| 1. |
- Chawade, Aakash, et al.
(författare)
-
Global expression profiling of low temperature induced genes in the chilling tolerant japonica rice jumli marshi
- 2013
-
Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 8:12, s. e81729-
-
Tidskriftsartikel (refereegranskat)abstract
- Low temperature is a key factor that limits growth and productivity of many important agronomical crops worldwide. Rice (Oryza sativa L.) is negatively affected already at temperatures below +10°C and is therefore denoted as chilling sensitive. However, chilling tolerant rice cultivars exist and can be commercially cultivated at altitudes up to 3,050 meters with temperatures reaching as low as +4°C. In this work, the global transcriptional response to cold stress (+4°C) was studied in the Nepalese highland variety Jumli Marshi (spp. japonica) and 4,636 genes were identified as significantly differentially expressed within 24 hours of cold stress. Comparison with previously published microarray data from one chilling tolerant and two sensitive rice cultivars identified 182 genes differentially expressed (DE) upon cold stress in all four rice cultivars and 511 genes DE only in the chilling tolerant rice. Promoter analysis of the 182 genes suggests a complex cross-talk between ABRE and CBF regulons. Promoter analysis of the 511 genes identified over-represented ABRE motifs but not DRE motifs, suggesting a role for ABA signaling in cold tolerance. Moreover, 2,101 genes were DE in Jumli Marshi alone. By chromosomal localization analysis, 473 of these cold responsive genes were located within 13 different QTLs previously identified as cold associated.
|
|
| 2. |
- Harbst, Katja, et al.
(författare)
-
Molecular and genetic diversity in the metastatic process of melanoma.
- 2014
-
Ingår i: Journal of Pathology. - : Wiley. - 0022-3417 .- 1096-9896. ; 233:1, s. 39-50
-
Tidskriftsartikel (refereegranskat)abstract
- Diversity between metastatic melanoma tumours in individual patients is known; however, the molecular and genetic differences remain unclear. To examine the molecular and genetic differences between metastatic tumours, we performed gene-expression profiling of 63 melanoma tumours obtained from 28 patients (two or three tumours/patient), followed by analysis of their mutational landscape, using targeted deep sequencing of 1697 cancer genes and DNA copy number analysis. Gene-expression signatures revealed discordant phenotypes between tumour lesions within a patient in 50% of the cases. In 18 of 22 patients (where matched normal tissue was available), we found that the multiple lesions within a patient were genetically divergent, with one or more melanoma tumours harbouring 'private' somatic mutations. In one case, the distant subcutaneous metastasis of one patient occurring 3 months after an earlier regional lymph node metastasis had acquired 37 new coding sequence mutations, including mutations in PTEN and CDH1. However, BRAF and NRAS mutations, when present in the first metastasis, were always preserved in subsequent metastases. The patterns of nucleotide substitutions found in this study indicate an influence of UV radiation but possibly also DNA alkylating agents. Our results clearly demonstrate that metastatic melanoma is a molecularly highly heterogeneous disease that continues to progress throughout its clinical course. The private aberrations observed on a background of shared aberrations within a patient provide evidence of continued evolution of individual tumours following divergence from a common parental clone, and might have implications for personalized medicine strategies in melanoma treatment. Published by John Wiley & Sons, Ltd. www.pathsoc.org.uk.
|
|
| 3. |
|
|
| 4. |
- Abdeldaim, Guma, 1969-, et al.
(författare)
-
Multiplex quantitative PCR for detection of lower respiratory tract infection and meningitis caused by Streptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis
- 2010
-
Ingår i: BMC Microbiology. - : Springer Science and Business Media LLC. - 1471-2180. ; 10, s. 310-
-
Tidskriftsartikel (refereegranskat)abstract
- Background. Streptococcus pneumoniae and Haemophilus influenzae cause pneumonia and as Neisseria meningitidis they are important agents of meningitis. Although several PCR methods have been described for these bacteria the specificity is an underestimated problem. Here we present a quantitative multiplex real-time PCR (qmPCR) for detection of S. pneumoniae (9802 gene fragment), H. influenzae (omp P6 gene) and N. meningitidis (ctrA gene). The method was evaluated on bronchoalveolar lavage (BAL) samples from 156 adults with lower respiratory tract infection (LRTI) and 31 controls, and on 87 cerebrospinal fluid (CSF) samples from meningitis patients. Results. The analytical sensitivity was not affected by using a combined mixture of reagents and a combined DNA standard (S. pneumoniae/H. influenzae/N. meningitidis) in single tubes. By blood- and BAL-culture and S. pneumoniae urinary antigen test, S. pneumoniae and H. influenzae were aetiological agents in 21 and 31 of the LTRI patients, respectively. These pathogens were identified by qmPCR in 52 and 72 of the cases, respectively, yielding sensitivities and specificities of 95% and 75% for S. pneumoniae, and 90% and 65% for H. influenzae, respectively. When using a cut-off of 105 genome copies/mL for clinical positivity the sensitivities and specificities were 90% and 80% for S. pneumoniae, and 81% and 85% for H. influenzae, respectively. Of 44 culture negative but qmPCR positive for H. influenzae, 41 were confirmed by fucK PCR as H. influenzae. Of the 103 patients who had taken antibiotics prior to sampling, S. pneumoniae and H. influenzae were identified by culture in 6% and 20% of the cases, respectively, and by the qmPCR in 36% and 53% of the cases, respectively. In 87 CSF samples S. pneumoniae and N. meningitidis were identified by culture and/or 16 S rRNA in 14 and 10 samples and by qmPCR in 14 and 10 samples, respectively, giving a sensitivity of 100% and a specificity of 100% for both bacteria. Conclusions. The PCR provides increased sensitivity and the multiplex format facilitates diagnosis of S. pneumoniae, H. influenzae and N. meningitidis and the assay enable detection after antibiotic treatment has been installed. Quantification increases the specificity of the etiology for pneumonia.
|
|
| 5. |
- Ahlsson, Fredrik, et al.
(författare)
-
Insulin Resistance, a Link between Maternal Overweight and Fetal Macrosomia in Nondiabetic Pregnancies
- 2010
-
Ingår i: Hormone research in paediatrics. - : S. Karger AG. - 1663-2818 .- 1663-2826. ; 74:4, s. 267-274
-
Tidskriftsartikel (refereegranskat)abstract
- Background/Aims: During the last decades the number of large for gestational age infants delivered by nondiabetic mothers has increased. Our aim was to investigate to what extent fetal growth in nondiabetic pregnant women can be explained by rates of maternal energy substrate production and resting energy expenditure. Methods: Twenty nonsmoking pregnant women without impaired glucose tolerance and with a wide range of fetal weights (0.2-2.7 SDS) were investigated at 36 weeks of gestation. Maternal lipolysis, glucose production, resting energy expenditure, body composition and insulin resistance were assessed.Results: Median (range) glucose production rate was 805 (653-1,337) mumol/min and that of glycerol, reflecting lipolysis, was 214 (110-576) mumol/min. Multiple linear regression analysis showed that maternal fat mass explained 36% of the variation in insulin resistance, accounting for 62% of the variation in glucose production. Further, glucose production explained 31% of the variation in fetal weight. Resting energy expenditure explained 51% of the variation in estimated fetal weight. Conclusion: Fetal weight is dependent on maternal glucose production, which is in turn determined by the degree of insulin resistance, induced in part by the maternal fat mass. The variation in maternal resting energy expenditure is closely related to fetal weight.
|
|
| 6. |
- Aronsson, Per, et al.
(författare)
-
An operational decision support tool for stump harvest
- 2011
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- A multi-criteria decision support tool was developed to optimise stump harvesting for energy in Sweden. The decision tool takes account of multiple, sometimes conflicting, criteria relating to stump harvest; energy and climate, economics, biodiversity, and soil and water. Data on harvested stems are used as primary input data in the tool. Such data are routinely collected in harvester computers. The tool effectively deals with mixed sets of data; quantitative harvest data are re-calculated to metric (e.g. stump biomass), and qualitative data (e.g. biodiversity implications) are incorporated. A digital terrain map derived from air-borne laser scanning provides basic data for estimating soil wetness, while digital maps of water courses, key habitats and protected areas, or other sensitive habitats, are used to identify potentially and practically harvestable stumps.In four sub-models, an index from 0 to 10 is calculated for each stump, with 0 representing ‘Not at all suitable’ and 10 ‘Highly suitable for extraction’. Through this, a stump of high value for wood-living species is assigned a low index in the biodiversity sub-model and a large, easily accessible stump is assigned a high index in the economic sub-model. When calculating the net index, the sub-indices can be weighted according to the preferences of the end-user.An energy and climate sub-model incorporates greenhouse gas (GHG) emissions from forest operations and the effect of advancing GHG emissions when stump biomass is incinerated instead of being left to decompose. In the economic sub-model the potential monetary return from each stump is calculated based on estimated revenue from harvested stump biomass and the costs of stump harvesting and forwarding operations (based on cost functions and GIS calculations of transport distances).The biodiversity sub-model considers four types of wood-dependent organisms (lichens, mosses, insects and fungi) in terms of their habitat requirements, vulnerability, sun exposure preferences, locality, etc. A panel of external experts has drawn up a grading scale of stump values for the different taxonomic groups. The proximity to key habitats and exposure to sunlight are derived from a spatial model.Soil and water issues are handled within a sub-model estimating the consequences for long-term soil fertility (nutrient cycling and soil compaction) and water (leaching of plant nutrients and mercury, and particle transport due to soil damage by heavy machinery).The tool offers the end-user possibilities to prioritise and plan for cost-effective stump harvesting, while minimising negative environmental impacts.
|
|
| 7. |
- Axelsson Olsson, Diana, et al.
(författare)
-
Amoebae and algae can prolong the survival of Campylobacter species in co-culture
- 2010
-
Ingår i: Experimental parasitology. - : Elsevier BV. - 0014-4894 .- 1090-2449. ; 126:1, s. 59-64
-
Tidskriftsartikel (refereegranskat)abstract
- Several species of free-living amoebae can cause disease in humans. However, in addition to the direct pathogenicity of e.g. Acanthamoebae and Naegleria species, they are recognized as environmental hosts, indirectly involved in the epidemiology of many pathogenic bacteria. Although several studies have demonstrated intracellular survival of many different bacteria in these species, the extent of such interactions as well as the implications for the epidemiology of the bacterial species involved, are largely unknown and probably underestimated. In this study, we evaluated eight different unicellular eukaryotic organisms, for their potential to serve as environmental hosts for Campylobacter species. These organisms include four amoebozoas (Acanthamoeba polyphaga, Acanthamoeba castellanii, Acanthamoeba rhysodes and Hartmanella vermiformis), one alveolate (Tetrahymena pyriformis), one stramenopile (Dinobryon sertularia), one eugoenozoa (Euglena gracilis) and one heterolobosea (Naegleria americana). Campylobacter spp. including Campylobacter jejuni, Campylobacter coli and Campylobacter lari are the most common cause of gastroenteritis in the western world. Survival and replication of these three species as well as Campylobacter hyointestinalis were assessed in co-cultures with the eukaryotic organisms. Campylobacter spp. generally survived longer in co-cultures, compared to when incubated in the corresponding growth media. The eukaryotic species that best promoted bacterial survival was the golden algae D. sertularia. Three species of amoebozoas, of the genus Acanthamoeba promoted both prolonged survival and replication of Campylobacter spp. The high abundance in lakes, ponds and water distribution networks of these organisms indicate that they might have a role in the epidemiology of campylobacteriosis, possibly contributing to survival and dissemination of these intestinal pathogens to humans and other animals. The results suggest that not only C. jejuni, but a variety of Campylobacter spp. can interact with different eukaryotic unicellular organisms.
|
|
| 8. |
- Axelsson Olsson, Diana, et al.
(författare)
-
Increase in Acid Tolerance of Campylobacter jejuni through Coincubation with Amoebae
- 2010
-
Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 76:13, s. 4194-4200
-
Tidskriftsartikel (refereegranskat)abstract
- Campylobacter jejuni is a recognized and common gastrointestinal pathogen in most parts of the world. Human infections are often food borne, and the bacterium is frequent among poultry and other food animals. However, much less is known about the epidemiology of C. jejuni in the environment and what mechanisms the bacterium depends on to tolerate low pH. The sensitive nature of C. jejuni stands in contrast to the fact that it is difficult to eradicate from poultry production, and even more contradictory is the fact that the bacterium is able to survive the acidic passage through the human stomach. Here we expand the knowledge on C. jejuni acid tolerance by looking at protozoa as a potential epidemiological pathway of infection. Our results showed that when C. jejuni cells were coincubated with Acanthamoeba polyphaga in acidified phosphate-buffered saline (PBS) or tap water, the bacteria could tolerate pHs far below those in their normal range, even surviving at pH 4 for 20 h and at pH 2 for 5 h. Interestingly, moderately acidic conditions (pH 4 and 5) were shown to trigger C. jejuni motility as well as to increase adhesion/internalization of bacteria into A. polyphaga. Taken together, the results suggest that protozoa may act as protective hosts against harsh conditions and might be a potential risk factor for C. jejuni infections. These findings may be important for our understanding of C. jejuni passage through the gastrointestinal tract and for hygiene practices used in poultry settings.
|
|
| 9. |
- Bergkvist, Linda, 1979-
(författare)
-
Towards a Framework for Relational-Oriented Management of Information Systems Outsourcing : Key Conditions Connected to Actors, Relationships and Process
- 2014
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Currently, client and supplier firms are struggling with how they can make their information systems (IS) outsourcing engagements more valuable. This research points to the importance of successful practice and outcome in IS outsourcing for achieving engagements of value. To enhance the understanding of IS outsourcing over time, a process perspective is applied. Further, this research is based on the contention that IS outsourcing is more likely to be successful if challenges are managed in a proactive manner and with a relationship perspective. Thus, understanding challenges in IS outsourcing requires a symmetric view on client and supplier.The thesis is based on two studies presented as three steps of research: development, validation and reconsideration of a conceptual framework. The licentiate study centred on the step of development whereas the present doctoral study has a focus on the steps of validation and reconsideration. The purpose of this study includes investigating how the management of successful practice and outcome in IS outsourcing can be enabled. To address the purpose, the IS outsourcing process is studied in a client–supplier relationship. This includes that different actor perspectives, including strategic, operative, and systems, are considered for a better understanding of the practice of IS outsourcing, the challenges, and how different actors convey successful IS outsourcing.The thesis contributes a framework for relational-oriented management of IS outsourcing, which provides the structure for understanding what needs to be managed in terms of key conditions, when and how in connection to actors, relationships, and process. Theoretical propositions, enhancing the understanding of the complexity of IS outsourcing as well as the number of challenges involved, are also presented. In brief, these propositions relate to the circumstance that IS outsourcing requires management on different levels and with different kinds of results in mind.
|
|
| 10. |
- Berntsson Svensson, Richard, et al.
(författare)
-
An investigation of how quality requirements are specified in industrial practice
- 2013
-
Ingår i: Information and Software Technology. - : Elsevier BV. - 0950-5849 .- 1873-6025. ; 55:7, s. 1224-1236
-
Tidskriftsartikel (refereegranskat)abstract
- Context: This paper analyses a sub-contractor specification in the mobile handset domain. Objective: The objective is to understand how quality requirements are specified and which types of requirements exist in a requirements specification from industry. Method: The case study is performed in the mobile handset domain, where a requirements specification was analyzed by categorizing and characterizing the pertaining requirements. Results: The requirements specification is written in structured natural language with unique identifiers for the requirements. Of the 2178 requirements, 827 (38%) are quality requirements. Of the quality requirements, 56% are quantified, i.e., having a direct metric in the requirement. The variation across the different sub-domains within the requirements specification is large. Conclusion: The findings from this study suggest that methods for quality requirements need to encompass many aspects to comprehensively support working with quality requirements. Solely focusing on, for example, quantification of quality requirements might overlook important requirements since there are many quality requirements in the studied specification where quantification is not appropriate. (C) 2013 Elsevier B.V. All rights reserved.
|
|
