1.
Munthe, Christian, 1962
(författare)
Precaution and Ethics: Handling risks, uncertainties and knowledge gaps in the regulation of new biotechnologies
2017
Bok (övrigt vetenskapligt/konstnärligt) abstract
This volume outlines and analyses ethical issues actualized by applying a precautionary approach to the regulation of new biotechnologies. It presents a novel way of categorizing and comparing biotechnologies from a precautionary standpoint. Based on this, it addresses underlying philosophical problems regarding the ethical assessment of decision-making under uncertainty and ignorance, and discusses how risks and possible benefits of such technologies should be balanced from an ethical standpoint. It argues on conceptual and ethical grounds for a technology neutral regulation as well as for a regulation that not only checks new technologies but also requires old, inferior ones to be phased out. It demonstrates how difficult ethical issues regarding the extent and ambition of precautionary policies need to be handled by such a regulation, and presents an overarching framework for doing so.
2.
Sandin, Per, et al.
(författare)
Technology neutrality and regulation of agricultural biotechnology
2018
Ingår i: Professionals in food chains: ethics, rules and responsibility. EurSafe 2018, Vienna, Austria 13 – 16 June 2018 / edited by: Svenja Springer, Herwig Grimm. - Wageningen, Netherlands : Wageningen Academic Publishers. - 9789086863211
Konferensbidrag (refereegranskat) abstract
Agricultural biotechnology, in particular genetically modified organisms (GMOs), is subject to regulation in many areas of the world, not least in the European Union (EU). A number of authors have argued that those regulatory processes are unfair, costly, and slow and that regulation therefore should move in the direction of increased ‘technology neutrality’. The issue is becoming more pressing, especially since new biotechnologies such as CRISPR increasingly blur the regulatory distinction between GMOs and non-GMOs. This paper offers a definition of technology neutrality, uses the EU GMO regulation as a starting point for exploring technology neutrality, and presents distinctions between variants of the call for technology neutral GMO regulation in the EU.
3.
Guschanski, Katerina, et al.
(författare)
The evolution of duplicate gene expression in mammalian organs
2017
Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 27:9, s. 1461-1474
Tidskriftsartikel (refereegranskat) abstract
Gene duplications generate genomic raw material that allows the emergence of novel functions, likely facilitating adaptive evolutionary innovations. However, global assessments of the functional and evolutionary relevance of duplicate genes in mammals were until recently limited by the lack of appropriate comparative data. Here, we report a large-scale study of the expression evolution of DNA-based functional gene duplicates in three major mammalian lineages (placental mammals, marsupials, egg-laying monotremes) and birds, on the basis of RNA sequencing (RNA-seq) data from nine species and eight organs. We observe dynamic changes in tissue expression preference of paralogs with different duplication ages, suggesting differential contribution of paralogs to specific organ functions during vertebrate evolution. Specifically, we show that paralogs that emerged in the common ancestor of bony vertebrates are enriched for genes with brain-specific expression and provide evidence for differential forces underlying the preferential emergence of young testis-and liver-specific expressed genes. Further analyses uncovered that the overall spatial expression profiles of gene families tend to be conserved, with several exceptions of pronounced tissue specificity shifts among lineage-specific gene family expansions. Finally, we trace new lineage-specific genes that may have contributed to the specific biology of mammalian organs, including the little-studied placenta. Overall, our study provides novel and taxonomically broad evidence for the differential contribution of duplicate genes to tissue-specific transcriptomes and for their importance for the phenotypic evolution of vertebrates.
4.
Seroussi, Eyal, et al.
(författare)
Identification of the Long-Sought Leptin in Chicken and Duck : Expression Pattern of the Highly GC-Rich Avian leptin Fits an Autocrine/Paracrine Rather Than Endocrine Function
2016
Ingår i: Endocrinology. - : The Endocrine Society. - 0013-7227 .- 1945-7170. ; 157:2, s. 737-751
Tidskriftsartikel (refereegranskat) abstract
More than 20 years after characterization of the key regulator of mammalian energy balance, leptin, we identified the leptin (LEP) genes of chicken (Gallus gallus) and duck (Anas platyrhynchos). The extreme guanine-cytosine content (similar to 70%), the location in a genomic region with low-complexity repetitive and palindromic sequence elements, the relatively low sequence conservation, and low level of expression have hampered the identification of these genes until now. In vitro-expressed chicken and duck leptins specifically activated signaling through the chicken leptin receptor in cell culture. In situ hybridization demonstrated expression of LEP mRNA in granular and Purkinje cells of the cerebellum, anterior pituitary, and in embryonic limb buds, somites, and branchial arches, suggesting roles in adult brain control of energy balance and during embryonic development. The expression patterns of LEP and the leptin receptor (LEPR) were explored in chicken, duck, and quail (Coturnix japonica) using RNA-sequencing experiments available in the Short Read Archive and by quantitative RT-PCR. In adipose tissue, LEP and LEPR were scarcely transcribed, and the expression level was not correlated to adiposity. Our identification of the leptin genes in chicken and duck genomes resolves a long lasting controversy regarding the existence of leptin genes in these species. This identification was confirmed by sequence and structural similarity, conserved exon-intron boundaries, detection in numerous genomic, and transcriptomic datasets and characterization by PCR, quantitative RT-PCR, in situ hybridization, and bioassays. Our results point to an autocrine/paracrine mode of action for bird leptin instead of being a circulating hormone as in mammals.
5.
6.
Ahmadi Afzadi, Masoud
(författare)
Genetic variation in resistance to fungal storage diseases in apple : inoculation-based screening, transcriptomics and biochemistry
2015
Doktorsavhandling (övrigt vetenskapligt/konstnärligt) abstract
Apple is one of the economically and culturally most important fruit crops and has many health-related benefits. Apple production is, however, sensitive to several fungal diseases including blue mold, caused by Penicillium expansum. Problems are more pronounced in organic production or in countries where postharvest application of fungicides is prohibited. To limit or overcome this problem, many studies have been focused on investigations of the mechanism of resistance/tolerance. No major gene(s) have as yet been identified, but quantitatively inherited traits, some of which are related to fruit texture and content of chemical compounds, have been shown to affect the ability of cultivars to withstand storage diseases. In the present thesis, inter-cultivar variation in terms of resistance to fungal storage diseases was investigated at two locations, i.e. Balsgård in Sweden and Njøs in Norway. The association of harvest date, fruit firmness and softening with lesion decay was investigated on large sets of cultivars. The contribution of four fruit texture-related genes (Md-ACO1, Md-ACS1, Md-Exp7 and Md-PG1) in explaining the fruit texture characteristics was examined. Fruit content of chemical compounds with a potential impact on disease resistance was also investigated, and finally the regulation of apple genes upon fungal infection was studied in order to identify candidate genes responsible for disease resistance. Inoculation-based screening indicated large variation across the investigated cultivars in terms of blue mold and bitter rot susceptibility. Harvest date and softening rate of fruits during storage had a large impact on resistance to fungal diseases, thus cultivars with moderate to firm fruits that soften comparatively little during storage could withstand the fungal infection comparatively well. Softening rate is, in its turn, closely associated with harvest date whereas four fruit texture-related genes had lower predictive power than expected. Quantifying the chemical compounds in the fruit samples revealed that some of these compounds, especially flavonols and procyanidin B2, could contribute to resistance against blue mold, whereas contents of malic acids or total titratable acidity had considerably less impact. Differential expression of FLS, LDOX, and CHS genes involved in biosynthesis of flavonoids and PGIP, TT10, WAK1 and CTL1 genes related to cell wall structure indicate the importance of fruit characteristics and biochemical compounds in the resistance mechanism.
7.
Andersson, Mariette, et al.
(författare)
Genome editing in potato via CRISPR-Cas9 ribonucleoprotein delivery
2018
Ingår i: Physiologia Plantarum. - : Wiley. - 0031-9317 .- 1399-3054. ; 164, s. 378-384
Tidskriftsartikel (refereegranskat) abstract
Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein-9 (CRISPR-Cas9) can be used as an efficient tool for genome editing in potato (Solanum tuberosum). From both a scientific and a regulatory perspective, it is beneficial if integration of DNA in the potato genome is avoided. We have implemented a DNA-free genome editing method, using delivery of CRISPR-Cas9 ribonucleoproteins (RNPs) to potato protoplasts, by targeting the gene encoding a granule bound starch synthase (GBSS, EC 2.4.1.242). The RNP method was directly implemented using previously developed protoplast isolation, transfection and regeneration protocols without further adjustments. Cas9 protein was preassembled with RNA produced either synthetically or by in vitro transcription. RNP with synthetically produced RNA (cr-RNP) induced mutations, i.e. indels, at a frequency of up to 9%, with all mutated lines being transgene-free. A mutagenesis frequency of 25% of all regenerated shoots was found when using RNP with in vitro transcriptionally produced RNA (IVT-RNP). However, more than 80% of the shoots with confirmed mutations had unintended inserts in the cut site, which was in the same range as when using DNA delivery. The inserts originated both from DNA template remnants from the in vitro transcription, and from chromosomal potato DNA. In 2-3% of the regenerated shoots from the RNP-experiments, mutations were induced in all four alleles resulting in a complete knockout of the GBSS enzyme function.
8.
Burra, Dharani
(författare)
Defence related molecular signalling in Potato : new perspectives from “- Omics”
2016
Doktorsavhandling (övrigt vetenskapligt/konstnärligt) abstract
Potato production is hampered by several pathogens and is subjected to intense chemical based disease control, use of which also has undesirable consequences. Resistance breeding programs have also shown limited success. Hence, there is a need to develop durable disease resistance. Omics-techniques enable new layers of knowledge regarding molecules and their interactions mediating defence, which can contribute to identification of durable resistance sources. A novel network-based approach was used to improve the existing annotation of gene probes on the genome based microarray. Approximately 8000 unannotated probes received a new annotation. This improved annotation was used to assess genome wide changes in transcripts and proteins in response to treatments with resistance inducers, β- amino butyric acid (BABA) and Phosphite based salt (Phi). Five thousand transcripts were significantly regulated 48 hours after 10mM BABA treatment while one was regulated with 1mM BABA. In coherence, 10 mM BABA but not 1 mM induced protection to the hemibiotroph Phytophthora infestans. No transcript was significantly regulated 48 hours after Phi treatment. Time course analysis revealed that Phi exerts a transient effect, as significant transcriptomic changes were observed only 3, 6 and 11 hours after treatment. In contrast, plants showed resistance to P. infestans even at 120 hours after Phi treatment. Phi and BABA dependent “Induced state” is not restricted to transcripts related to plant defence, as transcripts related to abiotic stress and primary metabolism were altered, while biotic stress and cell wall related proteins also increased in abundance. Furthermore, an in vitro based blackleg disease screening assay was developed to investigate Potato – Dickeya solani interactions. We show that salicylic (SA) and COI1 are necessary for defence in shoots and tubers to this necrotroph. We also screened a crossing population and identified “potential” D. solani susceptibility genes related to transcriptional regulation. We also show that while SA is necessary to restrict lesion development and pathogen growth in response to the necrotroph Alternaria solani, COI1 affects pathogen growth only. Transcriptomic analysis indicated that rapid defence response to A. solani involves biotic, abiotic and oxidative stress related transcripts regulated by SA and COI1. We identified a citrate binding protein, which is also induced by resistance inducers, as an SA-repressed susceptibility factor to A. solani. Finally, proteomics of PAMP triggered immunity revealed upregulation of oxidative stress proteins while proteins related to oxidative stress tolerance, GTP binding activity were specifically upregulated in effector triggered immunity interactions.
9.
10.
Calleja-Rodriguez, Ainhoa
(författare)
Quantitative Genetics and Genomic Selection of Scots pine
2019
Doktorsavhandling (övrigt vetenskapligt/konstnärligt) abstract
The final objective of tree improvement programs is to increase the frequency of favourable alleles in a population, for the traits of interest within the breeding programs. To achieve this, it is crucial to decompose the phenotypic variance accurately into its genetic and environmental components in order to obtain a precise estimation of genetic parameters and to increase genetic gains. The overall aim of this thesis was to increase the accuracy of genetic parameter estimation by incorporating new quantitative genetics models to the analysis of multiple traits in multiple trials of Scots pine, and to develop a genomic selection protocol to accelerate genetic gain. Factor analysis was incorporated to multivariate multi-environment analyses and it allowed to evaluate up to 19 traits simultaneously. As a result, precise patterns of genotype-by-environment interactions (G E) were observed for tree vitality and height; moreover, it was possible to detect the main driver of the G E: differences in temperature sum among sites. Traditional quantitative trait loci (QTL) analysis of phenotypic data was compared with the detection of QTL with estimated breeding values (EBV) for the first time in a three generation pedigree and, as outcome, it was noticed that if a QTL was associated to a EBV and to a phenotypic trait, the proportion of variance explained by the QTLEBV was higher than the QTL-phenotype. Additionally, several QTL were detected across several ages, which may make them suitable as candidates for early selection. Genomic selection (GS) could aid to reduce the breeding cycle by shortening the periods of progeny field testing, and consequently increasing genetic gains per year. Genomic predictions, including additive and non-additive effects through different prediction models were compared with traditional pedigree-based models; it was seen an overestimation of genetic parameters for pedigree-based models, even larger when nonadditive effects could not be discerned from additive and residual effects. Prediction accuracies and abilities of the genomic models were sufficient to achieve higher selection efficiencies and responses per year varying between 50-90% by shortening 50% the breeding cycle. For the selection of the top 50 individuals, higher gains were estimated if non-additive effects are incorporated to the models (7 – 117%).
