| 1. |
- Abrhámová, Kateřina, et al.
(författare)
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Truncating the spliceosomal 'rope protein' Prp45 results in Htz1 dependent phenotypes.
- 2024
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Ingår i: RNA Biology. - 1547-6286 .- 1555-8584. ; 21:1, s. 1-17
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Tidskriftsartikel (refereegranskat)abstract
- Spliceosome assembly contributes an important but incompletely understood aspect of splicing regulation. Prp45 is a yeast splicing factor which runs as an extended fold through the spliceosome, and which may be important for bringing its components together. We performed a whole genome analysis of the genetic interaction network of the truncated allele of PRP45 (prp45(1-169)) using synthetic genetic array technology and found chromatin remodellers and modifiers as an enriched category. In agreement with related studies, H2A.Z-encoding HTZ1, and the components of SWR1, INO80, and SAGA complexes represented prominent interactors, with htz1 conferring the strongest growth defect. Because the truncation of Prp45 disproportionately affected low copy number transcripts of intron-containing genes, we prepared strains carrying intronless versions of SRB2, VPS75, or HRB1, the most affected cases with transcription-related function. Intron removal from SRB2, but not from the other genes, partly repaired some but not all the growth phenotypes identified in the genetic screen. The interaction of prp45(1-169) and htz1Δ was detectable even in cells with SRB2 intron deleted (srb2Δi). The less truncated variant, prp45(1-330), had a synthetic growth defect with htz1Δ at 16°C, which also persisted in the srb2Δi background. Moreover, htz1Δ enhanced prp45(1-330) dependent pre-mRNA hyper-accumulation of both high and low efficiency splicers, genes ECM33 and COF1, respectively. We conclude that while the expression defects of low expression intron-containing genes contribute to the genetic interactome of prp45(1-169), the genetic interactions between prp45 and htz1 alleles demonstrate the sensitivity of spliceosome assembly, delayed in prp45(1-169), to the chromatin environment.
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| 2. |
- Biler, Michal, et al.
(författare)
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Quercetin and its analogues : optical and acido-basic properties
- 2017
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : ROYAL SOC CHEMISTRY. - 1463-9076 .- 1463-9084. ; 19:39, s. 26870-26879
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Tidskriftsartikel (refereegranskat)abstract
- This study is focused on eight structurally analogous natural flavonoids that exhibit a wide range of biological activities, which are of interest in pharmacy, cosmetics and the food industry. Using both experimental and theoretical approaches, we relate their fundamental physico-chemical properties to the structural motifs, with particular focus on UV/Vis absorption properties and pH dependence. We highlight the role of the C2-C3 double bond, whose presence or absence is responsible for the switch between absorption bands in the UVB and UVA regions, which is rationalized by strong modification of the involved molecular orbitals. After deprotonation in an alkaline environment, a typical switch in intensity at the maximum absorption wavelength (lambda(max)) is observed enabling the calculation of pK(a) values for compounds with a C2-C3 single bond, whereas a bathochromic shift of lambda(max) vs. pH is observed for the C2-C3 double bond containing compounds. These behaviors are also rationalized and understood by MO analysis. Interestingly, high pH (above 11 for ampelopsin and above 9 for myricetin) induces the formation of a long-wavelength peak arising from double and/or triple deprotonation. Substitution at position C3 by the OH group has almost no effect on lambda(max) for taxifolin and eriodictyol, whereas the effect is larger for quercetin and luteolin. An additional sugar moiety at C3 has a stabilizing effect and induces only minor changes in spectral behavior.
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| 3. |
- Koistinen, Ville Mikael, et al.
(författare)
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Interlaboratory coverage test on plant food bioactive compounds and their metabolites by mass spectrometry-based untargeted metabolomics
- 2018
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Ingår i: Metabolites. - : MDPI AG. - 2218-1989 .- 2218-1989. ; 8:3
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Tidskriftsartikel (refereegranskat)abstract
- Bioactive compounds present in plant-based foods, and their metabolites derived from gut microbiota and endogenous metabolism, represent thousands of chemical structures of potential interest for human nutrition and health. State-of-the-art analytical methodologies, including untargeted metabolomics based on high-resolution mass spectrometry, are required for the profiling of these compounds in complex matrices, including plant food materials and biofluids. The aim of this project was to compare the analytical coverage of untargeted metabolomics methods independently developed and employed in various European platforms. In total, 56 chemical standards representing the most common classes of bioactive compounds spread over a wide chemical space were selected and analyzed by the participating platforms (n = 13) using their preferred untargeted method. The results were used to define analytical criteria for a successful analysis of plant food bioactives. Furthermore, they will serve as a basis for an optimized consensus method.
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| 4. |
- Low, Dorrain Yanwen, et al.
(författare)
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Data sharing in PredRet for accurate prediction of retention time: Application to plant food bioactive compounds
- 2021
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Ingår i: Food Chemistry. - : Elsevier BV. - 0308-8146 .- 1873-7072. ; 357
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Tidskriftsartikel (refereegranskat)abstract
- Prediction of retention times (RTs) is increasingly considered in untargeted metabolomics to complement MS/MS matching for annotation of unidentified peaks. We tested the performance of PredRet (http://predret.org/) to predict RTs for plant food bioactive metabolites in a data sharing initiative containing entry sets of 29–103 compounds (totalling 467 compounds, >30 families) across 24 chromatographic systems (CSs). Between 27 and 667 predictions were obtained with a median prediction error of 0.03–0.76 min and interval width of 0.33–8.78 min. An external validation test of eight CSs showed high prediction accuracy. RT prediction was dependent on shape and type of LC gradient, and number of commonly measured compounds. Our study highlights PredRet's accuracy and ability to transpose RT data acquired from one CS to another CS. We recommend extensive RT data sharing in PredRet by the community interested in plant food bioactive metabolites to achieve a powerful community-driven open-access tool for metabolomics annotation.
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| 5. |
- Vinarov, Zahari, et al.
(författare)
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Current challenges and future perspectives in oral absorption research : An opinion of the UNGAP network
- 2021
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Ingår i: Advanced Drug Delivery Reviews. - : Elsevier. - 0169-409X .- 1872-8294. ; 171, s. 289-331
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Forskningsöversikt (refereegranskat)abstract
- Although oral drug delivery is the preferred administration route and has been used for centuries, modern drug discovery and development pipelines challenge conventional formulation approaches and highlight the insufficient mechanistic understanding of processes critical to oral drug absorption. This review presents the opinion of UNGAP scientists on four key themes across the oral absorption landscape: (1) specific patient populations, (2) regional differences in the gastrointestinal tract, (3) advanced formulations and (4) food-drug interactions. The differences of oral absorption in pediatric and geriatric populations, the specific issues in colonic absorption, the formulation approaches for poorly water-soluble (small molecules) and poorly permeable (peptides, RNA etc.) drugs, as well as the vast realm of food effects, are some of the topics discussed in detail. The identified controversies and gaps in the current understanding of gastrointestinal absorption-related processes are used to create a roadmap for the future of oral drug absorption research.
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