A General Strategy for Extrusion Bioprinting of Bio‐Macromolecular Bioinks through Alginate‐Templated Dual‐Stage Crosslinking

The recently developed 3D bioprinting technology has greatly improved the ability to generate biomimetic tissues that are structurally and functionally relevant to their human counterparts. The selection of proper biomaterials as the bioinks is a key step toward successful bioprinting. For example, viscosity of a bioink is an important rheological parameter to determine the flexibility in deposition of free‐standing structures and the maintenance of architectural integrity following bioprinting. This requirement, however, has greatly limited the selection of bioinks, especially for those naturally derived due to their commonly low mechanical properties. Here the generalization of a mechanism for extrusion bioprinting of bio‐macromolecular components, mainly focusing on collagen and its derivatives including gelatin and gelatin methacryloyl, is reported. Specifically, a templating strategy is adopted using a composite bioink containing both the desired bio‐macromolecular component and a polysaccharide alginate. The physically crosslinkable alginate component serves as the temporal structural support to stabilize the shape of the construct during bioprinting; upon subsequent chemical or physical crosslinking of the bio‐macromolecular component, alginate can be selectively removed to leave only the desired bio‐macromolecule. It is anticipated that this strategy is general, and can be readily expanded for use of a wide variety of other bio‐macromolecular bioinks.     

Biochemical sensors: The state of the art

The basic components of a (bio)chemical sensor and the main concepts involved in the (bio)chemical sensor methodology are considered in order to depict the state of the art of the development of research in this field, paying special attention to the evolution of the published scientific literature in analytical chemistry.     

Roles of paeoniflorin and senkyunolide I in SiWu decoction on antiplatelet and anticoagulation activities

Traditional Chinese medicine (TCM) is a complex system, which consists of numerous compounds with related mechanisms to maximize therapeutic efficacy with minimal adverse effects. Some new methods disclosing the contribution of these constituents as well as their relationship in the formula are necessary for elucidating the bio‐active constituents and the working mechanisms of TCM. In this study, depletion of target components using preparative HPLC followed by antiplatelet and anticoagulation activities evaluation was first applied to investigate the roles of paeoniflorin and senkyunolide I in a well‐known formula, SiWu decoction. The results showed that both paeoniflorin and senkyunolide I not only directly brought about some bio‐activities, but also indirectly made the contribution to the total bio‐activity reflection of SiWu decoction, especially the latter should deserve to be drawn attention to the research of complicated bio‐active constituents of TCM or its formula. So, the significant and effective approach will be very useful for the elucidation of the contribution of each different chemical constituent to the bio‐activity of a TCM formula. Furthermore, this study demonstrated the potential utilization of preparative HPLC in the research of TCM.     

Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs

Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black‐box method that is easily applied, but requires careful set‐up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work‐protocols developed in our groups for running successful QM/MM calculations.     

Threshold Sensing through a Synthetic Enzymatic Reaction–Diffusion Network

A wet stamping method to precisely control concentrations of enzymes and inhibitors in place and time inside layered gels is reported. By combining enzymatic reactions such as autocatalysis and inhibition with spatial delivery of components through soft lithographic techniques, a biochemical reaction network capable of recognizing the spatial distribution of an enzyme was constructed. The experimental method can be used to assess fundamental principles of spatiotemporal order formation in chemical reaction networks.     

Recent progress in plant cell culture

Conclusions Commercial application of plant cell cultures for the production of useful metabolites on a large scale has not yet been realized. However, some recently published papers and patents seem very attractive for industrial use because their results and techniques are apparently applicable to a large-scale production of metabolites. The author believes that commercial success using plant tissue cultures will be realized in the near future with advanced techniques if product selection is determined by economic and political principles. In 1982, the 5th International Congress of Plant Tissue and Cell Culture will be held in Japan and this undoubtedly will encourage research activity in our country.     

Peptide Nanomaterials Designed from Natural Supramolecular Systems

Natural supramolecular assemblies exhibit unique structural and functional properties that have been optimized over the course of evolution. Inspired by these natural systems, various bio‐nanomaterials have been developed using peptides, proteins, and nucleic acids as components. Peptides are attractive building blocks because they enable the important domains of natural protein assemblies to be isolated and optimized while retaining the original structures and functions. Furthermore, the peptide subunits can be conjugated with exogenous molecules such as peptides, proteins, nucleic acids, and metal nanoparticles to generate advanced functions. In this personal account, we summarize recent progress in the construction of peptide‐based nanomaterial designed from natural supramolecular systems, including (1) artificial viral capsids, (2) self‐assembled nanofibers, and (3) protein‐binding motifs. The peptides inspired by nature should provide new design principles for bio‐nanomaterials.     

Light‐Triggered Multifunctionality at Surfaces Mediated by Photolabile Protecting Groups

Photoremovable protecting groups (PRPGs) are applied to organic surfaces, thin polymer films, and hydrogels to achieve light‐based remote control of their (bio)chemical and physical properties. These can be localized (i.e. patterned), tunable by exposure dose, and generated on‐demand. Using PRPGs with independent response to different wavelengths, multifunctional materials with a number of individually addressable functional states can be generated. Light‐triggered polymerization, crosslinking, and degradation processes as well as release of attached molecules can be realized. Light‐responsive surfaces and materials based on PRPGs open interesting possibilities for the next generation of instructive materials for cell culture and tissue regeneration.     

Molecular computing: paths to chemical Turing machines

To comply with the rapidly increasing demand of information storage and processing, new strategies for computing are needed. The idea of molecular computing, where basic computations occur through molecular, supramolecular, or biomolecular approaches, rather than electronically, has long captivated researchers. The prospects of using molecules and (bio)macromolecules for computing is not without precedent. Nature is replete with examples where the handling and storing of data occurs with high efficiencies, low energy costs, and high-density information encoding. The design and assembly of computers that function according to the universal approaches of computing, such as those in a Turing machine, might be realized in a chemical way in the future; this is both fascinating and extremely challenging. In this perspective, we highlight molecular and (bio)macromolecular systems that have been designed and synthesized so far with the objective of using them for computing purposes. We also present a blueprint of a molecular Turing machine, which is based on a catalytic device that glides along a polymer tape and, while moving, prints binary information on this tape in the form of oxygen atoms.     

Umweltprobenbanken-eine wichtige Säule der Umweltbeobachtung

Natural events as well as human activities are affecting the environment and even with largescale monitoring programs it is not possible to completely assess the state of the environment. But a documentation of the environmental status with respect to its chemical composition can be realized with systematically collected representative environmental samples, which can be stored for decades at very low temperatures almost without degradation. Such ‘banking activity’ allows a current environmental monitoring and also a retrospective analysis for the determination of components which have not been analyzed at the time of sampling because of ta lack in analytical techniques or because they have not been known or considered environmentally relevant. The concept of environmental specimen banking and general procedures are described. Various examples illustrate the many facets of such activities.     

Functionalized Silicas for Metal‐Free and Metal‐Based Catalytic Applications: A Review in Perspective of Green Chemistry

Heterogeneous catalysis plays a key role in promoting green chemistry through many routes. The functionalizable reactive silanols highlight silica as a beguiling support for the preparation of heterogeneous catalysts. Metal active sites anchored on functionalized silica (FS) usually demonstrate the better dispersion and stability due to their firm chemical interaction with FSs. Having certain functional groups in structure, FSs can act as the useful catalysts for few organic reactions even without the need of metal active sites which are termed as the covetous reusable organocatalysts. Magnetic FSs have laid the platform where the effortless recovery of catalysts is realized just using an external magnet, resulting in the simplified reaction procedure. Using FSs of multiple functional groups, we can envisage the shortened reaction pathway and, reduced chemical uses and chemical wastes. Unstable bio‐molecules like enzymes have been stabilized when they get chemically anchored on FSs. The resultant solid bio‐catalysts exhibited very good reusability in many catalytic reactions. Getting provoked from the green chemistry aspects and benefits of FS‐based catalysts, we confer the recent literature and progress focusing on the significance of FSs in heterogeneous catalysis. This review covers the preparative methods, types and catalytic applications of FSs. A special emphasis is given to the metal‐free FS catalysts, multiple FS‐based catalysts and magnetic FSs. Through this review, we presume that the contribution of FSs to green chemistry can be well understood. The future perspective of FSs and the improvements still required for implementing FS‐based catalysts in practical applications have been narrated at the end of this review.     

Nanoparticles for the development of improved (bio)sensing systems

Nanoparticles serve as fundamental building blocks for nanobiotechnology, especially in several applications in the development of novel (bio)sensing systems. Nanoparticles can be used for modification of the surfaces of (bio)sensing transducers or as optical or electroactive labels to improve different aspects of performance, for example sensitivity, detection limit, multidetection capability, and response stability. Nanoparticles can be integrated into the transducer materials on an individual basis or inside other matrices to ensure the immobilization of recognition biomolecules and/or receptors which are the principal components of the (bio)sensing systems. Incorporation of nanoparticles into optical and electrochemical (bio)sensing systems, including their use in microfluidic based systems has the advantages of enabling the design of robust, easy to use, portable, and cost-effective devices.     

Nachhaltige Bausteine für die Kunststoff‐Herstellung

Plant oils are currently the principle resource for the production of bio‐based, high performance polymers, such as polyamides. This process is facilitated by giant strides in chemical catalysis and biotechnology, which allows conversion of vegetable oils in “drop‐in” chemical building blocks. These bio‐based polymer building blocks have equivalent chemical and physical properties as well as similar cost structures compared to conventional petrochemical synthesis feedstock. This allows integration of bio‐based resources into industrial production processes without significant adaptations in logistics or process configuration. However, only use of synergies between chemical and biotechnological unit operations will in future provide for sustainable and eco‐efficient process designs. To allow sustainable supply of bio‐oils to a growing chemical industry without a significant impact on food production demands development of alternative bio‐oil sourcing strategies. In this respect the development of processes for the production of microbial oils, which have equivalent chemical properties to their plant counterparts is imperative. One leading option is the biotechnological conversion of agricultural and food waste streams into microbial oils by combining enzymatic hydrolysis and fermentative production using oleaginous organisms, such as yeasts.     

Predicting the chemical reactivity of organic materials using a machine-learning approach

Stability and compatibility between chemical components are essential parameters that need to be considered in the selection of functional materials in configuring a system. In configuring devices such as batteries or solar cells, not only the functionality of individual constituting materials such as electrodes or electrolyte but also an appropriate combination of materials which do not undergo unwanted side reactions is critical in ensuring their reliable performance in long-term operation. While the universal theory that can predict the general chemical reactivity between materials is long awaited and has been the subject of studies with a rich history, traditional ways proposed to date have been mostly based on simple electronic properties of materials such as electronegativity, ionization energy, electron affinity and hardness/softness, and could be applied to only a small group of materials. Moreover, prediction has often been far from accurate and has failed to offer general implications; thus it was practically inadequate as a selection criterion from a large material database, i.e. data-driven material discovery. Herein, we propose a new model for predicting the general reactivity and chemical compatibility among a large number of organic materials, realized by a machine-learning approach. As a showcase, we demonstrate that our new implemented model successfully reproduces previous experimental results reported on side-reactions occurring in lithium–oxygen electrochemical cells. Furthermore, the mapping of chemical stability among more than 90 available electrolyte solvents and the representative redox mediators is realized by this approach, presenting an important guideline in the development of stable electrolyte/redox mediator couples for lithium–oxygen batteries.

Stability and compatibility between chemical components are essential parameters that need to be considered in the selection of functional materials in configuring a system.     

Reagentless fluorescent biosensors based on proteins for continuous monitoring systems

There is a lack of commercially available efficient and autonomous systems capable of continuous monitoring of (bio)chemical data for clinical, environmental, food, or industrial samples. The weakest link in the design of these systems is the (bio)chemical receptor (bCR). The bCR should have transducer ability, the recognition event should be a single reaction, and the bCR should be easily regenerated. Transport proteins and enzymes are well placed as bCR for optical continuous monitoring systems (OCMS). In this paper we review quantitative aspects and the main transducer strategies which have been developed for transport proteins, using periplasmic binding proteins (linking an environmentally sensitive fluorophore or FRET between two fluorophores) and concanavalin A (competitive reversible assays) as representative examples. Efficient immobilization systems and implementation in OCMS are also reviewed. Some kinds of enzymes can fulfil the necessary requirements to be appropriate bCR. Strategies using flavoenzymes chemically modified with fluorophores can be successfully implemented in OCMS and they are, in our opinion, the most appropriate option.     

Microfluidics in the “Open Space” for Performing Localized Chemistry on Biological Interfaces

Local interactions between (bio)chemicals and biological interfaces play an important role in fields ranging from surface patterning to cell toxicology. These interactions can be studied using microfluidic systems that operate in the “open space”, that is, without the need for the sealed channels and chambers commonly used in microfluidics. This emerging class of techniques localizes chemical reactions on biological interfaces or specimens without imposing significant “constraints” on samples, such as encapsulation, pre‐processing steps, or the need for scaffolds. They therefore provide new opportunities for handling, analyzing, and interacting with biological samples. The motivation for performing localized chemistry is discussed, as are the requirements imposed on localization techniques. Three classes of microfluidic systems operating in the open space, based on microelectrochemistry, multiphase transport, and hydrodynamic flow confinement of liquids are presented.     

A simple protocol for the comparative analysis of the structure and occurrence of biochemical pathways across superkingdoms

A biochemical pathway can be viewed as a series of chemical reactions occurring within a cell, each of which is carried out by one or more biological macromolecules (protein, RNA, or complexes thereof). Computational methods can be applied to assess whether one organism is able to perform a biochemical process of interest by checking whether its genome encodes all the components that are known to be necessary for the task. Here we present a simple strategy for collecting the above data that is based on, but not limited to, our experience on processes involving metal ions and metal-binding cofactors. The strategy is fully implemented in a bioinformatics package, Retrieval of Domains and Genome Browsing (RDGB), which is available from http://www.cerm.unifi.it/home/research/genomebrowsing.html . The use of RDGB allows users to perform all the operations that are needed to implement the aforementioned strategy with minimal intervention and to gather all results in an ordered manner, with a tabular summary. This minimizes the (bio)informatics needed, thus facilitating its use by nonexperts. As examples, we analyzed the pathways for the degradation of organic compounds containing one or two aromatic rings as well as the distribution of some proteins involved in Cu(A) assembly in more than a thousand prokaryotes.     

Interfacing the GROMOS (bio)molecular simulation software to quantum‐chemical program packages

The newly implemented quantum‐chemical/molecular‐mechanical (QM/MM) functionality of the Groningen molecular simulation (GROMOS) software for (bio)molecular simulation is described. The implementation scheme is based on direct coupling of the GROMOS C++ software to executables of the quantum‐chemical program packages MNDO and TURBOMOLE, allowing for an independent further development of these packages. The new functions are validated for different test systems using program and model testing techniques. The effect of truncating the QM/MM electrostatic interactions at various QM/MM cutoff radii is discussed and the application of semiempirical versus density‐functional Hamiltonians for a solute molecule in aqueous solution is compared. © 2012 Wiley Periodicals, Inc.     

Isotope dilution analysis for elemental speciation: a tutorial review

The identification and/or determination of the different (bio)chemical forms in which an element can be present in a given sample is called “speciation analysis.” In many cases, qualitative information is not enough and methods for the accurate and precise determination of the identified species need to be developed. In this review, we describe in some depth one of the most accurate approaches developed so far for such purpose: the application of isotope dilution analysis to quantitative elemental speciation.     

Liquid exclusion adsorption chromatography, a new technique for isocratic separation of nonionic surfactants. III. Two-dimensional separation of fatty alcohol ethoxylates

In this paper, a novel procedure for qualitative and quantitative analysis of the two-dimensional data obtained from GC-MS is investigated to determine chemical components of essential oils in Cortex Cinnamomi from four different producing areas. A new method named iterative optimization procedure (IOP) specially used to resolve embedded peaks is also developed. With the help of IOP and other chemometric techniques, such as heuristic evolving latent projections, evolving factor analysis, sub-window factor analysis and orthogonal projection resolution, and etc., the detection of the purity of chromatographic peaks can be first addressed, and then the overlapping peaks are resolved into the pure chromatogram and mass spectrum of each component. The similarity searches in the MS database are finally conducted to qualitatively determine the chemical components. The results obtained showed that the accuracy of qualitative and quantitative analysis could be greatly enhanced by chemometric resolution methods. The chemometric resolution techniques upon the two-dimensional data can be quite promising tools for the analysis of the complex samples like traditional Chinese medicine.