • 5.
    Augstein, Frauke
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Fysiologisk botanik.
    Carlsbecker, Annelie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Fysiologisk botanik.
    Getting to the Roots: A Developmental Genetic View of Root Anatomy and Function From Arabidopsis to Lycophytes2018Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 9, artikkel-id 1410Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Roots attach plants to the ground and ensure efficient and selective uptake of water and nutrients. These functions are facilitated by the morphological and anatomical structures of the root, formed by the activity of the root apical meristem (RAM) and consecutive patterning and differentiation of specific tissues with distinct functions. Despite the importance of this plant organ, its evolutionary history is not clear, but fossils suggest that roots evolved at least twice, in the lycophyte (clubmosses and their allies) and in the euphyllophyte (ferns and seed plants) lineages. Both lycophyte and euphyllophyte roots grow indeterminately by the action of an apical meristem, which is protected by a root cap. They produce root hairs, and in most species the vascular stele is guarded by a specialized endodermal cell layer. Hence, most of these traits must have evolved independently in these lineages. This raises the question if the development of these apparently analogous tissues is regulated by distinct or homologous genes, independently recruited from a common ancestor of lycophytes and euphyllophytes. Currently, there are few studies of the genetic and molecular regulation of lycophyte and fern roots. Therefore, in this review, we focus on key regulatory networks that operate in root development in the model angiosperm Arabidopsis. We describe current knowledge of the mechanisms governing RAM maintenance as well as patterning and differentiation of tissues, such as the endodermis and the vasculature, and compare with other species. We discuss the importance of comparative analyses of anatomy and morphology of extant and extinct species, along with analyses of gene regulatory networks and, ultimately, gene function in plants holding key phylogenetic positions to test hypotheses of root evolution.

  • 6. Bakker, Elisabeth S.
    et al.
    Veen, Ciska G. F.
    Ter Heerdt, Gerard J. N.
    Huig, Naomi
    Sarneel, Judith M
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Ecology and Biodiversity Group, Utrecht University, Utrecht, Netherlands; Plant Ecophysiology Group, Utrecht University, Utrecht, Netherlands.
    High grazing pressure of geese threatens conservation and restoration of reed belts2018Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 9, artikkel-id 1649Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Reed (Phragmites australis (Cav.) Trin. ex Steud.) beds are important habitat for marsh birds, but are declining throughout Europe. Increasing numbers of the native marsh bird, the Greylag goose (Anser anser L.), are hypothesized to cause reed bed decline and inhibit restoration of reed beds, but data are largely lacking. In this study, we experimentally tested the effect of grazing by Greylag geese on the growth and expansion of reed growing in belts along lake shorelines. After 5 years of protecting reed from-grazing with exclosures, reed stems were over 4-fold denser and taller than in the grazed plots. Grazing pressure was intense with 50-100% of the stems being grazed among years in the control plots open to grazing. After 5 years of protection we opened half of the exclosures and the geese immediately grazed almost 100% of the reed stems. Whereas this did not affect the reed stem density, the stem height was strongly reduced and similar to permanently grazed reed. The next year geese were actively chased away by management from mid-March to mid-June, which changed the maximum amount of geese from over 2300 to less than 50. As a result, reed stem density and height increased and the reed belt had recovered over the full 6 m length of the experimental plots. Lastly, we introduced reed plants in an adjacent lake where no reed was growing and geese did visit this area. After two years, the density of the planted reed was six to nine-fold higher and significantly taller in exclosures compared to control plots where geese had access to the reed plants. We conclude that there is a conservation dilemma regarding how to preserve and restore reed belts in the presence of high densities of Greylag geese as conservation of both reed belts and high goose numbers seems infeasible. We suggest that there are three possible solutions for this dilemma: (1) effects of the geese can be mediated by goose population management, (2) the robustness of the reed marshes can be increased, and (3) at the landscape level, spatial planning can be used to configure landscapes with large reed bed reserves surrounded by unmown, unfertilized meadows.

  • 7. Billault-Penneteau, Benjamin
    et al.
    Sandré, Aline
    Folgmann, Jessica
    Parniske, Martin
    Pawlowski, Katharina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Dryas as a Model for Studying the Root Symbioses of the Rosaceae2019Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, artikkel-id 661Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The nitrogen-fixing root nodule symbiosis is restricted to four plant orders: Fabales (legumes), Fagales, Cucurbitales and Rosales (Elaeagnaceae, Rhamnaceae, and Rosaceae). Interestingly all of the Rosaceae genera confirmed to contain nodulating species (i.e., Cercocarpus, Chamaebatia, Dryas, and Purshia) belong to a single subfamily, the Dryadoideae. The Dryas genus is particularly interesting from an evolutionary perspective because it contains closely related nodulating (Dryas drummondii) and non-nodulating species (Dryas octopetala). The close phylogenetic relationship between these two species makes Dryas an ideal model genus to study the genetic basis of nodulation by whole genome comparison and classical genetics. Therefore, we established methods for plant cultivation, transformation and DNA extraction for these species. We optimized seed surface sterilization and germination methods and tested growth protocols ranging from pots and Petri dishes to a hydroponic system. Transgenic hairy roots were obtained by adapting Agrobacterium rhizogenes-based transformation protocols for Dryas species. We compared several DNA extraction protocols for their suitability for subsequent molecular biological analysis. Using CTAB extraction, reproducible PCRs could be performed, but CsCI gradient purification was essential to obtain DNA in sufficient purity for high quality de novo genome sequencing of both Dryas species. Altogether, we established a basic toolkit for the culture, transient transformation and genetic analysis of Dryas sp.

  • 8. Bitocchi, Elena
    et al.
    Rau, Domenico
    Benazzo, Andrea
    Bellucci, Elisa
    Goretti, Daniela
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, 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 Traits2017Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 7, artikkel-id 2005Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 9.
    Boussardon, Clément
    et al.
    Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
    Martin-Magniette, Marie-Laure
    Godin, Béatrice
    Benamar, Abdelilah
    Vittrant, Benjamin
    Citerne, Sylvie
    Mary-Huard, Tristan
    Macherel, David
    Rajjou, Loïc
    Budar, Françoise
    Novel Cytonuclear Combinations Modify Arabidopsis thaliana Seed Physiology and Vigor2019Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, artikkel-id 32Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Dormancy and germination vigor are complex traits of primary importance for adaptation and agriculture. Intraspecific variation in cytoplasmic genomes and cytonuclear interactions were previously reported to affect germination in Arabidopsis using novel cytonuclear combinations that disrupt co-adaptation between natural variants of nuclear and cytoplasmic genomes. However, specific aspects of dormancy and germination vigor were not thoroughly explored, nor the parental contributions to the genetic effects. Here, we specifically assessed dormancy, germination performance and longevity of seeds from Arabidopsis plants with natural and new genomic compositions. All three traits were modified by cytonuclear reshuffling. Both depth and release rate of dormancy could be modified by a changing of cytoplasm. Significant changes on dormancy and germination performance due to specific cytonuclear interacting combinations mainly occurred in opposite directions, consistent with the idea that a single physiological consequence of the new genetic combination affected both traits oppositely. However, this was not always the case. Interestingly, the ability of parental accessions to contribute to significant cytonuclear interactions modifying the germination phenotype was different depending on whether they provided the nuclear or cytoplasmic genetic compartment. The observed deleterious effects of novel cytonuclear combinations (in comparison with the nuclear parent) were consistent with a contribution of cytonuclear interactions to germination adaptive phenotypes. More surprisingly, we also observed favorable effects of novel cytonuclear combinations, suggesting suboptimal genetic combinations exist in natural populations for these traits. Reduced sensitivity to exogenous ABA and faster endogenous ABA decay during germination were observed in a novel cytonuclear combination that also exhibited enhanced longevity and better germination performance, compared to its natural nuclear parent. Taken together, our results strongly support that cytoplasmic genomes represent an additional resource of natural variation for breeding seed vigor traits.

  • 10.
    Burman, Robert
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi, Avdelningen för farmakognosi.
    Yeshak, Mariamawit Y.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi, Avdelningen för farmakognosi. Univ Addis Ababa, Sch Pharm, Dept Pharmacognosy, Addis Ababa, Ethiopia..
    Larsson, Sonny
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi, Avdelningen för farmakognosi.
    Craik, David J.
    Univ Queensland, Inst Mol Biosci, Chem & Struct Biol Div, Craik Lab, Brisbane, Qld, Australia..
    Rosengren, K. Johan
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi, Avdelningen för farmakognosi. Univ Queensland, Sch Biomed Sci, Lab Peptide Struct Biol, Brisbane, Qld, Australia..
    Göransson, Ulf
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi, Avdelningen för farmakognosi.
    Distribution of circular proteins in plants: large-scale mapping of cyclotides in the Violaceae2015Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 6, artikkel-id 855Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    During the last decade there has been increasing interest in small circular proteins found in plants of the violet family (Violaceae). These so-called cyclotides consist of a circular chain of approximately 30 amino acids, including six cysteines forming three disulfide bonds, arranged in a cyclic cystine knot (CCK) motif. In this study we map the occurrence and distribution of cyclotides throughout the Violaceae. Plant material was obtained from herbarium sheets containing samples up to 200 years of age. Even the oldest specimens contained cyclotides in the preserved leaves, with no degradation products observable, confirming their place as one of the most stable proteins in nature. Over 200 samples covering 17 of the 23-31 genera in Violaceae were analyzed, and cyclotides were positively identified in 150 species. Each species contained a unique set of between one and 25 cyclotides, with many exclusive to individual plant species. We estimate the number of different cyclotides in the Violaceae to be 5000-25,000, and propose that cyclotides are ubiquitous among all Violaceae species. Twelve new cyclotides from six phylogenetically dispersed genera were sequenced. Furthermore, the first glycosylated derivatives of cyclotides were identified and characterized, further increasing the diversity and complexity of this unique protein family.

  • 11. Catalá, Rafael
    et al.
    Carrasco-López, Cristian
    Perea-Resa, Carlos
    Hernández-Verdeja, Tamara
    Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas-CSIC, Madrid, Spain.
    Salinas, Julio
    Emerging Roles of LSM Complexes in Posttranscriptional Regulation of Plant Response to Abiotic Stress2019Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, artikkel-id 167Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    It has long been assumed that the wide reprogramming of gene expression that modulates plant response to unfavorable environmental conditions is mainly controlled at the transcriptional level. A growing body of evidence, however, indicates that posttranscriptional regulatory mechanisms also play a relevant role in this control. Thus, the LSMs, a family of proteins involved in mRNA metabolism highly conserved in eukaryotes, have emerged as prominent regulators of plant tolerance to abiotic stress. Arabidopsis contains two main LSM ring-shaped heteroheptameric complexes, LSM1-7 and LSM2-8, with different subcellular localization and function. The LSM1-7 ring is part of the cytoplasmic decapping complex that regulates mRNA stability. On the other hand, the LSM2-8 complex accumulates in the nucleus to ensure appropriate levels of U6 snRNA and, therefore, correct pre-mRNA splicing. Recent studies reported unexpected results that led to a fundamental change in the assumed consideration that LSM complexes are mere components of the mRNA decapping and splicing cellular machineries. Indeed, these data have demonstrated that LSM1-7 and LSM2-8 rings operate in Arabidopsis by selecting specific RNA targets, depending on the environmental conditions. This specificity allows them to actively imposing particular gene expression patterns that fine-tune plant responses to abiotic stresses. In this review, we will summarize current and past knowledge on the role of LSM rings in modulating plant physiology, with special focus on their function in abiotic stress responses.

  • 12.
    Cheregi, Otilia
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Wagner, Raik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Funk, Christiane
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Insights into the Cyanobacterial Deg/HtrA Proteases2016Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 7, artikkel-id 694Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Proteins are the main machinery for all living processes in a cell; they provide structural elements, regulate biochemical reactions as enzymes, and are the interface to the outside as receptors and transporters. Like any other machinery proteins have to be assembled correctly and need maintenance after damage, e.g., caused by changes in environmental conditions, genetic mutations, and limitations in the availability of cofactors. Proteases and chaperones help in repair, assembly, and folding of damaged and misfolded protein complexes cost-effective, with low energy investment compared with neo-synthesis. Despite their importance for viability, the specific biological role of most proteases in vivo is largely unknown. Deg/HtrA proteases, a family of serinetype ATP-independent proteases, have been shown in higher plants to be involved in the degradation of the Photosystem II reaction center protein D1. The objective of this review is to highlight the structure and function of their cyanobacterial orthologs. Homology modeling was used to find specific features of the SynDeg/HtrA proteases of Synechocystis sp. PCC 6803. Based on the available data concerning their location and their physiological substrates we conclude that these Deg proteases not only have important housekeeping and chaperone functions within the cell, but also are needed for remodeling the cell exterior.

  • 13.
    Decker, Daniel
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Kleczkowski, Leszek
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Substrate Specificity and Inhibitor Sensitivity of Plant UDP-Sugar Producing Pyrophosphorylases2017Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 8, artikkel-id 1610Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    UDP-sugars are essential precursors for glycosylation reactions producing cell wall polysaccharides, sucrose, glycoproteins, glycolipids, etc. Primary mechanisms of UDP sugar formation involve the action of at least three distinct pyrophosphorylases using UTP and sugar-1-P as substrates. Here, substrate specificities of barley and Arabidopsis (two isozymes) UDP-glucose pyrophosphorylases (UGPase), Arabidopsis UDP-sugar pyrophosphorylase (USPase) and Arabidopsis UDP-N-acetyl glucosamine pyrophosphorylase2 (UAGPase2) were investigated using a range of sugar-1-phosphates and nucleoside-triphosphates as substrates. Whereas all the enzymes preferentially used UTP as nucleotide donor, they differed in their specificity for sugar-1-P. UGPases had high activity with D-Glc-1-P, but could also react with Fru-1-P and Fru-2-P (Km values over 10 mM). Contrary to an earlier report, their activity with Gal-1-P was extremely low. USPase reacted with a range of sugar-1-phosphates, including D-Glc-1-P, D-Gal-1-P, D-GalA-1-P (K-m of 1.3 mM), beta-L-Ara-1-P and alpha-D-Fuc-1-P (K-m of 3.4 mM), but not beta-L-Fuc-1-P. In contrast, UAGPase2 reacted only with D-GlcNAc-1-P, D-GalNAc-1-P (K-m of 1 mM) and, to some extent, D-Glc-1-P (Km of 3.2 mM). Generally, different conformations/substituents at C2, C4, and C5 of the pyranose ring of a sugar were crucial determinants of substrate specificity of a given pyrophosphorylase. Homology models of UDP-sugar binding to UGPase, USPase and UAGPase2 revealed more common amino acids for UDP binding than for sugar binding, reflecting differences in substrate specificity of these proteins. UAGPase2 was inhibited by a salicylate derivative that was earlier shown to affect UGPase and USPase activities, consistent with a common structural architecture of the three pyrophosphorylases. The results are discussed with respect to the role of the pyrophosphorylases in sugar activation for glycosylated end-products.

  • 14.
    Decker, Daniel
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Kleczkowski, Leszek A.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    UDP-Sugar Producing Pyrophosphorylases: Distinct and Essential Enzymes With Overlapping Substrate Specificities, Providing de novo Precursors for Glycosylation Reactions2019Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 9, artikkel-id 1822Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Nucleotide sugars are the key precursors for all glycosylation reactions and are required both for oligo- and polysaccharides synthesis and protein and lipid glycosylation. Among all nucleotide sugars, UDP-sugars are the most important precursors for biomass production in nature (e.g., synthesis of cellulose, hemicellulose, and pectins for cell wall production). Several recent studies have already suggested a potential role for UDP-Glc in plant growth and development, and UDP-Glc has also been suggested as a signaling molecule, in addition to its precursor function. In this review, we will cover primary mechanisms of formation of UDP-sugars, by focusing on UDP-sugar metabolizing pyrophosphorylases. The pyrophosphorylases can be divided into three families: UDP-Glc pyrophosphorylase (UGPase), UDP-sugar pyrophosphorylase (USPase), and UDP-N-acetyl glucosamine pyrophosphorylase (UAGPase), which can be distinguished both by their amino acid sequences and by differences in substrate specificity. Substrate specificities of these enzymes are discussed, along with structure-function relationships, based on their crystal structures and homology modeling. Earlier studies with transgenic plants have revealed that each of the pyrophosphorylases is essential for plant survival, and their loss or a decrease in activity results in reproductive impairment. This constitutes a problem when studying exact in vivo roles of the enzymes using classical reverse genetics approaches. Thus, strategies involving the use of specific inhibitors (reverse chemical genetics) are also discussed. Further characterization of the properties/roles of pyrophosphorylases should address fundamental questions dealing with mechanisms and control of carbohydrate synthesis and may allow to identify targets for manipulation of biomass production in plants.

  • 15. Demchenko, Kirill N.
    et al.
    Voitsekhovskaja, Olga V.
    Pawlowski, Katharina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Plasmodesmata without callose and calreticulin in higher plants - open channels for fast syrnplastic transport?2014Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 5Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Plasmodesmata (PD) represent membrane-lined channels that link adjacent plant cells across the cell wall. PD of higher plants contain a central tube of endoplasmic reticulum (ER) called desmotubule. Membrane and lumen proteins seem to be able to move through the desmotubule, but most transport processes through PD occur through the cytoplasmic annulus (Brunkard (Bale 2013). Calreticulin (CRT), a highly conserved Ca2+-binding protein found in all multicellular eukaryotes, predominantly located in the ER, was shown to localize to PD, though not all PD accumulate CRT. In nitrogen-fixing actinorhizal root nodules of the Australian tree Casuarina glauca, the primary walls of infected cells containing the microsymbiont become lignified upon infection. TEM analysis of these nodules showed that during the differentiation of infected cells, PD connecting infected cells, and connecting infected and adjacent uninfected cells, were reduced in number as well as diameter (Schubert eta, 2013). In contrast with PD connecting young infected cells, and most PD connecting mature infected and adjacent uninfected cells, PD connecting mature infected cells did not accumulate CRT. Furthermore, as shown here, these PD were not associated with callose, and based on their diameter, they probably had lost their desmotubules. We speculate that either this is a slow path to PD degradation, or that the loss of callose accumulation and presumably also desmotubules leads to the PD becoming open channels and improves metabolite exchange between cells.

  • 16.
    Demina, Irina V.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Maity, Pooja Jha
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Nagchowdhury, Anurupa
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Ng, Jason L. P.
    van der Graaff, Eric
    Demchenko, Kirill N.
    Roitsch, Thomas
    Mathesius, Ulrike
    Pawlowski, Katharina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Accumulation of and Response to Auxins in Roots and Nodules of the Actinorhizal Plant Datisca glomerata Compared to the Model Legume Medicago truncatula2019Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, artikkel-id 1085Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Actinorhizal nodules are structurally different from legume nodules and show a greater similarity to lateral roots. Because of the important role of auxins in lateral root and nodule formation, auxin profiles were examined in roots and nodules of the actinorhizal species Datisca glomerata and the model legume Medicago truncatula. The auxin response in roots and nodules of both species was analyzed in transgenic root systems expressing a beta-glucuronidase gene under control of the synthetic auxin-responsive promoter DR5. The effects of two different auxin on root development were compared for both species. The auxin present in nodules at the highest levels was phenylacetic acid (PAA). No differences were found between the concentrations of active auxins of roots vs. nodules, while levels of the auxin conjugate indole-3-acetic acid-alanine were increased in nodules compared to roots of both species. Because auxins typically act in concert with cytokinins, cytokinins were also quantified. Concentrations of cis-zeatin and some glycosylated cytokinins were dramatically increased in nodules compared to roots of D. glomerata, but not of M. truncatula. The ratio of active auxins to cytokinins remained similar in nodules compared to roots in both species. The auxin response, as shown by the activation of the DR5 promoter, seemed significantly reduced in nodules compared to roots of both species, suggesting the accumulation of auxins in cell types that do not express the signal transduction pathway leading to DR5 activation. Effects on root development were analyzed for the synthetic auxin naphthaleneacetic acid (NAA) and PAA, the dominant auxin in nodules. Both auxins had similar effects, except that the sensitivity of roots to PAA was lower than to NAA. However, while the effects of both auxins on primary root growth were similar for both species, effects on root branching were different: both auxins had the classical positive effect on root branching in M. truncatula, but a negative effect in D. glomerata. Such a negative effect of exogenous auxin on root branching has previously been found for a cucurbit that forms lateral root primordia in the meristem of the parental root; however, root branching in D. glomerata does not follow that pattern.

  • 17. Deng, Nan
    et al.
    Hou, Chen
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Hunan Cili Forest Ecosystem State Research Station, China.
    Liu, Caixia
    Li, Minghe
    Bartish, Igor
    Tian, Yuxin
    Chen, Wei
    Du, Changjian
    Jiang, Zeping
    Shi, Shengqing
    Significance of Photosynthetic Characters in the Evolution of Asian Gnetum (Gnetales)2019Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, artikkel-id 39Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Gnetum is a genus in the Gnetales that has a unique but ambiguous placement within seed plant phylogeny. Previous studies have shown that Gnetum has lower values of photosynthetic characters than those of other seed plants, but few Gnetum species have been studied, and those that have been studied are restricted to narrow taxonomic and geographic ranges. In addition, the mechanism underlying the lower values of photosynthetic characters in Gnetum remains poorly understood. Here, we investigated the photosynthetic characters of a Chinese lianoid species, i.e., Gnetum parvifolium, and co-occurring woody angiosperms growing in the wild, as well as seedlings of five Chinese Gnetum species cultivated in a greenhouse. The five Gnetum species had considerably lower values for photosynthesis parameters (net photosynthetic rate, transpiration rate, intercellular CO2 concentration, and stomatal conductance) than those of other seed plant representatives. Interrelated analyses revealed that the low photosynthetic capacity may be an intrinsic property of Gnetum, and may be associated with its evolutionary history. Comparison of the chloroplast genomes (cpDNAs) of Gnetum with those of other seed plant representatives revealed that 17 coding genes are absent from the cpDNAs of all species of Gnetum. This lack of multiple functional genes from the cpDNAs probably leads to the low photosynthetic rates of Gnetum. Our results provide a new perspective on the evolutionary history of the Gnetales, and on the ecophysiological and genomic attributes of tropical biomes in general. These results could also be useful for the breeding and cultivation of Gnetum.

  • 18.
    Dobrenel, Thomas
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Versailles, France; Université Paris-Sud–Université Paris-Saclay, Orsay, France.
    Mancera-Martinez, Eder
    Forzani, Celine
    Azzopardi, Marianne
    Davanture, Marlene
    Moreau, Manon
    Schepetilnikov, Mikhail
    Chicher, Johana
    Langella, Olivier
    Zivy, Michel
    Robaglia, Christophe
    Ryabova, Lyubov A.
    Hanson, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Meyer, Christian
    The Arabidopsis TOR Kinase Specifically Regulates the Expression of Nuclear Genes Coding for Plastidic Ribosomal Proteins and the Phosphorylation of the Cytosolic Ribosomal Protein S62016Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 7, artikkel-id 1611Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Protein translation is an energy consuming process that has to be fine-tuned at both the cell and organism levels to match the availability of resources. The target of rapamycin kinase (TOR) is a key regulator of a large range of biological processes in response to environmental cues. In this study, we have investigated the effects of TOR inactivation on the expression and regulation of Arabidopsis ribosomal proteins at different levels of analysis, namely from transcriptomic to phosphoproteomic. TOR inactivation resulted in a coordinated down-regulation of the transcription and translation of nuclear-encoded mRNAs coding for plastidic ribosomal proteins, which could explain the chlorotic phenotype of the TOR silenced plants. We have identified in the 5' untranslated regions (UTRs) of this set of genes a conserved sequence related to the 5' terminal oligopyrimidine motif, which is known to confer translational regulation by the TOR kinase in other eukaryotes. Furthermore, the phosphoproteomic analysis of the ribosomal fraction following TOR inactivation revealed a lower phosphorylation of the conserved Ser240 residue in the C-terminal region of the 40S ribosomal protein S6 (RPS6). These results were confirmed by Western blot analysis using an antibody that specifically recognizes phosphorylated Ser240 in RPS6. Finally, this antibody was used to follow TOR activity in plants. Our results thus uncover a multi-level regulation of plant ribosomal genes and proteins by the TOR kinase.

  • 19. Donev, Evgeniy
    et al.
    Gandla, Madhavi Latha
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Jönsson, Leif J.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Mellerowicz, Ewa J.
    Engineering non-cellulosic polysaccharides of wood for the biorefinery2018Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 9, artikkel-id 1537Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Non-cellulosic polysaccharides constitute approximately one third of usable woody biomass for human exploitation. In contrast to cellulose, these substances are composed of several different types of unit monosaccharides and their backbones are substituted by various groups. Their structural diversity and recent examples of their modification in transgenic plants and mutants suggest they can be targeted for improving wood-processing properties, thereby facilitating conversion of wood in a biorefinery setting. Critical knowledge on their structure-function relationship is slowly emerging, although our understanding of molecular interactions responsible for observed phenomena is still incomplete. This review: (1) provides an overview of structural features of major non-cellulosic polysaccharides of wood, (2) describes the fate of non-cellulosic polysaccharides during biorefinery processing, (3) shows how the non-cellulosic polysaccharides impact lignocellulose processing focused on yields of either sugars or polymers, and (4) discusses outlooks for the improvement of tree species for biorefinery by modifying the structure of non-cellulosic polysaccharides.

  • 20. Ferrando, Alejandro
    et al.
    Mar Castellano, M.
    Lison, Purificacion
    Leister, Dario
    Stepanova, Anna N.
    Hanson, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Editorial: Relevance of Translational Regulation on Plant Growth and Environmental Responses2017Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 8, artikkel-id 2170Artikkel i tidsskrift (Annet vitenskapelig)
  • 21.
    Grossmann, Jonas
    et al.
    Funct Genom Ctr Zurich, Zurich, Switzerland..
    Fernandez, Helena
    Univ Oviedo, Dept Organisms & Syst Biol BOS, Area Plant Physiol, Oviedo, Spain..
    Chaubey, Pururawa M.
    Univ Zurich, Inst Plant & Microbial Biol, Zurich Basel Plant Sci Ctr, Zurich, Switzerland.;Hadron Finsys GmbH, Pharma & Life Sci, Cham, Switzerland..
    Valdés, Ana Elisa
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Fysiologisk botanik. Linnean Ctr Plant Biol, Uppsala, Sweden.; Stockholm Univ, Dept Ecol Environm & Plant Sci, Stockholm, Sweden..
    Gagliardini, Valeria
    Univ Zurich, Inst Plant & Microbial Biol, Zurich Basel Plant Sci Ctr, Zurich, Switzerland..
    Canal, Maria J.
    Univ Oviedo, Dept Organisms & Syst Biol BOS, Area Plant Physiol, Oviedo, Spain..
    Russo, Giancarlo
    Funct Genom Ctr Zurich, Zurich, Switzerland..
    Grossniklaus, Ueli
    Univ Zurich, Inst Plant & Microbial Biol, Zurich Basel Plant Sci Ctr, Zurich, Switzerland..
    Proteogenomic Analysis Greatly Expands the Identification of Proteins Related to Reproduction in the Apogamous Fern Dryopteris affinis ssp affinis2017Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 8, artikkel-id 336Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Performing proteomic studies on non-model organisms with little or no genomic information is still difficult. However, many specific processes and biochemical pathways occur only in species that are poorly characterized at the genomic level. For example, many plants can reproduce both sexually and asexually, the first one allowing the generation of new genotypes and the latter their fixation. Thus, both modes of reproduction are of great agronomic value. However, the molecular basis of asexual reproduction is not well understood in any plant. In ferns, it combines the production of unreduced spores (diplospory) and the formation of sporophytes from somatic cells (apogamy). To set the basis to study these processes, we performed transcriptomics by next-generation sequencing (NGS) and shotgun proteomics by tandem mass spectrometry in the apogamous fern D. affinis ssp. affinis. For protein identification we used the public viridiplantae database (VPDB) to identify orthologous proteins from other plant species and new transcriptomics data to generate a "species-specific transcriptome database" (SSTDB). In total 1,397 protein clusters with 5,865 unique peptide sequences were identified (13 decoy proteins out of 1,410, protFDR 0.93% on protein cluster level). We show that using the SSTDB for protein identification increases the number of identified peptides almost four times compared to using only the publically available VPDB. We identified homologs of proteins involved in reproduction of higher plants, including proteins with a potential role in apogamy. With the increasing availability of genomic data from non -model species, similar proteogenomics approaches will improve the sensitivity in protein identification for species only distantly related to models.

  • 22. Grossmann, Jonas
    et al.
    Fernández, Helena
    Chaubey, Pururawa M.
    Valdés, Ana E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Linnean Centre for Plant Biology, Sweden.
    Gagliardini, Valeria
    Cañal, María J.
    Russo, Giancarlo
    Grossniklaus, Ueli
    Proteogenomic Analysis Greatly Expands the Identification of Proteins Related to Reproduction in the Apogamous Fern Dryopteris affinis ssp affinis2017Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 8, artikkel-id 336Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Performing proteomic studies on non-model organisms with little or no genomic information is still difficult. However, many specific processes and biochemical pathways occur only in species that are poorly characterized at the genomic level. For example, many plants can reproduce both sexually and asexually, the first one allowing the generation of new genotypes and the latter their fixation. Thus, both modes of reproduction are of great agronomic value. However, the molecular basis of asexual reproduction is not well understood in any plant. In ferns, it combines the production of unreduced spores (diplospory) and the formation of sporophytes from somatic cells (apogamy). To set the basis to study these processes, we performed transcriptomics by next-generation sequencing (NGS) and shotgun proteomics by tandem mass spectrometry in the apogamous fern D. affinis ssp. affinis. For protein identification we used the public viridiplantae database (VPDB) to identify orthologous proteins from other plant species and new transcriptomics data to generate a species-specific transcriptome database (SSTDB). In total 1,397 protein clusters with 5,865 unique peptide sequences were identified (13 decoy proteins out of 1,410, protFDR 0.93% on protein cluster level). We show that using the SSTDB for protein identification increases the number of identified peptides almost four times compared to using only the publically available VPDB. We identified homologs of proteins involved in reproduction of higher plants, including proteins with a potential role in apogamy. With the increasing availability of genomic data from non -model species, similar proteogenomics approaches will improve the sensitivity in protein identification for species only distantly related to models.

  • 23. Guerriero, Gea
    et al.
    Hausman, Jean-Francois
    Ezcurra, Ines
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    WD4O-Repeat Proteins in Plant Cell Wall Formation: Current Evidence and Research Prospects2015Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 6, artikkel-id 1112Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The metabolic complexity of living organisms relies on supramolecular protein structures which ensure vital processes, such as signal transduction, transcription, translation and cell wall synthesis. In eukaryotes WD40-repeat (WDR) proteins often function as molecular "hubs" mediating supramolecular interactions. WDR proteins may display a variety of interacting partners and participate in the assembly of complexes involved in distinct cellular functions. In plants, the formation of lignocellulosic biomass involves extensive synthesis of cell wall polysaccharides, a process that requires the assembly of large transmembrane enzyme complexes, intensive vesicle trafficking, interactions with the cytoskeleton, and coordinated gene expression. Because of their function as supramolecular hubs, WDR proteins could participate in each or any of these steps, although to date only few WDR proteins have been linked to the cell wall by experimental evidence. Nevertheless, several potential cell wall-related WDR proteins were recently identified using in silico approaches, such as analyses of co-expression, interactome and conserved gene neighborhood. Notably, some WDR genes are frequently genomic neighbors of genes coding for GT2-family polysaccharide synthases in eukaryotes, and this WDR-GT2 collinear microsynteny is detected in diverse taxa. In angiosperms, two WDR genes are collinear to cellulose synthase genes, CesAs, whereas in ascomycetous fungi several WDR genes are adjacent to chitin synthase genes, chs. In this Perspective we summarize and discuss experimental and in silico studies on the possible involvement of WDR proteins in plant cell wall formation. The prospects of biotechnological engineering for enhanced biomass production are discussed.

  • 24.
    Götmark, Frank
    et al.
    University of Gothenburg, Sweden.
    Götmark, Elin
    Chalmers University of Technology, Sweden;University of Gothenburg, Sweden.
    Jensen, Anna M.
    Linnéuniversitetet, Fakulteten för teknik (FTK), Institutionen för skog och träteknik (SOT).
    Why Be a Shrub?: a Basic Model and Hypotheses for the Adaptive Values of a Common Growth Form2016Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 7, artikkel-id 1095Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Shrubs are multi-stemmed short woody plants, more widespread than trees, important in many ecosystems, neglected in ecology compared to herbs and trees, but currently in focus due to their global expansion. We present a novel model based on scaling relationships and four hypotheses to explain the adaptive significance of shrubs, including a review of the literature with a test of one hypothesis. Our model describes advantages for a small shrub compared to a small tree with the same above-ground woody volume, based on larger cross-sectional stem area, larger area of photosynthetic tissue in bark and stem, larger vascular cambium area, larger epidermis (bark) area, and larger area for sprouting, and faster production of twigs and canopy. These components form our Hypothesis 1 that predicts higher growth rate for a small shrub than a small tree. This prediction was supported by available relevant empirical studies (14 publications). Further, a shrub will produce seeds faster than a tree (Hypothesis 2), multiple stems in shrubs insure future survival and growth if one or more stems die (Hypothesis 3), and three structural traits of short shrub stems improve survival compared to tall tree stems (Hypothesis 4)—all hypotheses have some empirical support. Multi-stemmed trees may be distinguished from shrubs by more upright stems, reducing bending moment. Improved understanding of shrubs can clarify their recent expansion on savannas, grasslands, and alpine heaths. More experiments and other empirical studies, followed by more elaborate models, are needed to understand why the shrub growth form is successful in many habitats.

  • 25. Hall, Hardy C.
    et al.
    Fakhrzadeh, Azadeh
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Luengo Hendriks, Cris L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Fischer, Urs
    Precision automation of cell type classification and sub-cellular fluorescence quantification from laser scanning confocal images2016Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 7, artikkel-id 119Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    While novel whole-plant phenotyping technologies have been successfully implemented into functional genomics and breeding programs, the potential of automated phenotyping with cellular resolution is largely unexploited. Laser scanning confocal microscopy has the potential to close this gap by providing spatially highly resolved images containing anatomic as well as chemical information on a subcellular basis. However, in the absence of automated methods, the assessment of the spatial patterns and abundance of fluorescent markers with subcellular resolution is still largely qualitative and time-consuming. Recent advances in image acquisition and analysis, coupled with improvements in microprocessor performance, have brought such automated methods within reach, so that information from thousands of cells per image for hundreds of images may be derived in an experimentally convenient time-frame. Here, we present a MATLAB-based analytical pipeline to (1) segment radial plant organs into individual cells, (2) classify cells into cell type categories based upon Random Forest classification, (3) divide each cell into sub-regions, and (4) quantify fluorescence intensity to a subcellular degree of precision for a separate fluorescence channel. In this research advance, we demonstrate the precision of this analytical process for the relatively complex tissues of Arabidopsis hypocotyls at various stages of development. High speed and robustness make our approach suitable for phenotyping of large collections of stem-like material and other tissue types.

  • 26. Hoeber, Stefanie
    et al.
    Fransson, Petra
    Prieto-Ruiz, Ines
    Manzoni, Stefano
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi.
    Weih, Martin
    Two Salix Genotypes Differ in Productivity and Nitrogen Economy When Grown in Monoculture and Mixture2017Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 8, artikkel-id 231Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Individual plant species or genotypes often differ in their demand for nutrients; to compete in a community they must be able to acquire more nutrients (i.e., uptake efficiency) and/or use them more efficiently for biomass production than their competitors. These two mechanisms are often complementary, as there are inherent trade-offs between them. In a mixed-stand, species with contrasting nutrient use patterns interact and may use their resources to increase productivity in different ways. Under contrasting nutrient availabilities, the competitive advantages conferred by either strategy may also shift, so that the interaction between resource use strategy and resource availability ultimately determines the performance of individual genotypes in mixtures. The aim was to investigate growth and nitrogen (N) use efficiency of two willow (Salix) genotypes grown in monoculture and mixture in a fertilizer contrast. We explored the hypotheses that (1) the biomass production of at least one of the involved genotypes should be greater when grown in mixture as compared to the corresponding monoculture when nutrients are the most growth-limiting factor; and (2) the N economy of individual genotypes differs when grown in mixture compared to the corresponding monoculture. The genotypes 'Tora' (Salix schwerinii x S. viminalis) and 'Loden' (S. dasyclados), with contrasting phenology and functional traits, were grown from cuttings in a growth container experiment under two nutrient fertilization treatments (high and low) in mono-and mixed-culture for 17 weeks. Under low nutrient level, 'Tora' showed a higher biomass production (aboveground biomass, leaf area productivity) and N uptake efficiency in mixture than in monoculture, whereas 'Loden' showed the opposite pattern. In addition, 'Loden' showed higher leaf N productivity but lower N uptake efficiency than 'Tora.' The results demonstrated that the specific functional trait combinations of individual genotypes affect their response to mixture as compared to monoculture. Plants grown in mixture as opposed to monoculture may thus increase biomass and vary in their response of N use efficiency traits. However, young plants were investigated here, and as we cannot predict mixture response in mature stands, our results need to be validated at field scale.

  • 27.
    Holm, Angelika
    et al.
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Hälsouniversitetet.
    Vikström, Elena
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Hälsouniversitetet.
    Quorum sensing communication between bacteria and human cells: signals, targets, and functions2014Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 5, nr 309Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Both direct and long-range interactions between pathogenic Pseudomonas aeruginosa bacteria and their eukaryotic hosts are important in the outcome of infections. For cell-to-cell communication, these bacteria employ the quorum sensing (QS) system to pass on information of the density of the bacterial population and collectively switch on virulence factor production, biofilm formation, and resistance development. Thus, QS allows bacteria to behave as a community to perform tasks which would be impossible for individual cells, e.g., to overcome defense and immune systems and establish infections in higher organisms. This review highlights these aspects of QS and our own recent research on how P aeruginosa communicates with human cells using the small QS signal molecules N-acyl homoserine lactones (AHL). We focus on how this conversation changes the behavior and function of neutrophils, macrophages, and epithelial cells and on how the signaling machinery in human cells responsible for the recognition of AHL. Understanding the bacteria host relationships at both cellular and molecular levels is essential for the identification of new targets and for the development of novel strategies to fight bacterial infections in the future.

  • 28.
    Hughes, P. William
    Max Planck Institute for Plant Breeding Research, Germany; University of Cologne, Germany.
    Minimal-Risk Seed Heteromorphism: Proportions of Seed Morphs for Optimal Risk-Averse Heteromorphic Strategies2018Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 9, artikkel-id 1412Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Seed heteromorphism is the reproductive strategy characterized by the simultaneous production of multiple seed types. While comparing heteromorphic to monomorphic strategies is mathematically simple, there is no explicit test for assessing which ratio of seed morphs minimizes fitness variance, and hence offers a basis for comparing different heteromorphic strategies. Such a test may be particularly valuable when more than two distinct morphs are present, since many strategies may have equivalent geometric fitnesses. As noted by Gillespie (1974), in these cases avoiding rare but evolutionarily important instances of severe reductions in fitness involves the minimization of variation in fitness—i.e., risk. Here I compute the optimal proportions of two or more seed morphs for heteromorphic strategies that either: (1) minimize total fitness variance; or (2) maximize the fitness-risk ratio—i.e., the “extra” fitness accrued per unit of “extra” fitness variance. This work thereby provides a testable null hypothesis to estimate the optimal frequencies of seed morphs when multiple heteromorphic strategies have evolved in environments with severe fitness risks. Moreover, it also permits the calculation of expected seed morph frequencies when more than two seed morphs are produced.

  • 29. Igamberdiev, Abir U.
    et al.
    Kleczkowski, Leszek A.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Optimization of ATP synthase function in mitochondria and chloroplasts via the adenylate kinase equilibrium2015Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 6, s. 10-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The bulk of ATP synthesis in plants is performed by ATP synthase, the main bioenergetics engine of cells, operating both in mitochondria and in chloroplasts. The reaction mechanism of ATP synthase has been studied in detail for over half a century; however, its optimal performance depends also on the steady delivery of ATP synthase substrates and the removal of its products. For mitochondrial ATP synthase, we analyze here the provision of stable conditions for (i) the supply of ADP and Mg2+, supported by adenylate kinase (AK) equilibrium in the intermembrane space, (ii) the supply of phosphate via membrane transporter in symport with H+ and (iii) the conditions of outflow of ATP by adenylate transporter carrying out the exchange of free adenylates. We also show that, in chloroplasts, AK equilibrates adenylates and governs Mg2+ contents in the stroma, optimizing ATP synthase and Calvin cycle operation, and affecting the import of inorganic phosphate in exchange with triose phosphates. It is argued that chemiosmosis is not the sole component of ATP synthase performance, which also depends on AK-mediated equilibrium of adenylates and Mg2+, adenylate transport, and phosphate release and supply.

  • 30. Igamberdiev, Abir U.
    et al.
    Kleczkowski, Leszek A.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    The Glycerate and Phosphorylated Pathways of Serine Synthesis in Plants: The Branches of Plant Glycolysis Linking Carbon and Nitrogen Metabolism2018Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 9, artikkel-id 318Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Serine metabolism in plants has been studied mostly in relation to photorespiration where serine is formed from two molecules of glycine. However, two other pathways of serine formation operate in plants and represent the branches of glycolysis diverging at the level of 3-phosphoglyceric acid. One branch (the glycerate serine pathway) is initiated in the cytosol and involves glycerate formation from 3phosphoglycerate, while the other (the phosphorylated serine pathway) operates in plastids and forms phosphohydroxypyruvate as an intermediate. Serine formed in these pathways becomes a precursor of glycine, formate and glycolate accumulating in stress conditions. The pathways can be linked to GABA shunt via transamination reactions and via participation of the same reductase for both glyoxylate and succinic semialdehyde. In this review paper we present a hypothesis of the regulation of redox balance in stressed plant cells via participation of the reactions associated with glycerate and phosphorylated serine pathways. We consider these pathways as important processes linking carbon and nitrogen metabolism and maintaining cellular redox and energy levels in stress conditions.

  • 31.
    Jarvi, Sari
    et al.
    Univ Turku, Dept Biochem, Mol Plant Biol, SF-20500 Turku, Finland..
    Isojarvi, Janne
    Univ Turku, Dept Biochem, Mol Plant Biol, SF-20500 Turku, Finland..
    Kangasjarvi, Saijaliisa
    Univ Turku, Dept Biochem, Mol Plant Biol, SF-20500 Turku, Finland..
    Salojarvi, Jarkko
    Univ Helsinki, Dept Biosci, Plant Biol, Helsinki, Finland..
    Mamedov, Fikret
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Suorsa, Marjaana
    Univ Turku, Dept Biochem, Mol Plant Biol, SF-20500 Turku, Finland..
    Aro, Eva-Mari
    Univ Turku, Dept Biochem, Mol Plant Biol, SF-20500 Turku, Finland..
    Photosystem II Repair and Plant Immunity: Lessons Learned from Arabidopsis Mutant Lacking the THYLAKOID LUMEN PROTEIN 18.32016Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 7, artikkel-id 405Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Chloroplasts play an important role in the cellular sensing of abiotic and biotic stress. Signals originating from photosynthetic light reactions, in the form of redox and pH changes, accumulation of reactive oxygen and electrophile species or stromal metabolites are of key importance in chloroplast retrograde signaling. These signals initiate plant acclimation responses to both abiotic and biotic stresses. To reveal the molecular responses activated by rapid fluctuations in growth light intensity, gene expression analysis was performed with Arabidopsis thaliana wild type and the tlp18.3 mutant plants, the latter showing a stunted growth phenotype under fluctuating light conditions (Biochem. J, 406, 415-425). Expression pattern of genes encoding components of the photosynthetic electron transfer chain did not differ between fluctuating and constant light conditions, neither in wild type nor in tlp18.3 plants, and the composition of the thylakoid membrane protein complexes likewise remained unchanged. Nevertheless, the fluctuating light conditions repressed in wild-type plants a broad spectrum of genes involved in immune responses, which likely resulted from shade-avoidance responses and their intermixing with hormonal signaling. On the contrary, in the tlp18.3 mutant plants there was an imperfect repression of defense-related transcripts upon growth under fluctuating light, possibly by signals originating from minor malfunction of the photosystem II (PSII) repair cycle, which directly or indirectly modulated the transcript abundances of genes related to light perception via phytochromes. Consequently, a strong allocation of resources to defense reactions in the tlp18.3 mutant plants presumably results in the stunted growth phenotype under fluctuating light.

  • 32. Järvi, Sari
    et al.
    Isojärvi, Janne
    Kangasjärvi, Säijaliisa
    Salojärvi, Jarkko
    Mamedov, Fikret
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Suorsa, Marjaana
    Aro, Eva-Mari
    Photosystem II repair and plant immunity: Lessons learned from Arabidopsis mutant lacking the thylakoid lumen protein 18.32016Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 7, artikkel-id 405Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Chloroplasts play an important role in the cellular sensing of abiotic and biotic stress. Signals originating from photosynthetic light reactions, in the form of redox and pH changes, accumulation of reactive oxygen and electrophile species or stromal metabolites are of key importance in chloroplast retrograde signaling. These signals initiate plant acclimation responses to both abiotic and biotic stresses. To reveal the molecular responses activated by rapid fluctuations in growth light intensity, gene expression analysis was performed with Arabidopsis thaliana wild type and the tlp18.3 mutant plants, the latter showing a stunted growth phenotype under fluctuating light conditions (Biochem. J, 406, 415–425). Expression pattern of genes encoding components of the photosynthetic electron transfer chain did not differ between fluctuating and constant light conditions, neither in wild type nor in tlp18.3 plants, and the composition of the thylakoid membrane protein complexes likewise remained unchanged. Nevertheless, the fluctuating light conditions repressed in wild-type plants a broad spectrum of genes involved in immune responses, which likely resulted from shade-avoidance responses and their intermixing with hormonal signaling. On the contrary, in the tlp18.3 mutant plants there was an imperfect repression of defense-related transcripts upon growth under fluctuating light, possibly by signals originating from minor malfunction of the photosystem II (PSII) repair cycle, which directly or indirectly modulated the transcript abundances of genes related to light perception via phytochromes. Consequently, a strong allocation of resources to defense reactions in the tlp18.3 mutant plants presumably results in the stunted growth phenotype under fluctuating light.

  • 33.
    Kabir, Ahmad H.
    et al.
    Plant and Crop Physiology Laboratory, Department of Botany, University of Rajshahi, Rajshahi, Bangladesh.
    Hossain, Mohammad M.
    Plant and Crop Physiology Laboratory, Department of Botany, University of Rajshahi, Rajshahi, Bangladesh.
    Khatun, Most A.
    Plant and Crop Physiology Laboratory, Department of Botany, University of Rajshahi, Rajshahi, Bangladesh.
    Mandal, Abul
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Haider, Syed A.
    Plant and Crop Physiology Laboratory, Department of Botany, University of Rajshahi, Rajshahi, Bangladesh.
    Role of Silicon Counteracting Cadmium Toxicity in Alfalfa (Medicago sativa L.)2016Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 7, artikkel-id 1117Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cadmium (Cd) is one of the most phytotoxic elements causing an agricultural problem and human health hazards. This work investigates whether and how silicon (Si) ameliorates Cd toxicity in Alfalfa. The addition of Si in Cd-stressed plants caused significant improvement in morpho-physiological features as well as total protein and membrane stability, indicating that Si does have critical roles in Cd detoxification in Alfalfa. Furthermore, Si supplementation in Cd stressed plants showed a significant decrease in Cd and Fe concentrations in both roots and shoots compared with Cd-stressed plants, revealing that Si-mediated tolerance to Cd stress is associated with Cd inhibition in Alfalfa. Results also showed no significant changes in the  expression of two metal chelators [MsPCS1 (phytochelatin synthase) and MsMT2  (metallothionein)] and PC (phytochelatin) accumulation, indicating that there may be no metal sequestration or change in metal sequestration following Si application under Cd stress in  Alfalfa. We further performed a targeted study on the effect of Si on Fe uptake mechanisms. We observed the consistent reduction in Fe reductase activity, expression of Fe-related genes [MsIRT1 (Fe transporter), MsNramp1 (metal transporter) and OsFRO1 (ferric chelate reductase] and Fe chelators (citrate and malate) by Si application to Cd stress in roots of Alfalfa. These results support that limiting Fe uptake through the down-regulation of Fe acquisition mechanisms confers Si-mediated alleviation of Cd toxicity in Alfalfa. Finally, an increase of catalase (CAT), ascorbate peroxidase (APX) and superoxide dismutase (SOD) activities along with elevated methionine and proline subjected to Si application might play roles, at least in part, to reduce H2O2 and to provide antioxidant defense against Cd stress in Alfalfa. The study shows evidence of the effect of Si on alleviating Cd toxicity in Alfalfa and can be further extended for phytoremediation of Cd toxicity in plants.

  • 34. Kiryushkin, Alexey S.
    et al.
    Ilina, Elena L.
    Puchkova, Vera A.
    Guseva, Elizaveta D.
    Pawlowski, Katharina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Demchenko, Kirill N.
    Lateral Root Initiation in the Parental Root Meristem of Cucurbits: Old Players in a New Position2019Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, artikkel-id 365Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    While in most higher plants, including the model system Arabidopsis thaliana, the formation of lateral root primordia is induced in the elongation zone of the parental root, in seven plant families, including Cucurbitaceae, an alternative root branching mechanism is established such that lateral roots are initiated directly in the apical meristem of the parental root. In Arabidopsis, the transcription factor GATA23 and MEMBRANE-ASSOCIATED KINASE REGULATOR4 (MAKR4) are involved in the gene regulatory network of lateral root initiation. Among all marker genes examined, these are the earliest known marker genes up-regulated by auxin during lateral root initiation. In this study, putative functional orthologs of Arabidopsis GATA23 and MAKR4 were identified in cucumber (Cucumis sativus) and squash (Cucurbita pepo). Both cucurbits contained 26 genes encoding GATA family transcription factors and only one MAKR4 gene. Phylogenetic and transcriptional analysis of up-regulation by auxin led to the identification of GATA23 putative functional orthologs in Cucurbitaceae - CpGATA24 and CsGATA24. In squash, CpMAKR4 was up-regulated by naphthylacetic acid (NM) and, similar to MAKR4 in Arabidopsis, indole-3-butyric acid (IBA). A detailed analysis of the expression pattern of CpGATA24 and CpMAKR4 in squash roots from founder cell specification until emergence of lateral root primordia was carried out using promoter-fluorescent reporter gene fusions and confocal microscopy. Their expression was induced in the protoxylem, and then expanded to founder cells in the pericycle. Thus, while the overall expression pattern of these genes was significantly different from that in Arabidopsis, in founder cells their expression was induced in the same order as in Arabidopsis. Altogether, these findings suggest that in Cucurbitaceae the putative functional orthologs of GATA23 and MAKR4 might play a role in founder cell specification and primordium positioning during lateral root initiation. The role of the protoxylem in auxin transport as a trigger of founder cells specification and lateral root initiation is discussed.

  • 35.
    Klemencic, Marina
    et al.
    Umea Univ, Dept Chem, Umea, Sweden. emencic, Marina; Dolinar, Marko.
    Asplund-Samuelsson, Johannes
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Proteinvetenskap, Systembiologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Dolinar, Marko
    Funk, Christiane
    Phylogenetic distribution and diversity of bacterial pseudo-orthocaspases underline their putative role in photosynthesis2019Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, artikkel-id 293Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Orthocaspases are prokaryotic caspase homologs – proteases, which cleave their substrates after positively charged residues using a conserved histidine – cysteine (HC) dyad situated in a catalytic p20 domain. However, in orthocaspases pseudo-variants have been identified, which instead of the catalytic HC residues contain tyrosine and serine, respectively. The presence and distribution of these presumably proteolytically inactive p20-containing enzymes has until now escaped attention. We have performed a detailed analysis of orthocaspases in all available prokaryotic genomes, focusing on pseudo-orthocaspases. Surprisingly we identified type I metacaspase homologs in filamentous cyanobacteria. While genes encoding pseudo-orthocaspases seem to be absent in Archaea, our results show conservation of these genes in organisms performing either anoxygenic photosynthesis (orders Rhizobiales, Rhodobacterales, and Rhodospirillales in Alphaproteobacteria) or oxygenic photosynthesis (all sequenced cyanobacteria, except Gloeobacter, Prochlorococcus, and Cyanobium). Contrary to earlier reports, we were able to detect pseudo-orthocaspases in all sequenced strains of the unicellular cyanobacteria Synechococcus and Synechocystis. In silico comparisons of the primary as well as tertiary structures of pseudo-p20 domains with their presumably proteolytically active homologs suggest that differences in their amino acid sequences have no influence on the overall structures. Mutations therefore affect most likely only the proteolytic activity. Our data provide an insight into diversification of pseudo-orthocaspases in Prokaryotes, their taxa-specific distribution, and allow suggestions on their taxa-specific function.

  • 36.
    Klemenčič, Marina
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
    Asplund-Samuelsson, Johannes
    Dolinar, Marko
    Funk, Christiane
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Phylogenetic Distribution and Diversity of Bacterial Pseudo-Orthocaspases Underline Their Putative Role in Photosynthesis2019Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, artikkel-id 293Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Orthocaspases are prokaryotic caspase homologs – proteases, which cleave their substrates after positively charged residues using a conserved histidine – cysteine (HC) dyad situated in a catalytic p20 domain. However, in orthocaspases pseudo-variants have been identified, which instead of the catalytic HC residues contain tyrosine and serine, respectively. The presence and distribution of these presumably proteolytically inactive p20-containing enzymes has until now escaped attention. We have performed a detailed analysis of orthocaspases in all available prokaryotic genomes, focusing on pseudo-orthocaspases. Surprisingly we identified type I metacaspase homologs in filamentous cyanobacteria. While genes encoding pseudo-orthocaspases seem to be absent in Archaea, our results show conservation of these genes in organisms performing either anoxygenic photosynthesis (orders Rhizobiales, Rhodobacterales, and Rhodospirillales in Alphaproteobacteria) or oxygenic photosynthesis (all sequenced cyanobacteria, except Gloeobacter, Prochlorococcus, and Cyanobium). Contrary to earlier reports, we were able to detect pseudo-orthocaspases in all sequenced strains of the unicellular cyanobacteria Synechococcus and Synechocystis. In silico comparisons of the primary as well as tertiary structures of pseudo-p20 domains with their presumably proteolytically active homologs suggest that differences in their amino acid sequences have no influence on the overall structures. Mutations therefore affect most likely only the proteolytic activity. Our data provide an insight into diversification of pseudo-orthocaspases in Prokaryotes, their taxa-specific distribution, and allow suggestions on their taxa-specific function.

  • 37. Kollars, Nicole M.
    et al.
    Henry, Amy K.
    Whalen, Matthew A.
    Boyer, Katharyn E.
    Cusson, Mathieu
    Eklöf, Johan S.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Hereu, Clara M.
    Jorgensen, Pablo
    Kiriakopolos, Stephanie L.
    Reynolds, Pamela L.
    Tomas, Fiona
    Turner, Mo S.
    Ruesink, Jennifer L.
    Meta-Analysis of Reciprocal Linkages between Temperate Seagrasses and Waterfowl with Implications for Conservation2017Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 8, artikkel-id 2119Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Multi-trophic conservation and management strategies may be necessary if reciprocal linkages between primary producers and their consumers are strong. While herbivory on aquatic plants is well-studied, direct top-down control of seagrass populations has received comparatively little attention, particularly in temperate regions. Herein, we used qualitative and meta-analytic approaches to assess the scope and consequences of avian (primarily waterfowl) herbivory on temperate seagrasses of the genus Zostera. Meta-analyses revealed widespread evidence of spatio-temporal correlations between Zostera and waterfowl abundances as well as strong top-down effects of grazing on Zostera. We also documented the identity and diversity of avian species reported to consume Zostera and qualitatively assessed their potential to exert top-down control. Our results demonstrate that Zostera and their avian herbivores are ecologically linked and we suggest that bird herbivory may influence the spatial structure, composition, and functioning of the seagrass ecosystem. Therefore, the consequences of avian herbivory should be considered in the management of seagrass populations. Of particular concern are instances of seagrass overgrazing by waterfowl which result in long-term reductions in seagrass biomass or coverage, with subsequent impacts on local populations of waterfowl and other seagrass-affiliated species. While our results showed that bird density and type may affect the magnitude of the top-down effects of avian herbivory, empirical research on the strength, context-dependency, and indirect effects of waterfowl-Zostera interactions remains limited. For example, increased efforts that explicitly measure the effects of different functional groups of birds on seagrass abundance and/or document how climate change-driven shifts in waterfowl migratory patterns impact seagrass phenology and population structure will advance research programs for both ecologists and managers concerned with the joint conservation of both seagrasses and their avian herbivores.

  • 38.
    Krautz, Robert
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    Arefin, Badrul
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    Theopold, Ulrich
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    Damage signals in the insect immune response2014Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 5, artikkel-id 342Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Insects and mammals share an ancient innate immune system comprising both humoral and cellular responses. The insect immune system consists of the fat body, which secretes effector molecules into the hemolymph and several classes of hemocytes, which reside in the hemolymph and of protective border epithelia. Key features of wound- and immune responses are shared between insect and mammalian immune systems including the mode of activation by commonly shared microbial (non-self) patterns and the recognition of these patterns by dedicated receptors. It is unclear how metazoan parasites in insects, which lack these shared motifs, are recognized. Research in recent years has demonstrated that during entry into the insect host, many eukaryotic pathogens leave traces that alert potential hosts of the damage they have afflicted. In accordance with terminology used in the mammalian immune systems, these signals have been dubbed danger- or damage-associated signals. Damage signals are necessary byproducts generated during entering hosts either by mechanical or proteolytic damage. Here, we briefly review the current stage of knowledge on how wound closure and wound healing during mechanical damage is regulated and how damage-related signals contribute to these processes. We also discuss how sensors of proteolytic activity induce insect innate immune responses. Strikingly damage-associated signals are also released from cells that have aberrant growth, including tumor cells. These signals may induce apoptosis in the damaged cells, the recruitment of immune cells to the aberrant tissue and even activate humoral responses. Thus, this ensures the removal of aberrant cells and compensatory proliferation to replace lost tissue. Several of these pathways may have been co-opted from wound healing and developmental processes.

  • 39.
    Kremnev, Dmitry
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Strand, Åsa
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Plastid encoded RNA polymerase activity and expression of photosynthesis genes required for embryo and seed development in Arabidopsis2014Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462XArtikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Chloroplast biogenesis and function is essential for proper plant embryo and seed development but the molecular mechanisms underlying the role of plastids during embryogenesis are poorly understood. Expression of plastid encoded genes is dependent on two different transcription machineries; a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. However, the division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear. We show here that PLASTID REDOX INSENSITIVE 2 (PRIN2) and CHLOROPLAST STEM-LOOP BINDING PROTEIN 41 kDa (CSP41b), two proteins identified in plastid nucleoid preparations, are essential for proper plant embryo development. Using Co-IP assays and native PAGE we have shown a direct physical interaction between PRIN2 and CSP41b. Moreover, PRIN2 and CSP41b form a distinct protein complex in vitro that binds DNA. The prin2.2 and csp41b-2 single mutants displayed pale phenotypes, abnormal chloroplasts with reduced transcript levels of photosynthesis genes and defects in embryo development. The respective csp41b-2prin2.2 homo/heterozygote double mutants produced abnormal white colored ovules and shrunken seeds. Thus, the csp41b-2prin2.2 double mutant is embryo lethal. In silico analysis of available array data showed that a large number of genes traditionally classified as PEP dependent genes are transcribed during early embryo development from the pre-globular stage to the mature-green-stage. Taken together, our results suggest that PEP activity and consequently the switch from NEP to PEP activity, is essential during embryo development and that the PRIN2-CSP41b DNA binding protein complex possibly is important for full PEP activity during this process.

  • 40. Krupinski, Pawel
    et al.
    Bozorg, Behruz
    Larsson, André
    Pietra, Stefano
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Grebe, Markus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Institute of Biochemistry and Biology, Plant Physiology, University of Potsdam, Potsdam, Germany.
    Jönsson, Henrik
    A Model Analysis of Mechanisms for Radial Microtubular Patterns at Root Hair Initiation Sites2016Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 7, artikkel-id 1560Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Plant cells have two main modes of growth generating anisotropic structures. Diffuse growth where whole cell walls extend in specific directions, guided by anisotropically positioned cellulose fibers, and tip growth, with inhomogeneous addition of new cell wall material at the tip of the structure. Cells are known to regulate these processes via molecular signals and the cytoskeleton. Mechanical stress has been proposed to provide an input to the positioning of the cellulose fibers via cortical microtubules in diffuse growth. In particular, a stress feedback model predicts a circumferential pattern of fibers surrounding apical tissues and growing primordia, guided by the anisotropic curvature in such tissues. In contrast, during the initiation of tip growing root hairs, a star-like radial pattern has recently been observed. Here, we use detailed finite element models to analyze how a change in mechanical properties at the root hair initiation site can lead to star-like stress patterns in order to understand whether a stress-based feedback model can also explain the microtubule patterns seen during root hair initiation. We show that two independent mechanisms, individually or combined, can be sufficient to generate radial patterns. In the first, new material is added locally at the position of the root hair. In the second, increased tension in the initiation area provides a mechanism. Finally, we describe how a molecular model of Rho-of-plant (ROP) GTPases activation driven by auxin can position a patch of activated ROP protein basally along a 2D root epidermal cell plasma membrane, paving the way for models where mechanical and molecular mechanisms cooperate in the initial placement and outgrowth of root hairs.

  • 41.
    Kunz, Sabine
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Gardeström, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Pesquet, Edouard
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Kleczkowski, Leszek
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Hexokinase 1 is required for glucose-induced repression of bZIP63, At5g22920, and BT2 in Arabidopsis2015Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 6, artikkel-id 525Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Simple sugars, like glucose (Glc) and sucrose (Suc), act as signals to modulate the expression of hundreds of genes in plants. Frequently, however, it remains unclear whether this regulation is induced by the sugars themselves or by their derivatives generated in the course of carbohydrate (CH) metabolism. In the present study, we tested the relevance of different CH metabolism and allocation pathways affecting expression patterns of five selected sugar-responsive genes (bZIP63, At5g22920, BT2, MGD2, and TPS9) in Arabidopsis thaliana. In general, the expression followed diurnal changes in the overall sugar availability. However, under steady growth conditions, this response was hardly impaired in the mutants for CH metabolizing/transporting proteins (adg1, sex1, sus1-4, sus5/6, and tpt2), including also hexokinase1 (HXK1) loss- and gain-of-function plants—gin2.1 and oe3.2, respectively. In addition, transgenic plants carrying pbZIP63::GUS showed no changes in reporter-gene-expression when grown on sugar under steady-state conditions. In contrast, short-term treatments of agar-grown seedlings with 1% Glc or Suc induced pbZIP63::GUS repression, which became even more apparent in seedlings grown in liquid media. Subsequent analyses of liquid-grown gin2.1 and oe3.2 seedlings revealed that Glc -dependent regulation of the five selected genes was not affected in gin2.1, whereas it was enhanced in oe3.2 plants for bZIP63, At5g22920, and BT2. The sugar treatments had no effect on ATP/ADP ratio, suggesting that changes in gene expression were not linked to cellular energy status. Overall, the data suggest that HXK1 does not act as Glc sensor controlling bZIP63, At5g22920, and BT2 expression, but it is nevertheless required for the production of a downstream metabolic signal regulating their expression.

  • 42. Kusano, Miyako
    et al.
    Jonsson, Pär
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Fukushima, Atsushi
    Gullberg, Jonas
    Sjöström, Michael
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Trygg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Moritz, Thomas
    Metabolite signature during short-day induced growth cessation in populus2011Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 2, artikkel-id 29Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The photoperiod is an important environmental signal for plants, and influences a wide range of physiological processes. For woody species in northern latitudes, cessation of growth is induced by short photoperiods. In many plant species, short photoperiods stop elongational growth after a few weeks. It is known that plant daylength detection is mediated by Phytochrome A (PHYA) in the woody hybrid aspen species. However, the mechanism of dormancy involving primary metabolism remains unclear. We studied changes in metabolite profiles in hybrid aspen leaves (young, middle, and mature leaves) during short-day-induced growth cessation, using a combination of gas chromatography–time-of-flight mass spectrometry, and multivariate projection methods. Our results indicate that the metabolite profiles in mature source leaves rapidly change when the photoperiod changes. In contrast, the differences in young sink leaves grown under long and short-day conditions are less distinct. We found short daylength induced growth cessation in aspen was associated with rapid changes in the distribution and levels of diverse primary metabolites. In addition, we conducted metabolite profiling of leaves of PHYA overexpressor (PHYAOX) and those of the control to find the discriminative metabolites between PHYAOX and the control under the short-day conditions. The metabolite changes observed in PHYAOX leaves, together with those in the source leaves, identified possible candidates for the metabolite signature (e.g., 2-oxo-glutarate, spermidine, putrescine, 4-amino-butyrate, and tryptophan) during short-day-induced growth cessation in aspen leaves.

  • 43.
    Le Hir, Rozenn
    et al.
    UMR1318 Institut Jean-Pierre Bourgin, INRA-AgroParisTech, INRA Centre de Versailles, Versailles, France.
    Bellini, Catherine
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). UMR1318 Institut Jean-Pierre Bourgin, INRA-AgroParisTech, INRA Centre de Versailles, Versailles, France.
    The plant-specific Dof transcription factors family: new players involved in vascular system development and functioning in Arabidopsis2013Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 4, s. Article Number: 164-Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    In higher plants phloem and xylem are responsible for long-distance transport of water, nutrients, and signals that act systemically at short or long-distance to coordinate developmental processes. The formation of the plant vascular system is a complex process that integrates signaling events and gene regulation at transcriptional and posttranscriptional levels. Thanks to transcriptomic and proteomic analysis we start to better understand the mechanisms underlying the formation and the functioning of the vascular system. The role of the DNA-binding with one finger (Dof TFs), a group of plant-specific transcription factors, recently emerged as part of the transcriptional regulatory networks acting on the formation and functioning of the vascular tissues. More than half of the members of this TF family are expressed in the vascular system. In addition some of them have been proposed to be mobile proteins, suggesting a possible role in the control of short- or long-distance signaling as well. This review summarizes the current knowledge on Dof TFs family in Arabidopsis with a special focus on their role in vascular development and functioning.

  • 44.
    Leijon, Felicia
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Glykovetenskap.
    Melzer, Michael
    Zhou, Qi
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Glykovetenskap.
    Srivastava, Vaibhav
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Glykovetenskap.
    Bulone, Vincent
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Glykovetenskap. ARC Centre of Excellence in Plant Cell Walls and School of Agriculture, Food and Wine, The University of Adelaide.
    Proteomic Analysis of Plasmodesmata From Populus Cell Suspension Cultures in Relation With Callose Biosynthesis.2018Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 9, artikkel-id 1681Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Plasmodesmata are channels that link adjacent cells in plant tissues through which molecular exchanges take place. They are involved in multiple processes vital to plant cells, such as responses to hormonal signaling or environmental challenges including osmotic stress, wounding and pathogen attack. Despite the importance of plasmodesmata, their proteome is not well-defined. Here, we have isolated fractions enriched in plasmodesmata from cell suspension cultures of Populus trichocarpa and identified 201 proteins that are enriched in these fractions, thereby providing further insight on the multiple functions of plasmodesmata. Proteomics analysis revealed an enrichment of proteins specifically involved in responses to stress, transport, metabolism and signal transduction. Consistent with the role of callose deposition and turnover in the closure and aperture of the plasmodesmata and our proteomic analysis, we demonstrate the enrichment of callose synthase activity in the plasmodesmata represented by several gene products. A new form of calcium-independent callose synthase activity was detected, in addition to the typical calcium-dependent enzyme activity, suggesting a role of calcium in the regulation of plasmodesmata through two forms of callose synthase activities. Our report provides the first proteomic investigation of the plasmodesmata from a tree species and the direct biochemical evidence for the occurrence of several forms of active callose synthases in these structures. Data are available via ProteomeXchange with identifier PXD010692.

  • 45.
    Li, Furong
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Gaillard, Marie-José
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Xu, Qinghai
    Hebei Normal Univ, Peoples Republic of China.
    Bunting, Mairi J.
    Univ Hull, UK.
    Li, Yuecong
    Hebei Normal Univ, Peoples Republic of China.
    Li, Jie
    Hebei Normal Univ, Peoples Republic of China.
    Mu, Huishuang
    Hebei Normal Univ, Peoples Republic of China.
    Lu, Jingyao
    Hebei Normal Univ, Peoples Republic of China.
    Zhang, Panpan
    Hebei Normal Univ, Peoples Republic of China.
    Zhang, Shengrui
    Hebei Normal Univ, Peoples Republic of China.
    Cui, Qiao-Yu
    Chinese Acad Sci, Peoples Republic of China.
    Zhang, Yahong
    Hebei Normal Univ, Peoples Republic of China.
    Shen, Wei
    Hebei Normal Univ, Peoples Republic of China.
    A Review of Relative Pollen Productivity Estimates From Temperate China for Pollen-Based Quantitative Reconstruction of Past Plant Cover2018Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 9, artikkel-id 1214Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Model-based quantitative reconstruction of past plant cover in Europe has shown great potential for: (i) testing hypotheses related to Holocene vegetation dynamics, biodiversity, and their relationships with climate and land use; (ii) studying long term interactions between climate and land use. Similar model-based quantitative reconstruction of plant cover in China has been restricted due to the lack of standardized datasets of existing estimates of relative pollen productivity (RPP). This study presents the first synthesis of all RPP values available to date for 39 major plant taxa from temperate China and proposes standardized RPP datasets that can be used for model-based quantitative reconstructions of past plant cover using fossil pollen records for the region. We review 11 RPP studies in temperate China based on modern pollen and related vegetation data around the pollen samples. The study areas include meadow, steppe and desert vegetation, various woodland types, and cultural landscapes. We evaluate the strategies of each study in terms of selection of study areas and distribution of study sites; pollen- and vegetation-data collection in field; vegetation-data collection from satellite images and vegetation maps; and data analysis. We compare all available RPP estimates, select values based on precise rules and calculate mean RPP estimates. We propose two standardized RPP datasets for 31 (Alt1) and 29 (Alt2) plant taxa. The ranking of mean RPPs (Alt-2) relative to Poaceae (= 1) for eight major taxa is: Artemisia (21) > Pinus (18.4) > Betula (12.5) > Castanea (11.5) > Elaeagnaceae (8.8) > Juglans (7.5) > Compositae (4.5) > Amaranthaceae/Chenopodiaceae (4). We conclude that although RPPs are comparable between Europe and China for some genera and families, they can differ very significantly, e.g., Artemisia, Compositae, and Amaranthaceae/Chenopodiaceae. For some taxa, we present the first RPP estimates e.g. Castanea, Elaeagnaceae, and Juglans. The proposed standardized RPP datasets are essential for model-based reconstructions of past plant cover using fossil pollen records from temperate China.

  • 46.
    Lopez-Goldar, Xose
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH). CSIC, Mision Biol Galicia, Pontevedra, Spain.;Ohio State Univ, Dept Plant Pathol, Columbus, OH 43210 USA.;INIA, Forest Res Ctr, Dept Forest Ecol & Genet, Madrid, Spain..
    Villari, Caterina
    Ohio State Univ, Dept Plant Pathol, Columbus, OH 43210 USA.;Univ Georgia, Daniel B Warnell Sch Forestry & Nat Resources, Athens, GA 30602 USA..
    Bonello, Pierluigi
    Ohio State Univ, Dept Plant Pathol, Columbus, OH 43210 USA..
    Borg-Karlson, Anna-Karin
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Organisk kemi.
    Grivet, Delphine
    INIA, Forest Res Ctr, Dept Forest Ecol & Genet, Madrid, Spain.;Univ Valladolid, INIA, Sustainable Forest Management Res Inst, Palencia, Spain..
    Zas, Rafael
    CSIC, Mision Biol Galicia, Pontevedra, Spain..
    Sampedro, Luis
    CSIC, Mision Biol Galicia, Pontevedra, Spain..
    Inducibility of Plant Secondary Metabolites in the Stem Predicts Genetic Variation in Resistance Against a Key Insect Herbivore in Maritime Pine2018Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 9, artikkel-id 1651Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Resistance to herbivores and pathogens is considered a key plant trait with strong adaptive value in trees, usually involving high concentrations of a diverse array of plant secondary metabolites (PSM). Intraspecific genetic variation and plasticity of PSM are widely known. However, their ecology and evolution are unclear, and even the implication of PSM as traits that provide direct effective resistance against herbivores is currently questioned. We used control and methyl jasmonate (MJ) induced clonal copies of genotypes within families from ten populations of the main distribution range of maritime pine to exhaustively characterize the constitutive and induced profile and concentration of PSM in the stem phloem, and to measure insect herbivory damage as a proxy of resistance. Then, we explored whether genetic variation in resistance to herbivory may be predicted by the constitutive concentration of PSM, and the role of its inducibility to predict the increase in resistance once the plant is induced. We found large and structured genetic variation among populations but not between families within populations in resistance to herbivory. The MJ-induction treatment strongly increased resistance to the weevil in the species, and the genetic variation in the inducibility of resistance was significantly structured among populations, with greater inducibility in the Atlantic populations. Genetic variation in resistance was largely explained by the multivariate concentration and profile of PSM at the genotypic level, rather than by bivariate correlations with individual PSM, after accounting for genetic relatedness among genotypes. While the constitutive concentration of the PSM blend did not show a clear pattern of resistance to herbivory, specific changes in the chemical profile and the increase in concentration of the PSM blend after MJ induction were related to increased resistance. To date, this is the first example of a comprehensive and rigorous approach in which inducibility of PSM in trees and its implication in resistance was analyzed excluding spurious associations due to genetic relatedness, often overlooked in intraspecific studies. Here we provide evidences that multivariate analyses of PSM, rather than bivariate correlations, provide more realistic information about the potentially causal relationships between PSM and resistance to herbivory in pine trees.

  • 47. Mazzuca, Silvia
    et al.
    Björk, Mats
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Beer, S.
    Felisberto, P.
    Gobert, S.
    Procaccini, G.
    Runcie, J.
    Silva, J.
    Borges, A. V.
    Brunet, C.
    Buapet, Pimchanok
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Champenois, W.
    Costa, M. M.
    D'Esposito, D.
    Gullström, Martin
    Lejeune, P.
    Lepoint, G.
    Olive, I.
    Rasmusson, Lina M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Richir, J.
    Ruocco, M.
    Serra, I. A.
    Spadafora, A.
    Santos, Rui
    Establishing research strategies, methodologies and technologies to link genomics and proteomics to seagrass productivity, community metabolism, and ecosystem carbon fluxes2013Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 4, artikkel-id 38Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A complete understanding of the mechanistic basis of marine ecosystem functioning is only possible through integrative and interdisciplinary research. This enables the prediction of change and possibly the mitigation of the consequences of anthropogenic impacts. One major aim of the European Cooperation in Science and Technology (COST) Action ES0609 Seagrasses productivity. From genes to ecosystem management, is the calibration and synthesis of various methods and the development of innovative techniques and protocols for studying seagrass ecosystems. During 10 days, 20 researchers representing a range of disciplines (molecular biology, physiology, botany, ecology, oceanography, and underwater acoustics) gathered at The Station de Recherches Sous-marines et Oceanographiques (STARESO, Corsica) to study together the nearby Posidonia oceanica meadow. STARESO is located in an oligotrophic area classified as pristine site where environmental disturbances caused by anthropogenic pressure are exceptionally low. The healthy P. oceanica meadow, which grows in front of the research station, colonizes the sea bottom from the surface to 37 m depth. During the study, genomic and proteomic approaches were integrated with ecophysiological and physical approaches with the aim of understanding changes in seagrass productivity and metabolism at different depths and along daily cycles. In this paper we report details on the approaches utilized and we forecast the potential of the data that will come from this synergistic approach not only for P. oceanica but for seagrasses in general.

  • 48.
    Montagnoli, Antonio
    et al.
    University of Insubria, Italy.
    Terzaghi, Mattia
    University of Insubria, Italy.
    Fulgaro, Nicoletta
    University of Insubria, Italy.
    Stoew, Borys
    RISE., Swedish ICT, Acreo.
    Wipenmyr, Jan
    RISE., Swedish ICT, Acreo.
    Ilver, Dag
    RISE., Swedish ICT, Acreo.
    Rusu, Cristina
    RISE., Swedish ICT, Acreo.
    Scippa, Gabriella S.
    University of Molise, Italy.
    Chiatante, Donato
    University of Insubria, Italy.
    Non-destructive phenotypic analysis of early stage tree seedling growth using an automated stereovision imaging method2016Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 7, artikkel-id 1644Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A plant phenotyping approach was applied to evaluate growth rate of containerized tree seedlings during the precultivation phase following seed germination. A simple and affordable stereo optical system was used to collect stereoscopic red-green-blue (RGB) images of seedlings at regular intervals of time. Comparative analysis of these images by means of a newly developed software enabled us to calculate (a) the increments of seedlings height and (b) the percentage greenness of seedling leaves. Comparison of these parameters with destructive biomass measurements showed that the height traits can be used to estimate seedling growth for needle-leaved plant species whereas the greenness trait can be used for broad-leaved plant species. Despite the need to adjust for plant type, growth stage and light conditions this new, cheap, rapid, and sustainable phenotyping approach can be used to study large-scale phenome variations due to genome variability and interaction with environmental factors.

  • 49.
    Muola, Anne
    et al.
    Abo Akad Univ, Environm & Marine Biol, Turku, Finland.;Swedish Univ Agr Sci, Dept Ecol, Uppsala, Sweden..
    Weber, Daniela
    Swedish Univ Agr Sci, Dept Plant Protect Biol, Alnarp, Sweden..
    Malm, Lisa E.
    Swedish Univ Agr Sci, Dept Ecol, Uppsala, Sweden..
    Egan, Paul A.
    Swedish Univ Agr Sci, Dept Plant Protect Biol, Alnarp, Sweden..
    Glinwood, Robert
    Swedish Univ Agr Sci, Dept Crop Prod Ecol, Uppsala, Sweden..
    Parachnowitsch, Amy L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Stenberg, Johan A.
    Swedish Univ Agr Sci, Dept Plant Protect Biol, Alnarp, Sweden..
    Direct and Pollinator-Mediated Effects of Herbivory on Strawberry and the Potential for Improved Resistance2017Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 8, artikkel-id 823Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The global decline in pollinators has partly been blamed on pesticides, leading some to propose pesticide-free farming as an option to improve pollination. However, herbivores are likely to be more prevalent in pesticide-free environments, requiring knowledge of their effects on pollinators, and alternative crop protection strategies to mitigate any potential pollination reduction. Strawberry leaf beetles (SLB) Galerucella spp. are important strawberry pests in Northern Europe and Russia. Given that SLB attack both leaf and flower tissue, we hypothesized pollinators would discriminate against SLB-damaged strawberry plants (Fragaria vesca, cultivar 'Rügen'), leading to lower pollination success and yield. In addition we screened the most common commercial cultivar 'Rugen' and wild Swedish F. vesca genotypes for SLB resistance to assess the potential for inverse breeding to restore high SLB resistance in cultivated strawberry. Behavioral observations in a controlled experiment revealed that the local pollinator fauna avoided strawberry flowers with SLB-damaged petals. Low pollination, in turn, resulted in smaller more deformed fruits. Furthermore, SLB-damaged flowers produced smaller fruits even when they were hand pollinated, showing herbivore damage also had direct effects on yield, independent of indirect effects on pollination. We found variable resistance in wild woodland strawberry to SLB and more resistant plant genotypes than the cultivar 'Rugen' were identified. Efficient integrated pest management strategies should be employed to mitigate both direct and indirect effects of herbivory for cultivated strawberry, including high intrinsic plant resistance.

  • 50. Murray, Michelle
    et al.
    Soh, Wuu Kuang
    Yiotis, Charilaos
    Batke, Sven
    Parnell, Andrew C.
    Spicer, Robert A.
    Lawson, Tracy
    Caballero, Rodrigo
    Stockholms universitet, Naturvetenskapliga fakulteten, Meteorologiska institutionen (MISU).
    Wright, Ian J.
    Purcell, Conor
    McElwain, Jennifer C.
    Convergence in Maximum Stomatal Conductance of C-3 Woody Angiosperms in Natural Ecosystems Across Bioclimatic Zones2019Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, artikkel-id 558Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Stomatal conductance (g(s)) in terrestrial vegetation regulates the uptake of atmospheric carbon dioxide for photosynthesis and water loss through transpiration, closely linking the biosphere and atmosphere and influencing climate. Yet, the range and pattern of g(s) in plants from natural ecosystems across broad geographic, climatic, and taxonomic ranges remains poorly quantified. Furthermore, attempts to characterize g(s) on such scales have predominantly relied upon meta-analyses compiling data from many different studies. This approach may be inherently problematic as it combines data collected using unstandardized protocols, sometimes over decadal time spans, and from different habitat groups. Using a standardized protocol, we measured leaf-level g(s) using porometry in 218 C-3 woody angiosperm species in natural ecosystems representing seven bioclimatic zones. The resulting dataset of 4273 g(s) measurements, which we call STraits (Stomatal Traits), was used to determine patterns in maximum g(s) (g(smax)) across bioclimatic zones and whether there was similarity in the mean g(smax) of C3 woody angiosperms across ecosystem types. We also tested for differential g(smax) in two broadly defined habitat groups - open-canopy and understory-subcanopy - within and across bioclimatic zones. We found strong convergence in mean g(smax) of C3 woody angiosperms in the understory-subcanopy habitats across six bioclimatic zones, but not in open-canopy habitats. Mean g(smax) in open-canopy habitats (266 +/- 100 mmol m(-2) s(-1)) was significantly higher than in understory-subcanopy habitats (233 +/- 86 mmol m(-2) s(-1)). There was also a central tendency in the overall dataset to operate toward a g(smax) of similar to 250 mmol m(-2) s(-1). We suggest that the observed convergence in mean g(smax) of C3 woody angiosperms in the understory-subcanopy is due to a buffering of g(smax) against macroclimate effects which will lead to differential response of C3 woody angiosperm vegetation in these two habitats to future global change. Therefore, it will be important for future studies of g(smax) to categorize vegetation according to habitat group.

12 1 - 50 of 76
RefereraExporteraLink til resultatlisten
Permanent link
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf