Neural network prediction of biomass digestibility based on structural features

Plots of biomass digestibility are linear with the natural logarithm of enzyme loading; the slope and intercept characterize biomass reactivity. The feed-forward back-propagation neural networks were performed to predict biomass digestibility by simulating the 1-, 6-, and 72-h slopes and intercepts of glucan, xylan, and total sugar hydrolyses of 147 poplar wood model samples with a variety of lignin contents, acetyl contents, and crystallinity indices. Regression analysis of the neural network models indicates that they performed satisfactorily. Increasing the dimensionality of the neural network input matrix allowed investigation of the influence glucan and xylan enzymatic hydrolyses have on each other. Glucan hydrolysis affected the last stage of xylan digestion, and xylan hydrolysis had no influence on glucan digestibility. This study has demonstrated that neural networks have good potential for predicting biomass digestibility over a wide range of enzyme loadings, thus providing the potential to design cost-effective pretreatment and saccharification processes.     

Structural features of distinctin affecting peptide biological and biochemical properties

The antimicrobial peptide distinctin consists of two peptide chains linked by a disulfide bridge; it presents a peculiar fold in water resulting from noncovalent dimerization of two heterodimeric molecules. To investigate the contribution of each peptide chain and the S-S bond to distinctin biochemical properties, different monomeric and homodimeric peptide analogues were synthesized and comparatively evaluated with respect to the native molecule. Our experiments demonstrate that the simultaneous occurrence of both peptide chains and the disulfide bond is essential for the formation of the quaternary structure of distinctin in aqueous media, able to resist protease action. In contrast, distinctin and monomeric and homodimeric analogues exhibited comparable antimicrobial activities, suggesting only a partial contribution of the S-S bond to peptide killing effectiveness. Relative bactericidal properties paralleled liposome permeabilization results, definitively demonstrating that microbial membranes are the main target of distinctin activity. Various biophysical experiments performed in membrane-mimicking media, before and after peptide addition, provided information about peptide secondary structure, lipid bilayer organization, and lipid-peptide orientation with respect to membrane surface. These data were instrumental in the generation of putative models of peptide-lipid supramolecular pore complexes.     

Fiber fractionation to understand the effect of mechanical refining on fiber structure and resulting enzymatic digestibility of biomass

Mechanical refining results in fiber deconstruction and modifications that enhance enzyme accessibility to carbohydrates. Further understanding of the morphological changes occurring to biomass during mechanical refining and the impacts of these changes on enzymatic digestibility is necessary to maximize yields and reduce energy consumption. Although the degree of fiber length reduction relative to fibrillation/delamination can be impacted by manipulating refining variables, mechanical refining of any type (PFI, disk, and valley beater) typically results in both phenomena. Separating the two is not straightforward. In this study, fiber fractionation based on particle size performed after mechanical refining of high-lignin pulp was utilized to successfully elucidate the relative impact of fibrillation/delamination and fiber cutting phenomena during mechanical refining. Compositional analysis showed that fines contain significantly more lignin than larger size fractions. Enzymatic hydrolysis results indicated that within fractions of uniform fiber length, fibrillation/delamination due to mechanical refining increased enzymatic conversion by 20–30 percentage points. Changes in fiber length had little effect on digestibility for fibers longer than ~0.5 mm. However, the digestibility of the fines fractions was high for all levels of refining even with the high-lignin content.     

Composition and enzymatic digestibility of Oregon grass straws

Samples of nine species or types of commercial grass seed straws grown in Oregon were analyzed and treated with anhydrous ammonia in the laboratory. Enzymatic digestibility of treated and untreated materials was determined using commercial cellulase and protease. The mean composition of all nine species/types (based on six each within-group replicates) was: crude protein, 5.4%; NDF, 72.2%; ADF, 43.6%; hemicellulose, 26.4%; cellulose, 34.8%; and lignin, 6.9%. Significant species/type compositional differences were found. From their composition, several of the grass straws appeared to have better nutritional value than most cereal straws. Enzymatic digestibility of all straws was improved by ammoniation (average increase, 62%). Enzymatic digestibility ranged from about 27–42% for untreated materials to 43–66% for NH₃-treated products.     

Pretreatments to enhance the digestibility of lignocellulosic biomass

Lignocellulosic biomass represents a rather unused source for biogas and ethanol production. Many factors, like lignin content, crystallinity of cellulose, and particle size, limit the digestibility of the hemicellulose and cellulose present in the lignocellulosic biomass. Pretreatments have as a goal to improve the digestibility of the lignocellulosic biomass. Each pretreatment has its own effect(s) on the cellulose, hemicellulose and lignin; the three main components of lignocellulosic biomass. This paper reviews the different effect(s) of several pretreatments on the three main parts of the lignocellulosic biomass to improve its digestibility. Steam pretreatment, lime pretreatment, liquid hot water pretreatments and ammonia based pretreatments are concluded to be pretreatments with high potentials. The main effects are dissolving hemicellulose and alteration of lignin structure, providing an improved accessibility of the cellulose for hydrolytic enzymes.     

Structural features affecting trafficking, processing, and secretion of Trypanosoma cruzi mucins

Trypanosoma cruzi is wrapped by a dense coat of mucin-type molecules encoded by complex gene families termed TcSMUG and TcMUC, which are expressed in the insect- and mammal-dwelling forms of the parasite, respectively. Here, we dissect the contribution of distinct post-translational modifications on the trafficking of these glycoconjugates. In vivo tracing and characterization of tagged-variants expressed by transfected epimastigotes indicate that although the N-terminal signal peptide is responsible for targeting TcSMUG products to the endoplasmic reticulum (ER), the glycosyl phosphatidylinositol (GPI)-anchor likely functions as a forward transport signal for their timely progression along the secretory pathway. GPI-minus variants accumulate in the ER, with only a minor fraction being ultimately released to the medium as anchorless products. Secreted products, but not ER-accumulated ones, display several diagnostic features of mature mucin-type molecules including extensive O-type glycosylation, Galf-based epitopes recognized by monoclonal antibodies, and terminal Galp residues that become readily sialylated upon addition of parasite trans-sialidases. Processing of N-glycosylation site(s) is dispensable for the overall TcSMUG mucin-type maturation and secretion. Despite undergoing different O-glycosylation elaboration, TcMUC reporters yielded quite similar results, thus indicating that (i) molecular trafficking signals are structurally and functionally conserved between mucin families, and (ii) TcMUC and TcSMUG products are recognized and processed by a distinct repertoire of stage-specific glycosyltransferases. Thus, using the fidelity of a homologous expression system, we have defined some biosynthetic aspects of T. cruzi mucins, key molecules involved in parasite protection and virulence.     

Structural features influential to enzymatic hydrolysis of cellulose-solvent-based pretreated pinewood and elmwood for ethanol production

Bioprocess and Biosystems Engineering - Dissolution of lignocelluloses in N-methylmorpholine-N-oxide (NMMO or NMO) at moderate conditions, e.g., 120 °C for 3 h under...     

Organosolv pretreatment of lignocellulosic biomass for enzymatic hydrolysis

Production of ethanol by bioconversion of lignocellulosic biomass has attracted much interest in recent years. However, the pretreatment process for increasing the enzymatic digestibility of cellulose has become a key step in commercialized production of cellulosic ethanol. During the last decades, many pretreatment processes have been developed for decreasing the biomass recalcitrance, but only a few of them seem to be promising. From the point of view for integrated utilization of lignocellulosic biomass, organosolv pretreatment provides a pathway for biorefining of biomass. This review presents the progress of organosolv pretreatment of lignocellulosic biomass in recent decades, especially on alcohol, organic acid, organic peracid and acetone pretreatments, and corresponding action mechanisms. Evaluation and prospect of organosolv pretreatment were performed. Finally, some recommendations for future investigation of this pretreatment method were given.     

Structural features affecting chiral resolution of cannabimimetic enantiomers by amylose 3,5-dimethylphenylcarbamate chiral stationary phase

The effect of structural features of six pairs of enantiomers of cannabimimetic compounds on their chromatographic resolution on an amylose tris(3,5-dimethylphenylcarbamate) chiral stationary phase was studied using various compositions of n-hexane with 2-propanol and ethanol. Structural analysis by molecular mechanics was also performed to verify that the 3D conformation within this family of compounds was preserved with substitution. The homologous enantiomeric pairs showed better resolution when there was an additional OH group near the chiral centers (position 7 on the cannabinoid structure). Better resolution was observed also for the enantiomeric pair that had the smaller alkyl side chain. These differences indicated that the additional OH group contributed to a better discrimination of the enantiomers by the chiral sites of the stationary phase and that the bulkier alkyl side chain reduced it. The chromatographic resolution of two enantiomeric pairs of nonclassical cannabinoids HU-249 and HU-250, HU-255 and HU-256, was compared both in ethanol and 2-propanol. Both enantiomeric pairs showed relatively high resolution and selectivity, but the rigid benzofuran analogs (HU-249 and HU-250) exhibited better resolution using 2-propanol, in spite of the flexibility of the open chain analog (HU-255 and HU-256) and its additional OH group. The elution order of all the cannabinoids was (+)/(?) using both solvents. Unusual solvent effects were displayed by one enantiomeric pair, Δ⁶-THC, which was resolved easily using 2-propanol, but whose elution order reversed with 1% ethanol in the mobile phase. Partial separation was obtained at 5% ethanol [elution order (+)/(?)] and full separation was obtained at 0.5% ethanol [elution order (?)/(+)]. © 1995 Wiley-Liss, Inc.     

Mechanism of lignin inhibition of enzymatic biomass deconstruction

Background

The conversion of plant biomass to ethanol via enzymatic cellulose hydrolysis offers a potentially sustainable route to biofuel production. However, the inhibition of enzymatic activity in pretreated biomass by lignin severely limits the efficiency of this process.

Results

By performing atomic-detail molecular dynamics simulation of a biomass model containing cellulose, lignin, and cellulases (TrCel7A), we elucidate detailed lignin inhibition mechanisms. We find that lignin binds preferentially both to the elements of cellulose to which the cellulases also preferentially bind (the hydrophobic faces) and also to the specific residues on the cellulose-binding module of the cellulase that are critical for cellulose binding of TrCel7A (Y466, Y492, and Y493).

Conclusions

Lignin thus binds exactly where for industrial purposes it is least desired, providing a simple explanation of why hydrolysis yields increase with lignin removal.

     

Methodological analysis for determination of enzymatic digestibility of cellulosic materials

Accurate measurement of enzymatic cellulose digestibility (X) is important in evaluating the efficiency of lignocellulose pretreatment technologies, assessing the performance of reconstituted cellulase mixtures, and conducting economic analysis for biorefinery processes. We analyzed the effect of sugars contained in enzymes solutions, usually added as a preservative, and random measurement errors on the accuracy of X calculated by various methods. The analysis suggests that exogenous sugars at levels measured in several commercial enzyme preparations significantly bias the results and that this error should be minimized by accounting for these sugars in the calculation of X. Additionally, a method of calculating X equating the ratio of the soluble glucose equivalent in the liquid phase after hydrolysis to the sum of the soluble glucose equivalent in the liquid phase and the insoluble glucose equivalent in the residual solid after hydrolysis was found to be the most accurate, particularly at high conversion levels (>ca. 50%).     

Cellulase digestibility of pretreated biomass is limited by cellulose accessibility

Attempts to correlate the physical and chemical properties of biomass to its susceptibility to enzyme digestion are often inconclusive or contradictory depending on variables such as the type of substrate, the pretreatment conditions and measurement techniques. In this study, we present a direct method for measuring the key factors governing cellulose digestibility in a biomass sample by directly probing cellulase binding and activity using a purified cellobiohydrolase (Cel7A) from Trichoderma reesei. Fluorescence-labeled T. reesei Cel7A was used to assay pretreated corn stover samples and pure cellulosic substrates to identify barriers to accessibility by this important component of cellulase preparations. The results showed cellulose conversion improved when T. reesei Cel7A bound in higher concentrations, indicating that the enzyme had greater access to the substrate. Factors such as the pretreatment severity, drying after pretreatment, and cellulose crystallinity were found to directly impact enzyme accessibility. This study provides direct evidence to support the notion that the best pretreatment schemes for rendering biomass more digestible to cellobiohydrolase enzymes are those that improve access to the cellulose in biomass cell walls, as well as those able to reduce the crystallinity of cell wall cellulose.     

Rapeseed-straw enzymatic digestibility enhancement by sodium hydroxide treatment under ultrasound irradiation

In this study, we carried out sodium hydroxide and sonication pretreatments of rapeseed straw (Brassica napus) to obtain monosugar suitable for production of biofuels. To optimize the pretreatment conditions, we applied a statistical response-surface methodology. The optimal pretreatment conditions using sodium hydroxide under sonication irradiation were determined to be 75.0 °C, 7.0 % sodium hydroxide, and 6.8 h. For these conditions, we predicted 97.3 % enzymatic digestibility. In repeated experiments to validate the predicted value, 98.9 ± 0.3 % enzymatic digestibility was obtained, which was well within the range of the predicted model. Moreover, sonication irradiation was found to have a good effect on pretreatment in the lower temperature range and at all concentrations of sodium hydroxide. According to scanning electron microscopy images, the surface area and pore size of the pretreated rapeseed straw were modified by the sodium hydroxide pretreatment under sonication irradiation.     

High‐level hemicellulosic arabinose predominately affects lignocellulose crystallinity for genetically enhancing both plant lodging resistance and biomass enzymatic digestibility in rice mutants

Rice is a major food crop with enormous biomass residue for biofuels. As plant cell wall recalcitrance basically decides a costly biomass process, genetic modification of plant cell walls has been regarded as a promising solution. However, due to structural complexity and functional diversity of plant cell walls, it becomes essential to identify the key factors of cell wall modifications that could not much alter plant growth, but cause an enhancement in biomass enzymatic digestibility. To address this issue, we performed systems biology analyses of a total of 36 distinct cell wall mutants of rice. As a result, cellulose crystallinity (CrI) was examined to be the key factor that negatively determines either the biomass enzymatic saccharification upon various chemical pretreatments or the plant lodging resistance, an integrated agronomic trait in plant growth and grain production. Notably, hemicellulosic arabinose (Ara) was detected to be the major factor that negatively affects cellulose CrI probably through its interlinking with β‐1,4‐glucans. In addition, lignin and G monomer also exhibited the positive impact on biomass digestion and lodging resistance. Further characterization of two elite mutants, Osfc17 and Osfc30, showing normal plant growth and high biomass enzymatic digestion in situ and in vitro, revealed the multiple GH9B candidate genes for reducing cellulose CrI and XAT genes for increasing hemicellulosic Ara level. Hence, the results have suggested the potential cell wall modifications for enhancing both biomass enzymatic digestibility and plant lodging resistance by synchronically overexpressing GH9B and XAT genes in rice.     

Structural features that govern enzymatic activity in carbonic anhydrase from a low-temperature adapted fish, Chionodraco hamatus

The carbonic anhydrase (CA) family of zinc metalloenzymes includes many known isozymes that have different subcellular distributions. The study described here focuses on identification of the structural features that define low-temperature adaptation in a Chionodraco hamatus protein, both for the reaction center, at an atomic level, and for the tertiary structure of the protein. To this aim, an x-ray absorption near-edge spectroscopy/Minuit x-ray absorption near-edge spectroscopy analysis of the reaction center was undertaken for both a structurally characterized human CAII and CA of C. hamatus. Higher structural levels were analyzed by sequence comparison and homology modeling. To establish whether the structural insights acquired in fish CAs are general, theoretical models were generated by homology modeling for three temperate-climate-adapted fish CAs. The measured structural differences between the two proteins are discussed in terms of the differences in the electrostatic potential between human CAII and CA of C. hamatus. We conclude that modulation of the interaction between the catalytic water molecule and the zinc ion could depend on the effect of the electrostatic potential distribution.     

纤维素酶与木质纤维素生物降解转化的研究进展

利用纤维素酶将预处理后的秸秆降解成可发酵性单糖,然后发酵生产所需的液体燃料及化工产品的技术,对于我国解决能源、环境、人口就业等难题有着巨大的积极影响。在木质纤维素生物降解转化工艺中,减少纤维素酶用量及提高酶解效率是降低木质纤维素降解成本的关键。纤维素酶系和木质纤维素酶水解技术的改进需要深入了解纤维素酶系统的组成及其协同作用、纤维素酶的结构与功能以及纤维素酶的生产技术。将就以上几个方面的研究进展进行讨论,并深入探讨了纤维素酶糖化能力的评价方法。