| 1. |
- Hathaway, Louise, et al.
(författare)
-
Geographically congruent large-scale patterns of plastid haplotype variation in the European herbs Silene dioica and S-latifolia (Caryophyllaceae)
- 2009
-
Ingår i: Botanical Journal of the Linnean Society. - 1095-8339. ; 161:2, s. 153-170
-
Tidskriftsartikel (refereegranskat)abstract
- The closely related dioecious herbs Silene latifolia and Silene dioica are widespread and predominantly sympatric in Europe. The species are interfertile, but morphologically and ecologically distinct. A study of large-scale patterns of plastid DNA (polymerase chain reaction-restriction fragment length polymorphism) haplotypes in a sample of 198 populations from most of the European ranges of both species revealed extensive interspecific haplotype sharing. Four of the 28 detected haplotypes were frequent (found in > 40 populations) and widespread. Three of these frequent haplotypes occurred in both species and the geographic distribution of each haplotype was broadly congruent in both species. Each of these three, shared and widespread haplotypes is likely to have colonized central and/or northern Europe after the last glaciation from one or more of refugial areas in southern Europe. Interspecific hybridization and plastid introgression within refugial regions and/or during the early stages of postglacial expansion is the most plausible explanation for the broadly similar distribution patterns of the shared, frequent chloroplast haplotypes in the two species. The fourth frequent, widespread haplotype was absent from S. latifolia and almost entirely restricted to Nordic S. dioica. It is most likely that this haplotype spread into the Nordic countries from a central or northern European source or from a refugial area in Russia. (c) 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 161, 153-170.
|
|
| 2. |
- Jakobsson, Anders, et al.
(författare)
-
Vetenskapskommunikation och skolutveckling som en del av den tredje uppgiften
- 2019
-
Ingår i: En historiker korsar sitt spår. - : Malmö universitet. - 9789178770335 - 9789178770458 ; , s. 221-237
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- I detta kapitel fokuserar vi hur universitetens samverkan med det omgivande samhället kan bidra med ny forskning och samtidigt verka för spridning av nya forskningsresultat. I forskarskolan Communicate science in school (CSiS) deltar tio lärare i en forskarutbildning där deltagarna efter avslutad utbildning erhåller en licentiatexamen i naturvetenskapernas didaktik. Ett viktigt syfte med forskarskolan är att fortlöpande samla förvaltningschefer, rektorer och forskarstuderande för att diskutera och förstärka skolutveckling i förskolan, grundskolan och gymnasieskolan på vetenskaplig grund. Det innebär att initiera samtal om hur de berörda lärarnas kunskaper ska komma kommunernas skolutveckling till godo efter avlagd examen. Gemensamt för samtliga forskarstuderande har varit att problematisera skolämnenas innehåll i relation till modern forskning i naturvetenskap och teknik men också att ta del av internationell utbildningsvetenskaplig forskning i relation till undervisningsformer och organisering av själva undervisningen.
|
|
| 3. |
- Kieler, Ida Nordang, et al.
(författare)
-
Genome wide association study in Swedish Labrador retrievers identifies genetic loci associated with hip dysplasia and body weight
- 2024
-
Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 14:1
-
Tidskriftsartikel (refereegranskat)abstract
- Genome wide association studies (GWAS) have been utilized to identify genetic risk loci associated with both simple and complex inherited disorders. Here, we performed a GWAS in Labrador retrievers to identify genetic loci associated with hip dysplasia and body weight. Hip dysplasia scores were available for 209 genotyped dogs. We identified a significantly associated locus for hip dysplasia on chromosome 24, with three equally associated SNPs (p = 4.3 x 10-7) in complete linkage disequilibrium located within NDRG3, a gene which in humans has been shown to be differentially expressed in osteoarthritic joint cartilage. Body weight, available for 85 female dogs, was used as phenotype for a second analysis. We identified two significantly associated loci on chromosome 10 (p = 4.5 x 10-7) and chromosome 31 (p = 2.5 x 10-6). The most associated SNPs within these loci were located within the introns of the PRKCE and CADM2 genes, respectively. PRKCE has been shown to play a role in regulation of adipogenesis whilst CADM2 has been associated with body weight in multiple human GWAS. In summary, we identified credible candidate loci explaining part of the genetic inheritance for hip dysplasia and body weight in Labrador retrievers with strong candidate genes in each locus previously implicated in the phenotypes investigated.
|
|
| 4. |
|
|
| 5. |
|
|
| 6. |
- Malm, Louise, et al.
(författare)
-
Guide to Semi-Quantitative Non-Targeted Screening Using LC/ESI/HRMS
- 2021
-
Ingår i: Molecules. - : MDPI AG. - 1431-5157 .- 1420-3049. ; 26:12
-
Forskningsöversikt (refereegranskat)abstract
- Non-targeted screening (NTS) with reversed phase liquid chromatography electrospray ionization high resolution mass spectrometry (LC/ESI/HRMS) is increasingly employed as an alternative to targeted analysis; however, it is not possible to quantify all compounds found in a sample with analytical standards. As an alternative, semi-quantification strategies are, or at least should be, used to estimate the concentrations of the unknown compounds before final decision making. All steps in the analytical chain, from sample preparation to ionization conditions and data processing can influence the signals obtained, and thus the estimated concentrations. Therefore, each step needs to be considered carefully. Generally, less is more when it comes to choosing sample preparation as well as chromatographic and ionization conditions in NTS. By combining the positive and negative ionization mode, the performance of NTS can be improved, since different compounds ionize better in one or the other mode. Furthermore, NTS gives opportunities for retrospective analysis. In this tutorial, strategies for semi-quantification are described, sources potentially decreasing the signals are identified and possibilities to improve NTS are discussed. Additionally, examples of retrospective analysis are presented. Finally, we present a checklist for carrying out semi-quantitative NTS.
|
|
| 7. |
- Pennegård, Eva, et al.
(författare)
-
Vetenskapskommunikation och skolutveckling som en del av det tredje uppdraget
- 2019
-
Ingår i: En historiker korsar sitt spår : En vänbok till Roger Johansson om att lära sig av historien och lära ut historia - En vänbok till Roger Johansson om att lära sig av historien och lära ut historia. - 9789178770335 - 9789178770458 ; , s. 231-233
-
Bokkapitel (populärvet., debatt m.m.)
|
|
| 8. |
- Poulsen, Liv la Cour, et al.
(författare)
-
Progressive changes in human follicular fluid composition over the course of ovulation : quantitative proteomic analyses
- 2019
-
Ingår i: Molecular and Cellular Endocrinology. - : Elsevier BV. - 0303-7207. ; 495:Sept.
-
Tidskriftsartikel (refereegranskat)abstract
- Follicular fluid (FF) acts as a vehicle for paracrine signalling between somatic cells of the follicle and the oocyte. To investigate changes in the protein composition of FF during ovulation, we conducted a prospective cohort study including 25 women undergoing fertility treatment. Follicular fluid was aspirated either before or 12, 17, 32 or 36 h after induction of ovulation (five patients per time point). Liquid chromatography-mass spectrometry was used to identify and quantify FF proteins. In total, 400 proteins were identified and the levels of 40 proteins changed significantly across ovulation, evaluated by analysis of covariance (adjusted p < 0.05) and on-off expression patterns. The majority peaked after 12–17 h, e.g., AREG (p < 0.0001), TNFAIP6 (p < 0.0001), and LDHB (p = 0.0316), while some increased to peak after 36 h e.g., ACPP (p < 0.0001), TIMP1 (p < 0.0001) and SERPINE1 (p = 0.0002). Collectively, this study highlights proteins and pathways of importance for ovulation and oocyte competence in humans.
|
|
| 9. |
- Prentice, Honor C, et al.
(författare)
-
Chloroplast DNA variation in the European herb Silene dioica (red campion): postglacial migration and interspecific introgression
- 2008
-
Ingår i: Plant Systematics and Evolution. - : Springer Science and Business Media LLC. - 1615-6110 .- 0378-2697. ; 272:1-4, s. 23-37
-
Tidskriftsartikel (refereegranskat)abstract
- Many recent studies of intraspecific geographic variation in maternally inherited chloroplast DNA (cpDNA) in European trees have revealed haplotype distributions that can be interpreted in terms of scenarios of postglacial migration and range expansion. However, there is still a lack of comparable information from widespread herb species. In the present study, we investigated the geographic distribution of cpDNA variation in 124 populations, covering a large part of the range of the widespread, dioecious, European herb, Silene dioica. PCR-RFLP analysis revealed 24 different cpDNA haplotypes. As in the majority of European tree species, the large-scale geographic distributions of the most common S. dioica haplotypes suggest that the species colonized Europe from more than one geographic source. Material from 16 populations of S. latifolia and five hybrid populations was also included in the study for comparative purposes. Five out of seven haplotypes detected in S. latifolia were shared with S. dioica. The similarity of the geographic distributions of the shared haplotypes in both species is consistent with a history of past and/or recent interspecific hybridization and introgression between these closely related plants. The two haplotypes detected only in S. latifolia were present in populations in the Mediterranean region – on the southern margin of the species’ area of sympatry, or outside the range of S. dioica.
|
|
| 10. |
- Priskorn, Lærke, et al.
(författare)
-
RUBIC (ReproUnion Biobank and Infertility Cohort) : A binational clinical foundation to study risk factors, life course, and treatment of infertility and infertility-related morbidity
- 2021
-
Ingår i: Andrology. - : Wiley. - 2047-2919 .- 2047-2927. ; 9:6, s. 1828-1842
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Infertility affects 15%–25% of all couples during their reproductive life span. It is a significant societal and public health problem with potential psychological, social, and economic consequences. Furthermore, infertility has been linked to adverse long-term health outcomes. Despite the advanced diagnostic and therapeutic techniques available, approximately 30% of infertile couples do not obtain a live birth after fertility treatment. For these couples, there are no further options to increase their chances of a successful pregnancy and live birth. Objectives: Three overall questions will be studied: (1) What are the risk factors and natural life courses of infertility, early embryonic loss, and adverse pregnancy outcomes? (2) Can we develop new diagnostic and prognostic biomarkers for fecundity and treatment success? And (3) what are the health characteristics of women and men in infertile couples at the time of fertility treatment and during long-term follow-up?. Material and Methods: ReproUnion Biobank and Infertility Cohort (RUBIC) is established as an add-on to the routine fertility management at Copenhagen University Hospital Departments in the Capital Region of Denmark and Reproductive Medicine Centre at Skåne University Hospital in Sweden. The aim is to include a total of 5000 couples equally distributed between Denmark and Sweden. The first patients were enrolled in June 2020. All eligible infertile couples are prospectively asked to participate in the project. Participants complete an extensive questionnaire and undergo a physical examination and collection of biospecimens (blood, urine, hair, saliva, rectal swabs, feces, semen, endometrial biopsies, and vaginal swabs). After the cohort is established, the couples will be linked to the Danish and Swedish national registers to obtain information on parental, perinatal, childhood, and adult life histories, including disease and medication history. This will enable us to understand the causes of infertility and identify novel therapeutic options for this important societal problem.
|
|
| 11. |
- Sepman, Helen, et al.
(författare)
-
Bypassing the Identification : MS2Quant for Concentration Estimations of Chemicals Detected with Nontarget LC-HRMS from MS2 Data
- 2023
-
Ingår i: Analytical Chemistry. - 0003-2700 .- 1520-6882. ; 95:33, s. 12329-12338
-
Tidskriftsartikel (refereegranskat)abstract
- Nontarget analysis by liquid chromatography-high-resolutionmass spectrometry (LC-HRMS) is now widely used to detect pollutants in the environment. Shifting away from targeted methods has led to detection of previously unseen chemicals, and assessing the risk posed by these newly detected chemicals is an important challenge. Assessing exposure and toxicity of chemicals detected with nontarget HRMS is highly dependent on the knowledge of the structure of the chemical. However, the majority of features detected in nontarget screening remain unidentified and therefore the risk assessment with conventional tools is hampered. Here, we developed MS2Quant, a machine learning model that enables prediction of concentration from fragmentation(MS2) spectra of detected, but unidentified chemicals. MS2Quant is an xgbTree algorithm-based regression model developed using ionization efficiency data for 1191 unique chemicals that spans 8 orders of magnitude. The ionization efficiency values are predicted from structural fingerprints that can be computed from the SMILES notation of the identified chemicals or from MS2 spectra of unidentified chemicals using SIRIUS+CSI: FingerID software. The root mean square errors of the training and test sets were 0.55(3.5x) and 0.80 (6.3x) log-units, respectively. In comparison, ionization efficiency prediction approaches that depend on assigning an unequivocal structure typically yield errors from 2x to 6x. The MS2Quant quantification model was validated on a set of 39 environmental pollutants and resulted in a mean prediction error of 7.4x, ageometric mean of 4.5x, and a median of 4.0x. For comparison, a model based on PaDEL descriptors that depends on unequivocal structural assignment was developed using the same dataset. The latter approach yielded a comparable mean prediction error of 9.5x, a geometricmean of 5.6x, and a median of 5.2x on the validation set chemicals when the top structural assignment was used as input. This confirms that MS2Quant enables to extract exposure information for unidentified chemicals which, although detected, have thus far been disregarded due to lack of accurate tools for quantification. TheMS2Quant model is available as an R-package in GitHub for improving discovery and monitoring of potentially hazardous environmental pollutants with nontarget screening.
|
|
| 12. |
- Sepman, Helen, et al.
(författare)
-
Scientometric review : Concentration and toxicity assessment in environmental non-targeted LC/HRMS analysis
- 2023
-
Ingår i: Trends in Environmental Analytical Chemistry. - 2214-1588. ; 40
-
Forskningsöversikt (refereegranskat)abstract
- Non-targeted screening with LC/HRMS is a go-to approach to discover relevant contaminants in environmental water samples that contain an abundance of chemicals. The rapidly increasing popularity of non-targeted LC/ HRMS screening has initiated development of a diverse set of methods for assessing the concentration and toxicity of the detected chemicals. This review aims to benchmark the trends in the environmental NTS literature with particular focus on (1) methods used for the quantification of tentatively identified chemicals that lack analytical standards, (2) methods for assessing the toxicity of detected chemicals, and (3) methods combining the former into a risk evaluation. Here we provide a scientometric review of these strategies based on the Web of Science referenced papers published between 2019 and 2022. General trends show that quantification and toxicity assessments are widely employed in NTS, reaching 66 % and 45 % over four years, respectively. Simultaneously, only 13 % of the papers covered here combine these results into a risk factor or similar. With this review we aim to highlight the advantages and gaps in the approaches used for concentration and toxicity assessment and provide guidelines for more homogeneous data interrogation and extrapolation.
|
|
| 13. |
- Souihi, Amina, et al.
(författare)
-
MultiConditionRT : Predicting liquid chromatography retention time for emerging contaminants for a wide range of eluent compositions and stationary phases
- 2022
-
Ingår i: Journal of Chromatography A. - : Elsevier BV. - 0021-9673 .- 1873-3778. ; 1666
-
Tidskriftsartikel (refereegranskat)abstract
- Structural elucidation of compounds detected with liquid chromatography coupled to high resolution mass spectrometry is a challenging and time-consuming step in the workflow of non-targeted analysis and often requires manual validation of the results. Retention time, alongside exact mass, isotope pattern, fragmentation spectra, and collision cross-section, is valuable information for ruling out unlikely structures and increasing the confidence in others. Different approaches to predict retention times have been used previously for reversed phase chromatography and hydrophilic interaction liquid chromatography (HILIC), but application is limited to a small set of mobile phases and gradient profiles. Here, we expand the toolbox available for retention time predictions by developing a random forest regression model for predicting retention times for four column types and twenty mobile phase systems. MultiConditionRT was built using a dataset containing 78 compounds analyzed with C18 reversed phase, mixed mode, HILIC, and biphenyl columns. In addition, different eluent compositions were used: both methanol and acetonitrile were combined with different aqueous phases with pH from 2.1 to 10.0 (formic acid, acetic acid, trifluoroacetic acid, formate, acetate, bicarbonate, and ammonia). The root mean square error (RMSE) of the test set predictions was 1.55 min for C18 reversed phase, 1.79 min for mixed-mode, 1.93 min for HILIC, and 1.56 min for biphenyl column. Additionally, MultiConditionRT can be applied to different gradient profiles with a general additive model-based calibration approach. The approach of MultiConditionRT was validated externally and internally with 356 and 151 compounds respectively, yielding an RMSE of 2.68 and 2.32 min. 324 and 84 of these compounds were not in the dataset used in the model development.
|
|
| 14. |
- Vipsjö, Lars, 1959-, et al.
(författare)
-
Sagospelet Skaraborg
- 2023
-
Annan publikation (populärvet., debatt m.m.)abstract
- KLUB-böckerna om Kira och Luppe är en barnboksserie som utspelar sig i gamla Skaraborgs län. Varje kommun har en egen bok med ett eget mytologiskt väsen ur den svenska folktron, exempelvis Jättinnan i Falköping, Näcken i Tibro och Gäddfrun i Grästorp.Spelet går ut på att lösa uppdrag genom att hitta på smarta och roliga sagor om skatter och väsen i Skaraborg. Spelarna kan hitta på sagor tillsammans, eller var för sig. De två olika spellägena gör att alla kan spela på det vis som passar dem bäst, kanske beroende på vad man gillar, eller hur gamla spelarna är.Till stöd för berättandet finns en karta över Skaraborg, vilken utgör spelplanen, och spelkort med bilder och spännande information om väsen, magi och skatter, kopplade till olika platser på kartan. Platserna går att besöka och skatterna finns faktiskt att se.KLUB Sagospelet Skaraborg har tagits fram i samarbete med Högskolan i Skövde, alla Skaraborgs kommuner, Västergötlands museum, Platåbergens geopark och Lokrantz förlag. Målgruppen är bred, från barn till alla som är intresserade av nordisk mytologi och av att själva dra en skröna.
|
|
