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Jens Nielsen

Publications and source records attributed to Jens Nielsen.

At least 37 records · Page 2Linked to original sources
PubMed2006

Long-term consequences of respiratory syncytial virus acute lower respiratory tract infection in early childhood in Guinea-bissau.

AIM: The study aimed to investigate long-term consequences of respiratory syncytial virus (RSV) positive acute lower respiratory tract infection (ALRI) in a low-income country according to severity of the initial infection. DESIGN: The study was a 1:1 matched case-control study of 335 RSV case children and 335 control children. The mean age of RSV ALRI was 0.9 year and at follow-up, 6.8 years. Case children were identified at the hospital and in the community with an antigen and an IgM test to diagnose RSV. Severe RSV infection was defined when a child was treated at the hospital, whereas disease was assumed less severe when a child was diagnosed at home and received no care in the hospital. RESULTS: At follow-up, forced expiratory volume in 1 second (FEV1) and peak flow were significantly lower in case children (odds ratio [OR] = 0.28; 95% confidence interval [CI] 0.10-0.79), the effect being particularly marked for children with severe RSV. Bronchitis at follow-up was reported more frequently among the case children with severe disease. Fewer case children had a positive skin-prick test for local allergens than control children (OR 0.64; 95% CI = 0.44-0.94). Specific IgE for dust mites and cockroach was elevated (52%) in both case and control children. However, specific IgE to peppertree was higher in the case children (OR 2.18; 95% CI = 1.17-4.07). All identified differences were particularly marked for children with severe RSV. CONCLUSION: Severe RSV infection in infancy was associated with decreased lung function in preschool age in Guinea-Bissau. Children with severe RSV disease had more long-term health problems than children with less severe disease.

Case-Control Studies↗
PubMed2006

Long-term treatment of pigs with low doses of monoclonal antibodies against porcine CD4 and CD8 antigens.

In vivo depletion of lymphocyte subsets allows investigation of the role of specific subsets in protective immunity. In the present study we evaluated the effects of long-term, low-dose treatment with murine monoclonal antibodies (mAbs) against porcine CD4 and CD8 surface antigens on lymphocyte subsets in pigs. Four-week-old pigs were treated by intramuscular injections of hybridoma cell culture supernatants containing anti-CD mAbs twice a week for a period of 5 weeks. The immunomodulatory effects of the treatments were assessed by flow cytometry (FCM) analysis of peripheral blood lymphocytes. Treatment with the anti-CD4 mAb almost completely eliminated the CD4(+) T-cell subset from the circulation after 2 weeks of therapy. This depletion persisted until the end of the experimental period 5 weeks after initiated therapy. Treatment with the anti-CD8 mAb was less effective, reducing the CD8(+) T-cell subset in peripheral blood by approximately 50% of the initial level after 3 weeks of therapy. Further, the anti-CD8 mAb-treated pigs showed a parallel increase in the CD4(+) T-cell subset from day 7. Two-colour FCM analysis indicated that a shift in phenotype from single-positive CD4(+)/CD8(-) to double-positive CD4(+)/CD8(+) T-cells might have occurred in these pigs. In the present experiment we demonstrated specific modulation of the peripheral blood T-lymphocyte population in pigs with continuous low-dose injections of specific mAb. The ability to modulate individual T-cell subsets should provide a method to elucidate their functionality in protection against infectious disease.

Animals↗
PubMed2006

Global transcriptional and physiological responses of Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine limitation.

The yeast Saccharomyces cerevisiae encounters a range of nitrogen sources at various concentrations in its environment. The impact of these two parameters on transcription and metabolism was studied by growing S. cerevisiae in chemostat cultures with l-glutamine, l-alanine, or l-ammonium in limitation and by growing cells in an excess of ammonium. Cells grown in l-alanine-limited cultures had higher biomass yield per nitrogen mole (19%) than those from ammonium-limited cultures. Whole-genome transcript profiles were analyzed with a genome-scale metabolic model that suggested increased anabolic activity in l-alanine-limited cells. The changes in these cells were found to be focused around pyruvate, acetyl coenzyme A, glyoxylate, and alpha-ketoglutarate via increased levels of ALT1, DAL7, PYC1, GDH2, and ADH5 and decreased levels of GDH3, CIT2, and ACS1 transcripts. The transcript profiles were then clustered. Approximately 1,400 transcripts showed altered levels when amino acid-grown cells were compared to those from ammonium. Another 400 genes had low transcript levels when ammonium was in excess. Overrepresentation of the GATAAG element in their promoters suggests that nitrogen catabolite repression (NCR) may be responsible for this regulation. Ninety-one genes had transcript levels on both l-glutamine and ammonium that were decreased compared to those on l-alanine, independent of the concentration. The GATAAG element in these genes suggests two groups of NCR-responsive genes, those that respond to high levels of nitrogen and those that respond to levels below 30 muM. In conclusion, our results reveal that the nitrogen source has substantial influence on the transcriptome of yeasts and that transcriptional changes may be correlated to physiology via a metabolic model.

Alanine↗
PubMed2006

Deletion of RTS1, encoding a regulatory subunit of protein phosphatase 2A, results in constitutive amino acid signaling via increased Stp1p processing.

In Saccharomyces cerevisiae, extracellular amino acids are sensed at the plasma membrane by the SPS sensor, consisting of the transporter homologue Ssy1p, Ptr3p, and the endoprotease Ssy5p. Amino acid sensing results in proteolytic truncation of the transcription factors Stp1p and Stp2p, followed by their relocation from the cytoplasm to the nucleus, where they activate transcription of amino acid permease genes. We screened a transposon mutant library for constitutively signaling mutants, with the aim of identifying down-regulating components of the SPS-mediated pathway. Three isolated mutants were carrying a transposon in the RTS1 gene, which encodes a regulatory subunit of protein phosphatase 2A. We investigated the basal activity of the AGP1 and BAP2 promoters in rts1delta cells and found increased transcription from these promoters, as well as increased Stp1p processing, even in the absence of amino acids. Based on our findings we propose that the phosphatase complex containing Rts1p keeps the SPS-mediated pathway down-regulated in the absence of extracellular amino acids by dephosphorylating a component of the pathway.

Amino Acid Transport Systems↗
PubMed2006

Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae.

BACKGROUND: Growth rate is central to the development of cells in all organisms. However, little is known about the impact of changing growth rates. We used continuous cultures to control growth rate and studied the transcriptional program of the model eukaryote Saccharomyces cerevisiae, with generation times varying between 2 and 35 hours. RESULTS: A total of 5930 transcripts were identified at the different growth rates studied. Consensus clustering of these revealed that half of all yeast genes are affected by the specific growth rate, and that the changes are similar to those found when cells are exposed to different types of stress (>80% overlap). Genes with decreased transcript levels in response to faster growth are largely of unknown function (>50%) whereas genes with increased transcript levels are involved in macromolecular biosynthesis such as those that encode ribosomal proteins. This group also covers most targets of the transcriptional activator RAP1, which is also known to be involved in replication. A positive correlation between the location of replication origins and the location of growth-regulated genes suggests a role for replication in growth rate regulation. CONCLUSION: Our data show that the cellular growth rate has great influence on transcriptional regulation. This, in turn, implies that one should be cautious when comparing mutants with different growth rates. Our findings also indicate that much of the regulation is coordinated via the chromosomal location of the affected genes, which may be valuable information for the control of heterologous gene expression in metabolic engineering.

Cell Growth Processes↗
PubMed2006

Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans.

BACKGROUND: Aspergillus nidulans (the asexual form of Emericella nidulans) is a model organism for aspergilli, which are an important group of filamentous fungi that encompasses human and plant pathogens as well as industrial cell factories. Aspergilli have a highly diversified metabolism and, because of their medical, agricultural and biotechnological importance, it would be valuable to have an understanding of how their metabolism is regulated. We therefore conducted a genome-wide transcription analysis of A. nidulans grown on three different carbon sources (glucose, glycerol, and ethanol) with the objective of identifying global regulatory structures. Furthermore, we reconstructed the complete metabolic network of this organism, which resulted in linking 666 genes to metabolic functions, as well as assigning metabolic roles to 472 genes that were previously uncharacterized. RESULTS: Through combination of the reconstructed metabolic network and the transcription data, we identified subnetwork structures that pointed to coordinated regulation of genes that are involved in many different parts of the metabolism. Thus, for a shift from glucose to ethanol, we identified coordinated regulation of the complete pathway for oxidation of ethanol, as well as upregulation of gluconeogenesis and downregulation of glycolysis and the pentose phosphate pathway. Furthermore, on change in carbon source from glucose to ethanol, the cells shift from using the pentose phosphate pathway as the major source of NADPH (nicotinamide adenine dinucleotide phosphatase, reduced form) for biosynthesis to use of the malic enzyme. CONCLUSION: Our analysis indicates that some of the genes are regulated by common transcription factors, making it possible to establish new putative links between known transcription factors and genes through clustering.

Aspergillus nidulans↗
PubMed2006

Atopic disposition, wheezing, and subsequent respiratory syncytial virus hospitalization in Danish children younger than 18 months: a nested case-control study.

OBJECTIVES: This study examined whether atopic disposition, wheezing, and atopic disorders increased the risk of hospitalizations because of respiratory syncytial virus in children between birth and 18 months of age. PATIENTS AND METHODS: Relative risks for respiratory syncytial virus hospitalization were studied in a nested 1:5 case-control design using exposure information obtained from interviews with mothers of 2564 case and 12,816 control children who had been followed prospectively from birth and until 18 months of age as participants in the Danish National Birth Cohort. Information on the children's ages at respiratory syncytial virus hospitalization, presentation of infrequent wheezing, recurrent wheezing, and atopic dermatitis were used to study these associations chronologically. RESULTS: The adjusted relative risk of respiratory syncytial virus hospitalization in the offspring was 1.11 for maternal atopic dermatitis, 1.72 for maternal asthma, and 1.23 for paternal asthma. Atopic dermatitis in the child was associated with an increased risk of subsequent respiratory syncytial virus hospitalization among infants <6 months of age. Infrequent wheezing was associated with a relative risk of subsequent respiratory syncytial virus hospitalization of 2.98 and recurrent wheezing with a relative risk of 5.90. These associations were present also if infants with medical risk factors were excluded from the analysis. CONCLUSIONS: Asthmatic disposition and wheezing were strong determinants of subsequent respiratory syncytial virus hospitalization in Danish children <18 months of age.

Case-Control Studies↗
PubMed2005

Evolutionary programming as a platform for in silico metabolic engineering.

BACKGROUND: Through genetic engineering it is possible to introduce targeted genetic changes and hereby engineer the metabolism of microbial cells with the objective to obtain desirable phenotypes. However, owing to the complexity of metabolic networks, both in terms of structure and regulation, it is often difficult to predict the effects of genetic modifications on the resulting phenotype. Recently genome-scale metabolic models have been compiled for several different microorganisms where structural and stoichiometric complexity is inherently accounted for. New algorithms are being developed by using genome-scale metabolic models that enable identification of gene knockout strategies for obtaining improved phenotypes. However, the problem of finding optimal gene deletion strategy is combinatorial and consequently the computational time increases exponentially with the size of the problem, and it is therefore interesting to develop new faster algorithms. RESULTS: In this study we report an evolutionary programming based method to rapidly identify gene deletion strategies for optimization of a desired phenotypic objective function. We illustrate the proposed method for two important design parameters in industrial fermentations, one linear and other non-linear, by using a genome-scale model of the yeast Saccharomyces cerevisiae. Potential metabolic engineering targets for improved production of succinic acid, glycerol and vanillin are identified and underlying flux changes for the predicted mutants are discussed. CONCLUSION: We show that evolutionary programming enables solving large gene knockout problems in relatively short computational time. The proposed algorithm also allows the optimization of non-linear objective functions or incorporation of non-linear constraints and additionally provides a family of close to optimal solutions. The identified metabolic engineering strategies suggest that non-intuitive genetic modifications span several different pathways and may be necessary for solving challenging metabolic engineering problems.

Algorithms↗
PubMed2005

Mortality patterns during a war in Guinea-Bissau 1998-99: changes in risk factors?

BACKGROUND: The crude mortality rate of the whole population and the mortality of children <5 years of age are the common indicators of the severity of a complex emergency situation. However, these indicators rarely take account of differences in socioeconomic conditions and vulnerability. METHODS: We followed a population in Guinea-Bissau, which fled when fighting took place in the capital during the war in 1998-99. The population stayed close to the area of conflict and returned as soon as a cease-fire was negotiated. A peace treaty was signed after half-a-year. The following 6 months was a period of returning and re-settlement, even though two outbreaks of fighting occurred. RESULTS: In the first half-year the mortality rate was 78% [mortality ratio (MR) = 1.78; 95% CI 1.61-1.97] increased and mortality for children <5 years of age doubled (MR = 2.07; 95% CI 1.79-2.38). In the last 6 months of the war, mortality was slightly increased for children and not at all for the total population. In the first half-year, households living in better houses and having members with schooling were less affected. In the 're-settlement' period two inequalities emerged; the largest ethnic group, Pepel, continued to have high mortality when the mortality of other groups declined; likewise girls continued to have an elevated mortality whereas mortality of boys declined. CONCLUSION: Whereas specific 'free' interventions reduced social inequalities for the groups affected, for the total population health-inequalities were slightly amplified during the war. Once the population returned to their urban homes, mortality fell to pre-war levels even though some fighting continued, limited humanitarian aid was available and the pre-war infra-structure had not been re-established.

Child, Preschool↗
PubMed2005

In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production.

In silico genome-scale cell models are promising tools for accelerating the design of cells with improved and desired properties. We demonstrated this by using a genome-scale reconstructed metabolic network of Saccharomyces cerevisiae to score a number of strategies for metabolic engineering of the redox metabolism that will lead to decreased glycerol and increased ethanol yields on glucose under anaerobic conditions. The best-scored strategies were predicted to completely eliminate formation of glycerol and increase ethanol yield with 10%. We successfully pursued one of the best strategies by expressing a non-phosphorylating, NADP(+)-dependent glyceraldehyde-3-phosphate dehydrogenase in S. cerevisiae. The resulting strain had a 40% lower glycerol yield on glucose while the ethanol yield increased with 3% without affecting the maximum specific growth rate. Similarly, expression of GAPN in a strain harbouring xylose reductase and xylitol dehydrogenase led to an improvement in ethanol yield by up to 25% on xylose/glucose mixtures.

Computer Simulation↗
PubMed2005

Global metabolite analysis of yeast: evaluation of sample preparation methods.

Sample preparation is considered one of the limiting steps in microbial metabolome analysis. Eukaryotes and prokaryotes behave very differently during the several steps of classical sample preparation methods for analysis of metabolites. Even within the eukaryote kingdom there is a vast diversity of cell structures that make it imprudent to blindly adopt protocols that were designed for a specific group of microorganisms. We have therefore reviewed and evaluated the whole sample preparation procedures for analysis of yeast metabolites. Our focus has been on the current needs in metabolome analysis, which is the analysis of a large number of metabolites with very diverse chemical and physical properties. This work reports the leakage of intracellular metabolites observed during quenching yeast cells with cold methanol solution, the efficacy of six different methods for the extraction of intracellular metabolites, and the losses noticed during sample concentration by lyophilization and solvent evaporation. A more reliable procedure is suggested for quenching yeast cells with cold methanol solution, followed by extraction of intracellular metabolites by pure methanol. The method can be combined with reduced pressure solvent evaporation and therefore represents an attractive sample preparation procedure for high-throughput metabolome analysis of yeasts.

Freeze Drying↗
PubMed2005

Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm.

MOTIVATION: Hierarchical and relocation clustering (e.g. K-means and self-organizing maps) have been successful tools in the display and analysis of whole genome DNA microarray expression data. However, the results of hierarchical clustering are sensitive to outliers, and most relocation methods give results which are dependent on the initialization of the algorithm. Therefore, it is difficult to assess the significance of the results. We have developed a consensus clustering algorithm, where the final result is averaged over multiple clustering runs, giving a robust and reproducible clustering, capable of capturing small signal variations. The algorithm preserves valuable properties of hierarchical clustering, which is useful for visualization and interpretation of the results. RESULTS: We show for the first time that one can take advantage of multiple clustering runs in DNA microarray analysis by collecting re-occurring clustering patterns in a co-occurrence matrix. The results show that consensus clustering obtained from clustering multiple times with Variational Bayes Mixtures of Gaussians or K-means significantly reduces the classification error rate for a simulated dataset. The method is flexible and it is possible to find consensus clusters from different clustering algorithms. Thus, the algorithm can be used as a framework to test in a quantitative manner the homogeneity of different clustering algorithms. We compare the method with a number of state-of-the-art clustering methods. It is shown that the method is robust and gives low classification error rates for a realistic, simulated dataset. The algorithm is also demonstrated for real datasets. It is shown that more biological meaningful transcriptional patterns can be found without conservative statistical or fold-change exclusion of data. AVAILABILITY: Matlab source code for the clustering algorithm ClusterLustre, and the simulated dataset for testing are available upon request from T.G. and O.W.

Algorithms↗
PubMed2005

Effect of sublingual misoprostol on severe postpartum haemorrhage in a primary health centre in Guinea-Bissau: randomised double blind clinical trial.

OBJECTIVE: To evaluate whether routine administration of sublingual misoprostol 600 microg after delivery reduces postpartum haemorrhage. DESIGN: Randomised double blind placebo controlled trial. SETTING: Primary health centre in Bissau, Guinea-Bissau, West Africa. PARTICIPANTS: 661 women undergoing vaginal delivery. INTERVENTION: Misoprostol 600 mug or placebo administered sublingually immediately after delivery. MAIN OUTCOME MEASURES: Postpartum haemorrhage, defined as a loss of > or = 500 ml and decrease in haemoglobin concentration after delivery. RESULTS: The incidence of postpartum haemorrhage was not significantly different between the two groups, the relative risk being 0.89 (95% confidence interval 0.76 to 1.04) in the misoprostol group compared with the placebo group. Mean blood loss was 10.5% (-0.5% to 20.4%) lower in the misoprostol group than in the control group. Severe postpartum haemorrhage of > or = 1000 ml or > or = 1500 ml occurred in 17% (56) and 8% (25) in the placebo group and 11% (37) and 2% (7) in the misoprostol group. Significantly fewer women in the misoprostol group experienced a loss of > or = 1000 ml (0.66, 0.45 to 0.98) or > or = 1500 ml (0.28, 0.12 to 0.64). The decrease in haemoglobin concentration tended to be less in the misoprostol group, the mean difference between the two groups being 0.16 mmol/l (-0.01 mmol/l to 0.32 mmol/l). CONCLUSION: Sublingual misoprostol reduces the frequency of severe postpartum haemorrhage.

Administration, Sublingual↗
PubMed2005

The next wave in metabolome analysis.

The metabolome of a cell represents the amplification and integration of signals from other functional genomic levels, such as the transcriptome and the proteome. Although this makes metabolomics a useful tool for the high-throughput analysis of phenotypes, the lack of a direct connection to the genome makes it difficult to interpret metabolomic data. Nevertheless, functional genomics has produced examples of the use of metabolomics to elucidate the phenotypes of otherwise silent mutations. Despite several successes, we believe that future metabolomic studies must focus on the accurate measurement of the concentrations of unambiguously identified metabolites. The research community must develop databases of metabolite concentrations in cells that are grown in several well-defined conditions if metabolomic data are to be integrated meaningfully with data from the other levels of functional-genomic analysis and to make a significant contribution to systems biology.

Animals↗
PubMed2005

Comparative metabolic network analysis of two xylose fermenting recombinant Saccharomyces cerevisiae strains.

The recombinant xylose fermenting strain Saccharomyces cerevisiae TMB3001 can grow on xylose, but the xylose utilisation rate is low. One important reason for the inefficient fermentation of xylose to ethanol is believed to be the imbalance of redox co-factors. In the present study, a metabolic flux model was constructed for two recombinant S. cerevisiae strains: TMB3001 and CPB.CR4 which in addition to xylose metabolism have a modulated redox metabolism, i.e. ammonia assimilation was shifted from being NADPH to NADH dependent by deletion of gdh1 and over-expression of GDH2. The intracellular fluxes were estimated for both strains in anaerobic continuous cultivations when the growth limiting feed consisted of glucose (2.5 g L-1) and xylose (13 g L-1). The metabolic network analysis with 13C labelled glucose showed that there was a shift in the specific xylose reductase activity towards use of NADH as co-factor rather than NADPH. This shift is beneficial for solving the redox imbalance and it can therefore partly explain the 25% increase in the ethanol yield observed for CPB.CR4. Furthermore, the analysis indicated that the glyoxylate cycle was activated in CPB.CR4.

Computer Simulation↗
PubMed2005

Modeling Lactococcus lactis using a genome-scale flux model.

BACKGROUND: Genome-scale flux models are useful tools to represent and analyze microbial metabolism. In this work we reconstructed the metabolic network of the lactic acid bacteria Lactococcus lactis and developed a genome-scale flux model able to simulate and analyze network capabilities and whole-cell function under aerobic and anaerobic continuous cultures. Flux balance analysis (FBA) and minimization of metabolic adjustment (MOMA) were used as modeling frameworks. RESULTS: The metabolic network was reconstructed using the annotated genome sequence from L. lactis ssp. lactis IL1403 together with physiological and biochemical information. The established network comprised a total of 621 reactions and 509 metabolites, representing the overall metabolism of L. lactis. Experimental data reported in the literature was used to fit the model to phenotypic observations. Regulatory constraints had to be included to simulate certain metabolic features, such as the shift from homo to heterolactic fermentation. A minimal medium for in silico growth was identified, indicating the requirement of four amino acids in addition to a sugar. Remarkably, de novo biosynthesis of four other amino acids was observed even when all amino acids were supplied, which is in good agreement with experimental observations. Additionally, enhanced metabolic engineering strategies for improved diacetyl producing strains were designed. CONCLUSION: The L. lactis metabolic network can now be used for a better understanding of lactococcal metabolic capabilities and potential, for the design of enhanced metabolic engineering strategies and for integration with other types of 'omic' data, to assist in finding new information on cellular organization and function.

Bacteria, Anaerobic↗
PubMed2005

High-throughput metabolic state analysis: the missing link in integrated functional genomics of yeasts.

The lack of comparable metabolic state assays severely limits understanding the metabolic changes caused by genetic or environmental perturbations. The present study reports the application of a novel derivatization method for metabolome analysis of yeast, coupled to data-mining software that achieve comparable throughput, effort and cost compared with DNA arrays. Our sample workup method enables simultaneous metabolite measurements throughout central carbon metabolism and amino acid biosynthesis, using a standard GC-MS platform that was optimized for this purpose. As an implementation proof-of-concept, we assayed metabolite levels in two yeast strains and two different environmental conditions in the context of metabolic pathway reconstruction. We demonstrate that these differential metabolite level data distinguish among sample types, such as typical metabolic fingerprinting or footprinting. More importantly, we demonstrate that this differential metabolite level data provides insight into specific metabolic pathways and lays the groundwork for integrated transcription-metabolism studies of yeasts.

Aerobiosis↗