Plant cell wall profiling by fast maximum likelihood reconstruction (FMLR) and region-of-interest (ROI) segmentation of solution-state 2D 1H-13C NMR spectra

Tetraploidization promotes radial stem growth in poplars

Somatic polyploidization often increases cell and organ size, thereby contributing to plant biomass production. However, as most woody plants do not undergo polyploidization, explaining the polyploidization effect on organ growth in trees remains difficult. Here we developed a new method to generate tetraploid lines in poplars through colchicine treatment of lateral buds. We found that tetraploidization induced cell enlargement in the stem, suggesting that polyploidization can increase cell size in woody plants that cannot induce polyploidization in normal development. Greenhouse growth analysis revealed that radial growth was enhanced in the basal stem of tetraploids, whereas longitudinal growth was retarded, producing the same amount of stem biomass as diploids. Woody biomass characteristics were also comparable in terms of wood substance density, saccharification efficiency, and cell wall profiling. Our results reveal tetraploidization as an effective strategy for improving woody biomass production when combined with technologies that promote longitudinal stem growth by enhancing metabolite production and/or transport.

Valorization of Chinese hickory shell as novel sources for the efficient production of xylooligosaccharides

Chinese hickory shell, a by-product of the food industry, is still not utilized and urgent to develop sustainable technologies for its valorization. This research focuses on the systematical evaluation of degraded products and xylooligosaccharide production with high yield from the shell via hydrothermal process. The pretreatment was carried out in a bath pressurized reactor at 140-220 °C for 0.5-2 h. The results indicated that the pretreatment condition strongly affected the chemical structures and compositions of the liquid fraction. The maximum yield of XOS (55.3 wt%) with limitation of by-products formation was achieved at 160 °C for 2 h. High temperature (220 °C) and short time (0.5 h) contributed to hydrolysis of xylooligosaccharide with high DP to yield 37.5 wt% xylooligosaccharide with DP from 2 to 6. Xylooligosaccharide obtained mainly consisted of xylan with branches according to the HSQC NMR analysis. Overall, the production of XOS with a high yield from food waste will facilitate the valorization of food waste in the biorefinery industry.

Metabolomics toward personalized medicine

Metabolomics, which is the metabolites profiling in biological matrices, is a key tool for biomarker discovery and personalized medicine and has great potential to elucidate the ultimate product of the genomic processes. Over the last decade, metabolomics studies have identified several relevant biomarkers involved in complex clinical phenotypes using diverse biological systems. Most diseases result in signature metabolic profiles that reflect the sums of external and internal cellular activities. Metabolomics has a major role in clinical practice as it represents >95% of the workload in clinical laboratories worldwide. Many of these metabolites require different analytical platforms, such as Nuclear Magnetic Resonance (NMR), Mass Spectrometry (MS), and Ultra Performance Liquid Chromatography (UPLC), while many clinically relevant metabolites are still not routinely amenable to detection using currently available assays. Combining metabolomics with genomics, transcriptomics, and proteomics studies will result in a significantly improved understanding of the disease mechanisms and the pathophysiology of the target clinical phenotype. This comprehensive approach will represent a major step forward toward providing precision medical care, in which individual is accounted for variability in genes, environment, and personal lifestyle. In this review, we compare and evaluate the metabolomics strategies and studies that focus on the discovery of biomarkers that have "personalized" diagnostic, prognostic, and therapeutic value, validated for monitoring disease progression and responses to various management regimens.

Comparative analysis of 1H NMR and 1H-13C HSQC NMR metabolomics to understand the effects of medium composition in yeast growth

In nuclear magnetic resonance (NMR) metabolomics, most of the studies have been focused on the analysis of one-dimensional proton (1D ¹H) NMR, whereas the analysis of other nuclei, such as ¹³C, or other NMR experiments are still underrepresented. The preference of 1D ¹H NMR metabolomics lies on the fact that it has good sensitivity and a short acquisition time, but it lacks spectral resolution because it presents a high degree of overlap. In this study, the growth metabolism of yeast ( Saccharomyces cerevisiae) was analyzed by 1D ¹H NMR and by two-dimensional (2D) ¹H-¹³C heteronuclear single quantum coherence (HSQC) NMR spectroscopy, leading to the detection of more than 50 metabolites with both analytical approaches. These two analyses allow for a better understanding of the strengths and intrinsic limitations of the two types of NMR approaches. The two data sets (1D and 2D NMR) were investigated with PCA, ASCA, and PLS DA chemometric methods, and similar results were obtained regardless of the data type used. However, data-analysis time for the 2D NMR data set was substantially reduced when compared with the data analysis of the corresponding ¹H NMR data set because, for the 2D NMR data, signal overlap was not a major problem and deconvolution was not required. The comparative study described in this work can be useful for the future design of metabolomics workflows, to assist in the selection of the most convenient NMR platform and to guide the posterior data analysis of biomarker selection.

Plant metabolism as studied by NMR spectroscopy

The study of plant metabolism impacts a broad range of domains such as plant cultural practices, plant breeding, human or animal nutrition, phytochemistry and green biotechnologies. Plant metabolites are extremely diverse in terms of structure or compound families as well as concentrations. This review attempts to illustrate how NMR spectroscopy, with its broad variety of experimental approaches, has contributed widely to the study of plant primary or specialized metabolism in very diverse ways. The review presents recent developments of one-dimensional and multi-dimensional NMR methods to study various aspects of plant metabolism. Through recent examples, it highlights how NMR has proved to be an invaluable tool for the global characterization of sample composition within metabolomic studies, and shows some examples of use for targeted phytochemistry, with a special focus on compound identification and quantitation. In such cases, NMR approaches are often used to provide snapshots of the plant sample composition. The review also covers dynamic aspects of metabolism, with a description of NMR techniques to measure metabolic fluxes - in most cases after stable isotope labelling. It is mainly intended for NMR specialists who would be interested to learn more about the potential of their favourite technique in plant sciences and about specific details of NMR approaches in this field. Therefore, as a practical guide, a paragraph on the specific precautions that should be taken for sample preparation is also included. In addition, since the quality of NMR metabolic studies is highly dependent on approaches to data processing and data sharing, a specific part is dedicated to these aspects. The review concludes with perspectives on the emerging methods that could change significantly the role of NMR in the field of plant metabolism by boosting its sensitivity. The review is illustrated throughout with examples of studies selected to represent diverse applications of liquid-state or HR-MAS NMR.

Toward the complete utilization of rice straw: Methane fermentation and lignin recovery by a combinational process involving mechanical milling, supporting material and nanofiltration

Rice straw was mechanically milled using a process consuming 1.9MJ/kg-biomass, and 10g/L of unmilled or milled rice straw was used as the carbon source for methane fermentation in a digester containing carbon fiber textile as the supporting material. Milling increased methane production from 226 to 419mL/L/day at an organic loading rate of 2180mg-dichromate chemical oxygen demand/L/day, corresponding to 260mLCH4/gVS. Storage of the fermentation effluent at room temperature decreased the weight of the milled rice straw residue from 3.81 to 1.00g/L. The supernatant of the effluent was subjected to nanofiltration. The black concentrates deposited on the nanofiltration membranes contained 53.0-57.9% lignin. Solution nuclear magnetic resonance showed that lignin aromatic components such as p-hydroxyphenyl (H), guaiacyl (G), and syringyl (S) were retained primarily, and major lignin interunit structures such as the β-O-4-H/G unit were absent. This combinational process will aid the complete utilization of rice straw.

Comprehensive evaluation of the liquid fraction during the hydrothermal treatment of rapeseed straw

BACKGROUND

The requirement for efficient and green conversion technologies has prompted hydrothermal processing as a promising treatment option for sustainable biorefinery industry. The treatment has been applied to process plenty of lignocellulose materials, yielding abundant high value-degraded products, especially the products in the liquid fraction. Therefore, it is essential to systematically evaluate the degraded products in aqueous fraction by comprehensive analysis and structural characterization during the treatment.

RESULTS

Rapeseed straw was hydrothermally treated at temperature ranging from 145 to 205 °C for various retention time (15, 30, 60 and 120 min), and the degraded polysaccharides and lignin products in aqueous phase were systematically evaluated by comprehensive analysis and structural characterization. Results showed that with an increase of severity, the polymers were gradually depolymerized resulting in a decrease of the molecular weight from 8430 (log R 0 3.26) to 2130 g/mol (log R 0 5.08), an increase of oligosaccharides from 19.44 (log R 0 2.88) to 99.94 g/kg (log R 0 4.32) and an increase of monosaccharides from 0.91 (log R 0 2.88) to 30.43 g/kg (log R 0 4.37). With the increase of monosaccharide degradation components (8.26 to 125.68 g/kg), the saccharides gradually decreased after its maximum value. The maximum yield of oligosaccharides (99.94 g/kg) accompanying a relatively low level of monosaccharides (17.77 g/kg) was obtained at a high temperature (190 °C) for a short reaction time (15 min). The degraded polysaccharides had a linear backbone of (1 → 4)-linked β-d-xylopyranosyl xylan decorated with branches based on 2D NMR spectra analysis. Lignin was strongly condensed with a decrease of S/G ratio as the severity increased. The yields of the degraded constitutions have a incomplete linear correlation with the treatment severity.

CONCLUSIONS

The liquid fractions obtained from hydrothermal treatment were subjected to comprehensive analysis and structural characterization. Results indicated that hydrothermal treatment had a significant influence on the composition and structure of the polysaccharides and lignin in the aqueous phase. The treatment could be adopted to obtain XOS-rich fraction with limited formation of by-products. In addition, the result was expected to further reveal the mechanisms of hydrothermal treatment on rapeseed straw and to facilitate the value-added applications of agricultural residues in the biorefinery industry.

Organosolv pretreatment of sorghum bagasse using a low concentration of hydrophobic solvents such as 1-butanol or 1-pentanol

BACKGROUND

The primary components of lignocellulosic biomass such as sorghum bagasse are cellulose, hemicellulose, and lignin. Each component can be utilized as a sustainable resource for producing biofuels and bio-based products. However, due to their complicated structures, fractionation of lignocellulosic biomass components is required. Organosolv pretreatment is an attractive method for this purpose. However, as organosolv pretreatment uses high concentrations of organic solvents (>50 %), decreasing the concentration necessary for fractionation would help reduce processing costs. In this study, we sought to identify organic solvents capable of efficiently fractionating sorghum bagasse components at low concentrations.

RESULTS

Five alcohols (ethanol, 1-propanol, 2-propanol, 1-butanol, and 1-pentanol) were used for organosolv pretreatment of sorghum bagasse at a concentration of 12.5 %. Sulfuric acid (1 %) was used as a catalyst. With 1-butanol and 1-pentanol, three fractions (black liquor, liquid fraction containing xylose, and cellulose-enriched solid fraction) were obtained after pretreatment. Two-dimensional nuclear magnetic resonance analysis revealed that the lignin aromatic components of raw sorghum bagasse were concentrated in the black liquor fraction, although the major lignin side-chain (β-O-4 linkage) was lost. Pretreatment with 1-butanol or 1-pentanol effectively removed p-coumarate, some guaiacyl, and syringyl. Compared with using no solvent, pretreatment with 1-butanol or 1-pentanol resulted in two-fold greater ethanol production from the solid fraction by Saccharomyces cerevisiae.

CONCLUSIONS

Our results revealed that a low concentration (12.5 %) of a highly hydrophobic solvent such as 1-butanol or 1-pentanol can be used to separate the black liquor from the solid and liquid fractions. The efficient delignification and visible separation of the lignin-rich fraction possible with this method simplify the fractionation of sorghum bagasse.

Precipitate obtained following membrane separation of hydrothermally pretreated rice straw liquid revealed by 2D NMR to have high lignin content

BACKGROUND

Hydrothermal pretreatment of lignocellulosic biomass such as rice straw can dissolve part of the lignin and hemicellulose into a liquid fraction, thus facilitating enzyme accessibility to cellulose in bioethanol production process. Lignin is awaited to be recovered after hydrothermal pretreatment for utilization as value-added chemical, and lignin recovery also means removal of fermentation inhibitors. To recover lignin with high content from the liquid fraction, it is necessary to separate lignin and hemicellulose-derived polysaccharide. Therefore, the following processes were applied: membrane separation with nanofiltration (NF) and enzymatic hydrolysis by hemicellulase. To clarify lignin-concentrated fraction obtained during these processes, the fates of lignin and polysaccharide components were pursued by a solution NMR method and confirmed by compositional analysis of each fraction.

RESULTS

After hydrothermal pretreatment of rice straw, the NF concentrate of the supernatant of liquid fraction was hydrolyzed by hemicellulase and the resulting black precipitate was recovered. In this black precipitate, the intensity of NMR spectra related to lignin aromatic regions increased and those related to polysaccharides decreased, compared to rice straw, the solid fraction after hydrothermal pretreatment, and the NF concentrate. The lignin content of the black precipitate was 65.8 %. Lignin in the black precipitate included 52.9 % of the acid-insoluble lignin and 19.4 % of the soluble lignin in the NF concentrate of supernatant of liquid fraction.

CONCLUSION

A precipitate with high lignin content was obtained from supernatants of the liquid fraction. These results suggested that precipitation of lignin was enhanced from concentrated mixtures of lignin and hemicellulosic polysaccharides by hydrolyzing the polysaccharides. Precipitation of lignin can contribute to lignin recovery from lignocellulosic biomass and, at the same time, allow more efficient ethanol production in the subsequent fermentation process.

Changes in Lignin and Polysaccharide Components in 13 Cultivars of Rice Straw following Dilute Acid Pretreatment as Studied by Solution-State 2D 1H-13C NMR

A renewable raw material, rice straw is pretreated for biorefinery usage. Solution-state two-dimensional (2D) 1H-13 C hetero-nuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectroscopy, was used to analyze 13 cultivars of rice straw before and after dilute acid pretreatment, to characterize general changes in the lignin and polysaccharide components. Intensities of most (15 of 16) peaks related to lignin aromatic regions, such as p-coumarate, guaiacyl, syringyl, p-hydroxyphenyl, and cinnamyl alcohol, and methoxyl, increased or remained unchanged after pretreatment. In contrast, intensities of most (11 of 13) peaks related to lignin aliphatic linkages or ferulate decreased. Decreased heterogeneity in the intensities of three peaks related to cellulose components in acid-insoluble residues resulted in similar glucose yield (0.45-0.59 g/g-dry biomass). Starch-derived components showed positive correlations (r = 0.71 to 0.96) with glucose, 5-hydroxymethylfurfural (5-HMF), and formate concentrations in the liquid hydrolysates, and negative correlations (r = -0.95 to -0.97) with xylose concentration and acid-insoluble residue yield. These results showed the fate of lignin and polysaccharide components by pretreatment, suggesting that lignin aromatic regions and cellulose components were retained in the acid insoluble residues and starch-derived components were transformed into glucose, 5-HMF, and formate in the liquid hydrolysate.

Experimental approaches to study plant cell walls during plant-microbe interactions

Plant cell walls provide physical strength, regulate the passage of bio-molecules, and act as the first barrier of defense against biotic and abiotic stress. In addition to providing structural integrity, plant cell walls serve an important function in connecting cells to their extracellular environment by sensing and transducing signals to activate cellular responses, such as those that occur during pathogen infection. This mini review will summarize current experimental approaches used to study cell wall functions during plant-pathogen interactions. Focus will be paid to cell imaging, spectroscopic analyses, and metabolic profiling techniques.

A gel-state 2D-NMR method for plant cell wall profiling and analysis: a model study with the amorphous cellulose and xylan from ball-milled cotton linters

Amorphous cellulose and xylan structures were analyzed using high-resolution 2D-NMR, and the NMR data were obtained in a DMSO-d₆/pyridine-d₅ (4 : 1) solvent system.