| 1. |
- Akhter, Shirin, et al.
(författare)
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Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway
- 2022
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 236:5, s. 1951-1963
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Tidskriftsartikel (refereegranskat)abstract
- Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.
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| 2. |
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| 3. |
- Imsland, Freyja, et al.
(författare)
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Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation underlying Dun camouflage colour in horses
- 2016
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 48:2, s. 152-158
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Tidskriftsartikel (refereegranskat)abstract
- Dun is a wild-type coat color in horses characterized by pigment dilution with a striking pattern of dark areas termed primitive markings. Here we show that pigment dilution in Dun horses is due to radially asymmetric deposition of pigment in the growing hair caused by localized expression of the T-box 3 (TBX3) transcription factor in hair follicles, which in turn determines the distribution of hair follicle melanocytes. Most domestic horses are non-dun, a more intensely pigmented phenotype caused by regulatory mutations impairing TBX3 expression in the hair follicle, resulting in a more circumferential distribution of melanocytes and pigment granules in individual hairs. We identified two different alleles (non-dun1 and non-dun2) causing non-dun color. non-dun2 is a recently derived allele, whereas the Dun and non-dun1 alleles are found in ancient horse DNA, demonstrating that this polymorphism predates horse domestication. These findings uncover a new developmental role for T-box genes and new aspects of hair follicle biology and pigmentation.
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| 4. |
- Jiang, Lin, et al.
(författare)
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ZBED6 Modulates the Transcription of Myogenic Genes in Mouse Myoblast Cells
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:4, s. e94187-
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Tidskriftsartikel (refereegranskat)abstract
- ZBED6 is a recently discovered transcription factor, unique to placental mammals, that has evolved from a domesticated DNA transposon. It acts as a repressor at the IGF2 locus. Here we show that ZBED6 acts as a transcriptional modulator in mouse myoblast cells, where more than 700 genes were differentially expressed after Zbed6-silencing. The most significantly enriched GO term was muscle protein and contractile fiber, which was consistent with increased myotube formation. Twenty small nucleolar RNAs all showed increased expression after Zbed6-silencing. The co-localization of histone marks and ZBED6 binding sites and the effect of Zbed6-silencing on distribution of histone marks was evaluated by ChIP-seq analysis. There was a strong association between ZBED6 binding sites and the H3K4me3, H3K4me2 and H3K27ac modifications, which are usually found at active promoters, but no association with the repressive mark H3K27me3. Zbed6-silencing led to increased enrichment of active marks at myogenic genes, in agreement with the RNA-seq findings. We propose that ZBED6 preferentially binds to active promoters and modulates transcriptional activity without recruiting repressive histone modifications.
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| 5. |
- Johansson, Björn, 1975, et al.
(författare)
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Discrete Event Simulation with Lifecycle Assessment Data at a Juice Manufacturing System
- 2008
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Ingår i: 2008 5th International Conference on Simulation and Modelling in the Food and Bio-Industry, FOODSIM 2008; Dublin; Ireland; 26 June 2008 through 28 June 2008. ; , s. 165-169
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Konferensbidrag (refereegranskat)abstract
- In order to measure and evaluate productivity and environmental parameters simultaneously and in consideration to each other, they need to be presented on the same basis and put up on the same table, at the same time. Otherwise, while considering only parts of the relevant parameters at a time, there is a great risk for sub-optimisation. The study presented in this paper shows one way of putting productivity parameters such as batch size, batch frequency, production planning, and resource management on the same table as environmental parameters such as emissions, waste and energy consumption. This is done through the use of lifecycle assessment in combination with discrete event simulation. The result gives an example of a sound basis for decision-making when changes are to be made in the juice production system at hand. The presented case study gives information on energy consumption, waste and pollutants such as CO2, NOx, SO2, and ethene generated from production of juice. Results show that some changes of the system improves both environment and productivity, others improves one and worsens the other!
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| 6. |
- Karlsson, Karin, et al.
(författare)
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Sodium content in processed food items in Sweden compared to other countries : a cross-sectional multinational study
- 2023
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Ingår i: Frontiers in Public Health. - : Frontiers Media S.A.. - 2296-2565. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundDietary sodium has a dose-response relationship with cardiovascular disease, and sodium intake in Sweden exceeds national and international recommendations. Two thirds of dietary sodium intake comes from processed foods, and adults in Sweden eat more processed foods than any other European country. We hypothesized that sodium content in processed foods is higher in Sweden than in other countries. The aim of this study was to investigate sodium content in processed food items in Sweden, and how it differs from Australia, France, Hong Kong, South Africa, the United Kingdom and the United States. MethodsData were collected from retailers by trained research staff using standardized methods. Data were categorized into 10 food categories and compared using Kruskal-Wallis test of ranks. Sodium content in the food items was compared in mg sodium per 100 g of product, based on the nutritional content labels on the packages. ResultsCompared to other countries, Sweden had among the highest sodium content in the "dairy" and "convenience foods" categories, but among the lowest in "cereal and grain products," "seafood and seafood products" and "snack foods" categories. Australia had the overall lowest sodium content, and the US the overall highest. The highest sodium content in most analyzed countries was found in the "meat and meat products" category. The highest median sodium content in any category was found among "sauces, dips, spreads and dressings" in Hong Kong. ConclusionThe sodium content differed substantially between countries in all food categories, although contrary to our hypothesis, processed foods overall had lower sodium content in Sweden than in most other included countries. Sodium content in processed food was nonetheless high also in Sweden, and especially so in increasingly consumed food categories, such as "convenience foods".
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| 7. |
- Lagerkvist, Carl-Johan, et al.
(författare)
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Country of origin or EU/non-EU labelling of beef? Comparing structural reliability and validity of discrete choice experiments for measurement of consumer preferences for origin and extrinsic quality cues
- 2014
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Ingår i: Food Quality and Preference. - : Elsevier BV. - 0950-3293 .- 1873-6343. ; 34, s. 50-61
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Tidskriftsartikel (refereegranskat)abstract
- The use of food labels and packaging information on place of origin and credence quality has increased, but it is still unclear how such information relates to consumer decisions and choices concerning the relative valuation of attributes. Valid measurement methods are needed to assess the importance attributed by the public to such information, but also to inform the industry about market demand. Discrete choice experiments (CEs) are frequently used to assess consumer preferences for food attributes. However, suitable methods are needed to reveal the probabilistic nature of preference data, so that heterogeneity can be explicitly accounted for. An R-index measure was modelled to account for choice probabilities in this study. Two surveys of Swedish residents, without (n=506) and with (n=278) a price vector, compared attribute importance for origin and extrinsic quality labelling of beef in CEs. Problems of structural reliability owing to unstable associations in attribute importance between formats were supported, but on levels rather than orderings. The R-index analysis of CE data revealed violations of attribute transitivity and dominance. Extending CE analysis to include choice probabilities may be useful for consumer profiling and for optimisation of product information. Labels with specific country-of-origin information instead of a wider EU/non-EU designation were the most determining attribute in this study.
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| 8. |
- Lamichhaney, Sangeet, et al.
(författare)
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Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring
- 2012
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 109:47, s. 19345-19350
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Tidskriftsartikel (refereegranskat)abstract
- The Atlantic herring (Clupea harengus), one of the most abundant marine fishes in the world, has historically been a critical food source in Northern Europe. It is one of the few marine species that can reproduce throughout the brackish salinity gradient of the Baltic Sea. Previous studies based on few genetic markers have revealed a conspicuous lack of genetic differentiation between geographic regions, consistent with huge population sizes and minute genetic drift. Here, we present a cost-effective genome-wide study in a species that lacks a genome sequence. We first assembled amuscle transcriptome and then aligned genomic reads to the transcripts, creating an "exome assembly," capturing both exons and flanking sequences. We then resequenced pools of fish from a wide geographic range, including the Northeast Atlantic, as well as different regions in the Baltic Sea, aligned the reads to the exome assembly, and identified 440,817 SNPs. The great majority of SNPs showed no appreciable differences in allele frequency among populations; however, several thousand SNPs showed striking differences, some approaching fixation for different alleles. The contrast between low genetic differentiation at most loci and striking differences at others implies that the latter category primarily reflects natural selection. A simulation study confirmed that the distribution of the fixation index F-ST deviated significantly from expectation for selectively neutral loci. This study provides insights concerning the population structure of an important marine fish and establishes the Atlantic herring as a model for population genetic studies of adaptation and natural selection.
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| 9. |
- Lappi, Veli-Matti, et al.
(författare)
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A Comparison of the Nutritional Qualities of Supermarket's Own and Regular Brands of Bread in Sweden
- 2020
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Ingår i: Nutrients. - : MDPI. - 2072-6643. ; 12:4
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Tidskriftsartikel (refereegranskat)abstract
- Processed food is associated with unhealthy qualities such as higher content of harmful fats, sugars and salt. The aim of our study was to compare the nutritional qualities of supermarket's own brands and regular brands of bread sold in Sweden. Additionally, we compared the nutritional qualities of gluten-free and gluten-containing bread. We collected information from the labels of 332 bread products available in the largest grocery store chains. The Australian Health Star Rating (HSR) system was used to quantify the nutritional quality of each bread product. We compared all supermarket's own brand products to regular brand products, and gluten-free to gluten-containing bread. The mean HSR for the supermarket's own brands was lower than the regular brands (3.6 vs. 3.7; p = 0.046). For the regular brand products, the fibre, sugar and total fat content were greater (p < 0.001, p = 0.002 and p = 0.021, respectively), while less protein (p = 0.009) compared to regular bread products. Gluten-free bread had a lower HSR than gluten-containing bread (mean 3.5 vs. 3.8, respectively; p < 0.001). The regular brand products were slightly healthier than the supermarket's own brands, primarily as a result of a higher fibre content. Gluten-free bread products were slightly unhealthier due to a lower protein content.
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| 10. |
- Mishra, Laxmi, et al.
(författare)
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Natural variation in cone-setting ability in Norway spruce
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The conifer Norway spruce (Picea abies) has an uneven cone-setting and initiates cones onlyevery 3rd to 5th year. The cone-setting is in large synchronised on the population level,resulting in good or bad cone-years. However, variation in cone-setting frequencies andnumber of cones produced per tree can be observed among different genotypes. Here, we aimto study the genetic basis for the natural variation in cone-setting ability. To this end, we haveset up a field trial consisting of 560 ramets representing eighteen P. abies genotypes and havemonitored the cone-setting in these trees since 2008. Using this material, we study the naturalvariation in regulatory elements of a key cone-setting regulator, Picea abies SQUAMOSABINDING PROTEIN LIKE1 (PaSPL1). We have previously established that the combinedaction of miRNA156 and miRNA529 negatively regulates PaSPL1. Here, we use massivelyparallel sequencing to study the expression of these and other microRNAs in the P. abiesgenotypes. While no direct link can be established between miRNA expression levels and cone-setting frequencies, we report on individual genotype differences that grade the relativeimportance of miR156 and miR529 in regulating PaSPL1 transcript levels. We also clone, andSanger sequence the putative promoter of PaSPL1 from the genotypes in the field trial. Byanalysing variation in SNP data, we identify putative Gibberellic Acid (GA) responsiveelements enriched in the genotype with the highest cone-setting frequency. As a complement,we also sequence the transcriptomes of three genotypes before and after GA-inductions. Thisanalysis shows that relatively more genes are activated in a low cone-setting genotype than ina high cone-setting genotype. We also demonstrate that GA-regulated MYB transcriptionfactors are upregulated upon GA induction, providing a possible link between GA-inducedcone-setting and the regulation of PaSPL1 that merits further studies.
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