http://publicationslist.org/data/nipe/atom.xml Peter Nilssonhttp://publicationslist.org/nipe$basepathfavicon.icoRecent additions to Peter Nilsson's PublicationsList.org pagehttp://publicationslist.org/publications.png2010-08-20T08:05:12Z http://publicationslist.org/nipe/refid88 2010-06-21T22:46:28Z

In the pursuit towards a systematic analysis of human diseases, array-based approaches within antibody proteomics offer high-throughput strategies to discover protein biomarkers in serum and plasma. To investigate the influence of sample preparation on such discovery attempts, we report on a systematic effort to compare serum and plasma protein profiles determined with an antibody suspension bead ...<br/><br/>Jochen M Schwenk, Ulrika Igel, Bernet S Kato, George Nicholson, Fredrik Karpe, Mathias Uhlén, Peter Nilsson (2010) <i>Proteomics</i> <i></i> <i></i> 10: 3 532-540<br/>

http://publicationslist.org/nipe/refid85 2010-06-21T22:46:28Z

In vitro antibody generation by panning a large universal gene library with phage display was employed to generate antibodies to more than 60 different antigens. Of particular interest was a comparison of pannings on 20 different SH2 domains provided by the Structural Genomics Consortium (SGC). Streamlined methods for high throughput antibody generation developed within the 'Antibody Factory' of t...<br/><br/>Michael Mersmann, Doris Meier, Jana Mersmann, Saskia Helmsing, Peter Nilsson, Susanne Gräslund, Karen Colwill, Michael Hust, Stefan Dübel (2010) <i>N Biotechnol</i> <i></i> <i></i> 27: 2 118-128<br/>

http://publicationslist.org/nipe/refid82 2010-02-19T14:15:40Z

Jochen M. Schwenk and Peter Nilsson (2010) <i>Protein Microarrys for Disease Analysis: Methods and Protocols (Methods in Molecular Biology)</i> <br/>

http://publicationslist.org/nipe/refid90 2010-08-13T21:28:02Z

To demonstrate the utility of phage display in generating highly specific antibodies, affinity selections were conducted on 20 related Src Homology 2 (SH2) domains (ABL1, ABL2, BTK, BCAR3, CRK, FYN, GRB2, GRAP2, LYN, LCK, NCK1, PTPN11 C, PIK3R1 C, PLCgamma1 C, RASA1 C, SHC1, SH2D1A, SYK N, VAV1 and the tandem domains of ZAP70). The domains were expressed in Escherichia coli, purified and used in a...<br/><br/>K Pershad, J D Pavlovic, S Gräslund, P Nilsson, K Colwill, A Karatt-Vellatt, D J Schofield, M R Dyson, T Pawson, B K Kay, J McCafferty (2010) <i>Protein Eng Des Sel</i> <i></i> <i></i> 23: 4 279-288<br/>

http://publicationslist.org/nipe/refid94 2010-08-04T20:26:54Z

ABSTRACT: BACKGROUND: Species of the crenarchaeon Sulfolobus harbour three replication origins in their single circular chromosome that are synchronously initiated during replication. RESULTS: We demonstrate that global gene expression in two Sulfolobus species is highly biased, such that early replicating genome regions are more highly expressed at all three origins. The bias by far exceeds what ...<br/><br/>Anders F Andersson, Erik A Pelve, Stefan Lindeberg, Magnus Lundgren, Peter Nilsson, Rolf Bernander (2010) <i>BMC Genomics</i> <i></i> <i></i> 11: 1 <br/>

http://publicationslist.org/nipe/refid95 2010-08-13T21:13:00Z

There is need for high-throughput methods for screening patient samples in the quest for potential biomarkers for diagnostics and patient care. Here, we have used a combination of undirected target selection, antibody suspension bead arrays and heat-induced epitope retrieval to allow for protein profiling of human plasma in a novel and systematic manner. Several antibodies were found to reveal alt...<br/><br/>Jochen M Schwenk, Ulrika Igel, Maja Neiman, Hanno Langen, Charlotte Becker, Anders Bjartell, Fredrik Ponten, Fredrik Wiklund, Henrik Grönberg, Peter Nilsson, Mathias Uhlen (2010) <i>Mol Cell Proteomics</i> <i></i> <i></i> : <br/>

http://publicationslist.org/nipe/refid92 2010-06-21T22:48:05Z

Jochen M Schwenk, Peter Nilsson (2010) <i> Protein Microarrays: Methods and Protocols (Methods in Molecular Biology)</i> <br/>

http://publicationslist.org/nipe/refid78 2009-07-28T09:07:35Z

BACKGROUND: Dried blood spot samples (DBSS) from newborns are widely used in neonatal screening for selected metabolic diseases and diagnostic possibilities for additional disorders are continuously being evaluated. Primary immunodeficiency disorders comprise a group of more than one hundred diseases, several of which are fatal early in life. Yet, a majority of the patients are not diagnosed due t...<br/><br/>Magdalena Janzi, Ronald Sjöberg, Jinghong Wan, Björn Fischler, Ulrika von Döbeln, Lourdes Isaac, Peter Nilsson, Lennart Hammarström (2009) <i>PLoS One</i> 4: 4 e5321<br/>

http://publicationslist.org/nipe/refid76 2009-11-16T07:43:32Z

Selective IgA deficiency in early life is quite common in Caucasian populations, but it is unclear whether it increases the risk of infections and allergic diseases during childhood. Serum IgA levels were measured in 2423 children at 4 years of age in a Swedish population based birth cohort (BAMSE). Parental questionnaires were repeatedly sent out during the child's first 8 years of life, collecti...<br/><br/>Magdalena Janzi, Inger Kull, Ronald Sjöberg, Jinghong Wan, Erik Melén, Narges Bayat, Eva Ostblom, Qiang Pan-Hammarström, Peter Nilsson, Lennart Hammarström (2009) <i>Clin Immunol</i> 133: 1 78-85<br/>

http://publicationslist.org/nipe/refid75 2009-01-08T11:34:01Z

Henrik Nordström, Kerstin Falk, Peter Nilsson and Åke Lundkvist (2009) <i>Detection of Highly Dangerous Pathogens - Microarray Methods for BSL 3 and BSL 4 Agents </i> <br/>

http://publicationslist.org/nipe/refid77 2009-07-28T09:06:26Z

OBJECTIVE: Tumours in the adrenocortex are common human tumours. Malignancy is however, rare, the yearly incidence being 0.5-2 per million inhabitants, but associated with a very aggressive behaviour. Adrenocortical tumours are often associated with altered hormone production with a variety of clinical symptoms. The aggressiveness of carcinomas together with the high frequency of adenomas calls fo...<br/><br/>Cecilia Laurell, David Velázquez-Fernández, Kristina Lindsten, Christofer Juhlin, Ulla Enberg, Janos Geli, Anders Höög, Magnus Kjellman, Joakim Lundeberg, Bertil Hamberger, Catharina Larsson, Peter Nilsson, Martin Bäckdahl (2009) <i>Eur J Endocrinol</i> 161: 1 141-152<br/>

http://publicationslist.org/nipe/refid91 2010-03-09T07:46:34Z

Many steps of optimization are needed to achieve large-scale fabrication of high-quality DNA microarrays. These steps involve the printing instrument, the probes to be printed, microarray slides, and spotting buffer together with the surrounding environment, such as humidity and temperature. Robust microarray production requires not only appropriate reagents, equipment, and established procedures,...<br/><br/>Annelie Waldén, Peter Nilsson (2009) <i>Methods Mol Biol</i> <i> DNA Microarrays for Biomedical Research, (Methods in Molecular Biology, Vol. 529)</i> <i></i> 529: 101-113<br/>

http://publicationslist.org/nipe/refid83 2009-10-07T07:10:10Z

BACKGROUND: The Central Dogma of biology holds, in famously simplified terms, that DNA makes RNA makes proteins, but there is considerable uncertainty regarding the general, genome-wide correlation between levels of RNA and corresponding proteins. Therefore, to assess degrees of this correlation we compared the RNA profiles (determined using both cDNA- and oligo-based microarrays) and protein prof...<br/><br/>Marcus Gry, Rebecca Rimini, Sara Strömberg, Anna Asplund, Fredrik Pontén, Mathias Uhlén, Peter Nilsson (2009) <i>BMC Genomics</i> <i></i> <i></i> 10: 1 <br/>

http://publicationslist.org/nipe/refid89 2010-03-09T07:47:55Z

Defining the protein profiles of tissues and organs is critical to understanding the unique characteristics of the various cell types in the human body. In this study, we report on an anatomically comprehensive analysis of 4842 protein profiles in 48 human tissues and 45 human cell lines. A detailed analysis of over 2 million manually annotated, high-resolution, immunohistochemistry-based images s...<br/><br/>Fredrik Pontén, Marcus Gry, Linn Fagerberg, Emma Lundberg, Anna Asplund, Lisa Berglund, Per Oksvold, Erik Björling, Sophia Hober, Caroline Kampf, Sanjay Navani, Peter Nilsson, Jenny Ottosson, Anja Persson, Henrik Wernérus, Kenneth Wester, Mathias Uhlén (2009) <i>Mol Syst Biol</i> <i></i> <i></i> 5: <br/>

http://publicationslist.org/nipe/refid84 2010-02-10T14:02:00Z

In recent years, affinity-based technologies have become important tools for serum profiling to uncover protein expression patterns linked to disease state or therapeutic effects. In this study, we describe a path towards the production of an antibody microarray to allow protein profiling of biotinylated human serum samples with reproducible sensitivity in the picomolar range. With the availabilit...<br/><br/>Rebecca Rimini, Jochen M Schwenk, Mårten Sundberg, Ronald Sjöberg, Daniel Klevebring, Marcus Gry, Mathias Uhlén, Peter Nilsson (2009) <i>J Proteomics</i> 73: 2 252-266<br/>

http://publicationslist.org/nipe/refid69 2008-07-02T04:50:51Z

BACKGROUND: Basal cell carcinomas (BCCs) are prevalent tumours with uniform histology that develop without any known precursor lesion. Alterations in the sonic hedgehog-patched1 signalling pathway are accepted as necessary events for tumorigenesis, and mutations in the patched1 gene are frequently present in tumours. OBJECTIVES: To analyse transcript profiles in BCC. METHODS: We used laser-assiste...<br/><br/>A Asplund, M Gry Björklund, C Sundquist, S Strömberg, K Edlund, A Ostman, P Nilsson, F Pontén, J Lundeberg (2008) <i>Br J Dermatol</i> <i></i> <i></i> 158: 3 527-538<br/>

http://publicationslist.org/nipe/refid68 2009-10-07T07:16:01Z

Vitiligo is a complex, polygenic disorder characterized by patchy loss of skin pigmentation due to abnormal melanocyte function. Both genetic and environmental etiological factors have been proposed for vitiligo and lack of molecular markers renders difficulties to predict development and progression of the disease. Identification of dysregulated genes has the potential to unravel biological pathw...<br/><br/>Sara Strömberg, Marcus Gry Björklund, Anna Asplund, Rebecca Rimini, Joakim Lundeberg, Peter Nilsson, Fredrik Pontén, Mats J Olsson (2008) <i>Pigment Cell Melanoma Res</i> <i></i> <i></i> 21: 2 162-171<br/>

http://publicationslist.org/nipe/refid67 2008-07-02T04:50:51Z

Antigenic variation is a subtle process of fundamental importance to the survival of a microbial pathogen. In Plasmodium falciparum malaria, PfEMP1 is the major variable antigen and adhesin expressed at the surface of the infected erythrocyte, which is encoded for by members of a family of 60 var-genes. Peri-nuclear repositioning and epigenetic mechanisms control their mono-allelic expression. The...<br/><br/>Bobo W Mok, Ulf Ribacke, Niloofar Rasti, Fred Kironde, Qijun Chen, Peter Nilsson, Mats Wahlgren (2008) <i>PLoS ONE</i> <i></i> <i></i> 3: 4 e1982<br/>

http://publicationslist.org/nipe/refid70 2008-10-15T11:09:36Z

Antibody microarrays offer a powerful tool to screen for target proteins in complex samples. Here, we describe an approach for systematic analysis of serum, based on antibodies and using color-coded beads for the creation of antibody arrays in suspension. This method, adapted from planar antibody arrays, offers a fast, flexible, and multiplexed procedure to screen larger numbers of serum samples, ...<br/><br/>Jochen M Schwenk, Marcus Gry, Rebecca Rimini, Mathias Uhlén, Peter Nilsson (2008) <i>J Proteome Res</i> <i></i> <i></i> 7: 8 3168-3179<br/>

http://publicationslist.org/nipe/refid71 2009-10-07T07:16:01Z

Generation of monospecific antibodies (msAbs) (multiepitope) through affinity purification of polyclonal antisera is a plausible strategy for high-throughput production of affinity reagents toward large sets of proteins. These antibodies are generated using readily accessible gene sequence information from publicly available databases. The resulting antibodies have the potential to be used in a va...<br/><br/>Linda Paavilainen, Henrik Wernérus, Peter Nilsson, Mathias Uhlén, Sophia Hober, Kenneth Wester, Fredrik Pontén (2008) <i>Appl Immunohistochem Mol Morphol</i> <i></i> <i></i> 16: 5 493-502<br/>

http://publicationslist.org/nipe/refid73 2009-10-07T07:16:01Z

An attractive path forward in proteomics is to experimentally annotate the human protein complement of the genome in a genecentric manner. Using antibodies, it might be possible to design protein-specific probes for a representative protein from every protein-coding gene and to subsequently use the antibodies for systematical analysis of cellular distribution and subcellular localization of protei...<br/><br/>Lisa Berglund, Erik Björling, Per Oksvold, Linn Fagerberg, Anna Asplund, Cristina Al-Khalili Szigyarto, Anja Persson, Jenny Ottosson, Henrik Wernérus, Peter Nilsson, Emma Lundberg, Asa Sivertsson, Sanjay Navani, Kenneth Wester, Caroline Kampf, Sophia Hober, Fredrik Pontén, Mathias Uhlén (2008) <i>Mol Cell Proteomics</i> <i></i> <i></i> 7: 10 2019-2027<br/>

http://publicationslist.org/nipe/refid24 2007-11-02T07:05:17Z

Antigenic variation is a survival mechanism developed by the malaria parasite Plasmodium falciparum in order to allow for the establishment of a chronic infection. Here we have studied clonal differences in the transcriptomes of two isogenic P. falciparum clones (3D7S8.4 and 3D7AH1S2) of distinct adhesive and antigenic phenotypes employing a P. falciparum 70-mer oligonucleotide microarray. Fifteen...<br/><br/>Bobo W Mok, Ulf Ribacke, Gerhard Winter, Ben H Yip, Chuen-Seng Tan, Victor Fernandez, Qijun Chen, Peter Nilsson, Mats Wahlgren (2007) <i>Mol Biochem Parasitol</i> <i></i> <i></i> 151: 2 184-192<br/>

http://publicationslist.org/nipe/refid23 2007-11-02T07:05:17Z

Advances in antibody production render a growing supply of affinity reagents for immunohistochemistry (IHC), and tissue microarray (TMA) technologies facilitate simultaneous analysis of protein expression in a multitude of tissues. However, collecting validated IHC data remains a bottleneck problem, as the standard method is manual microscopical analysis. Here we present a high-throughput strategy...<br/><br/>Sara Strömberg, Marcus Gry Björklund, Caroline Asplund, Anna Sköllermo, Anja Persson, Kenneth Wester, Caroline Kampf, Peter Nilsson, Ann-Catrin Andersson, Mathias Uhlen, Juha Kononen, Fredrik Ponten, Anna Asplund (2007) <i>Proteomics</i> <i></i> <i></i> 7: 13 2142-2150<br/>

http://publicationslist.org/nipe/refid27 2007-11-02T07:05:17Z

p53 triggers apoptosis in response to cellular stress. We analyzed p53-dependent gene and protein expression in response to hypoxia using wild-type p53-carrying or p53 null HCT116 colon carcinoma cells. Hypoxia induced p53 protein levels and p53-dependent apoptosis in these cells. cDNA microarray analysis revealed that only a limited number of genes were regulated by p53 upon hypoxia. Most classic...<br/><br/>T Liu, C Laurell, G Selivanova, J Lundeberg, P Nilsson, K G Wiman (2007) <i>Cell Death Differ</i> <i></i> <i></i> 14: 3 411-421<br/>

http://publicationslist.org/nipe/refid22 2007-11-02T07:05:17Z

The extent to which duplications and deletions occur in the Plasmodium falciparum genome, outside of the subtelomeres, and their contribution to the virulence of the malaria parasite is not known. Here we show the presence of multiple genome wide copy number polymorphisms (CNPs) covering 82 genes, the most extensive spanning a cumulative size of 110kilobases. CNPs were identified in both laborator...<br/><br/>Ulf Ribacke, Bobo W Mok, Valtteri Wirta, Johan Normark, Joakim Lundeberg, Fred Kironde, Thomas G Egwang, Peter Nilsson, Mats Wahlgren (2007) <i>Mol Biochem Parasitol</i> <i></i> <i></i> 155: 1 33-44<br/>

http://publicationslist.org/nipe/refid25 2007-11-02T07:05:17Z

Estrogens cause intrahepatic cholestasis in susceptible women during pregnancy, after administration of oral contraceptives, or during postmenopausal hormone replacement therapy. 17alpha-Ethinylestradiol (EE) is a synthetic estrogen widely used to cause experimental cholestasis in rodents with the aim of examining molecular mechanisms involved in this disease. EE actions on the liver are thought t...<br/><br/>L A Henríquez-Hernández, A Flores-Morales, R Santana-Farré, M Axelson, P Nilsson, G Norstedt, L Fernández-Pérez (2007) <i>J Pharmacol Exp Ther</i> <i></i> <i></i> 320: 2 695-705<br/>

http://publicationslist.org/nipe/refid61 2010-03-31T13:10:18Z

Objective: Chronic fatigue syndrome (CFS) is an illness defined by unexplained disabling fatigue lasting longer than six months, together with at least four out of eight specified symptoms. The etiology and pathophysiology of CFS are to a large degree unknown. Since much remains unclear about CFS we wanted to investigate transcript expression levels in peripheral blood mononuclear cells to identif...<br/><br/>Gräns, H., Evengård, B. and Nilsson, P. (2007) <i>J Chronic Fatigue Syndrome</i> 14: 3 7-25<br/>

http://publicationslist.org/nipe/refid1 2007-11-02T06:58:23Z

Zhichao Pei, Hui Yu, Matthias Theurer, Annelie Waldén, Peter Nilsson, Mingdi Yan, Olof Ramström (2007) <i>Chembiochem</i> <i></i> <i></i> 8: 2 166-168<br/>

http://publicationslist.org/nipe/refid5 2007-11-02T06:58:23Z

BACKGROUND: Various types of amplification techniques have been developed in order to enable microarray gene expression analysis when the amount of starting material is limited. The two main strategies are linear amplification, using in vitro transcription, and exponential amplification, based on PCR. We have evaluated the performance of a linear and an in-house developed exponential amplification...<br/><br/>Cecilia Laurell, Valtteri Wirta, Peter Nilsson, Joakim Lundeberg (2007) <i>J Biotechnol</i> <i></i> <i></i> 127: 4 638-646<br/>

http://publicationslist.org/nipe/refid4 2007-11-02T06:58:23Z

One of the major challenges of antibody-based proteomics is the quality assurance of the generated antibodies to ensure specificity to the target protein. Here we describe a single tube multiplex approach to simultaneously analyze the binding of antibodies to a large number of different antigens. This bead-based assay utilizes the full multiplexing capacity theoretically offered by the Luminex sus...<br/><br/>Jochen M Schwenk, Johan Lindberg, Mårten Sundberg, Mathias Uhlén, Peter Nilsson (2007) <i>Mol Cell Proteomics</i> <i></i> <i></i> 6: 1 125-132<br/>

http://publicationslist.org/nipe/refid28 2007-11-02T07:05:17Z

BACKGROUND: The mechanisms underlying the progression of prostate cancer to androgen-resistant cancer are still not fully understood. Here, we studied the genetic events associated with this transformation. METHODS: The androgen sensitive prostate cancer cells line LNCaP-FGC and its androgen resistant subline LNCaP-r were investigated using SKY, CGH, and cDNA microarray. RESULTS: Karyotypically, s...<br/><br/>See-Tong Pang, Wen-Hui Weng, Amilcar Flores-Morales, Björn Johansson, Mohammad R Pourian, Peter Nilsson, Ake Pousette, Catharina Larsson, Gunnar Norstedt (2006) <i>Prostate</i> <i></i> <i></i> 66: 2 157-172<br/>

http://publicationslist.org/nipe/refid35 2007-11-02T07:10:51Z

Stems and branches of angiosperm trees form tension wood (TW) when exposed to a gravitational stimulus. One of the main characteristics of TW, which distinguishes it from normal wood, is the formation of fibers with a thick inner gelatinous cell wall layer mainly composed of crystalline cellulose. Hence TW is enriched in cellulose, and deficient in lignin and hemicelluloses. An expressed sequence ...<br/><br/>Sara Andersson-Gunnerås, Ewa J Mellerowicz, Jonathan Love, Bo Segerman, Yasunori Ohmiya, Pedro M Coutinho, Peter Nilsson, Bernard Henrissat, Thomas Moritz, Björn Sundberg (2006) <i>Plant J</i> <i></i> <i></i> 45: 2 144-165<br/>

http://publicationslist.org/nipe/refid30 2007-11-02T07:10:51Z

The genetic nature of tree adaptation to drought stress was examined by utilizing variation in the drought response of a full-sib second generation (F(2)) mapping population from a cross between Populus trichocarpa (93-968) and P. deltoides Bart (ILL-129) and known to be highly divergent for a vast range of phenotypic traits. We combined phenotyping, quantitative trait loci (QTL) analysis and micr...<br/><br/>Nathaniel Robert Street, Oskar Skogström, Andreas Sjödin, James Tucker, Maricela Rodríguez-Acosta, Peter Nilsson, Stefan Jansson, Gail Taylor (2006) <i>Plant J</i> <i></i> <i></i> 48: 3 321-341<br/>

http://publicationslist.org/nipe/refid34 2007-11-02T07:10:51Z

In recent years microarray technology has been used increasingly to acquire knowledge about the pathogenic processes involved in rheumatoid arthritis. The present study investigated variations in gene expression in synovial tissues within and between patients with rheumatoid arthritis. This was done by applying microarray technology on multiple synovial biopsies obtained from the same knee joints....<br/><br/>Johan Lindberg, Erik af Klint, Ann-Kristin Ulfgren, André Stark, Tove Andersson, Peter Nilsson, Lars Klareskog, Joakim Lundeberg (2006) <i>Arthritis Res Ther</i> <i></i> <i></i> 8: 2 <br/>

http://publicationslist.org/nipe/refid32 2007-11-02T07:10:51Z

A new and flexible technology for high throughput analysis of antibody specificity and affinity is presented. The method is based on microfluidics and takes advantage of compact disks (CDs) in which the centrifugal force moves fluids through microstructures containing immobilized metal affinity chromatography columns. Analyses are performed as a sandwich assay, where antigen is captured to the col...<br/><br/>Cecilia Eriksson, Charlotta Agaton, Rikard Kånge, Mårten Sundberg, Peter Nilsson, Bo Ek, Mathias Uhlén, Magnus Gustafsson, Sophia Hober (2006) <i>J Proteome Res</i> <i></i> <i></i> 5: 7 1568-1574<br/>

http://publicationslist.org/nipe/refid31 2007-11-02T07:10:51Z

The pentose metabolism of Archaea is largely unknown. Here, we have employed an integrated genomics approach including DNA microarray and proteomics analyses to elucidate the catabolic pathway for D-arabinose in Sulfolobus solfataricus. During growth on this sugar, a small set of genes appeared to be differentially expressed compared with growth on D-glucose. These genes were heterologously overex...<br/><br/>Stan J J Brouns, Jasper Walther, Ambrosius P L Snijders, Harmen J G van de Werken, Hanneke L D M Willemen, Petra Worm, Marjon G J de Vos, Anders Andersson, Magnus Lundgren, Hortense F M Mazon, Robert H H van den Heuvel, Peter Nilsson, Laurent Salmon, Willem M de Vos, Phillip C Wright, Rolf Bernander, John van der Oost (2006) <i>J Biol Chem</i> <i></i> <i></i> 281: 37 27378-27388<br/>

http://publicationslist.org/nipe/refid26 2007-11-02T07:05:17Z

The increasing accessibility and use of microarrays in transcriptomics has accentuated the need for purpose-designed storage and analysis tools. Here we present UPSC-BASE, a database for analysis and storage of Populus DNA microarray data. A microarray analysis pipeline has also been established to allow consistent and efficient analysis (from small to large scale) of samples in various experiment...<br/><br/>Andreas Sjödin, Max Bylesjö, Oskar Skogström, Daniel Eriksson, Peter Nilsson, Patrik Rydén, Stefan Jansson, Jan Karlsson (2006) <i>Plant J</i> <i></i> <i></i> 48: 5 806-817<br/>

http://publicationslist.org/nipe/refid2 2007-11-02T06:58:23Z

We examined the gene expression profiles in arthroscopic biopsies retrieved from 10 rheumatoid arthritis patients before and after anti-TNF treatment with infliximab to investigate whether such profiles can be used to predict responses to the therapy, and to study effects of the therapy on the profiles. Responses to treatment were assessed using European League Against Rheumatism response criteria...<br/><br/>Johan Lindberg, Erik af Klint, Anca Irinel Catrina, Peter Nilsson, Lars Klareskog, Ann-Kristin Ulfgren, Joakim Lundeberg (2006) <i>Arthritis Res Ther</i> <i></i> <i></i> 8: 6 <br/>

http://publicationslist.org/nipe/refid6 2007-11-02T06:58:23Z

Monospecific antibodies dfdfdfdf (msAbs) generated through antigen specific purification of polyclonal antisera are valuable tools in proteome analyses. However, proteome wide generation of msAbs would require extensive immunization programs. Therefore, it would be desirable to develop efficient immunization and purification methods to reduce the number of animals needed for such antibody-based re...<br/><br/>Karin Larsson, Kenneth Wester, Peter Nilsson, Mathias Uhlén, Sophia Hober, Henrik Wernérus (2006) <i>J Immunol Methods</i> <i></i> <i></i> 315: 1-2 110-120<br/>

http://publicationslist.org/nipe/refid7 2007-11-02T06:58:23Z

A great many platforms and versions of the microarray technology, with different characteristics and applications, have been developed. This review will describe some key issues in reliability and performance with the two most commonly used platforms for gene expression analysis, in situ-synthesized oligonucleotide microarrays or GeneChips and spotted microarrays. Some recent advances and new appl...<br/><br/>Maria Sievertzon, Peter Nilsson, Joakim Lundeberg (2006) <i>Expert Rev Mol Diagn</i> <i></i> <i></i> 6: 3 481-492<br/>

http://publicationslist.org/nipe/refid3 2007-11-02T06:58:23Z

BACKGROUND: Transcript half-lives differ between organisms, and between groups of genes within the same organism. The mechanisms underlying these differences are not clear, nor are the biochemical properties that determine the stability of a transcript. To address these issues, genome-wide mRNA decay studies have been conducted in eukaryotes and bacteria. In contrast, relatively little is known ab...<br/><br/>Anders F Andersson, Magnus Lundgren, Stefan Eriksson, Magnus Rosenlund, Rolf Bernander, Peter Nilsson (2006) <i>Genome Biol</i> <i></i> <i></i> 7: 10 <br/>

http://publicationslist.org/nipe/refid33 2007-11-02T07:10:51Z

In the exploding field of gene expression techniques such as DNA microarrays, there are still few general probabilistic methods for analysis of variance. Linear models and ANOVA are heavily used tools in many other disciplines of scientific research. The usual F-statistic is unsatisfactory for microarray data, which explore many thousand genes in parallel, with few replicates. We present three pot...<br/><br/>Ingrid Lönnstedt, Rebecca Rimini, Peter Nilsson (2005) <i>Stat Appl Genet Mol Biol</i> <i></i> <i></i> 4: <br/>

http://publicationslist.org/nipe/refid8 2007-11-02T06:58:23Z

A great need exists for the systematic generation of specific antibodies to explore the human proteome. Here, we show that antibodies specific to human proteins can be generated in a high-throughput manner involving stringent affinity purification using recombinant protein epitope signature tags (PrESTs) as immunogens and affinity-ligands. The specificity of the generated affinity reagents, here c...<br/><br/>Peter Nilsson, Linda Paavilainen, Karin Larsson, Jenny Odling, Mårten Sundberg, Ann-Catrin Andersson, Caroline Kampf, Anja Persson, Cristina Al-Khalili Szigyarto, Jenny Ottosson, Erik Björling, Sophia Hober, Henrik Wernérus, Kenneth Wester, Fredrik Pontén, Mathias Uhlen (2005) <i>Proteomics</i> <i></i> <i></i> 5: 17 4327-4337<br/>

http://publicationslist.org/nipe/refid10 2007-11-02T06:58:23Z

BACKGROUND: Transcriptional profiling using microarrays has developed into a key molecular tool for the elucidation of gene function and gene regulation. Microarray platforms based on either oligonucleotides or purified amplification products have been utilised in parallel to produce large amounts of data. Irrespective of platform examined, the availability of genome sequence or a large number of ...<br/><br/>Valtteri Wirta, Anders Holmberg, Morten Lukacs, Peter Nilsson, Pierre Hilson, Mathias Uhlén, Rishikesh P Bhalerao, Joakim Lundeberg (2005) <i>BMC Biotechnol</i> <i></i> <i></i> 5: <br/>

http://publicationslist.org/nipe/refid11 2007-11-02T06:58:23Z

MOTIVATION: Microarray experiments using probes covering a whole transcriptome are expensive to initiate, and a major part of the costs derives from synthesizing gene-specific PCR primers or hybridization probes. The high costs may force researchers to limit their studies to a single organism, although comparing gene expression in different species would yield valuable information. RESULTS: We hav...<br/><br/>Anders Andersson, Rolf Bernander, Peter Nilsson (2005) <i>Bioinformatics</i> <i></i> <i></i> 21: 3 325-332<br/>

http://publicationslist.org/nipe/refid9 2007-11-02T06:58:23Z

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...<br/><br/>Mathias Uhlén, Erik Björling, Charlotta Agaton, Cristina Al-Khalili Szigyarto, Bahram Amini, Elisabet Andersen, Ann-Catrin Andersson, Pia Angelidou, Anna Asplund, Caroline Asplund, Lisa Berglund, Kristina Bergström, Harry Brumer, Dijana Cerjan, Marica Ekström, Adila Elobeid, Cecilia Eriksson, Linn Fagerberg, Ronny Falk, Jenny Fall, Mattias Forsberg, Marcus Gry Björklund, Kristoffer Gumbel, Asif Halimi, Inga Hallin, Carl Hamsten, Marianne Hansson, My Hedhammar, Görel Hercules, Caroline Kampf, Karin Larsson, Mats Lindskog, Wald Lodewyckx, Jan Lund, Joakim Lundeberg, Kristina Magnusson, Erik Malm, Peter Nilsson, Jenny Odling, Per Oksvold, Ingmarie Olsson, Emma Oster, Jenny Ottosson, Linda Paavilainen, Anja Persson, Rebecca Rimini, Johan Rockberg, Marcus Runeson, Asa Sivertsson, Anna Sköllermo, Johanna Steen, Maria Stenvall, Fredrik Sterky, Sara Strömberg, Mårten Sundberg, Hanna Tegel, Samuel Tourle, Eva Wahlund, Annelie Waldén, Jinghong Wan, Henrik Wernérus, Joakim Westberg, Kenneth Wester, Ulla Wrethagen, Lan Lan Xu, Sophia Hober, Fredrik Pontén (2005) <i>Mol Cell Proteomics</i> <i></i> <i></i> 4: 12 1920-1932<br/>

http://publicationslist.org/nipe/refid42 2007-11-02T07:10:51Z

BACKGROUND: Poplar (Populus sp.) has emerged as the main model system for molecular and genetic studies of forest trees. A Populus expressed sequence tag (EST) database (POPULUSDB) was previously created from 19 cDNA libraries each originating from different Populus tree tissues, and opened to the public in September 2004. We used this dataset for in silico transcript profiling of a particular pro...<br/><br/>Charleen Moreau, Nikolay Aksenov, Maribel García Lorenzo, Bo Segerman, Christiane Funk, Peter Nilsson, Stefan Jansson, Hannele Tuominen (2005) <i>Genome Biol</i> <i></i> <i></i> 6: 4 <br/>

http://publicationslist.org/nipe/refid36 2007-11-02T07:10:51Z

BACKGROUND: Distinguishing between adrenocortical adenomas and carcinomas is often difficult. Our aim was to investigate the differences in transcriptional profiles between benign and malignant adrenocortical neoplasms using complementary DNA microarray techniques. METHODS: We studied 7 patients with adrenocortical carcinomas and 13 with adenomas. Histopathology was reviewed in all patients; clini...<br/><br/>David Velázquez-Fernández, Cecilia Laurell, Janos Geli, Anders Höög, Jacob Odeberg, Magnus Kjellman, Joakim Lundeberg, Bertil Hamberger, Peter Nilsson, Martin Bäckdahl (2005) <i>Surgery</i> <i></i> <i></i> 138: 6 1087-1094<br/>

http://publicationslist.org/nipe/refid43 2007-11-02T07:10:51Z

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...<br/><br/>Henrik Aspeborg, Jarmo Schrader, Pedro M Coutinho, Mark Stam, Asa Kallas, Soraya Djerbi, Peter Nilsson, Stuart Denman, Bahram Amini, Fredrik Sterky, Emma Master, Göran Sandberg, Ewa Mellerowicz, Björn Sundberg, Bernard Henrissat, Tuula T Teeri (2005) <i>Plant Physiol</i> <i></i> <i></i> 137: 3 983-997<br/>

http://publicationslist.org/nipe/refid40 2007-11-02T07:10:51Z

OBJECTIVES: Several cancer prevention programmes have previously been executed using treatment of antioxidant compounds. The antioxidant N-acetyl L-cysteine (NAC), a membrane-permeable aminothiol, is a sulfhydryl reductant reducing oxidised glutathione, as well as being a precursor of intracellular cysteine and glutathione. A previous report based on the cellular response to NAC treatment showed t...<br/><br/>Esther Edlundh-Rose, Ilya Kupershmidt, Anna C Gustafsson, Tiziana Parasassi, Annalucia Serafino, Luisa Bracci-Laudiero, Giulia Greco, Ewa K Krasnowska, Maria-Concetta Romano, Thomas Lundeberg, Peter Nilsson, Joakim Lundeberg (2005) <i>Pathobiology</i> <i></i> <i></i> 72: 4 203-212<br/>

http://publicationslist.org/nipe/refid41 2007-11-02T07:10:51Z

The genetic variability of Helicobacter pylori is known to be high compared to that of many other bacterial species. H. pylori is adapted to the human stomach, where it persists for decades, and adaptation to each host results in every individual harboring a distinctive bacterial population. Although clonal variants may exist within such a population, all isolates are generally genetically related...<br/><br/>Annelie Lundin, Britta Björkholm, Ilya Kupershmidt, Magnus Unemo, Peter Nilsson, Dan I Andersson, Lars Engstrand (2005) <i>Infect Immun</i> <i></i> <i></i> 73: 8 4818-4822<br/>

http://publicationslist.org/nipe/refid39 2007-11-02T07:10:51Z

There is a great need for comprehensive proteomic analysis of large patient cohorts of plasma and serum samples to identify biomarkers of human diseases. Here we describe a new antibody-based proteomic approach involving a reverse array format where serum samples are spotted on a microarray. This enables all samples to be screened for their content of a certain serum protein in a single experiment...<br/><br/>Magdalena Janzi, Jenny Odling, Qiang Pan-Hammarström, Mårtenn Sundberg, Joakim Lundeberg, Mathias Uhlén, Lennart Hammarström, Peter Nilsson (2005) <i>Mol Cell Proteomics</i> <i></i> <i></i> 4: 12 1942-1947<br/>

http://publicationslist.org/nipe/refid38 2007-11-02T07:10:51Z

H Gräns, P Nilsson, B Evengard (2005) <i>J Intern Med</i> <i></i> <i></i> 258: 4 388-390<br/>

http://publicationslist.org/nipe/refid37 2007-11-02T07:10:51Z

A flavivirus microarray was developed for detection and identification of yellow fever (YF), West Nile, Japanese encephalitis (JE), and the dengue 1-4 viruses, which are causing severe human disease all over the world. The microarray was based on 500-nucleotide probe fragments from five different parts of the seven viral genomes. A low-stringent amplification method targeting the corresponding reg...<br/><br/>Henrik Nordström, Kerstin I Falk, Gunnel Lindegren, Mehrdad Mouzavi-Jazi, Annelie Waldén, Fredrik Elgh, Peter Nilsson, Ake Lundkvist (2005) <i>J Med Virol</i> <i></i> <i></i> 77: 4 528-540<br/>

http://publicationslist.org/nipe/refid51 2007-11-02T07:20:29Z

DNA microarrays combine high-precision technology with advanced molecular biology to achieve high-throughput screening of DNA fragments. In this study, we investigated the potential of the cDNA microarray technique to identify and discriminate PCR derived amplicons from genetically highly similar viruses. The wide range of sequence variation among hantaviruses makes them suitable as a model for th...<br/><br/>Henrik Nordström, Patrik Johansson, Quan-Gen Li, Ake Lundkvist, Peter Nilsson, Fredrik Elgh (2004) <i>J Med Virol</i> <i></i> <i></i> 72: 4 646-655<br/>

http://publicationslist.org/nipe/refid59 2010-03-31T13:13:59Z

Cellulose is synthesized in plant cell walls by large membrane-bound protein complexes proposed to contain several copies of the catalytic subunit of the cellulose synthase, CesA. Here we report identification of 10 distinct CesA genes within a database of 100,000 ESTs of the hybrid aspen, Populus tremula (L.) × P. tremuloides (Michx.). Expression analyses in normal wood undergoing xylogenesis an...<br/><br/>Djerbi, S., Aspeborg, H., Nilsson, P., Sundberg, B., Mellerowicz, E., Blomqvist, K. and Teeri, T. T. (2004) <i>Cellulose</i> 11: 3-4 301-312<br/>

http://publicationslist.org/nipe/refid54 2007-11-02T07:23:52Z

Deletions and duplications of genomic segments commonly cause developmental disorders. The resolution and efficiency in diagnosing such gene-dosage alterations can be drastically increased using microarray-based comparative genomic hybridization (array-CGH). However, array-CGH currently relies on spotting genomic clones as targets, which confers severe limitations to the approach including resolut...<br/><br/>Kiran Kumar Mantripragada, Isabel Tapia-Páez, Elisabeth Blennow, Peter Nilsson, Anna Wedell, Jan P Dumanski (2004) <i>Int J Mol Med</i> <i></i> <i></i> 13: 2 273-279<br/>

http://publicationslist.org/nipe/refid12 2007-11-02T06:58:23Z

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 stu...<br/><br/>Anders Andersson, Johanna Keskitalo, Andreas Sjödin, Rupali Bhalerao, Fredrik Sterky, Kirsten Wissel, Karolina Tandre, Henrik Aspeborg, Richard Moyle, Yasunori Ohmiya, Rishikesh Bhalerao, Amy Brunner, Petter Gustafsson, Jan Karlsson, Joakim Lundeberg, Ove Nilsson, Göran Sandberg, Steven Strauss, Björn Sundberg, Mathias Uhlen, Stefan Jansson, Peter Nilsson (2004) <i>Genome Biol</i> <i></i> <i></i> 5: 4 <br/>

http://publicationslist.org/nipe/refid53 2007-11-02T07:23:52Z

Here we describe an amplification method for global transcript analysis. The strategy relies on amplification of cDNA tags (signature tags) achieved by random fragmentation of the cDNAs to short tags of similar length, isolation of the 3' ends and then PCR amplification of the 3'-end signature tag population. This method minimizes biased amplification that may occur during parallel amplification o...<br/><br/>Maria Sievertzon, Charlotta Agaton, Peter Nilsson, Joakim Lundeberg (2004) <i>Biotechniques</i> <i></i> <i></i> 36: 2 253-259<br/>

http://publicationslist.org/nipe/refid44 2007-11-02T07:10:51Z

The establishment of the dormant state in meristems involves considerable physiological and metabolic alterations necessary for surviving unfavourable growth conditions. However, a global molecular analysis of dormancy in meristems has been hampered by the difficulty in isolating meristem cells. We used cryosectioning to isolate purified cambial meristem cells from the woody plant Populus tremula ...<br/><br/>Jarmo Schrader, Richard Moyle, Rupali Bhalerao, Magnus Hertzberg, Joakim Lundeberg, Peter Nilsson, Rishikesh P Bhalerao (2004) <i>Plant J</i> <i></i> <i></i> 40: 2 173-187<br/>

http://publicationslist.org/nipe/refid72 2010-06-21T22:46:28Z

In this paper we aim to create a reference data collection of Northern blot results and demonstrate how such a collection can enable a quantitative comparison of modern expression profiling techniques, a central component of functional genomics studies. Historically, Northern blots were the de facto standard for determining RNA transcript levels. However, driven by the demand for analysis of large...<br/><br/>Danielle Kemmer, Margareta Faxén, Emily Hodges, Jonathan Lim, Elena Herzog, Elsebrit Ljungström, Anders Lundmark, Mary K Olsen, Raf Podowski, Erik L L Sonnhammer, Peter Nilsson, Mark Reimers, Boris Lenhard, Steven L Roberds, Claes Wahlestedt, Christer Höög, Pankaj Agarwal, Wyeth W Wasserman (2004) <i>Comp Funct Genomics</i> <i></i> <i></i> 5: 8 584-595<br/>

http://publicationslist.org/nipe/refid47 2007-11-02T07:10:51Z

Chromosome replication origins were mapped in vivo in the two hyperthermophilic archaea, Sulfolobus acidocaldarius and Sulfolobus solfataricus, by using microarray-based marker frequency analysis. Bidirectional replication was found to be initiated in near synchrony from three separate sites in both organisms. Two of the three replication origins in each species were located in the vicinity of a c...<br/><br/>Magnus Lundgren, Anders Andersson, Lanming Chen, Peter Nilsson, Rolf Bernander (2004) <i>Proc Natl Acad Sci U S A</i> <i></i> <i></i> 101: 18 7046-7051<br/>

http://publicationslist.org/nipe/refid45 2007-11-02T07:10:51Z

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...<br/><br/>Fredrik Sterky, Rupali R Bhalerao, Per Unneberg, Bo Segerman, Peter Nilsson, Amy M Brunner, Laurence Charbonnel-Campaa, Jenny Jonsson Lindvall, Karolina Tandre, Steven H Strauss, Björn Sundberg, Petter Gustafsson, Mathias Uhlén, Rishikesh P Bhalerao, Ove Nilsson, Göran Sandberg, Jan Karlsson, Joakim Lundeberg, Stefan Jansson (2004) <i>Proc Natl Acad Sci U S A</i> <i></i> <i></i> 101: 38 13951-13956<br/>

http://publicationslist.org/nipe/refid46 2007-11-02T07:10:51Z

Plant growth is the result of cell proliferation in meristems, which requires a careful balance between the formation of new tissue and the maintenance of a set of undifferentiated stem cells. Recent studies have provided important information on several genetic networks responsible for stem cell maintenance and regulation of cell differentiation in the apical meristems of shoots and roots. Nothin...<br/><br/>Jarmo Schrader, Jeanette Nilsson, Ewa Mellerowicz, Anders Berglund, Peter Nilsson, Magnus Hertzberg, Göran Sandberg (2004) <i>Plant Cell</i> <i></i> <i></i> 16: 9 2278-2292<br/>

http://publicationslist.org/nipe/refid55 2007-11-02T07:23:52Z

We describe a microfluidic approach for allele-specific extension of fluorescently labeled nucleotides for scoring of single-nucleotide polymorphism (SNP). The method takes advantage of the fact that the reaction kinetics differs between matched and mismatched configurations of allele-specific primers hybridized to DNA template. A microfluidic flow-through device for biochemical reactions on beads...<br/><br/>Aman Russom, Afshin Ahmadian, Helene Andersson, Peter Nilsson, Göran Stemme (2003) <i>Electrophoresis</i> <i></i> <i></i> 24: 1-2 158-161<br/>

http://publicationslist.org/nipe/refid48 2007-11-02T07:10:51Z

Transgenic lines of hybrid aspen with elevated levels of gibberellin (GA) show greatly increased numbers of xylem fibres and increases in xylem fibre length. These plants therefore provide excellent models for studying secondary growth. We have used cDNA microarry analysis to investigate how gene transcription in the developing xylem is affected by GA-induced growth. A recent investigation has sho...<br/><br/>Maria Israelsson, Maria E Eriksson, Magnus Hertzberg, Henrik Aspeborg, Peter Nilsson, Thomas Moritz (2003) <i>Plant Mol Biol</i> <i></i> <i></i> 52: 4 893-903<br/>

http://publicationslist.org/nipe/refid56 2007-11-02T07:27:07Z

A Ahmadian, A Russom, H Andersson, M Uhlén, G Stemme, P Nilsson (2002) <i>Biotechniques</i> 32: 4 <br/>

http://publicationslist.org/nipe/refid14 2007-11-02T06:58:23Z

Various approaches to the study of differential gene expression are applied to compare cell lines and tissue samples in a wide range of biological contexts. The compromise between focusing on only the important genes in certain cellular processes and achieving a complete picture is critical for the selection of strategy. We demonstrate how global microarray technology can be used for the explorati...<br/><br/>T Andersson, P Unneberg, P Nilsson, J Odeberg, J Quackenbush, J Lundeberg (2002) <i>Biotechniques</i> <i></i> <i></i> 32: 6 1348-50, 1352, 1354-6, 1358<br/>

http://publicationslist.org/nipe/refid13 2007-11-02T06:58:23Z

Pyrosequencing is a four-enzyme bioluminometric DNA sequencing technique based on a DNA sequencing by synthesis principle. Currently, the technique is limited to analysis of short DNA sequences exemplified by single-nucleotide polymorphism analysis. In order to expand the field for pyrosequencing, the read length needs to be improved and efforts have been made to purify reaction components as well...<br/><br/>Maria Ehn, Afshin Ahmadian, Peter Nilsson, Joakim Lundeberg, Sophia Hober (2002) <i>Electrophoresis</i> <i></i> <i></i> 23: 19 3289-3299<br/>

http://publicationslist.org/nipe/refid49 2007-11-02T07:16:39Z

The large vascular meristem of poplar trees with its highly organized secondary xylem enables the boundaries between different developmental zones to be easily distinguished. This property of wood-forming tissues allowed us to determine a unique tissue-specific transcript profile for a well defined developmental gradient. RNA was prepared from different developmental stages of xylogenesis for DNA ...<br/><br/>M Hertzberg, H Aspeborg, J Schrader, A Andersson, R Erlandsson, K Blomqvist, R Bhalerao, M Uhlén, T T Teeri, J Lundeberg, B Sundberg, P Nilsson, G Sandberg (2001) <i>Proc Natl Acad Sci U S A</i> <i></i> <i></i> 98: 25 14732-14737<br/>

http://publicationslist.org/nipe/refid57 2010-03-31T13:16:47Z

The suitability of valve-less micropumps in biochemistry has been shown. Fluids encountered in various biochemical methods that are problematic for other micropumps have been pumped with good performance. The pump is fabricated as a silicon-glass stack with a new process involving three subsequent deep reactive ion etching steps. Some of the main advantages of the valve-less diffuser pump are the ...<br/><br/>H Andersson, W van der Wijngaart, P Nilsson, P Enoksson and G Stemme (2001) <i>Sensors Actuat B</i> 72: 259-265<br/>

http://publicationslist.org/nipe/refid15 2007-11-02T06:58:23Z

Escherichia coli (E. coli) single-stranded binding protein (SSB) is a valuable protein for various biotechnical applications, such as PCR and DNA sequencing. Here we describe an efficient expression and purification scheme where the tendency of SSB to aggregate at low salt concentration and high protein concentration is avoided. The method contains fewer steps of purification and results in high p...<br/><br/>M Ehn, P Nilsson, M Uhlén, S Hober (2001) <i>Protein Expr Purif</i> <i></i> <i></i> 22: 1 120-127<br/>

http://publicationslist.org/nipe/refid16 2007-11-02T06:58:23Z

Microarray technology is becoming an important comprehensive tool to study gene expression in plants. However, the use of this technology is limited by the large amount of sample tissue needed for microarray analysis. Generally, 50-200 microg of total RNA and 1-2 microg of mRNA is required for each hybridisation, which is equivalent to 50-100 mg of plant tissue. This requirement for large amounts ...<br/><br/>M Hertzberg, M Sievertzon, H Aspeborg, P Nilsson, G Sandberg, J Lundeberg (2001) <i>Plant J</i> <i></i> <i></i> 25: 5 585-591<br/>

http://publicationslist.org/nipe/refid18 2007-11-02T06:58:23Z

Here, we describe a new approach for mutational scanning of PCR products through hybridization analysis between complementary oligonucleotides. Sets of overlapping probe oligonucleotides complementary to wild-type (WT) sequence are hybridized to microbead-immobilized PCR products under solution-like conditions. Mismatch-hybridization situations between a mutant sample and probe oligonucleotides re...<br/><br/>P Nilsson, A Larsson, J Lundeberg, M Uhlén, P A Nygren (1999) <i>Biotechniques</i> <i></i> <i></i> 26: 2 308-316<br/>

http://publicationslist.org/nipe/refid17 2007-11-02T06:58:23Z

The effect on oligonucleotide-template duplex stability upon cohybridization of adjacently annealing oligonucleotides, the modular primer effect, was studied with biosensor technology. DNA and peptide nucleic acid (PNA) hexamer modules and sensor chip-immobilized template DNA strands were designed for analysis of nick, overlap, and gap modular hybridization situations. The fast hybridization kinet...<br/><br/>P Nilsson, D O'meara, F Edebratt, B Persson, M Uhlén, J Lundeberg, P Nygren (1999) <i>Anal Biochem</i> <i></i> <i></i> 269: 1 155-161<br/>

http://publicationslist.org/nipe/refid19 2007-11-02T06:58:23Z

Real-time biospecific interaction analysis was employed to monitor direct capture of a hepatitis C virus (HCV) derived polymerase chain reaction (PCR) product by nucleic acid hybridization. Different formats for hybridization were used to study the interaction between a single-stranded HCV PCR product and capture oligonucleotides immobilized on a sensor chip via streptavidin-biotin chemistry. By e...<br/><br/>D O'Meara, P Nilsson, P A Nygren, M Uhlén, J Lundeberg (1998) <i>Anal Biochem</i> <i></i> <i></i> 255: 2 195-203<br/>

http://publicationslist.org/nipe/refid60 2010-03-31T13:25:28Z

Nilsson, P., Persson, B., Uhlén, M. and Nygren, P.-Å (1997) <i>Laboratory methods for the detection of mutations and polymorphisms in DNA</i> p253-261,<br/>

http://publicationslist.org/nipe/refid50 2007-11-02T07:16:39Z

A novel strategy for real-time analysis of oligonucleotide probe hybridization based on detection by surface plasmon resonance is described. The design of the analysis, exploiting the rapid dissociation kinetics of short oligonucleotides from their hybridization templates, allows monitoring in genuine sensor mode of equilibrium hybridization responses, circumventing the need for regeneration betwe...<br/><br/>B Persson, K Stenhag, P Nilsson, A Larsson, M Uhlén, P Nygren (1997) <i>Anal Biochem</i> <i></i> <i></i> 246: 1 34-44<br/>

http://publicationslist.org/nipe/refid20 2007-11-02T06:58:23Z

Two different strategies for scanning and screening of mutations in polymerase chain reaction (PCR) products by hybridization analysis are described, employing real-time biospecific interaction analysis (BIA) for detection. Real-time BIA was used to detect differences in hybridization responses between PCR products and different 17-mer oligonucleotide probes. For the analysis using a biosensor ins...<br/><br/>P Nilsson, B Persson, A Larsson, M Uhlén, P A Nygren (1997) <i>J Mol Recognit</i> <i></i> <i></i> 10: 1 7-17<br/>

http://publicationslist.org/nipe/refid52 2007-11-02T07:20:29Z

A system for production of recombinant Fc fragments of human IgG in Escherichia coli has been developed to allow for structural and functional studies of human Fc. The genes for the Fc fragments of human IgG subclasses 1 and 3, designated Fc(1) and Fc(3), were cloned from a human spleen cDNA library. The interactions to Staphylococcal protein A (SpA), a bacterial Fc receptor, that interacts with h...<br/><br/>L Jendeberg, P Nilsson, A Larsson, P Denker, M Uhlén, B Nilsson, P A Nygren (1997) <i>J Immunol Methods</i> <i></i> <i></i> 201: 1 25-34<br/>

http://publicationslist.org/nipe/refid21 2007-11-02T06:58:23Z

The potential of real-time biospecific interaction analysis technology for applications in molecular biology is described. DNA fragments are immobilized onto a biosensor surface using the high-affinity streptavidin-biotin system and subsequently used to monitor different unit operations in molecular biology, e.g., DNA strand separation, DNA hybridization kinetics, and enzymatic modifications. A mo...<br/><br/>P Nilsson, B Persson, M Uhlén, P A Nygren (1995) <i>Anal Biochem</i> <i></i> <i></i> 224: 1 400-408<br/>

http://publicationslist.org/nipe/refid29 2007-11-02T07:05:17Z

A novel system is described for mild elution of fusion proteins by competitive elution. The approach is based on displacement of immobilized fusions containing a monovalent IgG-binding staphylococcal protein A fragment (Z) from an IgG-affinity matrix by a divalent fragment fused to a serum-albumin-binding region derived from streptococcal protein G. Using real-time interaction analysis, the bindin...<br/><br/>J Nilsson, P Nilsson, Y Williams, L Pettersson, M Uhlén, P A Nygren (1994) <i>Eur J Biochem</i> <i></i> <i></i> 224: 1 103-108<br/>