| 1. |
- Bellini, Catherine, 1962-
(författare)
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A synthetic auxin for cloning mature trees
- 2024
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696.
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 2. |
- de Oliveira, Ana Henriques
(författare)
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RsbX and stress response in Listeria monocytogenes
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Listeria monocytogenes is a ubiquitous foodborne Gram-positive bacterium. Despite being mainly a soil bacterium, it can reach the food processing environment and contaminate food destined for human consumption, causing outbreaks. Because of its pathogenicity, it poses a danger for certain high-risk groups, including children, elderly, and immune-compromised people, as well as pregnant women, being capable of causing a life-threatening systemic infection known as listeriosis.All bacteria require an efficient transcriptional response and its fine-tuned modulation in order to survive the different stresses it encounters. This is especially true for L. monocytogenes, which presents an impressive range of stress adaptions that allows it survival in certain extreme conditions such as low temperature, low pH and high osmolarity. The alternative Sigma factor B, SigB, is responsible for the expression of the general stress response of this bacterium and plays a key role in the survival and adaption to new environments. The activation of SigB requires an intricate system of partner switching mechanisms, involving anti-sigma and anti-anti-sigma factors, triggered by a number of phosphorylation and dephosphorylation events that culminates with SigB being available to interact with RNA polymerase and lead the transcription of the general stress response regulon. At the top of this signal transduction pathway lies a large multi-protein complex, known as the stressosome. It is formed by RsbR (and its paralogs), RsbS and RsbT and is believed to function as a sensory hub for environmental stimuli. After signal detection, the stressosome proteins are phosphorylated and the complex goes through conformational changes that will ultimately allow for SigB activation. The reset of the stressosome to its pre-stress conformation, is hypothesized to be exerted by a putative phosphatase, RsbX, which most likely dephosphorylates the stressosome proteins post-stress.The role of RsbX in modulating the activity and conformation of the stressosome as well as in subsequent regulation of SigB activity was investigated. RsbX was shown to be required for maintaining SigB levels and activity low in non-stressed conditions as well as for proper SigB mediated stress adaptation. A ΔrsbX mutant strain was shown to have a very slight growth defect, but it also exhibited impaired motility, reduced biofilm formation, as well as a more acid resistant phenotype. The absence of RsbX was shown to alter the composition of the stressosome without drastically affecting its phosphorylation pattern. In general, RsbX was shown to play a crucial role in modulating the signal transduction pathways by preventing SigB activation under non-stressed conditions.Strains that acquire sigB operon mutations have been shown to have a growth advantage under certain mild stress conditions recurrent in a laboratory set. These strains were shown to outcompete the wild-type strain when grown in these conditions, demonstrating how a deficient SigB activity poses an advantage to the cell. On the other hand, and the ΔrsbX mutant strain was shown to have a growth disadvantage, since it was outcompeted by the wild-type strain when co-cultured. The data highlights the significant cost stress protection presents to this pathogen, since deploying the general stress response is a burden on cellular resources, and in its absence the cell can redirect energy for growth. In contrast, in the presence of a lethal stress (low pH) the strains with impaired SigB activity showed a reduced survival and an overall increased sensitivity to the stress. Hence demonstrating that in a more stressful condition the high cost of the general stress response regulon is outweighed by the protection benefits it confers to the cell. The importance of RsbX, which prevents unnecessary SigB activation, is even more evident. RsbX is not only critical to shut down the general stress response post-stress and subsequent recovery of homeostasis, but it also keeps SigB activity to low levels in non-stressed conditions, avoiding unwarranted gene expression and contributing to important energy saving. SigB also plays an important role in the transition of L. monocytogenes from a saprophytic to a pathogenic lifestyle. Even though most of the virulence factors are under the control of PrfA, the master regulator of virulence, SigB is fundamental in the survival of the bacteria inside the host’s gastro-intestinal tract (e.g., stomach high acidity and bile salt release in the duodenum), as well as in the early stages of infection, such as internalization into not phagocytic cells. Because of the importance of SigB for virulence, we speculated if RsbX, by controlling activity of SigB, would also impact the virulence of the bacteria. The data showed somewhat contradicting results, but in general it suggests that even though the expression of the virulence genes responsible for the uptake of the bacteria are increased in a strain lacking RsbX compared with the wild-type strain, the effect on the general infectivity of this strain was either minimal or not existent at all. A reason for this could be the suggested growth defect caused by the absence of RsbX, which could also jeopardize the bacteria’s ability to efficiently grow within infected cells or organisms.Overall, RsbX seems to play a crucial role for L. monocytogenes, since it is responsible to maintain a very important, but extremely costly, stress protection mechanism in an inactive mode in absence of stress. Its functions span from alteration of stressosome conformation and subsequent modulation of stress response, to homeostasis recovery, motility, biofilm formation, stress survival, and even to indirect impact in the bacteria’s infectivity. This shows the diversified, but impactful range of effects RsbX seems to have for the bacterial cell.
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| 3. |
- Ekström, Magnus, 1966-, et al.
(författare)
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Estimating density from presence/absence data in clustered populations
- 2021
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- 1. Inventories of plant populations are fundamental in ecological research and monitoring, butsuch surveys are often prone to field assessment errors. Presence/ absence (P/A) samplingmay have advantages over plant cover assessments for reducing such errors. However, thelinking between P/A data and plant density depends on model assumptions for plant spatialdistributions. Previous studies have shown, for example, how that plant density can beestimated under Poisson model assumptions on the plant locations. In this study, newmethods are developed and evaluated for linking P/A data with plant density assuming thatplants occur in clustered spatial patterns.2. New theory was derived for estimating plant density under Neyman–Scott-type cluster models such as the Matérn and Thomas cluster processes. Suggested estimators, correspondingconfidence intervals and a proposed goodness-of-fit test were evaluated in a Monte Carlosimulation study assuming a Matérn cluster process. Furthermore, the estimators were applied to plant data from environmental monitoring in Sweden to demonstrate their empiricalapplication.3. The simulation study showed that our methods work well for large enough sample sizes.The judgment of what is ’large enough’ is often difficult, but simulations indicate that asample size is large enough when the sampling distributions of the parameter estimators aresymmetric or mildly skewed. Bootstrap may be used to check whether this is true. Theempirical results suggest that the derived methodology may be useful for estimating densityof plants such as Leucanthemum vulgare and Scorzonera humilis.4. By developing estimators of plant density from P/A data under realistic model assumptions about plants’ spatial distributions, P/A sampling will become a more useful tool forinventories of plant populations. Our new theory is an important step in this direction.
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| 4. |
- Essalhi, Mohamed, et al.
(författare)
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10 - Thermo-osmosis
- 2021. - 1
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Ingår i: Osmosis Engineering. - : Elsevier. - 9780128210161 ; , s. 279-312
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- The existence of nonisothermal transport of liquids through a gelatin membrane was first described by Lippmann in 1907, and 5 years later, it was investigated by Aubert in more detail using membranes of gelatin pig’s bladder, parchment paper and viscose. In this phenomenon, there is no liquid/vapor phase transition and it is known as thermo-osmosis (TO) or thermal osmosis (TO). Lippmann also observed TO in air, obviously without prior knowledge of the work of Feddersen and Reynolds. However, at that time the lack of theory on irreversible processes prevented the progress towards understanding this phenomenon.
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| 5. |
- Heuchel, Alisa, 1990-
(författare)
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Game of crops : genetic composition and adaptation of seed orchard crops
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Orchard populations are artificial and intensively managed populations of elite, best-performing trees that are established for mass production of genetically improved seeds. Seed orchards connect cycles of selection, breeding, and testing of plus-trees with the deployment of the improved seeds at the operational plantations. Long reproductive cycles and rotation age, irregular flowering of trees pose serious threats to the economic success of tree breeding and urge efficiency monitoring. This thesis describes genetic functioning of Swedish seed orchard of Scots pine and Norway spruce, diversity levels of orchard crops, their performance in the field in connection with their genetic background, and possible ways to stimulate flowering. It is especially relevant now when molecular technologies became more affordable and allow more intensive sampling and genome coverage.We detected differences between the two species in all genetic parameters and higher diversity levels in Scots pine crops. Crop diversity was at acceptable level though slightly reduced compared to reference population. We detected great variation in flowering in orchard parents, and the influence of linear deployment strategy on diversity, reproductive success, and effective number of orchard parents. Frost tolerance of a crop depended on the origin of orchard parents but up to a smaller extent than was previously expected.Seedlings orchard crops perform well in the field, and do not suffer from increased mortality while their counterparts from controlled crosses have variable performance and tend to form G-by-E interactions. Overall, selected seed sources perform better than forest seed lots, and this superiority is independent from the silvicultural methods at the between-sites level. Site preparation methods and planting positions play a larger role at each location and may enhance survival and growth. Seed weight correlates positively with height, while diameter is more affected by the planting position.Topgrafting showed varying degree of success but efficiently reduced time to flowering to 1 year after the grafting procedure. The extent of male and female flowering was dramatically different, and for satisfactory cone crops, there is a great need in the application of flowering stimulation methods.This is a first systematic attempt to analyse genetic background of mating and population structure of several crops from different orchards of the two species. It describes the success of Swedish tree breeding strategy in conserving genetic diversity, improving survival and economic traits, and provides the assessment of linear deployment strategy with the advanced molecular techniques. We emphasize the urgent need to efficiently stimulate flowering in both species for securing orchard production and balanced genetic composition.
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| 6. |
- Hussain, Adil, et al.
(författare)
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CRISPR/Cas9-mediated gene editing in grain crops
- 2020
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Ingår i: Recent Advances in Grain Crops Research. - : IntechOpen. - 9781789854503 - 9781789854497 - 9781789856439 ; , s. 1-12
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- The development of reliable and efficient techniques for making precise targeted changes in the genome of living organisms has been a long-standing objective of researchers throughout the world. In plants, different methods, each with several different variations, have been developed for this purpose, though many of them are hampered either by providing only temporary modification of gene function or unpredictable off-target results. The recent discovery of clustered regularly interspaced short palindromic repeats (CRISPRs) and the CRISPR-associated 9 (Cas9) nucleases started a new era in genome editing. Basically, the CRISPR/Cas system is a natural immune response of prokaryotes to resist foreign genetic elements entering via plasmids and phages. Through this naturally occurring gene editing system, bacteria create DNA segments known as CRISPR arrays that allow them to "remember" foreign genetic material for protection against it and other similar sequences in the future. This system has now been adopted by researchers in laboratory to create a short guide RNA that binds to specific target sequences of DNA in eukaryotic genome, and the Cas9 enzyme cuts the DNA at the targeted location. Once cut, the cell's endogenous DNA repair machinery is used to add, delete, or replace pieces of genetic material. Though CRISPR/Cas9 technology has been recently developed, it has started to be regularly used for gene editing in plants as well as animals to good success. It has been proved as an efficient transgene-free technique. A simple search on PubMed (NCBI) shows that among all plants, 80 different studies published since 2013 involved CRISPR/Cas9-mediated genome editing in rice. Of these, 20, 13, and 24 papers have been published in 2019, 2018, and 2017, respectively. Furthermore, 20 different studies published since 2014 utilized CRISPR/Cas9 system for gene editing in wheat, where five of these studies were published in 2019 and seven were published in 2018. Genomes of other grain crops edited through this technique include maize, sorghum, barley, etc. This indicates the high utility of this technique for gene editing in grain crops. Here we emphasize on CRISPR/Cas9-mediated gene editing in rice, wheat, and maize.
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| 7. |
- Martin, Carlos
(författare)
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Pretreatment of crop residues for bioconversion
- 2021
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Ingår i: Agronomy. - : MDPI. - 2073-4395. ; 11:5
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Decreasing the dependence on fossil resources as raw materials for the production of fuels, platform chemicals, and commodities is an imperative requirement of today’s industry and society in order to alleviate the threats related to climate change [...]
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| 8. |
- Martin, Carlos, et al.
(författare)
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Special issue “Pretreatment and Bioconversion of Crop Residues II” : introduction to the collection
- 2024
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Ingår i: Agronomy. - : MDPI. - 2073-4395. ; 14:5
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Bioconversion in biorefineries is a way to valorize residues from agriculture and food processing. Pretreatment is an important step in the bioconversion of lignocellulosic materials, including crop residues. This Special Issue includes nine articles on several pretreatment and bioconversion approaches applied to different agricultural residues and food-processing by-products. The materials addressed in this collection cover straw from wheat, rye, and miscanthus, olive tree pruning residue, almond shells and husks, avocado waste, sweet sorghum bagasse, soybean meal, and residues of non-edible oilseeds.
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| 9. |
- Mishra, Laxmi S., 1983-
(författare)
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FtsH metalloproteases and their pseudo-proteases in the chloroplast envelope of Arabidopsis thaliana
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- By cleaving peptide bonds, proteases either activate or degrade proteins and maintain protein quality control in response to various developmental stimuli and environmental factors. My work has focused on elucidating the role of the filamentation temperature sensitive protein H (FtsH) proteases. FtsHs belong to a membrane-embedded class of proteases found in eubacteria, animals and plants, which are located in the organelles of endosymbiosis (mitochondria and chloroplasts). They possess an AAA+ (ATPase associated with various cellular activities) and a peptidase M41 domain containing the HEXXH consensus sequence in the Zn2+ metalloprotease domain. FtsH proteases are known to form ring-like homo- or hetero-hexameric complexes. Arabidopsis thaliana, the model plant used in this study, contains seventeen AtFtsH proteases, of which twelve are presumably proteolytically active and five presumably proteolytic inactive members, known as AtFtsHi (i for inactive). In AtFtsHi members, the HEXXH motif is either deleted (AtFtsHi3) or mutated (AtFtsHi1, 2, 4, 5). Twelve AtFtsHs (AtFtsH 1, 2, 5–9, 11, 12 and AtFtsHi 1-5) are targeted to the chloroplast, whereas the remaining three (AtFtsH 3, 4 and 10) are mitochondrial. In Paper I, we demonstrate that AtFtsH12 interacts with AtFtsHi1, 2, 4, 5 to form a heteromeric complex. Abundance of these AtFtsH12-AtFtsHi complexes alters the accumulation of TIC (translocon on the inner chloroplast membrane) complexes. Transgenic mi12 (miRNA) knockdown plants that express lower amounts of AtFtsH12 displayed a pale-seedling and an aberrant chloroplast phenotype. mi12 plants displayed lowered total chlorophyll (Chla+Chlb) amount compared to wild type (WT), complementation lines and native AtFtsH12 promoter overexpressor (ox12) lines. Our biochemical studies identified drastic modifications in the total proteome of mi12 seedlings. N-terminome analyses of mi12 seedlings showed undisturbed plastidic protein maturation. In Paper II, we have shown that single mutants depleted in AtFTSHI1, 2, 4 or 5 are embryo-lethal, suggesting the pseudo-proteases to have an indispensable role in seed germination. This study further identified “weak” Atftshi1, Atftshi4, Atftshi3-1(kd) and Atftshi3-2 homozygous mutants, which develop into plants with altered photosynthetic efficiency. Field experiments were performed to determine the Darwinian fitness of these homozygous as well as heterozygous AtFtsHi mutants. The results suggested AtFtsHi enzymes to be critical during early developmental stages. A complete Atftshi3 knockdown mutant (Atftshi3-1(kd)) was identified (described in Paper III), which is not embryo-lethal and tolerates drought better than WT plants. Atftshi3-1(kd) leaves were smaller with fewer and smaller stomatal aperture. Above ground, Atftshi3-1(kd) leaves displayed lowered stomatal conductance and increased WUEi (intrinsic water-use efficiency), while below ground, the root-associated bacterial community showed a typical drought stress response. Upregulated transcripts of the ABA-responsive genes in leaves of Atftshi3-1(kd) compared to WT indicate the drought tolerance to be controlled independently of ABA. To conclude, AtFtsHi pseudo-proteases affect various stages of plant development and abiotic stress management, especially drought.
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| 10. |
- Pilotto, Francesca, et al.
(författare)
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Biodiversity shifts : data-driven insights from modern ecology, archaeology, and quaternary sciences
- 2024
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- To understand the implications of past changes in climate, landscape and human activity on contemporary biodiversity patterns, data from modern and palaeoecological studies must be connected. The Strategic Environmental Archaeology Database (SEAD) provides access to big data from archaeology and Quaternary science and is an enormous potential resource for investigating past changes in biodiversity. By linking SEAD to SBDI, past species distributions can be analysed for their implications for landscape and climate change. Recent macroecological research using SEAD/ SBDI illustrates trends in Late Holocene anthropogenic landscape change in north-western Europe. Over the past few thousand years, humans have impacted insect biodiversity as much as climate change did after the last Ice Age. This demonstrates that data from archaeology, and the consequences of human activity, are essential for fulfilling the promi- se of using data driven ecology for guiding future conservation practices in response to climate change.
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