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Tuskan, G. A., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., . . . et al, . (2006). The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, 313(5793), 1596-1604
Open this publication in new window or tab >>The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
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2006 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 313, no 5793, p. 1596-1604Article in journal (Refereed) Published
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.

Keywords
cinnamyl alcohol-dehydrogenase, arabidopsis-thaliana, hybrid poplar, gene-expression, transcriptional regulators, phenylpropanoid metabolism, gravitational induction, lignin biosynthesis, resistance genes, quaking aspen
Identifiers
urn:nbn:se:kth:diva-15989 (URN)10.1126/science.1128691 (DOI)000240498900035 ()2-s2.0-33748760611 (Scopus ID)
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2017-12-12Bibliographically approved
Uhlén, M., Björling, E., Agaton, C., Al-Khalili Szigyarto, C., Amini, B., Andersen, E., . . . Pontén, F. (2005). A human protein atlas for normal and cancer tissues based on antibody proteomics. Molecular & Cellular Proteomics, 4(12), 1920-1932
Open this publication in new window or tab >>A human protein atlas for normal and cancer tissues based on antibody proteomics
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2005 (English)In: Molecular & Cellular Proteomics, ISSN 1535-9476, E-ISSN 1535-9484, Vol. 4, no 12, p. 1920-1932Article in journal (Refereed) Published
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.

Keywords
MESSENGER-RNA, FACTOR TFIIH, IN-VITRO, EXPRESSION, FAMILY, MICROARRAYS, SUBUNIT, DISPLAY, GENES, CRIM1
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-14023 (URN)10.1074/mcp.M500279-MCP200 (DOI)000233774200008 ()2-s2.0-29244477844 (Scopus ID)
Note

QC 20100708

Available from: 2010-07-08 Created: 2010-07-08 Last updated: 2017-12-12Bibliographically approved
Unneberg, P., Stromberg, M., Lundeberg, J., Jansson, S. & Sterky, F. (2005). Analysis of 70,000 EST sequences to study divergence between two closely related Populus species. Tree Genetics & Genomes, 1(3), 109-115
Open this publication in new window or tab >>Analysis of 70,000 EST sequences to study divergence between two closely related Populus species
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2005 (English)In: Tree Genetics & Genomes, ISSN 1614-2942, Vol. 1, no 3, p. 109-115Article in journal (Refereed) Published
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.

Keywords
EST, SNP, assembly, cDNA library analysis, ortholog, functional genomics, gene discovery, plant, selection, evolution, poplar, tags
Identifiers
urn:nbn:se:kth:diva-15339 (URN)10.1007/s11295-005-0014-0 (DOI)000244896200004 ()2-s2.0-33746913459 (Scopus ID)
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05Bibliographically approved
Aspeborg, H., Schrader, J., Coutinho, P. M., Stam, M., Kallas, A., Djerbi, S., . . . Teeri, T. T. (2005). Carbohydrate-active enzymes involved in the secondary cell wall biogenesis in hybrid aspen. Plant Physiology, 137(3), 983-997
Open this publication in new window or tab >>Carbohydrate-active enzymes involved in the secondary cell wall biogenesis in hybrid aspen
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2005 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 137, no 3, p. 983-997Article in journal (Refereed) Published
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.

Keywords
arabidopsis-thaliana, cellulose synthesis, gene-expression, mesophyll-cells, xyloglucan galactosyltransferase, functional genomics, beta-galactosidase, tracheary elements, catalytic subunit, molecular-cloning
National Category
Plant Biotechnology
Identifiers
urn:nbn:se:kth:diva-14637 (URN)10.1104/pp.104.055087 (DOI)000227957200021 ()15734915 (PubMedID)2-s2.0-20444437284 (Scopus ID)
Note

QC 20100525

Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2017-12-12Bibliographically approved
Sterck, L., Rombauts, S., Jansson, S., Sterky, F., Rouze, P. & Van de Peer, Y. (2005). EST data suggest that poplar is an ancient polyploid. New Phytologist, 167(1), 165-170
Open this publication in new window or tab >>EST data suggest that poplar is an ancient polyploid
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2005 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 167, no 1, p. 165-170Article in journal (Refereed) Published
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.

Keywords
EST (expressed sequence tag) data, evolution, fossil record, genome duplication, K-S dating, polyploidy, Populus (poplar), expressed sequence tags, nucleotide substitution, phylogenetic analysis, functional genomics, duplicate genes, arabidopsis, model, evolution, populus, program
Identifiers
urn:nbn:se:kth:diva-14794 (URN)10.1111/j.1469-8137.2005.01378.x (DOI)000229581600017 ()2-s2.0-21244483590 (Scopus ID)
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2017-12-12Bibliographically approved
Lindskog, M., Berglund, L., Uhlén, M. & Sterky, F. (2005). Selection of antigenic protein fragments for antibody-based proteomics. Molecular & Cellular Proteomics, 4(8), S63-S63
Open this publication in new window or tab >>Selection of antigenic protein fragments for antibody-based proteomics
2005 (English)In: Molecular & Cellular Proteomics, ISSN 1535-9476, E-ISSN 1535-9484, Vol. 4, no 8, p. S63-S63Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC, 2005
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-242464 (URN)000202995300177 ()
Note

QC 20190205

Available from: 2019-02-05 Created: 2019-02-05 Last updated: 2019-02-05Bibliographically approved
Lindskog, M., Rockberg, J., Uhlén, M. & Sterky, F. (2005). Selection of protein epitopes for antibody production. BioTechniques, 38(5), 723-727
Open this publication in new window or tab >>Selection of protein epitopes for antibody production
2005 (English)In: BioTechniques, ISSN 0736-6205, E-ISSN 1940-9818, Vol. 38, no 5, p. 723-727Article in journal (Refereed) Published
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.

Keywords
Antibodies, Arrays, Computer software, Data acquisition, Enzymes, Escherichia coli, Genes, Java programming language, Optimization, Basic local alignment search tool (BLAST), Microarrays, Protein functional analysis, Transmembranes
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-8827 (URN)10.2144/05385ST02 (DOI)000229057100010 ()2-s2.0-17844392695 (Scopus ID)
Note
QC 20100907Available from: 2005-11-30 Created: 2005-11-30 Last updated: 2017-12-14Bibliographically approved
Unneberg, P., Strömberg, M. & Sterky, F. (2005). SNP discovery using advanced algorithms and neural networks. Bioinformatics, 21(10), 2528-2530
Open this publication in new window or tab >>SNP discovery using advanced algorithms and neural networks
2005 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 21, no 10, p. 2528-2530Article in journal (Refereed) Published
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.

Keywords
access to information, algorithm, article, artificial neural network, forage, gene frequency, information processing, priority journal, single nucleotide polymorphism, statistical analysis, validation process
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-5172 (URN)10.1093/bioinformatics/bti354 (DOI)000229285600053 ()15746291 (PubMedID)2-s2.0-19544386177 (Scopus ID)
Note
QC 20100929. Uppdaterad från Manuskript till Artikel (20100929). Tidigare titel: "SNP discovery usin advanced algorithms and nuural networks".Available from: 2004-10-08 Created: 2004-10-08 Last updated: 2017-12-04Bibliographically approved
Djerbi, S., Lindskog, M., Arvestad, L., Sterky, F. & Teeri, T. (2005). The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes. Planta, 221(5), 739-746
Open this publication in new window or tab >>The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes
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2005 (English)In: Planta, ISSN 0032-0935, E-ISSN 1432-2048, Vol. 221, no 5, p. 739-746Article in journal (Refereed) Published
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.

Keywords
Populus, paleopolyploids, cellulose synthase, gene duplication, paralogues
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-6245 (URN)10.1007/s00425-005-1498-4 (DOI)000230490200013 ()2-s2.0-22444446783 (Scopus ID)
Note
QC 20101001. Uppdaterad från In press till Published (20101001).Available from: 2005-09-13 Created: 2005-09-13 Last updated: 2017-12-14Bibliographically approved
Sterky, F., Bhalerao, R. R., Unneberg, P., Segerman, B., Nilsson, P., Brunner, A. M., . . . Jansson, S. (2004). A Populus EST resource for plant functional genomics. Proceedings of the National Academy of Sciences of the United States of America, 101(38), 13951-13956
Open this publication in new window or tab >>A Populus EST resource for plant functional genomics
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2004 (English)In: 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) Published
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.

Keywords
gene-expression, draft sequence, arabidopsis, poplar, evolution, biology
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-23752 (URN)10.1073/pnas.0401641101 (DOI)000224069800046 ()2-s2.0-4644282569 (Scopus ID)
Note
QC 20100525 QC 20110916Available from: 2010-08-10 Created: 2010-08-10 Last updated: 2017-12-12Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-3281-8088

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