Change search
Refine search result
1 - 29 of 29
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1.
    Ahmadian, Afshin
    et al.
    KTH, Superseded Departments, Biotechnology.
    Gharizadeh, B.
    Gustafsson, A. C.
    Sterky, Fredrik
    KTH, Superseded Departments, Biotechnology.
    Nyrén, Pål
    KTH, Superseded Departments, Biochemistry and Biotechnology.
    Uhlén, Mathias
    KTH, Superseded Departments, Biotechnology.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Single-nucleotide polymorphism analysis by pyrosequencing2000In: Analytical Biochemistry, ISSN 0003-2697, E-ISSN 1096-0309, Vol. 280, no 1, p. 103-110Article in journal (Refereed)
    Abstract [en]

    There is a growing demand for high-throughput methods for analysis of single-nucleotide polymorphic (SNP) positions. Here, we have evaluated a novel sequencing approach, pyrosequencing, for such purposes. Pyrosequencing is a sequencing-by-synthesis method in which a cascade of enzymatic reactions yields detectable light, which is proportional to incorporated nucleotides. One feature of typing SNPs with pyrosequencing is that each allelic variant will give a unique sequence compared to the two other variants. These variants can easily be distinguished by a pattern recognition software. The software displays the allelic: alternatives and allows for direct comparison with the pyrosequencing raw data. For optimal determination of SNPs, various protocols of nucleotide dispensing order were investigated. Here, we demonstrate that typing of SNPs can efficiently be performed by pyrosequencing using an automated system for parallel analysis of 96 samples in approximately 5 min, suitable for large-scale screening and typing of SNPs.

  • 2.
    Andersson, Anders
    et al.
    KTH, Superseded Departments, Biotechnology.
    Keskitalo, J.
    Sjödin, A.
    Bhalerao, Rupali
    KTH, Superseded Departments, Biotechnology.
    Sterky, Fredrik
    KTH, Superseded Departments, Biotechnology.
    Wissel, K.
    Tandre, K.
    Aspeborg, Henrik
    KTH, Superseded Departments, Biotechnology.
    Moyle, R.
    Ohmiya, Y.
    Brunner, A.
    Gustafsson, P.
    Karlsson, J.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Nilsson, O.
    Sandberg, G.
    Strauss, S.
    Sundberg, B.
    Uhlén, Mathias
    KTH, Superseded Departments, Biotechnology.
    Jansson, S.
    Nilsson, Peter
    KTH, Superseded Departments, Biotechnology.
    A transcriptional timetable of autumn senescence2004In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 5, no 4, p. R24-Article in journal (Refereed)
    Abstract [en]

    Background: We have developed genomic tools to allow the genus Populus ( aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag ( EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results: On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree ( Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions: We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.

  • 3.
    Aspeborg, Henrik
    et al.
    KTH, School of Biotechnology (BIO).
    Schrader, J.
    Coutinho, P. M.
    Stam, M.
    Kallas, A.
    Djerbi, S.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Denman, S.
    Amini, B.
    Sterky, Fredrik
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Master, E.
    Sandberg, G.
    Mellerowicz, E.
    Sundberg, B.
    Henrissat, B.
    Teeri, Tuula T.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Carbohydrate-active enzymes involved in the secondary cell wall biogenesis in hybrid aspen2005In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 137, no 3, p. 983-997Article in journal (Refereed)
    Abstract [en]

    Wood formation is a fundamental biological process with significant economic interest. While lignin biosynthesis is currently relatively well understood, the pathways leading to the synthesis of the key structural carbohydrates in wood fibers remain obscure. We have used a functional genomics approach to identify enzymes involved in carbohydrate biosynthesis and remodeling during xylem development in the hybrid aspen Populus tremula x tremuloides. Microarrays containing cDNA clones from different tissue-specific libraries were hybridized with probes obtained from narrow tissue sections prepared by cryosectioning of the developing xylem. Bioinformatic analyses using the sensitive tools developed for carbohydrate-active enzymes allowed the identification of 25 xylem-specific glycosyltransferases belonging to the Carbohydrate-Active EnZYme families GT2, GT8, GT14, GT31, GT43, GT47, and GT61 and nine glycosidases (or transglycosidases) belonging to the Carbohydrate-Active EnZYme families GH9, GH10, GH16, GH17, GH19, GH28, GH35, and GH51. While no genes encoding either polysaccharide lyases or carbohydrate esterases were found among the secondary wall-specific genes, one putative O-acetyltransferase was identified. These wood-specific enzyme genes constitute a valuable resource for future development of engineered fibers with improved performance in different applications.

  • 4. Bhalerao, R.
    et al.
    Keskitalo, J.
    Sterky, Fredrik
    KTH, Superseded Departments, Biotechnology.
    Erlandsson, R.
    Bjorkbacka, H.
    Birve, S. J.
    Karlsson, J.
    Gardestrom, P.
    Gustafsson, P.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Jansson, S.
    Gene expression in autumn leaves2003In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 131, no 2, p. 430-442Article in journal (Refereed)
    Abstract [en]

    Two cDNA libraries were prepared, one from leaves of a field-grown aspen (Populus tremula) tree, harvested just before any visible sign of leaf senescence in the autumn, and one from young but fully expanded leaves of greenhouse-grown aspen (Populus tremula X tremuloides). Expressed sequence tags (ESTs; 5,128 and 4,841, respectively) were obtained from the two libraries. A semiautomatic method of annotation and functional classification of the ESTs, according to a modified Munich Institute of Protein Sequences classification scheme, was developed, utilizing information from three different databases. The patterns of gene expression in the two libraries were strikingly different. In the autumn leaf library, ESTs encoding metallothionein, early light-inducible proteins, and cysteine proteases were most abundant. Clones encoding other proteases and proteins involved in respiration and breakdown of lipids and pigments, as well as stress-related genes, were also well represented. We identified homologs to many known senescence-associated genes, as well as seven different genes encoding cysteine proteases, two encoding aspartic proteases, five encoding metallothioneins, and 35 additional genes that were up-regulated in autumn leaves. We also indirectly estimated the rate of plastid protein synthesis in the autumn leaves to be less that 10% of that in young leaves.

  • 5.
    Djerbi, Soraya
    et al.
    KTH, School of Biotechnology (BIO).
    Lindskog, Mats
    KTH, School of Biotechnology (BIO).
    Arvestad, Lars
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis and Computer Science, NADA.
    Sterky, Fredrik
    KTH, School of Biotechnology (BIO).
    Teeri, Tuula
    KTH, School of Biotechnology (BIO).
    The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes2005In: Planta, ISSN 0032-0935, E-ISSN 1432-2048, Vol. 221, no 5, p. 739-746Article in journal (Refereed)
    Abstract [en]

    The genome sequence of Populus trichocarpa was screened for genes encoding cellulose synthases by using full-length cDNA sequences and ESTs previously identified in the tissue specific cDNA libraries of other poplars. The data obtained revealed 18 distinct CesA gene sequences in P. trichocarpa. The identified genes were grouped in seven gene pairs, one group of three sequences and one single gene. Evidence from gene expression studies of hybrid aspen suggests that both copies of at least one pair, CesA3-1 and CesA3-2, are actively transcribed. No sequences corresponding to the gene pair, CesA6-1 and CesA6-2, were found in Arabidopsis or hybrid aspen, while one homologous gene has been identified in the rice genome and an active transcript in Populus tremuloides. A phylogenetic analysis suggests that the CesA genes previously associated with secondary cell wall synthesis originate from a single ancestor gene and group in three distinct subgroups. The newly identified copies of CesA genes in P. trichocarpa give rise to a number of new questions concerning the mechanism of cellulose synthesis in trees.

  • 6. Dujon, B
    et al.
    Albermann, K
    Aldea, M
    Alexandraki, D
    Ansorge, W
    Arino, J
    Benes, V
    Bohn, C
    BolotinFukuhara, M
    Bordonne, R
    Boyer, J
    Camasses, A
    Casamayor, A
    Casas, C
    Cheret, G
    Cziepluch, C
    DaignanFornier, B
    Dang, V
    deHaan, M
    Delius, H
    Durand, P
    Fairhead, C
    Feldmann, H
    Gaillon, L
    Galisson, F
    Gamo, J
    Gancedo, C
    Goffeau, A
    Goulding, E
    Grivell, A
    Habbig, B
    Hand, J
    Hani, J
    Hattenhorst, U
    Hebling, U
    Hernando, Y
    Herrero, E
    Heumann, K
    Hiesel, R
    Hilger, F
    Hofmann, B
    Hollenberg, P
    Hughes, B
    Jauniaux, C
    Kalogeropoulos, A
    Katsoulou, C
    Kordes, E
    Lafuente, J
    Landt, O
    Louis, J
    Maarse, C
    Madania, A
    Mannhaupt, G
    Marck, C
    Martin, P
    Mewes, W
    Michaux, G
    Paces, V
    ParleMcDermott, G
    Pearson, M
    Perrin, A
    Pettersson, B
    Poch, O
    Pohl, M
    Poirey, R
    Portetelle, D
    Pujol, A
    Purnelle, B
    Rad, R
    Rechmann, S
    Schwager, C
    Schweizer, M
    Sor, F
    Sterky, Fredrik
    KTH, Superseded Departments, Biotechnology.
    Tarassov, A
    Teodoru, C
    Tettelin, H
    Thierry, A
    Tobiasch, E
    Tzermia, M
    Uhlen, Mathias
    KTH, Superseded Departments, Biotechnology.
    Unseld, M
    Valens, M
    Vandenbol, M
    Vetter, I
    Vicek, C
    Voet, M
    Volckaert, G
    Voss, H
    Wambutt, R
    Wedler, H
    Wiemann, S
    Winsor, B
    Wolfe, H
    Zollner, A
    Zumstein, E
    Kleine, K
    The nucleotide sequence of Saccharomyces cerevisiae chromosome XV1997In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 387, no 6632, p. 98-102Article in journal (Refereed)
    Abstract [en]

    Chromosome XV was one of the last two chromosomes of Saccharomyces cerevisiae to be discovered(1). It is the third-largest yeast chromosome after chromosomes XII and IV, and is very similar in size to chromosome VII. It alone represents 9% of the yeast genome (8% if ribosomal DNA is included). When systematic sequencing of chromosome XV was started, 93 genes or markers were identified, and most of them were mapped(2). However, very little else was known about chromosome XV which, in contrast to shorter chromosomes, had not been the object of comprehensive genetic or molecular analysis. It was therefore decided to start sequencing chromosome XV only in the third phase of the European Yeast Genome Sequencing Programme, after experience was gained on chromosomes III, XI and II (refs 3-5). The sequence of chromosome XV has been determined from a set of partly overlapping cosmid clones derived from a unique yeast strain, and physically mapped at 3.3-kilobase resolution before sequencing. As well as numerous new open reading frames (ORFs) and genes encoding tRNA or small RNA molecules, the sequence of 1,091,283 base pairs confirms the high proportion of orphan genes and reveals a number of ancestral and successive duplications with other yeast chromosomes.

  • 7. Finkelstein, D.
    et al.
    Ewing, R.
    Gollub, J.
    Sterky, Fredrik
    KTH, Superseded Departments, Biotechnology.
    Cherry, J. M.
    Somerville, S.
    Microarray data quality analysis: lessons from the AFGC project2002In: Plant Molecular Biology, ISSN 0167-4412, E-ISSN 1573-5028, Vol. 48, no 02-jan, p. 119-131Article in journal (Refereed)
    Abstract [en]

    Genome-wide expression profiling with DNA microarrays has and will provide a great deal of data to the plant scientific community. However, reliability concerns have required the development data quality tests for common systematic biases. Fortunately, most large-scale systematic biases are detectable and some are correctable by normalization. Technical replication experiments and statistical surveys indicate that these biases vary widely in severity and appearance. As a result, no single normalization or correction method currently available is able to address all the issues. However, careful sequence selection, array design, experimental design and experimental annotation can substantially improve the quality and biological of microarray data. In this review, we discuss these issues with reference to examples from the Arabidopsis Functional Genomics Consortium (AFGC) microarray project.

  • 8. Gray-Mitsumune, Madoka
    et al.
    Mellerowicz, Ewa J.
    Abe, Hisashi
    Schrader, Jarmo
    Winzell, Anders
    KTH, Superseded Departments, Biotechnology.
    Sterky, Fredrik
    KTH, Superseded Departments, Biotechnology.
    Blomqvist, Kristina
    KTH, Superseded Departments, Biotechnology.
    McQueen-Mason, Simon
    Teeri, Tuula T.
    KTH, Superseded Departments, Biotechnology.
    Sundberg, Björn
    Expansins abundant in secondary xylem belong to subgroup a of the alpha-expansin gene family (1 w )2004In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 135, no 3, p. 1552-1564Article in journal (Refereed)
    Abstract [en]

    Differentiation of xylem cells in dicotyledonous plants involves expansion of the radial primary cell walls and intrusive tip growth of cambial derivative cells prior to the deposition of a thick secondary wall essential for xylem function. Expansins are cell wall-residing proteins that have an ability to plasticize the cellulose-hemicellulose network of primary walls. We found expansin activity in proteins extracted from the cambial region of mature stems in a model tree species hybrid aspen (Populus tremula X Populus tremuloides Michx). We identified three a-expansin genes (PttEXP1, PttEXP2, and PttEXP8) and one beta-expansin gene (PttEXPB1) in a cambial region expressed sequence tag library, among which PttEXP1 was most abundantly represented. Northern-blot analyses in aspen vegetative organs and tissues showed that PttEXP1 was specifically expressed in mature stems exhibiting secondary growth, where it was present in the cambium and in the radial expansion zone. By contrast, PttEXP2 was mostly expressed in developing leaves. In situ reverse transcription-PCR provided evidence for accumulation of mRNA of PttEXP1 along with ribosomal rRNA at the tips of intrusively growing xylem fibers, suggesting that PttEXP1 protein has a role in intrusive tip growth. An examination of tension wood and leaf cDNA libraries identified another expansin, PttEXP5, very similar to PttEXP1, as the major expansin in developing tension wood, while PttEXP3 was the major expansin expressed in developing leaves. Comparative analysis of expansins expressed in woody stems in aspen, Arabidopsis, and pine showed that the most abundantly expressed expansins share sequence similarities, belonging to the subfamily A of alpha-expansins and having two conserved motifs at the beginning and end of the mature protein, RIPVG and KNFRV, respectively. This conservation suggests that these genes may share a specialized, not yet identified function.

  • 9. Johansson, H.
    et al.
    Sterky, Fredrik
    KTH, Superseded Departments, Biotechnology.
    Amini, B.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Kleczkowski, L. A.
    Molecular cloning and characterization of a cDNA encoding poplar UDP-glucose dehydrogenase, a key gene of hemicellulose/pectin formation2002In: Biochimica et Biophysica Acta, Gene Structure and Expression, ISSN 0167-4781, E-ISSN 1879-2634, Vol. 1576, no 02-jan, p. 53-58Article in journal (Refereed)
    Abstract [en]

    Plant UDP-glucose dehydrogenase (UGDH) is an important enzyme in the formation of hemicellulose and pectin, the components of newly formed cell walls. A cDNA clone (Ugdh) corresponding to UGDH was isolated from a cDNA library prepared from cambial zone of poplar (Populus tremula x tremuloides). Within the 1824-nucleotide (nt)-long clone, an open reading frame encoded a protein of 481 amino acids (aa), with a calculated molecular weight of 53.1 kDa. The derived aa sequence showed 90% and 63% identity with UGDHs from soybean and bovine liver, respectively, and had highly conserved aa motifs believed to be of importance for nt binding and catalytic efficiency. In poplar, the Ugdh corresponds to one or two genes, as found by genomic Southern analysis. The gene was expressed predominantly in differentiating xylem and young leaves, with little expression in the phloem zone of the stem. The expression pattern matched that of UGDH protein, as found by immunoblotting. In leaves, the Ugdh expression was upregulated by a short-term feeding with sucrose, sorbitol and polyethylene glycol, and this effect was to some extent mimicked by light exposure. The data suggest that Ugdh is regulated via an osmoticum-dependent pathway, possibly related to the availability of osmotically active carbohydrate precursors to UDPglucose, a substrate of UGDH.

  • 10. Johansson, H
    et al.
    Sterky, Fredrik
    KTH, Superseded Departments, Biotechnology.
    Mohammad Amini, Amini Bahram
    KTH, Superseded Departments, Biotechnology.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Kleczkowski, L A
    Molecular cloning of UPD-glucose dehydrogenase from cambium of poplar (Populus tremula x tremuloides)Article in journal (Other academic)
  • 11. Karpinska, B.
    et al.
    Karlsson, M.
    Srivastava, M.
    Stenberg, A.
    Schrader, J.
    Sterky, Fredrik
    KTH, Superseded Departments, Biotechnology.
    Bhalerao, R.
    Wingsle, G.
    MYB transcription factors are differentially expressed and regulated during secondary vascular tissue development in hybrid aspen2004In: Plant Molecular Biology, ISSN 0167-4412, E-ISSN 1573-5028, Vol. 56, no 2, p. 255-270Article in journal (Refereed)
    Abstract [en]

    More than 120,000 poplar ESTs have been sequenced from 20 different cDNA libraries by the Swedish Centre for Tree Functional Genomics. We screened this EST collection for MYB transcription factors involved in secondary vascular tissue formation, and genes assigned as PttMYB3Ra, PttMYB4a and PttMYB21a were selected for further characterisation. Three MYB genes showed different expression patterns in various organs, tissues and stem sub-sections representing different developmental stages of vascular tissue formation. Furthermore, the analysis showed that PttMYB21a expression was much higher in secondary cell wall formation zone of xylem and phloem fibers than in other developmental zones. Transgenic hybrid aspen plants, expressing the 3'-part of the PttMYB21a gene in antisense orientation were generated to assess the function of PttMYB21a gene in vascular tissue formation and lignification. All transgenic lines showed reduced growth and had fewer internodes compared to the wild-type. The analysis of selected lines showed that acid soluble lignin present in the bark was higher in transgenic lines as compared to wild-type plants. Moreover a higher transcript level of caffeoyl-CoA 3-O-methyltransferase [CCoAOMT];EC2.1.1.104) was found in the phloem of the transgenic plants, suggesting that PttMYB21a might function as a transcriptional repressor.

  • 12.
    Lindskog, M.
    et al.
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Berglund, L.
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Uhlén, Mathias
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Sterky, Fredrik
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Selection of antigenic protein fragments for antibody-based proteomics2005In: Molecular & Cellular Proteomics, ISSN 1535-9476, E-ISSN 1535-9484, Vol. 4, no 8, p. S63-S63Article in journal (Other academic)
  • 13.
    Lindskog, Mats
    et al.
    KTH, School of Biotechnology (BIO).
    Berglund, L.
    Hamsten, Carl
    KTH, School of Biotechnology (BIO).
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO).
    Sterky, Fredrik
    KTH, School of Biotechnology (BIO).
    Processing of high sequence similarity proteins in antibody-based proteomicsManuscript (Other academic)
  • 14.
    Lindskog, Mats
    et al.
    KTH, School of Biotechnology (BIO).
    Rockberg, Johan
    KTH, School of Biotechnology (BIO).
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO).
    Sterky, Fredrik
    KTH, School of Biotechnology (BIO).
    Selection of protein epitopes for antibody production2005In: BioTechniques, ISSN 0736-6205, E-ISSN 1940-9818, Vol. 38, no 5, p. 723-727Article in journal (Refereed)
    Abstract [en]

    Protein functional analysis in the post-genomic era is a huge task that has to be approached by different methods in parallel. The use of protein-specific antibodies in conjunction with tissue microarrays has proven to be one important technology. In this study, we present a strategy for the optimized design of protein subfragments for subsequent antibody production. The fragments are selected based on a principle of lowest sequence similarity to other human proteins, optimally to generate antibodies with high selectivity. Furthermore, the fragments should have properties optimized for efficient protein production in Escherichia coli. The strategy has been implemented in Bishop, which is a Java-based software enabling the high-throughput production of protein fragments. Bishop allows for the avoidance of certain restriction enzyme sites, transmembrane regions, and signal peptides. A Basic Local Alignment Search Tool (BLAST) scanning procedure permits the selection of fragments of a selected size with a minimal sequence similarity to other proteins. The software and the strategy were evaluated on a human test data set and verified to fulfill the requested criteria.

  • 15. Nguyen, N
    et al.
    Samuelson, Patrik
    KTH, Superseded Departments, Biotechnology.
    Sterky, Fredrik
    KTH, Superseded Departments, Biotechnology.
    Merle-Poitte, C
    Robert, A
    Baussant, T
    Haeuw, F
    Uhlen, Mathias
    KTH, Superseded Departments, Biotechnology.
    Binz, H
    Ståhl, Stefan
    KTH, Superseded Departments, Biotechnology.
    Chromosomal sequencing using a PCR-based biotin-capture method allowed isolation of the complete gene for the outer membrane protein A of Klebsiella pneumoniae1998In: Gene, ISSN 0378-1119, E-ISSN 1879-0038, Vol. 210, no 1, p. 93-101Article in journal (Refereed)
    Abstract [en]

    By employing a novel biotin-and PCR-assisted capture method, which allows determination of unknown sequences on chromosomal DNA. the gene for the outer membrane protein A (OmpA) of Klebsiella pneumoniae has been isolated and sequenced to completion. The method involves linear amplification of DNA from a biotinylated primer annealing to a region with known sequence. After capture of the amplified single-stranded DNA on to paramagnetic beads, unspecifically annealing primers, i.e. arbitrary primers, were used to generate fragments with only partly determined nt sequences. The homology of the sequenced gene to ompAs of related bacteria is discussed. The ompA gene was assembled for intracellular expression in Escherichia coli, and two different fusion proteins were produced and recovered with good yields. The importance of the novel chromosomal sequencing method for gene isolation in general and the potential use of the OmpA fusion proteins are discussed. (C) 1998 Elsevier Science B.V.

  • 16. Sterck, L.
    et al.
    Rombauts, S.
    Jansson, S.
    Sterky, Fredrik
    KTH, School of Biotechnology (BIO), Proteomics.
    Rouze, P.
    Van de Peer, Y.
    EST data suggest that poplar is an ancient polyploid2005In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 167, no 1, p. 165-170Article in journal (Refereed)
    Abstract [en]

    We analysed the publicly available expressed sequence tag (EST) collections for the genus Populus to examine whether evidence can be found for large-scale gene-duplication events in the evolutionary past of this genus. The ESTs were clustered into unigenes for each poplar species examined. Gene families were constructed for all proteins deduced from these unigenes, and K-S dating was performed on all paralogs within a gene family. The fraction of paralogs was then plotted against the K-S values, which resulted in a distribution reflecting the age of duplicated genes in poplar. Sufficient EST data were available for seven different poplar species spanning four of the six sections of the genus Populus. For all these species, there was evidence that a large-scale gene-duplication event had occurred. From our analysis it is clear that all poplar species have shared the same large-scale gene-duplication event, suggesting that this event must have occurred in the ancestor of poplar, or at least very early in the evolution of the Populus genus.

  • 17.
    Sterky, Fredrik
    KTH, Superseded Departments, Biotechnology.
    Sequencing of genes and genomes1998Doctoral thesis, comprehensive summary (Other scientific)
  • 18.
    Sterky, Fredrik
    et al.
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Berglund, L.
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Lindskog, M.
    KTH, School of Biotechnology (BIO).
    Rockberg, Johan
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Al-Khalili Szigyarto, Cristina
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Uhlén, Mathias
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Strategies and software for design of protein Epitopes within HPR2004In: Molecular & Cellular Proteomics, ISSN 1535-9476, E-ISSN 1535-9484, Vol. 3, no 10, p. S4-S4Article in journal (Other academic)
  • 19.
    Sterky, Fredrik
    et al.
    KTH, Superseded Departments, Biotechnology.
    Bhalerao, Rupali R.
    KTH, Superseded Departments, Biotechnology.
    Unneberg, Per
    KTH, Superseded Departments, Biotechnology.
    Segerman, B.
    Nilsson, Peter
    KTH, Superseded Departments, Biotechnology.
    Brunner, A. M.
    Charbonnel-Campaa, L.
    Lindvall, J. J.
    Tandre, K.
    Strauss, S. H.
    Sundberg, B.
    Gustafsson, P.
    Uhlén, Mathias
    KTH, Superseded Departments, Biotechnology.
    Nilsson, O.
    Sandberg, G.
    Karlsson, J.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Jansson, S.
    A Populus EST resource for plant functional genomics2004In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 101, no 38, p. 13951-13956Article in journal (Refereed)
    Abstract [en]

    Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide >4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (POPULUSDB) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.

  • 20.
    Sterky, Fredrik
    et al.
    KTH, Superseded Departments, Biotechnology.
    Holmberg, Anders
    Alexandersson, G
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Uhlen, Mathias
    KTH, Superseded Departments, Biotechnology.
    Direct sequencing of bacterial artificial chromosomes (BACs) and prokaryotic genomes by biotin-capture PCR1998In: Journal of Biotechnology, ISSN 0168-1656, E-ISSN 1873-4863, Vol. 60, no 1-2, p. 119-129Article in journal (Refereed)
    Abstract [en]

    Determination of unknown DNA sequences adjacent to known segments is an important task in genome-related research. We have applied the methodology of biotin-capture PCR for direct sequencing of bacterial artificial chromosomes (BACs) and bacterial genomes. The strategy involves extension of a biotinylated primer from a known locus into unknown regions of the template to yield single-stranded DNA, which is immobilised onto paramagnetic beads. An arbitrary primer initiates extension from the unknown region and back towards the known locus. The arbitrary primer contains a universal primer 'handle', which is utilised for subsequent amplification. The PCR products are then directly sequenced by solid-phase or cycle sequencing. The fact that BACs or bacterial chromosomes can be sequenced without prior purification or subcloning might be useful in numerous applications, such as gap-filling, sequencing of regulatory regions upstream known genes and determination of intron/exon-boundaries.

  • 21.
    Sterky, Fredrik
    et al.
    KTH, Superseded Departments, Biotechnology.
    Holmberg, Anders
    KTH, Superseded Departments, Biotechnology.
    Pettersson, B
    Uhlen, Mathias
    KTH, Superseded Departments, Biotechnology.
    The sequence of a 30 kb fragment on the left arm of chromosome XV from Saccharomyces cerevisiae reveals 15 open reading frames, five of which correspond to previously identified genes1996In: Yeast, ISSN 0749-503X, E-ISSN 1097-0061, Vol. 12, no 10B, p. 1091-1095Article in journal (Refereed)
    Abstract [en]

    We report the sequence of a 30 469 bp long DNA fragment on the left arm of chromosome XV of Saccharomyces cerevisiae. The fragment contains 15 open reading frames (ORFs) of al least 300 bp. Five previously sequenced yeast genes, PHO80, TIR2, SLG1, the gene encoding the subtilisin-like protease III precursor and the gene coding for ATP-dependent permease, are found among these ORFs. By DNA sequence comparison, two ORFs identified previously reported expressed sequence tags from yeast. Of the proteins encoded by the remaining eight ORFs, six show similarities to proteins from different organisms and two lack detectable similarity with any amino acid sequence described in public data banks. The DNA sequence has been deposited in GenBank under Accession Number U43491.

  • 22.
    Sterky, Fredrik
    et al.
    KTH, Superseded Departments, Biotechnology.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Sequence analysis of genes and genomes2000In: Journal of Biotechnology, ISSN 0168-1656, E-ISSN 1873-4863, Vol. 76, no 1, p. 1-31Article, review/survey (Refereed)
    Abstract [en]

    A major step towards understanding of the genetic basis of an organism is the complete sequence determination of all genes in its genome. The development of powerful techniques for DNA sequencing has enabled sequencing of large amounts of gene fragments and even complete genomes. Important new techniques for physical mapping, DNA sequencing and sequence analysis have been developed. To increase the throughput, automated procedures for sample preparation and new software for sequence analysis have been applied. This review describes the development of new sequencing methods and the optimisation of sequencing strategies for whole genome and cDNA analysis, as well as discusses issues regarding sequence analysis and annotation.

  • 23. Sterky, Fredrik
    et al.
    Regan, S
    Karlsson, J
    Hertzberg, M
    Rohde, A
    Holmberg, Anders
    Mohammad Amini, Amini Bahram
    KTH, Superseded Departments, Biotechnology.
    Bhalerao, R
    Larsson, M
    Villarroel, R
    Van Montagu, M
    Sandberg, G
    Olsson, O
    Teeri, T
    Boerjan, W
    Gustafsson, P
    Uhlen, Mathias
    KTH, Superseded Departments, Biotechnology.
    Sundberg, B
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Gene discovery in the wood-forming tissues of poplar: Analysis of 5,692 expressed sequence tags1998In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 95, no 22, p. 13330-13335Article in journal (Refereed)
    Abstract [en]

    A rapidly growing area of genome research is the generation of expressed sequence tags (ESTs) in which large numbers of randomly selected cDNA clones are partially sequenced. The collection of ESTs reflects the level and complexity of gene expression in the sampled tissue, To date, the majority of plant ESTs are from nonwoody plants such as Arabidopsis, Brassica, maize, and rice. Here, we present a large-scale production of ESTs from the wood-forming tissues of two poplars, Populus tremula L, x tremuloides Michx, and Populus trichocarpa 'Trichobel.' The 5,692 ESTs analyzed represented a total of 3,719 unique transcripts for the two cDNA libraries, Putative functions could be assigned to 2,245 of these transcripts that corresponded to 820 protein functions. Of specific interest to forest biotechnology are the 4% of ESTs involved in various processes of cell wall formation, such as lignin and cellulose synthesis, 5% similar to developmental regulators and members of known signal transduction pathways, and 2% involved in hormone biosynthesis. An additional 12% of the ESTs show ed no significant similarity to any other DNA or protein sequences in existing databases. The absence of these sequences from public databases may indicate a specific role for these proteins in wood formation. The cDNA libraries and the accompanying database are valuable resources for forest research directed toward understanding the genetic control of wood formation and future endeavors to modify wood and fiber properties for industrial use.

  • 24.
    Sterky, Fredrik
    et al.
    KTH, Superseded Departments, Biotechnology.
    Sievertzon, M
    Molecular cloning of a cDNA encoding a cytosolic form of phosphoglucomutase from cambium of poplar (Populus tremula x tremuloides)1998Article in journal (Other academic)
  • 25. Tuskan, G. A.
    et al.
    DiFazio, S.
    Jansson, S.
    Bohlmann, J.
    Grigoriev, I.
    Hellsten, U.
    Putnam, N.
    Ralph, S.
    Rombauts, S.
    Salamov, A.
    Schein, J.
    Sterck, L.
    Sterky, Fredrik
    KTH, School of Biotechnology (BIO), Proteomics.
    et al,
    The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)2006In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 313, no 5793, p. 1596-1604Article in journal (Refereed)
    Abstract [en]

    We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

  • 26.
    Uhlén, Mathias
    et al.
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Björling, Erik
    KTH, School of Biotechnology (BIO).
    Agaton, Charlotta
    KTH, School of Biotechnology (BIO).
    Al-Khalili Szigyarto, Cristina
    KTH, School of Biotechnology (BIO).
    Amini, Bahram
    KTH, School of Biotechnology (BIO).
    Andersen, Elisabet
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Andersson, Ann-Catrin
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Angelidou, Pia
    KTH, School of Biotechnology (BIO).
    Asplund, Anna
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Asplund, Caroline
    KTH, School of Biotechnology (BIO).
    Berglund, Lisa
    KTH, School of Biotechnology (BIO).
    Bergström, Kristina
    KTH, School of Biotechnology (BIO).
    Brumer, Harry
    KTH, School of Biotechnology (BIO).
    Cerjan, Dijana
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Ekström, Marica
    KTH, School of Biotechnology (BIO).
    Elobeid, Adila
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Eriksson, Cecilia
    KTH, School of Biotechnology (BIO).
    Fagerberg, Linn
    KTH, School of Biotechnology (BIO).
    Falk, Ronny
    KTH, School of Biotechnology (BIO).
    Fall, Jenny
    KTH, School of Biotechnology (BIO).
    Forsberg, Mattias
    KTH, School of Biotechnology (BIO).
    Gry Björklund, Marcus
    KTH, School of Biotechnology (BIO).
    Gumbel, Kristoffer
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Halimi, Asif
    KTH, School of Biotechnology (BIO).
    Hallin, Inga
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Hamsten, Carl
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Hansson, Marianne
    KTH, School of Biotechnology (BIO).
    Hedhammar, My
    KTH, School of Biotechnology (BIO).
    Hercules, Görel
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Kampf, Caroline
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Larsson, Karin
    KTH, School of Biotechnology (BIO).
    Lindskog, Mats
    KTH, School of Biotechnology (BIO).
    Lodewyckx, Wald
    KTH, School of Biotechnology (BIO).
    Lund, Jan
    KTH, School of Biotechnology (BIO).
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO).
    Magnusson, Kristina
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Malm, Erik
    KTH, School of Biotechnology (BIO).
    Nilsson, Peter
    KTH, School of Biotechnology (BIO).
    Ödling, Jenny
    KTH, School of Biotechnology (BIO).
    Oksvold, Per
    KTH, School of Biotechnology (BIO).
    Olsson, Ingmarie
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Öster, Emma
    KTH, School of Biotechnology (BIO).
    Ottosson, Jenny
    KTH, School of Biotechnology (BIO).
    Paavilainen, Linda
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Persson, Anja
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Rimini, Rebecca
    KTH, School of Biotechnology (BIO).
    Rockberg, Johan
    KTH, School of Biotechnology (BIO).
    Runeson, Marcus
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Sivertsson, Åsa
    KTH, School of Biotechnology (BIO).
    Sköllermo, Anna
    KTH, School of Biotechnology (BIO).
    Steen, Johanna
    KTH, School of Biotechnology (BIO).
    Stenvall, Maria
    KTH, School of Biotechnology (BIO).
    Sterky, Fredrik
    KTH, School of Biotechnology (BIO).
    Strömberg, Sara
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Sundberg, Mårten
    KTH, School of Biotechnology (BIO).
    Tegel, Hanna
    KTH, School of Biotechnology (BIO).
    Tourle, Samuel
    KTH, School of Biotechnology (BIO).
    Wahlund, Eva
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Waldén, Annelie
    KTH, School of Biotechnology (BIO).
    Wan, Jinghong
    KTH, School of Biotechnology (BIO), Molecular Biotechnology (closed 20130101).
    Wernérus, Henrik
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Westberg, Joakim
    KTH, School of Biotechnology (BIO).
    Wester, Kenneth
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Wrethagen, Ulla
    KTH, School of Biotechnology (BIO).
    Xu, Lan Lan
    KTH, School of Biotechnology (BIO).
    Hober, Sophia
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Pontén, Fredrik
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    A human protein atlas for normal and cancer tissues based on antibody proteomics2005In: Molecular & Cellular Proteomics, ISSN 1535-9476, E-ISSN 1535-9484, Vol. 4, no 12, p. 1920-1932Article in journal (Refereed)
    Abstract [en]

    Antibody-based proteomics provides a powerful approach for the functional study of the human proteome involving the systematic generation of protein-specific affinity reagents. We used this strategy to construct a comprehensive, antibody-based protein atlas for expression and localization profiles in 48 normal human tissues and 20 different cancers. Here we report a new publicly available database containing, in the first version, similar to 400,000 high resolution images corresponding to more than 700 antibodies toward human proteins. Each image has been annotated by a certified pathologist to provide a knowledge base for functional studies and to allow queries about protein profiles in normal and disease tissues. Our results suggest it should be possible to extend this analysis to the majority of all human proteins thus providing a valuable tool for medical and biological research.

  • 27. Unneberg, Per
    et al.
    Stromberg, Michael
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology.
    Jansson, Stefan
    Sterky, Fredrik
    KTH, School of Biotechnology (BIO), Proteomics.
    Analysis of 70,000 EST sequences to study divergence between two closely related Populus species2005In: Tree Genetics & Genomes, ISSN 1614-2942, Vol. 1, no 3, p. 109-115Article in journal (Refereed)
    Abstract [en]

    The Populus genus has evolved as the model organism for forest tree genomics, which has been further emphasised with the sequencing of the Populus trichocarpa genome. Populus species are widely spread over the Northern Hemisphere and provide a great source of genetic diversity, which can be used for mapping of quantitative trait loci, positional cloning, association mapping and studies in environmental adaptation. Collections of expressed sequence tags (ESTs) are rich sources in studies of genetic diversity. Here, we report on an in-depth analysis of 70,000 ESTs from two Populus species, Populus tremula and Populus trichocarpa. We present data on the level of conservation in transcript sequences and supply a collection of potential single nucleotide polymorphisms.

  • 28.
    Unneberg, Per
    et al.
    KTH, Superseded Departments, Biotechnology.
    Strömberg, Michael
    KTH, Superseded Departments, Biotechnology.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Jansson, Stefan
    Sterky, Fredrik
    KTH, Superseded Departments, Biotechnology.
    Unravelling differences in the transcriptome of two closely related populus specialManuscript (Other academic)
  • 29.
    Unneberg, Per
    et al.
    KTH, School of Biotechnology (BIO).
    Strömberg, Michael
    KTH, School of Biotechnology (BIO).
    Sterky, Fredrik
    KTH, School of Biotechnology (BIO).
    SNP discovery using advanced algorithms and neural networks2005In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 21, no 10, p. 2528-2530Article in journal (Refereed)
    Abstract [en]

    Forage is an application which uses two neural networks for detecting single nucleotide polymorphisms (SNPs). Potential SNP candidates are identified in multiple alignments. Each candidate is then represented by a vector of features, which is classified as SNP or monomorphic by the networks. A validated dataset of SNPs was constructed from experimentally verified SNP data and used for network training and method evalutation.

1 - 29 of 29
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf