Sök i SwePub databas

  Utökad sökning

Träfflista för sökning "hsv:(NATURVETENSKAP) hsv:(Biologiska vetenskaper) hsv:(Biokemi och molekylärbiologi) "

Sökning: hsv:(NATURVETENSKAP) hsv:(Biologiska vetenskaper) hsv:(Biokemi och molekylärbiologi)

Sortera/gruppera träfflistan
  • Larsson, Daniel, 1981- (författare)
  • Exploring the Molecular Dynamics of Proteins and Viruses
  • 2012
  • Doktorsavhandling (övrigt vetenskapligt)abstract
    • Knowledge about structure and dynamics of the important biological macromolecules — proteins, nucleic acids, lipids and sugars — helps to understand their function. Atomic-resolution structures of macromolecules are routinely captured with X-ray crystallography and other techniques. In this thesis, simulations are used to explore the dynamics of the molecules beyond the static structures.Viruses are machines constructed from macromolecules. Crystal structures of them reveal little to no information about their genomes. In simulations of empty capsids, we observed a correlation between the spatial distribution of chloride ions in the solution and the position of RNA in crystals of satellite tobacco necrosis virus (STNV) and satellite tobacco mosaic virus (STMV). In this manner, structural features of the non-symmetric RNA could also be inferred.The capsid of STNV binds calcium ions on the icosahedral symmetry axes. The release of these ions controls the activation of the virus particle upon infection. Our simulations reproduced the swelling of the capsid upon removal of the ions and we quantified the water permeability of the capsid. The structure and dynamics of the expanded capsid suggest that the disassembly is initiated at the 3-fold symmetry axis.Several experimental methods require biomolecular samples to be injected into vacuum, such as mass-spectrometry and diffractive imaging of single particles. It is therefore important to understand how proteins and molecule-complexes respond to being aerosolized. In simulations we mimicked the dehydration process upon going from solution into the gas phase. We find that two important factors for structural stability of proteins are the temperature and the level of residual hydration. The simulations support experimental claims that membrane proteins can be protected by a lipid micelle and that a non-membrane protein could be stabilized in a reverse micelle in the gas phase. A water-layer around virus particles would impede the signal in diffractive experiments, but our calculations estimate that it should be possible to determine the orientation of the particle in individual images, which is a prerequisite for three-dimensional reconstruction.
  • Xu, Bo, 1980- (författare)
  • Evolutionary and Pharmacological Studies of NPY and QRFP Receptors
  • 2014
  • Doktorsavhandling (övrigt vetenskapligt)abstract
    • The neuropeptide Y (NPY) system consists of 3-4 peptides and 4-7 receptors in vertebrates. It has powerful effects on appetite regulation and is involved in many other biological processes including blood pressure regulation, bone formation and anxiety. This thesis describes studies of the evolution of the NPY system by comparison of several vertebrate species and structural studies of the human Y2 receptor, which reduces appetite, to identify amino acid residues involved in peptide-receptor interactions.The NPY system was studied in zebrafish (Danio rerio), western clawed frog (Xenopus tropicalis), and sea lamprey (Petromyzon marinus). The receptors were cloned and functionally expressed and their pharmacological profiles were determined using the native peptides in either binding studies or a signal transduction assay. Some peptide-receptor preferences were observed, indicating functional specialization.A receptor family closely related to the NPY receptors, called the QRFP receptors, was investigated. A QRFP receptor was cloned from amphioxus, Branchistoma floridae, showing that the receptor arose before the origin of the vertebrates. Evolutionary studies demonstrated that the ancestral vertebrate had as many as four QRFP receptors, only one of which remains in mammals today. This correlates with the NPY receptor family, located in the same chromosomal regions, which had seven members in the ancestral vertebrate but only 4-5 in living mammals. Some vertebrates have considerably more complex NPY and QRFP receptor systems than humans and other mammals.Two studies investigated interactions of NPY-family peptides with the human Y2 receptor. Candidate residues, selected based on structural modeling and docking, were mutated to disrupt possible interactions with peptide ligands. The modified receptors were expressed in cultured cells and investigated by measuring binding and functional responses. Several receptor residues were found to influence peptide-receptor interactions, some of which are involved in maintaining receptor structure. In a pilot study, the kinetics of peptide-receptor interaction were found to be very slow, of the order several hours.In conclusion, this thesis clarifies evolutionary relationships for the complex NPY and QRFP peptide-receptor systems and improves the structural models of the human NPY-family receptors, especially Y2. These results will hopefully facilitate drug design for targeting of NPY-family receptors.
  • Wedin, Mats, et al. (författare)
  • Slippery when wet : phylogeny and character evolution in the gelatinous cyanobacterial lichens (Peltigerales, Ascomycetes)
  • 2009
  • Ingår i: Molecular Phylogenetics and Evolution. - San Diego : Academic Press. - 1055-7903 .- 1095-9513. ; 53:3, s. 862-871
  • Tidskriftsartikel (refereegranskat)abstract
    • Many lichen fungi form symbioses with filamentous Nostoc cyanobacteria, which cause the lichen to swell and become extremely gelatinous when moist. Within the Lecanoromycetes, such gelatinous lichens are today mainly classified in the Collemataceae (Peltigerales, Ascomycota). We performed Bayesian MCMC, maximum likelihood, and maximum parsimony analyses of three independent markers (mtSSU rDNA, nuLSU rDNA, and RPB1), to improve our understanding of the phylogeny and classification in the Peltigerales, as well as the evolution of morphological characters that have been used for classification purposes in this group. The Collemataceae and the non-gelatinous Parmariaceae are paraphyletic but can be re-circumscribed as monophyletic if Leciophysma, Physma, Ramalodium and Staurolemma are transferred to the Parmariaceae. The gelatinous taxa transferred to the Parmariaceae deviate from other Collemataceae in having simple ascospores, and several also have a ring-shaped exciple as in other Pannariaceae, rather than the disc-shaped exciple found in the typical Collemataceae. Both Collema and Leptogium are non-monophyletic. The re-circumscribed Collemataceae shares a distinct ascus type with the sister group Placynthiaceae and the Coccocarpiaceae, whereas Parmariaceae includes a variety of structures. All Parmariaceae have one-celled ascospores, whereas all Collemataceae have two- or multi-celled spores. Reconstructions of the number of character state transformations in exciple structure, thallus gelatinosity, and ascus apex structure indicate that the number of transformations is distinctly higher than the minimum possible. Most state transformations in the exciple took place from a ring-shaped to a disc-shaped exciple. Depending on the reconstruction method, most or all transformations in thallus structure took place from a non-gelatinous to a gelatinous thallus. Gains and losses of internal structures in the ascus apex account for all or a vast majority of the number of transformations in the ascus, whereas direct transformations between asci with internal structures appear to have been rare.
  • Klevebring, Daniel, 1981- (författare)
  • On Transcriptome Sequencing
  • 2009
  • Doktorsavhandling (övrigt vetenskapligt)abstract
    • This thesis is about the use of massive DNA sequencing to investigate the transcriptome. During recent decades, several studies have made it clear that the transcriptome comprises a more complex set of biochemical machinery than was previously believed. The majority of the genome can be expressed as transcripts; and overlapping and antisense transcription is widespread. New technologies for the interroga- tion of nucleic acids have made it possible to investigate such cellular phenomena in much greater detail than ever before. For each application, special requirements need to be met. The work presented in this thesis focuses on the transcrip- tome and the development of technology for its analysis. In paper I, we report our development of an automated approach for sample preparation. The procedure was benchmarked against a publicly available reference data set, and we note that our approach outperformed similar manual procedures in terms of reproducibility. In the work reported in papers II-IV, we used different massive sequencing technologies to investigate the transcriptome. In paper II we describe a concatemerization approach that increased throughput by 65% using 454 sequencing,and we identify classes of transcripts not previously described in Populus. Papers III and IV both report studies based on SOLiD sequencing. In the former, we investigated transcripts and proteins for 13% of the human gene and detected a massive overlap for the upper 50% transcriptional levels. In the work described in paper IV, we investigated transcription in non-genic regions of the genome and detected expression from a high number of previ- ously unknown loci.
  • Boija, Ann, et al. (författare)
  • CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II
  • 2017
  • Ingår i: Molecular Cell. - 1097-2765 .- 1097-4164. ; 68:3, s. 491-503.e5
  • Tidskriftsartikel (refereegranskat)abstract
    • Transcription activation involves RNA polymerase II (Pol II) recruitment and release from the promoter into productive elongation, but how specific chromatin regulators control these steps is unclear. Here, we identify a novel activity of the histone acetyltransferase p300/CREB-binding protein (CBP) in regulating promoter-proximal paused Pol II. We find that Drosophila CBP inhibition results in "dribbling" of Pol II from the pause site to positions further downstream but impedes transcription through the +1 nucleosome genome-wide. Promoters strongly occupied by CBP and GAGA factor have high levels of paused Pol II, a unique chromatin signature, and are highly expressed regardless of cell type. Interestingly, CBP activity is rate limiting for Pol II recruitment to these highly paused promoters through an interaction with TFIIB but for transit into elongation by histone acetylation at other genes. Thus, CBP directly stimulates both Pol II recruitment and the ability to traverse the first nucleosome, thereby promoting transcription of most genes.
  • Danielsson, Frida, et al. (författare)
  • Majority of differentially expressed genes are down-regulated during malignant transformation in a four-stage model
  • 2013
  • Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - 0027-8424 .- 1091-6490. ; 110:17, s. 6853-6858
  • Tidskriftsartikel (refereegranskat)abstract
    • The transformation of normal cells to malignant, metastatic tumor cells is a multistep process caused by the sequential acquirement of genetic changes. To identify these changes, we compared the transcriptomes and levels and distribution of proteins in a four-stage cell model of isogenically matched normal, immortalized, transformed, and metastatic human cells, using deep transcriptome sequencing and immunofluorescence microscopy. The data show that similar to 6% (n = 1,357) of the human protein-coding genes are differentially expressed across the stages in the model. Interestingly, the majority of these genes are down-regulated, linking malignant transformation to dedifferentiation. The up-regulated genes are mainly components that control cellular proliferation, whereas the down-regulated genes consist of proteins exposed on or secreted from the cell surface. As many of the identified gene products control basic cellular functions that are defective in cancers, the data provide candidates for follow-up studies to investigate their functional roles in tumor formation. When we further compared the expression levels of four of the identified proteins in clinical cancer cohorts, similar differences were observed between benign and cancer cells, as in the cell model. This shows that this comprehensive demonstration of the molecular changes underlying malignant transformation is a relevant model to study the process of tumor formation.
  • Devine, Ellenor, 1977- (författare)
  • Cyanobacterial Hydrogen Metabolism : Regulation and Maturation of Hydrogenases
  • 2011
  • Doktorsavhandling (övrigt vetenskapligt)abstract
    • In times with elevated CO2 levels and global warming there is a need of finding alternatives to carbon based energy carriers. One such environmental friendly solution could be H2 produced by living organisms. Cyanobacteria are good candidates since they can produce H2 from sunlight and water through the combination of photosynthesis and H2 producing enzymes i.e. nitrogenases and/or [NiFe]-hydrogenases. This thesis investigates the maturation and transcriptional regulation of [NiFe]-hydrogenases in cyanobacteria, with a special focus on hydrogenase specific proteases. The core of all hydrogenases consists of the small and large subunit. The large subunit in which the catalytic site is located goes through an extenstive maturation process which ends with a proteolytic cleavage performed by a hydrogenase specific protease (HupW/HoxW). This thesis shows that within the maturation process of hydrogenases, the proteolytic cleavage is probably the only step that is specific with respect to different types of hydrogenases i.e. one type of protease cleaves only one type of hydrogenase. Further in-silico analysis revealed that these proteases and the hydrogenases might have co-evolved since ancient time and that the specificity observed could be the result of a conserved amino acid sequence which differs between the two types of proteases (HupW/HoxW). A number of different transcription factors were revealed and shown to interact with the promoter regions of several of the genes encoding maturation proteins. The results indicate that the hydrogenase specific proteases are regulated on a transcriptional level in a similar manner as the hydrogenases they cleave. This thesis contributes with knowledge concerning transcriptional regulation and protein regulation of hydrogenases which will be useful for designing genetically engineered cyanobacteria with an improved and adjustable H2 production.
  • Diamanti, Riccardo, et al. (författare)
  • Comparative structural analysis provides new insights into the function of R2-like ligand-binding oxidase
  • 2022
  • Ingår i: FEBS Letters. - : John Wiley & Sons. - 0014-5793 .- 1873-3468. ; 596:12, s. 1600-1610
  • Tidskriftsartikel (refereegranskat)abstract
    • R2-like ligand-binding oxidase (R2lox) is a ferritin-like protein that harbours a heterodinuclear manganese–iron active site. Although R2lox function is yet to be established, the enzyme binds a fatty acid ligand coordinating the metal centre and catalyses the formation of a tyrosine–valine ether cross-link in the protein scaffold upon O2 activation. Here, we characterized the ligands copurified with R2lox by mass spectrometry-based metabolomics. Moreover, we present the crystal structures of two new homologs of R2lox, from Saccharopolyspora erythraea and Sulfolobus acidocaldarius, at 1.38 Å and 2.26 Å resolution, respectively, providing the highest resolution structure for R2lox, as well as new insights into putative mechanisms regulating the function of the enzyme.
  • Ekblom, Robert, et al. (författare)
  • Major histocompatibility complex variation and mate choice in a lekking bird, the great snipe (Gallinago media)
  • 2004
  • Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 13:12, s. 3821-3828
  • Tidskriftsartikel (refereegranskat)abstract
    • Genes of the major histocompatibility complex (MHC) play a major part in the activation of the vertebrate immune system. In addition, they also appear to function as cues for mate choice. In mammals especially, several kinds of MHC-dependent mate choice have been hypothesized and observed. These include choice of mates that share no or few alleles with the choosing individual, choice of mates with alleles that differ as much as possible from the choosing individual, choice of heterozygous mates, choice of certain genotypes and choice of rare alleles. We investigated these different aspects of mate choice in relation to MHC in a lekking bird species, the great snipe (Gallinago media). We found no evidence for MHC disassortative mating, no preference for males with many MHC alleles and no preference for rare alleles. However, we did find that some allelic lineages were more often found in males with mating success than in males without mating success. Females do not seem to use themselves as references for the MHC-dependent mate choice, rather they seem to prefer males with certain allele types. We speculate that these alleles may be linked to resistance to common parasites.
  • Farnelid, Hanna, et al. (författare)
  • Nitrogenase Gene Amplicons from Global Marine Surface Waters Are Dominated by Genes of Non-Cyanobacteria
  • 2011
  • Ingår i: PLOS ONE. - 1932-6203. ; 6:4, s. e19223-
  • Tidskriftsartikel (refereegranskat)abstract
    • Cyanobacteria are thought to be the main N-2-fixing organisms (diazotrophs) in marine pelagic waters, but recent molecular analyses indicate that non-cyanobacterial diazotrophs are also present and active. Existing data are, however, restricted geographically and by limited sequencing depths. Our analysis of 79,090 nitrogenase (nifH) PCR amplicons encoding 7,468 unique proteins from surface samples (ten DNA samples and two RNA samples) collected at ten marine locations worldwide provides the first in-depth survey of a functional bacterial gene and yield insights into the composition and diversity of the nifH gene pool in marine waters. Great divergence in nifH composition was observed between sites. Cyanobacteria-like genes were most frequent among amplicons from the warmest waters, but overall the data set was dominated by nifH sequences most closely related to non-cyanobacteria. Clusters related to Alpha-, Beta-, Gamma-, and Delta-Proteobacteria were most common and showed distinct geographic distributions. Sequences related to anaerobic bacteria (nifH Cluster III) were generally rare, but preponderant in cold waters, especially in the Arctic. Although the two transcript samples were dominated by unicellular cyanobacteria, 42% of the identified non-cyanobacterial nifH clusters from the corresponding DNA samples were also detected in cDNA. The study indicates that non-cyanobacteria account for a substantial part of the nifH gene pool in marine surface waters and that these genes are at least occasionally expressed. The contribution of non-cyanobacterial diazotrophs to the global N-2 fixation budget cannot be inferred from sequence data alone, but the prevalence of non-cyanobacterial nifH genes and transcripts suggest that these bacteria are ecologically significant.
Skapa referenser, mejla, bekava och länka
Typ av publikation
tidskriftsartikel (4965)
doktorsavhandling (852)
annan publikation (412)
forskningsöversikt (304)
bokkapitel (148)
konferensbidrag (120)
visa fler...
licentiatavhandling (39)
rapport (9)
patent (8)
bok (4)
recension (4)
samlingsverk (redaktörskap) (1)
konstnärligt arbete (1)
proceedings (redaktörskap) (1)
visa färre...
Typ av innehåll
refereegranskat (5206)
övrigt vetenskapligt (1629)
populärvet., debatt m.m. (31)
Uhlén, Mathias (111)
Lammi, Mikko, 1961- (87)
Langel, Ülo (86)
Mannervik, Bengt (82)
Lindblad, Peter (69)
Widersten, Mikael (69)
visa fler...
Los, Marek Jan (60)
von Heijne, Gunnar (54)
Nilsson, Peter (49)
Ehrenberg, Måns (46)
Åqvist, Johan (46)
Mamedov, Fikret (45)
Brodelius, Peter (45)
Helminen, Heikki (42)
Löfblom, John (41)
Styring, Stenbjörn (40)
Kamerlin, Shina C. L ... (40)
Lundberg, Emma (39)
Sanyal, Suparna (38)
Glaser, Elzbieta (38)
El-Seedi, Hesham (37)
Lundeberg, Joakim (37)
Lindberg, Pia (37)
Högbom, Martin (36)
Ståhl, Stefan (36)
Bulone, Vincent (36)
Schwenk, Jochen M. (35)
Tammi, Markku (35)
Månsson, Alf (34)
Gräslund, Astrid (33)
Tolmachev, Vladimir (33)
Funk, Christiane (33)
Stenmark, Pål (33)
Sjöberg, Britt-Marie (33)
Ivarsson, Ylva (32)
Lindahl, Erik (31)
Nilsson, Mats (30)
Hellman, Lars (30)
Nilsson Ekdahl, Kris ... (30)
Hober, Sophia (30)
Pontén, Fredrik (29)
Eriksson Karlström, ... (28)
Danielson, U. Helena (28)
Hofer, Anders (28)
Berglund, Per (27)
Helleday, Thomas (27)
Brumer, Harry (27)
Persson, Bengt L. (27)
Ott, Martin (27)
Berndt, Kurt D (27)
visa färre...
Uppsala universitet (2377)
Stockholms universitet (1359)
Umeå universitet (1293)
Kungliga Tekniska Högskolan (1212)
Karolinska Institutet (477)
Linköpings universitet (314)
visa fler...
Linnéuniversitetet (306)
Örebro universitet (212)
Södertörns högskola (209)
Lunds universitet (172)
Sveriges Lantbruksuniversitet (110)
Högskolan i Skövde (69)
Göteborgs universitet (64)
Chalmers tekniska högskola (41)
Jönköping University (30)
Malmö universitet (30)
Karlstads universitet (30)
RISE (29)
Luleå tekniska universitet (24)
Högskolan i Borås (12)
Högskolan i Halmstad (10)
Mälardalens universitet (9)
Mittuniversitetet (9)
Högskolan Kristianstad (8)
Naturhistoriska riksmuseet (7)
Högskolan Dalarna (6)
Gymnastik- och idrottshögskolan (5)
Högskolan Väst (1)
Högskolan i Gävle (1)
VTI - Statens väg- och transportforskningsinstitut (1)
visa färre...
Engelska (6846)
Svenska (13)
Ryska (4)
Spanska (1)
Finska (1)
Kinesiska (1)
visa fler...
Koreanska (1)
visa färre...
Forskningsämne (UKÄ/SCB)
Naturvetenskap (6866)
Medicin och hälsovetenskap (913)
Teknik (159)
Lantbruksvetenskap (83)
Samhällsvetenskap (13)
Humaniora (4)


Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.

pil uppåt Stäng

Kopiera och spara länken för att återkomma till aktuell vy