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1. Enzymatic regioselective acylation of nucleosides in biomass-derived 2-methyltetrahydrofuran: kinetic study and enzyme substrate recognition.

Author

Gao WL, Li N, and Zong MH

Subjects
Acylation, Bacterial Proteins metabolism, Biomass, Bioreactors, Kinetics, Lipase metabolism, Penicillium enzymology, Stereoisomerism, Substrate Specificity, Biotechnology methods, Enzymes, Immobilized metabolism, Furans metabolism, Nucleosides chemistry, Nucleosides metabolism
Abstract

Enzymatic regioselective acylation of pyrimidine nucleosides was mediated by immobilized lipase from Penicillium expansum in 2-methyltetrahydrofuran (MeTHF), a bio-solvent derived from biomass. Despite of the moderate dissolution ability of MeTHF toward nucleosides, the initial enzymatic reaction rate was much higher in this eco-friendly solvent than in other commonly used organic solvents. This could be explained by the lower apparent activation energy of the enzymatic reaction (24.5 vs. 43.3-57.1kJ/mol) and the higher catalytic efficiency of the enzyme (Vmax/Km, 5.8 vs. 1.1-2.9h(-1)) in MeTHF. The enzymatic acylation of a group of ribonucleosides afforded the desirable 5'-esters with the conversions of 96-99% and 5'-regioselectivities of 96 to >99%. In enzymatic acylation of 2'-deoxynucleosides, however, 5'-regioselectivities showed a clear dependence on the 5-substituents present in the base moiety although the substrate conversions reached >98% within 1-3h. In the cases of 2',3'-dideoxynucleoside analogs, the reaction rate decreased markedly due to the lack of 3'-hydroxyl., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Published
2013
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2. Effects of drying-induced fiber hornification on enzymatic saccharification of lignocelluloses.

Author

Luo X and Zhu JY

Subjects
Cell Wall metabolism, Cellulose analysis, Cellulose chemistry, Cellulose metabolism, Industrial Waste, Lignin physiology, Substrate Specificity, Water analysis, Biotechnology methods, Cellulase metabolism, Desiccation, Lignin metabolism, Paper, Wood
Abstract

This study investigated the effect of fiber hornification during drying on lignocellulosic substrate enzymatic saccharification. Two chemically pretreated wood substrates and one commercial bleached kraft hardwood pulp were used. Heat drying at 105 and 150°C and air drying at 50% RH and 23.8°C for different durations were applied to produce substrate with various degrees of hornification. It was found that substrate enzymatic digestibilities (SEDs) of hornified substrates made from the same never-dried sample correlate very well to an easily measurable parameter, water retention value (WRV), and can be fitted by a Boltzmann function. The hornification-produced SED reduction at a given degree of hornification as the percentage of the total SED reduction when the substrate is completely hornified depends on two parameters. The first is WRV¯, which is primarily a function of the effective enzyme molecule size, and Δ, which is related to the substrate pore size distribution shape. The low values of SED(CH), SED of a completely hornified substrate, obtained from curve fittings for the three sets of samples studied, suggest that enzyme accessibility to cellulose is mainly through the pores in the cell wall rather than substrate external surface. The SEDs of hornified substrates were found to correlate to Simons' staining measurements well. A new parameter was proposed to better correlate enzyme accessibility to cellulose using the two-color Simons' staining technique., (Published by Elsevier Inc.)

Published
2011
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3. Effect of hot-water extraction on alkaline pulping of bagasse.

Author

Lei Y, Liu S, Li J, and Sun R

Subjects
Cellulose metabolism, Hot Temperature, Hydrogen-Ion Concentration, Paper, Water, Alkalies chemistry, Biotechnology methods, Cellulose chemistry, Sodium Hydroxide chemistry
Abstract

The effect of hot-water extraction on alkaline pulping was investigated. The properties of black liquor and pulp strength of bagasse were analyzed. The extraction was conducted at 160 degrees C for 30min where 13.2% of the mass was dissolved in the extraction liquor. Untreated bagasse and extracted bagasse were digested by soda and soda-AQ processes at 17% and 15.5% (with 0.1% AQ) alkali charge (NaOH). Cooking temperatures were 160 degrees C and 155 degrees C respectively. The pulp from extracted bagasse had a lower Kappa number and a higher viscosity compared to the pulp from the untreated bagasse. The black liquor from pulping extracted bagasse had a lower solid content, a lower viscosity and a lower silica content, but a higher heating value than that from pulping of untreated bagasse. Hot-water extraction resulted in a significant decrease in bleaching chemical consumption and the formation of chlorinated organics. Pulp strength properties such as the tensile index and the burst index were found to be lower, but the tear index, bulk, opacity and pulp freeness were found to be higher when hot-water extraction was applied., (Copyright 2010 Elsevier Inc. All rights reserved.)

Published
2010
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4. Bioethanol fermentation by recombinant E. coli FBR5 and its robust mutant FBHW using hot-water wood extract hydrolyzate as substrate.

Author

Liu T, Lin L, Sun Z, Hu R, and Liu S

Subjects
Acer chemistry, Acer metabolism, Ethanol chemistry, Fermentation, Hot Temperature, Hydrogen-Ion Concentration, Hydrolysis, Nuclear Magnetic Resonance, Biomolecular, Polysaccharides metabolism, Sterilization, Water, Xylose metabolism, Biofuels microbiology, Bioreactors microbiology, Biotechnology methods, Escherichia coli metabolism, Ethanol metabolism
Abstract

Hemicellulose is a potential by-product currently under-utilized in the papermaking industry. It is a hetero-carbohydrate polymer. For hardwood hemicelluloses, D-xylose is the major component upon depolymerization. At SUNY-ESF, wood extracts were obtained by extracting sugar maple wood chips with hot water at an elevated temperature. The wood extracts were then concentrated and acid hydrolyzed. Ethanologenic bacteria, E. coli FBR5, had a good performance in pure xylose medium for ethanol production. However, FBR5 was strongly inhibited in dilute sulfuric acid hydrolyzate of hot-water wood extract. FBR5 was challenged by hot-water wood extract hydrolyzate in this study. After repeated strain adaptation, an improved strain: E. coli FBHW was obtained. Fermentation experiments indicated that FBHW was resistant to the toxicity of hydrolyzate in the fermentation media of concentrated hydrolyzate, and xylose was completely utilized by the strain to produce ethanol. FBHW was grown in the concentrated hydrolyzate without any detoxification treatment and has yielded 36.8g/L ethanol., (Copyright 2010 Elsevier Inc. All rights reserved.)

Published
2010
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5. Woody biomass: Niche position as a source of sustainable renewable chemicals and energy and kinetics of hot-water extraction/hydrolysis.

Author

Liu S

Subjects
Hot Temperature, Hydrolysis, Water, Biofuels, Biomass, Biotechnology methods, Conservation of Natural Resources methods, Wood
Abstract

The conversion of biomass to chemicals and energy is imperative to sustaining our way of life as known to us today. Fossil chemical and energy sources are traditionally regarded as wastes from a distant past. Petroleum, natural gas, and coal are not being regenerated in a sustainable manner. However, biomass sources such as algae, grasses, bushes and forests are continuously being replenished. Woody biomass represents the most abundant and available biomass source. Woody biomass is a reliably sustainable source of chemicals and energy that could be replenished at a rate consistent with our needs. The biorefinery is a concept describing the collection of processes used to convert biomass to chemicals and energy. Woody biomass presents more challenges than cereal grains for conversion to platform chemicals due to its stereochemical structures. Woody biomass can be thought of as comprised of at least four components: extractives, hemicellulose, lignin and cellulose. Each of these four components has a different degree of resistance to chemical, thermal and biological degradation. The biorefinery concept proposed at ESF (State University of New York - College of Environmental Science and Forestry) aims at incremental sequential deconstruction, fractionation/conversion of woody biomass to achieve efficient separation of major components. The emphasis of this work is on the kinetics of hot-water extraction, filling the gap in the fundamental understanding, linking engineering developments, and completing the first step in the biorefinery processes. This first step removes extractives and hemicellulose fractions from woody biomass. While extractives and hemicellulose are largely removed in the extraction liquor, cellulose and lignin largely remain in the residual woody structure. Xylo-oligomers and acetic acid in the extract are the major components having the greatest potential value for development. Extraction/hydrolysis involves at least 16 general reactions that could be divided into four categories: adsorption of proton onto woody biomass, hydrolysis reactions on the woody biomass surface, dissolution of soluble substances into the extraction liquor, and hydrolysis and dehydration decomposition in the extraction liquor. The extraction/hydrolysis rates are significantly simplified when the reactivity of all the intermonomer bonds are regarded as identical within each macromolecule, and the overall reactivity are identical for all the extractable macromolecules on the surface. A pseudo-first order extraction rate expression has been derived based on concentrations in monomer units. The reaction rate constant is however lower at the beginning of the extraction than that towards the end of the extraction. Furthermore, the H-factor and/or severity factor can be applied to lump the effects of temperature and residence time on the extraction process, at least for short times. This provides a means to control and optimize the performance of the extraction process effectively., (Copyright 2010 Elsevier Inc. All rights reserved.)

Published
2010
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6. Effect of phosphoric acid pretreatment on enzymatic hydrolysis of microcrystalline cellulose.

Author

Zhang J, Zhang B, Zhang J, Lin L, Liu S, and Ouyang P

Subjects
Adsorption, Cellobiose chemistry, Cellobiose metabolism, Cellulose metabolism, Glucose chemistry, Glucose metabolism, Hydrolysis, Photoelectron Spectroscopy, Surface Properties, Biotechnology methods, Cellulose chemistry, Phosphoric Acids chemistry
Abstract

Microcrystalline cellulose (MCC) was pretreated with phosphoric acid at 323K for 10h. X-ray diffraction (XRD) and Atomic Force Microscope (AFM) analyses revealed that the fiber surface morphology of pretreated MCC (P-MCC) were uneven and rough with the crystalline diffraction peaks of P-MCC decreased to a distinct range. The X-ray Photoelectron Spectroscopy (XPS) analysis showed that the uneven and rough surface of P-MCC could enhance the adsorption of cellulose to the molecular surface of cellulose, which is one of the key factors affecting enzymatic hydrolysis of cellulose. A reversible first order kinetics was employed to describe the adsorption kinetics of cellulase to MCC and P-MCC, and the adsorption rate constants of MCC and P-MCC were found to be 0.016, 0.024, 0.041, and 0.095, 0.149, 0.218min(-1), respectively at 278K, 293K and 308K. The activation energies of MCC and P-MCC hydrolysis reactions were found to be 22.257 and 19.721kJ mol(-1). The major hydrolysis products of MCC and P-MCC were cellobiose and glucose. Hydrolysis of MCC for 120h resulted in yields of glucose (7.21%), cellobiose (13.16%) and total sugars (20.37%). However, after the pretreatment with phosphoric acid, the corresponding sugar yields resulted from enzymatic hydrolysis of P-MCC were increased to 24.10%, 41.42%, and 65.52%; respectively, which were 3.34, 3.15, and 3.22 times of the sugars yields from enzymatic hydrolysis of MCC., (Copyright 2010 Elsevier Inc. All rights reserved.)

Published
2010
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7. Rare earths stick to rare cyanobacteria: Future potential for bioremediation and recovery of rare earth elements

Author

Michael Paper, Max Koch, Patrick Jung, Michael Lakatos, Tom Nilges, and Thomas B. Brück

Subjects
Histology, Biomedical Engineering, Bioengineering and Biotechnology, cyanobacteria, biosorption, mechanism, rare earth elements, ion exchange, Bioengineering, ddc, Biotechnology
Abstract

Biosorption of metal ions by phototrophic microorganisms is regarded as a sustainable and alternative method for bioremediation and metal recovery. In this study, 12 cyanobacterial strains, including 7 terrestrial and 5 aquatic cyanobacteria, covering a broad phylogenetic diversity were investigated for their potential application in the enrichment of rare earth elements through biosorption. A screening for the maximum adsorption capacity of cerium, neodymium, terbium, and lanthanum was conducted in which Nostoc sp. 20.02 showed the highest adsorption capacity with 84.2–91.5 mg g-1. Additionally, Synechococcus elongatus UTEX 2973, Calothrix brevissima SAG 34.79, Desmonostoc muscorum 90.03, and Komarekiella sp. 89.12 were promising candidate strains, with maximum adsorption capacities of 69.5–83.4 mg g-1, 68.6–83.5 mg g-1, 44.7–70.6 mg g-1, and 47.2–67.1 mg g-1 respectively. Experiments with cerium on adsorption properties of the five highest metal adsorbing strains displayed fast adsorption kinetics and a strong influence of the pH value on metal uptake, with an optimum at pH 5 to 6. Studies on binding specificity with mixed-metal solutions strongly indicated an ion-exchange mechanism in which Na+, K+, Mg2+, and Ca2+ ions are replaced by other metal cations during the biosorption process. Depending on the cyanobacterial strain, FT-IR analysis indicated the involvement different functional groups like hydroxyl and carboxyl groups during the adsorption process. Overall, the application of cyanobacteria as biosorbent in bioremediation and recovery of rare earth elements is a promising method for the development of an industrial process and has to be further optimized and adjusted regarding metal-containing wastewater and adsorption efficiency by cyanobacterial biomass.

Published
2023

8. Isolation and Investigation of Natural Rare Earth Metal Chelating Agents From Calothrix brevissima - A Step Towards Unraveling the Mechanisms of Metal Biosorption

Author

Jurkowski, Wojciech, Paper, Michael, and Brück, Thomas B.

Subjects
Histology, complexation, Biomedical Engineering, mechanism, rare earth elements, calothrix, Bioengineering, cyanobacteria, TP248.13-248.65, biosorption, Biotechnology
Abstract

In this study water soluble compounds that form complexes with Rare Earth Elements (REE) and other metals were isolated from Calothrix brevissima biomass with chromatographic methods for the first time. Molecular characterization showed that the isolated compounds are most likely polysaccharides comprised of arabinose, xylose, mannose, galactose and glucose. FT-IR analysis revealed functional groups involved in the binding mechanism of Tb are likely sulfate- and to a lesser extend hydroxyl-groups. The binding specificity of the isolated compounds was investigated with different metal solutions. Here, ions of the alkali and alkaline earth metals Na, K, Mg and Ca showed no competition for Tb-binding even at 10-fold excess concentration. Ions of the elements Co and Pb on the other hand replaced Tb at higher concentrations. Addition of the isolated compounds significantly reduced the precipitation of Eu at pH-values between 6.7 and 9.5, indicating that the interaction between the isolated chelators and Rare Earth Metals is stable even at high pH-values.

Published
2022

9. Efficient Green Light Acclimation of the Green Algae Picochlorum sp. Triggering Geranylgeranylated Chlorophylls

Author

Michael Paper, Matthias Glemser, Martina Haack, Jan Lorenzen, Norbert Mehlmer, Tobias Fuchs, Gerhard Schenk, Daniel Garbe, Dirk Weuster-Botz, Wolfgang Eisenreich, Michael Lakatos, and Thomas B. Brück

Subjects
Histology, Biomedical Engineering, Bioengineering and Biotechnology, green light, photosynthesis, chlorophyll derivatives, light adaption mechanism, geranylgeranylated, eukaryotic microalgae, Bioengineering, Biotechnology, ddc
Abstract

In analogy to higher plants, eukaryotic microalgae are thought to be incapable of utilizing green light for growth, due to the “green gap” in the absorbance profiles of their photosynthetic pigments. This study demonstrates, that the marine chlorophyte Picochlorum sp. is able to grow efficiently under green light emitting diode (LED) illumination. Picochlorum sp. growth and pigment profiles under blue, red, green and white LED illumination (light intensity: 50–200 μmol m−2 s−1) in bottom-lightened shake flask cultures were evaluated. Green light-treated cultures showed a prolonged initial growth lag phase of one to 2 days, which was subsequently compensated to obtain comparable biomass yields to red and white light controls (approx. 0.8 gDW L−1). Interestingly, growth and final biomass yields of the green light-treated sample were higher than under blue light with equivalent illumination energies. Further, pigment analysis indicated, that during green light illumination, Picochlorum sp. formed unknown pigments (X1-X4). Pigment concentrations increased with illumination intensity and were most abundant during the exponential growth phase. Mass spectrometry and nuclear magnetic resonance data indicated, that pigments X1-X2 and X3-X4 are derivatives of chlorophyll b and a, which harbor C=C bonds in the phytol side chain similar to geranylgeranylated chlorophylls. Thus, for the first time, the natural accumulation of large pools (approx. 12 mg gDW−1) of chlorophyll intermediates with incomplete hydrogenation of their phytyl chains is demonstrated for algae under monochromatic green light (Peak λ 510 nm, full width at half maximum 91 nm). The ability to utilize green light offers competitive advantages for enhancing biomass production, particularly under conditions of dense cultures, long light pathways and high light intensity. Green light acclimation for an eukaryotic microalgae in conjunction with the formation of new aberrant geranylgeranylated chlorophylls and high efficiency of growth rates are novel for eukaryotic microalgae. Illumination with green light could enhance productivity in industrial processes and trigger the formation of new metabolites–thus, underlying mechanisms require further investigation.

Published
2021

10. Bioorthogonal click chemistry for fluorescence imaging of choline phospholipids in plants

Author

Kathrin Schrick, Janet M. Paper, and Thiya Mukherjee

Subjects
0106 biological sciences, 0301 basic medicine, Cell signaling, Arabidopsis thaliana, Membrane lipids, Phospholipid, Fluorescence labeling, Plant Science, lcsh:Plant culture, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Phosphatidylcholine, Genetics, Propargylcholine, Choline, lcsh:SB1-1110, lcsh:QH301-705.5, Phospholipids, Alexa Fluor, Click chemistry, fungi, Methodology, food and beverages, Plant cell, ESI-MS/MS, 030104 developmental biology, Membrane, lcsh:Biology (General), chemistry, Biochemistry, lipids (amino acids, peptides, and proteins), 010606 plant biology & botany, Biotechnology
Abstract

Background Phospholipids are important structural and signaling molecules in plant membranes. Some fluorescent dyes can stain general lipids of membranes, but labeling and visualization of specific lipid classes have yet to be developed for most components of the membrane. New techniques for visualizing membrane lipids are needed to further delineate their dynamic structural and signaling roles in plant cells. In this study we examined whether propargylcholine, a bioortholog of choline, can be used to label the major membrane lipid, phosphatidylcholine, and other choline phospholipids in plants. We established that propargylcholine is readily taken up by roots, and that its incorporation is not detrimental to plant growth. After plant tissue is harvested and fixed, a click-chemistry reaction covalently links the alkyne group of propargylcholine to a fluorescently-tagged azide, resulting in specific labeling of choline phospholipids. Results Uptake of propargylcholine, followed by click chemistry with fluorescein or Alexa Fluor 594 azide was used to visualize choline phospholipids in cells of root, leaf, stem, silique and seed tissues from Arabidopsis thaliana. Co-localization with various subcellular markers indicated coinciding fluorescent signals in cell membranes, such as the tonoplast and the ER. Among different cell types in the leaf epidermis, guard cells displayed strong labeling. Mass spectrometry-based lipidomic analysis of the various plant tissues revealed that incorporation of propargylcholine was strongest in roots with approximately 50% of total choline phospholipids being labeled, but it was also incorporated in the other tissues including seeds. Phospholipid profiling confirmed that, in each tissue analyzed, incorporation of the bioortholog had little impact on the pool of choline plus choline-like phospholipids or other lipid species. Conclusion We developed and validated a click-chemistry based method for fluorescence imaging of choline phospholipids using a bioortholog of choline, propargylcholine, in various cell-types and tissues from Arabidopsis. This click-chemistry method provides a direct way to metabolically tag and visualize specific lipid molecules in plant cells. This work paves the way for future studies addressing in situ localization of specific lipids in plants. Electronic supplementary material The online version of this article (10.1186/s13007-018-0299-2) contains supplementary material, which is available to authorized users.

Published
2018

11. α-Fucosidases with different substrate specificities from two species of Fusarium

Author

Jonathan D. Walton, Janet M. Paper, John S. Scott-Craig, Mareike Bongers, Richard E. Wiemels, Ahmed Faik, David Cavalier, and Melissa S. Borrusch

Subjects
alpha-L-Fucosidase, Genetics, Subfamily, Sequence Homology, Amino Acid, Sequence analysis, Molecular Sequence Data, Fungal genetics, food and beverages, Sequence alignment, Sequence Analysis, DNA, General Medicine, Biology, biology.organism_classification, Applied Microbiology and Biotechnology, Substrate Specificity, Pichia pastoris, Microbiology, Fusarium, Fusarium oxysporum, Glycosides, DNA, Fungal, Sequence Alignment, Gene, Trichoderma reesei, Biotechnology
Abstract

Two fungal-secreted α-fucosidases and their genes were characterized. FoFCO1 was purified from culture filtrates of Fusarium oxysporum strain 0685 grown on l-fucose and its encoding gene identified in the sequenced genome of strain 4287. FoFCO1 was active on p-nitrophenyl-α-fucoside (pNP-Fuc), but did not defucosylate a nonasaccharide (XXFG) fragment of pea xyloglucan. A putative α-fucosidase gene (FgFCO1) from Fusarium graminearum was expressed in Pichia pastoris. FgFCO1 was ∼1,800 times less active on pNP-Fuc than FoFCO1, but was able to defucosylate the XXFG nonasaccharide. Although FgFCO1 and FoFCO1 both belong to Glycosyl Hydrolase family 29, they share

Published
2012

12. Stripped: contribution of cyanobacterial extracellular polymeric substances to the adsorption of rare earth elements from aqueous solutions

Author

Michael Paper, Patrick Jung, Max Koch, Michael Lakatos, Tom Nilges, and Thomas B. Brück

Subjects
extracellular polymeric substances, polysaccharides, Komarekiella, Nostoc, Desmonostoc, biosorption, Biotechnology, TP248.13-248.65
Abstract

The transformation of modern industries towards enhanced sustainability is facilitated by green technologies that rely extensively on rare earth elements (REEs) such as cerium (Ce), neodymium (Nd), terbium (Tb), and lanthanum (La). The occurrence of productive mining sites, e.g., is limited, and production is often costly and environmentally harmful. As a consequence of increased utilization, REEs enter our ecosystem as industrial process water or wastewater and become highly diluted. Once diluted, they can hardly be recovered by conventional techniques, but using cyanobacterial biomass in a biosorption-based process is a promising eco-friendly approach. Cyanobacteria can produce extracellular polymeric substances (EPS) that show high affinity to metal cations. However, the adsorption of REEs by EPS has not been part of extensive research. Thus, we evaluated the role of EPS in the biosorption of Ce, Nd, Tb, and La for three terrestrial, heterocystous cyanobacterial strains. We cultivated them under N-limited and non-limited conditions and extracted their EPS for compositional analyses. Subsequently, we investigated the metal uptake of a) the extracted EPS, b) the biomass extracted from EPS, and c) the intact biomass with EPS by comparing the amount of sorbed REEs. Maximum adsorption capacities for the tested REEs of extracted EPS were 123.9–138.2 mg g−1 for Komarekiella sp. 89.12, 133.1–137.4 mg g−1 for Desmonostoc muscorum 90.03, and 103.5–129.3 mg g−1 for Nostoc sp. 20.02. A comparison of extracted biomass with intact biomass showed that 16% (Komarekiella sp. 89.12), 28% (Desmonostoc muscorum 90.03), and 41% (Nostoc sp. 20.02) of REE adsorption was due to the biosorption of the extracellular EPS. The glucose- rich EPS (15%–43% relative concentration) of all three strains grown under nitrogen-limited conditions showed significantly higher biosorption rates for all REEs. We also found a significantly higher maximum adsorption capacity of all REEs for the extracted EPS compared to cells without EPS and untreated biomass, highlighting the important role of the EPS as a binding site for REEs in the biosorption process. EPS from cyanobacteria could thus be used as efficient biosorbents in future applications for REE recycling, e.g., industrial process water and wastewater streams.

Published
2023
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13. Efficient Green Light Acclimation of the Green Algae Picochlorum sp. Triggering Geranylgeranylated Chlorophylls

Author

Michael Paper, Matthias Glemser, Martina Haack, Jan Lorenzen, Norbert Mehlmer, Tobias Fuchs, Gerhard Schenk, Daniel Garbe, Dirk Weuster-Botz, Wolfgang Eisenreich, Michael Lakatos, and Thomas B. Brück

Subjects
green light, photosynthesis, chlorophyll derivatives, light adaption mechanism, geranylgeranylated, eukaryotic microalgae, Biotechnology, TP248.13-248.65
Abstract

In analogy to higher plants, eukaryotic microalgae are thought to be incapable of utilizing green light for growth, due to the “green gap” in the absorbance profiles of their photosynthetic pigments. This study demonstrates, that the marine chlorophyte Picochlorum sp. is able to grow efficiently under green light emitting diode (LED) illumination. Picochlorum sp. growth and pigment profiles under blue, red, green and white LED illumination (light intensity: 50–200 μmol m−2 s−1) in bottom-lightened shake flask cultures were evaluated. Green light-treated cultures showed a prolonged initial growth lag phase of one to 2 days, which was subsequently compensated to obtain comparable biomass yields to red and white light controls (approx. 0.8 gDW L−1). Interestingly, growth and final biomass yields of the green light-treated sample were higher than under blue light with equivalent illumination energies. Further, pigment analysis indicated, that during green light illumination, Picochlorum sp. formed unknown pigments (X1-X4). Pigment concentrations increased with illumination intensity and were most abundant during the exponential growth phase. Mass spectrometry and nuclear magnetic resonance data indicated, that pigments X1-X2 and X3-X4 are derivatives of chlorophyll b and a, which harbor C=C bonds in the phytol side chain similar to geranylgeranylated chlorophylls. Thus, for the first time, the natural accumulation of large pools (approx. 12 mg gDW−1) of chlorophyll intermediates with incomplete hydrogenation of their phytyl chains is demonstrated for algae under monochromatic green light (Peak λ 510 nm, full width at half maximum 91 nm). The ability to utilize green light offers competitive advantages for enhancing biomass production, particularly under conditions of dense cultures, long light pathways and high light intensity. Green light acclimation for an eukaryotic microalgae in conjunction with the formation of new aberrant geranylgeranylated chlorophylls and high efficiency of growth rates are novel for eukaryotic microalgae. Illumination with green light could enhance productivity in industrial processes and trigger the formation of new metabolites–thus, underlying mechanisms require further investigation.

Published
2022
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14. Isolation and Investigation of Natural Rare Earth Metal Chelating Agents From Calothrix brevissima - A Step Towards Unraveling the Mechanisms of Metal Biosorption

Author

Wojciech Jurkowski, Michael Paper, and Thomas B. Brück

Subjects
biosorption, cyanobacteria, rare earth elements, mechanism, calothrix, complexation, Biotechnology, TP248.13-248.65
Abstract

In this study water soluble compounds that form complexes with Rare Earth Elements (REE) and other metals were isolated from Calothrix brevissima biomass with chromatographic methods for the first time. Molecular characterization showed that the isolated compounds are most likely polysaccharides comprised of arabinose, xylose, mannose, galactose and glucose. FT-IR analysis revealed functional groups involved in the binding mechanism of Tb are likely sulfate- and to a lesser extend hydroxyl-groups. The binding specificity of the isolated compounds was investigated with different metal solutions. Here, ions of the alkali and alkaline earth metals Na, K, Mg and Ca showed no competition for Tb-binding even at 10-fold excess concentration. Ions of the elements Co and Pb on the other hand replaced Tb at higher concentrations. Addition of the isolated compounds significantly reduced the precipitation of Eu at pH-values between 6.7 and 9.5, indicating that the interaction between the isolated chelators and Rare Earth Metals is stable even at high pH-values.

Published
2022
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15. Tuning gelatin-based hydrogel towards bioadhesive ocular tissue engineering applications

Author

Miguel Gonzalez-Andrades, James Chodosh, Sina Sharifi, Tom Eirik Mollnes, Rakibul Islam, Felisa Reyes-Ortega, Per H. Nilsson, David Alba-Molina, Claes H. Dohlman, Mohammad Mirazul Islam, Darrell J. Koza, Hannah Sharifi, [Sharifi,S, Islam,MM, Sharifi,H, Dohlman,CH, Chodosh,J, Gonzalez-Andrades,M] Massachusetts Eye and Ear and Schepens Eye Research Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA. [Islam, Nilsson,PH, Mollnes,TE, ] Department of Immunology, Oslo University Hospital, Rikshospitalet, University of Oslo, Oslo, Norway. [Koza,D] Department of Physical Sciences, Eastern Connecticut State University, Willimantic, CT, USA. [Nilsson,PH] Linnaeus Center for Biomaterials Chemistry, Linnaeus University, Kalmar, Sweden. [Mollnes,TE] Research Laboratory, Nordland Hospital, Bodø, Norway. [Mollnes,TE] Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway. [Reyes-Ortega,F, Alba-Molina,D, Gonzalez-Andrades,M] Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Department of Ophthalmology, Reina Sofia University Hospital and University of Cordoba, Cordoba, Spain. [Mollnes,TE] Faculty of Health Sciences, K.G. Jebsen TREC, University of Tromsø, Norway., and This paper was supported by the Boston-KPro research fund and NIH/NEI P30EY003790 (Core-PA). R.S. was supported in part by the K99 grant from NIH award no. K99 EY030553. This work was performed in part at the Center for Nanoscale Systems (CNS), Harvard University, a member of the National Nanotechnology Coordinated Infrastructure Network (NNCI), which is supported by the National Science Foundation under NSF award no. 1541959. F.R-O and D.A-M were supported by the research project ICI19/00006, funded by Instituto de Salud Carlos III and co-funded by European Union (ERDF/ESF, 'A way to make Europe'/'Investing in your future'). F.R-O additionally acknowledges funding from Plan Andaluz de Investigación, Desarrollo e Innovación (PAIDI2020) Fellowship supported by Consejería de Economía, Conocimiento, Empresas y Universidad, Junta de Andalucía co-funded by Fondo Social Europeo de Andalucía 2014-2020.

Subjects
Biocompatible, Glycidyl methacrylate, Light, Anatomy::Digestive System::Liver [Medical Subject Headings], Anatomy::Urogenital System::Urinary Tract::Kidney [Medical Subject Headings], Analytical, Diagnostic and Therapeutic Techniques and Equipment::Equipment and Supplies::Bandages [Medical Subject Headings], Analytical, Diagnostic and Therapeutic Techniques and Equipment::Equipment and Supplies::Surgical Equipment::Surgical Fixation Devices::Tissue Adhesives [Medical Subject Headings], 02 engineering and technology, Gelatin, Metacrilatos, Anatomy::Cardiovascular System::Blood Vessels::Arteries::Aorta [Medical Subject Headings], Cornea, Extracellular matrix, chemistry.chemical_compound, Chemicals and Drugs::Organic Chemicals::Ethers::Ethers, Cyclic::Epoxy Compounds [Medical Subject Headings], Materiales biocompatibles, Biology (General), Materials of engineering and construction. Mechanics of materials, Disciplines and Occupations::Natural Science Disciplines::Biological Science Disciplines::Biotechnology::Biomimetics [Medical Subject Headings], Phenomena and Processes::Physical Phenomena::Optical Phenomena::Light [Medical Subject Headings], Adhesion, 021001 nanoscience & nanotechnology, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Bioprinting [Medical Subject Headings], VDP::Medical disciplines: 700::Basic medical, dental and veterinary science disciplines: 710, Chemicals and Drugs::Amino Acids, Peptides, and Proteins::Proteins::Scleroproteins::Gelatin [Medical Subject Headings], Anatomy::Sense Organs::Eye::Anterior Eye Segment::Cornea [Medical Subject Headings], Gelatina, Technology and Food and Beverages::Technology, Industry, and Agriculture::Manufactured Materials::Adhesives [Medical Subject Headings], TA401-492, Methacrylates, Biomimetic, 0210 nano-technology, Biotechnology, food.ingredient, Materials science, Biocompatibility, QH301-705.5, Bioadhesive, 0206 medical engineering, Biomedical Engineering, Article, Tissue adhesives, Hidrogeles, Biomaterials, Adhesivos tisulares, Natural-based hydrogel, food, Biomimética, Chemicals and Drugs::Complex Mixtures::Colloids::Gels::Hydrogels [Medical Subject Headings], Anatomy::Tissues::Lymphoid Tissue::Spleen [Medical Subject Headings], VDP::Medisinske Fag: 700::Basale medisinske, odontologiske og veterinærmedisinske fag: 710, Luz, 020601 biomedical engineering, Córnea, Transplantation, chemistry, Chemicals and Drugs::Organic Chemicals::Carboxylic Acids::Acids, Acyclic::Acrylates::Methacrylates [Medical Subject Headings], Adhesive, Biomedical engineering
Abstract

Gelatin based adhesives have been used in the last decades in different biomedical applications due to the excellent biocompatibility, easy processability, transparency, non-toxicity, and reasonable mechanical properties to mimic the extracellular matrix (ECM). Gelatin adhesives can be easily tuned to gain different viscoelastic and mechanical properties that facilitate its ocular application. We herein grafted glycidyl methacrylate on the gelatin backbone with a simple chemical modification of the precursor, utilizing epoxide ring-opening reactions and visible light-crosslinking. This chemical modification allows the obtaining of an elastic protein-based hydrogel (GELGYM) with excellent biomimetic properties, approaching those of the native tissue. GELGYM can be modulated to be stretched up to 4 times its initial length and withstand high tensile stresses up to 1.95 MPa with compressive strains as high as 80% compared to Gelatin-methacryloyl (GeIMA), the most studied derivative of gelatin used as a bioadhesive. GELGYM is also highly biocompatible and supports cellular adhesion, proliferation, and migration in both 2 and 3-dimensional cell-cultures. These characteristics along with its super adhesion to biological tissues such as cornea, aorta, heart, muscle, kidney, liver, and spleen suggest widespread applications of this hydrogel in many biomedical areas such as transplantation, tissue adhesive, wound dressing, bioprinting, and drug and cell delivery., Graphical abstract Image 1, Highlights • Gelatin based adhesives have been used in the last decades in different biomedical applications. • Gelatin adhesives can be easily tuned to gain different viscoelastic and mechanical properties that facilitate its ocular application. • We herein grafted glycidyl methacrylate on the gelatin backbone with a simple chemical modification of the precursor. • Epoxide ring-opening reactions and visible light-crosslinking allows the obtaining of an elastic gelatin-based hydrogel (GELGYM). • GELGYM shows excellent biomimetic properties, approaching those of the native tissue.

Published
2021

16. Left Ventricle Quantification Challenge: A Comprehensive Comparison and Evaluation of Segmentation and Regression for Mid-Ventricular Short-Axis Cardiac MR Data

Author

Georgios Tziritas, Yeonggul Jang, Jin Ma, Fumin Guo, Quanzheng Li, Tiancong Hua, Xiang Li, Lihong Liu, Angélica Atehortúa, James R. Clough, Zhiqiang Hu, Eric Kerfoot, Vicente Grau, Enzo Ferrante, Matthew Ng, Guanyu Yang, Mireille Garreau, Alejandro Debus, Elias Grinias, Jiahui Li, Wufeng Xue, Shuo Li, Wenjun Yan, Ilkay Oksuz, Hao Xu, Shenzhen University, Beijing University of Posts and Telecommunications (BUPT), Peking University [Beijing], King‘s College London, Istanbul Technical University (ITÜ), University of Oxford [Oxford], University of Toronto, Massachusetts General Hospital [Boston], University of Crete [Heraklion] (UOC), Fudan University [Shanghai], Universidad Nacional de Colombia [Bogotà] (UNAL), Laboratoire Traitement du Signal et de l'Image (LTSI), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche en Information Biomédicale sino-français (CRIBS), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Southeast University [Jiangsu]-Institut National de la Santé et de la Recherche Médicale (INSERM), Yonsei University, Universidad Nacional del Litoral [Santa Fe] (UNL), Laboratory of Image Science and Technology [Nanjing] (LIST), Southeast University [Jiangsu]-School of Computer Science and Engineering, University of Western Ontario (UWO), The paper is partially supported by the Natural Science Foundation of China under Grants 61801296. The workof Eric Kerfoot was supported by an EPSRC programmeGrant (EP/P001009/1) and the Wellcome EPSRC Centre for Medical Engineering at the School of Biomedical Engineering and Imaging Sciences, Kings College London (WT203148/Z/16/Z). The work of Angelica Atehortua was supported by Colciencias-Colombia, Grant No. 647 (2015 call for National PhD studies) and Université de Rennes 1. The work of Alejandro Debus was supported by the Santa Fe Science, Technology and Innovation Agency (AS ACTEI), Government of the Province of Santa Fe, through Project AC-00010-18,Resolution N 117/14., University of Oxford, Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Rennes (UR)-Southeast University [Jiangsu]-Institut National de la Santé et de la Recherche Médicale (INSERM), and Jonchère, Laurent

Subjects
Short axis, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, Computer science, Heart Ventricles, Magnetic Resonance Imaging, Cine, Article, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Health Information Management, medicine, Humans, Segmentation, Electrical and Electronic Engineering, [SPI.SIGNAL] Engineering Sciences [physics]/Signal and Image processing, Ground truth, Cardiac cycle, business.industry, Heart, Pattern recognition, Image segmentation, Magnetic Resonance Imaging, Regression, [SDV.MHEP.CSC] Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Computer Science Applications, [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, medicine.anatomical_structure, Ventricle, 030220 oncology & carcinogenesis, Artificial intelligence, business, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, Cardiac phase, Biotechnology
Abstract

Automatic quantification of the left ventricle (LV) from cardiac magnetic resonance (CMR) images plays an important role in making the diagnosis procedure efficient, reliable, and alleviating the laborious reading work for physicians. Considerable efforts have been devoted to LV quantification using different strategies that include segmentation-based (SG) methods and the recent direct regression (DR) methods. Although both SG and DR methods have obtained great success for the task, a systematic platform to benchmark them remains absent because of differences in label information during model learning. In this paper, we conducted an unbiased evaluation and comparison of cardiac LV quantification methods that were submitted to the Left Ventricle Quantification (LVQuan) challenge, which was held in conjunction with the Statistical Atlases and Computational Modeling of the Heart (STACOM) workshop at the MICCAI 2018. The challenge was targeted at the quantification of 1) areas of LV cavity and myocardium, 2) dimensions of the LV cavity, 3) regional wall thicknesses (RWT), and 4) the cardiac phase, from mid-ventricle short-axis CMR images. First, we constructed a public quantification dataset Cardiac-DIG with ground truth labels for both the myocardium mask and these quantification targets across the entire cardiac cycle. Then, the key techniques employed by each submission were described. Next, quantitative validation of these submissions were conducted with the constructed dataset. The evaluation results revealed that both SG and DR methods can offer good LV quantification performance, even though DR methods do not require densely labeled masks for supervision. Among the 12 submissions, the DR method LDAMT offered the best performance, with a mean estimation error of 301 mm $^2$ for the two areas, 2.15 mm for the cavity dimensions, 2.03 mm for RWTs, and a 9.5% error rate for the cardiac phase classification. Three of the SG methods also delivered comparable performances. Finally, we discussed the advantages and disadvantages of SG and DR methods, as well as the unsolved problems in automatic cardiac quantification for clinical practice applications.

Published
2021

18. Real-time analysis of the behaviour of groups of mice via a depth-sensing camera and machine learning

Author

Philippe Faure, Jean-Christophe Olivo-Marin, Fabrice de Chaumont, Nicolas Torquet, Albane Imbert, Stephane Dallongeville, Anne-Marie Le Sourd, Thomas Bourgeron, Elodie Ey, Thierry Legou, Thibault Lagache, Analyse d'images biologiques - Biological Image Analysis (BIA), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique humaine et fonctions cognitives - Human Genetics and Cognitive Functions (GHFC (UMR_3571 / U-Pasteur_1)), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Neurosciences Paris Seine (NPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche et Innovation Technologique (CITECH), Institut Pasteur [Paris], Laboratoire Parole et Langage (LPL), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), This work was partially funded by the Institut Pasteur, the Bettencourt-Schueller Foundation, the Cognacq–Jay Foundation, the Conny–Maeva Foundation, the ERANET–NEURON SYNPATHY program, the Agence Nationale de la Recherche through grant number ANR-10-LABX-62-IBEID, France-BioImaging infrastructure through grant number ANR-10-INBS-04 and the INCEPTION program through grant number ANR-16-CONV-0005, the Centre National de la Recherche Scientifique, the University Paris Diderot, the BioPsy Labex, the Institut National du Cancer through grant number TABAC-16–022, the Foundation for Medical Research (Equipe DEQ20130326488), the Innovative Medicines Initiative Joint Undertaking through grant agreement number 115300, resources of which are composed of financial contributions from the European Union’s Seventh Framework Program (FP7/2007–2013) and EFPIA companies in kind contribution., The authors thank Y. Archambeau and P. Ollivon at the workshop of the Institut Pasteur for building the first 12 setups and advising on hardware, W. Meiniel for the mathematical proof for decisions of head/tail probability, Microsoft France for their technical support, P. Spinicelli for optical engineering and reading of the paper, R. Marée for machine learning support, B. König for advice and reading of biological experiments, J. N. Crawley for reading and providing comments on the manuscript, A. Barmpoutis for providing us with the early Kinect 2 driver and support, N. Chenouard for driving the use of the machine learning solution, P. Dugast for drawing the mice in the different behavioural events, A. Engelberg for checking the English, S. Wagner and R. Accardi for RFID advice, M. Marim for website development, and X. Montagutelli and M. Bérard for animal facility support., Analyse d'images biologiques - BioImage Analysis (AIQ), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Institut Pasteur [Paris], Neuroscience Paris Seine (NPS), Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Male, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Biomedical Engineering, Video Recording, Medicine (miscellaneous), Bioengineering, Nerve Tissue Proteins, Mouse tracking, Biology, Machine learning, computer.software_genre, Machine Learning, 03 medical and health sciences, Mice, 0302 clinical medicine, [INFO.INFO-TS]Computer Science [cs]/Signal and Image Processing, Animals, Autistic Disorder, Real time analysis, Social Behavior, Mice, Knockout, Behavior, Animal, business.industry, Microfilament Proteins, Computer Science Applications, Disease Models, Animal, 030104 developmental biology, Phenotype, Mutation, Identification (biology), Female, Artificial intelligence, business, computer, 030217 neurology & neurosurgery, Biotechnology, Behavioral Research
Abstract

Preclinical studies of psychiatric disorders use animal models to investigate the impact of environmental factors or genetic mutations on complex traits such as decision-making and social interactions. Here, we introduce a method for the real-time analysis of the behaviour of mice housed in groups of up to four over several days and in enriched environments. The method combines computer vision through a depth-sensing infrared camera, machine learning for animal and posture identification, and radio-frequency identification to monitor the quality of mouse tracking. It tracks multiple mice accurately, extracts a list of behavioural traits of both individuals and the groups of mice, and provides a phenotypic profile for each animal. We used the method to study the impact of Shank2 and Shank3 gene mutations—mutations that are associated with autism—on mouse behaviour. Characterization and integration of data from the behavioural profiles of Shank2 and Shank3 mutant female mice revealed their distinctive activity levels and involvement in complex social interactions. A method that combines a depth-sensing camera and machine learning can track the movements of up to four mice in real time and for several days, extracting both individual and group behavioural traits.

Published
2019

19. Hydrophobic properties conferred to Kraft pulp by a laccase-catalysed treatment with lauryl gallate

Author

Céline Reynaud, Michel Petit-Conil, Sandra Tapin-Lingua, Graziano Elegir, Stéphanie Baumberger, Intechfibers, FCBA, New Mat Div, Domaine Univ, Paper Div, Innovhub ssi, Intechfibers, Ctr Tech Papier, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, ENCELPA, ANRT, and Institut Technologique Forêt Cellulose Bois-construction Ameublement (FCBA)

Subjects
Paper, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, Absorption of water, Hydrophobicity, MODELS, Bioengineering, Kappa number, 01 natural sciences, Applied Microbiology and Biotechnology, Acetone, GALLIC ACID, chemistry.chemical_compound, Adsorption, 010608 biotechnology, Organic chemistry, Gallic acid, Laccase, 010405 organic chemistry, Green Chemistry Technology, General Medicine, Wood, 0104 chemical sciences, chemistry, Kraft process, Papermaking, Lauryl gallate, Dodecanol, Hydrophobic and Hydrophilic Interactions, Biotechnology
Abstract

Hydrophobic properties were conferred to a high-lignin-content Kraft pulp by a laccase-catalysed treatment in the presence of lauryl gallate (LG). The treatment resulted in a two-fold increase in contact angle and conferred water absorption resistance to the pulp. Kappa number was increased, indicating that some phenolic compounds were incorporated in the pulp. A control treatment with LG alone did not affect water absorption, demonstrating that laccase was essential to attain these new properties. The loss of hydrophobicity after an acetone Soxhlet extraction highlighted that adsorbed acetone-soluble compounds played a key role in the properties. GC-FID and HPSEC-UV analysis of the acetone extract indicated the formation of dodecanol and different phenolic oligomers. SEM images showed the treatment-induced changes in the fibre network. Additional experiments with various reaction times and reactant concentrations highlighted the role of LG oxidation products in the introduction of absorption resistance. (C) 2013 Elsevier B.V. All rights reserved.

Published
2013

20. Valorisation of local agro-industrial processing waters as growth media for polyhydroxyalkanoates (PHA) production

Author

Patrick Loulergue, Stéphane Bruzaud, Nicolas Hachet, Jean-Luc Audic, Yves-Marie Corre, Adélaïde Le Grand, Véronique Le Tilly, Anne Elain, Magali Le Fellic, Laboratoire d'Ingénierie des Matériaux de Bretagne (LIMATB), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO), Plateforme technologique ProDiaBio (PFT ProDiaBio), Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), The authors acknowledge the regions of Bretagne and Pays de Loire for funding. We are grateful to Breizpack and Valorial pole for their help and to the industrial partners of PHApack consortium: Europlastiques, Séché Environnement, Triballat Noyal and Cap Ouest, for their contribution to this research program. We are also thankful to Mélanie Blanche Barbat and Laureen Van Steenberge for their contribution to this work. We thank Maja Bumke Scheer for taking time to help us improve the paper., Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 02 engineering and technology, Bacterial growth, Batch fermentation, 01 natural sciences, Polyhydroxyalkanoates, Stachyose, chemistry.chemical_compound, Marine bacterium, 010608 biotechnology, [CHIM]Chemical Sciences, Food science, Growth medium, Halomonas, biology, business.industry, 021001 nanoscience & nanotechnology, biology.organism_classification, 6. Clean water, Biotechnology, Agro-industrial processing waters, chemistry, Fermentation, Biodegradable plastic, Valorisation, 0210 nano-technology, business, Agronomy and Crop Science
Abstract

International audience; Polyhydroxyalkanoates (PHA) are bacterial polyesters usually produced from costly sugars or volatile fatty acids (VFAs). In this work, two processing waters rich in vegetable proteins and reducing sugars, i.e., a mixture of saccharose and stachyose in Leguminous Processing Water (LPW) and a mixture of glucose and fructose in Fruit Processing Water (FPW), were tested as growth medium for PHA production in a two-stage fermentation with a unique marine bacterial species: Halomonas i4786. In preliminary shake flask experiments, it was shown that the two media can effectively support the bacterial growth and the accumulation of PHA (evaluated using Nile Red staining). In batch cultivation mode in a 5-L fermentor, PHA productivities of 1.6 g L−1 and 1.8 g L−1 were further achieved within 72 h, in LPW and FPW respectively. Polymer characterization by Differential Scanning Calorimetry and Steric Exclusion Chromatography indicated that the two substrates led to the biosynthesis of polymers with different chain length, distribution and crystallinity. To summarize, these results show that by-products derived from local agri-food industry can be used as a user-adapted and cost-effective source to produce bio-sourced and biodegradable plastic materials

Published
2016

21. RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans

Author

Jean-Yves Coppée, Gaëlle Lelandais, Odile Sismeiro, Sophie Lemoine, Frédéric Devaux, Stéphane Le Crom, Rajendra Prasad, Maria Bernard, Sanjiveeni Dhamgaye, Membrane Biology Laboratory, Jawaharlal Nehru University (JNU), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA), Transcriptome et Epigénome (PF2), Institut Pasteur [Paris], Génomique des Microorganismes (LGM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), The work presented in this paper has been supported in part by grants to R.P. from Indo-French Center for the Promotion of Advanced Scientific Research (IFC-3403-2/2006) and DST INT/SWISS/P-31/2009., Institut de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Institut Pasteur [Paris] (IP), BMC, Ed., Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Candida albicans, beta-Glucans, lcsh:QH426-470, lcsh:Biotechnology, Repressor, RNA-Seq, Drug resistance, Multidrug resistance, Fungal Proteins, 03 medical and health sciences, Drug Resistance, Fungal, lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Transcriptional regulation, Genetics, CZF1, Gene, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, Sequence Analysis, RNA, Gene Expression Profiling, biology.organism_classification, Yeast, 3. Good health, Multiple drug resistance, Gene expression profiling, lcsh:Genetics, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], RNA-seq, Biotechnology, Transcription Factors, Research Article
Abstract

Background Drug susceptible clinical isolates of Candida albicans frequently become highly tolerant to drugs during chemotherapy, with dreadful consequences to patient health. We used RNA sequencing (RNA-seq) to analyze the transcriptomes of a CDR (Candida Drug Resistance) strain and its isogenic drug sensitive counterpart. Results RNA-seq unveiled differential expression of 228 genes including a) genes previously identified as involved in CDR, b) genes not previously associated to the CDR phenotype, and c) novel transcripts whose function as a gene is uncharacterized. In particular, we show for the first time that CDR acquisition is correlated with an overexpression of the transcription factor encoding gene CZF1. CZF1 null mutants were susceptible to many drugs, independently of known multidrug resistance mechanisms. We show that CZF1 acts as a repressor of β-glucan synthesis, thus negatively regulating cell wall integrity. Finally, our RNA-seq data allowed us to identify a new transcribed region, upstream of the TAC1 gene, which encodes the major CDR transcriptional regulator. Conclusion Our results open new perspectives of the role of Czf1 and of our understanding of the transcriptional and post-transcriptional mechanisms that lead to the acquisition of drug resistance in C. albicans, with potential for future improvements of therapeutic strategies.

Published
2012

22. BMC Genomics

Author

Grace C. Davey, Penelope K. Lindeque, Richard Reinhardt, Christophe Klopp, Pascal Favrel, Dario Moraga, Pierre Boudry, Sylvie Lapegue, Patrick Prunet, Arnaud Huvet, Julien de Lorgeril, Jeanne Moal, Viviane Boulo, Elodie Fleury, Christophe Lelong, Christopher Sauvage, Patrick Wincker, François Moreews, Michel Mathieu, Frédérick Gavory, Arnaud Tanguy, Caroline Fabioux, Charlotte Corporeau, Evelyne Bachère, Jenny P. Shaw, Yannick Gueguen, Laboratoire Environnement Ressources Morbihan Pays de Loire (LERMPL), LITTORAL (LITTORAL), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Physiologie et Ecophysiologie des Mollusques Marins (PE2M), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Ecosystèmes lagunaires : organisation biologique et fonctionnement (ECOLAG), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Brest (UBO), Plymouth Marine Laboratory (PML), Max-Planck-Institut für Molekulare Genetik (MPIMG), Max-Planck-Gesellschaft, Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE), Institut National de la Recherche Agronomique (INRA), Génétique fonctionnelle, agronomie et santé [IFR 140] (GFAS), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Diagnostics Centre (NDC), National University of Ireland [Galway] (NUI Galway), Laboratoire de Génétique et Pathologie (LGP), Amélioration génétique, du contrôle des performances et de la santé des mollusques marins (AGSAE), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Systèmes d'Elevage, Nutrition Animale et Humaine (SENAH), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Rennes, Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Laboratoire de Physiologie des Invertébrés (LPI), Physiologie Fonctionnelle des Organismes Marins (PFOM), The research presented in this paper was performed within the framework of several research projects funded by: Genoscope (11/AP2006-2007), Marine Genomics Network of Excellence (GOCE-CT-2004-505403), the European project 'Aquafirst' (513692) in the Sixth Framework Program, ANR 'CgPhysiogène' (ANR-06-GANI-0009) and 'Gametogenes' (ANR-08-GENM-041), ANR-06-GANI-0009,CgPhysiogene,Bases moléculaires des fonctions physiologiques de l'huître Crassostrea gigas : interactions hôte/pathogène/milieu(2006), ANR-08-GENM-0041,Gametogenes,Génomiques de la gamétogénèse chez l'huître creuse Crassostrea gigas(2008), Laboratoire Laboratoire Environnement Ressources Morbihan Pays de Loire (LER/MPL), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Adaptation et Biologie des Invertébrés en Conditions Extrêmes (ABICE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Plymouth Marine Laboratory, Institut National de la Recherche Agronomique (INRA)-IFR140, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Ecole Nationale Supérieure Agronomique de Rennes-Institut National de la Recherche Agronomique (INRA), Unité de Biométrie et Intelligence Artificielle de Toulouse [Castanet-Tolosan] (UBIA), Institut National de la Recherche Agronomique (INRA)-Plateforme bioinformatique du GIS GENOTOUL - Génopole Toulouse Midi-Pyrénées, Laboratoire de Physiologie des Invertébrés [Plouzané] (LPI), Adaptation et diversité en milieu marin (AD2M), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Station biologique de Roscoff (SBR), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Oyster, genome annotation, génomique fonctionnelle, computer.software_genre, Genome, User-Computer Interface, single nucleotide polymorphisms, Databases, Genetic, crassostrea gigas, structure du génome, Expressed Sequence Tags, base de données, 0303 health sciences, Expressed sequence tag, biology, Database, 04 agricultural and veterinary sciences, Genomics, crustacea, Pacific oyster, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], energy-balance, factor-beta superfamily, DNA microarray, expression des gènes, Biotechnology, lcsh:QH426-470, Sequence analysis, lcsh:Biotechnology, kappa-b, Polymorphism, Single Nucleotide, génomique, 03 medical and health sciences, biology.animal, lcsh:TP248.13-248.65, Genetics, summer mortality, Animals, Crassostrea, 030304 developmental biology, Gene Library, Whole genome sequencing, [SDV.GEN]Life Sciences [q-bio]/Genetics, huître, cell-development, génome, Gene Expression Profiling, linkage maps, Sequence Analysis, DNA, biology.organism_classification, lcsh:Genetics, coquillage, 040102 fisheries, 0401 agriculture, forestry, and fisheries, identification, marine genomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Microsatellite Repeats
Abstract

Background Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available. Description In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster. Conclusion A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as protein or nucleotide hits, to select and download relevant elements. This database constitutes one of the most developed genomic resources accessible among Lophotrochozoans, an orphan clade of bilateral animals. These data will accelerate the development of both genomics and genetics in a commercially-important species with the highest annual, commercial production of any aquatic organism.

Published
2009