| 1. |
- Madin, Joshua S., et al.
(author)
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A synthesis of bacterial and archaeal phenotypic trait data
- 2020
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In: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 7:1
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Journal article (peer-reviewed)abstract
- A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for approximately 170,000 strain-level and 15,000 species-aggregated records. It spans all habitats including soils, marine and fresh waters and sediments, host-associated and thermal. Trait data can find use in clarifying major dimensions of ecological strategy variation across species. They can also be used in conjunction with species and abundance sampling to characterize trait mixtures in communities and responses of traits along environmental gradients.
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| 2. |
- Berglund, Anna-Karin, 1979, et al.
(author)
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Nucleotide pools dictate the identity and frequency of ribonucleotide incorporation in mitochondrial DNA. : Mapping ribonucleotides in mitochondrial DNA
- 2017
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In: PLoS genetics. - : Public Library of Science (PLoS). - 1553-7404 .- 1553-7390. ; 13:2
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Journal article (peer-reviewed)abstract
- Previous work has demonstrated the presence of ribonucleotides in human mitochondrial DNA (mtDNA) and in the present study we use a genome-wide approach to precisely map the location of these. We find that ribonucleotides are distributed evenly between the heavy- and light-strand of mtDNA. The relative levels of incorporated ribonucleotides reflect that DNA polymerase γ discriminates the four ribonucleotides differentially during DNA synthesis. The observed pattern is also dependent on the mitochondrial deoxyribonucleotide (dNTP) pools and disease-causing mutations that change these pools alter both the absolute and relative levels of incorporated ribonucleotides. Our analyses strongly suggest that DNA polymerase γ-dependent incorporation is the main source of ribonucleotides in mtDNA and argues against the existence of a mitochondrial ribonucleotide excision repair pathway in human cells. Furthermore, we clearly demonstrate that when dNTP pools are limiting, ribonucleotides serve as a source of building blocks to maintain DNA replication. Increased levels of embedded ribonucleotides in patient cells with disturbed nucleotide pools may contribute to a pathogenic mechanism that affects mtDNA stability and impair new rounds of mtDNA replication.
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| 3. |
- Bergman, Jan, et al.
(author)
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Studies of the reactions between indole-2,3-diones (isatins) and 2-aminobenzylamine
- 2003
-
In: Tetrahedron. - 0040-4020 .- 1464-5416. ; 59:7, s. 1033-1048
-
Journal article (peer-reviewed)abstract
- Reflux of equimolecular amounts 2-aminobenzylamine and isatins in acetic acid produced indolo[3,2-c]quinolin-6-ones in good yields. A proposed mechanism involving initial formation of a spiro compound is given. This isolable intermediate subsequently rearranges via a sequential isocyanate ring opening and a cyclisation process to a urea derivative which finally cyclized to the indolo[3,2-c]quinolin-6-ones. The urea derivative could be prepared separately and cyclized selectively to indolo[3,2-c]quinolin-6-one. Reaction of N-acetylisatin with 2-aminobenzylamine at room temperature yielded the 1,4-benzodiazepinone 3-(2-acetamidophenyl)-1,5-dihydro-1,4-benzodiazepin-2one whereas its isomer 2(2-acetamidophenyl)-4,5-dihydro-1,4-benzodiazepin-3-one was obtained from 2-(2-acetylaminophenyl)-N-(2-aminobenzyl)-2-oxoacetamide in acetic acid at room temperature. The previously unknown linear isomer of indolo[3,2-c]quinolin-6-one, i.e. indolo[2,3-blquinolin-11-one, has been prepared by thermal (260degreesC) cyclization of methyl 2-phenylamino indole-3-carboxylate, which in turn was prepared in two steps from methyl indole-3-carboxyl ate. (C) 2003 Elsevier Science Ltd. All rights reserved.
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| 4. |
- Casey, John R., et al.
(author)
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Basin-scale biogeography of marine phytoplankton reflects cellular-scale optimization of metabolism and physiology
- 2022
-
In: Science advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 8:3
-
Journal article (peer-reviewed)abstract
- Extensive microdiversity within Prochlorococcus, the most abundant marine cyanobacterium, occurs at scales from a single droplet of seawater to ocean basins. To interpret the structuring role of variations in genetic potential, as well as metabolic and physiological acclimation, we developed a mechanistic constraint-based modeling framework that incorporates the full suite of genes, proteins, metabolic reactions, pigments, and biochemical compositions of 69 sequenced isolates spanning the Prochlorococcus pangenome. Optimizing each strain to the local, observed physical and chemical environment along an Atlantic Ocean transect, we predicted variations in strain-specific patterns of growth rate, metabolic configuration, and physiological state, defining subtle niche subspaces directly attributable to differences in their encoded metabolic potential. Predicted growth rates covaried with observed ecotype abundances, affirming their significance as a measure of fitness and inferring a nonlinear density dependence of mortality. Our study demonstrates the potential to interpret global-scale ecosystem organization in terms of cellular-scale processes.
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| 5. |
- Chen, Song, et al.
(author)
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Compressive fatigue limit of four types of dental restorative materials
- 2016
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In: Journal of The Mechanical Behavior of Biomedical Materials. - : Elsevier BV. - 1751-6161 .- 1878-0180. ; 61, s. 283-289
-
Journal article (peer-reviewed)abstract
- The purpose of this study was to evaluate the quasi-static compressive strength and the compressive fatigue limit of four different dental restorative materials, before and after aging in distilled water for 30 days. A conventional glass ionomer cement (Fuji IX GP; IG), a zinc-reinforced glass ionomer cement (Chemfil rock; CF), a light curable resin-reinforced glass ionomer cement (Fuji II LC; LC) and a resin-based composite (Quixfil; QF) were investigated. Cylindrical specimens (4 mm in diameter and 6 mm in height) were prepared according to the manufacturer's instructions. The compressive fatigue limit was obtained using the staircase method. Samples were tested in distilled water at 37 degrees C, at a frequency of 10 Hz with 10(5) cycles set as run-out. 17 fatigue samples were tested for each group. Two-way ANOVA and one-way ANOVA followed by Tukey's post-hoc test were used to analyze the results. Among the four types of materials, the resin-based composite exhibited the highest compressive strength (244 +/- 13.0 MPa) and compressive fatigue limit (134 +/- 7.8 MPa), followed by the light-cured resin reinforced glass ionomer cement (168 +/- 8.5 MPa and 92 +/- 6.6 MPa, respectively) after one day of storage in distilled water. After being stored for 30 days, all specimens showed an increase in compressive strength. Aging showed no effect on the compressive fatigue limit of the resin-based composite and the light-cured resin reinforced glass ionomer cement, however, the conventional glass ionomer cements showed a drastic decrease (37% for IG, 31% for CF) in compressive fatigue limit. In conclusion, in the present study, resin modified GIC and resin-based composite were found to have superior mechanical properties to conventional GIC.
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| 6. |
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| 7. |
- Corell, Hanna, 1977, et al.
(author)
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Depth distribution of larvae critically affects their dispersal and the efficiency of marine protected areas
- 2012
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In: Marine Ecology Progress Series. - : Inter-Research Science Center. - 0171-8630 .- 1616-1599. ; 467, s. 29-46
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Journal article (peer-reviewed)abstract
- This study aims to improve estimates of dispersal by including information on larval traits, and in particular to explore how larval depth distribution affects connectivity and MPA (marine protected area) functionality in the Baltic Sea. A field survey showed that both invertebrates and fish differed in their larval depth distribution, ranging from surface waters to >100 m. A biophysical model of larval dispersal in the Baltic Sea showed that decreased depth distribution increased average dispersal distance 2.5-fold, decreased coastal retention and local recruitment, and substantially increased connectivity. Together with pelagic larval duration (PLD), depth distribution explained 80% of total variation in dispersal distance, whereas spawning season, and geographic and annual variations in circulation had only marginal effects. Median dispersal distances varied between 8 and 46 km, with 10% of simulated trajectories dispersing 30 to 160 km depending on drift depth and PLD. In the Baltic Sea, the majority of shallow Natura 2000 MPAs are <8 km in diameter. In the present study, only 1 of the 11 assessed larval taxa would have a recruitment >10% within MPAs of this size. Connectivity between MPAs was expected to be low for most larval trait combinations. Our simulations and the empirical data suggest that the MPA size within the Natura 2000 system is considerably below what is required for local recruitment of most sessile invertebrates and sedentary fish. Future designs of MPA networks would benefit from spatially explicit biophysical models that consider dispersal and connectivity for complex circulation patterns and informed larval traits.
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| 8. |
- Corell, Hanna, 1977-, et al.
(author)
-
Larval depth distribution critically affects dispersal and the efficiency of marine protected areas
-
In: Marine Ecology Progress Series. - 0171-8630 .- 1616-1599.
-
Journal article (peer-reviewed)abstract
- This study aims to improve estimates of dispersal by including information on larval traits, and in particular to explore how larval depth distribution affects connectivity and MPA functionality in the Baltic Sea. A field survey showed that both invertebrates and fish differed in their larval depth distribution ranging from surface waters to more than 100 m. A biophysical model of larval dispersal in the Baltic Sea showed that decreased depthdistribution increased average dispersal distance 2.5 times, decreased coastal retention and local recruitment, and increased connectivity substantially. Together with pelagic larval duration (PLD), depth distribution explained 80% of total variation in dispersal distance, whereas spawning season, geographic and annual variations in circulation had only marginal effects. Median dispersal distances varied between 8 and 46 km, with 10% of simulated trajectories dispersing beyond 30-160 km depending on drift depth and PLD. In the Baltic Sea, the majority of shallow Natura 2000 MPAs are smaller than 8 km. In the present study, only one of the 11 assessed larval taxa would have a local recruitment >10% within MPAs of this size. Connectivity between MPAs was expected to be low for most larval trait combinations. Our simulations and the empirical data suggest that the MPA size within the Natura2000 system is considerably below what is required for local recruitment of most sessile invertebrates and sedentary fish. Future designs of MPA networks would benefit from spatially explicit biophysical models that consider dispersal and connectivity for complex circulation patterns and informed larval traits.
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| 9. |
- Engqvist, Martin, 1983, et al.
(author)
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Directed evolution of gloeobacter violaceus rhodopsin spectral properties
- 2015
-
In: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 427:1, s. 205-220
-
Journal article (peer-reviewed)abstract
- Proton-pumping rhodopsins (PPRs) are photoactive retinal-binding proteins that transport ions across biological membranes in response to light. These proteins are interesting for light-harvesting applications in bioenergy production, in optogenetics applications in neuroscience, and as fluorescent sensors of membrane potential. Little is known, however, about how the protein sequence determines the considerable variation in spectral properties of PPRs from different biological niches or how to engineer these properties in a given PPR. Here we report a comprehensive study of amino acid substitutions in the retinal-binding pocket of Gloeobacter violaceus rhodopsin (GR) that tune its spectral properties. Directed evolution generated 70 GR variants with absorption maxima shifted by up to ± 80 nm, extending the protein's light absorption significantly beyond the range of known natural PPRs. While proton-pumping activity was disrupted in many of the spectrally shifted variants, we identified single tuning mutations that incurred blue and red shifts of 42 nm and 22 nm, respectively, that did not disrupt proton pumping. Blue-shifting mutations were distributed evenly along the retinal molecule while red-shifting mutations were clustered near the residue K257, which forms a covalent bond with retinal through a Schiff base linkage. Thirty eight of the identified tuning mutations are not found in known microbial rhodopsins. We discovered a subset of red-shifted GRs that exhibit high levels of fluorescence relative to the WT (wild-type) protein.
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| 10. |
- Engqvist, Martin, 1983, et al.
(author)
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GLYCOLATE OXIDASE3, a Glycolate Oxidase Homolog of Yeast l-Lactate Cytochrome c Oxidoreductase, Supports l-Lactate Oxidation in Roots of Arabidopsis
- 2015
-
In: Plant Physiology. - : Oxford University Press (OUP). - 1532-2548 .- 0032-0889. ; 169:2, s. 1042-1061
-
Journal article (peer-reviewed)abstract
- In roots of Arabidopsis (Arabidopsis thaliana), L-lactate is generated by the reduction of pyruvate via L-lactate dehydrogenase, but this enzyme does not efficiently catalyze the reverse reaction. Here, we identify the Arabidopsis glycolate oxidase (GOX) paralogs GOX1, GOX2, and GOX3 as putative L-lactate-metabolizing enzymes based on their homology to CYB2, the L-lactate cytochrome c oxidoreductase from the yeast Saccharomyces cerevisiae. We found that GOX3 uses L-lactate with a similar efficiency to glycolate; in contrast, the photorespiratory isoforms GOX1 and GOX2, which share similar enzymatic properties, use glycolate with much higher efficiencies than L-lactate. The key factor making GOX3 more efficient with L-lactate than GOX1 and GOX2 is a 5- to 10-fold lower Km for the substrate. Consequently, only GOX3 can efficiently metabolize L-lactate at low intracellular concentrations. Isotope tracer experiments as well as substrate toxicity tests using GOX3 loss-offunction and overexpressor plants indicate that L-lactate is metabolized in vivo by GOX3. Moreover, GOX3 rescues the lethal growth phenotype of a yeast strain lacking CYB2, which cannot grow on L-lactate as a sole carbon source. GOX3 is predominantly present in roots and mature to aging leaves but is largely absent from young photosynthetic leaves, indicating that it plays a role predominantly in heterotrophic rather than autotrophic tissues, at least under standard growth conditions. In roots of plants grown under normoxic conditions, loss of function of GOX3 induces metabolic rearrangements that mirror wild-type responses under hypoxia. Thus, we identified GOX3 as the enzyme that metabolizes L-lactate to pyruvate in vivo and hypothesize that it may ensure the sustainment of low levels of L-lactate after its formation under normoxia.
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| 11. |
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| 12. |
- Gigolashvili, T., et al.
(author)
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HAG2/MYB76 and HAG3/MYB29 exert a specific and coordinated control on the regulation of aliphatic glucosinolate biosynthesis in Arabidopsis thaliana
- 2008
-
In: New Phytologist. - : Wiley. - 1469-8137 .- 0028-646X. ; 177:3, s. 627-642
-
Journal article (peer-reviewed)abstract
- In a previous transactivation screen, two Arabidopsis thaliana R2R3-MYB transcription factors, HAG2/MYB76 and HAG3/MYB29, along with the already characterized HAG1/MYB28, were identified as putative regulators of aliphatic glucosinolate biosynthesis. • Molecular and biochemical characterization of HAG2/MYB76 and HAG3/MYB29 functions was performed using transformants with increased or repressed transcript levels. Real-time PCR assays, cotransformation assays and measurements of glucosinolate contents were used to assess the impact of both MYB factors on the steady-state level of glucosinolate biosynthetic genes and accumulation of aliphatic glucosinolates. • Both HAG2/MYB76 and HAG3/MYB29 were shown to be positive regulators of aliphatic glucosinolate biosynthesis. Expression of promoter-β- glucuronidase (GUS) fusions indicated GUS activities in both vegetative and generative organs, with distinct characteristics for each MYB factor. HAG1/MYB28, HAG2/MYB76 and HAG3/MYB29 reciprocally transactivated each other in the control of aliphatic glucosinolate biosynthesis and downregulated the expression of genes involved in the control of indolic glucosinolate biosynthesis, pointing to a reciprocal negative regulation of these two pathways. • All three HAG transcription factors exert a coordinated control on aliphatic glucosinolate biosynthesis.
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| 13. |
- Kreisel, Katrin, 1991, et al.
(author)
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DNA polymerase η contributes to genome-wide lagging strand synthesis.
- 2019
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In: Nucleic acids research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 47:5, s. 2425-2435
-
Journal article (peer-reviewed)abstract
- DNA polymerase η (pol η) is best known for its ability to bypass UV-induced thymine-thymine (T-T) dimers and other bulky DNA lesions, but pol ηalso has other cellular roles. Here, we present evidence that pol η competes with DNA polymerases α and δfor the synthesis of the lagging strand genome-wide, where it also shows a preference for T-T in the DNA template. Moreover, we found that the C-terminus of pol η,which contains a PCNA-Interacting Protein motif is required for pol ηto function in lagging strand synthesis. Finally, we provide evidence that a pol η dependent signature is also found to be lagging strand specific in patients with skin cancer. Taken together, these findings provide insight into the physiological role of DNA synthesis by pol η and have implications for our understanding of how our genome is replicated to avoid mutagenesis, genome instability and cancer.
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| 14. |
- Kreisel, Katrin, 1991, et al.
(author)
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Simultaneous mapping and quantitation of ribonucleotides in human mitochondrial DNA
- 2017
-
In: Journal of Visualized Experiments. - : MyJove Corporation. - 1940-087X. ; 2017
-
Journal article (peer-reviewed)abstract
- © 2017. Established approaches to estimate the number of ribonucleotides present in a genome are limited to the quantitation of incorporated ribonucleotides using short synthetic DNA fragments or plasmids as templates and then extrapolating the results to the whole genome. Alternatively, the number of ribonucleotides present in a genome may be estimated using alkaline gels or Southern blots. More recent in vivo approaches employ Next-generation sequencing allowing genome-wide mapping of ribonucleotides, providing the position and identity of embedded ribonucleotides. However, they do not allow quantitation of the number of ribonucleotides which are incorporated into a genome. Here we describe how to simultaneously map and quantitate the number of ribonucleotides which are incorporated into human mitochondrial DNA in vivo by Next-generation sequencing. We use highly intact DNA and introduce sequence specific double strand breaks by digesting it with an endonuclease, subsequently hydrolyzing incorporated ribonucleotides with alkali. The generated ends are ligated with adapters and these ends are sequenced on a Next-generation sequencing machine. The absolute number of ribonucleotides can be calculated as the number of reads outside the recognition site per average number of reads at the recognition site for the sequence specific endonuclease. This protocol may also be utilized to map and quantitate free nicks in DNA and allows adaption to map other DNA lesions that can be processed to 5´-OH ends or 5´-phosphate ends. Furthermore, this method can be applied to any organism, given that a suitable reference genome is available. This protocol therefore provides an important tool to study DNA replication, 5´-end processing, DNA damage, and DNA repair.
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| 15. |
- Li, Feiran, 1993, et al.
(author)
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Different routes of protein folding contribute to improved protein production in saccharomyces cerevisiae
- 2020
-
In: mBio. - 2161-2129 .- 2150-7511. ; 11:6, s. 1-12
-
Journal article (peer-reviewed)abstract
- Protein folding is often considered the flux controlling process in protein synthesis and secretion. Here, two previously isolated Saccharomyces cerevisiae strains with increased α-amylase productivity were analyzed in chemostat cultures at different dilution rates using multi-omics data. Based on the analysis, we identified different routes of the protein folding pathway to improve protein production. In the first strain, the increased abundance of proteins working on the folding process, coordinated with upregulated glycogen metabolism and trehalose metabolism, helped increase α-amylase productivity 1.95-fold compared to the level in the original strain in chemostat culture at a dilution rate of 0.2/h. The second strain further strengthened the folding precision to improve protein production. More precise folding helps the cell improve protein production efficiency and reduce the expenditure of energy on the handling of misfolded proteins. As calculated using an enzyme-constrained genome-scale metabolic model, the second strain had an increased productivity of 2.36-fold with lower energy expenditure than that of the original under the same condition. Further study revealed that the regulation of N-glycans played an important role in the folding precision control and that overexpression of the glucosidase Cwh41p can significantly improve protein production, especially for the strains with improved folding ca-pacity but lower folding precision. Our findings elucidated in detail the mechanisms in two strains having improved protein productivity and thereby provided novel insights for industrial recombinant protein production as well as demonstrating how multi-omics analysis can be used for identification of novel strain-engineering targets. IMPORTANCE Protein folding plays an important role in protein maturation and se-cretion. In recombinant protein production, many studies have focused on the folding pathway to improve productivity. Here, we identified two different routes for improving protein production by yeast. We found that improving folding precision is a better strategy. Dysfunction of this process is also associated with several aberrant protein-associated human diseases. Here, our findings about the role of glucosidase Cwh41p in the precision control system and the characterization of the strain with a more precise folding process could contribute to the development of novel therapeutic strategies. © 2020 Qi et al.
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| 16. |
- Mathew, Renny, 1982-, et al.
(author)
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Nuclear Magnetic Resonance and Metadynamics Simulations Reveal the Atomistic Binding of ʟ-Serine and O-Phospho-ʟ-Serine at Disordered Calcium Phosphate Surfaces of Biocements
- 2022
-
In: Chemistry of Materials. - : American Chemical Society (ACS). - 0897-4756 .- 1520-5002. ; 34:19, s. 8815-8830
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Journal article (peer-reviewed)abstract
- Interactions between biomolecules and structurally disordered calcium phosphate (CaP) surfaces are crucial for the regulation of bone mineralization by noncollagenous proteins, the organization of complexes of casein and amorphous calcium phosphate (ACP) in milk, as well as for structure–function relationships of hybrid organic/inorganic interfaces in biomaterials. By a combination of advanced solid-state NMR experiments and metadynamics simulations, we examine the detailed binding of O-phospho-l-serine (Pser) and l-serine (Ser) with ACP in bone-adhesive CaP cements, whose capacity of gluing fractured bone together stems from the close integration of the organic molecules with ACP over a subnanometer scale. The proximity of each carboxy, aliphatic, and amino group of Pser/Ser to the Ca2+ and phosphate species of ACP observed from the metadynamics-derived models agreed well with results from heteronuclear solid-state NMR experiments that are sensitive to the 13C–31P and 15N–31P distances. The inorganic/organic contacts in Pser-doped cements are also contrasted with experimental and modeled data on the Pser binding at nanocrystalline HA particles grown from a Pser-bearing aqueous solution. The molecular adsorption is driven mainly by electrostatic interactions between the negatively charged carboxy/phosphate groups and Ca2+ cations of ACP, along with H bonds to either protonated or nonprotonated inorganic phosphate groups. The Pser and Ser molecules anchor at their phosphate/amino and carboxy/amino moieties, respectively, leading to an extended molecular conformation across the surface, as opposed to an “upright standing” molecule that would result from the binding of one sole functional group.
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| 17. |
- McIsaac, R.S., et al.
(author)
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Directed evolution of a far-red fluorescent rhodopsin
- 2014
-
In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 111:36, s. 13034-13039
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Journal article (peer-reviewed)abstract
- Microbial rhodopsins are a diverse group of photoactive transmembrane proteins found in all three domains of life. A member of this protein family, Archaerhodopsin-3 (Arch) of halobacterium Halorubrum sodomense, was recently shown to function as a fluorescent indicator of membrane potential when expressed in mammalian neurons. Arch fluorescence, however, is very dim and is not optimal for applications in live-cell imaging. We used directed evolution to identify mutations that dramatically improve the absolute brightness of Arch, as confirmed biochemically and with livecell imaging (in Escherichia coli and human embryonic kidney 293 cells). In some fluorescent Arch variants, the pKaof the protonated Schiff-base linkage to retinal is near neutral pH, a useful feature for voltage-sensing applications. These bright Arch variants enable labeling of biological membranes in the far-red/infrared and exhibit the furthest red-shifted fluorescence emission thus far reported for a fluorescent protein (maximal excitation/emission at ∼620 nm/730 nm).
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| 18. |
- Naumovska, M, et al.
(author)
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Tomographic ultrasound for three-dimensional visualization of temporal arteries
-
In: Scandinavian Journal of Rheumatology. - 0300-9742.
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Journal article (peer-reviewed)abstract
- ObjectiveConventional two-dimensional ultrasound has been assessed for the non-invasive diagnosis of giant cell arteritis (GCA), but the results are operator dependent, resulting in low sensitivity. Tomographic three-dimensional (3D) ultrasound is a novel technique that enables the objective documentation of vessel geometry. Here, for the first time, its utility is assessed for visualizing temporal arteries.MethodThe temporal artery of 14 healthy subjects and three subjects with suspected GCA was examined using tomographic 3D ultrasound.ResultsThis technique enabled 3D mapping of the architecture of the temporal artery. The inner and outer vessel diameters showed considerable interindividual variability. However, calculation of the vessel wall fraction revealed the combination of vessel wall thickening and lumen narrowing, which may be indicative of GCA.ConclusionsThis proof-of-concept study indicates that tomographic 3D ultrasound can be used for objective mapping of the temporal artery. The technique must be evaluated regarding its diagnostic sensitivity in GCA before it can be introduced in clinical practice.
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| 19. |
- Nilsson, Avlant, 1985, et al.
(author)
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Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis
- 2020
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 117:19, s. 10294-10304
-
Journal article (peer-reviewed)abstract
- Many cancer cells consume glutamine at high rates; counterintuitively, they simultaneously excrete glutamate, the first intermediate in glutamine metabolism. Glutamine consumption has been linked to replenishment of tricarboxylic acid cycle (TCA) intermediates and synthesis of adenosine triphosphate (ATP), but the reason for glutamate excretion is unclear. Here, we dynamically profile the uptake and excretion fluxes of a liver cancer cell line (HepG2) and use genome-scale metabolic modeling for in-depth analysis. We find that up to 30% of the glutamine is metabolized in the cytosol, primarily for nucleotide synthesis, producing cytosolic glutamate. We hypothesize that excreting glutamate helps the cell to increase the nucleotide synthesis rate to sustain growth. Indeed, we show experimentally that partial inhibition of glutamate excretion reduces cell growth. Our integrative approach thus links glutamine addiction to glutamate excretion in cancer and points toward potential drug targets.
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| 20. |
- Pires, Marcel V., et al.
(author)
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The influence of alternative pathways of respiration that utilize branched-chain amino acids following water shortage in Arabidopsis
- 2016
-
In: Plant, Cell and Environment. - : Wiley. - 1365-3040 .- 0140-7791. ; 39:6, s. 1304-1319
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Journal article (peer-reviewed)abstract
- During dark-induced senescence isovaleryl-CoA dehydrogenase (IVDH) and D-2-hydroxyglutarate dehydrogenase (D-2HGDH) act as alternate electron donors to the ubiquinol pool via the electron-transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase (ETF/ETFQO) pathway. However, the role of this pathway in response to other stresses still remains unclear. Here, we demonstrated that this alternative pathway is associated with tolerance to drought in Arabidopsis. In comparison with wild type (WT) and lines overexpressing D-2GHDH, loss-of-function etfqo-1, d2hgdh-2 and ivdh-1 mutants displayed compromised respiration rates and were more sensitive to drought. Our results demonstrated that an operational ETF/ETFQO pathway is associated with plants' ability to withstand drought and to recover growth once water becomes replete. Drought-induced metabolic reprogramming resulted in an increase in tricarboxylic acid (TCA) cycle intermediates and total amino acid levels, as well as decreases in protein, starch and nitrate contents. The enhanced levels of the branched-chain amino acids in loss-of-function mutants appear to be related to their increased utilization as substrates for the TCA cycle under water stress. Our results thus show that mitochondrial metabolism is highly active during drought stress responses and provide support for a role of alternative respiratory pathways within this response.
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| 21. |
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| 22. |
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| 23. |
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| 24. |
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| 25. |
- Svahn, Fedrik, et al.
(author)
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A novel method for producing electron transparent thin films of inat interfaces between cells and biomaterials
- 2008
-
In: Journal of materials science. Materials in medicine. - : Springer Science and Business Media LLC. - 0957-4530 .- 1573-4838. ; 19:1, s. 467-470
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Journal article (peer-reviewed)abstract
- Transmission electron microscopy (TEM) investigations of intact interfaces of cells and brittle biomaterials have proven difficult using common TEM preparation techniques. This paper describes a technique to fabricate thin sections for TEM investigation of intact interfaces between human monocytes and sintered hydroxylapatite by the use of focused ion beam (FIB) microscopy. The interfaces were examined using energy filtered TEM.
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| 26. |
- Ting, Miriam, et al.
(author)
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Classification and Effects of Implant Surface Modification on the Bone : Human Cell-Based In Vitro Studies
- 2017
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In: Journal of Oral Implantology. - : ALLEN PRESS INC. - 0160-6972 .- 1548-1336. ; 43:1, s. 58-83
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Research review (peer-reviewed)abstract
- Implant surfaces are continuously being improved to achieve faster osseointegration and a stronger bone to implant interface. This review will present the various implant surfaces, the parameters for implant surface characterization, and the corresponding in vitro human cell-based studies determining the strength and quality of the bone-implant contact. These in vitro cell-based studies are the basis for animal and clinical studies and are the prelude to further reviews on how these surfaces would perform when subjected to the oral environment and functional loading.
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| 27. |
- Wanrooij, Paulina H., et al.
(author)
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Elimination of rNMPs from mitochondrial DNA has no effect on its stability
- 2020
-
In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 117:25, s. 14306-14313
-
Journal article (peer-reviewed)abstract
- Ribonucleotides (rNMPs) incorporated in the nuclear genome are a well-established threat to genome stability and can result in DNA strand breaks when not removed in a timely manner. However, the presence of a certain level of rNMPs is tolerated in mitochondrial DNA (mtDNA) although aberrant mtDNA rNMP content has been identified in disease models. We investigated the effect of incorporated rNMPs on mtDNA stability over the mouse life span and found that the mtDNA rNMP content increased during early life. The rNMP content of mtDNA varied greatly across different tissues and was defined by the rNTP/dNTP ratio of the tissue. Accordingly, mtDNA rNMPs were nearly absent in SAMHD1(-/-) mice that have increased dNTP pools. The near absence of rNMPs did not, however, appreciably affect mtDNA copy number or the levels of mtDNA molecules with deletions or strand breaks in aged animals near the end of their life span. The physiological rNMP load therefore does not contribute to the progressive loss of mtDNA quality that occurs as mice age.
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| 28. |
- Wanrooij, Paulina H., et al.
(author)
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Ribonucleotides incorporated by the yeast mitochondrial DNA polymerase are not repaired
- 2017
-
In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 114:47, s. 12466-12471
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Journal article (peer-reviewed)abstract
- Incorporation of ribonucleotides into DNA during genome replication is a significant source of genomic instability. The frequency of ribonucleotides in DNA is determined by deoxyribonucleoside triphosphate/ribonucleoside triphosphate (dNTP/rNTP) ratios, by the ability of DNA polymerases to discriminate against ribonucleotides, and by the capacity of repair mechanisms to remove incorporated ribonucleotides. To simultaneously compare how the nuclear and mitochondrial genomes incorporate and remove ribonucleotides, we challenged these processes by changing the balance of cellular dNTPs. Using a collection of yeast strains with altered dNTP pools, we discovered an inverse relationship between the concentration of individual dNTPs and the amount of the corresponding ribonucleotides incorporated in mitochondrial DNA, while in nuclear DNA the ribonucleotide pattern was only altered in the absence of ribonucleotide excision repair. Our analysis uncovers major differences in ribonucleotide repair between the two genomes and provides concrete evidence that yeast mitochondria lack mechanisms for removal of ribonucleotides incorporated by the mtDNA polymerase. Furthermore, as cytosolic dNTP pool imbalances were transmitted equally well into the nucleus and the mitochondria, our results support a view of the cytosolic and mitochondrial dNTP pools in frequent exchange. © 2017, National Academy of Sciences. All rights reserved.
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