Ingunn Berget | Nofima - Academia.edu (original) (raw)

Papers by Ingunn Berget

Research paper thumbnail of Unveiling an abundant core microbiota in the human adult colon by a phylogroup-independent searching approach

The ISME Journal, 2011

The potential presence of widespread and stable bacterial core phylogroups in the human colon has... more The potential presence of widespread and stable bacterial core phylogroups in the human colon has promoted considerable attention. Despite major efforts, no such phylogroups have yet been identified. Therefore, using a novel phylogroup-and tree-independent approach, we present a reanalysis of 1 114 722 V2 region and 71 550 near full-length 16S rRNA sequences from a total of 210 human beings, with widespread geographic origin, ethnic background and diet, in addition to a wide range of other mammals. We found two highly prevalent core phylogroups (cores 1 and 2), belonging to the clostridial family Lachnospiraceae. These core phylogroups showed a log-normal distribution among human individuals, while non-core phylogroups showed more skewed distributions towards individuals with low levels compared with the log-normal distribution. Molecular clock analyses suggest that core 2 co-evolved with the radiation of vertebrates, while core 1 co-evolved with the mammals. Taken together, the stability, prevalence and potential functionality support the fact that the identified core phylogroups are pivotal in maintaining gut homeostasis and health.

Research paper thumbnail of Statistisk metodikk for å lage robuste produktresepter gjennom optimal prosessering og effektiv råvareutnyttelse i næringsmiddelindustrien

Research paper thumbnail of Discriminatory power, typability, and accuracy of single nucleotide extension microarrays

Journal of AOAC International

Despite great conceptual promise, the use of microarrays in typing approaches has not yet gained ... more Despite great conceptual promise, the use of microarrays in typing approaches has not yet gained wide acceptance. The establishment of proper criteria for determining discriminatory power as well as typability and the accuracy of microarray data remains to be solved. Purely experimental estimations of these parameters would far exceed what is experimentally practical. We therefore used simulations in combination with experimental results in parameter estimations. Our assay was based on 26 single nucleotide polymorphisms (SNPs) identified in the Campylobacterjejuni Multi Locus Sequence Typing (MLST) database (http:///pubmist.org/campylobacter/). The SNPs were detected using a single nucleotide extension (SNE) typing microarray. Unknown isolates were assigned to the known sequence type(s) by calculating weighted sum of matches minus a weighted sum of mismatches between predicted and candidate genotype. The weights were set according to the Bayesian posterior probability of the SNP cla...

Research paper thumbnail of MALDI-TOF mass spectrometry for quantitative gene expression analysis of acid responses in Staphylococcus aureus

Journal of Microbiological Methods, 2009

Microorganisms are constantly exposed to new and altered growth conditions, and respond by changi... more Microorganisms are constantly exposed to new and altered growth conditions, and respond by changing gene expression patterns. Several methods for studying gene expression exist. During the last decade, the analysis of microarrays has been one of the most common approaches applied for large scale gene expression studies. A relatively new method for gene expression analysis is MassARRAY, which combines real competitive-PCR and MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry. In contrast to microarray methods, MassARRAY technology is suitable for analysing a larger number of samples, though for a smaller set of genes. In this study we compare the results from MassARRAY with microarrays on gene expression responses of Staphylococcus aureus exposed to acid stress at pH 4.5. RNA isolated from the same stress experiments was analysed using both the MassARRAY and the microarray methods. The MassARRAY and microarray methods showed good correlation. Both MassARRAY and microarray estimated somewhat lower fold changes compared with quantitative real-time PCR (qRT-PCR). The results confirmed the up-regulation of the urease genes in acidic environments, and also indicated the importance of metal ion regulation. This study shows that the MassARRAY technology is suitable for gene expression analysis in prokaryotes, and has advantages when a set of genes is being analysed for an organism exposed to many different environmental conditions.

Research paper thumbnail of Sorting of raw materials with focus on multiple end-product properties

Journal of Chemometrics, 2002

In industry, variability in raw material quality often leads to unstable end-product quality. By ... more In industry, variability in raw material quality often leads to unstable end-product quality. By sorting the raw materials into homogeneous groups, stability and quality of the end-product can be improved. The optimal splitting and the corresponding optimal process settings in each category can be found by fuzzy clustering. In the single-response case the distance between groups and objects is defined as the predicted response's distance to the target. When there are multiple responses, the distance between an object and a category can be based either on a quadratic loss function that weights the different responses or on desirability functions. Another approach is to put restrictions on the less important responses when optimizing the process variables. These three methods are discussed and illustrated by an example. The constrained approach was not suited for the example treated, while the other two approaches gave similar solutions to the optimization problem. Copyright © 2002 John Wiley & Sons, Ltd.

Research paper thumbnail of Optimal sorting of raw materials for use in different products

Chemometrics and Intelligent Laboratory Systems, 2003

Often one type of raw material is used for different, but related products. Since raw material qu... more Often one type of raw material is used for different, but related products. Since raw material quality can be variable, some batches/entities of raw materials may be better suited for one type of product than others. A methodology for sorting raw materials into different categories, which can be used to make different types of products, is presented. The process variables for each product are optimised within each product/category simultaneously as the optimal splitting is found. The presented methodology can also be applied in situations where the goal is to split the raw materials into those that need additives and those that do not. The methodology is illustrated with an example where the product categories considered are bread baked with or without DATEM, which is an additive commonly used in the baking industry. D

Research paper thumbnail of New modifications and applications of fuzzy C-means methodology

Computational Statistics & Data Analysis, 2008

Research paper thumbnail of Properties of prediction sorting

Journal of Chemometrics, 2004

One of the major sources of unwanted variation in an industrial process is the raw material quali... more One of the major sources of unwanted variation in an industrial process is the raw material quality. However, if the raw materials are sorted into more homogeneous groups before production, each group can be treated differently. In this way the raw materials can be better utilized and the stability of the end product may be improved. Prediction sorting is a methodology for doing this. The procedure is founded on the fuzzy c-means algorithm where the distance in the objective function is based on the predicted end product quality. Usually empirical models such as linear regression are used for predicting the end product quality. By using simulations and bootstrapping, this paper investigates how the uncertainties connected with empirical models affect the optimization of the splitting and the corresponding process variables. The results indicate that the practical consequences of uncertainties in regression coefficients are small. Copyright © 2004 John Wiley & Sons, Ltd.

Research paper thumbnail of A strategy for finding relevant clusters; with an application to microarray data

Journal of Chemometrics, 2005

Cluster analysis is a helpful tool for explorative analysis of large and complex data. Most clust... more Cluster analysis is a helpful tool for explorative analysis of large and complex data. Most clustering methods will, however, find clusters also in random data. An important aspect of cluster analysis is therefore to distinguish real and artificial clusters, as this will make interpretation of the clusters easier. In some cases, certain types of clusters are more interesting than others. When working with gene expression data, examples of such clusters are gene clusters with high between-sample variability or clusters with a certain expression profile. Here we present a strategy with the ability to search for such clusters. The clustering is done sequentially. For each sequence, the data is separated into ‘interesting’ and ‘rest’ using the fuzzy c-means algorithm with noise clustering. The interesting cluster is defined by adding a penalty function to the usual clustering criterion. The penalty function is constructed in such a way that clusters without the interesting properties are given a high penalty. The strategy is presented in a general frame, and can be adjusted by defining different criteria for each type of cluster that is of interest. The methodology is presented and demonstrated in the context of microarray gene expression analysis, using real and simulated data, but can be used for any type of data where cluster analysis may be a helpful tool. Copyright © 2006 John Wiley & Sons, Ltd.

Research paper thumbnail of Unveiling an abundant core microbiota in the human adult colon by a phylogroup-independent searching approach

Research paper thumbnail of Optimal Sorting of Raw Materials, Based on the Predicted EndProduct Quality

Quality Engineering, 2002

ABSTRACT Raw material variation is one of the most important factors causing unstable end-product... more ABSTRACT Raw material variation is one of the most important factors causing unstable end-product quality. A methodology for sorting raw materials into homogenous groups with constant and optimized processing within each group is presented. The sorting criterion is based on the squared distance between the predicted response and its target value. The raw materials are split into homogenous categories by a partitioning algorithm related to the fuzzy-c-means algorithm. The method has been tested for raw material properties in one and two dimensions and with different degrees of fuzziness. The method shows good flexibility and can also be used with a penalty function penalizing unfavorable process settings.

Research paper thumbnail of Using unclassified observations for improving classifiers

Journal of Chemometrics, 2004

Methodologies for updating a classifier using unclassified observations are discussed. The focus ... more Methodologies for updating a classifier using unclassified observations are discussed. The focus is on classifiers based on linear or quadratic discriminant analysis. A semi-supervised clustering based on the Gustafson–Kessel algorithm for fuzzy clustering is carried out for all data, both classified and unclassified observations. The resulting fuzzy means and covariance matrices are used to update the classifier. It has formerly been shown that this methodology can reduce the misclassification rate. In this paper a modified approach is suggested for situations with errors in the data for the unclassified objects. To handle such situations, a noise cluster is introduced in the cluster analysis, and dubious points are allocated to this cluster. The proposed modifications are tested on simulated data. The results indicate that the misclassification rates are lower than or at the same level as with the original updating procedure. Copyright © 2004 John Wiley & Sons, Ltd.

Research paper thumbnail of Transcript profiling of candidate genes in testis of pigs exhibiting large differences in androstenone levels

BMC Genetics, 2010

Background: Boar taint is an unpleasant odor and flavor of the meat and occurs in a high proporti... more Background: Boar taint is an unpleasant odor and flavor of the meat and occurs in a high proportion of uncastrated male pigs. Androstenone, a steroid produced in testis and acting as a sex pheromone regulating reproductive function in female pigs, is one of the main compounds responsible for boar taint. The primary goal of the present investigation was to determine the differential gene expression of selected candidate genes related to levels of androstenone in pigs. Results: Altogether 2560 boars from the Norwegian Landrace and Duroc populations were included in this study. Testicle samples from the 192 boars with most extreme high or low levels of androstenone in fat were used for RNA extraction, and 15 candidate genes were selected and analyzed by real-competitive PCR analysis. The genes Cytochrome P450 c17 (CYP17A1), Steroidogenic acute regulatory protein (STAR), Aldo-keto reductase family 1 member C4 (AKR1C4), Short-chain dehydrogenase/reductase family member 4 (DHRS4), Ferritin light polypeptide (FTL), Sulfotransferase family 2A, dehydroepiandrosterone-preferring member 1 (SULT2A1), Cytochrome P450 subfamily XIA polypeptide 1 (CYP11A1), Cytochrome b5 (CYB5A), and 17-beta-Hydroxysteroid dehydrogenase IV (HSD17B4) were all found to be significantly (P < 0.05) up-regulated in high androstenone boars in both Duroc and Landrace. Furthermore, Cytochrome P450 c19A2 (CYP19A2) was down-regulated and progesterone receptor membrane component 1 (PGRMC1) was up-regulated in high-androstenone Duroc boars only, while CYP21 was significantly down-regulated (2.5) in high-androstenone Landrace only. The genes Nuclear Receptor co-activator 4 (NCOA4), Sphingomyrlin phosphodiesterase 1 (SMPD1) and 3β-hydroxysteroid dehydrogenase (HSD3B) were not significantly differentially expressed in any breeds. Additionally, association studies were performed for the genes with one or more detected SNPs. Association between SNP and androstenone level was observed in CYB5A only, suggesting cis-regulation of the differential transcription in this gene. Conclusion: A large pig material of highly extreme androstenone levels is investigated. The current study contributes to the knowledge about which genes that is differentially expressed regard to the levels of androstenone in pigs. Results in this paper suggest that several genes are important in the regulation of androstenone level in boars and warrant further evaluation of the above mentioned candidate genes, including analyses in different breeds, identification of causal mutations and possible gene interactions.

Research paper thumbnail of Gene expression profiles in liver of pigs with extreme high and low levels of androstenone

BMC Veterinary Research, 2008

Background: Boar taint is the unpleasant odour and flavour of the meat of uncastrated male pigs t... more Background: Boar taint is the unpleasant odour and flavour of the meat of uncastrated male pigs that is primarily caused by high levels of androstenone and skatole in adipose tissue. Androstenone is a steroid and its levels are mainly genetically determined. Studies on androstenone metabolism have, however, focused on a limited number of genes. Identification of additional genes influencing levels of androstenone may facilitate implementation of marker assisted breeding practices. In this study, microarrays were used to identify differentially expressed genes and pathways related to androstenone metabolism in the liver from boars with extreme levels of androstenone in adipose tissue.

Research paper thumbnail of Changes in lipid metabolism associated gene transcripts during porcine adipogenesis

Comparative Biochemistry and Physiology B-biochemistry & Molecular Biology, 2009

Pigs are recognised as suitable biomedical models to study obesity and obesity-related diseases; ... more Pigs are recognised as suitable biomedical models to study obesity and obesity-related diseases; however, little is known about adipose tissue development and adipogenesis in pigs. In this study, the temporal expression of key genes involved in lipid metabolism was investigated during porcine adipogenesis and the metabolic fate of exogenously administered palmitic acid (16:0) was examined in differentiating preadipocytes. The expression of genes encoding elongases and desaturases increased simultaneously with those involved in fatty acid and triacylglycerol synthesis during porcine adipogenesis, and a high biosynthesis of monounsaturated fatty acids was measured prior to storage in differentiating preadipocytes. Although the total fatty acid oxidation in differentiating preadipocytes was low, differentiating cells showed increased expression of hormone-sensitive lipase and mitochondrial and peroxisomal genes. These data provide new insight into the temporal expression of genes involved in lipid metabolism during porcine adipogenesis and suggest a possible role of elongation and desaturation events prior to lipid accumulation in porcine adipocytes.

Research paper thumbnail of Gene expression profiles in testis of pigs with extreme high and low levels of androstenone

BMC Genomics, 2007

Background: Boar taint is a major obstacle when using uncastrated male pigs for swine production.... more Background: Boar taint is a major obstacle when using uncastrated male pigs for swine production. One of the main compounds causing this taint is androstenone, a pheromone produced in porcine testis. Here we use microarrays to study the expression of thousands of genes simultaneously in testis of high and low androstenone boars. The study allows identification of genes and pathways associated with elevated androstenone levels, which is essential for recognising potential molecular markers for breeding purposes.

Research paper thumbnail of Depot specific differences during adipogenesis of porcine stromal-vascular cells

Cell Biology International, 2008

Recently a role of adipose tissue as an endocrine organ secreting factors involved in the regulat... more Recently a role of adipose tissue as an endocrine organ secreting factors involved in the regulation of whole-body energy homeostasis has emerged. Preadipocytes in different fat depots have distinct adipogenic potential and the metabolic activity differs between mature adipocytes of different depot origins. Here we describe the proliferation and differentiation of stromal-vascular cells derived from subcutaneous and visceral fat depots of adult pigs. We demonstrate that subcutaneous porcine preadipocytes proliferate more actively and that individual subcutaneous adipocytes have a more rapid accumulation of triacylglycerols than visceral cells. During differentiation, subcutaneous and visceral preadipocytes showed similar gene expression patterns with increased expression of adiponectin (APM1), adipocyte-specific fatty acid binding protein (FABP4), catalase (CAT), and peroxisome proliferator-activated receptor gamma 2 (PPARG2). Furthermore, initial data showing depot-originated effects on the expression of CAT, carnitine palmitoyl transferase 1B (CPT1B) and FABP4 suggest possible depot specific differences in the function and metabolism of mature porcine adipocytes. Ó

Research paper thumbnail of Differential gene expression of fatty acid binding proteins during porcine adipogenesis

Comparative Biochemistry and Physiology B-biochemistry & Molecular Biology, 2008

Four different subtypes of fatty acid binding proteins i.e. liver-type FABP1, heart/muscle-type F... more Four different subtypes of fatty acid binding proteins i.e. liver-type FABP1, heart/muscle-type FABP3, adipocyte-type FABP4 and epithelial/epidermal-type FABP5 are expressed in adipose tissue. However, only the regulatory role of FABP4 in adipogenesis has been thoroughly investigated. To increase the knowledge on possible roles of these FABP subtypes in preadipocyte differentiation, gene expression patterns were examined during adipogenesis in pig (Sus scrofa). FABP1 expression was induced in proliferating cells, whereas FABP3, FABP4 and FABP5 expression increased throughout preadipocyte differentiation. Interestingly, the FABP4 and FABP5 expression increased early in the differentiation, followed by FABP3 later in the differentiation process. This indicates a role of FABP4 and FABP5 in intracellular fatty acid transport during initiation of differentiation, whereas, FABP3 likely is involved in the transport of fatty acids during intermediate stages of adipogenesis. In this study we demonstrate that FABP3, FABP4 and FABP5 expression is correlated with that of the peroxisome proliferator-activated receptors alpha and gamma (PPARA and PPARG). Altogether, this suggests a role of FABP1 during cell proliferation, whereas a coordinated expression of FABP3, FABP4 and FABP5 together with that of PPARA, PPARG1 and PPARG2 might be critical for the metabolic regulation during porcine adipogenesis.

Research paper thumbnail of Genomic organization and transcript profiling of the bovine toll-like receptor gene cluster TLR6- TLR1- TLR10

Gene, 2006

Toll-like receptors (TLRs) are a family of recognition receptors playing a crucial role in the in... more Toll-like receptors (TLRs) are a family of recognition receptors playing a crucial role in the innate immune system. Different combinations of TLRs are thought to be crucial for effective immune response, thus insight into the organization and expression of TLRs is important for understanding disease resistance. Mastitis is the most frequent and costly disease in dairy production, and the innate immune system is considered to be important in the first line defence against this disease. In the present paper we have characterized the genomic organization of TLR6-TLR1-TLR10 in a ∼50 kb region of bovine chromosome 6, including 5′-untranslated exons not previously described. A method for gene expression analysis was developed and used for transcription profiling of the three paralogous genes in different bovine tissues. The expression analysis showed similar expression profiles for TLR1 and TLR6, which indicate a co-regulation of these two genes in cattle. TLR10 had a different expression profile, pointing toward a stronger functional diversification compared to TLR1 and TLR6. The differences in expression are in accordance with the evolutionary history of this gene cluster, where TLR10 diverged from the common ancestral gene before the duplication event that created TLR1 and TLR6.

Research paper thumbnail of Unveiling an abundant core microbiota in the human adult colon by a phylogroup-independent searching approach

The ISME Journal, 2011

The potential presence of widespread and stable bacterial core phylogroups in the human colon has... more The potential presence of widespread and stable bacterial core phylogroups in the human colon has promoted considerable attention. Despite major efforts, no such phylogroups have yet been identified. Therefore, using a novel phylogroup-and tree-independent approach, we present a reanalysis of 1 114 722 V2 region and 71 550 near full-length 16S rRNA sequences from a total of 210 human beings, with widespread geographic origin, ethnic background and diet, in addition to a wide range of other mammals. We found two highly prevalent core phylogroups (cores 1 and 2), belonging to the clostridial family Lachnospiraceae. These core phylogroups showed a log-normal distribution among human individuals, while non-core phylogroups showed more skewed distributions towards individuals with low levels compared with the log-normal distribution. Molecular clock analyses suggest that core 2 co-evolved with the radiation of vertebrates, while core 1 co-evolved with the mammals. Taken together, the stability, prevalence and potential functionality support the fact that the identified core phylogroups are pivotal in maintaining gut homeostasis and health.

Research paper thumbnail of Statistisk metodikk for å lage robuste produktresepter gjennom optimal prosessering og effektiv råvareutnyttelse i næringsmiddelindustrien

Research paper thumbnail of Discriminatory power, typability, and accuracy of single nucleotide extension microarrays

Journal of AOAC International

Despite great conceptual promise, the use of microarrays in typing approaches has not yet gained ... more Despite great conceptual promise, the use of microarrays in typing approaches has not yet gained wide acceptance. The establishment of proper criteria for determining discriminatory power as well as typability and the accuracy of microarray data remains to be solved. Purely experimental estimations of these parameters would far exceed what is experimentally practical. We therefore used simulations in combination with experimental results in parameter estimations. Our assay was based on 26 single nucleotide polymorphisms (SNPs) identified in the Campylobacterjejuni Multi Locus Sequence Typing (MLST) database (http:///pubmist.org/campylobacter/). The SNPs were detected using a single nucleotide extension (SNE) typing microarray. Unknown isolates were assigned to the known sequence type(s) by calculating weighted sum of matches minus a weighted sum of mismatches between predicted and candidate genotype. The weights were set according to the Bayesian posterior probability of the SNP cla...

Research paper thumbnail of MALDI-TOF mass spectrometry for quantitative gene expression analysis of acid responses in Staphylococcus aureus

Journal of Microbiological Methods, 2009

Microorganisms are constantly exposed to new and altered growth conditions, and respond by changi... more Microorganisms are constantly exposed to new and altered growth conditions, and respond by changing gene expression patterns. Several methods for studying gene expression exist. During the last decade, the analysis of microarrays has been one of the most common approaches applied for large scale gene expression studies. A relatively new method for gene expression analysis is MassARRAY, which combines real competitive-PCR and MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry. In contrast to microarray methods, MassARRAY technology is suitable for analysing a larger number of samples, though for a smaller set of genes. In this study we compare the results from MassARRAY with microarrays on gene expression responses of Staphylococcus aureus exposed to acid stress at pH 4.5. RNA isolated from the same stress experiments was analysed using both the MassARRAY and the microarray methods. The MassARRAY and microarray methods showed good correlation. Both MassARRAY and microarray estimated somewhat lower fold changes compared with quantitative real-time PCR (qRT-PCR). The results confirmed the up-regulation of the urease genes in acidic environments, and also indicated the importance of metal ion regulation. This study shows that the MassARRAY technology is suitable for gene expression analysis in prokaryotes, and has advantages when a set of genes is being analysed for an organism exposed to many different environmental conditions.

Research paper thumbnail of Sorting of raw materials with focus on multiple end-product properties

Journal of Chemometrics, 2002

In industry, variability in raw material quality often leads to unstable end-product quality. By ... more In industry, variability in raw material quality often leads to unstable end-product quality. By sorting the raw materials into homogeneous groups, stability and quality of the end-product can be improved. The optimal splitting and the corresponding optimal process settings in each category can be found by fuzzy clustering. In the single-response case the distance between groups and objects is defined as the predicted response's distance to the target. When there are multiple responses, the distance between an object and a category can be based either on a quadratic loss function that weights the different responses or on desirability functions. Another approach is to put restrictions on the less important responses when optimizing the process variables. These three methods are discussed and illustrated by an example. The constrained approach was not suited for the example treated, while the other two approaches gave similar solutions to the optimization problem. Copyright © 2002 John Wiley & Sons, Ltd.

Research paper thumbnail of Optimal sorting of raw materials for use in different products

Chemometrics and Intelligent Laboratory Systems, 2003

Often one type of raw material is used for different, but related products. Since raw material qu... more Often one type of raw material is used for different, but related products. Since raw material quality can be variable, some batches/entities of raw materials may be better suited for one type of product than others. A methodology for sorting raw materials into different categories, which can be used to make different types of products, is presented. The process variables for each product are optimised within each product/category simultaneously as the optimal splitting is found. The presented methodology can also be applied in situations where the goal is to split the raw materials into those that need additives and those that do not. The methodology is illustrated with an example where the product categories considered are bread baked with or without DATEM, which is an additive commonly used in the baking industry. D

Research paper thumbnail of New modifications and applications of fuzzy C-means methodology

Computational Statistics & Data Analysis, 2008

Research paper thumbnail of Properties of prediction sorting

Journal of Chemometrics, 2004

One of the major sources of unwanted variation in an industrial process is the raw material quali... more One of the major sources of unwanted variation in an industrial process is the raw material quality. However, if the raw materials are sorted into more homogeneous groups before production, each group can be treated differently. In this way the raw materials can be better utilized and the stability of the end product may be improved. Prediction sorting is a methodology for doing this. The procedure is founded on the fuzzy c-means algorithm where the distance in the objective function is based on the predicted end product quality. Usually empirical models such as linear regression are used for predicting the end product quality. By using simulations and bootstrapping, this paper investigates how the uncertainties connected with empirical models affect the optimization of the splitting and the corresponding process variables. The results indicate that the practical consequences of uncertainties in regression coefficients are small. Copyright © 2004 John Wiley & Sons, Ltd.

Research paper thumbnail of A strategy for finding relevant clusters; with an application to microarray data

Journal of Chemometrics, 2005

Cluster analysis is a helpful tool for explorative analysis of large and complex data. Most clust... more Cluster analysis is a helpful tool for explorative analysis of large and complex data. Most clustering methods will, however, find clusters also in random data. An important aspect of cluster analysis is therefore to distinguish real and artificial clusters, as this will make interpretation of the clusters easier. In some cases, certain types of clusters are more interesting than others. When working with gene expression data, examples of such clusters are gene clusters with high between-sample variability or clusters with a certain expression profile. Here we present a strategy with the ability to search for such clusters. The clustering is done sequentially. For each sequence, the data is separated into ‘interesting’ and ‘rest’ using the fuzzy c-means algorithm with noise clustering. The interesting cluster is defined by adding a penalty function to the usual clustering criterion. The penalty function is constructed in such a way that clusters without the interesting properties are given a high penalty. The strategy is presented in a general frame, and can be adjusted by defining different criteria for each type of cluster that is of interest. The methodology is presented and demonstrated in the context of microarray gene expression analysis, using real and simulated data, but can be used for any type of data where cluster analysis may be a helpful tool. Copyright © 2006 John Wiley & Sons, Ltd.

Research paper thumbnail of Unveiling an abundant core microbiota in the human adult colon by a phylogroup-independent searching approach

Research paper thumbnail of Optimal Sorting of Raw Materials, Based on the Predicted EndProduct Quality

Quality Engineering, 2002

ABSTRACT Raw material variation is one of the most important factors causing unstable end-product... more ABSTRACT Raw material variation is one of the most important factors causing unstable end-product quality. A methodology for sorting raw materials into homogenous groups with constant and optimized processing within each group is presented. The sorting criterion is based on the squared distance between the predicted response and its target value. The raw materials are split into homogenous categories by a partitioning algorithm related to the fuzzy-c-means algorithm. The method has been tested for raw material properties in one and two dimensions and with different degrees of fuzziness. The method shows good flexibility and can also be used with a penalty function penalizing unfavorable process settings.

Research paper thumbnail of Using unclassified observations for improving classifiers

Journal of Chemometrics, 2004

Methodologies for updating a classifier using unclassified observations are discussed. The focus ... more Methodologies for updating a classifier using unclassified observations are discussed. The focus is on classifiers based on linear or quadratic discriminant analysis. A semi-supervised clustering based on the Gustafson–Kessel algorithm for fuzzy clustering is carried out for all data, both classified and unclassified observations. The resulting fuzzy means and covariance matrices are used to update the classifier. It has formerly been shown that this methodology can reduce the misclassification rate. In this paper a modified approach is suggested for situations with errors in the data for the unclassified objects. To handle such situations, a noise cluster is introduced in the cluster analysis, and dubious points are allocated to this cluster. The proposed modifications are tested on simulated data. The results indicate that the misclassification rates are lower than or at the same level as with the original updating procedure. Copyright © 2004 John Wiley & Sons, Ltd.

Research paper thumbnail of Transcript profiling of candidate genes in testis of pigs exhibiting large differences in androstenone levels

BMC Genetics, 2010

Background: Boar taint is an unpleasant odor and flavor of the meat and occurs in a high proporti... more Background: Boar taint is an unpleasant odor and flavor of the meat and occurs in a high proportion of uncastrated male pigs. Androstenone, a steroid produced in testis and acting as a sex pheromone regulating reproductive function in female pigs, is one of the main compounds responsible for boar taint. The primary goal of the present investigation was to determine the differential gene expression of selected candidate genes related to levels of androstenone in pigs. Results: Altogether 2560 boars from the Norwegian Landrace and Duroc populations were included in this study. Testicle samples from the 192 boars with most extreme high or low levels of androstenone in fat were used for RNA extraction, and 15 candidate genes were selected and analyzed by real-competitive PCR analysis. The genes Cytochrome P450 c17 (CYP17A1), Steroidogenic acute regulatory protein (STAR), Aldo-keto reductase family 1 member C4 (AKR1C4), Short-chain dehydrogenase/reductase family member 4 (DHRS4), Ferritin light polypeptide (FTL), Sulfotransferase family 2A, dehydroepiandrosterone-preferring member 1 (SULT2A1), Cytochrome P450 subfamily XIA polypeptide 1 (CYP11A1), Cytochrome b5 (CYB5A), and 17-beta-Hydroxysteroid dehydrogenase IV (HSD17B4) were all found to be significantly (P < 0.05) up-regulated in high androstenone boars in both Duroc and Landrace. Furthermore, Cytochrome P450 c19A2 (CYP19A2) was down-regulated and progesterone receptor membrane component 1 (PGRMC1) was up-regulated in high-androstenone Duroc boars only, while CYP21 was significantly down-regulated (2.5) in high-androstenone Landrace only. The genes Nuclear Receptor co-activator 4 (NCOA4), Sphingomyrlin phosphodiesterase 1 (SMPD1) and 3β-hydroxysteroid dehydrogenase (HSD3B) were not significantly differentially expressed in any breeds. Additionally, association studies were performed for the genes with one or more detected SNPs. Association between SNP and androstenone level was observed in CYB5A only, suggesting cis-regulation of the differential transcription in this gene. Conclusion: A large pig material of highly extreme androstenone levels is investigated. The current study contributes to the knowledge about which genes that is differentially expressed regard to the levels of androstenone in pigs. Results in this paper suggest that several genes are important in the regulation of androstenone level in boars and warrant further evaluation of the above mentioned candidate genes, including analyses in different breeds, identification of causal mutations and possible gene interactions.

Research paper thumbnail of Gene expression profiles in liver of pigs with extreme high and low levels of androstenone

BMC Veterinary Research, 2008

Background: Boar taint is the unpleasant odour and flavour of the meat of uncastrated male pigs t... more Background: Boar taint is the unpleasant odour and flavour of the meat of uncastrated male pigs that is primarily caused by high levels of androstenone and skatole in adipose tissue. Androstenone is a steroid and its levels are mainly genetically determined. Studies on androstenone metabolism have, however, focused on a limited number of genes. Identification of additional genes influencing levels of androstenone may facilitate implementation of marker assisted breeding practices. In this study, microarrays were used to identify differentially expressed genes and pathways related to androstenone metabolism in the liver from boars with extreme levels of androstenone in adipose tissue.

Research paper thumbnail of Changes in lipid metabolism associated gene transcripts during porcine adipogenesis

Comparative Biochemistry and Physiology B-biochemistry & Molecular Biology, 2009

Pigs are recognised as suitable biomedical models to study obesity and obesity-related diseases; ... more Pigs are recognised as suitable biomedical models to study obesity and obesity-related diseases; however, little is known about adipose tissue development and adipogenesis in pigs. In this study, the temporal expression of key genes involved in lipid metabolism was investigated during porcine adipogenesis and the metabolic fate of exogenously administered palmitic acid (16:0) was examined in differentiating preadipocytes. The expression of genes encoding elongases and desaturases increased simultaneously with those involved in fatty acid and triacylglycerol synthesis during porcine adipogenesis, and a high biosynthesis of monounsaturated fatty acids was measured prior to storage in differentiating preadipocytes. Although the total fatty acid oxidation in differentiating preadipocytes was low, differentiating cells showed increased expression of hormone-sensitive lipase and mitochondrial and peroxisomal genes. These data provide new insight into the temporal expression of genes involved in lipid metabolism during porcine adipogenesis and suggest a possible role of elongation and desaturation events prior to lipid accumulation in porcine adipocytes.

Research paper thumbnail of Gene expression profiles in testis of pigs with extreme high and low levels of androstenone

BMC Genomics, 2007

Background: Boar taint is a major obstacle when using uncastrated male pigs for swine production.... more Background: Boar taint is a major obstacle when using uncastrated male pigs for swine production. One of the main compounds causing this taint is androstenone, a pheromone produced in porcine testis. Here we use microarrays to study the expression of thousands of genes simultaneously in testis of high and low androstenone boars. The study allows identification of genes and pathways associated with elevated androstenone levels, which is essential for recognising potential molecular markers for breeding purposes.

Research paper thumbnail of Depot specific differences during adipogenesis of porcine stromal-vascular cells

Cell Biology International, 2008

Recently a role of adipose tissue as an endocrine organ secreting factors involved in the regulat... more Recently a role of adipose tissue as an endocrine organ secreting factors involved in the regulation of whole-body energy homeostasis has emerged. Preadipocytes in different fat depots have distinct adipogenic potential and the metabolic activity differs between mature adipocytes of different depot origins. Here we describe the proliferation and differentiation of stromal-vascular cells derived from subcutaneous and visceral fat depots of adult pigs. We demonstrate that subcutaneous porcine preadipocytes proliferate more actively and that individual subcutaneous adipocytes have a more rapid accumulation of triacylglycerols than visceral cells. During differentiation, subcutaneous and visceral preadipocytes showed similar gene expression patterns with increased expression of adiponectin (APM1), adipocyte-specific fatty acid binding protein (FABP4), catalase (CAT), and peroxisome proliferator-activated receptor gamma 2 (PPARG2). Furthermore, initial data showing depot-originated effects on the expression of CAT, carnitine palmitoyl transferase 1B (CPT1B) and FABP4 suggest possible depot specific differences in the function and metabolism of mature porcine adipocytes. Ó

Research paper thumbnail of Differential gene expression of fatty acid binding proteins during porcine adipogenesis

Comparative Biochemistry and Physiology B-biochemistry & Molecular Biology, 2008

Four different subtypes of fatty acid binding proteins i.e. liver-type FABP1, heart/muscle-type F... more Four different subtypes of fatty acid binding proteins i.e. liver-type FABP1, heart/muscle-type FABP3, adipocyte-type FABP4 and epithelial/epidermal-type FABP5 are expressed in adipose tissue. However, only the regulatory role of FABP4 in adipogenesis has been thoroughly investigated. To increase the knowledge on possible roles of these FABP subtypes in preadipocyte differentiation, gene expression patterns were examined during adipogenesis in pig (Sus scrofa). FABP1 expression was induced in proliferating cells, whereas FABP3, FABP4 and FABP5 expression increased throughout preadipocyte differentiation. Interestingly, the FABP4 and FABP5 expression increased early in the differentiation, followed by FABP3 later in the differentiation process. This indicates a role of FABP4 and FABP5 in intracellular fatty acid transport during initiation of differentiation, whereas, FABP3 likely is involved in the transport of fatty acids during intermediate stages of adipogenesis. In this study we demonstrate that FABP3, FABP4 and FABP5 expression is correlated with that of the peroxisome proliferator-activated receptors alpha and gamma (PPARA and PPARG). Altogether, this suggests a role of FABP1 during cell proliferation, whereas a coordinated expression of FABP3, FABP4 and FABP5 together with that of PPARA, PPARG1 and PPARG2 might be critical for the metabolic regulation during porcine adipogenesis.

Research paper thumbnail of Genomic organization and transcript profiling of the bovine toll-like receptor gene cluster TLR6- TLR1- TLR10

Gene, 2006

Toll-like receptors (TLRs) are a family of recognition receptors playing a crucial role in the in... more Toll-like receptors (TLRs) are a family of recognition receptors playing a crucial role in the innate immune system. Different combinations of TLRs are thought to be crucial for effective immune response, thus insight into the organization and expression of TLRs is important for understanding disease resistance. Mastitis is the most frequent and costly disease in dairy production, and the innate immune system is considered to be important in the first line defence against this disease. In the present paper we have characterized the genomic organization of TLR6-TLR1-TLR10 in a ∼50 kb region of bovine chromosome 6, including 5′-untranslated exons not previously described. A method for gene expression analysis was developed and used for transcription profiling of the three paralogous genes in different bovine tissues. The expression analysis showed similar expression profiles for TLR1 and TLR6, which indicate a co-regulation of these two genes in cattle. TLR10 had a different expression profile, pointing toward a stronger functional diversification compared to TLR1 and TLR6. The differences in expression are in accordance with the evolutionary history of this gene cluster, where TLR10 diverged from the common ancestral gene before the duplication event that created TLR1 and TLR6.