Natural Biological Systems Research Articles

Macroscopic handedness inversion of terbium coordination polymers achieved by doping homochiral ligand analogues.

Inspired by natural biological systems, chiral or handedness inversion by altering external and internal conditions to influence intermolecular interactions is an attractive topic for regulating chiral self-assembled materials. For coordination polymers, the regulation of their helical handedness remains little reported compared to polymers and supramolecules. In this work, we choose the chiral ligands R-pempH2 (pempH2 = (1-phenylethylamino)methylphosphonic acid) and R-XpempH2 (X = F, Cl, Br) as the second ligand, which can introduce C-H⋯π and C-H⋯X interactions, doped into the reaction system of the Tb(R-cyampH)3·3H2O (cyampH2 = (1-cyclohexylethylamino)methylphosphonic acid) coordination polymer, which itself can form a right-handed superhelix by van der Waals forces, and a series of superhelices R-1H-x, R-2F-x, R-3Cl-x, and R-4Br-x with different doping ratios x were obtained, whose handedness is related to the second ligand and its doping ratio, indicating the decisive role of interchain interactions of different strengths in the helical handedness. This study could provide a new pathway for the design and self-assembly of chiral materials with controllable handedness and help the further understanding of the mechanism of self-assembly of coordination polymers forming macroscopic helical systems.

ОСОБЕННОСТИ ЭКОСИСТЕМЫ БИОЛОГИЧЕСКИХ ПРУДОВ В ПРОЦЕССЕ ЕСТЕСТВЕННОЙ ОЧИСТКИ ЖИВОТНОВОДЧЕСКИХ СТОКОВ

The article presents the indicators of pig manure wastewater treatment in natural biological systems. It has been established that the ecosystem of the biopond cascade is not stable and depends on the temperature conditions of the external environment.

Interfering with Color Response by Porphyrin-Related Compounds in the MTT Tetrazolium-Based Colorimetric Assay.

Porphyrin compounds are widely distributed in various natural products and biological systems. In this study, effects of porphyrin-related compounds including zinc protoporphyrin (ZnPP), protoporphyrin IX (PPIX), cyanocobalamin (CBL), hemin, and zinc phthalocyanine (ZnPC) were analyzed on color response of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) tetrazolium-based assay, a commonly-used method for analyzing cell viability. Color responses of MTT formazan formed in cells treated with ZnPP, PPIX, or ZnPC were significantly reduced even at submicromolar concentrations without affecting cell viability, whereas hemin and CBL did not. ZnPP, PPIX, and ZnPC rapidly induced degradation of MTT formazan already-produced by cells when exposed to light, but not under a dark condition. Photosensitizing properties of the three compounds were also verified through extensive generation of reactive oxygen species under light. The porphyrins did not affect the stability of water-soluble formazans including XTT, WST-1, WST-8, and MTS formazans. Several factors including different light sources and antioxidants modulated the degradation process of MTT formazan by the porphyrins. The results suggest that certain porphyrin compounds could cause a severe artifact in the MTT assay through rapid degradation of formazan dye due to their photosensitizing property, which needs to be considered carefully in the related assays.

Programmable Synthesis of Biobased Materials Using Cell-Free Systems.

Motivated by the intricate mechanisms underlying biomolecule syntheses in cells that chemistry is currently unable to mimic, researchers have harnessed biological systems for manufacturing novel materials. Cell-free systems (CFSs) utilizing the bioactivity of transcriptional and translational machineries in vitro are excellent tools that allow supplementation of exogenous materials for production of innovative materials beyond the capability of natural biological systems. Herein, recent studies that have advanced the ability to expand the scope of biobased materials using CFS are summarized and approaches enabling the production of high-value materials, prototyping of genetic parts and modules, and biofunctionalization are discussed. By extending the reach of chemical and enzymatic reactions complementary to cellular materials, CFSs provide new opportunities at the interface of materials science and synthetic biology.

Stiffness optimization design for TPMS architected cellular materials

The unique topology-driven versatility of natural biological systems has motivated the material science research community to design and synthesize architected cellular materials for different engineering disciplines. However, the lattice cell design of architected cellular materials is highly arbitrary, making the design of architected cellular materials very difficult. In order to overcome these problems, an innovative triple period minimal surface (TPMS) lattice type distribution algorithm based on the maximum strain energy principle is proposed in this paper to optimize the stiffness of the structure. The algorithm establishes the mapping relationship between the relative density of TPMS lattice cells and the surface bias parameter t by generating a voxel model, obtains the equivalent mechanical properties of lattice cells as a function of relative density by homogenization algorithm and function fitting, establishes a TPMS lattice database, and innovatively distributes the TPMS lattice types by selecting the maximum strain energy lattice cells on the basis of the topology optimization results. The experimental results show that the stiffness of the multi-TPMS lattice structure is improved by 55.89% and 30.15%, respectively, compared with the two single lattice structures.

Review article-Amalgamation, scrutinizing, and biological evaluation of the antimicrobial aptitude of thiosemicarbazide Schiff bases derivatives metal complexes

The initial report, there has been a tremendous development of Schiff base ligands and their metal complexes which Since have captured the attention of researchers owing to an increasing number of applications of these compounds to a variety of fields. Thiosemicarbazones owing to their unique characteristics including multiple bonding modes, application as bioinorganic processes because of N, O, and S as donor atoms, excellent complexing ability, and broad-spectrum biological activities with minimum toxicity owing to –N-C = S moiety. The Schiff bases ligands have structural similarities with natural biological systems that’s why metal complexes of Schiff bases derivatives have been applied for catalytic activities and biological studies. Literature supported the practical employment of Schiff bases metal complexes in the area of material science to biological sciences Therefore, the review summarized the amalgamation, scrutinizing and substantiating the antimicrobial aptitude of thiosemicarbazide derivatives of Schiff Bases metal complexes.

Cooperative stability renders protein complex formation more robust and controllable

Protein complexes are the fundamental units of many biological functions. Despite their many advantages, one major adverse impact of protein complexes is accumulations of unassembled subunits that may disrupt other processes or exert cytotoxic effects. Synthesis of excess subunits can be inhibited via negative feedback control or they can be degraded more efficiently than assembled subunits, with this latter being termed cooperative stability. Whereas controlled synthesis of complex subunits has been investigated extensively, how cooperative stability acts in complex formation remains largely unexplored. To fill this knowledge gap, we have built quantitative models of heteromeric complexes with or without cooperative stability and compared their behaviours in the presence of synthesis rate variations. A system displaying cooperative stability is robust against synthesis rate variations as it retains high dimer/monomer ratios across a broad range of parameter configurations. Moreover, cooperative stability can alleviate the constraint of limited supply of a given subunit and makes complex abundance more responsive to unilateral upregulation of another subunit. We also conducted an in silico experiment to comprehensively characterize and compare four types of circuits that incorporate combinations of negative feedback control and cooperative stability in terms of eight systems characteristics pertaining to optimality, robustness and controllability. Intriguingly, though individual circuits prevailed for distinct characteristics, the system with cooperative stability alone achieved the most balanced performance across all characteristics. Our study provides theoretical justification for the contribution of cooperative stability to natural biological systems and represents a guideline for designing synthetic complex formation systems with desirable characteristics.

Geometry and size optimization of stiffener layout for three-dimensional box structures with maximization of natural frequencies

Based on the growth mechanism of natural biological branching systems and inspiration from the morphology of plant root tips, a bionic design method called Improved Adaptive Growth Method (IAGM) has been proposed in the authors’ previous research and successfully applied to the reinforcement optimization of three-dimensional box structures with respect to natural frequencies. However, as a kind of ground structure methods, the final layout patterns of stiffeners obtained by using the IAGM are highly subjected to their ground structures, which restricts the optimization effect and freedom to further improve the dynamic performance of structures. To solve this problem, a novel post-processing geometry and size optimization approach is proposed in this article. This method takes the former layout optimization result as start, and iteratively finds the optimal layout angles, locations, and lengths of stiffeners with a few design variables by optimizing the positions of some specific node lines called active node lines. At the same time, thicknesses of stiffeners are also optimized to further improve natural frequencies of three-dimensional box structures. Using this method, stiffeners can be successfully separated from their ground structures and further effectively improve natural frequencies of three-dimensional box structures with less material consumption. Typical numerical examples are illustrated to validate the effectiveness and advantages of the suggested method.

Recent Advances of Nanomaterials-Based Molecularly Imprinted Electrochemical Sensors.

Molecularly imprinted polymer (MIP) is illustrated as an analogue of a natural biological antibody-antigen system. MIP is an appropriate substrate for electrochemical sensors owing to its binding sites, which match the functional groups and spatial structure of the target analytes. However, the irregular shapes and slow electron transfer rate of MIP limit the sensitivity and conductivity of electrochemical sensors. Nanomaterials, famous for their prominent electron transfer capacity and specific surface area, are increasingly employed in modifications of MIP sensors. Staying ahead of traditional electrochemical sensors, nanomaterials-based MIP sensors represent excellent sensing and recognition capability. This review intends to illustrate their advances over the past five years. Current limitations and development prospects are also discussed.

Recent progress in biologically active indole hybrids: a mini review.

The indole moiety is one of the most widespread heterocycles found in both natural products and biological systems. Indoles have important biological activities including anticancer, antioxidant, anti-inflammatory, antifungal, anticholinesterase, and antibacterial properties. Scientists are therefore interested in the synthesis of biologically active indole-based hybrids such as indole-coumarin, indole-chalcone, indole-isatin, indole-pyrimidine and so on, with the aim of improving activity, selectivity, and mitigating side effects. This review will discuss the newly synthesized indole-based hybrids along with their biological activity which will be useful in drug discovery and development.

Dichotomous feedback: a signal sequestration-based feedback mechanism for biocontroller design

We introduce a new design framework for implementing negative feedback regulation in synthetic biology, which we term ‘dichotomous feedback’. Our approach is different from current methods, in that it sequesters existing fluxes in the process to be controlled, and in this way takes advantage of the process’s architecture to design the control law. This signal sequestration mechanism appears in many natural biological systems and can potentially be easier to realize than ‘molecular sequestration’ and other comparison motifs that are nowadays common in biomolecular feedback control design. The loop is closed by linking the strength of signal sequestration to the process output. Our feedback regulation mechanism is motivated by two-component signalling systems, where a second response regulator could be competing with the natural response regulator thus sequestering kinase activity. Here, dichotomous feedback is established by increasing the concentration of the second response regulator as the level of the output of the natural process increases. Extensive analysis demonstrates how this type of feedback shapes the signal response, attenuates intrinsic noise while increasing robustness and reducing crosstalk.

Suitability and Sensitivity of the Potential Distribution of Cyclobalanopsis glauca Forests under Climate Change Conditions in Guizhou Province, Southwestern China

Global climate change is becoming increasingly prominent and has already begun to influence natural biological systems. Assessing the potential impact of climate change on ecosystems is an important research topic of the International Geosphere-Biosphere Programme (IGBP). Based on current distribution data, climate data, climate change scenarios (RCP8.5 scenario, 2070–2099), and application of the MaxEnt model, this study assessed suitability and sensitivity of the potential distribution of Cyclobalanopsis glauca forests under climate change conditions in Guizhou Province. The results were as follows: (1) Area under the curve values of training data and texting data indicated excellent performance of the model; (2) Compared to the current climate, areas of probability <0.4 were decreased, and the other areas presented an increasing trend under the RCP8.5 scenario; (3) Positive sensitivity areas were much larger than negative sensitivity areas under climate change. In either case, slight sensitivity areas accounted for the largest proportion; (4) The mean altitude of slight sensitivity areas measured the lowest, and highly negative sensitivity areas were the highest.

Computational Design of Single-Peptide Nanocages with Nanoparticle Templating.

Protein complexes perform a diversity of functions in natural biological systems. While computational protein design has enabled the development of symmetric protein complexes with spherical shapes and hollow interiors, the individual subunits often comprise large proteins. Peptides have also been applied to self-assembly, and it is of interest to explore such short sequences as building blocks of large, designed complexes. Coiled-coil peptides are promising subunits as they have a symmetric structure that can undergo further assembly. Here, an α-helical 29-residue peptide that forms a tetrameric coiled coil was computationally designed to assemble into a spherical cage that is approximately 9 nm in diameter and presents an interior cavity. The assembly comprises 48 copies of the designed peptide sequence. The design strategy allowed breaking the side chain conformational symmetry within the peptide dimer that formed the building block (asymmetric unit) of the cage. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) techniques showed that one of the seven designed peptide candidates assembled into individual nanocages of the size and shape. The stability of assembled nanocages was found to be sensitive to the assembly pathway and final solution conditions (pH and ionic strength). The nanocages templated the growth of size-specific Au nanoparticles. The computational design serves to illustrate the possibility of designing target assemblies with pre-determined specific dimensions using short, modular coiled-coil forming peptide sequences.

Heterologous overexpression and preliminary antimicrobial activity test of salmocin M, a novel colicin M-like bacteriocin against Salmonella sp.

Currently, it is extremely important to identify and describe new alternative compounds with potential antimicrobial properties. Since various natural biological systems are capable of producing active compounds with such properties, many of them have been the subject of intensive study. The aim of this work was to heterologously overexpress, purify and preliminarily investigate the antimicrobial activity of a novel bacteriocin found in Salmonella species. Overexpressed protein shows an amino acid structure homologous to the well-known colicin M and was never expressed previously in the E. coli platform. Purified salmocin M showed an inhibition spectrum against Salmonella and E. coli strains. To determine its potential as an antimicrobial agent for use in medicine or the food industry, preliminary antimicrobial tests against pathogenic bacteria were carried out. Our research demonstrates that bacteriocin can be produced efficiently in bacterial expression systems, which are one of the cheapest and the most popular platforms for recombinant protein production. Moreover, preliminary results of microbiological tests showed its activity against most of the bacterial strains in a dose-dependent manner.Graphical abstract

Biodegradability of Polyolefin-Based Compositions: Effect of Natural Rubber.

Recently, environmental problems caused by the overproduction and consumption of synthetic polymer materials led to an urgent need to develop efficient methods for processing plastics. The accumulation of polymer waste for their subsequent incineration does not solve the problem due to the limited areas of landfills for waste storage. In addition, the incineration of polymer waste can cause toxic air pollution, which, in turn, does not contribute to an improvement in the environmental situation. Recycling plastics, although a more environmentally friendly waste disposal method, requires significant labor and energy costs and can be performed a limited number of times. Thus, the most promising solution to this problem is the creation of biodegradable polymers capable of degradation with the formation of simpler chemical structures (water, carbon dioxide, biomass, etc.), which are easily included in the metabolic processes of natural biological systems. The article provides an overview of the main trends in the creation of biodegradable composites for the needs of agriculture. Also, the article proposes a new composition based on polyethylene with natural rubber that surpasses existing biodegradable materials in a number of physical and mechanical characteristics and has the ability to complete biodegradation in 60 months. It is shown that the studies carried out to date indicate that these composites are highly promising for the creation of biodegradable packaging materials with good performance characteristics. Thus, it was concluded that further research on composites based on polyethylene and natural rubber is important.

Photochemistry in a capsule: controlling excited state dynamics via confinement.

Exerting control on excited state processes has been a long-held goal in photochemistry. One approach to achieve control has been to mimic biological systems in Nature (e.g., photosynthesis) that has perfected it over millions of years by performing the reactions in highly organized assemblies such as membranes and proteins by restricting the freedom of reactants and directing them to pursue a select pathway. The duplication of this concept at a smaller scale in the laboratory involves the use of highly confined and organized assemblies as reaction containers. This article summarizes the studies in the author's laboratory using a synthetic, well-defined reaction container known as octa acid (OA). OA, unlike most commonly known cavitands, forms a capsule in water and remains closed during the lifetime of the excited states of included molecules. Thus, the described excited state chemistry occurs in a small space with hydrophobic characteristics. Examples where the photophysical and photochemical properties are dramatically altered, compared to that in organic solvents wherein the molecules are freely soluble, are presented to illustrate the value of a restricted environment in controlling the dynamics of molecules on an excited state surface. While the ground state complexation of the guest and host is controlled by well-known concepts of tight-fit, lock and key, complementarity, etc., free space around the guest is necessary for it to be able to undergo structural transformations in the excited state, where the time is short. This article highlights the role of free space during the dynamics of molecules within a confined, inflexible reaction cavity.

Research progress of bio-inspired radiative cooling

As a new type of cooling technology, radiative cooling achieves temperature reduction through spectral regulation. Compared with the traditional active cooling technologies such as absorption-based cooling and compression-based cooling, the radiative cooling offers unique advantages, which are of great significance in environmental protection and energy utilization. First of all, the basic principle of radiative cooling and the radiative cooling within the natural biological systems are introduced in this review. The biological systems achieve their regulations of radiative cooling through controlling the materials, microstructures and behaviors in the systems, which also provide inspiration for us to explore new radiative cooling materials and devices. We also summarize the various mechanisms of radiative cooling in the biological systems and the optimization of such cooling structures. The recent research progress of bio-inspired radiative cooling is also presented. At the end, the outlook of the research directions, potential applications, and the material fabrication approaches for bio-inspired radiative cooling are discussed. The radiative cooling materials and devices with high power output and intelligent control should be an important development direction of bio-inspired radiative cooling in the future. With the integration of advanced micro/nano fabrication technology, bio-inspired radiative cooling will have a broader market and much room of applications in the future.

Ferric ion detection mechanism of a dicarboxylic cellulose nanocrystal and a 7-amino-4-methylcoumarin based fluorescent chemosensor.

As one of Earth's most widely distributed and abundant elements, iron impacts the natural environment and biological systems. Therefore, developing a simple, rapid, and accurate Fe3+ detection method is vital. Fluorescent dicarboxylic cellulose nanocrystals (FDCN) with selective quenching of Fe3+ were synthesized using 7-amino-4-methylcoumarin (AMC), and dicarboxylic cellulose nanocrystals (DCN) prepared by sequential periodate–chlorite oxidation. The sensing characteristics and detection mechanism of FDCN for Fe3+ were studied by fluorescence spectrophotometry, Fourier-transform infrared spectroscopy (FTIR), the Stern–Volmer equation, Job's plot method, and the Benesi–Hildebrand equation. The results showed that FDCN was highly selective for Fe3+, and other metal ions did not reduce the selectivity. High sensitivity with a detection limit of 0.26 μM and a Stern–Volmer quenching constant of 0.1229 were also achieved. The coordination between Fe3+ and the carboxylic, hydroxyl, and amide groups on the surface of FDCN and the carbonyl of coumarin lactones to form FDCN/Fe3+ complexes prevented the intramolecular charge transfer (ICT) process and led to the fluorescence quenching of FDCN. EDTA restored the fluorescence emission of quenched FDCN. The complexation stoichiometry of Fe3+ to FDCN was 1 : 1, and the association constant was 3.23 × 104 M−1. The high hydrophilicity, sensitivity, and selectivity of FDCN for Fe3+ make the chemosensor suitable for Fe3+ trace detection in drinking water and biology.

Organometallic catalysis in aqueous and biological environments: harnessing the power of metal carbenes.

Translating the power of transition metal catalysis to the native habitats of enzymes can significantly expand the possibilities of interrogating or manipulating natural biological systems, including living cells and organisms. This is especially relevant for organometallic reactions that have shown great potential in the field of organic synthesis, like the metal-catalyzed transfer of carbenes. While, at first sight, performing metal carbene chemistry in aqueous solvents, and especially in biologically relevant mixtures, does not seem obvious, in recent years there has been a growing number of reports demonstrating the feasibility of the task. Either using small molecule metal catalysts or artificial metalloenzymes, a number of carbene transfer reactions that tolerate aqueous and biorelevant media are being developed. This review intends to summarize the most relevant contributions, and establish the state of the art in this emerging research field.

An in situ real time probe spacing correction method for multi-needle heat pulse sap flow sensors

Probe spacing of sap flow sensors affects the quantification of sap flow in plants. The assumption of nocturnal zero flow conditions, required by most non-destructive methods for probe spacing calibration, is often invalid in natural biological systems and extremely hard to validate with in situ measurements. Our study aims to present a novel method for accurate in situ determination of probe spacing. The method uses nonlinear curve fitting with two mathematical models applied during low flow conditions. Numerical simulations were conducted with three types of probe misalignment and demonstrated that errors in heat pulse velocity (Vh) (< 2.0%) is less than the error associated with commonly-used probe spacing correction methods. Field experiment on European beech (Fagus sylvatica L.) comparisons with corrected probe spacing applied to the heat ratio (HR) and Sapflow+ method produced improved sap flux densities, with both methods agreeing very well (root mean square deviation < 1 cm3 cm−2 h−1). The proposed method allows real time probe spacing measurements at low flow rates, alleviating some uncertainties associated with zero flow assumption. The new method can hence successfully be used to estimate in situ probe spacing for operational measurements of sap flux density.