| 1. |
- Kehoe, Laura, et al.
(author)
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Make EU trade with Brazil sustainable
- 2019
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Journal article (other academic/artistic)
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| 2. |
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| 3. |
- Persson, Erik, et al.
(author)
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Philosophical aspects of astrobiology
- 2013
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In: The History and Philosophy of Astrobiology : Perspectives on Extraterrestrial Life and the Human Mind - Perspectives on Extraterrestrial Life and the Human Mind. - : Cambridge Scholars Publishing. - 9781443850353 ; , s. 29-48
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Book chapter (peer-reviewed)
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| 4. |
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| 5. |
- Andreanidis, Christos, et al.
(author)
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On the Design and Development of a Tabletop Robot for Interaction with Children
- 2023
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In: 2023 IEEE/ASME International Conference on Advanced Intelligent Mechatronics, AIM 2023. - : Institute of Electrical and Electronics Engineers (IEEE). ; , s. 1232-1237
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Conference paper (peer-reviewed)abstract
- This article presents a novel emotionally expressive robot platform targeting social engagement with children. This platform was implemented in accordance with UNICEF's policy guidance on artificial intelligence (AI) for children, focusing on factors such as safety, transparency, reliability and explainability. The robot prototype is presented from a design and development perspective, outlining all utilized electromechanical components that enable its 11 degrees-of-freedom and sensing functions. Preliminary evaluation results are provided in terms of dependability and expressiveness of basic emotions, thus demonstrating the robot's potential to facilitate trustworthy and secure interactions with children.
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| 6. |
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| 7. |
- Bjermo, Helena, et al.
(author)
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Effects of n-6 PUFAs compared with SFAs on liver fat, lipoproteins, and inflammation in abdominal obesity : a randomized controlled trial
- 2012
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In: American Journal of Clinical Nutrition. - : Elsevier BV. - 0002-9165 .- 1938-3207. ; 95:5, s. 1003-1012
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Journal article (peer-reviewed)abstract
- BACKGROUND: Replacing SFAs with vegetable PUFAs has cardiometabolic benefits, but the effects on liver fat are unknown. Increased dietary n-6 PUFAs have, however, also been proposed to promote inflammation-a yet unproven theory. OBJECTIVE: We investigated the effects of PUFAs on liver fat, systemic inflammation, and metabolic disorders. DESIGN: We randomly assigned 67 abdominally obese subjects (15% had type 2 diabetes) to a 10-wk isocaloric diet high in vegetable n-6 PUFA (PUFA diet) or SFA mainly from butter (SFA diet), without altering the macronutrient intake. Liver fat was assessed by MRI and magnetic resonance proton (1H) spectroscopy (MRS). Proprotein convertase subtilisin/kexin type-9 (PCSK9, a hepatic LDL-receptor regulator), inflammation, and adipose tissue expression of inflammatory and lipogenic genes were determined. RESULTS: A total of 61 subjects completed the study. Body weight modestly increased but was not different between groups. Liver fat was lower during the PUFA diet than during the SFA diet [between-group difference in relative change from baseline; 16% (MRI; P < 0.001), 34% (MRS; P = 0.02)]. PCSK9 (P = 0.001), TNF receptor-2 (P < 0.01), and IL-1 receptor antagonist (P = 0.02) concentrations were lower during the PUFA diet, whereas insulin (P = 0.06) tended to be higher during the SFA diet. In compliant subjects (defined as change in serum linoleic acid), insulin, total/HDL-cholesterol ratio, LDL cholesterol, and triglycerides were lower during the PUFA diet than during the SFA diet (P < 0.05). Adipose tissue gene expression was unchanged. CONCLUSIONS: Compared with SFA intake, n-6 PUFAs reduce liver fat and modestly improve metabolic status, without weight loss. A high n-6 PUFA intake does not cause any signs of inflammation or oxidative stress. Downregulation of PCSK9 could be a novel mechanism behind the cholesterol-lowering effects of PUFAs.
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| 8. |
- Björklund, Emmelie, et al.
(author)
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Involvement of Fatty Acid Amide Hydrolase and Fatty Acid Binding Protein 5 in the Uptake of Anandamide by Cell Lines with Different Levels of Fatty Acid Amide Hydrolase Expression: A Pharmacological Study
- 2014
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In: PLOS ONE. - : PLoS ONE. - 1932-6203. ; 9:7, s. e103479-
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Journal article (peer-reviewed)abstract
- Background:The endocannabinoid ligand anandamide (AEA) is removed from the extracellular space by a process ofcellular uptake followed by metabolism. In many cells, such as the RBL-2H3 cell line, inhibition of FAAH activity reduces theobserved uptake, indicating that the enzyme regulates uptake by controlling the intra- : extracellular AEA concentrationgradient. However, in other FAAH-expressing cells, no such effect is seen. It is not clear, however, whether these differencesare methodological in nature or due to properties of the cells themselves. In consequence, we have reinvestigated the roleof FAAH in gating the uptake of AEA.Methodology/Principal Findings: The effects of FAAH inhibition upon AEA uptake were investigated in four cell lines: AT1rat prostate cancer, RBL-2H3 rat basophilic leukaemia, rat C6 glioma and mouse P19 embryonic carcinoma cells. SemiquantitativePCR for the cells and for a rat brain lysate confirmed the expression of FAAH. No obvious expression of atranscript with the expected molecular weight of FLAT was seen. FAAH expression differed between cells, but all four couldaccumulate AEA in a manner inhibitable by the selective FAAH inhibitor URB597. However, there was a difference in thesensitivities seen in the reduction of uptake for a given degree of FAAH inhibition produced by a reversible FAAH inhibitor,with C6 cells being more sensitive than RBL-2H3 cells, despite rather similar expression levels and activities of FAAH. Thefour cell lines all expressed FABP5, and AEA uptake was reduced in the presence of the FABP5 inhibitor SB-FI-26, suggestingthat the different sensitivities to FAAH inhibition for C6 and RBL2H3 cells is not due to differences at the level of FABP-5.Conclusions/Significance: When assayed using the same methodology, different FAAH-expressing cells display differentsensitivities of uptake to FAAH inhibition.
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| 9. |
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| 10. |
- Cederlund, Ella, et al.
(author)
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Characterization of new medium-chain alcohol dehydrogenases adds resolution to duplications of the class I/III and the sub-class I genes
- 2011
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In: Chemico-Biological Interactions. - : Elsevier Science B.V., Amsterdam.. - 0009-2797 .- 1872-7786. ; 191:03-jan
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Journal article (peer-reviewed)abstract
- Four additional variants of alcohol and aldehyde dehydrogenases have been purified and functionally characterized, and their primary structures have been determined. The results allow conclusions about the structural and evolutionary relationships within the large family of MDR alcohol dehydrogenases from characterizations of the pigeon (Columba livia) and dogfish (Scyliorhinus canicula) major liver alcohol dehydrogenases. The pigeon enzyme turns out to be of class I type and the dogfish enzyme of class III type. This result gives a third type of evidence, based on purifications and enzyme characterization in lower vertebrates, that the classical liver alcohol dehydrogenase originated by a gene duplication early in the evolution of vertebrates. It is discernable as the major liver form at about the level in-between cartilaginous and osseous fish. The results also show early divergence within the avian orders. Structures were determined by Edman degradations, making it appropriate to acknowledge the methodological contributions of Pehr Edman during the 65 years since his thesis at Karolinska Institutet, where also the present analyses were performed.
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| 11. |
- Dobsicek Trefna, Hana, 1979, et al.
(author)
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Antenna Applicator for Microwave Hyperthermia Treatment of Pediatric Brain Cancer
- 2014
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In: 8th European Conference on Antennas and Propagation, EuCAP 2014, The Hague, The Netherlands 6-11 April 2014. - 9788890701849
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Conference paper (other academic/artistic)abstract
- A novel antenna applicator for microwave hyperthermia allowing treatment of deep brain tumors is proposed. The applicator consists of up to 16 antennas placed around the head in a helmet-like set-up and operates at a frequency range of 430-1000~MHz. The self-grounded bow-tie antennas are housed in a molded plastic enclosure with the shape of a truncated cone. The inner space of the enclosure is filled with distilled water. The antennas are attached to a perimetric water bolus with a thickness of 2 cm and aligned with the head shape. The focusing ability of the applicator was investigated on a homogeneous SAM model and on a model of a 13-year old patient containing a spherical tumor of 2 cm radius. Two different tumor positions were investigated: the right frontal lobe and the central brain. The obtained SAR distributions are favorable, although a relatively high level of energy is also absorbed on the surface of the body. This heating is however not expected to cause problems as it can be cooled by blood perfusion and water bolus. Our results show that focused microwave heating in the brain is feasible and warrants further verification on phantoms.
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| 12. |
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| 13. |
- Eriksson, Hanna, et al.
(author)
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Quantitative membrane proteomics applying narrow range peptide isoelectric focusing for studies of small cell lung cancer resistance mechanisms
- 2008
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In: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 28:5C, s. 3275-3276
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Journal article (peer-reviewed)abstract
- Drug resistance is often associated with upregulation of membrane-associated drug-efflux systems, and thus global membrane proteomics methods are valuable tools in the search for novel components of drug resistance phenotypes. Herein we have compared the microsomal proteome from the lung cancer cell line H69 and its isogenic Doxorubicin-resistant subcell line H69AR. The method used includes microsome preparation, iTRAQ labeling followed by narrow range peptide IEF in an immobilized pH-gradient (IPG-IEF) and LC-MS/MS analysis. We demonstrate that the microsomal preparation and iTRAQ labeling is reproducible regarding protein content and composition. The rationale using narrow range peptide IPG-IEF separation is demonstrated by its ability to: (i) lowering the complexity of the sample by two-thirds while keeping high proteome coverage (96%), (ii) providing high separation efficiency, and (iii) allowing for peptide validation and possibly identifications of post-transcriptional modifications. After analyzing one-fifth of the IEF fractions (effective pH range of 4.0-4.5), a total of 3704 proteins were identified, among which 527 were predicted to be membrane proteins. One of the proteins found to be differentially expressed was Serca 2, a calcium pump located in the ER membrane that potentially could result in changes of apoptotic response toward Doxorubicin.
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| 14. |
- Fulton, Joel, et al.
(author)
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Heterodimers of photoreceptor-specific nuclear receptor (PNR/NR2E3) and peroxisome proliferator-activated receptor-gamma (PPAR gamma) are disrupted by retinal disease-associated mutations
- 2017
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In: Cell Death and Disease. - : Springer Science and Business Media LLC. - 2041-4889. ; 8
-
Journal article (peer-reviewed)abstract
- Photoreceptor-specific nuclear receptor (PNR/NR2E3) and Tailless homolog (TLX/NR2E1) are human orthologs of the NR2E group, a subgroup of phylogenetically related members of the nuclear receptor (NR) superfamily of transcription factors. We assessed the ability of these NRs to form heterodimers with other members of the human NRs representing all major subgroups. The TLX ligand-binding domain (LBD) did not appear to form homodimers or interact directly with any other NR tested. The PNR LBD was able to form homodimers, but also exhibited robust interactions with the LBDs of peroxisome proliferator-activated receptor-gamma (PPAR gamma)/NR1C3 and thyroid hormone receptor b (TRb) TR beta/NR1A2. The binding of PNR to PPAR. was specific for this paralog, as no interaction was observed with the LBDs of PPAR alpha/NR1C1 or PPAR delta/NR1C2. In support of these findings, PPAR. and PNR were found to be co-expressed in human retinal tissue extracts and could be co-immunoprecipitated as a native complex. Selected sequence variants in the PNR LBD associated with human retinopathies, or a mutation in the dimerization region of PPAR. LBD associated with familial partial lipodystrophy type 3, were found to disrupt PNR/PPAR gamma complex formation. Wild-type PNR, but not a PNR309G mutant, was able to repress PPAR gamma-mediated transcription in reporter assays. In summary, our results reveal novel heterodimer interactions in the NR superfamily, suggesting previously unknown functional interactions of PNR with PPAR. and TR beta that have potential importance in retinal development and disease.
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| 15. |
- Fulton, Joel, et al.
(author)
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Heterodimers of photoreceptor-specific nuclear receptor (PNR/NR2E3) and peroxisome proliferator-activated receptor-γ (PPARγ) are disrupted by retinal disease-associated mutations
- 2017
-
In: Cell Death and Disease. - : Springer Science and Business Media LLC. - 2041-4889. ; 8:3, s. 2677-2677
-
Journal article (peer-reviewed)abstract
- Photoreceptor-specific nuclear receptor (PNR/NR2E3) and Tailless homolog (TLX/NR2E1) are human orthologs of the NR2E group, a subgroup of phylogenetically related members of the nuclear receptor (NR) superfamily of transcription factors. We assessed the ability of these NRs to form heterodimers with other members of the human NRs representing all major subgroups. The TLX ligand-binding domain (LBD) did not appear to form homodimers or interact directly with any other NR tested. The PNR LBD was able to form homodimers, but also exhibited robust interactions with the LBDs of peroxisome proliferator-activated receptor-γ (PPARγ)/NR1C3 and thyroid hormone receptor b (TRb) TRβ/NR1A2. The binding of PNR to PPARγ was specific for this paralog, as no interaction was observed with the LBDs of PPARα/NR1C1 or PPARδ/NR1C2. In support of these findings, PPARγ and PNR were found to be co-expressed in human retinal tissue extracts and could be co-immunoprecipitated as a native complex. Selected sequence variants in the PNR LBD associated with human retinopathies, or a mutation in the dimerization region of PPARγ LBD associated with familial partial lipodystrophy type 3, were found to disrupt PNR/PPARγ complex formation. Wild-type PNR, but not a PNR309G mutant, was able to repress PPARγ-mediated transcription in reporter assays. In summary, our results reveal novel heterodimer interactions in the NR superfamily, suggesting previously unknown functional interactions of PNR with PPARγ and TRβ that have potential importance in retinal development and disease.
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| 16. |
- Garcia, Danilo, 1973, et al.
(author)
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IRT analyses of the Swedish Dark Triad Dirty Dozen
- 2018
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In: Heliyon. - : Elsevier BV. - 2405-8440. ; 4:3
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Journal article (peer-reviewed)abstract
- Background: The Dark Triad (i.e., Machiavellianism, narcissism, and psychopathy) can be captured quickly with 12 items using the Dark Triad Dirty Dozen (Jonason and Webster, 2010). Previous Item Response Theory (IRT) analyses of the original English Dark Triad Dirty Dozen have shown that all three subscales adequately tap into the dark domains of personality. The aim of the present study was to analyze the Swedish version of the Dark Triad Dirty Dozen using IRT.Method: 570 individuals (n(males) = 326, n(females) = 242, and 2 unreported), including university students and white-collar workers with an age range between 19 and 65 years, responded to the Swedish version of the Dark Triad Dirty Dozen (Garcia et al., 2017a, b).Results: Contrary to previous research, we found that the narcissism scale provided most information, followed by psychopathy, and finally Machiavellianism. Moreover, the psychopathy scale required a higher level of the latent trait for endorsement of its items than the narcissism and Machiavellianism scales. Overall, all items provided reasonable amounts of information and are thus effective for discriminating between individuals. The mean itemdiscriminations (alphas) were 1.92 for Machiavellianism, 2.31 for narcissism, and 1.99 for psychopathy.Conclusion: This is the first study to provide IRT analyses of the Swedish version of the Dark Triad Dirty Dozen. Our findings add to a growing literature on the Dark Triad Dirty Dozen scale in different cultures and highlight psychometric characteristics, which can be used for comparative studies. Items tapping into psychopathy showed higher thresholds for endorsement than the other two scales. Importantly, the narcissism scale seems to provide more information about a lack of narcissism, perhaps mirroring cultural conditions.
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| 17. |
- Garcia, Danilo, 1973, et al.
(author)
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IRT Analyses of the Swedish Version of the Dark Triad Dirty Dozen
- 2018
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In: 30th APS Annual Convention, San Francisco, CA, USA.
-
Conference paper (other academic/artistic)abstract
- The Dark Triad Dirty Dozen is one of the quickest ways to measure the Dark Triad. Item Response Theory analyses of the Swedish version showed that all items contributed with substantial information. However, items tapping into psychopathy showed higher thresholds for endorsement than Machiavellianism, and in particular narcissism.
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| 18. |
- Giuffrida, L., et al.
(author)
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Manipulation of laser-accelerated proton beam profiles by nanostructured and microstructured targets
- 2017
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In: Physical Review Accelerators and Beams. - 2469-9888. ; 20:8, s. 081301-
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Journal article (peer-reviewed)abstract
- Nanostructured and microstructured thin foils have been fabricated and used experimentally as targets to manipulate the spatial profile of proton bunches accelerated through the interaction with high intensity laser pulses (6 x 1019 W/cm(2)). Monolayers of polystyrene nanospheres were placed on the rear surfaces of thin plastic targets to improve the spatial homogeneity of the accelerated proton beams. Moreover, thin targets with grating structures of various configurations on their rear sides were used tomodify the proton beam divergence. Experimental results are presented, discussed, and supported by 3D particle-in-cell numerical simulations.
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| 19. |
- Giuffrida, L., et al.
(author)
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Nano and micro structured targets to modulate the spatial profile of laser driven proton beams
- 2017
-
In: Journal of Instrumentation. - 1748-0221. ; 12:3, s. article no C03040 -
-
Journal article (peer-reviewed)abstract
- Nano and micro structured thin (μ m-scale) foils were designed, fabricated and irradiated with the high intensity laser system operating at LLC (Lund Laser Centre, Sweden) in order to systematically study and improve the main proton beam parameters. Nano-spheres deposited on the front (laser irradiated) surface of a flat Mylar foil enabled a small enhancement of the maximum energy and number of the accelerated protons. Nano-spheres on the rear side allowed to modify the proton beam spatial profile. In particular, with nanospheres deposited on the rear of the target, the proton beam spatial homogeneity was clearly enhanced. Silicon nitride thin foils having micro grating structures (with different step dimensions) on the rear surface were also used as targets to influence the divergence of the proton beam and drastically change its shape through a sort of stretching effect. The target fabrication process used for the different target types is described, and representative experimental results are shown and discussed along with supporting 3D particle-in-cell simulations. © 2017 IOP Publishing Ltd and Sissa Medialab srl.
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| 20. |
- Hambäck, Peter A., et al.
(author)
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Insekter och spindlar i anlagda våtmarker : Intressanta fynd från en systematisk undersökning i Uppland och södra Halland
- 2022
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In: Entomologisk tidskrift. - 0013-886X. ; 143:1-2, s. 47-66
-
Journal article (peer-reviewed)abstract
- Wetland area has decreased dramatically compared with preindustrial times, and in manyagricultural areas almost all wetlands have been drained to gain cropland. The trend hasin recent years been reversed because society has realized the many benefits of wetlandfunctions, such as for nutrient retention and flood control. In this study we inventoried 75 wetlands in Uppland and Halland for insects and spiders with Malaise traps, pitfall traps andsuction sampling. Most included wetlands are constructed, because the main purpose was toexamine if these wetlands also can be good for arthropod diversity, but we also included somemore natural wetlands as comparison. In total, we identified more than 25,000 individualsof more than 900 species of Coleoptera, Araneae, Diptera and Heteroptera. We found onenew species for Sweden, Hilara manicata Meigen 1822, and 37 new regional records. Alarge number of species found are considered threatened or else rare. Some wetlands closeto Mälaren were particularly interesting, with three species (Hypsosinga heri (Hahn 1831),Rhaphium antennatum (Charlier 1835) and Bagous robustus Brisout de Barneville 1863)that have no records nearby during recent times. These and other species found in the studyshow that constructed wetlands can provide good habitats for arthropod biodiversity andrare species, particularly if wetland shores are grazed and trampled by cattle.
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| 21. |
- Hedlund, Joel, 1978-, et al.
(author)
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Analysis of ancient sequence motifs in the H+ -PPase family
- 2006
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In: The FEBS Journal. - : Wiley. - 1742-464X .- 1742-4658. ; 273, s. 5183-5193
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Journal article (peer-reviewed)abstract
- The unique family of membrane-bound proton-pumping inorganic pyrophosphatases, involving pyrophosphate as the alternative to ATP, was investigated by characterizing 166 members of the UniProtKB ⁄ Swiss-Prot + UniProtKB ⁄TrEMBL databases and available completed genomes, using sequence comparisons and a hidden Markov model based upon a conserved 57-residue region in the loop between transmembrane segments 5 and 6. The hidden Markov model was also used to search the approximately one million sequences recently reported from a large-scale sequencing project of organisms in the Sargasso Sea, resulting in additional 164 partial pyrophosphatase sequences. The strongly conserved 57-residue region was found to contain two nonapeptidyl sequences, mainly consisting of the four ‘very early’ proteinaceous amino acid residues Gly, Ala, Val and Asp, compatible with an ancient origin of the inorganic pyrophosphatases. The nonapeptide patterns have charged amino acid residues at positions 1, 5 and 9, are apparent binding sites for the substrate and parts of the active site, and were shown to be so specific for these enzymes that they can be used for functional assignments of unannotated genomes.
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| 22. |
- Hedlund, Joel, 1978-
(author)
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Bioinformatic protein family characterisation
- 2010
-
Doctoral thesis (other academic/artistic)abstract
- Biological research is necessary; not only to further our understanding of the processes of life, but also to combat disease, hunger and environmental damage.Bioinformatics is the science of handling biological information. It entails integrating, structuring and analysing the ever-increasing amounts of available biological data. In practise it means using computers to analyse huge amounts of very complicated data taken from a field that is only partially understood, to see the hidden trends and connections, and to draw useful conclusions.My thesis work has mainly concerned the study of protein families, which are groups of evolutionarily related proteins. I have analysed known protein families and created predictive models for them, and developed algorithms for defining new protein families. My principal techniques have been sequence alignments and hidden Markov models (HMM). To aid my work, I have written a lot of software, including MSAView, a visualiser for multiple sequence alignments (MSA).In this thesis, the protein family of inorganic pyrophosphatases (H+-PPases) is studied, as well as the two protein superfamilies BRICHOS and MDR (medium-chain dehydrogenases/reductases). The H+-PPases are tightly membrane bound, proton pumping, dimeric enzymes with ~700-residue subunits and found in bacteria, plants and eukaryotic parasites, and which use pyrophosphate as an alternative to ATP. The BRICHOS superfamily is only present in higher eukaryotes, but encompasses at least 8 protein families with a wide range of functions and disease associations, such as respiratory distress syndrome, dementia and cancer. The sequences are typically ~200 residues with even shorter functional forms. Finally, MDR, is a large and complex protein superfamily; it currently has over 16000 members, it is present in all kingdoms of life, the pairwise sequence identity is typically around 25 %, the chain lengths vary as does the oligomericity, and the members are partaking in a multitude of biological processes. The member families include the classical liver alcohol dehydrogenase (ADH), quinone reductase, leukotriene B4 dehydrogenase, and many more forms. There are at least 25 human MDR genes excluding close homologues. There are HMMs available for detecting MDR superfamily membership, but none for the individual families.For the H+-PPase family, we characterised member sequences found using an HMM of a conserved 57-residue region thought to form part of the active site. This region was found to contain two highly conserved nonapeptides, mainly consisting of the four “very early” residues Gly, Ala, Val and Asp, compatible with an ancient origin of the family. The two patterns have charged amino acid residues at positions 1, 5 and 9, are apparent binding sites for the substrate and parts of the active site, and were shown to be so specific for these enzymes that they can be used for automated annotation of new sequences.For the BRICHOS superfamily, we were able to find three previously unknown member families; group A, which may be ancestral to the ITM2 families (integral membrane protein 2); group B, which is a close relative to the gastrokine families, and group C, which appears to be a truly novel, disjoint BRICHOS family. The C-terminal region of group C has nearly identical sequences in all species ranging from fish to man and is seemingly unique to this family, indicating critical functional or structural properties.For the MDR superfamily, we characterised and built stable HMMs for 17 member families using an empiric approach. From our experiences we were able to develop an algorithm for automated HMM refinement that uses relationships in data to produce stable and reliable classifiers, and we used it to produce HMMs for 86 distinct MDR families. We have made the program freely available and it can be readily applied to other protein families. We also developed a web site (http://mdr–enzymes.org) that makes our findings directly useful also for non-bioinformaticians.In our analyses of the 86 families, we found that MDR forms with 2 Zn2+ ions in general are dehydrogenases, while MDR forms with no Zn2+ in general are reductases. Furthermore, in Bacteria, MDRs without Zn2+ are more frequent than those with Zn2+, while the opposite is true for eukaryotic MDRs, indicating that Zn2+ has been recruited into the MDR superfamily after the initial life kingdom separations.Multiple sequence alignments (MSA) play a central part in most work on protein families, and are integral to many bioinformatic methods. With the ongoing explosive increase of available sequence data, the scales of bioinformatic projects are growing, and efficient and human-friendly data visualisation becomes increasingly challenging, but is still essential for making new interpretations and discovering unexpected properties of the data.Ideally, visualisation should be comprehensive and detailed, and never distract with irrelevant information. It needs to offer natural and responsive ways of exploring the data, as well as provide consistent views in order to facilitate comparisons between datasets. I therefore developed MSAView, which is a fast, modular, configurable and extensible package for analysing and visualising MSAs and sequence features. It has a graphical user interface and a powerful command line client, and can be imported as a package into any Python program. It has a plugin architecture and a user extendable preset library. It can integrate and display data from online sources and launch external viewers for showing additional details. It also includes two new conservation measures; alignment divergences, which indicate atypical residues or deletions, and sequence conformances, which highlight sequences that differ from their siblings at crucial positions.In conclusion, this thesis details my work in analysing two protein superfamilies and one protein family using bioinformatic methods; developing an algorithm for automated generation of stable and reliable HMMs, as well as a new conservation measure, and a software platform for working with aligned sequences.
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| 23. |
- Hedlund, Joel, et al.
(author)
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BRICHOS - a superfamily of multidomain proteins with diverse functions.
- 2009
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In: BMC research notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 2, s. 180-
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Journal article (peer-reviewed)abstract
- ABSTRACT: BACKGROUND: The BRICHOS domain has been found in 8 protein families with a wide range of functions and a variety of disease associations, such as respiratory distress syndrome, dementia and cancer. The domain itself is thought to have a chaperone function, and indeed three of the families are associated with amyloid formation, but its structure and many of its functional properties are still unknown. FINDINGS: The proteins in the BRICHOS superfamily have four regions with distinct properties. We have analysed the BRICHOS proteins focusing on sequence conservation, amino acid residue properties, native disorder and secondary structure predictions. Residue conservation shows large variations between the regions, and the spread of residue conservation between different families can vary greatly within the regions. The secondary structure predictions for the BRICHOS proteins show remarkable coherence even where sequence conservation is low, and there seems to be little native disorder. CONCLUSIONS: The greatly variant rates of conservation indicates different functional constraints among the regions and among the families. We present three previously unknown BRICHOS families; group A, which may be ancestral to the ITM2 families; group B, which is a close relative to the gastrokine families, and group C, which appears to be a truly novel, disjoint BRICHOS family. The C-terminal region of group C has nearly identical sequences in all species ranging from fish to man and is seemingly unique to this family, indicating critical functional or structural properties.
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| 24. |
- Hedlund, Joel, 1978-, et al.
(author)
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Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement
- 2010
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In: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 11, s. 534-
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Journal article (peer-reviewed)abstract
- Backgroun: The Medium-chain Dehydrogenases/Reductases (MDR) form a protein superfamily whose size and complexity defeats traditional means of subclassification; it currently has over 15000 members in the databases, the pairwise sequence identity is typically around 25%, there are members from all kingdoms of life, the chain-lengths vary as does the oligomericity, and the members are partaking in a multitude of biological processes. There are profile hidden Markov models (HMMs) available for detecting MDR superfamily members, but none for determining which MDR family each protein belongs to. The current torrential influx of new sequence data enables elucidation of more and more protein families, and at an increasingly fine granularity. However, gathering good quality training data usually requires manual attention by experts and has therefore been the rate limiting step for expanding the number of available models. Result: We have developed an automated algorithm for HMM refinement that produces stable and reliable models for protein families. This algorithm uses relationships found in data to generate confident seed sets. Using this algorithm we have produced HMMs for 86 distinct MDR families and 34 of their subfamilies which can be used in automated annotation of new sequences. We find that MDR forms with 2 Zn2+ ions in general are dehydrogenases, while MDR forms with no Zn2+ in general are reductases. Furthermore, in Bacteria MDRs without Zn2+ are more frequent than those with Zn2+, while the opposite is true for eukaryotic MDRs, indicating that Zn2+ has been recruited into the MDR superfamily after the initial life kingdom separations. We have also developed a web site http://mdr-enzymes.org webcite that provides textual and numeric search against various characterised MDR family properties, as well as sequence scan functions for reliable classification of novel MDR sequences. Conclusion: Our method of refinement can be readily applied to create stable and reliable HMMs for both MDR and other protein families, and to confidently subdivide large and complex protein superfamilies. HMMs created using this algorithm correspond to evolutionary entities, making resolution of overlapping models straightforward. The implementation and support scripts for running the algorithm on computer clusters are available as open source software, and the database files underlying the web site are freely downloadable. The web site also makes our findings directly useful also for non-bioinformaticians.
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| 25. |
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