| 1. |
|
|
| 2. |
|
|
| 3. |
- Bräutigam, Marcus, 1968, et al.
(författare)
-
Development of Swedish winter oat with gene technology and molecular breeding
- 2006
-
Ingår i: J. Seed Science. - 0039-6990. ; 116:1-2, s. 12-35
-
Tidskriftsartikel (refereegranskat)abstract
- In Sweden, oat (Avena sativa) is only grown as a spring crop. A Swedish winter oat, on the other hand, would give increased yields and would secure oat in Swedish agriculture. During three consecutive winters we performed field trials with oat aiming at identifying potential winter material. More than 300 varieties, originating from breeding programs all over the world, were tested. Plants were rated according to winter survival, vigour and general performance during the following growth season and more than 20 lines were identified that were cold hardier than present commercial oat varieties. In parallel experiments a cDNA library was constructed from cold induced English winter oat (Gerald) and ca 10000 EST sequences were generated. After data mining a UniGene set of 2800 oat genes was obtained. By detailed analysis of microarray data from cold stressed Arabidopsis and by advanced bioinformatics, gene interactions in the complex cold induced signal transduction pathway were deduced. By comparison to the oat UniGene set, several genes potentially involved in the regulation of cold hardiness in oat were identified. An Agrobacterium mediated transformation protocol was developed for one oat genotype. Key regulatory genes in cold acclimation will be introduced to oat by genetic transformation or modified by TILLING. Such genes will be used as molecular markers in intogression of winter hardiness to commercial oat.
|
|
| 4. |
- Bräutigam, Marcus, 1968, et al.
(författare)
-
Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa
- 2005
-
Ingår i: BMC Plant Biol. - : Springer Science and Business Media LLC. - 1471-2229. ; 5
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Oat is an important crop in North America and northern Europe. In Scandinavia, yields are limited by the fact that oat cannot be used as a winter crop. In order to develop such a crop, more knowledge about mechanisms of cold tolerance in oat is required. RESULTS: From an oat cDNA library 9792 single-pass EST sequences were obtained. The library was prepared from pooled RNA samples isolated from leaves of four-week old Avena sativa (oat) plants incubated at +4 degrees C for 4, 8, 16 and 32 hours. Exclusion of sequences shorter than 100 bp resulted in 8508 high-quality ESTs with a mean length of 710.7 bp. Clustering and assembly identified a set of 2800 different transcripts denoted the Avena sativa cold induced UniGene set (AsCIUniGene set). Taking advantage of various tools and databases, putative functions were assigned to 1620 (58%) of these genes. Of the remaining 1180 unclassified sequences, 427 appeared to be oat-specific since they lacked any significant sequence similarity (Blast E values > 10(-10)) to any sequence available in the public databases. Of the 2800 UniGene sequences, 398 displayed significant homology (BlastX E values < or = 10(-10)) to genes previously reported to be involved in cold stress related processes. 107 novel oat transcription factors were also identified, out of which 51 were similar to genes previously shown to be cold induced. The CBF transcription factors have a major role in regulating cold acclimation. Four oat CBF sequences were found, belonging to the monocot cluster of DREB family ERF/AP2 domain proteins. Finally in the total EST sequence data (5.3 Mbp) approximately 400 potential SSRs were found, a frequency similar to what has previously been identified in Arabidopsis ESTs. CONCLUSION: The AsCIUniGene set will now be used to fabricate an oat biochip, to perform various expression studies with different oat cultivars incubated at varying temperatures, to generate molecular markers and provide tools for various genetic transformation experiments in oat. This will lead to a better understanding of the cellular biology of this important crop and will open up new ways to improve its agronomical properties.
|
|
| 5. |
- Bucin, Dragan, et al.
(författare)
-
Heart transplantation across the antibodies against HLA and ABO
- 2006
-
Ingår i: Transplant International. - : Frontiers Media SA. - 1432-2277 .- 0934-0874. ; 19:3, s. 239-244
-
Tidskriftsartikel (refereegranskat)abstract
- We have intentionally performed heart transplantation in a 5-year-old child, despite the most unfavourable risk factors for patient survival; the presence of high level of antibodies against donor's human leucocyte antigen (HLA) class I/II and blood group antigens. Pretransplant treatment by mycophenolate mofetil, prednisolone, tacrolimus, intravenous immunoglobulin, rituximab, protein-A immunoadsorption (IA) and plasma exchange reduced antibody titres against the donor's lymphocytes from 128 to 16 and against the donor's blood group antigen from 256 to 0. The patient was urgently transplanted with a heart from an ABO incompatible donor (A(1) to O). A standard triple-drug immunosuppressive protocol was used. No hyperacute rejection was seen. Antibodies against the donor's HLA antigens remained at a low level despite three acute rejections. Rising anti-A(1) blood group antibodies preceded the second rejection and were reduced by two blood group-specific IAs and remained at a low level. The patient is doing well despite the persistence of donor-reactive antibodies.
|
|
| 6. |
- Chawade, Aakash, 1980, et al.
(författare)
-
Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors
- 2007
-
Ingår i: BMC GENOMICS. - : Springer Science and Business Media LLC. - 1471-2164. ; 8
-
Tidskriftsartikel (refereegranskat)abstract
- Background With the advent of microarray technology, it has become feasible to identify virtually all genes in an organism that are induced by developmental or environmental changes. However, relying solely on gene expression data may be of limited value if the aim is to infer the underlying genetic networks. Development of computational methods to combine microarray data with other information sources is therefore necessary. Here we describe one such method. Results By means of our method, previously published Arabidopsis microarray data from cold acclimated plants at six different time points, promoter motif sequence data extracted from ~24,000 Arabidopsis promoters and known transcription factor binding sites were combined to construct a putative genetic regulatory interaction network. The inferred network includes both previously characterised and hitherto un-described regulatory interactions between transcription factor (TF) genes and genes that encode other TFs or other proteins. Part of the obtained transcription factor regulatory network is presented here. More detailed information is available in the additional files. Conclusion The rule-based method described here can be used to infer genetic networks by combining data from microarrays, promoter sequences and known promoter binding sites. This method should in principle be applicable to any biological system. We tested the method on the cold acclimation process in Arabidopsis and could identify a more complex putative genetic regulatory network than previously described. However, it should be noted that information on specific binding sites for individual TFs were in most cases not available. Thus, gene targets for the entire TF gene families were predicted. In addition, the networks were built solely by a bioinformatics approach and experimental verifications will be necessary for their final validation. On the other hand, since our method highlights putative novel interactions, more directed experiments could now be performed.
|
|
| 7. |
- Dura, Elzbieta, et al.
(författare)
-
Towards Information Fusion in Pathway Evaluation : Encoding Relations in Biomedical Texts
- 2006
-
Ingår i: 9th International Conference on Information Fusion. - : IEEE. - 9781424409532
-
Konferensbidrag (refereegranskat)abstract
- The long-term goal of the research presented in this paper is to incorporate linguistic text analysis into a system for evaluation of biological pathways. In this system, relations extracted from biomedical texts will be compared with pathways encoded in existing specialized databases. In this way, the biologist's conclusions regarding the plausibility and/or novelty of a certain relation between genes, proteins, etc., can be supported by fused information from biological databases and biological literature. We aim at overcoming the shortcomings of existing systems for information retrieval by proposing a method based on thorough linguistic analysis of a large text corpus. In this paper, we present a comparative analysis of two corpora: one consisting of biomedical texts from PubMed, the other one of general English prose. The results stress the importance of taking multiword entries into account when constructing a system for extracting biological relations from texts
|
|
| 8. |
- Gawronska, Barbara, et al.
(författare)
-
Towards an Automated Analysis of Biomedical Abstracts
- 2006
-
Ingår i: Data Integration in the Life Sciences. - Berlin, Heidelberg : Springer. - 9783540365938 ; , s. 50-65
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- An essential part of bioinformatic research concerns the iterative process of validating hypotheses by analyzing facts stored in databases and in published literature. This process can be enhanced by language technology methods, in particular by automatic text understanding. Since it is becoming increasingly difficult to keep up with the vast number of scientific articles being published, there is a need for more easily accessible representations of the current knowledge. The goal of the research described in this paper is to develop a system aimed to support the large-scale research on metabolic and regulatory pathways by extracting relations between biological objects from descriptions found in literature. We present and evaluate the procedures for semantico-syntactic tagging, dividing the text into parts concerning previous research and current research, syntactic parsing, and transformation of syntactic trees into logical representations similar to the pathway graphs utilized in the Kyoto Encyclopaedia of Genes and Genomes.
|
|
| 9. |
- Gawronska, Barbara, et al.
(författare)
-
Tracking biological relations in texts : a Referent Grammar based approach
- 2005
-
Ingår i: Proceedings of the workshop Biomedical Ontologies and Text Processing, in connection to ECCB/05. ; , s. 15-22
-
Konferensbidrag (refereegranskat)abstract
- In this paper, we describe a method for extracting biological relations (in the first place, relations used in the KEGG ontology of biological pathways) from scientific texts. The main assumption is that correct syntactic analysis combined with domain-specific heuristics provides a good basis for relation extraction. We propose an algorithm that searches through the syntactic trees produced by a parser based on a formalism called Referent Grammar (inspired by Categorial Grammar), identifies relations mentioned in the sentence, and classifies them with respect to their semantic class and epistemic status (facts, counterfactuals, hypotheses).
|
|
| 10. |
- Hägg, Daniel, 1974, et al.
(författare)
-
Expression profiling of macrophages from subjects with atherosclerosis to identify novel susceptibility genes.
- 2008
-
Ingår i: International journal of molecular medicine. - 1107-3756 .- 1791-244X. ; 21:6, s. 697-704
-
Tidskriftsartikel (refereegranskat)abstract
- Although a number of environmental risk factors for atherosclerosis have been identified, heredity seems to be a significant independent risk factor. The aim of our study was to identify novel susceptibility genes for atherosclerosis. The screening process consisted of three steps. First, expression profiles of macrophages from subjects with atherosclerosis were compared to macrophages from control subjects. Secondly, the subjects were genotyped for promoter region polymorphisms in genes with altered gene expression. Thirdly, a population of subjects with coronary heart disease and control subjects were genotyped to test for an association with identified polymorphisms that affected gene expression. Twenty-seven genes were differentially expressed in both macrophages and foam cells from subjects with atherosclerosis. Three of these genes, IRS2, CD86 and SLC11A1 were selected for further analysis. Foam cells from subjects homozygous for the C allele at the -765C-->T SNP located in the promoter region of IRS2 had increased gene expression compared to foam cells from subjects with the nonCC genotype. Also, macrophages and foam cells from subjects homozygous for allele 2 at a repeat element in the promoter region of SLC11A1 had increased gene expression compared to macrophages and foam cells from subjects with the non22 genotype. Genotyping of 512 pairs of subjects with coronary heart disease (CHD) and matched controls revealed that subjects homozygous for C of the IRS2 SNP had an increased risk for CHD; odds ratio 1.43, p=0.010. Immunohistochemical staining of human carotid plaques showed that IRS2 expression was localised to macrophages and endothelial cells in vivo. Our method provides a reliable approach for identifying susceptibility genes for atherosclerosis, and we conclude that elevated IRS2 gene expression in macrophages may be associated with an increased risk of CHD.
|
|
