| 1. |
- Lahti, Leo, et al.
(författare)
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Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data
- 2013
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 1
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Tidskriftsartikel (refereegranskat)abstract
- Accumulating evidence indicates that the intestinal microbiota regulates our physiology and metabolism. Bacteria marketed as probiotics confer health benefits that may arise from their ability to affect the microbiota. Here high-throughput screening of the intestinal microbiota was carried out and integrated with serum lipidomic profiling data to study the impact of probiotic intervention on the intestinal ecosystem, and to explore the associations between the intestinal bacteria and serum lipids. We performed a comprehensive intestinal microbiota analysis using a phylogenetic microarray before and after Lactobacillus rhamnosus GG intervention. While a specific increase in the L. rhamnosus-related bacteria was observed during the intervention, no other changes in the composition or stability of the microbiota were detected. After the intervention, lactobacilli returned to their initial levels. As previously reported, also the serum lipid profiles remained unaltered during the intervention. Based on a high-resolution microbiota analysis, intake of L. rhamnosus GG did not modify the composition of the intestinal ecosystem in healthy adults, indicating that probiotics confer their health effects by other mechanisms. The most prevailing association between the gut microbiota and lipid profiles was a strong positive correlation between uncultured phylotypes of Ruminococcus gnavus-group and polyunsaturated serum triglycerides of dietary origin. Moreover, a positive correlation was detected between serum cholesterol and Collinsella (Coriobacteriaceae). These associations identified with the spectrometric lipidome profiling were corroborated by enzymatically determined cholesterol and triglyceride levels. Actinomycetaceae correlated negatively with triglycerides of highly unsaturated fatty acids while a set of Proteobacteria showed negative correlation with ether phosphatidylcholines. Our results suggest that several members of the Firmicutes, Actinobacteria and Proteobacteria may be involved in the metabolism of dietary and endogenous lipids, and provide a scientific rationale for further human studies to explore the role of intestinal microbes in host lipid metabolism.
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| 2. |
- Ræbild, Anders, et al.
(författare)
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Polyploidy – A tool in adapting trees to future climate changes? A review of polyploidy in trees
- 2024
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Ingår i: Forest Ecology and Management. - : Elsevier. - 0378-1127 .- 1872-7042. ; 560, s. 121767-121767
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Forskningsöversikt (refereegranskat)abstract
- Polyploidy, or genome doubling, has occurred repeatedly through plant evolution. While polyploid plants are used extensively in agriculture and horticulture, they have so far found limited use in forestry. Here we review the potentials of polyploid trees under climate change, and investigate if there is support for increased use. We find that polyploid trees like other plants have consistent increases in cell sizes compared to diploids, and that leaf-area based rates of photosynthesis tend to increase with increasing levels of ploidy. While no particular trend could be discerned in terms of biomass between trees of different ploidy levels, physiology is affected by polyploidization and several studies point towards a high potential for polyploid trees to adapt to drought stress. The ploidy level of most tree species is unknown, and analysis of geographical patterns in frequencies of polyploid trees are inconclusive. Artificial polyploid trees are often created by colchicine and in a few cases these have been successfully applied in forestry, but the effects of induced polyploidization in many economically important tree species remains untested. Polyploids would also be increasingly useful in tree breeding programs, to create synthetic hybrids or sterile triploids that could control unwanted spreading of germplasm in nature. In conclusion, this review suggests that polyploid trees may be superior under climate change in some cases, but that the potential of polyploids is not yet fully known and should be evaluated on a case-to-case basis for different tree species.
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| 3. |
- Rai, Neha, et al.
(författare)
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The photoreceptor UVR8 mediates the perception of both UV-B and UV-A wavelengths up to 350 nm of sunlight with responsivity moderated by cryptochromes
- 2020
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Ingår i: Plant, Cell and Environment. - : John Wiley & Sons. - 0140-7791 .- 1365-3040. ; 43:6, s. 1513-1527
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Tidskriftsartikel (refereegranskat)abstract
- The photoreceptors UV RESISTANCE LOCUS 8 (UVR8) and CRYPTOCHROMES 1 and 2 (CRYs) play major roles in the perception of UV-B (280–315 nm) and UV-A/blue radiation (315–500 nm), respectively. However, it is poorly understood how they function in sunlight. The roles of UVR8 and CRYs were assessed in a factorial experiment with Arabidopsis thaliana wild-type and photoreceptor mutants exposed to sunlight for 6 h or 12 h under five types of filters with cut-offs in UV and blue-light regions. Transcriptome-wide responses triggered by UV-B and UV-A wavelengths shorter than 350 nm (UV-Asw) required UVR8 whereas those induced by blue and UV-A wavelengths longer than 350 nm (UV-Alw) required CRYs. UVR8 modulated gene expression in response to blue light while lack of CRYs drastically enhanced gene expression in response to UV-B and UV-Asw. These results agree with our estimates of photons absorbed by these photoreceptors in sunlight and with in vitro monomerization of UVR8 by wavelengths up to 335 nm. Motif enrichment analysis predicted complex signaling downstream of UVR8 and CRYs. Our results highlight that it is important to use UV waveband definitions specific to plants’ photomorphogenesis as is routinely done in the visible region.
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| 4. |
- Westrin, Karl Johan, 1989-
(författare)
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The art of transcriptome reconstruction : with applications in Picea abies (L.) H. Karst.
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Transcriptome reconstruction is an important component in the bioinformatical part of transcriptome studies. When a reference genome is missing, highly fragmented or incomplete, a de novo transcriptome assembly is the transcriptome reconstruction approach of choice, since in such situations, a simple alignment (or mapping) would not necessarily give all theinformation concerning splice junctions, isoforms or even the full extent of the gene. Several methods for de novo transcriptome assembly have been suggested, but many of these methods lack sufficient ability to recover isoforms or are memory intense, which requires themethods to be executed on computing clusters.One species, whose published reference genome is highly fragmented, is the Norway spruce (Picea abies (L.) H. Karst.) – a conifer, very important for Swedish forestry ande conomy, but with a long juvenile phase and irregular cone setting, the demand of cultivated seeds is larger than the supply. Thus, there is a desire to understand the molecular biology behind the cone setting in P. abies, not least regarding gene expression and its regulation. This doctoral dissertation addresses these problems by describing the biological background in general, followed by an introduction to theoretical computational problems relatedto the methods applied for transcriptome reconstruction, which then are described in depth themselves, as is P. abies.Paper I uses a novel de novo assembler to detect connections between scaffolds in the P. abies genome, and also studies P. abies var acrocona, a mutant with shorter juvenile phase and more regular cone setting than the wild type, in order to detect how cone setting is initiated. By means of allele-specific expression analysis, this study detects a SNP ina miRNA binding site on a novel gene, a mutation which is coherent with the acroconaphenotype.Paper II and paper III both introduce one novel de novo transcriptome assembler each: Paper II describes the assembly method applied in paper I, with the focus torecover a comprehensive list of isoforms. It accomplished this, thus providing higher recallthan the other tested assemblers, but with an increased use of computational resources. In turn, paper III introduces a lightweight assembly method, which is the first assembly method employing the ant colony system (ACS) meta-heuristic. It is more rapid than theother tested assemblers and requires less memory (never more than half of the second most memory efficient method), but provides low recall.Paper IV applies reference based transcriptome assembly to improve the gene annotation of a new, chromosome-scale, P. abies reference genome, which is being prepared at the moment. This study pinpoints the locations in the assembled genome of six previously described genes, but which the annotation missed – until now. Furthermore, for two annotatedgenes, this study found and verified one novel transcript isoform each.Paper V studies the natural variation in cone setting in P. abies, and also the gene expression pre and post treatment of gibberellic acid (GA), known to stimulate floweringin plants. P. abies genotypes with lower cone setting ability turns out to get more genesactivated post GA treatment, compared to genotypes with higher cone setting ability.
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