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Trygg, Johan
Publications (10 of 146) Show all publications
Obudulu, O., Mähler, N., Skotare, T., Bygdell, J., Abreu, I. N., Ahnlund, M., . . . Tuominen, H. (2018). A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees. BMC Genomics, 19, Article ID 11.
Open this publication in new window or tab >>A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees
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2018 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 19, article id 11Article in journal (Refereed) Published
Abstract [en]

Background: Secretory Carrier-Associated Membrane Proteins (SCAMPs) are highly conserved 32–38 kDa proteins that are involved in membrane trafficking. A systems approach was taken to elucidate function of SCAMPs in wood formation of Populus trees. Phenotypic and multi-omics analyses were performed in woody tissues of transgenic Populus trees carrying an RNAi construct for Populus tremula x tremuloides SCAMP3 (PttSCAMP3;Potri.019G104000).

Results: The woody tissues of the transgenic trees displayed increased amounts of both polysaccharides and lignin oligomers, indicating increased deposition of both the carbohydrate and lignin components of the secondary cell walls. This coincided with a tendency towards increased wood density as well as significantly increased thickness of the suberized cork in the transgenic lines. Multivariate OnPLS (orthogonal projections to latent structures) modeling of five different omics datasets (the transcriptome, proteome, GC-MS metabolome, LC-MS metabolome and pyrolysis-GC/MS metabolome) collected from the secondary xylem tissues of the stem revealed systemic variation in the different variables in the transgenic lines, including changes that correlated with the changes in the secondary cell wall composition. The OnPLS model also identified a rather large number of proteins that were more abundant in the transgenic lines than in the wild type. Several of these were related to secretion and/or endocytosis as well as both primary and secondary cell wall biosynthesis.

Conclusions: Populus SCAMP proteins were shown to influence accumulation of secondary cell wall components, including polysaccharides and phenolic compounds, in the woody tissues of Populus tree stems. Our multi-omics analyses combined with the OnPLS modelling suggest that this function is mediated by changes in membrane trafficking to fine-tune the abundance of cell wall precursors and/or proteins involved in cell wall biosynthesis and transport. The data provides a multi-level source of information for future studies on the function of the SCAMP proteins in plant stem tissues.

Place, publisher, year, edition, pages
Springer Publishing Company, 2018
Keywords
Secretory Carrier-Associated Membrane Protein (SCAMP), Populus, Wood chemistry, Wood density, Biomass, Bioprocessing, Cork, Multi-omics
National Category
Cell Biology
Identifiers
urn:nbn:se:umu:diva-143890 (URN)10.1186/s12864-017-4411-1 (DOI)000419232000004 ()
Funder
Swedish Research Council Formas, 232-2009-1698
Available from: 2018-01-12 Created: 2018-01-12 Last updated: 2018-06-09Bibliographically approved
Rahnama, L., Peterson, G., Kazemnejad, A., Trygg, J. & Peolsson, A. (2018). Alterations in the Mechanical Response of Deep Dorsal Neck Muscles in Individuals Experiencing Whiplash-Associated Disorders Compared to Healthy Controls: An Ultrasound Study. American Journal of Physical Medicine & Rehabilitation, 97(2), 75-82
Open this publication in new window or tab >>Alterations in the Mechanical Response of Deep Dorsal Neck Muscles in Individuals Experiencing Whiplash-Associated Disorders Compared to Healthy Controls: An Ultrasound Study
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2018 (English)In: American Journal of Physical Medicine & Rehabilitation, ISSN 0894-9115, E-ISSN 1537-7385, Vol. 97, no 2, p. 75-82Article in journal (Refereed) Published
Abstract [en]

Objective: The aim of this study was to investigate and compare the mechanical responses of dorsal neck muscles in individuals with whiplash-associated disorders (WAD) versus healthy individuals.

Design: This study included 36 individuals with WAD (26 women and 10 men) and 36 healthy controls (26 women and 10 men). Ultrasound imaging with speckle tracking was used to measure deformation and deformation rate in five dorsal neck muscles during a neck extension task.

Results: Compared with controls, individuals with WAD showed higher deformations of the semispinalis cervicis (P = 0.02) and multifidus (P = 0.002) muscles and higher deformation rates (P = 0.03 and 0.0001, respectively). Among individuals with WAD, multifidus deformation and deformation rate were significantly associated with pain, disability, and fatigue (r = 0.31-0.46, P = 0.0001-0.01).

Conclusions: These findings indicate that the mechanical responses of the deep dorsal neck muscles differ between individuals with WAD and healthy controls, possibly reflecting that these muscles use altered strategies while performing a neck extension task. This finding provides new insight into neck muscles pathology in patients with chronic WAD and may help improve rehabilitation programs.

Place, publisher, year, edition, pages
LIPPINCOTT WILLIAMS & WILKINS, 2018
Keywords
Whiplash Injury, Neck Muscle, Cervical Spine, Ultrasonography
National Category
Physiotherapy
Identifiers
urn:nbn:se:umu:diva-144947 (URN)10.1097/PHM.0000000000000845 (DOI)000423729500004 ()29016400 (PubMedID)
Available from: 2018-02-23 Created: 2018-02-23 Last updated: 2018-06-09Bibliographically approved
Galindo-Prieto, B., Trygg, J. & Geladi, P. (2017). A new approach for variable influence on projection (VIP) in O2PLS models. Chemometrics and Intelligent Laboratory Systems, 160, 110-124
Open this publication in new window or tab >>A new approach for variable influence on projection (VIP) in O2PLS models
2017 (English)In: Chemometrics and Intelligent Laboratory Systems, ISSN 0169-7439, E-ISSN 1873-3239, Vol. 160, p. 110-124Article in journal (Refereed) Published
Abstract [en]

A novel variable influence on projection approach for O2PLS® models, named VIPO2PLS, is presented in this paper. VIPO2PLS is a model-based method for judging the importance of variables. Its cornerstone is the 2-way formalism of the O2PLS models; i.e. the use of both predictive and orthogonal normalized loadings of the two modelled data matrices, and also a new weighting system based on the sum of squares of both data blocks (X, Y). The VIPO2PLS algorithm has been tested in one synthetic data set and two real cases, and the outcomes have been compared to the PLS-VIP, VIPOPLS, and i-PLS methods. The purpose is to achieve a sharper and enhanced model interpretation of O2PLS models by using the new VIPO2PLS method for assessing the importance of both X- and Y- variables.

Place, publisher, year, edition, pages
Elsevier, 2017
Keywords
Multi-block variable selection, O2PLS, VIP, Variable importance, Model interpretation, Multivariate calibration
National Category
Chemical Sciences Computer and Information Sciences
Identifiers
urn:nbn:se:umu:diva-128916 (URN)10.1016/j.chemolab.2016.11.005 (DOI)000392684100013 ()
Available from: 2016-12-19 Created: 2016-12-19 Last updated: 2018-06-09Bibliographically approved
Kuess, P., Andrzejewski, P., Nilsson, D., Georg, P., Knoth, J., Susani, M., . . . Nyholm, T. (2017). Association between pathology and texture features of multi parametric MRI of the prostate. Physics in Medicine and Biology, 62(19), 7833-7854
Open this publication in new window or tab >>Association between pathology and texture features of multi parametric MRI of the prostate
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2017 (English)In: Physics in Medicine and Biology, ISSN 0031-9155, E-ISSN 1361-6560, Vol. 62, no 19, p. 7833-7854Article in journal (Refereed) Published
Abstract [en]

The role of multi-parametric (mp)MRI in the diagnosis and treatment of prostate cancer has increased considerably. An alternative to visual inspection of mpMRI is the evaluation using histogram-based (first order statistics) parameters and textural features (second order statistics). The aims of the present work were to investigate the relationship between benign and malignant sub-volumes of the prostate and textures obtained from mpMR images. The performance of tumor prediction was investigated based on the combination of histogram-based and textural parameters. Subsequently, the relative importance of mpMR images was assessed and the benefit of additional imaging analyzed. Finally, sub-structures based on the PI-RADS classification were investigated as potential regions to automatically detect maligned lesions. Twenty-five patients who received mpMRI prior to radical prostatectomy were included in the study. The imaging protocol included T2, DWI, and DCE. Delineation of tumor regions was performed based on pathological information. First and second order statistics were derived from each structure and for all image modalities. The resulting data were processed with multivariate analysis, using PCA (principal component analysis) and OPLS-DA (orthogonal partial least squares discriminant analysis) for separation of malignant and healthy tissue. PCA showed a clear difference between tumor and healthy regions in the peripheral zone for all investigated images. The predictive ability of the OPLS-DA models increased for all image modalities when first and second order statistics were combined. The predictive value reached a plateau after adding ADC and T2, and did not increase further with the addition of other image information. The present study indicates a distinct difference in the signatures between malign and benign prostate tissue. This is an absolute prerequisite for automatic tumor segmentation, but only the first step in that direction. For the specific identified signature, DCE did not add complementary information to T2 and ADC maps.

Keywords
textural features, mpMRI, prostate cancer, haralick texture features
National Category
Radiology, Nuclear Medicine and Medical Imaging
Identifiers
urn:nbn:se:umu:diva-142316 (URN)10.1088/1361-6560/aa884d (DOI)000425829000002 ()28837046 (PubMedID)
Available from: 2017-11-27 Created: 2017-11-27 Last updated: 2018-06-09Bibliographically approved
Checa, A., Idborg, H., Zandian, A., Sar, D. G., Surowiec, I., Trygg, J., . . . Wheelock, C. E. (2017). Dysregulations in circulating sphingolipids associate with disease activity indices in female patients with systemic lupus erythematosus: a cross-sectional study. Lupus, 26(10), 1023-1033
Open this publication in new window or tab >>Dysregulations in circulating sphingolipids associate with disease activity indices in female patients with systemic lupus erythematosus: a cross-sectional study
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2017 (English)In: Lupus, ISSN 0961-2033, E-ISSN 1477-0962, Vol. 26, no 10, p. 1023-1033Article in journal (Refereed) Published
Abstract [en]

Objective The objective of this study was to investigate the association of clinical and renal disease activity with circulating sphingolipids in patients with systemic lupus erythematosus.

Methods We used liquid chromatography tandem mass spectrometry to measure the levels of 27 sphingolipids in plasma from 107 female systemic lupus erythematosus patients and 23 controls selected using a design of experiment approach. We investigated the associations between sphingolipids and two disease activity indices, the Systemic Lupus Activity Measurement and the Systemic Lupus Erythematosus Disease Activity Index. Damage was scored according to the Systemic Lupus International Collaborating Clinics damage index. Renal activity was evaluated with the British Island Lupus Activity Group index. The effects of immunosuppressive treatment on sphingolipid levels were evaluated before and after treatment in 22 female systemic lupus erythematosus patients with active disease.

Results Circulating sphingolipids from the ceramide and hexosylceramide families were increased, and sphingoid bases were decreased, in systemic lupus erythematosus patients compared to controls. The ratio of C-16:0-ceramide to sphingosine-1-phosphate was the best discriminator between patients and controls, with an area under the receiver-operating curve of 0.77. The C-16:0-ceramide to sphingosine-1-phosphate ratio was associated with ongoing disease activity according to the Systemic Lupus Activity Measurement and the Systemic Lupus Erythematosus Disease Activity Index, but not with accumulated damage according to the Systemic Lupus International Collaborating Clinics Damage Index. Levels of C-16:0- and C-24:1-hexosylceramides were able to discriminate patients with current versus inactive/no renal involvement. All dysregulated sphingolipids were normalized after immunosuppressive treatment.

Conclusion We provide evidence that sphingolipids are dysregulated in systemic lupus erythematosus and associated with disease activity. This study demonstrates the utility of simultaneously targeting multiple components of a pathway to establish disease associations.

Place, publisher, year, edition, pages
SAGE PUBLICATIONS LTD, 2017
Keywords
Systemic lupus erythematosus, sphingolipids, disease activity
National Category
Rheumatology and Autoimmunity Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-139613 (URN)10.1177/0961203316686707 (DOI)000407822000002 ()28134039 (PubMedID)
Available from: 2017-10-09 Created: 2017-10-09 Last updated: 2018-06-09Bibliographically approved
Surowiec, I., Vikström, L., Hector, G., Johansson, E., Vikström, C. & Trygg, J. (2017). Generalized Subset Designs in Analytical Chemistry. Analytical Chemistry, 89(12), 6491-6497
Open this publication in new window or tab >>Generalized Subset Designs in Analytical Chemistry
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2017 (English)In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 89, no 12, p. 6491-6497Article in journal (Refereed) Published
Abstract [en]

Design of experiments (DOE) is an established methodology in research, development, manufacturing, and production for screening, optimization, and robustness testing. Two-level fractional factorial designs remain the preferred approach due to high information content while keeping the number of experiments low. These types of designs, however, have never been extended to a generalized multilevel reduced design type that would be capable to include both qualitative and quantitative factors. In this Article we describe a novel generalized fractional factorial design. In addition, it also provides complementary and balanced subdesigns analogous to a fold-over in two-level reduced factorial designs. We demonstrate how this design type can be applied with good results in three different applications in analytical chemistry including (a) multivariate calibration using microwave resonance spectroscopy for the determination of water in tablets, (b) stability study in drug product development, and (c) representative sample selection in clinical studies. This demonstrates the potential of generalized fractional factorial designs to be applied in many other areas of analytical chemistry where representative, balanced, and complementary subsets are required, especially when a combination of quantitative and qualitative factors at multiple levels exists.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2017
National Category
Analytical Chemistry
Identifiers
urn:nbn:se:umu:diva-137804 (URN)10.1021/acs.analchem.7b00506 (DOI)000404087600031 ()28497952 (PubMedID)
Available from: 2017-07-27 Created: 2017-07-27 Last updated: 2018-06-09Bibliographically approved
Brynolfsson, P., Nilsson, D., Torheim, T., Asklund, T., Thellenberg Karlsson, C., Trygg, J., . . . Garpebring, A. (2017). Haralick texture features from apparent diffusion coefficient (ADC) MRI images depend on imaging and pre-processing parameters. Scientific Reports, 7, Article ID 4041.
Open this publication in new window or tab >>Haralick texture features from apparent diffusion coefficient (ADC) MRI images depend on imaging and pre-processing parameters
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2017 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 4041Article in journal (Refereed) Published
Abstract [en]

In recent years, texture analysis of medical images has become increasingly popular in studies investigating diagnosis, classification and treatment response assessment of cancerous disease. Despite numerous applications in oncology and medical imaging in general, there is no consensus regarding texture analysis workflow, or reporting of parameter settings crucial for replication of results. The aim of this study was to assess how sensitive Haralick texture features of apparent diffusion coefficient (ADC) MR images are to changes in five parameters related to image acquisition and pre-processing: noise, resolution, how the ADC map is constructed, the choice of quantization method, and the number of gray levels in the quantized image. We found that noise, resolution, choice of quantization method and the number of gray levels in the quantized images had a significant influence on most texture features, and that the effect size varied between different features. Different methods for constructing the ADC maps did not have an impact on any texture feature. Based on our results, we recommend using images with similar resolutions and noise levels, using one quantization method, and the same number of gray levels in all quantized images, to make meaningful comparisons of texture feature results between different subjects.

Place, publisher, year, edition, pages
Nature Publishing Group, 2017
National Category
Radiology, Nuclear Medicine and Medical Imaging
Identifiers
urn:nbn:se:umu:diva-134993 (URN)10.1038/s41598-017-04151-4 (DOI)000403874900024 ()28642480 (PubMedID)
Note

Originally included in thesis in manuscript form.

Available from: 2017-05-15 Created: 2017-05-15 Last updated: 2018-06-09Bibliographically approved
Orikiiriza, J., Surowiec, I., Lindquist, E., Bonde, M., Magambo, J., Muhinda, C., . . . Normark, J. (2017). Lipid response patterns in acute phase paediatric Plasmodium falciparum malaria. Metabolomics, 13(4), Article ID 41.
Open this publication in new window or tab >>Lipid response patterns in acute phase paediatric Plasmodium falciparum malaria
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2017 (English)In: Metabolomics, ISSN 1573-3882, E-ISSN 1573-3890, Vol. 13, no 4, article id 41Article in journal (Refereed) Published
Abstract [en]

Introduction: Several studies have observed serum lipid changes during malaria infection in humans. All of them were focused at analysis of lipoproteins, not specific lipid molecules. The aim of our study was to identify novel patterns of lipid species in malaria infected patients using lipidomics profiling, to enhance diagnosis of malaria and to evaluate biochemical pathways activated during parasite infection.

Methods: Using a multivariate characterization approach, 60 samples were representatively selected, 20 from each category (mild, severe and controls) of the 690 study participants between age of 0.5–6 years. Lipids from patient’s plasma were extracted with chloroform/methanol mixture and subjected to lipid profiling with application of the LCMS-QTOF method.

Results: We observed a structured plasma lipid response among the malaria-infected patients as compared to healthy controls, demonstrated by higher levels of a majority of plasma lipids with the exception of even-chain length lysophosphatidylcholines and triglycerides with lower mass and higher saturation of the fatty acid chains. An inverse lipid profile relationship was observed when plasma lipids were correlated to parasitaemia.

Conclusions: This study demonstrates how mapping the full physiological lipid response in plasma from malaria-infected individuals can be used to understand biochemical processes during infection. It also gives insights to how the levels of these molecules relate to acute immune responses.

Keywords
Lipidomics profiling, Malaria, Plasmodium falciparum, Triacylglycerides, Lysophosphatidylcholines
National Category
Infectious Medicine
Identifiers
urn:nbn:se:umu:diva-133729 (URN)10.1007/s11306-017-1174-2 (DOI)000394544900010 ()28286460 (PubMedID)
Available from: 2017-05-05 Created: 2017-05-05 Last updated: 2018-06-09Bibliographically approved
Surowiec, I., Johansson, E., Torell, F., Idborg, H., Gunnarsson, I., Svenungsson, E., . . . Trygg, J. (2017). Multivariate strategy for the sample selection and integration of multi-batch data in metabolomics. Metabolomics, 13(10), Article ID 114.
Open this publication in new window or tab >>Multivariate strategy for the sample selection and integration of multi-batch data in metabolomics
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2017 (English)In: Metabolomics, ISSN 1573-3882, E-ISSN 1573-3890, Vol. 13, no 10, article id 114Article in journal (Refereed) Published
Abstract [en]

Introduction Availability of large cohorts of samples with related metadata provides scientists with extensive material for studies. At the same time, recent development of modern high-throughput 'omics' technologies, including metabolomics, has resulted in the potential for analysis of large sample sizes. Representative subset selection becomes critical for selection of samples from bigger cohorts and their division into analytical batches. This especially holds true when relative quantification of compound levels is used.

Objectives We present a multivariate strategy for representative sample selection and integration of results from multi-batch experiments in metabolomics.

Methods Multivariate characterization was applied for design of experiment based sample selection and subsequent subdivision into four analytical batches which were analyzed on different days by metabolomics profiling using gas-chromatography time-of-flight mass spectrometry (GC-TOFMS). For each batch OPLS-DA (R) was used and its p(corr) vectors were averaged to obtain combined metabolic profile. Jackknifed standard errors were used to calculate confidence intervals for each metabolite in the average p(corr) profile.

Results A combined, representative metabolic profile describing differences between systemic lupus erythematosus (SLE) patients and controls was obtained and used for elucidation of metabolic pathways that could be disturbed in SLE.

Conclusion Design of experiment based representative sample selection ensured diversity and minimized bias that could be introduced at this step. Combined metabolic profile enabled unified analysis and interpretation.

Place, publisher, year, edition, pages
SPRINGER, 2017
Keywords
OPLS, Metabolomics, Multi-batch analysis, Representative sample selection
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-140022 (URN)10.1007/s11306-017-1248-1 (DOI)000410911200007 ()28890672 (PubMedID)
Note

Open Access, link to the Creative Commons license: https://creativecommons.org/licenses/by/4.0/

Available from: 2017-09-29 Created: 2017-09-29 Last updated: 2018-06-09Bibliographically approved
Bygdell, J., Srivastava, V., Obudulu, O., Srivastava, M. K., Nilsson, R., Sundberg, B., . . . Wingsle, G. (2017). Protein expression in tension wood formation monitored at high tissue resolution in Populus. Journal of Experimental Botany, 68(13), 3405-3417
Open this publication in new window or tab >>Protein expression in tension wood formation monitored at high tissue resolution in Populus
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2017 (English)In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 13, p. 3405-3417Article in journal (Refereed) Published
Abstract [en]

Tension wood (TW) is a specialized tissue with contractile properties that is formed by the vascular cambium in response to gravitational stimuli. We quantitatively analysed the proteomes of Populus tremula cambium and its xylem cell derivatives in stems forming normal wood (NW) and TW to reveal the mechanisms underlying TW formation. Phloem-, cambium-, and wood-forming tissues were sampled by tangential cryosectioning and pooled into nine independent samples. The proteomes of TW and NW samples were similar in the phloem and cambium samples, but diverged early during xylogenesis, demonstrating that reprogramming is an integral part of TW formation. For example, 14-3-3, reactive oxygen species, ribosomal and ATPase complex proteins were found to be up-regulated at early stages of xylem differentiation during TW formation. At later stages of xylem differentiation, proteins involved in the biosynthesis of cellulose and enzymes involved in the biosynthesis of rhamnogalacturonan-I, rhamnogalacturonan-II, arabinogalactan-II and fasciclin-like arabinogalactan proteins were up-regulated in TW. Surprisingly, two isoforms of exostosin family proteins with putative xylan xylosyl transferase function and several lignin biosynthesis proteins were also up-regulated, even though xylan and lignin are known to be less abundant in TW than in NW. These data provided new insight into the processes behind TW formation.

Place, publisher, year, edition, pages
Oxford University Press, 2017
Keywords
cell wall, cellulose, lignin, Populus, proteomics, tension wood, tissue resolution, xylogenesis
National Category
Plant Biotechnology Botany
Identifiers
urn:nbn:se:umu:diva-139165 (URN)10.1093/jxb/erx186 (DOI)000408119100011 ()
Available from: 2017-09-08 Created: 2017-09-08 Last updated: 2018-06-09Bibliographically approved
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