Structural analyses and yeast production of the β-1,3-1,4-glucanase catalytic module encoded by the licB gene of Clostridium thermocellum

Deciphering the structure of a distinctive trimodular cellulosomal licheninase (RfGH16_21), a family 16 glycoside hydrolase from Ruminococcus flavefaciens by computational and experimental methods

In order to know the insights of a unique naturally existing trimodular licheninase from GH16 family, sub-family 21 (RfGH16_21) from Ruminococcus flavefaciens, its structure was modeled to understand its functional relations to reveal information regarding modifying the enzyme for improved properties with enhanced catalytic efficiency. Homology modeling revealed three tandem repeats of β-jelly roll like folds linked by natural linkers. Catalytic pockets and the catalytically important amino acids in each tandem repeat of RfGH16_21 determined by multiple sequence alignment and structure superposition with its homologues indicated that two Glu residues are involved in a retaining-type of catalytic mechanism. Sequential molecular docking revealed maximum binding energy with mixed linked cellotriose showing that cellotriose is the lowest oligomeric hydrolysed product formed by the catalytic action of endo-β-1,3-1,4-glucanase. Molecular dynamic (MD) simulation of RfGH16_21-cellotriose complex confirmed the structural specificity of catalytic residues and increased stability of enzyme in presence of ligand as compared to simulated RfGH16_21 alone. The binding affinity of cellotriose towards the three tandem repeats of RfGH16_21 was also confirmed by calculating total binding Gibbs free energy, i.e. -100.8 ± 2.6 KJ/mol, by using g_mmpbsa tool. The stability of the protein was determined by protein melting analysis that showed Ca2+ and Mg2+ ions imparted structural stability to RfGH16_21. Dynamic light scattering analysis of RfGH16_21 showed monodispersity and hydrodynamic radius of 4.0 nm at 2.0 mg/mL protein concentration, which was comparable with the radius of gyration of 3.2 nm determined by MD simulation showing the protein to be in monomeric form.Communicated by Ramaswamy H. Sarma.

Specificity of a β-porphyranase produced by the carrageenophyte red alga Chondrus crispus and implications of this unexpected activity on red algal biology

The carrageenophyte red alga Chondrus crispus produces three family 16 glycoside hydrolases (CcGH16-1, CcGH16-2, and CcGH16-3). Phylogenetically, the red algal GH16 members are closely related to bacterial GH16 homologs from subfamilies 13 and 14, which have characterized marine bacterial β-carrageenase and β-porphyranase activities, respectively, yet the functions of these CcGH16 hydrolases have not been determined. Here, we first confirmed the gene locus of the ccgh16-3 gene in the alga to facilitate further investigation. Next, our biochemical characterization of CcGH16-3 revealed an unexpected β-porphyranase activity, since porphyran is not a known component of the C. crispus extracellular matrix. Kinetic characterization was undertaken on natural porphyran substrate with an experimentally determined molecular weight. We found CcGH16-3 has a pH optimum between 7.5 and 8.0; however, it exhibits reasonably stable activity over a large pH range (pH 7.0-9.0). CcGH16-3 has a K_M of 4.0 ± 0.8 μM, a k_cat of 79.9 ± 6.9 s^-1, and a k_cat/K_M of 20.1 ± 1.7 μM^-1 s^-1. We structurally examined fine enzymatic specificity by performing a subsite dissection. CcGH16-3 has a strict requirement for D-galactose and L-galactose-6-sulfate in its -1 and +1 subsites, respectively, whereas the outer subsites are less restrictive. CcGH16-3 is one of a handful of algal enzymes characterized with a specificity for a polysaccharide unknown to be found in their own extracellular matrix. This β-porphyranase activity in a carrageenophyte red alga may provide defense against red algal pathogens or provide a competitive advantage in niche colonization.

A chemiluminescence aptasensor for sensitive detection of alpha-fetoprotein based on hemin@ZIF-67

In this work, hemin@ZIF-67 composites were prepared and were used to construct a chemiluminescence (CL) aptasensor for alpha-fetoprotein (AFP) detection. Hemin is a catalytic porphyrin with two carboxylate groups that can covalently bond to metal ions. A hemin/ZIF-67 composite was prepared via covalent bonding between the carboxyl groups of hemin and the cobalt ion of ZIF-67, and these materials were characterized by scanning electron microscopy (SEM), infrared spectroscopy (IR), and X-ray diffraction (XRD). Hemin@ZIF-67 was used as the peroxidase material, and the aptamer of alpha-fetoprotein was modified on its surface by electrostatic adsorption. Then a simple CL aptasensor was constructed based on the CL system of luminol-H₂O₂-NaOH. Under the optimal conditions, the CL intensity value was linearly proportional to the concentration of AFP in the range of 4 × 10^-10 to 200 × 10^-10 mg/mL. The detection limit was 1.3 × 10^-10 mg/mL. Thus the aptasensor enables highly sensitive and selective detection of AFP.

Production of trans-free interesterified fat using indigenously immobilized lipase

Enzymatic interesterification was carried out between high-oleic canola oil and fully hydrogenated soybean oil using indigenously immobilized Thermomyces lanuginosus lipas substrate concentration, moisture content of enzyme, and enzyme load. Interesterification resulted in a decrease in the concentration of tri-unsaturated and trisaturated TAG and an increase of mono- and di-saturated TAG as observed by reversed-phase HPLC. The alteration in TAG composition and the presence of new TAG species after interesterification was correlated with extended plasticity characterized by lower slip melting point with a significant change in functionality and consistency of the interesterified product. Thermal and structural properties of the blends before and after interesterification were assessed by differential scanning calorimetry (DSC), X-ray diffraction and polarized light microscopy. Trans-fat analysis indicated the absence of any trans fatty acid in the final interesterified product. The resultant interesterified products with varying slip melting points can be used in the formulation of healthier fat and oil products and address a critical industrial demand for trans free formulations for base-stocks of spreads, margarines, and confectionary fats.

A novel design for passive misscromixers based on topology optimization method

In this paper, a series of novel passive micromixers, called topological micromixers with reversed flow (TMRFX), are proposed. The reversed flow in the microchannels can enhance chaotic advection and produce better mixing performance. Therefore the maximum of reversed flow is chosen as the objective function of the topology optimization problem. Because the square-wave unit is easier to fabricate and have better mixing performance than many other serpentine micromixers, square-wave structure becomes the original geometry structure. By simulating analysis, the series of TMRFX, namely TMRF, TMRF0.75, TMRF0.5, TMRF0.25, mix better than the square-wave micromixer at various Reynolds numbers (Re), but pressure drops of TMRFX are much higher. Lots of intensive numerical simulations are conducted to prove that TMRF and TMRF0.75 have remarkable advantages on mixing over other micromixers at various Re. The mixing performance of TMRF0.75 is similar to TMRF's. What's more, TMRF have a larger pressure drop than TMRF0.75, which means that TMRF have taken more energy than TMRF0.75. For a wide range of Re (Re ≤ 0.1 and Re ≥ 10), TMRF0.75 delivers a great performance and the mixing efficiency is greater than 95 %. Even in the range of 0.1-10 for the Re, the mixing efficiency of TMRF0.75 is higher than 85 %.

A Genome Wide Association Study of arabinoxylan content in 2-row spring barley grain

In barley endosperm arabinoxylan (AX) is the second most abundant cell wall polysaccharide and in wheat it is the most abundant polysaccharide in the starchy endosperm walls of the grain. AX is one of the main contributors to grain dietary fibre content providing several health benefits including cholesterol and glucose lowering effects, and antioxidant activities. Due to its complex structural features, AX might also affect the downstream applications of barley grain in malting and brewing. Using a high pressure liquid chromatography (HPLC) method we quantified AX amounts in mature grain in 128 spring 2-row barley accessions. Amounts ranged from ~ 5.2 μg/g to ~ 9 μg/g. We used this data for a Genome Wide Association Study (GWAS) that revealed three significant quantitative trait loci (QTL) associated with grain AX levels which passed a false discovery threshold (FDR) and are located on two of the seven barley chromosomes. Regions underlying the QTLs were scanned for genes likely to be involved in AX biosynthesis or turnover, and strong candidates, including glycosyltransferases from the GT43 and GT61 families and glycoside hydrolases from the GH10 family, were identified. Phylogenetic trees of selected gene families were built based on protein translations and were used to examine the relationship of the barley candidate genes to those in other species. Our data reaffirms the roles of existing genes thought to contribute to AX content, and identifies novel QTL (and candidate genes associated with them) potentially influencing the AX content of barley grain. One potential outcome of this work is the deployment of highly associated single nucleotide polymorphisms markers in breeding programs to guide the modification of AX abundance in barley grain.

GH16 and GH81 family β-(1,3)-glucanases in Aspergillus fumigatus are essential for conidial cell wall morphogenesis

The fungal cell wall is a rigid structure because of fibrillar and branched β-(1,3)-glucan linked to chitin. Softening of the cell wall is an essential phenomenon during fungal morphogenesis, wherein rigid cell wall structures are cleaved by glycosylhydrolases. During the search for glycosylhydrolases acting on β-(1,3)-glucan, we identified seven genes in the Aspergillus fumigatus genome coding for potential endo-β-(1,3)-glucanase. ENG1 (previously characterized and named ENGL1, Mouyna et al., ), belongs to the Glycoside-Hydrolase 81 (GH81) family, while ENG2 to ENG7, to GH16 family. ENG1 and four GH16 genes (ENG2-5) were expressed in the resting conidia as well as during germination, suggesting an essential role during A. fumigatus morphogenesis. Here, we report the effect of sequential deletion of AfENG2-5 (GH16) followed by AfENG1 (GH81) deletion in the Δeng2,3,4,5 mutant. The Δeng1,2,3,4,5 mutant showed conidial defects, with linear chains of conidia unable to separate while the germination rate was not affected. These results show, for the first time in a filamentous fungus, that endo β-(1,3)-glucanases are essential for proper conidial cell wall assembly and thus segregation of conidia during conidiation.

A Highly Reliable and Cost-Efficient Multi-Sensor System for Land Vehicle Positioning

In this paper, we propose a novel positioning solution for land vehicles which is highly reliable and cost-efficient. The proposed positioning system fuses information from the MEMS-based reduced inertial sensor system (RISS) which consists of one vertical gyroscope and two horizontal accelerometers, low-cost GPS, and supplementary sensors and sources. First, pitch and roll angle are accurately estimated based on a vehicle kinematic model. Meanwhile, the negative effect of the uncertain nonlinear drift of MEMS inertial sensors is eliminated by an H∞ filter. Further, a distributed-dual-H∞ filtering (DDHF) mechanism is adopted to address the uncertain nonlinear drift of the MEMS-RISS and make full use of the supplementary sensors and sources. The DDHF is composed of a main H∞ filter (MHF) and an auxiliary H∞ filter (AHF). Finally, a generalized regression neural network (GRNN) module with good approximation capability is specially designed for the MEMS-RISS. A hybrid methodology which combines the GRNN module and the AHF is utilized to compensate for RISS position errors during GPS outages. To verify the effectiveness of the proposed solution, road-test experiments with various scenarios were performed. The experimental results illustrate that the proposed system can achieve accurate and reliable positioning for land vehicles.