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Lignocellulose feedstock (LCF) provides a sustainable source of components to produce bioenergy, biofuel, and novel biomaterials. Besides hard and soft wood, so-called low-input plants such as Miscanthus are interesting crops to be investigated as potential feedstock for the second generation biorefinery. The status quo regarding the availability and composition of different plants, including grasses and fast-growing trees (i.e., Miscanthus, Paulownia), is reviewed here. The second focus of this review is the potential of multivariate data processing to be used for biomass analysis and quality control. Experimental data obtained by spectroscopic methods, such as nuclear magnetic resonance (NMR) and Fourier-transform infrared spectroscopy (FTIR), can be processed using computational techniques to characterize the 3D structure and energetic properties of the feedstock building blocks, including complex linkages. Here, we provide a brief summary of recently reported experimental data for structural analysis of LCF biomasses, and give our perspectives on the role of chemometrics in understanding and elucidating on LCF composition and lignin 3D structure.
The antiradical and antimicrobial activity of lignin and lignin-based films are both of great interest for applications such as food packaging additives. The polyphenolic structure of lignin in addition to the presence of O-containing functional groups is potentially responsible for these activities. This study used DPPH assays to discuss the antiradical activity of HPMC/lignin and HPMC/lignin/chitosan films. The scavenging activity (SA) of both binary (HPMC/lignin) and ternary (HPMC/lignin/chitosan) systems was affected by the percentage of the added lignin: the 5% addition showed the highest activity and the 30% addition had the lowest. Both scavenging activity and antimicrobial activity are dependent on the biomass source showing the following trend: organosolv of softwood > kraft of softwood > organosolv of grass. Testing the antimicrobial activities of lignins and lignin-containing films showed high antimicrobial activities against Gram-positive and Gram-negative bacteria at 35 °C and at low temperatures (0-7 °C). Purification of kraft lignin has a negative effect on the antimicrobial activity while storage has positive effect. The lignin release in the produced films affected the activity positively and the chitosan addition enhances the activity even more for both Gram-positive and Gram-negative bacteria. Testing the films against spoilage bacteria that grow at low temperatures revealed the activity of the 30% addition on HPMC/L1 film against both B. thermosphacta and P. fluorescens while L5 was active only against B. thermosphacta. In HPMC/lignin/chitosan films, the 5% addition exhibited activity against both B. thermosphacta and P. fluorescens.
Miscanthus x giganteus Stem Versus Leaf-Derived Lignins Differing in Monolignol Ratio and Linkage
(2019)
As a renewable, Miscanthus offers numerous advantages such as high photosynthesis activity (as a C4 plant) and an exceptional CO2 fixation rate. These properties make Miscanthus very attractive for industrial exploitation, such as lignin generation. In this paper, we present a systematic study analyzing the correlation of the lignin structure with the Miscanthus genotype and plant portion (stem versus leaf). Specifically, the ratio of the three monolignols and corresponding building blocks as well as the linkages formed between the units have been studied. The lignin amount has been determined for M. x giganteus (Gig17, Gig34, Gig35), M. nagara (NagG10), M. sinensis (Sin2), and M. robustus (Rob4) harvested at different time points (September, December, and April). The influence of the Miscanthus genotype and plant component (leaf vs. stem) has been studied to develop corresponding structure-property relationships (i.e., correlations in molecular weight, polydispersity, and decomposition temperature). Lignin isolation was performed using non-catalyzed organosolv pulping and the structure analysis includes compositional analysis, Fourier transform infradred (FTIR), ultraviolet/visible (UV-Vis), hetero-nuclear single quantum correlation nuclear magnetic resonsnce (HSQC-NMR), thermogravimetric analysis (TGA), and pyrolysis gaschromatography/mass spectrometry (GC/MS). Structural differences were found for stem and leaf-derived lignins. Compared to beech wood lignins, Miscanthus lignins possess lower molecular weight and narrow polydispersities (<1.5 Miscanthus vs. >2.5 beech) corresponding to improved homogeneity. In addition to conventional univariate analysis of FTIR spectra, multivariate chemometrics revealed distinct differences for aromatic in-plane deformations of stem versus leaf-derived lignins. These results emphasize the potential of Miscanthus as a low-input resource and a Miscanthus-derived lignin as promising agricultural feedstock.
Herein we report an update to ACPYPE, a Python3 tool that now properly converts AMBER to GROMACS topologies for force fields that utilize nondefault and nonuniform 1–4 electrostatic and nonbonded scaling factors or negative dihedral force constants. Prior to this work, ACPYPE only converted AMBER topologies that used uniform, default 1–4 scaling factors and positive dihedral force constants. We demonstrate that the updated ACPYPE accurately transfers the GLYCAM06 force field from AMBER to GROMACS topology files, which employs non-uniform 1–4 scaling factors as well as negative dihedral force constants. Validation was performed using β-d-GlcNAc through gas-phase analysis of dihedral energy curves and probability density functions. The updated ACPYPE retains all of its original functionality, but now allows the simulation of complex glycomolecular systems in GROMACS using AMBER-originated force fields. ACPYPE is available for download at https://github.com/alanwilter/acpype.
Bond graph software can simulate bond graph models without the user needing to manually derive equations. This offers the power to model larger and more complex systems than in the past. Multibond graphs (those with vector bonds) offer a compact model which further eases handling multibody systems. Although multibond graphs can be simulated successfully, the use of vector bonds can present difficulties. In addition, most qualitative, bond graph–based exploitation relies on the use of scalar bonds. This article discusses the main methods for simulating bond graphs of multibody systems, using a graphical software platform. The transformation between models with vector and scalar bonds is presented. The methods are then compared with respect to both time and accuracy, through simulation of two benchmark models. This article is a tutorial on the existing methods for simulating three-dimensional rigid and holonomic multibody systems using bond graphs and discusses the difficulties encountered. It then proposes and adapts methods for simulating this type of system directly from its bond graph within a software package. The value of this study is in giving practical guidance to modellers, so that they can implement the adapted method in software.
Intact Transition Epitope Mapping - Targeted High-Energy Rupture of Extracted Epitopes (ITEM-THREE)
(2019)
Epitope mapping, which is the identification of antigenic determinants, is essential for the design of novel antibody-based therapeutics and diagnostic tools. ITEM-THREE is a mass spectrometry-based epitope mapping method that can identify epitopes on antigens upon generating an immune complex in electrospray-compatible solutions by adding an antibody of interest to a mixture of peptides from which at least one holds the antibody's epitope. This mixture is nano-electrosprayed without purification. Identification of the epitope peptide is performed within a mass spectrometer that provides an ion mobility cell sandwiched in-between two collision cells and where this ion manipulation setup is flanked by a quadrupole mass analyzer on one side and a time-of-flight mass analyzer on the other side. In a stepwise fashion, immune-complex ions are separated from unbound peptide ions and dissociated to release epitope peptide ions. Immune complex-released peptide ions are separated from antibody ions and fragmented by collision induced dissociation. Epitope-containing peptide fragment ions are recorded, and mass lists are submitted to unsupervised data base search thereby retrieving both, the amino acid sequence of the epitope peptide and the originating antigen. ITEM-THREE was developed with antiTRIM21 and antiRA33 antibodies for which the epitopes were known, subjecting them to mixtures of synthetic peptides of which one contained the respective epitope. ITEM-THREE was then successfully tested with an enzymatic digest of His-tagged recombinant human β-actin and an antiHis-tag antibody, as well as with an enzymatic digest of recombinant human TNFα and an antiTNFα antibody whose epitope was previously unknown.
This work addresses the issue of finding an optimal flight zone for a side-by-side tracking and following Unmanned Aerial Vehicle(UAV) adhering to space-restricting factors brought upon by a dynamic Vector Field Extraction (VFE) algorithm. The VFE algorithm demands a relatively perpendicular field of view of the UAV to the tracked vehicle, thereby enforcing the space-restricting factors which are distance, angle and altitude. The objective of the UAV is to perform side-by-side tracking and following of a lightweight ground vehicle while acquiring high quality video of tufts attached to the side of the tracked vehicle. The recorded video is supplied to the VFE algorithm that produces the positions and deformations of the tufts over time as they interact with the surrounding air, resulting in an airflow model of the tracked vehicle. The present limitations of wind tunnel tests and computational fluid dynamics simulation suggest the use of a UAV for real world evaluation of the aerodynamic properties of the vehicle’s exterior. The novelty of the proposed approach is alluded to defining the specific flight zone restricting factors while adhering to the VFE algorithm, where as a result we were capable of formalizing a locally-static and a globally-dynamic geofence attached to the tracked vehicle and enclosing the UAV.
Plant sap-feeding insects are widespread, having evolved to occupy diverse environmental niches despite exclusive feeding on an impoverished diet lacking in essential amino acids and vitamins. Success depends exquisitely on their symbiotic relationships with microbial symbionts housed within specialized eukaryotic bacteriocyte cells. Each bacteriocyte is packed with symbionts that are individually surrounded by a host-derived symbiosomal membrane representing the absolute host-symbiont interface. The symbiosomal membrane must be a dynamic and selectively permeable structure to enable bidirectional and differential movement of essential nutrients, metabolites, and biosynthetic intermediates, vital for growth and survival of host and symbiont. However, despite this crucial role, the molecular basis of membrane transport across the symbiosomal membrane remains unresolved in all bacteriocyte-containing insects. A transport protein was immuno-localized to the symbiosomal membrane separating the pea aphid Acyrthosiphon pisum from its intracellular symbiont Buchnera aphidicola. The transporter, A. pisum nonessential amino acid transporter 1, or ApNEAAT1 (gene: ACYPI008971), was characterized functionally following heterologous expression in Xenopus oocytes, and mediates both inward and outward transport of small dipolar amino acids (serine, proline, cysteine, alanine, glycine). Electroneutral ApNEAAT1 transport is driven by amino acid concentration gradients and is not coupled to transmembrane ion gradients. Previous metabolite profiling of hemolymph and bacteriocyte, alongside metabolic pathway analysis in host and symbiont, enable prediction of a physiological role for ApNEAAT1 in bidirectional host-symbiont amino acid transfer, supplying both host and symbiont with indispensable nutrients and biosynthetic precursors to facilitate metabolic complementarity.
We present a systematization of usable security principles, guidelines and patterns to facilitate the transfer of existing knowledge to researchers and practitioners. Based on a literature review, we extracted 23 principles, 11 guidelines and 47 patterns for usable security and identified their interconnection. The results indicate that current research tends to focus on only a subset of important principles. The fact that some principles are not yet addressed by any design patterns suggests that further work on refining these patterns is needed. We developed an online repository, which stores the harmonized principles, guidelines and patterns. The tool enables users to search for relevant guidance and explore it in an interactive and programmatic manner. We argue that both the insights presented in this article and the web-based repository will be highly valuable for students to get a good overview, practitioners to implement usable security and researchers to identify areas of future research.
Scratch assays enable the study of the migration process of an injured adherent cell layer in vitro. An apparatus for the reproducible performance of scratch assays and cell harvesting has been developed that meets the requirements for reproducibility in tests as well as easy handling. The entirely autoclavable setup is divided into a sample translation and a scratching system. The translational system is compatible with standard culture dishes and can be modified to adapt to different cell culture systems, while the scratching system can be adjusted according to angle, normal force, shape, and material to adapt to specific questions and demanding substrates. As a result, a fully functional prototype can be presented. This system enables the creation of reproducible and clear scratch edges with a low scratch border roughness within a monolayer of cells. Moreover, the apparatus allows the collection of the migrated cells after scratching for further molecular biological investigations without the need for a second processing step. For comparison, the mechanical properties of manually performed scratch assays are evaluated.
Bioinspired stem cell-based hard tissue engineering includes numerous aspects: The synthesis and fabrication of appropriate scaffold materials, their analytical characterization, and guided osteogenesis using the sustained release of osteoinducing and/or osteoconducting drugs for mesenchymal stem cell differentiation, growth, and proliferation. Here, the effect of silicon- and silicate-containing materials on osteogenesis at the molecular level has been a particular focus within the last decade. This review summarizes recently published scientific results, including material developments and analysis, with a special focus on silicon hybrid bone composites. First, the sources, bioavailability, and functions of silicon on various tissues are discussed. The second focus is on the effects of calcium-silicate biomineralization and corresponding analytical methods in investigating osteogenesis and bone formation. Finally, recent developments in the manufacturing of Si-containing scaffolds are discussed, including in vitro and in vivo studies, as well as recently filed patents that focus on the influence of silicon on hard tissue formation.
The choice of suitable semiconducting metal oxide (MOX) gas sensors for the detection of a specific gas or gas mixture is time-consuming since the sensor’s sensitivity needs to be characterized at multiple temperatures to find its optimal operating conditions. To obtain reliable measurement results, it is very important that the power for the sensor’s integrated heater is stable, regulated and error-free (or error-tolerant). Especially the error-free requirement can be only be achieved if the power supply implements failure-avoiding and failure-detection methods. The biggest challenge is deriving multiple different voltages from a common supply in an efficient way while keeping the system as small and lightweight as possible. This work presents a reliable, compact, embedded system that addresses the power supply requirements for fully automated simultaneous sensor characterization for up to 16 sensors at multiple temperatures. The system implements efficient (avg. 83.3% efficiency) voltage conversion with low ripple output (<32 mV) and supports static or temperature-cycled heating modes. Voltage and current of each channel are constantly monitored and regulated to guarantee reliable operation. To evaluate the proposed design, 16 sensors were screened. The results are shown in the experimental part of this work.