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Sjödin, Marcus O.D.
Alternative names
Publications (10 of 11) Show all publications
Shepherd, T. R., Du, L., Liljeruhm, J., Samudyata, ., Wang, J., Sjödin, M. O. .., . . . Forster, A. C. (2017). De novo design and synthesis of a 30-cistron translation-factor module. Nucleic Acids Research, 45(18), 10895-10905
Open this publication in new window or tab >>De novo design and synthesis of a 30-cistron translation-factor module
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2017 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 45, no 18, p. 10895-10905Article in journal (Refereed) Published
Abstract [en]

Two of the many goals of synthetic biology are synthesizing large biochemical systems and simplifying their assembly. While several genes have been assembled together by modular idempotent cloning, it is unclear if such simplified strategies scale to very large constructs for expression and purification of whole pathways. Here we synthesize from oligodeoxyribonucleotides a completely de-novo-designed, 58-kb multigene DNA. This BioBrick plasmid insert encodes 30 of the 31 translation factors of the PURE translation system, each His-tagged and in separate transcription cistrons. Dividing the insert between three high-copy expression plasmids enables the bulk purification of the aminoacyl-tRNA synthetases and translation factors necessary for affordable, scalable reconstitution of an in vitro transcription and translation system, PURE 3.0.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2017
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-340137 (URN)10.1093/nar/gkx753 (DOI)000413107400046 ()28977654 (PubMedID)
Funder
NIH (National Institute of Health), R01-AI0727453Swedish Research Council, NT 2011-5787Swedish Research Council, NT 2016-1Swedish Research Council, 2016-1
Available from: 2018-01-29 Created: 2018-01-29 Last updated: 2018-01-29Bibliographically approved
Sjödin, M. O. .., Wetterhall, M., Kultima, K. & Artemenko, K. (2013). Comparative study of label and label-free techniques using shotgun proteomics for relative protein quantification. Journal of chromatography. B, 928, 83-92
Open this publication in new window or tab >>Comparative study of label and label-free techniques using shotgun proteomics for relative protein quantification
2013 (English)In: Journal of chromatography. B, ISSN 1570-0232, E-ISSN 1873-376X, Vol. 928, p. 83-92Article in journal (Refereed) Published
Abstract [en]

The analytical performance of three different strategies, iTRAQ (isobaric tag for relative and absolute quantitation), dimethyl labeling (DML) and label free (LF) for relative protein quantification using shotgun proteomics have been evaluated. The methods have been explored using samples containing (i) Bovine proteins in known ratios and (ii) Bovine proteins in known ratios spiked into E.Coli. The latter case mimics the actual conditions in a typical biological sample with a few differentially expressed proteins and a bulk of proteins with unchanged ratios. Additionally, the evaluation was performed on both Q-TOF and LTQ-FTICR mass spectrometers. LF LTQ-FTICR was found to have the highest proteome coverage (94 %) while the highest accuracy based on the artificially regulated proteins was found for DML LTQ-FTICR (54%). A good linearity (r2: 0.61-0.96) was shown for all methods within selected dynamic ranges. All methods were found to consistently underestimate bovine protein ratios when matrix proteins were added. However LF LTQ-FTICR was more tolerant towards a compression effect.  A single peptide was demonstrated to be sufficient for a reliable quantification using iTRAQ. A ranking system utilizing several parameters important for quantitative proteomics demonstrated that the overall performance of the five different methods were; DML LTQ-FTICR > iTRAQ QTOF > LF LTQ-FTICR > DML Q-TOF > LF Q-TOF.

Keywords
Relative quantification, Proteomics, Mass spectrometry, Stable isotope labeling, Label free
National Category
Analytical Chemistry
Research subject
Analytical Chemistry
Identifiers
urn:nbn:se:uu:diva-180105 (URN)10.1016/j.jchromb.2013.03.027 (DOI)000319236700011 ()
Note

De två (2) sista författarna delar sistaförfattarskapet.

Available from: 2012-08-29 Created: 2012-08-29 Last updated: 2019-04-29Bibliographically approved
Wetterhall, M., Sjödin, M. O., Bergquist, J., Hillered, L., Hjort, K. & Dahlin, A. P. (2012). Mapping the protein distribution within a microdialysis sampling system by on-surface enzymatic digestion in combination with mass spectrometry. In: Monitoring Molecules in Neuroscience: 14th International Conference, September 16 – 20, London, U.K.. Paper presented at Monitoring Molecules in Neuroscience: 14th International Conference, September 16 – 20, London, U.K..
Open this publication in new window or tab >>Mapping the protein distribution within a microdialysis sampling system by on-surface enzymatic digestion in combination with mass spectrometry
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2012 (English)In: Monitoring Molecules in Neuroscience: 14th International Conference, September 16 – 20, London, U.K., 2012Conference paper, Published paper (Refereed)
National Category
Analytical Chemistry Engineering and Technology
Research subject
Engineering Science with specialization in Microsystems Technology
Identifiers
urn:nbn:se:uu:diva-188862 (URN)
Conference
Monitoring Molecules in Neuroscience: 14th International Conference, September 16 – 20, London, U.K.
Available from: 2012-12-20 Created: 2012-12-20 Last updated: 2013-02-08Bibliographically approved
Dahlin, A. P., Hjort, K., Hillered, L., Sjödin, M. O. .., Bergquist, J. & Wetterhall, M. (2012). Multiplexed quantification of proteins adsorbed to surface-modified and non-modified microdialysis membranes. Analytical and Bioanalytical Chemistry, 402(6), 2057-2067
Open this publication in new window or tab >>Multiplexed quantification of proteins adsorbed to surface-modified and non-modified microdialysis membranes
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2012 (English)In: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 402, no 6, p. 2057-2067Article in journal (Refereed) Published
Abstract [en]

A simple and straightforward method for discovery and quantification of proteins adsorbed onto delicate and sensitive membrane surfaces is presented. The adsorbed proteins were enzymatically cleaved while still adsorbed onto the membranes using an on-surface enzymatic digestion (oSED). This was followed by isobaric tagging, nanoliquid chromatography, and tandem mass spectrometry. Protein adsorption on tri-block copolymer Poloxamer 407 surface-modified microdialysis (MD) membranes were compared with protein adsorption on unmodified MD membranes. Ventricular cerebrospinal fluid (vCSF) kept at 37 °C was used as sample matrix. In total, 19 proteins were quantified in two biological replicates. The surface-modified membranes adsorbed 33% less proteins than control membranes and the most abundant proteins were subunits of hemoglobin and clusterin. The adsorption of clusterin on the modified membranes was on average 36% compared to control membranes. The most common protein in vCSF, Albumin, was not identified adsorbed to the surface at all. It was also experimentally verified that oSED, in conjunction with tandem mass spectrometry can be used to quantify femtomole amounts of proteins adsorbed on limited and delicate surfaces, such as MD membranes. The method has great potential and can be used to study much more complex protein adsorption systems than previously reported.

National Category
Chemical Sciences Medical and Health Sciences Engineering and Technology
Research subject
Engineering Science with specialization in Microsystems Technology
Identifiers
urn:nbn:se:uu:diva-166977 (URN)10.1007/s00216-011-5614-y (DOI)000300308400008 ()
Available from: 2012-01-18 Created: 2012-01-18 Last updated: 2017-12-08Bibliographically approved
Dahlin, A. P., Hjort, K., Hillered, L., Sjödin, M. O., Bergquist, J. & Wetterhall, M. (2012). Quantification of Proteins Adsorbed to Surface Modified and Non-Modified Microdialysis Membranes using on-Surface Enzymatic Digestion (oSED) iTRAQ-MALDI-TOF/TOF MS. In: 60th ASMS Conference on Mass Spectrometry and Allied Topics, May 20 - 24, Vancouver, Canada: . Paper presented at 60th ASMS Conference on Mass Spectrometry and Allied Topics, May 20 - 24, Vancouver, Canada.
Open this publication in new window or tab >>Quantification of Proteins Adsorbed to Surface Modified and Non-Modified Microdialysis Membranes using on-Surface Enzymatic Digestion (oSED) iTRAQ-MALDI-TOF/TOF MS
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2012 (English)In: 60th ASMS Conference on Mass Spectrometry and Allied Topics, May 20 - 24, Vancouver, Canada, 2012Conference paper, Published paper (Refereed)
National Category
Analytical Chemistry Engineering and Technology
Research subject
Engineering Science with specialization in Microsystems Technology
Identifiers
urn:nbn:se:uu:diva-188854 (URN)
Conference
60th ASMS Conference on Mass Spectrometry and Allied Topics, May 20 - 24, Vancouver, Canada
Available from: 2012-12-20 Created: 2012-12-20 Last updated: 2014-01-09
Wetterhall, M., Shevchenko, G., Artemenko, K. A., Sjödin, M. O. .. & Bergquist, J. (2011). Analysis of membrane and hydrophilic proteins simultaneously derived from the mouse brain using cloud-point extraction. Analytical and Bioanalytical Chemistry, 400(9), 2827-2836
Open this publication in new window or tab >>Analysis of membrane and hydrophilic proteins simultaneously derived from the mouse brain using cloud-point extraction
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2011 (English)In: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 400, no 9, p. 2827-2836Article in journal (Refereed) Published
Abstract [en]

In this study, a temperature-induced phase fractionation known as cloud-point extraction (CPE) with the non-ionic surfactant Triton X-114 was used to simultaneously extract, concentrate, and fractionate hydrophobic and hydrophilic proteins from mouse brain tissue. Two bottom-up proteomic techniques were used to comprehensively identify the extracted proteins. The first "shotgun"-based approach included tryptic digestion of the proteins followed by reversed-phase nanoliquid chromatography (RP-nanoLC) in combination with electrospray ionization (ESI) tandem mass spectrometry (MS/MS). In the second approach, the extracted intact proteins were first separated by one-dimensional (1D) gel electrophoresis and then in-gel digested with trypsin and analyzed with nanoLC-MS/MS. In total, 1,825 proteins were unambiguously identified and the percentage of membrane proteins was 26% which is at the reported genome expression levels of 20-30%. The protein overlap between the two approaches was high. The majority (77%) of the identifications in the first approach was also found by the second method. The protein overlap between the CPE-extracted hydrophilic and hydrophobic fractions was rather small (16-23%) for both methods, which indicates a good phase separation. A quantitative evaluation of the CPE with iTRAQ labeling and nanoLC-ESI-MS/MS analysis gave iTRAQ ratios at the expected levels and an overall variation of the entire method at 17-31%. The results indicate very reproducible sample preparation and analysis methods that readily can be applied on large-scale sample sets.

Keywords
Cloud-point extraction (CPE), Brain, Proteomics, Membrane proteins (MPs), Mass spectrometry (MS), iTRAQ
National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-154958 (URN)10.1007/s00216-011-5037-9 (DOI)000291037800016 ()21553125 (PubMedID)
Available from: 2011-06-14 Created: 2011-06-14 Last updated: 2017-12-11Bibliographically approved
Amelina, H., Sjödin, M. O. .., Bergquist, J. & Cristobal, S. (2011). Quantitative subproteomic analysis of age-related changes in mouse liver peroxisomes by iTRAQ LC-MS/MS. Journal of chromatography. B, 879(30), 3393-3400
Open this publication in new window or tab >>Quantitative subproteomic analysis of age-related changes in mouse liver peroxisomes by iTRAQ LC-MS/MS
2011 (English)In: Journal of chromatography. B, ISSN 1570-0232, E-ISSN 1873-376X, Vol. 879, no 30, p. 3393-3400Article in journal (Refereed) Published
Abstract [en]

Aging is a complex multifactorial phenomenon, which is believed to result from the accumulation of cellular damage to biological macromolecules. Peroxisomes recently emerged as another important source of reactive oxygen species (ROS) production in addition to mitochondria. However, the role of these organelles in the process of aging is still not clear. The aim of this study was to characterize the changes in protein expression profiles of young (10 weeks old) versus old (18 months old) mouse liver peroxisome-enriched fractions. We have applied shotgun proteomic approach based on liquid chromatography and tandem mass spectrometry (LC-MS/MS) combined with iTRAQ (isobaric tags for relative and absolute quantitation) labeling that allows comparative quantitative multiplex analysis. Our analysis led to identification and quantification of 150 proteins, 8 out of which were differentially expressed between two age groups at a statistically significant level (p < 0.05), with folds ranging from 1.2 to 4.1. These proteins involved in peroxisornal beta-oxidation, detoxification of xenobiotics and production of ROS. Noteworthy, differences in liver proteome have been observed between as well as within different age groups. In conclusion, our subproteomic quantitative study suggests that mouse liver proteome is sufficiently maintained until certain age.

Keywords
Liquid chromatography, Tandem mass spectrometry, Peroxisomes, Aging, Liver, iTRAQ
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-166066 (URN)10.1016/j.jchromb.2011.08.044 (DOI)000297396200006 ()
Available from: 2012-01-12 Created: 2012-01-10 Last updated: 2017-12-08Bibliographically approved
Elhamili, A., Wetterhall, M., Sjödin, M. O. .., Sebastiano, R. & Bergquist, J. (2010). Analysis of peptides using N-methylpolyvinylpyridium as silica surface modifier for CE-ESI-MS. Electrophoresis, 31(7), 1151-1156
Open this publication in new window or tab >>Analysis of peptides using N-methylpolyvinylpyridium as silica surface modifier for CE-ESI-MS
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2010 (English)In: Electrophoresis, ISSN 0173-0835, E-ISSN 1522-2683, Vol. 31, no 7, p. 1151-1156Article in journal (Refereed) Published
Abstract [en]

In this study, the N-methylpolyvinylpyridinuim polymer has for the first time been used as a silica surface modifier for CE in combination with ESI MS (CE-ESI-MS). The compatibility for ESI-MS was demonstrated by the analysis of peptides and protein digests. The N-methylpolyvinylpyridium surface interacts electrostatically with the ionized silanol groups, giving a cationic surface with a reversed EOF. The surface modifier gave rapid and repeatable separations of peptides, proteins and protein digests at acidic pH for more than 4 h of continuous use. The CE separation yielded peak efficiencies of up to 4.3 x 10(5) plates/m. The surface coating is highly compatible with ESI and facilitates the separation and analysis of complex peptide mixtures as shown by the analysis of BSA digests.

Keywords
CE, ESI, MS, N-methylpolyvinylpyridinuim, peptides
National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-125809 (URN)10.1002/elps.200900536 (DOI)000276811000005 ()20209570 (PubMedID)
Available from: 2010-05-28 Created: 2010-05-28 Last updated: 2017-12-12Bibliographically approved
Sjödin, M. O. D. (2010). Analytical Strategies for Protein Biomarker Discovery in the Central Nervous System using Mass Spectrometry. (Licentiate dissertation). Uppsala universitet
Open this publication in new window or tab >>Analytical Strategies for Protein Biomarker Discovery in the Central Nervous System using Mass Spectrometry
2010 (English)Licentiate thesis, comprehensive summary (Other academic)
Place, publisher, year, edition, pages
Uppsala universitet, 2010
National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-153766 (URN)
Available from: 2011-06-23 Created: 2011-05-18 Last updated: 2011-06-23Bibliographically approved
Shevchenko, G., Sjödin, M. O. .., Malmström, D., Wetterhall, M. & Bergquist, J. (2010). Cloud-point extraction and delipidation of porcine brain proteins in combination with bottom-up mass spectrometry approaches for proteome analysis. Journal of Proteome Research, 9(8), 3903-3911
Open this publication in new window or tab >>Cloud-point extraction and delipidation of porcine brain proteins in combination with bottom-up mass spectrometry approaches for proteome analysis
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2010 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 9, no 8, p. 3903-3911Article in journal (Refereed) Published
Abstract [en]

In this study, temperature-induced phase fractionation also known as cloud-point extraction (CPE) with the nonionic surfactant Triton X-114 was used to simultaneously extract hydrophobic and hydrophilic proteins from porcine brain tissue. Various protein precipitation/delipidation procedures were investigated to efficiently remove lipids and detergents while retaining maximum protein recoveries. The best performing delipidation method was then used in combination with CPE to compare three different mass spectrometry (MS) based "bottom-up" proteomic approaches for protein analysis of the porcine brain. In the first approach, the intact proteins were initially separated by one-dimensional (1D) gel electrophoresis. The excised protein bands were digested with trypsin, and the peptides were separated by reversed phase nanoliquid chromatography (RP-nanoLC) followed by electrospray ionization (ESI) tandem mass spectrometry (MS/MS) analysis. The other bottom-up proteomic approaches were based on first enzymatical digestion of the proteins followed by RP-nanoLC separation in combination with matrix assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF/TOF MS) or on the combination of in-solution isoelectric focusing (IEF) with ESI-nanoLC-MS/MS of the IEF separated peptides. In total, we found and unambiguously identified 331 unique proteins. The overlap between different techniques was about 10%, showing that the use of multiple proteomic approaches is beneficial to yield a better coverage of the proteome. Furthermore, the overlap between the CPE extracted hydrophilic and hydrophobic proteins was rather small (9-16%), indicating an efficient sample preparation technique to extract and separate hydrophilic and hydrophobic proteins from brain tissue. The percentage of identified membrane proteins was 27%, which is in accordance to the fact that about one-third of all genes in various organisms encode for this class of proteins. The results indicate that cloud point extraction is a promising sample preparation tool, which allows simultaneous in depth studies of brain derived membrane proteins as well as hydrophilic proteins. This technique can be very useful when studying human central nervous system (CNS) tissue or animal models of neurological diseases.

Place, publisher, year, edition, pages
ACS, 2010
Keywords
cloud-point extraction (CPE), delipidation, central nervous system (CNS), brain, bottom-up proteomics, membrane proteins (MPs), mass spectrometry (MS)
National Category
Chemical Sciences
Research subject
Analytical Chemistry
Identifiers
urn:nbn:se:uu:diva-130276 (URN)10.1021/pr100116k (DOI)000280583700014 ()20586484 (PubMedID)
Available from: 2010-09-08 Created: 2010-09-06 Last updated: 2017-12-12Bibliographically approved
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