| 41. |
- Hallingbäck, Henrik, et al.
(författare)
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Genome Wide Associations of Growth, Phenology, and Plasticity Traits in Willow [Salix viminalis (L.)]
- 2019
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- The short rotation biomass crop willow (Salix genera) has been of interest for bioenergy but recently also for biofuel production. For a faster development of new varieties molecular markers could be used as selection tool in an early stage of the breeding cycle. To identify markers associated with growth traits, genome-wide association mapping was conducted using a population of 291 Salix viminalis accessions collected across Europe and Russia and a large set of genotyping-by-sequencing markers. The accessions were vegetatively propagated and planted in replicated field experiments, one in Southern Sweden and one in Central Sweden. Phenology data, including bud burst and leaf senescence, as well as different growth traits were collected and measured repeatedly between 2010 and 2017 at both field environments. A value of the plasticity for each accession was calculated for all traits that were measured the same year in both environments as the normalized accession value in one environment subtracted by the corresponding value in the other environment. Broad-sense accession heritabilities and narrow-sense chip heritabilities ranged from 0.68 to 0.95 and 0.45 to 0.99, respectively for phenology traits and from 0.56 to 0.85 and 0.24 to 0.97 for growth traits indicating a considerable genetic component for most traits. Population structure and kinship between accessions were taken into account in the association analyses. In total, 39 marker-trait associations were found where four were specifically connected to plasticity and interestingly one particular marker was associated to several different plasticity growth traits. Otherwise association consistency was poor, possibly due to accession by environment interactions which were demonstrated by the low structure adjusted accession correlations across environments (ranging from 0.40 to 0.58). However, one marker association with biomass fresh weight was repeatedly observed in the same environment over two harvest years. For some traits where several associations were found, the markers jointly explained over 20% of the accession variation. The result from this study using a population of unrelated accessions has given useful information about marker-trait associations especially highlighting marker-plasticity associations and genotype-by-environment interactions as important factors to take account of in future strategies of Salix breeding.
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| 42. |
- Harikrishnan, Srilakshmy L., et al.
(författare)
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Sequence and gene expression evolution of paralogous genes in willows
- 2015
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Whole genome duplications (WGD) have had strong impacts on species diversification by triggering evolutionary novelties, however, relatively little is known about the balance between gene loss and forces involved in the retention of duplicated genes originating from a WGD. We analyzed putative Salicoid duplicates in willows, originating from the Salicoid WGD, which took place more than 45Mya. Contigs were constructed by de novo assembly of RNA-seq data derived from leaves and roots from two genotypes. Among the 48,508 contigs, 3,778 pairs were, based on fourfold synonymous third-codon transversion rates and syntenic positions, predicted to be Salicoid duplicates. Both copies were in most cases expressed in both tissues and 74% were significantly differentially expressed. Mean Ka/Ks was 0.23, suggesting that the Salicoid duplicates are evolving by purifying selection. Gene Ontology enrichment analyses showed that functions related to DNA- and nucleic acid binding were over-represented among the non-differentially expressed Salicoid duplicates, while functions related to biosynthesis and metabolism were over-represented among the differentially expressed Salicoid duplicates. We propose that the differentially expressed Salicoid duplicates are regulatory neo- and/or subfunctionalized, while the non-differentially expressed are dose sensitive, hence, functionally conserved. Multiple evolutionary processes, thus drive the retention of Salicoid duplicates in willows.
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| 43. |
- Hillier, Ladeana W, et al.
(författare)
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
- 2004
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 432:7018, s. 695-716
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Tidskriftsartikel (refereegranskat)abstract
- We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
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| 44. |
- Höglund, Solveig, et al.
(författare)
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Willow resistance to a galling insect is driven by a lack of induced susceptibility not an induced defense
- 2015
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Ingår i: Arthropod-Plant Interactions. - : Springer Science and Business Media LLC. - 1872-8855 .- 1872-8847. ; 9, s. 447-455
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Tidskriftsartikel (refereegranskat)abstract
- Gall-forming insects need to manipulate host plant's growth to access food resources. Because of this intimate relationship, a hypersensitive response (HR) is thought to be an important plant defense mechanism to kill the insect before a gall is formed. Few data exist, however, that unambiguously demonstrate that HR is causally linked to resistance against galling insects. Variation in Salix viminalis resistance to the gall midge Dasineura marginemtorquens is governed by only a few genes. Although the HR is considered to be an important resistance mechanism, an earlier study based on quantitative trait locus (QTL) analysis of data sets in which resistance was expressed, has shown that larval mortality is related to a single locus in a genomic region that does not contain a locus for HR, thus challenging previous suppositions that resistance is causally linked to the expression of a HR. The present study aims to test whether or not a HR causes the observed variation in willow resistance to D. marginemtorquens. By increasing the number of markers in the genomic region of interest and reanalyzing the QTL, we have enhanced the level of resolution, so permitting a more conclusive analysis than has previously been possible. The analysis identifies two genomic regions responding to gall midge attack. Importantly, the locus for resistance (measured as neonate larval mortality) and the locus for the HR are located in different regions, strongly contradicting the induced defense hypothesis. The analysis found that resistance and susceptibility were highly correlated because the allele associated with resistance was also associated with an absence of galls. It is suggested that a lack of induced susceptibility, rather than induced defense, explains the 'resistance' of S. viminalis to D. marginemtorquens.
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| 45. |
- Klingberg, Gunilla, et al.
(författare)
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How old are you? : a systematic review investigating the relationship between age and mandibular third molar maturity
- 2023
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 18:5, s. 1-14
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Forskningsöversikt (refereegranskat)abstract
- Introduction and objective: Radiographic evaluation of the maturity of mandibular third molars is a common method used for age estimation of adolescents and young adults. The aim of this systematic review was to examine the scientific base for the relationship between a fully matured mandibular third molar based on Demirjian's method and chronological age, in order to assess whether an individual is above or below the age of 18 years.Methods: The literature search was conducted in six databases until February 2022 for studies reporting data evaluating the tooth maturity using Demirjian´s method (specifically stage H) within populations ranging from 8 to 30 years (chronological age). Two reviewers screened the titles and abstracts identified through the search strategy independently. All studies of potential relevance according to the inclusion criteria were obtained in full text, after which they were assessed for inclusion by two independent reviewers. Any disagreement was resolved by a discussion. Two reviewers independently evaluated the risk of bias using the assessment tool QUADAS-2 and extracted the data from the studies with low or moderate risk of bias. Logistic regression was used to estimate the relationship between chronological age and proportion of subjects with a fully matured mandibular third molar (Demirjian´s tooth stage H).Results: A total of 15 studies with low or moderate risk of bias were included in the review. The studies were conducted in 13 countries and the chronological age of the investigated participants ranged from 3 to 27 years and the number of participants ranged between 208 and 5,769. Ten of the studies presented the results as mean age per Demirjian´s tooth stage H, but only five studies showed the distribution of developmental stages according to validated age. The proportion of subjects with a mandibular tooth in Demirjian´s tooth stage H at 18 years ranged from 0% to 22% among males and 0 to 16% in females. Since the studies were too heterogenous to perform a meta-analysis or a meaningful narrative review, we decided to refrain from a GRADE assessment.Conclusion: The identified literature does not provide scientific evidence for the relationship between Demirjian´s stage H of a mandibular third molar and chronologic age in order to assess if an individual is under or above the age of 18 years.
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| 46. |
- Liu, Lei Conze, et al.
(författare)
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Transcriptome profiling of tobacco (Nicotiana tabacum) pollen and pollen tubes
- 2017
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 18
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Tidskriftsartikel (refereegranskat)abstract
- Background: Pollen tube growth is essential for plant reproduction and represents a widely employed model to investigate polarized cell expansion, a process important for plant morphogenesis and development. Cellular and regulatory mechanisms underlying pollen tube elongation are under intense investigation, which stands to greatly benefit from a comprehensive understanding of global gene expression profiles in pollen and pollen tubes. Here, RNA sequencing technology was applied to de novo assemble a Nicotiana tabacum male gametophytic transcriptome and to compare transcriptome profiles at two different stages of gametophyte development: mature pollen grains (MPG) and pollen tubes grown for six hours in vitro (PT6).Results: De novo assembly of data obtained by 454 sequencing of a normalized cDNA library representing tobacco pollen and pollen tube mRNA (pooled mRNA isolated from mature pollen grains [MPG] and from pollen tubes grown in vitro for 3 [PT3] or 6 [PT6] hours) resulted in the identification of 78,364 unigenes. Among these unigenes, which mapped to 24,933 entries in the Sol Genomics Network (SGN) N. tabacum unigene database, 24,672 were predicted to represent full length cDNAs. In addition, quantitative analyses of data obtained by Illumina sequencing of two separate non-normalized MPG and PT6 cDNA libraries showed that 8979 unigenes were differentially expressed (differentially expressed unigenes: DEGs) between these two developmental stages at a FDR q-value of <0.0001. Interestingly, whereas most of these DEGs were downregulated in PT6, the minor fraction of DEGs upregulated in PT6 was enriched for GO (gene ontology) functions in pollen tube growth or fertilization.Conclusions: A major output of our study is the development of two different high-quality databases representing the tobacco male gametophytic transcriptome and containing encompassing information about global changes in gene expression after pollen germination. Quantitative analyses of these databases 1) indicated that roughly 30% of all tobacco genes are expressed in the male gametophyte, and 2) support previous observations suggesting a global reduction of transcription after pollen germination. Interestingly, a small number of genes, many of which predicted to function in pollen tube growth or fertilization, were found to be upregulated in elongating pollen tubes despite globally reduced transcription.
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| 47. |
- Mogren, Sofia, et al.
(författare)
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Mast Cell Proteases Promote Diverse Effects on the Plasminogen Activation System and Wound Healing in A549 Alveolar Epithelial Cells
- 2022
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Ingår i: Cells. - : MDPI AG. - 2073-4409. ; 11:18
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Tidskriftsartikel (refereegranskat)abstract
- Tissue damage, epithelial alterations, and intraepithelial presence of mast cells (MCs) are characteristics of asthma pathogenesis. Increased alveolar infiltration of MC populations has also been identified as a feature of asthma and other chronic respiratory diseases. The asthma associated receptor, urokinase plasminogen activator receptor (uPAR), has been shown to regulate bronchial epithelial repair responses. However, the impact of MC tryptase and chymase on functional properties and expression of uPAR in alveolar epithelial cells have not been fully investigated. Alveolar epithelial cell migration and wound healing were investigated using holographic live cell imaging of A549 cells in a wound scratch model post stimulation with tryptase or chymase. The expression of uPAR was investigated on the protein and gene level from cellular supernatants and in bronchoalveolar lavage fluid fractions from allergic asthmatics. We found that tryptase improved wound healing capacity, cellular migration and membrane bound uPAR expression. Chymase reduced gap closure capacity, cellular migration and membrane bound uPAR expression but increased soluble uPAR release. Our data suggest a dual regulatory response from the MC proteases in events related to uPAR expression and wound healing which could be important features in asthmatic disease.
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| 48. |
- Mogren, Sofia, et al.
(författare)
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Mast cell tryptase enhances wound healing by promoting migration in human bronchial epithelial cells
- 2021
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Ingår i: Cell Adhesion and Migration. - : Informa UK Limited. - 1933-6918 .- 1933-6926. ; 15:1, s. 202-214
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Tidskriftsartikel (refereegranskat)abstract
- Epithelial damage and increase of intraepithelial mast cells (MC) are characteristics of asthma. The role of MC mediator tryptase and the protease-activated receptor-2 (PAR2) on epithelial wound healing is not fully investigated. Stimulation of bronchial epithelial cells (BECs) with tryptase promoted gap closure, migration and cellular speed compared to controls. Stimulated BECs had higher expression of migration marker CD151 compared to controls. Proliferation marker KI67 was upregulated in tryptase-stimulated BECs compared to controls. Treatment with PAR2 antagonist I-191 reduced gap closure, migration and cell speed compared to BECs stimulated with tryptase. We found that tryptase enhances epithelial wound healing by increased migration and proliferation, which is in part regulated via PAR2. Our data suggest that tryptase might be beneficial in tissue repair under baseline conditions. However, in a pathological context such as asthma with increased numbers of activated MCs, it might lead to epithelial remodeling and loss of function.
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| 49. |
- Nordström, Erik
(författare)
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Samordnad individuell plan (SIP) : Professionellas samt barn och föräldrars erfarenheter
- 2016
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Introduktion. Många barn och unga idag har så pass komplexa behov att de behöver samtidiga insatser från olika huvudmän. Insatserna blir alltmer specialiserade och fragmenterade, vilket kräver att professioner inom hälso- och sjukvård, socialtjänst och skola samverkar. Det finns också ett lagstiftat krav sedan 2010 på samverkan i form av Samordnad individuell plan (SIP). SIP möjliggör för barn och föräldrar att få överblick och få samordnade insatser av hälso- och sjukvården och socialtjänsten genom möte, planering och dokumenterade insatser.Syftet med avhandlingen var att beskriva professionellas, barn och föräldrars erfarenhet av samordnad individuell plan (SIP).Design och metod. Två deskriptiva studier genomfördes i ett län i södra Sverige. Delstudie 1 bestod av tolv fokusgruppsintervjuer med sammanlagt 71 personer med olika yrkeskategorier inom hälso- och sjukvården, socialtjänsten och skolan. Delstudie 2 bestod av semi-strukturerade intervjuer med sammantaget tretton barn och föräldrar från olika familjer. Bägge studierna analyserades med kvalitativ metod.Resultat. Resultatet i delstudie 1 visar att verksamheterna gör en primär avvägning mellan samverkan och sitt respektive kärnuppdrag; vårdande, pedagogisk och utredande. Samverkan skedde genom en pendling mellan hindrande och främjande faktorer. Hindrande faktorer består av olika mandat och behov, tvång till närvaro, ifrågasättande och klander, samt tidsramar och prioriteringar. Främjande faktorer är likartad tolkning av gemensamma avtal, ömsesidig respektoch kollegialt lärande, gemensam terminologi och dokumentation, samt intresse för samverkan. Delstudie 2 visar att barn och föräldrars upplevelse av delaktighet i form av SIP ökade över tid och att de över tid upplevde att de fick ett samordnat stöd från olika vårdgivare, som barnen och/eller föräldrarna innan SIP ofta själva fick samordna. Detta mål uppnåddes först efter initialt motstånd och konkurrens mellan olika verksamheter, och det underlättade att skapa relationer och allianser med professionella för att nå detta mål. Resultatet diskuteras utifrån fyra olika stadier av samverkan och förutsättningar för att intentionerna med SIP avseende delaktighet skall uppnås.Konklusion och praktiska implikationer. SIP tycks ha potential att bidra till en förbättrad samverkan om de professionella visar ömsesidig kollegial respekt och har fokus på barn och föräldrars behov. Detta kan lättare uppnås om professionella inte lägger för stor vikt vid skydda den egna verksamhetens agenda istället för en samverkansagenda. Detta bekräftas av delstudie 2 som visar att barn och föräldrar uppfattar att det finns intentioner att göra brukaren delaktig, men att denna intention hindras av oenighet, skilda intentioner och bristande samsyn mellan verksamheter, och barn och föräldrar får utstå förvirring och fragmentering av insatserna under lång tid, vilket kan utsätta barnet för risker. Om SIP skall bli det verktyg för helhetslösning och brukardelaktighet som det är avsett att vara, så behöver de berörda professionerna uppnå en bredare samsyn kring SIP för att uppfylla intentionen med en samverkan med utökad brukardelaktighet.
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| 50. |
- Pucholt, Pascal, et al.
(författare)
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Allelic incompatibility can explain female biased sex ratios in dioecious plants
- 2017
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 18
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Tidskriftsartikel (refereegranskat)abstract
- Background: Biased sex ratios are common among dioecious plant species despite the theoretical prediction of selective advantage of even sex ratios. Albeit the high prevalence of deviations from even sex ratios, the genetic causes to sex biases are rarely known outside of a few model species. Here we present a mechanism underlying the female biased sex ratio in the dioecious willow species Salix viminalis.Results: We compared the segregation pattern of genome-wide single nucleotide polymorphism markers in two contrasting bi-parental pedigree populations, the S3 with even sex ratio and the S5 with a female biased sex ratio. With the segregation analysis and comparison between the two populations, we were able to demonstrate that sex determination and sex ratio distortion are controlled by different genetic mechanisms. We furthermore located the sex ratio distorter locus to a Z/W-gametologous region on chromosome 15, which was in close linkage with the sex determination locus. Interestingly, all males in the population with biased sex ratio have in this sex ratio distorter locus the same genotype, meaning that males with the Z(1)/Z(3)-genotype were missing from the population, thereby creating the 2: 1 female biased sex ratio.Conclusions: We attribute the absence of Z(1)/Z(3) males to an allelic incompatibility between maternally and paternally inherited alleles in this sex ratio distorter locus. Due to the tight linkage with the sex determination locus only male individuals are purged from the population at an early age, presumably before or during seed development. We showed that such allelic incompatibility could be stably maintained over evolutionary times through a system of overdominant or pseudooverdominant alleles. Thus, it is possible that the same mechanism generates the female biased sex ratio in natural willow populations.
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