| 1. |
- GUSTAFSSON, L, et al.
(författare)
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LOW GENETIC-VARIATION IN SWEDISH POPULATIONS OF THE RARE SPECIES VICIA-PISIFORMIS (FABACEAE) REVEALED WITH RFLP (RDNA) AND RAPD
- 1994
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Ingår i: Plant Systematics and Evolution. - 0378-2697 .- 1615-6110. ; 189:3-4, s. 133-148
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Tidskriftsartikel (refereegranskat)abstract
- Nine Swedish populations, 1-5 individuals/population, and one cultivated individual of the rare species Vicia pisiformis were investigated for genetic variation. In hybridizations with two rDNA probes using 8 restriction enzymes, only two individuals belonging to one population were polymorphic. A map of the rDNA gene cluster was constructed for four of the restriction enzymes used. Two of the polymorphic sites were mapped and were found to be located outside regions coding for rRNA, presumably caused by single point mutations or small deletions. The repeat length of the rDNA region was c. 10,000 bp, which corresponds well with the size found for other species belonging to Fabaceae. No length polymorphism was found in the intergenic spacer, contrary to the situation found for most other plant species investigated for rDNA variation. The haplotype diversity for the species (Hsp Shannon) was very low (0.055). Within-population values (Hpop) was 0 for all populations except the variable one, which had 0.301. PCR amplification with 6 random primers also revealed very low levels of genetic diversity. A polymorphism was observed in a limited number of individuals for four populations. Hsp was 0.065 and HpopBAR was 0.050. The average D value (Wetton) for the PCR haplotypes was 0.99.
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| 2. |
- Andersson, Anders, et al.
(författare)
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A transcriptional timetable of autumn senescence
- 2004
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 5:4, s. R24-
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 3. |
- Bhalerao, RP, et al.
(författare)
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Cloning of the cpce and cpcf genes from synechococcus sp pcc-6301 and their inactivation in synechococcus sp pcc-7942
- 1994
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Ingår i: Plant Molecular Biology. - 0167-4412 .- 1573-5028. ; 26:1, s. 313-326
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Tidskriftsartikel (refereegranskat)abstract
- Two open reading frames denoted as cpcE and cpcF were cloned and sequenced from Synechococcus sp. PCC 6301. The cpcE and cpcF genes are located downstream of the cpcB2A2 gene cluster in the phycobilisome rod operon and can be transcribed independently of the upstream cpcB2A2 gene cluster. The cpcE and cpcF genes were separately inactivated by insertion of a kanamycin resistance cassette in Synechococcus sp. PCC 7942 to generate mutants R2EKM and R2FKM, respectively, both of which display a substantial reduction in spectroscopically detectable phycocyanin. The levels of beta- and alpha-phycocyanin polypeptides were reduced in the R2EKM and R2FKM mutants although the phycocyanin and linker genes are transcribed at normal levels in the mutants as in the wild type indicating the requirement of the functional cpcE and cpcF genes for normal accumulation of phycocyanin. Two biliprotein fractions were isolated on sucrose density gradient from the R2EKM/R2FKM mutants. The faster sedimenting fraction consisted of intact phycobilisomes. The slower sedimenting biliprotein fraction was found to lack phycocyanin polypeptides, thus no free phycocyanin was detected in the mutants. Characterization of the phycocyanin from the mutants revealed that it was chromophorylated, had a lambda(max) similar to that from the wild type and could be assembled into the phycobilisome rods. Thus, although phycocyanin levels are reduced in the R2EKM and R2FKM mutants, the remaining phycocyanin seems to be chromophorylated and similar to that in the wild type with respect to phycobilisome rod assembly and energy transfer to the core.
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| 4. |
- Bhalerao, RP, et al.
(författare)
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Cloning of the phycobilisome rod linker genes from the cyanobacterium synechococcus sp pcc-6301 och their inactivation in synechococcus sp pcc-7942
- 1993
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Ingår i: Molecular General Genetics. - 0026-8925 .- 1432-1874. ; 237:1-2, s. 89-96
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Tidskriftsartikel (refereegranskat)abstract
- The phycobilisome rod linker genes in the two closely related cyanobacteria Synechococcus sp. PCC 6301 and Synechococcus sp. PCC 7942 were studied. Southern blot analysis showed that the genetic organization of the phycobilisome rod operon is very similar in the two strains. The phycocyanin gene pair is duplicated and separated by a region of about 2.5 kb. The intervening region between the duplicated phycocyanin gene pair was cloned from Synechococcus sp. PCC 6301 and sequenced. Analysis of this DNA sequence revealed the presence of three open reading frames corresponding to 273, 289 and 81 amino acids, respectively. Insertion of a kanamycin resistance cassette into these open reading frames indicated that they corresponded to the genes encoding the 30, 33 and 9 kDa rod linkers, respectively, as judged by the loss of specific linkers from the phycobilisomes of the insertional mutants. Amino acid compositions of the 30 and 33 kDa linkers derived from the DNA sequence were found to deviate from those of purified 33 and 30 kDa linkers in the amounts of glutamic acid/glutamine residues. On the basis of similarity of the amino acid sequence of the rod linkers between Synechococcus sp. PCC 6301 and Calothrix sp. PCC 7601 we name the genes encoding the 30, 33 and 9 kDa linkers cpcH, cpcI and cpcD, respectively. The three linker genes were found to be co-transcribed on an mRNA of 3700 nucleotides. However, we also detected a smaller species of mRNA, of 3400 nucleotides, which would encode only the cpcH and cpcI genes. The 30 kDa linker was still found in phycobilisome rods lacking the 33 kDa linker and the 9 kDa linker was detected in mutants lacking the 33 or the 30 kDa linkers. Free phycocyanin was found in the mutants lacking the 33 or the 30 kDa linkers, whereas no free phycocyanin could be found in the mutant lacking the 9 kDa linker.
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| 5. |
- Bhalerao, RP, et al.
(författare)
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Factors influencing the phycobilisome rod composition of the cyanobacterium synechococcus sp pcc-7942 : effects of reduced phycocyanin content, lack of rod-linkers, and over-expression of the rod-terminating linker
- 1994
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Ingår i: Physiologia Plantarum. - 0031-9317 .- 1399-3054. ; 90:1, s. 187-197
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Tidskriftsartikel (refereegranskat)abstract
- Four novel mutants with altered phycobilisomes were constructed in the cyanobacterium Synechococcus 7942 to study factors influencing the rod length and composition. These mutants show (1) reduced phycocyanin content, (2) reduced phycocyanin content combined with loss of the 33 kDa linker, (3) loss of the 30 kDa rod-linker and (4) overexpression of the 9 kDa rod terminating linker. For these mutants we determined the 33 to 27 kDa and 30 to 27 kDa linker ratios in the isolated phycobilisomes and compared these ratios with those in the wild type. The 30 kDa linker can be incorporated into the rods in absence of the 33 kDa linker. The incorporation of the 30 kDa linker is lower in absence of the 33 kDa linker. When the 30 kDa linker is missing, an increase in the level of the 33 kDa linker is seen, indicating that there could be an excess of the 33 kDa linker in the cells. Our results also show that a reduction in the phycocyanin content causes a decrease in the rod length simultaneously with a reduction of the 30/27 linker ratio, without altering the 33/27 ratio. Reduced phycocyanin content and absence of the 33 kDa linker cause a dramatic reduction in the incorporation of the 30 kDa linker into the rods in the mutant B2SMIKM. Over-expression of the 9 kDa linker results in a decreased incorporation of both the 33 and 30 kDa linkers into the rods, the effect being more pronounced for the 30 kDa linker. This result indicates that the level of the 9 kDa linker relative to those of the 33 and the 30 kDa linkers may be an important determinant of the phycobilisome rod length.
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| 6. |
- Bhalerao, Rupali, et al.
(författare)
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Gene expression in autumn leaves
- 2003
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 131:2, s. 430-442
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 7. |
- Bhalerao, RP, et al.
(författare)
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Structure and energy-transfer of the phycobilisome in a linker protein replacement mutant of cyanobacterium synechococcus-7942
- 1991
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Ingår i: Biochimica et Biophysica Acta. - 0006-3002 .- 1878-2434. ; 1060:1, s. 59-66
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Tidskriftsartikel (refereegranskat)abstract
- The role of the linker proteins in the biogenesis and energy transfer of the phycobilisome rod was monitored by making insertional inactivation in the cpcI gene coding for the core-proximal 33 kilodalton (kDa) protein in the cyanobacterium Synechococcus 7942. The insertion leaves the cpcH gene coding for the core-distal 30 kDa protein intact and functional. Analysis of the phycobilisome protein composition of the cpcI mutant shows that the 30 kDa protein is present in normal amounts in the rod, indicating that the 30 kDa linker protein can replace the 33 kDa protein in the biogenesis and structural integrity of the rod. The absorption and fluorescence characteristics of the mutated phycobilisome is almost indistinguishable from that of the wild-type of the same rod length. The fluorescence kinetics from the cpcI mutant show that the dominating decay component has a lifetime from phycocyanin of 69 ps as compared to 72 ps found for the wild-type phycobilisome with the same rod length. The results show that replacing the 33 kDa for the 30 kDa linker in the rod does not alter the energy harvesting or the energy transfer characteristics of the rod in contrast to what has been concluded from data obtained from in vitro experiments. We conclude that the linker polypeptides have only a minor influence on the energy transfer characteristics of the rod but are mainly involved in determining the length of the rod in response to changing environmental light conditions.
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| 8. |
- Bhalerao, RP, et al.
(författare)
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The structure of phycobilisomes in mutants of synechococcus sp strain pcc-7942 devoid of specific linker polypeptides
- 1995
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Ingår i: Photochemistry and Photobiology. - 0031-8655 .- 1751-1097. ; 61:3, s. 298-302
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Tidskriftsartikel (refereegranskat)abstract
- The effect of elimination of the 30, 33 and 9 kDa phycobilisome rod-linker polypeptides on rod length was examined by electron microscopy of phycobilisomes isolated from wild-type Synechococcus sp. strain PCC 7942 and from genetically engineered mutants with lesions in the genes encoding the rod-linker polypeptides. The maximum rod length in the absence of the 33 kDa linker polypeptide was two phycocyanin hexamers, whereas rods with up to five hexamers were found in the mutant strain lacking the 30 kDa linker polypeptide. Elimination of the 9 kDa linker polypeptide did not have a significant effect on rod length. Finally, mutants lacking either the 30 or 33 kDa rod-associated linker polypeptides had an increased number of rods that terminated with a phycocyanin trimer. These observations are discussed with respect to the role of the linker polypeptides in the biosynthesis of the rod substructure.
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| 9. |
- Bröchner, Jan, 1948, et al.
(författare)
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Accelerated planning for urban housing infills: coordination strategies
- 2021
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Ingår i: European Planning Studies. - : Informa UK Limited. - 0965-4313 .- 1469-5944. ; 29:6, s. 1113-1131
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Tidskriftsartikel (refereegranskat)abstract
- The outcome of local policies to satisfy residential demand by accelerating urban planning and development is studied here for an infill programme with about 30 plans and a target of 7,000 new suburban dwellings, launched by a mid-sized Swedish city, Gothenburg. Interviews with developers and officials, questionnaires, policy and planning documents including appeals have been analyzed. Three municipal strategies for acceleration were applied: interdepartmental coordination, collaboration with developers and parallel processing of plans and permits. Plans were produced more rapidly, but the goal of parallel work on building permits was seldom achieved. A complex pattern of delay causes has been found and is discussed in the light of coordination strategies. Strong initial focus on the physical design in the detailed development plan overshadowed the need for an early identification of coordination issues throughout the stages of implementation. This emerges as one reason why developers have been reluctant or unable to start detailed design early on, instead of embracing the principle of parallel planning and preparation for a building permit.
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| 10. |
- Bylesjö, Max, et al.
(författare)
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LAMINA : a tool for rapid quantification of leaf size and shape parameters
- 2008
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Ingår i: BMC Plant Biology. - : BMC. - 1471-2229. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Background: An increased understanding of leaf area development is important in a number of fields: in food and non-food crops, for example short rotation forestry as a biofuels feedstock, leaf area is intricately linked to biomass productivity; in paleontology leaf shape characteristics are used to reconstruct paleoclimate history. Such fields require measurement of large collections of leaves, with resulting conclusions being highly influenced by the accuracy of the phenotypic measurement process.Results: We have developed LAMINA (Leaf shApe deterMINAtion), a new tool for the automated analysis of images of leaves. LAMINA has been designed to provide classical indicators of leaf shape (blade dimensions) and size (area), which are typically required for correlation analysis to biomass productivity, as well as measures that indicate asymmetry in leaf shape, leaf serration traits, and measures of herbivory damage (missing leaf area). In order to allow Principal Component Analysis (PCA) to be performed, the location of a chosen number of equally spaced boundary coordinates can optionally be returned.Conclusion: We demonstrate the use of the software on a set of 500 scanned images, each containing multiple leaves, collected from a common garden experiment containing 116 clones of Populus tremula (European trembling aspen) that are being used for association mapping, as well as examples of leaves from other species. We show that the software provides an efficient and accurate means of analysing leaf area in large datasets in an automated or semi-automated work flow.
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