Efficient Degradation of Alginate And Preparation of Unsaturated Monosaccharides By A Novel Alginate Lyase And Effects of Domain Truncation On Biochemical Characteristics, Degradation Patterns

BackgroundBrown algae are considered promising crops for the production of sustainable biofuels. However, its commercial application has been limited by lack of efficient methods for converting alginate into fermentable sugars. Recently, exo-type alginate lyases have received extensive attention due to their excellent ability of conversion of alginate into 4-deoxy-L-erythro-5-hexoseulose uronate (DEH), a promising material for bioethanol production and biorefinery systems.ResultsHerein, we cloned and characterized a novel alginate lyase AlyPL17 from Pedobacter hainanensis NJ-02. It possessed outstanding catalytic efficiency towards polymannuronic acid (polyM), polyguluronic acid (polyG) and alginate sodium, with kcat of 39.42 + 1.9 s-1, 32.53 + 0.88 s-1, and 38.30 + 2.12 s-1, respectively. In addition, AlyPL17 adopts a unique hybrid action mode to degrade alginate by the synergistic effect of two domains. Furthermore, the combination of AlyPL17 and AlyPL6 exhibited apparently synergistic effect for the preparation of unsaturated monosaccharides. ConclusionOverall, the results show that AlyPL17 is a PL17 exo-type alginate lyase with high activity and a high conversion rate at low/moderate temperatures, which provides a useful enzymatic tool for the conversion of brown algae into biofuels and enhance our understanding of the function of modular domain of alginate lyase.

Numerical Simulation on the Whole Sinking Process of Open Caisson with an Improved SPH Method

The phenomena of dynamic change in the material interfaces and mechanical properties are often involved in the caisson construction. Using conventional methods to simulate these phenomena is quite difficult due to the extremely large deformation. In this study, we proposed an improved soil-water-caisson interaction algorithm with the method of smoothed-particle hydrodynamics (SPH). This algorithm dealt with the support domain truncation of the particles near the blade and applied δ − SPH to avoid the pressure fluctuation. Meanwhile, the application of dynamic particles birth and death method could simulate the whole sinking process of an open caisson with underwater soil excavation. According to the comparison between SPH simulation and centrifuge test, the distribution of sidewall effective soil pressure was consistent, which indicated promising applicability of the algorithm. It should be noted that the considerable excess pore water pressure appeared in the surrounding soil under the blade. With the dissipation of the pressure over time, the effective soil stress increased correspondingly, and it would lead to the increasing difficulty of the sinking process. Therefore, the caisson should be avoided to stop for a long time during the sinking process or it would cause the stagnation of sinking. This algorithm could simulate engineering problems involving underwater construction effectively and provide theoretical and technical support for underwater excavation, shield tunneling, and other engineering problems.

Accurate Spectral Collocation Computation of High Order Eigenvalues for Singular Schrödinger Equations

We are concerned with the study of some classical spectral collocation methods, mainly Chebyshev and sinc as well as with the new software system Chebfun in computing high order eigenpairs of singular and regular Schrödinger eigenproblems. We want to highlight both the qualities as well as the shortcomings of these methods and evaluate them in conjunction with the usual ones. In order to resolve a boundary singularity, we use Chebfun with domain truncation. Although it is applicable with spectral collocation, a special technique to introduce boundary conditions as well as a coordinate transform, which maps an unbounded domain to a finite one, are the special ingredients. A challenging set of “hard”benchmark problems, for which usual numerical methods (f. d., f. e. m., shooting, etc.) fail, were analyzed. In order to separate “good”and “bad”eigenvalues, we have estimated the drift of the set of eigenvalues of interest with respect to the order of approximation and/or scaling of domain parameter. It automatically provides us with a measure of the error within which the eigenvalues are computed and a hint on numerical stability. We pay a particular attention to problems with almost multiple eigenvalues as well as to problems with a mixed spectrum.

Implementation of the Marchenko Multiple Elimination algorithm

The Marchenko multiple elimination and transmission compensation schemes retrieve primary reflections in the two-way traveltime domain without model information or using adaptive subtraction. Both schemes are derived from projected Marchenko equations and similar to each other, but use different time-domain truncation operators. The Marchenko multiple elimination scheme retrieves a new dataset without internal multiple reflections. The transmission compensated Marchenko multiple elimination scheme does the same and additionally compensates for transmission losses in the primary reflections. Both schemes can be solved with an iterative algorithm based on a Neumann series. At each iteration, a convolution or correlation between the projected focusing function and the measured reflection response are performed and after each convolution or correlation, a truncation in the time domain is applied. After convergence, the resulting projected focusing function is used for retrieving the transmission compensated primary reflections and the projected Green’s function is used for the physical primary reflections. We demonstrate that internal multiples are removed by using time-windowed input data that only contain primary reflections. We evaluate both schemes in detail and develop an iterative implementation that reproduces the presented numerical examples. The software is part of our open-source suite of programs and fits into the Seismic Unix software suite of the Colorado School of Mines.

Efficient calculation of transient eddy current response from multi-layer cylindrical conductive media

The transient response from a transmitter–receiver coil system inside a multi-layer cylindrical conductive configuration is obtained. The particular set-up applies to well logging as well as to eddy current tube testing. In this work, a number of improvements are presented to existing models for an efficient calculation of the induced voltage. These include: domain truncation, novel treatment of arbitrary number of layers in order to avoid computational overflows and efficient time response calculation. The latter is based on a combination of Laplace inversion techniques for short- and long-time transient responses. This article is part of the theme issue ‘Advanced electromagnetic non-destructive evaluation and smart monitoring’.

Hsp22 with an N-Terminal Domain Truncation Mediates a Reduction in Tau Protein Levels

Misfolding, aggregation and accumulation of proteins are toxic elements in the progression of a broad range of neurodegenerative diseases. Molecular chaperones enable a cellular defense by reducing or compartmentalizing these insults. Small heat shock proteins (sHsps) engage proteins early in the process of misfolding and can facilitate their proper folding or refolding, sequestration, or clearance. Here, we evaluate the effects of the sHsp Hsp22, as well as a pseudophosphorylated mutant and an N-terminal domain deletion (NTDΔ) variant on tau aggregation in vitro and tau accumulation and aggregation in cultured cells. Hsp22 wild-type (WT) protein had a significant inhibitory effect on heparin-induced aggregation in vitro and the pseudophosphorylated mutant Hsp22 demonstrated a similar effect. When co-expressed in a cell culture model with tau, these Hsp22 constructs significantly reduced soluble tau protein levels when transfected at a high ratio relative to tau. However, the Hsp22 NTDΔ protein drastically reduced the soluble protein expression levels of both tau WT and tau P301L/S320F even at lower transfection ratios, which resulted in a correlative reduction of the triton-insoluble tau P301L/S320F aggregates.

The rice NLR pair Pikp-1/Pikp-2 initiates cell death through receptor cooperation rather than negative regulation

Plant NLR immune receptors are multidomain proteins that can function as specialized sensor/helper pairs. Paired NLR immune receptors are generally thought to function via negative regulation, where one NLR represses the activity of the second and detection of pathogen effectors relieves this repression to initiate immunity. However, whether this mechanism is common to all NLR pairs is not known. Here, we show that the rice NLR pair Pikp-1/Pikp-2, which confers resistance to strains of the blast pathogen Magnaporthe oryzae (syn. Pyricularia oryzae) expressing the AVR-PikD effector, functions via receptor cooperation, with effector-triggered activation requiring both NLRs to trigger the immune response. To investigate the mechanism of Pikp-1/Pikp-2 activation, we expressed truncated variants of these proteins, and made mutations in previously identified NLR sequence motifs. We found that any domain truncation, in either Pikp-1 or Pikp-2, prevented cell death in the presence of AVR-PikD, revealing that all domains are required for activity. Further, expression of individual Pikp-1 or Pikp-2 domains did not result in cell death. Mutations in the conserved P-loop and MHD sequence motifs in both Pikp-1 and Pikp-2 prevented cell death activation, demonstrating that these motifs are required for the function of the two partner NLRs. Finally, we showed that Pikp-1 and Pikp-2 associate to form homo- and hetero-complexes in planta in the absence of AVR-PikD; on co-expression the effector binds to Pikp-1 generating a tripartite complex. Taken together, we provide evidence that Pikp-1 and Pikp-2 form a fine-tuned system that is activated by AVR-PikD via receptor cooperation rather than negative regulation.

Elements of the Endomucin Extracellular Domain Essential for VEGF-Induced VEGFR2 Activity

Endomucin (EMCN) is the type I transmembrane glycoprotein, mucin-like component of the endothelial cell glycocalyx. We have previously shown that EMCN is necessary for vascular endothelial growth factor (VEGF)-induced VEGF receptor 2 (VEGFR2) internalization and downstream signaling. To explore the structural components of EMCN that are necessary for its function and the molecular mechanism of EMCN in VEGF-induced endothelial functions, we generated a series of mouse EMCN truncation mutants and examined their ability to rescue VEGF-induced endothelial functions in human primary endothelial cells (EC) in which endogenous EMCN had been knocked down using siRNA. Expression of the mouse full-length EMCN (FL EMCN) and the extracellular domain truncation mutants ∆21-81 EMCN and ∆21-121 EMCN, but not the shortest mutant ∆21-161 EMCN, successfully rescued the VEGF-induced EC migration, tube formation, and proliferation. ∆21-161 EMCN failed to interact with VEGFR2 and did not facilitate VEGFR2 internalization. Deletion of COSMC (C1GalT1C1) revealed that the abundant mucin-type O-glycans were not required for its VEGFR2-related functions. Mutation of the two N-glycosylation sites on ∆21-121 EMCN abolished its interaction with VEGFR2 and its function in VEGFR2 internalization. These results reveal ∆21-121 EMCN as the minimal extracellular domain sufficient for VEGFR2-mediated endothelial function and demonstrate an important role for N-glycosylation in VEGFR2 interaction, internalization, and angiogenic activity.