| 1. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 2. |
- Baronti, Lorenzo, et al.
(författare)
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Base-pair conformational switch modulates miR-34a targeting of Sirt1 mRNA
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 583:7814, s. 139-144
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Tidskriftsartikel (refereegranskat)abstract
- MicroRNAs (miRNAs) regulate the levels of translation of messenger RNAs (mRNAs). At present, the major parameter that can explain the selection of the target mRNA and the efficiency of translation repression is the base pairing between the 'seed' region of the miRNA and its counterpart mRNA(1). Here we use R-1 rho relaxation-dispersion nuclear magnetic resonance(2) and molecular simulations(3) to reveal a dynamic switch-based on the rearrangement of a single base pair in the miRNA-mRNA duplex-that elongates a weak five-base-pair seed to a complete seven-base-pair seed. This switch also causes coaxial stacking of the seed and supplementary helix fitting into human Argonaute 2 protein (Ago2), reminiscent of an active state in prokaryotic Ago(4,5). Stabilizing this transient state leads to enhanced repression of the target mRNA in cells, revealing the importance of this miRNA-mRNA structure. Our observations tie together previous findings regarding the stepwise miRNA targeting process from an initial 'screening' state to an 'active' state, and unveil the role of the RNA duplex beyond the seed in Ago2. Repression of a messenger RNA by a cognate microRNA depends not only on complementary base pairing, but also on the rearrangement of a single base pair, producing a conformation that fits better within the human Ago2 protein.
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| 3. |
- Both, P., et al.
(författare)
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Discrimination of epimeric glycans and glycopeptides using IM-MS and its potential for carbohydrate sequencing
- 2014
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Ingår i: Nature Chemistry. - 1755-4330 .- 1755-4349. ; 6:1, s. 65-74
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Tidskriftsartikel (refereegranskat)abstract
- Mass spectrometry is the primary analytical technique used to characterize the complex oligosaccharides that decorate cell surfaces. Monosaccharide building blocks are often simple epimers, which when combined produce diastereomeric glycoconjugates indistinguishable by mass spectrometry. Structure elucidation frequently relies on assumptions that biosynthetic pathways are highly conserved. Here, we show that biosynthetic enzymes can display unexpected promiscuity, with human glycosyltransferase pp-a-GanT2 able to utilize both uridine diphosphate N-acetylglucosamine and uridine diphosphate N-acetylgalactosamine, leading to the synthesis of epimeric glycopeptides in vitro. Ion-mobility mass spectrometry ( IM-MS) was used to separate these structures and, significantly, enabled characterization of the attached glycan based on the drift times of the monosaccharide product ions generated following collision-induced dissociation. Finally, ion-mobility mass spectrometry following fragmentation was used to determine the nature of both the reducing and non-reducing glycans of a series of epimeric disaccharides and the branched pentasaccharide Man3 glycan, demonstrating that this technique may prove useful for the sequencing of complex oligosaccharides.
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| 4. |
- Chassagne, Pierre, et al.
(författare)
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Structural Studies of the O-Acetyl-Containing O-Antigen from a Shigella flexneri Serotype 6 Strain and Synthesis of Oligosaccharide Fragments Thereof
- 2013
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Ingår i: European Journal of Organic Chemistry. - : Wiley. - 1434-193X .- 1099-0690. ; :19, s. 4085-4106
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Tidskriftsartikel (refereegranskat)abstract
- Extensive analysis by NMR spectroscopy of the delipidated lipopolysaccharide of Shigella flexneri serotype 6 strain MDC 2924-71 confirmed the most recently reported structure of the O-antigen repeating unit as {4)--D-GalpA-(13)--D-GalpNAc-(12)--L-Rhap3Ac/4Ac-(12)--L-Rhap-(1}, and revealed the non-stoichiometric acetylation at O-3C/4C. Input from the CASPER program helped to ascertain the fine distribution of the three possible patterns of O-acetylation. The non-O-acetylated repeating unit (ABCD) corresponded to about 2/3 of the population, while 1/4 was acetylated at O-3C (3AcCDAB), and 1/10 at O-4C (4AcCDAB). Di- to tetrasaccharides with a GalpA residue (A) at their reducing end were synthesized as their propyl glycosides following a multistep linear strategy relying on late-stage acetylation at O-3C. Thus, the 3C-O-acetylated and non-O-acetylated targets were synthesized from common protected intermediates. Rhamnosylation was most efficiently achieved by using imidate donors, including at O-4 of a benzyl galacturonate acceptor. In contrast, a thiophenyl 2-deoxy-2-trichloroacetamido-D-galactopyranoside precursor was preferred for chain elongation involving residue B. Final Pd/C-mediated deprotection ensured O-acetyl stability. All of the target molecules represent parts of the O-antigen of S. flexneri 6, a prevalent serotype. Non-O-acetylated oligosaccharides are also fragments of the Escherichia coli O147 O-antigen.
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| 5. |
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| 6. |
- Fontana, Carolina, 1980-
(författare)
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NMR spectroscopy in structural and conformational analysis of bacterial polysaccharides
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Carbohydrates constitute one of the three major classes of biomolecules found in all living cells and, unlike nucleic acids and proteins, their polymeric structures are not based on a template. The structural diversity of these molecules confers them an enormous capacity to encode information in biological systems, acting as efficient mediators in the interaction of the cell with the environment. In order to understand the roles of glycans in biological processes it is of key importance to have a detailed understanding of their structures and conformational preferences, and NMR spectroscopy is one of most powerful techniques for the study of these molecules in solution.This thesis is focused on the structural and conformational analysis of lipopolysaccharides from Gram-negative bacteria. In the first two projects (Chapter 2 and 3) the structural analyses of the biological repeating units of the O-antigen polysaccharides from E. coli O174ab and O115 are described; in both cases a combination of NMR spectroscopy and gas chromatography techniques were used. Special emphasis was made in the characterization of the O-acetylation patterns observed in the native O-antigen polysaccharide from E. coli O115. Chapter 4 describes the development of a new methodology for the determination of the absolute configuration of monosaccharide components of glycans. This methodology was used in the structural elucidation of the O-antigen PS of E. coli O155 (Chapter 5) that was carried out in a semi-automated manner using the program CASPER and unassigned NMR data. The conformational preferences of O-antigen PS of E. coli O5ac and O5ab are analyzed in Chapter 6, using a combination of NMR spectroscopy and molecular modeling methods. In Chapter 7 the structural analysis is focused on the core region of the LPS, and the structures of the deacylated lipooligosaccharides of three rough mutants of B. melitesis are reported. In several of the aforementioned chapters, the biosynthetic aspects behind the assembly of the respective PSs were examined on the bases of genetic information available in the NCBI and ECODAB databases. Finally, in Chapter 8, different NMR pulse sequences available for the study of proteins and nucleic acids were evaluated and optimized for the structural analysis of 13C uniformly-labeled oligo- and polysaccharides.
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| 7. |
- Fontana, Carolina, et al.
(författare)
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NMR structure analysis of uniformly 13C-labeled carbohydrates
- 2014
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Ingår i: Journal of Biomolecular NMR. - : Springer Science and Business Media LLC. - 0925-2738 .- 1573-5001. ; 59:2, s. 95-110
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Tidskriftsartikel (refereegranskat)abstract
- In this study, a set of nuclear magnetic resonance experiments, some of them commonly used in the study of C-13-labeled proteins and/or nucleic acids, is applied for the structure determination of uniformly C-13-enriched carbohydrates. Two model substances were employed: one compound of low molecular weight [(UL-C-13)-sucrose, 342 Da] and one compound of medium molecular weight (C-13-enriched O-antigenic polysaccharide isolated from Escherichia coli O142, similar to 10 kDa). The first step in this approach involves the assignment of the carbon resonances in each monosaccharide spin system using the anomeric carbon signal as the starting point. The C-13 resonances are traced using C-13-C-13 correlations from homonuclear experiments, such as (H)CC-CT-COSY, (H)CC-NOESY, CC-CT-TOCSY and/or virtually decoupled (H)CC-TOCSY. Based on the assignment of the C-13 resonances, the H-1 chemical shifts are derived in a straightforward manner using one-bond H-1-C-13 correlations from heteronuclear experiments (HC-CT-HSQC). In order to avoid the (1) J (CC) splitting of the C-13 resonances and to improve the resolution, either constant-time (CT) in the indirect dimension or virtual decoupling in the direct dimension were used. The monosaccharide sequence and linkage positions in oligosaccharides were determined using either C-13 or H-1 detected experiments, namely CC-CT-COSY, band-selective (H)CC-TOCSY, HC-CT-HSQC-NOESY or long-range HC-CT-HSQC. However, due to the short T-2 relaxation time associated with larger polysaccharides, the sequential information in the O-antigen polysaccharide from E. coli O142 could only be elucidated using the H-1-detected experiments. Exchanging protons of hydroxyl groups and N-acetyl amides in the C-13-enriched polysaccharide were assigned by using HC-H2BC spectra. The assignment of the N-acetyl groups with N-15 at natural abundance was completed by using HN-SOFAST-HMQC, HNCA, HNCO and C-13-detected (H)CACO spectra.
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| 8. |
- Fontana, Carolina, et al.
(författare)
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Primary Structure of Glycans by NMR Spectroscopy
- 2023
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Ingår i: Chemical Reviews. - : American Chemical Society (ACS). - 0009-2665 .- 1520-6890. ; 123:3, s. 1040-1102
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Forskningsöversikt (refereegranskat)abstract
- Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a 1H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.
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| 9. |
- Fontana, Carolina, et al.
(författare)
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Rapid structural elucidation of polysaccharides employing predicted functions of glycosyltransferases and NMR data : Application to the O-antigen of Escherichia coli O59
- 2014
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Ingår i: Glycobiology. - : Oxford University Press (OUP). - 0959-6658 .- 1460-2423. ; 24:5, s. 450-457
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Tidskriftsartikel (refereegranskat)abstract
- A computerized method that uses predicted functions of glycosyltransferases (GTs) in conjunction with unassigned NMR data has been developed for the structural elucidation of bacterial polysaccharides (PSs). In this approach, information about the action of GTs (consisting of possible sugar residues used as donors and/or acceptors, as well as the anomeric configuration and/or substitution position in the respective glycosidic linkages) is extracted from the Escherichia coli O-antigen database and is submitted, together with the unassigned NMR data, to the CASPER program. This time saving methodology, which alleviates the need for chemical analysis, was successfully implemented in the structural elucidation of the O-antigen PS of E. coli O59. The repeating unit of the O-specific chain was determined using the O-deacylated PS and has a branched structure, namely, -> 6)[alpha-d-GalpA3Ac/4Ac-(1 -> 3)]-alpha-d-Manp-(1 -> 3)-alpha-d-Manp-(1 -> 3)-beta-d-Manp-(1 -> 3)-alpha-d-GlcpNAc-(1 ->. The identification of the O-acetylation positions was efficiently performed by comparison of the H-1,C-13 HSQC NMR spectra of the O-deacylated lipopolysaccharide and the lipid-free PS in conjunction with chemical shift predictions made by the CASPER program. The side-chain d-GalpA residue carries one equivalent of O-acetyl groups at the O-3 and O-4 positions distributed in the LPS in a 3:7 ratio, respectively. The presence of O-acetyl groups in the repeating unit of the E. coli O59 PS is consistent with the previously proposed acetyltransferase WclD in the O-antigen gene cluster.
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| 10. |
- Fontana, Carolina, et al.
(författare)
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Structural Elucidation of the O-Antigen Polysaccharide from Escherichia coli O181
- 2015
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Ingår i: ChemistryOpen. - : Wiley. - 2191-1363. ; 4:1, s. 47-55
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Tidskriftsartikel (refereegranskat)abstract
- Shiga-toxin-producing Escherichia coli (STEC) is an important pathogen associated to food-borne infection in humans; strains of E.coli O181, isolated from human cases of diarrhea, have been classified as belonging to this pathotype. Herein, the structure of the O-antigen polysaccharide (PS) from E.coli O181 has been investigated. The sugar analysis showed quinovosamine (QuiN), glucosamine (GlcN), galactosamine (GalN), and glucose (Glc) as major components. Analysis of the high-resolution mass spectrum of the oligosaccharide (OS), obtained by dephosphorylation of the O-deacetylated PS with aqueous 48% hydrofluoric acid, revealed a pentasaccharide composed of two QuiNAc, one GlcNAc, one GalNAc, and one Glc residue. The H-1 and (CNMR)-C-13 chemical shift assignments of the OS were carried out using 1D and 2D NMR experiments, and the OS was sequenced using a combination of tandem mass spectrometry (MS/MS) data and NMR (CNMR)-C-13 glycosylation shifts. The structure of the native PS was determined using NMR spectroscopy, and it consists of branched pentasaccharide repeating units joined by phosphodiester linkages: -> 4)[alpha-L-QuipNAc-(1 -> 3)]-alpha-D-GalpNAc6Ac-(1 -> 6)-alpha-D-Glcp-(1 -> P-4)-alpha-L-QuipNAc-(1 -> 3)-beta-D-GlcpNAc-(1 ->; the O-acetyl groups represent 0.4 equivalents per repeating unit. Both the OS and PSs exhibit rare conformational behavior since two of the five anomeric proton resonances could only be observed at an elevated temperature.
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