Natural Biological Systems Research Articles

State-of-the-Art Review of Enzyme-Induced Calcite Precipitation (EICP) for Ground Improvement: Applications and Prospects

The global construction industry consumes huge amounts of mined materials that are considered unsustainable for earth resources. In addition, Portland cement which is a key element in concrete and most construction materials is considered one of the main contributors to worldwide CO2 emissions. On the other hand, natural cemented soil deposits are examples of sustainable structures that have survived decades of severe environmental conditions. Mimicking these natural biological systems provide an alternative to the current practices of construction materials production. Enzyme-induced carbonate precipitation (EICP) is a bio-inspired technique based on the precipitation of calcium carbonate for enhancing the geo-mechanical properties of soils. In this technique, calcium carbonate acts as a cementitious agent that binds the soil particles together at the points of contact, hence, increasing the strength and stiffness of treated soils, while relatively reducing the soil permeability and porosity. The achieved enhancements make EICP useful for applications such as ground improvement, construction materials, and erosion control over traditional binders. This paper presents a state-of-the-art review of EICP for ground improvement including the fundamental basics of EICP treatment. The paper also discusses the chemical and physical factors affecting the performance of EICP such as enzyme source, enzyme activity and solution constitutes. Moreover, the paper reviews the different methods and testing techniques used in the application of EICP for soil treatment. Furthermore, the paper compares EICP with other biomineralization techniques in terms of performance and applicability on ground improvement. Finally, the paper discusses the research gaps and existing challenges concerning the commercialization and large-scale implementation of the technology.

Highly selective and sensitive fluorescent probe possessing AIEE and ICT properties for rapid detection of Pb2+ in aqueous medium and its applications in living cells.

In this paper, a novel rapid, highly selective and sensitive Pb2+ fluorescent probe (E)-N'-((2-(4'-(diphenylamino)-[1,1'-biphenyl]-4-yl)-2H-1,2,3-triazol-4-yl)methylene) (DBTBH) was synthesized. The probe DBTBH not only exhibited more excellent selectivity and sensitivity to Pb2+ detection compared with other analytes (include metal ions and anions) in H2 O:THF solution (v:v = 9:1, 10 mM Tris-HCl, 1 mM KI, pH 7.4), but also had excellent optical properties such as aggregation-induced emission enhancement (AIEE) and intramolecular charge transfer (ICT). Detection limit of the probe DBTBH towards Pb2+ was 4.49 × 10-8 M. The possible mechanism was verified by 1 H NMR titration and HR-MS. Furthermore, the successful detection of Pb2+ by DBTBH in real water samples and HeLa cells indicated that DBTBH has great potential for selective recognition of Pb2+ in the natural environment and biological systems. These findings will provide a promising new idea for designing better Pb2+ fluorescent probes in the future.

Biosynthesis of iron oxide nanoparticles from dates, characterization, and investigation of anticarcinogenic and antimicrobial properties

Nanomaterial synthesis using natural biological systems, especially plant-based green synthesis has evinced great excitement and interest. In this study, iron oxide nanomaterials were synthesized from three different varieties of date palms obtained from Srivilliputhur, Tamil Nadu, India. The extract of date palms reduced ferric chloride in solution and facilitated the formation of iron oxide nanomaterials. Phytochemical studies of the extracts obtained from all three varieties of date palms indicated the presence of phenols. The synthesized nanomaterials were characterized by UV-VIS spectroscopy, SEM, EDAX, XRD and FTIR methods. The ability of the synthesized nanomaterials to inhibit human microbial pathogens proliferation was tested in Staphylococcus sp. and Bacillus sp. by turbidity method and recorded the maximum antimicrobial property against Bacillus sp. in the iron nanomaterial synthesized from Sukhri date palm. The cytotoxic potential of the iron oxide nanomaterials was assessed against two human cancer cell lines (A-549 and MDA-MB-231) by MTT assay. The substantial cytotoxicity response was detected from the iron oxide nanomaterials made from Sukhri date palm.

"Minimal metabolism": A key concept to investigate the origins and nature of biological systems.

The systems view on life and its emergence from complex chemistry has remarkably increased the scientific attention on metabolism in the last two decades. However, during this time there has not been much theoretical discussion on what constitutes a metabolism and what role it actually played in biogenesis. A critical and updated review on the topic is here offered, including some references to classical models from last century, but focusing more on current and future research. Metabolism is considered as intrinsically related to the living but not necessarily equivalent to it. More precisely, the idea of "minimal metabolism", in contrast to previous, top-down conceptions, is formulated as a heuristic construct, halfway between chemistry and biology. Thus, rather than providing a complete or final characterization of metabolism, our aim is to encourage further investigations on it, particularly in the context of life's origin, for which some concrete methodological suggestions are provided. Also see the video abstract here: https://youtu.be/DP7VMKk2qpA.

Green Synthesis of Nanomaterials.

Nanotechnology is considered one of the paramount forefronts in science over the last decade. Its versatile implementations and fast-growing demand have paved the way for innovative measures for the synthesis of higher quality nanomaterials. In the early stages, traditional synthesis methods were utilized, and they relied on both carcinogenic chemicals and high energy input for production of nano-sized material. The pollution produced as a result of traditional synthesis methods induces a need for environmentally safer synthesis methods. As the downfalls of climate change become more abundant, the scientific community is persistently seeking solutions to combat the devastation caused by toxic production methods. Green methods for nanomaterial synthesis apply natural biological systems to nanomaterial production. The present review highlights the history of nanoparticle synthesis, starting with traditional methods and progressing towards green methods. Green synthesis is a method just as effective, if not more so, than traditional synthesis; it provides a sustainable approach to nanomaterial manufacturing by using naturally sourced starting materials and relying on low energy processes. The recent use of active molecules in natural biological systems such as bacteria, yeast, algae and fungi report successful results in the synthesis of various nanoparticle systems. Thus, the integration of green synthesis in scientific research and mass production provides a potential solution to the limitations of traditional synthesis methods.

Biophysical Measurement Strategies for Antiviral Drug Development: Recent Progress in Virus-Mimetic Platforms Down to the Single Particle Level.

The rapid growth in the global human population has increased the prevalence of emerging infectious diseases, which poses a major risk to public health. In search of effective clinical solutions, the acquisition of knowledge and understanding of biomolecular processes associated with viral pathogens represents a prerequisite. In this context, biophysical engineering approaches are particularly promising since they can resolve biomolecular interactions systematically by circumventing the complexities associated with experiments involving natural biological systems. The engineering approaches encompass the design and construction of biomimetic platforms that simulate the physiological system. This approach enables us to characterize, measure, and quantitatively analyze biomolecular interactions.In this Account, we summarize biophysical measurements that our group has successfully adopted to develop broad-spectrum antiviral drugs based on the lipid envelope antiviral disruption (LEAD) strategy, targeting the structural integrity of the outer viral membrane to abrogate viral infectivity. We particularly focus on the engineering aspects related to the design and construction of the tethered lipid vesicle platform, which closely mimics the viral membrane. We first outline the development of the LEAD agents screening platform that integrates soft matter design components with biomaterials and surface functionalization strategies to facilitate parallel measurements tracking peptide-induced destabilization of nanoscale, virus-mimicking vesicles with tunable size and composition. Then, we describe how this platform can be effectively employed to gain insights into the membrane curvature dependency of certain peptides. The fundamental knowledge acquired through this systematic process is crucial in the identification and subsequent development of antiviral drug candidates. In particular, we highlight the development of curvature-sensitive α-helical (AH) peptides as a broad-spectrum antiviral agent that has been demonstrated as an effective therapeutic treatment against multiple enveloped viruses. Also, we introduce a tethered cluster of vesicles to mimic clusters of enveloped viruses, exhibiting higher infectivity levels in the biological system. Then, we discuss key considerations, including experimental artifacts, namely dye leakage and imaging-related photobleaching, and corresponding corrective measures to improve the accuracy of quantitative interpretation. With the ongoing development and application of the tethered lipid vesicle platform, there is a compelling opportunity to explore fundamental biointerfacial science and develop a new class of broad-spectrum antiviral agents to prepare for the future membrane-enveloped viral pandemics.

A isophorone based colorimetric and ratiometric probe: Synthesis and rapid detection of cyanide in aqueous medium and its application in bioimaging

A simple colorimetric and fluorescent sensor for cyanide based on phenolic substituted dicyanoisophorone derivative (2) has been synthesized. The absorption spectra of chemosensor 2 showed large bathochromic shift (ca. 240 nm) upon titration with CN− while the solution color changed from yellow to green. The absorption ratios (A685/A446) responses of chemosensor 2 showed a favorable linear relationship with the CN− concentration and the detection limitation had been calculated to be 0.15 μM. Meanwhile, the fluorescence intensity of 2 can be quenched upon reacting with CN− over other anions. More importantly, chemosensor 2 can react instantaneously with cyanide in aqueous solution, and to visualize CN− in living HeLa cells by means of dramatic decrease of fluorescence intensity. Thus, the present sensor could be applicable in detecting cyanide ion both in natural water samples and biological systems conveniently.

INFLUENCE OF MAGNESIUM (Mg) SOURCE ON THE Cordyceps militaris (L.) MUSHROOM MYCELIUM GROWTH

Magnesium (Mg) is an element with a role in oxidation processes. The optimal concentration of magnesium for the development of fungi is associated with an optimal concentration of phosphorus (P), which through its essential constituents, is an important element for the existence of biological systems in nature through nucleic acids, phospholipids, phosphoglycerides, phytin and phosphates. Magnesium has a role in the activity of certain enzymes and in respiration, being a component of protein substances with a special importance for microorganisms being included in reducing and phosphorylating enzymes and for protein synthesis. In this study, magnesium sulphate (MgSO4), which is an accessible source of both magnesium and sulphur, as well as magnesium carbonate (MgCO3) were used as sources of magnesium, both being used in different concentrations in the growth medium. The culture medium or substrate influences the growth of the fungal mycelium, through the mineral, nutritive and stimulating substances in their composition. Using experimental culture media, an isolated tissue culture was performed from 2 strains of Cordyceps militaris (L.) fungus. The culture was performed in Petri dishes, incubated at a temperature of 24 ° C, aiming to increase the mycelium for 15 days. The highest increase was recorded by strain CI 32 with the addition of magnesium sulphate.

Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers.

Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.

Key interactions with deazariboflavin cofactor for light-driven energy transfer in Xenopus (6\u20134) photolyase

Photolyases are flavoenzymes responsible for light-driven repair of carcinogenic crosslinks formed in DNA by UV exposure. They possess two non-covalently bound chromophores: flavin adenine dinucleotide (FAD) as a catalytic center and an auxiliary antenna chromophore that harvests photons and transfers solar energy to the catalytic center. Although the energy transfer reaction has been characterized by time-resolved spectroscopy, it is strikingly important to understand how well natural biological systems organize the chromophores for the efficient energy transfer. Here, we comprehensively characterized the binding of 8-hydroxy-7,8-didemethyl-5-deazariboflavin (8-HDF) to Xenopus (6–4) photolyase. In silico simulations indicated that a hydrophobic amino acid residue located at the entrance of the binding site dominates translocation of a loop upon binding of 8-HDF, and a mutation of this residue caused dysfunction of the efficient energy transfer in the DNA repair reaction. Mutational analyses of the protein combined with modification of the chromophore suggested that Coulombic interactions between positively charged residues in the protein and the phenoxide moiety in 8-HDF play a key role in accommodation of 8-HDF in the proper direction. This study provides a clear evidence that Xenopus (6–4) photolyase can utilize 8-HDF as the light-harvesting chromophore. The obtained new insights into binding of the natural antenna molecule will be helpful for the development of artificial light-harvesting chromophores and future characterization of the energy transfer in (6–4) photolyase by spectroscopic studies.

Співпраця України та ЄС у сфері сталого розвитку: огляд перспектив

The results of the study of the concept of sustainable development and the benefits of implementing this concept in Ukraine based on the experience of the European Union are presented. It is established that the basis for the formation of the basic principles of sustainable development is the relationship of environmental, economic and social factors of human development, the solution of which is possible only on a comprehensive basis, taking into account the balance of interests of nature and society. Peculiarities of cooperation between Ukraine and the EU in the field of sustainable development are analyzed. The concept of sustainable development involves the identification of three approaches: economic, social and environmental, reflecting their particular importance, the existence of interconnections and interdependencies, while ignoring at least one of them can undermine the overall stability of the system. The economic approach in the concept of sustainable development is based on the need for rational use of scarce resources at the disposal of society and the use of environmentally friendly methods of production and technology. An important aspect of social stability is the fair distribution of goods. The environmental component is intended to ensure the integrity of physical and biological natural systems in the process of their interaction with economic and social systems The necessity for Ukraine to form and implement new directions is substantiated state investment policy, due to economic and social reforms aimed at economic growth, the formation of new ones effective mechanisms for attracting investment, creating conditions for implementation conceptual foundations of the strategy of sustainable development and ensuring European integration processes. These sustainable development components reflect a single value creation process and characterize individual aspects of human activity that reflect a single value creation process. The necessity of rational use of limited resources at the disposal of society and the use of environmentally friendly methods of production and technologies are pointed out. The importance of a clear understanding of the mechanisms of interaction between environmental, social and economic components of the concept that serve as a means of achieving development goals is determined.

Synthetic neural-like computing in microbial consortia for pattern recognition

Complex biological systems in nature comprise cells that act collectively to solve sophisticated tasks. Synthetic biological systems, in contrast, are designed for specific tasks, following computational principles including logic gates and analog design. Yet such approaches cannot be easily adapted for multiple tasks in biological contexts. Alternatively, artificial neural networks, comprised of flexible interactions for computation, support adaptive designs and are adopted for diverse applications. Here, motivated by the structural similarity between artificial neural networks and cellular networks, we implement neural-like computing in bacteria consortia for recognizing patterns. Specifically, receiver bacteria collectively interact with sender bacteria for decision-making through quorum sensing. Input patterns formed by chemical inducers activate senders to produce signaling molecules at varying levels. These levels, which act as weights, are programmed by tuning the sender promoter strength Furthermore, a gradient descent based algorithm that enables weights optimization was developed. Weights were experimentally examined for recognizing 3 × 3-bit pattern.

Recent Progress in the Design and Medical Application of In Situ Self-Assembled Polypeptide Materials.

Inspired by molecular self-assembly, which is ubiquitous in natural environments and biological systems, self-assembled peptides have become a research hotspot in the biomedical field due to their inherent biocompatibility and biodegradability, properties that are afforded by the amide linkages forming the peptide backbone. This review summarizes the biological advantages, principles, and design strategies of self-assembled polypeptide systems. We then focus on the latest advances in in situ self-assembly of polypeptides in medical applications, such as oncotherapy, materials science, regenerative medicine, and drug delivery, and then briefly discuss their potential challenges in clinical treatment.

Back to the Future: Reintegrating Biology to Understand How Past Eco-evolutionary Change Can Predict Future Outcomes.

During the last few decades, biologists have made remarkable progress in understanding the fundamental processes that shape life. But despite the unprecedented level of knowledge now available, large gaps still remain in our understanding of the complex interplay of eco-evolutionary mechanisms across scales of life. Rapidly changing environments on Earth provide a pressing need to understand the potential implications of eco-evolutionary dynamics, which can be achieved by improving existing eco-evolutionary models and fostering convergence among the sub-fields of biology. We propose a new, data-driven approach that harnesses our knowledge of the functioning of biological systems to expand current conceptual frameworks and develop corresponding models that can more accurately represent and predict future eco-evolutionary outcomes. We suggest a roadmap toward achieving this goal. This long-term vision will move biology in a direction that can wield these predictive models for scientific applications that benefit humanity and increase the resilience of natural biological systems. We identify short, medium, and long-term key objectives to connect our current state of knowledge to this long-term vision, iteratively progressing across three stages: (1) utilizing knowledge of biological systems to better inform eco-evolutionary models, (2) generating models with more accurate predictions, and (3) applying predictive models to benefit the biosphere. Within each stage, we outline avenues of investigation and scientific applications related to the timescales over which evolution occurs, the parameter space of eco-evolutionary processes, and the dynamic interactions between these mechanisms. The ability to accurately model, monitor, and anticipate eco-evolutionary changes would be transformational to humanity's interaction with the global environment, providing novel tools to benefit human health, protect the natural world, and manage our planet's biosphere.

Intelligent Polymers, Fibers and Applications.

Intelligent materials, also known as smart materials, are capable of reacting to various external stimuli or environmental changes by rearranging their structure at a molecular level and adapting functionality accordingly. The initial concept of the intelligence of a material originated from the natural biological system, following the sensing–reacting–learning mechanism. The dynamic and adaptive nature, along with the immediate responsiveness, of the polymer- and fiber-based smart materials have increased their global demand in both academia and industry. In this manuscript, the most recent progress in smart materials with various features is reviewed with a focus on their applications in diverse fields. Moreover, their performance and working mechanisms, based on different physical, chemical and biological stimuli, such as temperature, electric and magnetic field, deformation, pH and enzymes, are summarized. Finally, the study is concluded by highlighting the existing challenges and future opportunities in the field of intelligent materials.

An Overview of Herbal Antiviral Compounds Against Dengue Virus (A. Aegypti)

Dengue is the current prevalent disease caused by vector A. aegypti having four serotypes DENV 1,2,3,4. Natural biological systems are disrupted by the repeated use of synthetic repellants and often result in the development of resistance against dengue virus. These problems have emphasized the need for the development of new strategies for the selective control of mosquito larvae. Therefore antiviral active compounds are extracted from natural herbs to treat dengue virus. The aim of this paper is to review some opportunities in the development of anti-dengue drugs from celery, black seed, ponneem, Cucurbitaceae U. tomentosa, Gastrodiaelata Bl, L. alba and L. citriodora, Vitextrifolia and citrus plants like lemon, orange which might be helpful to control the epidemic.

BioMaster: An Integrated Database and Analytic Platform to Provide Comprehensive Information About BioBrick Parts.

Synthetic biology seeks to create new biological parts, devices, and systems, and to reconfigure existing natural biological systems for custom-designed purposes. The standardized BioBrick parts are the foundation of synthetic biology. The incomplete and flawed metadata of BioBrick parts, however, are a major obstacle for designing genetic circuit easily, quickly, and accurately. Here, a database termed BioMaster http://www.biomaster-uestc.cn was developed to extensively complement information about BioBrick parts, which includes 47,934 items of BioBrick parts from the international Genetically Engineered Machine (iGEM) Registry with more comprehensive information integrated from 10 databases, providing corresponding information about functions, activities, interactions, and related literature. Moreover, BioMaster is also a user-friendly platform for retrieval and analyses of relevant information on BioBrick parts.

Methodology for sustainable development of industrial ecosystems

The article contains methodological aspects of sustainable development of industrial ecosystems. The relevance of the study is confirmed by the fact that the promotion of inclusive and sustainable industry and further investment in physical infrastructure, innovation and research are essential for long-term economic development. It has been concluded that the COVID-19 pandemic has such destabilizing consequences that it threatens to halt or even reverse progress towards the Sustainable Development Goals. However, a fairly rapid recovery of industry after coping with the coronavirus pandemic is possible, unlike the economy as a whole, which will require a much longer recovery period. The article proposes the architecture of the methodology for the sustainable development of industrial ecosystems, which includes five levels (paradigm, meta-level, ontology, meanings and directly ecosystem level). The paradigm in the study is the super task, the mental model of the transition to a new economy, to a new way of industrial production, to a new thinking. The meta-level of methodology is represented by the principles of sustainable development of industrial ecosystems, theoretical provisions (hypotheses, fundamental approaches, basic theories, laws of development). At the ontological level, the methodology for the sustainable development of industrial ecosystems uses digital twins, basic organizational and managerial mechanisms (procedures, tools, structures). The semantic level includes a conceptual apparatus (glossary), as well as applied theories and concepts of the sustainable development of industrial ecosystems. The ecosystem level of the methodology for sustainable development of industrial ecosystems combines the concepts of economic, ecological and natural-biological systems. The sustainable development of the industrial ecosystem is proposed to be managed at six levels (methodological, ideological, conceptual, modelling, application and technology). The conclusion concluded that an ecosystem-based economic model achieves the highest production efficiency compared to a traditional economy model and a platform-based digital model.

Parasitemia Evaluation in Mice Infected with Schistosoma mansoni.

Schistosomiasis is a neglected tropical disease. Its treatment relies on the use of a single drug, praziquantel. Due to treatment limitations, an alternative for schistosomiasis chemotherapy is required; thus, a better understanding of parasite biology and host-parasite interactions is valuable to aid the identification of new anti-Schistosoma drugs. The parasite has a complex life cycle, which results in challenges regarding the evaluation of Schistosoma mansoni development and mammalian infection establishment. Accordingly, this protocol describes methodologies to evaluate: (1) adult worm growth; (2) reproduction; and (3) granuloma formation; and consequently allows more comprehensive knowledge of S. mansoni development in a natural biological system.

Digital twin for smart electricity distribution networks

This paper presents the results of composing a digital model of critical states of the power distribution network with intelligent control. A specific example of a power network with thirty transformer substations connected by main and reserve cables is discussed. The analysis of critical events occurring in the power system was carried out, and a set of decision rules was formed to counter these events. A practical need was noted for regular updating and expansion of the list of critical events and corresponding parrying rules. It is shown that it is expedient to use faceted active neural networks with a structure similar to that of the controlled object as a digital twin model of intelligent control of the system under consideration. The use of such neural networks based on the rule “one event - one ensemble of neurons” provides the digital duplicate model with the ability to unlimited cumulative expansion, similar to the evolutionary property of natural biological systems.