| 1. |
- Abarenkov, Kessy, et al.
(författare)
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The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered
- 2024
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Ingår i: Nucleic Acids Research. - 0305-1048 .- 1362-4962. ; 52:D1, s. D791-D797
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Tidskriftsartikel (refereegranskat)abstract
- UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into similar to 2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms. Graphical Abstract
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| 2. |
- Goldkuhl, Lisa, 1983, et al.
(författare)
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Impact of Birthing Room Design on Maternal Childbirth Experience: Results From the Room4Birth Randomized Trial
- 2023
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Ingår i: HERD. - : SAGE Publications. - 2167-5112 .- 1937-5867. ; 16:1, s. 200-218
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To study the effect of the birthing room design on nulliparous women’s childbirth experience up to 1 year after birth. Background: Although it is known that the birth environment can support or hinder birth processes, the impact of the birthing room design on maternal childbirth experience over time is insufficiently studied. Methods: The Room4Birth randomized controlled trial was conducted at a labor ward in Sweden. Nulliparous women in active stage of spontaneous labor were randomized (n = 406) to either a regular birthing room (n = 202) or a new birthing room designed with more person-centered considerations (n = 204). Childbirth experiences were measured 2 hr, 3 months, and 12 months after birth by using a Visual Analogue Scale of Overall Childbirth Experience (VAS-OCE), the Fear of Birth Scale (FOBS), and the Childbirth Experience Questionnaire (CEQ2). Results: Women randomized to the new room had a more positive childbirth experience reported on the VAS-OCE 3 months (p =.002) and 12 months (p =.021) after birth compared to women randomized to a regular room. Women in the new room also scored higher in the total CEQ2 score (p =.039) and within the CEQ2 subdomain own capacity after 3 months (p =.028). The remaining CEQ2 domains and the FOBS scores did not differ between the groups. Conclusions: These findings show that a birthing room offering more possibilities to change features and functions in the room according to personal needs and requirements, positively affects the childbirth experience of nulliparous women 3 and 12 months after they have given birth.
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| 3. |
- Goldkuhl, Lisa, 1983, et al.
(författare)
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Room4Birth – The effect of giving birth in a hospital birthing room designed with person-centred considerations: A Swedish randomised controlled trial
- 2022
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Ingår i: Sexual and Reproductive Healthcare. - : Elsevier BV. - 1877-5764 .- 1877-5756. ; 32
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To evaluate if a birthing room designed with person-centred considerations improves labour and birth outcomes for nulliparous women when compared to regular birthing rooms. Methods: A randomised controlled trial was conducted at a Swedish labour ward between January 2019 and October 2020. Nulliparous women in spontaneous labour were randomised either to a birthing room designed with person-centred considerations (New room) or a Regular room. The primary outcome was a composite of four variables: vaginal non-instrumental birth; no oxytocin augmentation; postpartum blood loss < 1000 ml; and a positive childbirth experience. To detect a difference of 8% between the groups, 1274 study participants were needed, but the trial was terminated early due to consequences of the Covid-19 pandemic. Results: A total of 406 women were randomised; 204 to the New room and 202 to the Regular room. There was no significant difference in the primary outcome between the groups (42.2% versus 35.1%; odds ratio: 1.35, 95% Confidence Interval 0.90–2.01; p = 0.18). Participants in the New room used epidural analgesia to a lower extent (54.4% versus 65.3%, relative risk: 0.83, 95% Confidence Interval 0.71–0.98; p = 0.03) and reported to a higher degree that the room contributed to a sense of safety, control, and integrity (p=<0.001). Conclusions: The hypothesis that the New room would improve the primary outcome could not be verified. Considering the early discontinuation of the study, results should be interpreted with caution. Nevertheless, analyses of our secondary outcomes emphasise the experiential value of the built birth environment in improving care for labouring women.
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| 4. |
- Gupta, G., et al.
(författare)
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Exploiting Mass Spectrometry to Unlock the Mechanism of Nanoparticle-Induced Inflammasome Activation
- 2023
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Ingår i: Acs Nano. - : AMER CHEMICAL SOC. - 1936-0851 .- 1936-086X. ; 17:17
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Tidskriftsartikel (refereegranskat)abstract
- Nanoparticles (NPs) elicit sterile inflammation, but the underlying signaling pathways are poorly understood. Here, we report that human monocytes are particularly vulnerable to amorphous silica NPs, as evidenced by single-cell-based analysis of peripheral blood mononuclear cells using cytometry by time-of-flight (CyToF), while silane modification of the NPs mitigated their toxicity. Using human THP-1 cells as a model, we observed cellular internalization of silica NPs by nanoscale secondary ion mass spectrometry (nanoSIMS) and this was confirmed by transmission electron microscopy. Lipid droplet accumulation was also noted in the exposed cells. Furthermore, time-of-flight secondary ion mass spectrometry (ToF-SIMS) revealed specific changes in plasma membrane lipids, including phosphatidylcholine (PC) in silica NP-exposed cells, and subsequent studies suggested that lysophosphatidylcholine (LPC) acts as a cell autonomous signal for inflammasome activation in the absence of priming with a microbial ligand. Moreover, we found that silica NPs elicited NLRP3 inflammasome activation in monocytes, whereas cell death transpired through a non-apoptotic, lipid peroxidation-dependent mechanism. Together, these data further our understanding of the mechanism of sterile inflammation.
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| 5. |
- Hinchcliffe, James, 1992, et al.
(författare)
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Comparative survival and growth performance of European lobster Homarus gammarus post-larva reared on novel feeds
- 2020
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Ingår i: Aquaculture Research. - : Hindawi Limited. - 1355-557X .- 1365-2109. ; 51:1, s. 102-113
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Tidskriftsartikel (refereegranskat)abstract
- One approach to ongrow juvenile European lobster, Homarus gammarus, is to utilize land based rearing systems, incorporating automated feeding, individual culture and provision of stable pelleted feeds, preferably using sustainable ingredients. We initiated three feeding experiments to investigate the general suitability of ingredients produced from seafood by-products as novel feeds for H. gammarus, in terms of promoting survival, development and growth of post-larval lobsters from post-larvae (PL) stage IV to the first juvenile stage (stage V). The first experiment was designed to screen an array of candidate, locally produced, novel protein sources on growth performance parameters. This initial experiment revealed that PL reared on a raw (i.e. wet, unprocessed shrimp) feed used as a reference showed superior performance to those reared on experimental feeds containing fishmeal, herring protein isolate or mussel meal; however, a novel type of shrimp meal, produced by flocculation from waste water, promoted the best PL performance of any experimental feed. A second experiment was designed to test the effect of drying method and to optimize the form of a wet shrimp reference feed used by lobster hatcheries. This showed that the performance of PL reared on experimental freeze-dried shrimp feed was not significantly different to those reared on the wet, unprocessed shrimp used as a reference feed. However, lobsters offered experimental oven-dried shrimp feed (with or without an immune supplement) resulted in significantly lower survival or growth performance. A third and final experiment was designed in an attempt to improve a candidate herring-based protein source, by supplementing with nutrients found in shrimp. However, the results showed that PL reared on the wet reference shrimp feed still showed superior growth and survival than those reared on a herring feed alone, or supplemented with additives found in shrimp meal (either glucosamine, astaxanthin or both supplements combined). The high survival and growth, low incidence of moulting problems and high availability of waste shrimp material, suggest that non-heat-treated shrimp products are a promising feed ingredient for post-larval European lobsters.
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| 6. |
- Luo, Hao, 1992, et al.
(författare)
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Genome-scale insights into the metabolic versatility of Limosilactobacillus reuteri
- 2021
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Ingår i: BMC Biotechnology. - : Springer Science and Business Media LLC. - 1472-6750. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Limosilactobacillus reuteri (earlier known as Lactobacillus reuteri) is a well-studied lactic acid bacterium, with some specific strains used as probiotics, that exists in different hosts such as human, pig, goat, mouse and rat, with multiple body sites such as the gastrointestinal tract, breast milk and mouth. Numerous studies have confirmed the beneficial effects of orally administered specific L. reuteri strains, such as preventing bone loss and promoting regulatory immune system development. L. reuteri ATCC PTA 6475 is a widely used strain that has been applied in the market as a probiotic due to its positive effects on the human host. Its health benefits may be due, in part, to the production of beneficial metabolites. Considering the strain-specific effects and genetic diversity of L. reuteri strains, we were interested to study the metabolic versatility of these strains. Results In this study, we aimed to systematically investigate the metabolic features and diversities of L. reuteri strains by using genome-scale metabolic models (GEMs). The GEM of L. reuteri ATCC PTA 6475 was reconstructed with a template-based method and curated manually. The final GEM iHL622 of L. reuteri ATCC PTA 6475 contains 894 reactions and 726 metabolites linked to 622 metabolic genes, which can be used to simulate growth and amino acids utilization. Furthermore, we built GEMs for the other 35 L. reuteri strains from three types of hosts. The comparison of the L. reuteri GEMs identified potential metabolic products linked to the adaptation to the host. Conclusions The GEM of L. reuteri ATCC PTA 6475 can be used to simulate metabolic capabilities and growth. The core and pan model of 35 L. reuteri strains shows metabolic capacity differences both between and within the host groups. The GEMs provide a reliable basis to investigate the metabolism of L. reuteri in detail and their potential benefits on the host.
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| 7. |
- Mc Conville, Jennifer R, 1978, et al.
(författare)
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Assessing the potential to use serious gaming in planning processes for sanitation designed for resource recovery
- 2023
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Ingår i: Environmental Science and Policy. - 1873-6416 .- 1462-9011. ; 145, s. 262-274
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Tidskriftsartikel (refereegranskat)abstract
- There is an urgent need for innovations in the sanitation sector to minimize environmental impacts and maximize resource recovery. Uptake of innovations may require changes in established technical practices, organisational norms and/or individual behaviours. Achieving change in any of these areas requires influencing cognitive, normative and relational learning processes. Serious games have been identified a potential tool for planners and environmental managers to influence such learning processes. This study designed the serious game RECLAIM to share knowledge about resource recovery from sanitation and to support attitude-change and collaboration between players. A structured framework was applied to assess if the game: 1) increased understanding of resource recovery (cognitive learning), 2) changed worldviews (normative learning), 3) led to more collaboration (relational learning), and 4) was a positive experience. Proof-of-concept testing of the game in Uganda found that it was positively received. The game provided cognitive learning on environmental and health impacts, resource recovery, and sanitation in general. Players gained an appreciation of the need for collaboration and it was deemed to have the potential to influence worldviews of a larger stakeholder group. Future recommendations include embedding the game in planning processes, including several gaming sessions that would strengthen cognition learning and the potential for changing practices.
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| 8. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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How, not if, is the question mycologists should be asking about DNA-based typification
- 2023
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :96, s. 143-157
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Tidskriftsartikel (refereegranskat)abstract
- Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings chal-lenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.
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| 9. |
- Schneider, Kara, et al.
(författare)
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Using reporters of different misfolded proteins reveals differential strategies in processing protein aggregates
- 2022
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Ingår i: Journal of Biological Chemistry. - : Elsevier BV. - 0021-9258 .- 1083-351X. ; 298:11
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Tidskriftsartikel (refereegranskat)abstract
- The accumulation of misfolded proteins is a hallmark of aging and many neurodegenerative diseases, making it important to understand how the cellular machinery recognizes and processes such proteins. A key question in this respect is whether misfolded proteins are handled in a similar way regardless of their genetic origin. To approach this question, we compared how three different misfolded proteins, guk1-7, gus1-3, and pro3-1, are handled by the cell. We show that all three are nontoxic, even though highly overexpressed, highlighting their usefulness in analyzing the cellular response to misfolding in the absence of severe stress. We found significant differences between the aggregation and disaggregation behavior of the misfolded proteins. Specifically, gus1-3 formed some aggregates that did not efficiently recruit the protein disaggregase Hsp104 and did not colocalize with the other misfolded reporter proteins. Strikingly, while all three misfolded proteins generally coaggregated and colocalized to specific sites in the cell, disaggregation was notably different; the rate of aggregate clearance of pro3-1 was faster than that of the other misfolded proteins, and its clearance rate was not hindered when pro3-1 colocalized with a slowly resolved misfolded protein. Finally, we observed using super-resolution light microscopy as well as immunogold labeling EM in which both showed an even distribution of the different misfolded proteins within an inclusion, suggesting that misfolding characteristics and remodeling, rather than spatial compartmentalization, allows for differential clearance of these misfolding reporters residing in the same inclusion. Taken together, our results highlight how properties of misfolded proteins can significantly affect processing.
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| 10. |
- Warwas, Niklas, et al.
(författare)
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Marine yeast (Candida sake) cultured on herring brine side streams is a promising feed ingredient and omega-3 source for rainbow trout (Oncorhynchus mykiss)
- 2023
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Ingår i: Aquaculture. - : Elsevier BV. - 0044-8486 .- 1873-5622. ; 571
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Tidskriftsartikel (refereegranskat)abstract
- A major challenge for the aquaculture industry is the supply of sustainable feeds. A promising model to achieve this is to utilize circular flows where feed ingredients, such as single cell protein, are cultivated using side streams of the food industry. The aim of this study was to evaluate the marine yeast Candida sake, produced on herring brine side streams, as a source of protein and immune stimulant in feed for salmonid fish. The dry C. sake product contained 54% protein (3.3% lysine and 0.8% methionine) and 13% lipids (1.1% eicosapentaenoic, EPA, and 1% docosahexaenoic acid, DHA). Four experimental diets were designed and tested in a 9-week feeding trial using juvenile rainbow trout (Oncorhynchus mykiss). A control diet containing both fish and plant-based ingredients constituted the base feed to which 20% (to evaluate effects on digestibility, growth and intestinal physiology), 20% heat-treated (to evaluate effects of downstream processing) and 3% (to evaluate immune stimulatory properties, replacing 3% soy protein concentrate) C. sake was added. The apparent digestibility coefficient of C. sake for protein, fat and gross energy was above 80%, and for amino acids above 90% regardless of treatment, suggesting a high bioavailability of C. sake. All three yeast containing diets performed equally to the control regarding specific growth rate, feed conversion ratio and functional intestinal health. These results suggest that C. sake is a promising alternative protein source for circular feeds in the salmonid industry. The presence of EPA and DHA represents an added value. The heat treatment increased the apparent digestibility coefficient of dry matter by 8% but decreased amino acid digestibility by on average 3%, indicating that heat treatment may not be the optimal downstream processing technique. Furthermore, the inclusion of 3% C. sake increased the intestinal lamina propria width and TGF-beta transcription, indicating an immune stimulating effect. Future research is needed to understand these immune modulatory effects of C. sake supplementation.
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