Biopolymer Analytical Platform (BAP)

The Biopolymer Analytical Platform (former UPSC Plant Cell Wall and Carbohydrate Analytical Facility) has been an official KBC facility since 2018 and is dedicated to research on cell walls of terrestrial and aquatic plants, and biopolymer materials among KBC groups.

Equip­ment and competence for applying a large range of standard methods have been established with various sample preparation equipment, permanently installed equipment for conventional wet chemical methods and state-of-the-art analytical instrument setups.

Our competence for the analysis of lignocellulose and secondary xylem, besides fine detection of soluble sugars and starch in these materials, includes: carbohydrate composition, lignin composition, lignin and carbohydrate structures and molecular size distributions of poly­mers. Conventional wet chemistry methods such as Updegraff cellulose and Klason/thioglycolic acid/acetylbromide lignin have been optimized in order to reduce the amount of sample material required. The availability of parallel cell wall analytical methodologies for both model systems (Arabidopsis and Populus) facilitates and accelerates the research process with other plant species.

 

 

The established methods include many dif­ferent protocols to analyze monosaccharide composition of a whole sample or fractionated cell walls. The instrumental backbone for many of those methods is gas chromatography/mass spectrometry or flame ionization detection (GC/MS(FID)). The facility offers two instruments for analytical pyrolysis-GC/MS (Py-GC/MS) that quickly yield highly reproducible and comprehensive chemical fingerprinting of carbohydrate and lignin types, while a third is permanently available for sugar analysis.

For characterizing a wide variety of polymers, there is an analytical size exclusion chromatography (SEC) setup with a quadruple detector array for multi-angle laser light scattering (MALLS), viscometry, refrac­tive index (RI) and UV absorbance detection. Ion chromatography (IC) is also available for the analysis of monosaccharides without derivatization, as well as oligosac­charides that can be collected for further characterization.

Recently, increasing number of researchers related to bioenergy, renewable resources and novel biomaterials conducted analyses at the lab.

 

Steering committee:

A steering committee oversees the work of the facility and decides what techniques should be developed.

• Totte Niittylä, Assoc. Prof., Dept. of Forest Genetics and Plant Physiology, SLU
• Ewa Mellerowicz, Prof., Dept. of Forest Genetics and Plant Physiology, SLU
• Hannele Tuominen, Assoc. Prof., Dept. of Plant Physiology, UmU
• Leif Jönsson, Prof., Dept. of Chemistry, UmU
• Ola Sundman, PhD, Dept. of Chemistry, UmU
• Junko Takahashi-Schmidt, PhD, Dept. of Forest Genetics and Plant Physiology, SLU

Contacts:

Totte Niittylä (This email address is being protected from spambots. You need JavaScript enabled to view it.): Responsible scientist

Junko Takahashi-Schmidt (This email address is being protected from spambots. You need JavaScript enabled to view it.): Laboratory manager

Available analyses and the charge (2018.04.23 updated):

{tab=Internal KBC groups}

Type of analysis		Charged per	Annual fee payers (10,000 kr/year)	Non annual fee payers
Soluble sugar (glucose, fructose and sucrose)		1 Elisa plate (96-well)	300 kr	600 kr
Starch		1 Elisa plate (96-well)	400	800
Updegraff cellulose (crystalline cellulose)		1 sample	40	80
Anthrone assay only		1 sample	20	40
Klason lignin (acid insoluble lignin)		1 sample	40	80
Thioglycolic acid (TGA) lignin		1 sample	40	80
Acetylbromide lignin		1 sample	40	80
Biphenyl assay for uronic acids		1 Elisa plate (96-well)	400	800
Total carbohydrate (Dubois)		1 sample	20	40
Hexose/6-deoxyhexose (Dische)		1 sample	20	40
Pyrolysis-GC/MS		1 sample	60	120
TMS sugars with GC/MS		1 sample	120	240
Alditol acetate sugars with GC/FID		1 sample	120	240
GC/FID or MS only		1 sample	60	120
TFA/monosaccharide with IC		1 sample	100	200
Apha-amylase (Roche) for AIR2		1ul	0,5	0,5

{tab=External academic groups}

Type of analysis		Charged per	External Groups
Soluble sugar (glucose, fructose and sucrose)		1 Elisa plate (96-well)	1200 kr
Starch		1 Elisa plate (96-well)	1600
Updegraff cellulose (crystalline cellulose)		1 sample	160
Anthrone assay only		1 sample	80
Klason lignin (acid insoluble lignin)		1 sample	160
Thioglycolic acid (TGA) lignin		1 sample	160
Acetylbromide lignin		1 sample	160
Biphenyl assay for uronic acids		1 Elisa plate (96-well)	1600
Total carbohydrate (Dubois)		1 sample	80
Hexose/6-deoxyhexose (Dische)		1 sample	80
Pyrolysis-GC/MS		1 sample	240
TMS sugars with GC/MS		1 sample	480
Alditol acetate sugars with GC/FID		1 sample	480
GC/FID or MS only		1 smaple	240
TFA/monosaccharide with IC		1 sample	400
Apha-amylase (Roche) for AIR2		1ul	1

{tab=External industrial groups}
Coming Soon
{tab=Additional information}
1. It is also possible to do: 1) preparation of alcohol insoluble residue (AIR) and removal of extractives, 2) analysis of acetylation/methyl esterification.
2. It is possible to do size exclusion chromatography (SEC) in collaboration with Leif Jönsson's group and Ola Sundman’s group in the Department of Chemistry, Umeå University. Please contact us.
3. Method development fee
If you would like to try a new method with us, we can do so in the form of project. For starting up, we need to charge the method development fee for covering the cost of necessary materials.
Half year: 6 000 kr, 1 year: 11 000 kr
4. Sample preparation by a Cell Wall Lab staff
When you have a lack of lab workers, although you have a lot of samples to be analyzed in the cell wall lab…  We can give you a hand when it is needed with the additional sample preparation fee.
1h: 600 kr
Examples:
1) TMS sample preparation (ca. 10h)
2) TMS data processing & peak identification (ca. 2h)
3) Py-GC/MS extra processing & peak identification (ca. half day)
4) Py-GC/MS sample preparation
5) Cleaning ion source in MSD due to special samples

Selected publications including analyses in the facility:

• Wang Z, Wu G and Jönsson LJ (2018). Effects of impregnation of softwood with sulfuric acid and sulfur dioxide on chemical and physical characteristics, enzymatic digestibility, and fermentability. Bioresource Technology 247: 200–208.

• Roach M, Arrivault S, Mahboubi A, Krohn N, Sulpice R, Stitt M and Niittylä T (2017). Spatially-resolved metabolic analysis reveals a central role for transcriptional control in carbon allocation to wood. Journal of Experimenal Botany 68: 3529-3539.
• Rende U, Wang W, Gandla ML, Jönsson LJ and Niittylä T (2017). Cytosolic invertase contributes to the supply of substrate for cellulose biosynthesis in developing wood. New Phytologist 214: 796-807.
• Pawar P M-A, Ratke C, Balasubramanian VK, Chong SL, Gandla ML, Adriasola M, Sparrman T, Hedenström M, Szwaj K, Derba-Maceluch M, Gaertner C, Mouille G, Ezcurra I, Tenkanen M, Jönsson LJ and Mellerowicz EJ (2017). Downregulation of RWA genes in hybrid aspen affects xylan acetylation and wood saccharification. New Phytologist 214: 1491–1505.
• Pawar P M-A, Derba-Maceluch M, Chong SL, Gandla ML, Bashar SS, Sparrman T, Ahvenainen P, Hedenström M, Özparpucu M, Rüggeberg M, Serimaa R, Lawoko M, Tenkanen M, Jönsson LJ and Mellerowicz EJ (2017). In muro deacetylation of xylan affects lignin properties and improves saccharification of aspen wood. Biotechnology for Biofuels 10:98.
  
• Soucémarianadin LN, Erhagen B, Nilsson MB, Öquist MG, Immerzeel P and Schleucher J (2017). Two dimensional NMR spectroscopy for molecular characterization of soil organic matter: Application to boreal soils and litter. Organic Geochemistry 113: 184-195.
  
• Garcia-Bravo A, Bouchet S, Tolu J, Björn E, Mateos-Rivera A and Bertillson S (2017). Molecular composition of organic matter controls methylmercury formation in boreal lakes. Nature Communications doi 10.1038/ncomms14255.
  
• Tolu J, Rydberg J, Meyer-Jacob C, Gerber L and Bindler R (2017). Spatial variability of organic matter molecular composition and elemental geochemistry in surface sediments of a small boreal Swedish lake. Biogeosciences 14: 1773-1792.
  
• Ninnes S, Tolu J, Meyer-Jacob C, Mighall, TM and Bindler R (2017). Investigating molecular changes in organic matter composition in two Holocene lake-sediment records from central Sweden using pyrolysis GC-MS. Journal of geophysical research - Biogeosciences 122: 1423-1438.
  
• Martín C, Wei M, Xiong S and Jönsson LJ (2017). Enhancing saccharification of cassava stems by starch hydrolysis prior to pretreatment. Industrial Crops and Products 97: 21-31.
  
• Escamez S, Gandla ML, Derba-Maceluch M, Lundqvist SO, Mellerowicz EJ, Jönsson LJ and Tuominen H (2017). A collection of genetically engineered Populus trees reveals wood biomass traits that predict glucose yield from enzymatic hydrolysis. bioRxiv 124396
• Pawar PM-A, Derba-Maceluch M, Chong S-L, Gómez LD, Miedes E, Banasiak A, Ratke C, Gaertner C, Mouille G, McQueen-Mason SJ, Molina A, Sellstedt A, Tenkanen M and Mellerowicz EJ (2016). Expression of fungal acetyl xylan esterase in Arabidopsis thaliana improves saccharification of stem lignocellulose. Plant Biotechnology Journal 14: 387–397.
• Normark M, Pommer L, Gräsvik J, Hedenström M, Gorzsás A, Winestrand S and Jönsson LJ (2016). Biochemical conversion of torrefied Norway spruce after pretreatment with acid or ionic liquid. BioEnergy Research 9: 355-368.
• Gao Q, Budarin VL, Cieplik M, Gronnow M and Jansson S (2016). PCDDs, PCDFs and PCNs in products of microwave-assisted pyrolysis of woody biomass - Distribution among solid, liquid and gaseous phases and effects of material composition. Chemosphere 145: 193-199.
• Mahboubi A, Linden P, Hedenström M, Moritz T and Niittylä T (2015). Carbon-13 tracking after 13CO2 supply revealed diurnal patterns of wood formation in aspen. Plant Physiology 168: 478-489.
• Serk H, Gorzsás A, Tuominen H and Pesquet E (2015). Cooperative lignification of xylem tracheary elements. Plant Signal Behavior 10(4):e1003753. doi: 10.1080/15592324.2014.1003753.
• Derba-Maceluch M, Awano T, Takahashi J, Lucenius J, Ratke C, Kontro I, Busse-Wicher M, Kosik O, Tanaka R, Winzéll A, Kallas Å, Lesniewska J, Berthold F, Immerzeel P, Teeri TT, Ezcurra I, Dupree P, Serimaa R, and Mellerowicz EJ (2015). Suppression of xylan transglycosylase PtxtXyn10A affects cellulose microfibril angle in secondary wall in aspen wood. New Phytologist 205: 666–681.
• Gandla ML, Derba-Maceluch M, Liu X, Gerber L, Master ER, Mellerowicz EJ and Jönsson LJ (2015). Expression of a fungal glucuronoyl esterase in Populus: effects on wood properties and saccharification efficiency. Phytochemistry 112: 210–220.
• Normark M, Pommer L, Gräsvik J, Hedenström M, Gorzsás A, Winestrand S and Jönsson LJ (2015). Biochemical conversion of torrefied Norway spruce after pretreatment with acid or ionic liquid. BioEnergy Research DOI 10.1007/s12155-015-9698-7.
• Tolu J, Gerber L, Boily JF and Bindler R (2015). High-throughput characterization of sediment organic matter by pyrolysis–gas chromatography/mass spectrometry and multivariate curve resolution: A promising analytical tool in (paleo)limnology. Analytica Chimica Acta 880: 93–102.
• Chong SL, Derba-Maceluch M, Koutaniemi S, Gómez LD, McQueen-Mason SJ, Tenkanen M and Mellerowicz EJ (2015). Active fungal GH115 α-glucuronidase produced in Arabidopsis thaliana affects only the UX1-reactive glucuronate decorations on native glucuronoxylans. BMC Biotechnology 15:56.
• Gerber L, Zhang B, Roach M, Rende U, Gorzsás A, Kumar M, Burgert I, Niittylä T and Sundberg B (2014). Deficient sucrose synthase activity in developing wood does not specifically affect cellulose biosynthesis, but causes an overall decrease in cell wall polymers. New Phytologist 203: 1220 – 1230.
• Mahboubi A, Ratke C, Gorzsás A, Kumar M, Mellerowicz EJ and Niittylä T (2013). Aspen SUCROSE TRANSPORTER 3 allocates carbon into wood fibers. Plant Physiology 163: 1729-1740.
• Pesquet E, Zhang B, Gorzsás A, Puhakainen T, Serk H, Escamez S, Barbier O, Gerber L, Courtois- Moreau C, Alatalo E, Paulin L, Kangasjärvi J, Sundberg B, Goffner D and Tuominen H (2013). Non-Cell-Autonomous Postmortem Lignification of Tracheary Elements in Zinnia elegans. Plant Cell 25(4): 1314-1328.
• Kudahettige RL, Holmgren M, Imerzeel P and Sellstedt A (2012). Characterization of Bioethanol Production from Hexoses and Xylose by the White Rot Fungus Trametes versicolor. BioEnergy Research 5: 277-285.
• Roach M, Gerber L, Sandquist D, Gorzsas A, Hedenström M, Kumar M, Steinhauser MC, Feil R, Daniel G, Stitt M, Sundberg B and Niittylä T (2012). Fructokinase is required for carbon partitioning to cellulose in aspen wood. Plant Journal 70: 967 – 977.
• Gerber L, Eliasson M, Trygg J, Moritz T and Sundberg B (2012). Multivariate curve resolution provides a high-throughput data processing pipeline for pyrolysis–gas chromatography/mass spectrometry. Journal of analytical and applied Pyrolysis 95: 95-100.

Facility Funding

The facility was initially funded by FuncFiber in order to enable basic cell wall chemical characterizations in its projects. Additional funding has been provided to maintain the instruments and to develop techniques in particular by UPSC Berzelii Centre, Spruce Genome Project (Knut and Alice Wallenberg Foundation), Bio4Energy, TC4F and Value Tree and KBC Scientific Board. Large numbers of samples have been analyzed in association with BioImprove projects.