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This comprehensive review explores the cutting-edge advancements in snake venom research, focusing on the integration of proteomics, genomics, transcriptomics, and bioinformatics. Highlighting the transformative impact of these technologies, the review delves into the genetic and ecological factors driving venom evolution, the complex molecular composition of venoms, and the regulatory mechanisms underlying toxin production. The application of synthetic biology and multi-omics approaches, collectively known as venomics, has revolutionized the field, providing deeper insights into venom function and its therapeutic potential. Despite significant progress, challenges such as the functional characterization of toxins and the development of cost-effective antivenoms remain. This review also discusses the future directions of venom research, emphasizing the need for interdisciplinary collaborations and new technologies (mRNAs, cryo-electron microscopy for structural determinations of toxin complexes, synthetic biology, and other technologies) to fully harness the biomedical potential of venoms and toxins from snakes and other animals. [ABSTRACT FROM AUTHOR]

Vanilla flavour is widely used in various industries and is the most broadly used flavouring agent in the food industry. The demand for this flavour is, therefore, extremely high, yet vanilla bean extracts can only meet about 1% of the overall demand. Vanillin, the main constituent of vanilla flavour, can easily be obtained through chemical synthesis. Nonetheless, consumer demands for natural products and environmentally friendly industrial processes drive the development of biotechnological approaches for its production. Some microorganisms can naturally produce vanillin when fed with various substrates, including eugenol, isoeugenol, and ferulic acid. The characterisation of the genes and enzymes involved in these bioconversion pathways, as well as progress in the understanding of vanillin biosynthesis in Vanilla orchids, allowed the development of genetic engineering and synthetic biology approaches to increase vanillin production in naturally vanillin-producing microorganisms, or to implement novel vanillin biosynthetic pathways in microbial chassis. This review summarises and discusses these genetic engineering and synthetic biology approaches for the microbial production of vanillin. [ABSTRACT FROM AUTHOR]

Panax japonicus C. A. Meyer is renowned for its significant therapeutic effects and is commonly used worldwide. Its active ingredients, triterpenoid saponins, show variation in content among different tissues. The tissue-specific distribution of saponins is potentially related to the expression of vital genes in the biosynthesis pathway. In this study, the contents of five saponins (ginsenoside Ro, chikusetsusaponin IV, chikusetsusaponin IVa, ginsenoside Rg1, and ginsenoside Rb1) in three different tissues were determined by HPLC. Transcriptome sequencing analysis identified differentially expressed genes (DEGs) involved in triterpenoid saponin biosynthesis, highlighting significant correlations between saponin contents and the expression levels of 10 cytochrome p450 monooxygenase (CYP) and 3 UDP-glycosyltransferase (UGT) genes. Cloning, sequencing, and prokaryotic expression of UGT genes confirmed the molecular weights of UGT proteins. Gene sequence alignment and phylogenetic analysis provided preliminary insights into UGT gene functions. Meanwhile, the function of one UGT gene was characterized in the yeast. These findings advance our understanding of the triterpenoid saponin biosynthesis in P. japonicus and support future research in traditional Chinese medicine (TCM) and synthetic biology. [ABSTRACT FROM AUTHOR]

The document "Microalgae Biotechnology: Methods and Applications" discusses the potential of microalgae as sustainable chassis for biotechnology, emphasizing their ability to produce valuable compounds and remediate pollutants. Advances in genetic tools and techniques, such as CRISPR/Cas9, are crucial for enhancing microalgal biotechnology. The document also highlights the use of synthetic biology to produce antimicrobial peptides in microalgae, offering a sustainable solution to combat antibiotic resistance. Additionally, innovations in cost-effective microalgae cultivation techniques, such as optimized culture mediums and photobioreactors, are essential for making microalgal products economically viable. [Extracted from the article]

Vesicular stomatitis virus (VSV) is a prototype RNA virus that has been instrumental in advancing our understanding of viral molecular biology and has applications in vaccine development, cancer therapy, antiviral screening, and more. Current VSV genome plasmids for purchase or contract virus services provide limited options for modification, restricted to predefined cloning sites and insert locations. Improved methods and tools to engineer VSV will unlock further insights into long-standing virology questions and new opportunities for innovative therapies. Here, we report the design and construction of a full-length VSV genome. The 11,161 base pair synthetic VSV (synVSV) was assembled from four modularized DNA fragments. Following rescue and titration, phenotypic analysis showed no significant differences between natural and synthetic viruses. To demonstrate the utility of a synthetic virology platform, we then engineered VSV with a foreign glycoprotein, a common use case for studying viral entry and developing anti-virals. To show the freedom of design afforded by this platform, we then modified the genome of VSV by rearranging the gene order, switching the positions of VSV-P and VSV-M genes. This work represents a significant technical advance, providing a flexible, cost-efficient platform for the rapid construction of VSV genomes, facilitating the development of innovative therapies. [ABSTRACT FROM AUTHOR]

The field of computational protein engineering has been transformed by recent advancements in machine learning, artificial intelligence, and molecular modeling, enabling the design of proteins with unprecedented precision and functionality. Computational methods now play a crucial role in enhancing the stability, activity, and specificity of proteins for diverse applications in biotechnology and medicine. Techniques such as deep learning, reinforcement learning, and transfer learning have dramatically improved protein structure prediction, optimization of binding affinities, and enzyme design. These innovations have streamlined the process of protein engineering by allowing the rapid generation of targeted libraries, reducing experimental sampling, and enabling the rational design of proteins with tailored properties. Furthermore, the integration of computational approaches with high-throughput experimental techniques has facilitated the development of multifunctional proteins and novel therapeutics. However, challenges remain in bridging the gap between computational predictions and experimental validation and in addressing ethical concerns related to AI-driven protein design. This review provides a comprehensive overview of the current state and future directions of computational methods in protein engineering, emphasizing their transformative potential in creating next-generation biologics and advancing synthetic biology. [ABSTRACT FROM AUTHOR]

Synthetic biology has advanced in creating artificial microbial and algal communities, but technical and evolutionary complexities still pose significant challenges. Traditional methods, like microscopy and pigment analysis, are limited in throughput and resolution. In contrast, advancements in full-spectrum cytometry enabled high-throughput, multidimensional analysis of single cells based on size, complexity, and spectral fingerprints, offering more precision and flexibility than conventional flow cytometry. This study uses full-spectrum cytometry to analyze synthetic algal–microbial communities, enabling rapid species identification and enumeration. The workflow involves recording individual spectral signatures from monocultures, using autofluorescence to capture populations of interest, and creating a spectral library for further analysis. This spectral library was used for the analysis of the synthetic phytoplankton communities, revealing differences in spectral signatures. Moreover, the synthetic consortium experiment monitored algal growth, comparing results from different instruments, highlighting the advantages of the spectral virtual filter system for precise population separation and abundance tracking. By capturing the entire emission spectrum of each cell, this method enhances understanding of algal–microbial community dynamics and responses to environmental stressors. The development of standardized spectral libraries would improve the characterization of algal communities, further advancing synthetic biology and phytoplankton ecology research. [ABSTRACT FROM AUTHOR]

This document is an editorial from the International Journal of Molecular Sciences titled "Application of Nanostructures in Biology and Medicine." It discusses the wide range of applications for nanomaterials in various fields, including energy, medicine, and industry. The document highlights the potential of nanoparticles and nanodevices in areas such as synthetic biology, drug delivery platforms, brain-computer interfaces, nanoelectronics, nanophotonics, and quantum communications technologies. The editorial also provides an overview of recent research in applied nanoscience, including materials science, chemistry, molecular and cell biology, and biotechnology. It features specific studies on the use of microparticles in pharmaceutics, metal-based nanoparticles in cancer therapy, nanoparticles in combating animal diseases, nanoparticles in wastewater treatment, chemical applications of mesoporous nanomaterials, and a new approach to assessing cell viability for implant development. [Extracted from the article]

Ginkgo biloba is an ancient plant that has survived up until the present day. Gingko biloba is a rich source of valuable secondary metabolites, particularly terpene trilactones (TTLs) such as ginkgolides and bilobalides, which are obtained from the leaves and seeds of the plant. TTLs have pharmacological properties, including anticancer, anti-dementia, antidepressant, antidiabetic, anti-inflammatory, anti-hypertensive, antiplatelet, immunomodulatory, and neuroprotective effects. However, ginkgo is a very-slow-growing tree that takes approximately 30 years to reach maturity. In addition, the accumulation of TTLs in these plants is affected by age, sex, and seasonal and geographical variations. Therefore, plant cell cultures have been established in ginkgo to produce TTLs. Extensive investigations have been conducted to optimize the culture media, growth regulators, nutrients, immobilization, elicitation, and precursor-feeding strategies for the production of TTLs in vitro. In addition, metabolic engineering and synthetic biology methods have been used for the heterologous production of TTLs. In this review, we present the research strategies applied to cell cultures for the production of TTLs. [ABSTRACT FROM AUTHOR]

Cell-free protein synthesis (CFPS) has emerged as a powerful tool for protein production, with applications ranging from basic research to biotechnology and pharmaceutical development. However, enhancing the efficiency of CFPS systems remains a crucial challenge for realizing their full potential. Computational strategies offer promising avenues for optimizing CFPS efficiency by providing insights into complex biological processes and enabling rational design approaches. This review provides a comprehensive overview of the computational approaches aimed at enhancing CFPS efficiency. The introduction outlines the significance of CFPS and the role of computational methods in addressing efficiency limitations. It discusses mathematical modeling and simulation-based approaches for predicting protein synthesis kinetics and optimizing CFPS reactions. The review also delves into the design of DNA templates, including codon optimization strategies and mRNA secondary structure prediction tools, to improve protein synthesis efficiency. Furthermore, it explores computational techniques for engineering cell-free transcription and translation machinery, such as the rational design of expression systems and the predictive modeling of ribosome dynamics. The predictive modeling of metabolic pathways and the energy utilization in CFPS systems is also discussed, highlighting metabolic flux analysis and resource allocation strategies. Machine learning and artificial intelligence approaches are being increasingly employed for CFPS optimization, including neural network models, deep learning algorithms, and reinforcement learning for adaptive control. This review presents case studies showcasing successful CFPS optimization using computational methods and discusses applications in synthetic biology, biotechnology, and pharmaceuticals. The challenges and limitations of current computational approaches are addressed, along with future perspectives and emerging trends, such as the integration of multi-omics data and advances in high-throughput screening. The conclusion summarizes key findings, discusses implications for future research directions and applications, and emphasizes opportunities for interdisciplinary collaboration. This review offers valuable insights and prospects regarding computational strategies to enhance CFPS efficiency. It serves as a comprehensive resource, consolidating current knowledge in the field and guiding further advancements. [ABSTRACT FROM AUTHOR]

Punicic acid (PuA) is a conjugated fatty acid with a wide range of nutraceutical properties naturally present in pomegranate seed oil. To meet the rising demand for pomegranate seed oil, a single-cell oil enriched in PuA provides a sustainable biomass-derived alternative. This study describes the production of a PuA-enriched single-cell oil through the engineering of the red yeast Rhodotorula toruloides grown in glucose and a low-cost substrate, crude glycerol. The gene for Punica granatum fatty acid conjugase, PgFADX, was randomly integrated into the genome of R. toruloides without disrupting the carotenoid synthesis. In shake flask studies, the effects of three promoters (PPGI1, PNAR1, and PPMA1) on PuA production were evaluated. PuA titers of 105.77 mg/L and 72.81 mg/L were obtained from engineered cells expressing PgFADX from the PPMA1 promoter cultivated for 72 h in glucose and for 168 h in crude glycerol, respectively. Furthermore, the detailed lipid analysis revealed a high enrichment PuA in the triacylglycerol lipid structures, even without substantial modifications to the metabolic pathways. This report demonstrates the high potential of R. toruloides in the upcycling of a low-cost substrate, crude glycerol, into a value-added product such as PuA. The findings support the feasibility of using engineered R. toruloides for sustainable production of PuA-enriched single-cell oil. [ABSTRACT FROM AUTHOR]

Simple Summary: Rice production is strongly affected by environmental stresses such as drought, heat and salt. Rice plants have developed intricate molecular mechanisms to deal with these challenges. Researchers have identified crucial genes, proteins and metabolic pathways involved in these responses through transcriptomic and proteomic studies. Understanding these molecular mechanisms can help in developing new stress-resistant varieties, thus ensuring stable production under adverse environmental conditions. This review aims to provide a straightforward summary of the progress in understanding the molecular mechanisms of rice's response to various environmental stresses through transcriptomic and proteomic studies. Rice (Oryza sativa L.) is grown nearly worldwide and is a staple food for more than half of the world's population. With the rise in extreme weather and climate events, there is an urgent need to decode the complex mechanisms of rice's response to environmental stress and to breed high-yield, high-quality and stress-resistant varieties. Over the past few decades, significant advancements in molecular biology have led to the widespread use of several omics methodologies to study all aspects of plant growth, development and environmental adaptation. Transcriptomics and proteomics have become the most popular techniques used to investigate plants' stress-responsive mechanisms despite the complexity of the underlying molecular landscapes. This review offers a comprehensive and current summary of how transcriptomics and proteomics together reveal the molecular details of rice's response to environmental stresses. It also provides a catalog of the current applications of omics in comprehending this imperative crop in relation to stress tolerance improvement and breeding. The evaluation of recent advances in CRISPR/Cas-based genome editing and the application of synthetic biology technologies highlights the possibility of expediting the development of rice cultivars that are resistant to stress and suited to various agroecological environments. [ABSTRACT FROM AUTHOR]

The broad range of applications offered by synthetic biology and bioengineering has revolutionized the ability to design and redesign microorganisms to express specific functions, overcoming the limitations of natural biological systems. This advancement has been achieved through the use of mathematical models and genetic circuits, enabling the precise design of synthetic microbial communities. These are defined as artificially created communities through co-cultures of selected species that share similar characteristics and environments. Reprogramming an organism is carried out by inserting synthetic genetic circuits, which are designed in a controlled manner to obtain biotechnological products beneficial to humans, their health, and the environment. The potential applications in medicine, bioremediation, industry, and pharmaceuticals make the research of synthetic microbial communities a promising field for the future. However, the implementation of synthetic microbial communities carries potential risks, such as horizontal gene transfer and possible environmental impacts. It is crucial to carefully evaluate these functions and risks, considering biocontainment and the associated ethical and ecological implications. [ABSTRACT FROM AUTHOR]

Borosins are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) with α-N-methylated backbones. Although the first mature compound of borosin was reported in 1997, the biosynthetic pathway was elucidated 20 years later. Until this work, borosins have been able to be categorized into 11 types based on the features of their protein structure and core peptides. Type III borosins were reported only in fungi initially. In order to explore the sources and potential of type III borosins, a precise genome mining work of type III borosins was conducted in bacteria and KchMA's self-methylation activity was validated by biochemical experiment. Furthermore, a commercial protease and AI-assisted rational design was employed to engineer KchMA for the capacity to produce various N-methylated peptides. Our work demonstrates that type III borosins are abundant not only in eukaryotes but also in bacteria and have immense potential as a tool for synthetic biology. [ABSTRACT FROM AUTHOR]

Exploiting the inherent compatibility of DNA-based data storage with living cells, various cellular recording approaches have been developed for recording and retrieving biologically relevant signals in otherwise inaccessible locations, such as inside the body. This review provides an overview of the current state of engineered cellular memory systems, highlighting their design principles, advantages, and limitations. We examine various technologies, including CRISPR-Cas systems, recombinases, retrons, and DNA methylation, that enable these recording systems. Additionally, we discuss potential strategies for improving recording accuracy, scalability, and durability to address current limitations in the field. This emerging modality of biological measurement will be key to gaining novel insights into diverse biological processes and fostering the development of various biotechnological applications, from environmental sensing to disease monitoring and beyond. [ABSTRACT FROM AUTHOR]

Plastic wastes, widely distributed in the environment, can be transformed into microplastics, posing a huge threat to ecosystems and human health due to their stability and adsorbability to other toxic pollutants (e.g., heavy metals and antibiotics). Recently, microbial degradation of (micro)plastics has gained widespread attention because of its green and sustainable properties. Microbial degradation of (micro)plastics is based on the cascade effects of various enzymes secreted by microorganisms, which can convert (micro)plastics into oligomers and monomers, or even mineralize them into CO2 and H2O. The microbial degradation of (micro)plastics is affected by multiple factors, such as microbial species, plastic properties, and environmental conditions. Currently, limited efficient plastic-degrading microorganisms have been discovered, and their degradation mechanisms are still unclear. Furthermore, the efficiency of microbial degradation needs to be improved for future application. Therefore, this review systematically summarizes the sources and properties of existing plastics, identifies pure cultures and mixed cultures for plastic degradation, and examines their influencing factors. In particular, the microbial degradation behaviors of (micro)plastics, including relevant enzymes, degradation efficiency, and degradation mechanisms, were thoroughly discussed. Additionally, the augmentation technologies coupling with microbial degradation, such as advanced oxidation, electrochemical, and genetic engineering technologies, were introduced and highlighted for their potential prospects. This review provides a reference for future research and development of (micro)plastic biodegradation technology. [ABSTRACT FROM AUTHOR]

This comprehensive review investigates the potential of cyanobacteria, particularly nitrogen-fixing strains, in addressing global challenges pertaining to plastic pollution and carbon emissions. By analyzing the distinctive characteristics of cyanobacteria, including their minimal growth requirements, high photosynthetic efficiency, and rapid growth rates, this study elucidates their crucial role in transforming carbon sequestration, biofuel generation, and biodegradable plastic production. The investigation emphasizes cyanobacteria's efficiency in photosynthesis, positioning them as optimal candidates for cost-effective bioplastic production with minimized land usage. Furthermore, the study explores their unconventional yet promising utilization in biodiesel production, mitigating environmental concerns such as sulfur emissions and the presence of aromatic hydrocarbons. The resulting biodiesel exhibits significant combustion potential, establishing cyanobacteria as a viable option for sustainable biofuel production. Through a comprehensive assessment of both achievements and challenges encountered during the commercialization process, this review offers valuable insights into the diverse contributions of cyanobacteria. Its objective is to provide guidance to researchers, policymakers, and industries interested in harnessing bio-inspired approaches for structural and sustainable applications, thereby advancing global efforts towards environmentally conscious plastic and biofuel production. [ABSTRACT FROM AUTHOR]

Creating propositions for the near and distant future requires a design to catch the tide of the times and move with or against trends. In addition, appropriate, adaptable, flexible, and transformational projects are needed in light of changes in science, technology, social, economic, political, and demographic fields over time. Humanity is facing a period in which science and developing technologies will be even more important in solving food safety, health, and environmental problems. Adapting to and mitigating climate change; reducing pollution, waste, and biodiversity loss; and feeding a growing global population with safe food are key challenges facing the agri-food industry and the food supply chain, requiring systemic transformation in agricultural systems and sustainable future agri-food. The aim of this review is to compile scientific evidence and data, define, and create strategies for the future in terms of food security, safety, and sufficiency; future sustainable foods and alternative protein sources; factors affecting food and nutrition security and agriculture; and promising food systems such as functional foods, novel foods, synthetic biology, and 3D food printing. In this review, the safety, conservation, nutritional, sensory, welfare, and potential challenges and limitations of food systems and the opportunities to overcome them on the basis of new approaches, innovative interpretations, future possibilities, and technologies are discussed. Additionally, this review also offers suggestions for future research and food trends in light of future perspectives. This article focuses on future sustainable foods, alternative protein sources, and novel efficient food systems, highlights scientific and technological advances and new research directions, and provides a significant perspective on sustainability. [ABSTRACT FROM AUTHOR]

The development of cross-reactive vaccines is one of the central aims of modern vaccinology. Continuous mutation and the emergence of new SARS-CoV-2 variants and subvariants create the problem of universal coronavirus vaccine design. Previously, the authors devised three recombinant coronavirus antigens, which were based on the sequence collected in 2019 (the Wuhan variant) and produced in an E. coli bacterial expression system. The present work has shown, for the first time, that these recombinant antigens induce the production of antibodies that clearly interact with produced in CHO full-length S-protein of the Omicron variant. The immunogenicity of these recombinant antigens was studied in formulations with different adjuvants: Freund's adjuvant, Al(OH)3 and an adjuvant based on spherical particles (SPs), which are structurally modified plant virus. All adjuvanted formulations effectively stimulated Omicron-specific IgG production in mice. These universal coronavirus antigens could be considered the main component for the further development of broad-spectrum coronavirus vaccines for the prevention of SARS-CoV-2 infection. The present work also provides evidence that the synthetic biology approach is a promising strategy for the development of highly cross-reactive vaccines. Moreover, it is important to note that the bacterial expression system might be appropriate for the production of antigenically active universal antigens. [ABSTRACT FROM AUTHOR]

Advancements in D-allulose production have seen significant strides in recent years, focusing on enzymatic conversion methods. Key developments include traditional immobilization techniques, the discovery of novel enzymes, directed evolution studies, and biosynthesis through metabolic pathway modification. Enzymatic conversion, particularly utilizing D-allulose 3-epimerase, remains fundamental for industrial-scale production. Innovative immobilization strategies, such as functionalized nano-beads and magnetic MOF nanoparticles, have significantly enhanced enzyme stability and reusability. Directed evolution has led to improved enzyme thermostability and catalytic efficiency, while synthetic biology methods, including phosphorylation-driven and thermodynamics-driven pathways, have optimized production processes. High-throughput screening methods have been crucial in identifying and refining enzyme variants for industrial applications. Collectively, these advancements not only enhance production efficiency and cost-effectiveness but also adhere to sustainable and economically viable manufacturing practices. The past five years have witnessed critical developments with significant potential impact on the commercial viability and global demand for allulose. [ABSTRACT FROM AUTHOR]

Cis-regulatory elements (CREs) play a pivotal role in orchestrating interactions with trans-regulatory factors such as transcription factors, RNA-binding proteins, and noncoding RNAs. These interactions are fundamental to the molecular architecture underpinning complex and diverse biological functions in living organisms, facilitating a myriad of sophisticated and dynamic processes. The rapid advancement in the identification and characterization of these regulatory elements has been marked by initiatives such as the Encyclopedia of DNA Elements (ENCODE) project, which represents a significant milestone in the field. Concurrently, the development of CRE detection technologies, exemplified by massively parallel reporter assays, has progressed at an impressive pace, providing powerful tools for CRE discovery. The exponential growth of multimodal functional genomic data has necessitated the application of advanced analytical methods. Deep learning algorithms, particularly large language models, have emerged as invaluable tools for deconstructing the intricate nucleotide sequences governing CRE function. These advancements facilitate precise predictions of CRE activity and enable the de novo design of CREs. A deeper understanding of CRE operational dynamics is crucial for harnessing their versatile regulatory properties. Such insights are instrumental in refining gene therapy techniques, enhancing the efficacy of selective breeding programs, pushing the boundaries of genetic innovation, and opening new possibilities in microbial synthetic biology. [ABSTRACT FROM AUTHOR]

This article discusses the use of filamentous fungi as industrial strains for the production of high-value compounds. Filamentous fungi, such as Aspergillus oryzae and Trametes versicolor, have shown great potential in synthesizing secondary metabolites, producing proteins, and enhancing enzyme production. Genetic engineering and genome editing have played a significant role in developing efficient production strains. The article also explores strategies for the development of fungal biofactories, including classical and recent methods for strain improvement. Additionally, the role of -omics technologies in understanding fungal biology and optimizing fungal strains for specific industrial applications is discussed. Overall, the article highlights the efforts of the scientific community to develop sustainable filamentous fungal strains for industrial purposes. [Extracted from the article]

Since the development of recombinant DNA technologies, the need to establish biosafety and biosecurity measures to control genetically modified organisms has been clear. Auxotrophies, or conditional suicide switches, have been used as firewalls to avoid horizontal or vertical gene transfer, but their efficacy has important limitations. The use of xenobiological systems has been proposed as the ultimate biosafety tool to circumvent biosafety problems in genetically modified organisms. Xenobiology is a subfield of Synthetic Biology that aims to construct orthogonal biological systems based on alternative biochemistries. Establishing true orthogonality in cell-based or cell-free systems promises to improve and assure that we can progress in synthetic biology safely. Although a wide array of strategies for orthogonal genetic systems have been tested, the construction of a host harboring fully orthogonal genetic system, with all parts operating in an orchestrated, integrated, and controlled manner, still poses an extraordinary challenge for researchers. In this study, we have performed a thorough review of the current literature to present the main advances in the use of xenobiology as a strategy for biocontainment, expanding on the opportunities and challenges of this field of research. [ABSTRACT FROM AUTHOR]

The rational design, activity prediction, and adaptive application of biological elements (bio-elements) are crucial research fields in synthetic biology. Currently, a major challenge in the field is efficiently designing desired bio-elements and accurately predicting their activity using vast datasets. The advancement of artificial intelligence (AI) technology has enabled machine learning and deep learning algorithms to excel in uncovering patterns in bio-element data and predicting their performance. This review explores the application of AI algorithms in the rational design of bio-elements, activity prediction, and the regulation of transcription-factor-based biosensor response performance using AI-designed elements. We discuss the advantages, adaptability, and biological challenges addressed by the AI algorithms in various applications, highlighting their powerful potential in analyzing biological data. Furthermore, we propose innovative solutions to the challenges faced by AI algorithms in the field and suggest future research directions. By consolidating current research and demonstrating the practical applications and future potential of AI in synthetic biology, this review provides valuable insights for advancing both academic research and practical applications in biotechnology. [ABSTRACT FROM AUTHOR]

Cordyceps militaris is considered to be of great medicinal potential due to its remarkable pharmacological effects, safety, and edible characteristics. With the completion of the genome sequence and the advancement of efficient gene-editing technologies, coupled with the identification of gene functions in Cordyceps militaris, this fungus is poised to emerge as an outstanding strain for medicinal engineering applications. This review focuses on the development and application of genomic editing techniques, including Agrobacterium tumefaciens-mediated transformation (ATMT), PEG-mediated protoplast transformation (PMT), and CRISPR/Cas9. Through the application of these techniques, researchers can engineer the biosynthetic pathways of valuable secondary metabolites to boost yields; such metabolites include cordycepin, polysaccharides, and ergothioneine. Furthermore, by identifying and modifying genes that influence the growth, disease resistance, and tolerance to environmental stress in Cordyceps militaris, it is possible to stimulate growth, enhance desirable traits, and increase resilience to unfavorable conditions. Finally, the green sustainable industrial development of C. militaris using agricultural waste to produce high-value-added products and the future research directions of C. militaris were discussed. This review will provide future directions for the large-scale production of bioactive ingredients, molecular breeding, and sustainable development of C. militaris. [ABSTRACT FROM AUTHOR]

This paper aims to highlight the physiological actions exerted by eumelanin present in several organs/tissues of the human body and to rationalise the often conflicting functional roles played by this biopolymer on the basis of its peculiar properties. Besides pigmentary disorders, a growing number of organ injuries and degenerative pathologies are presently ascribed to the modification of physiological eumelanin levels in terms of alterations in its chemical/structural features, and of a partial loss or uneven distribution of the pigment. The present review analyses the more recent research dedicated to the physiological and pathological actions of eumelanin and provides an insight into some melanogenesis-associated diseases of the skin, eye, ear, and brain, including the most significant neurodegenerative disorders. Also described are the potentialities of therapies based on the localised supply of exogeneous EU and the opportunities that EU produced via synthetic biology offers in order to redesign therapeutical and diagnostic applications. [ABSTRACT FROM AUTHOR]

This paper presents a novel method for fabricating fluidic circuits using laser printing technology. The method allows for rapid prototyping of macrofluidic devices with control over fluid manipulation and environmental conditions. We employed a high-resolution laser cutter to etch fluidic channels into various substrates, optimizing parameters such as laser power, speed, and substrate material. Our results demonstrate excellent performance in controlling fluid flow and maintaining environmental conditions, handling a wide range of fluids and flow rates. The devices were tested in multiple settings such as with high school students and in research laboratories in universities. We tested the laser-printed macrofluidcs mechanically for durability. We present previous works in microbiology with plants, microbial, and mammalian cell lines showing reliable operation with minimal leakage and consistent fluid dynamics. The versatility and scalability of this approach make it a promising tool for advancing research and innovation in fluidics, providing a robust platform for growing, manipulating, and experimenting with diverse biological systems from cells to whole organisms. We conclude that laser-printed macrofluidics can significantly contribute to fields such as biomedical research, synthetic biology, tissue engineering, and STEM education. [ABSTRACT FROM AUTHOR]

Withanolides are naturally occurring steroidal lactones found in certain species of the Withania genus, especially Withania somnifera (commonly known as Ashwagandha). These compounds have gained considerable attention due to their wide range of therapeutic properties and potential applications in modern medicine. To meet the rapidly growing demand for withanolides, innovative approaches such as in vitro culture techniques and synthetic biology offer promising solutions. In recent years, synthetic biology has enabled the production of engineered withanolides using heterologous systems, such as yeast and bacteria. Additionally, in vitro methods like cell suspension culture and hairy root culture have been employed to enhance withanolide production. Nevertheless, one of the primary obstacles to increasing the production of withanolides using these techniques has been the intricacy of the biosynthetic pathways for withanolides. The present article examines new developments in withanolide production through in vitro culture. A comprehensive summary of viable traditional methods for producing withanolide is also provided. The development of withanolide production in heterologous systems is examined and emphasized. The use of machine learning as a potent tool to model and improve the bioprocesses involved in the generation of withanolide is then discussed. In addition, the control and modification of the withanolide biosynthesis pathway by metabolic engineering mediated by CRISPR are discussed. [ABSTRACT FROM AUTHOR]

To realize the design process of bionic mechatronic systems, involving mapping from engineering to biology and inversion from biology to engineering, a novel design paradigm is introduced that integrates BioTRIZ with multi-factor coupling bionics. In the mapping stage from engineering to biology, BioTRIZ is employed to frame the concrete engineering issue as a general conflicting problem. The biological solution is refined by amalgamating the BioTRIZ solution derived from the contradiction matrix with biological instances. In the inversion stage of biology to engineering, a novel approach is proposed for constructing a bionic multi-factor coupling model, drawing inspiration from the establishment of biological multi-factor coupling model. This allows for a seamless correspondence between biological elements, such as morphology and behavior, and their respective engineering counterparts, including structure and algorithms. This correspondence ultimately achieves the engineering conceptual model that is rooted in biological principles. The practical application of this methodology is exemplified through a multi-biometric fusion bionic active vision system, underscoring its feasibility and efficacy. [ABSTRACT FROM AUTHOR]

Nucleic acid chemistry is a huge research area that has received new impetus due to the recent explosive success of oligonucleotide therapy. In order for an oligonucleotide to become clinically effective, its monomeric parts are subjected to modifications. Although a large number of redesigned natural nucleic acids have been proposed in recent years, the vast majority of them are combinations of simple modifications proposed over the past 50 years. This review is devoted to the main modifications of the sugar phosphate backbone of natural nucleic acids known to date. Here, we propose a systematization of existing knowledge about modifications of nucleic acid monomers and an acceptable classification from the point of view of chemical logic. The visual representation is intended to inspire researchers to create a new type of modification or an original combination of known modifications that will produce unique oligonucleotides with valuable characteristics. [ABSTRACT FROM AUTHOR]

From sea shores to the abysses of the deep ocean, marine ecosystems have provided humanity with valuable medicinal resources. The use of marine organisms is discussed in ancient pharmacopoeias of different times and geographic regions and is still deeply rooted in traditional medicine. Thanks to present-day, large-scale bioprospecting and rigorous screening for bioactive metabolites, the ocean is coming back as an untapped resource of natural compounds with therapeutic potential. This renewed interest in marine drugs is propelled by a burgeoning research field investigating the molecular mechanisms by which newly identified compounds intervene in the pathophysiology of human diseases. Of great clinical relevance are molecules endowed with anti-inflammatory and immunomodulatory properties with emerging applications in the management of chronic inflammatory disorders, autoimmune diseases, and cancer. Here, we review the historical development of marine pharmacology in the Eastern and Western worlds and describe the status of marine drug discovery. Finally, we discuss the importance of conducting sustainable exploitation of marine resources through biotechnology. [ABSTRACT FROM AUTHOR]

Glycosylation is one of the most common and important modifications in natural products (NPs), which can alter the biological activities and properties of NPs, effectively increase structural diversity, and improve pharmacological activities. The biosynthesis of glycosylation in natural products involves multiple complex biological processes, which are coordinated by many enzymes. UDP-glycosyltransferases (UGTs) play a crucial role in glycosylation modification, and have attracted long-term and widespread research attention. UGTs can catalyze the O-, C-, S-, and N-glycosylation of different substrates, producing a variety of glycosides with broad biological activity, while improving the solubility, stability, bioavailability, pharmacological activity, and other functions of NPs. In recent years, the rapid development of synthetic biology and advanced manufacturing technologies, especially the widespread application of artificial intelligence in the field of synthetic biology, has led to a series of new discoveries in the biosynthesis of NP glycosides by UGT. This work summarizes the latest progress and challenges in the field of NP glycosylation, covering the research results and potential applications of glycosylated derivatives of terpenes, flavonoids, polyphenols, aromatic compounds, and other compounds in terms of biogenesis. Looking to the future, research may leverage artificial intelligence-driven synthetic biology techniques to decipher genes related to the synthetic pathway, which is expected to further promote the large-scale synthesis and application of glycosylated NPs, and increase the diversity of NPs in the pharmaceutical, functional food, and cosmetic industries. [ABSTRACT FROM AUTHOR]

Synthetic biology is an exciting new area of research that combines science and engineering to design and build new biological functions and systems. Predictably, with the development of synthetic biology, more efficient and economical photosynthetic microalgae chassis will be successfully constructed, making it possible to break through laboratory research into large-scale industrial applications. The synthesis of a range of biochemicals has been demonstrated in cyanobacteria; however, low product titers are the biggest barrier to the commercialization of cyanobacterial biotechnology. This review summarizes the applied improvement strategies from the perspectives of cyanobacteria chassis cells and synthetic biology. The harvest advantages of cyanobacterial products and the latest progress in improving production strategies are discussed according to the product status. As cyanobacteria synthetic biology is still in its infancy, apart from the achievements made, the difficulties and challenges in the application and development of cyanobacteria genetic tool kits in biochemical synthesis, environmental monitoring, and remediation were assessed. [ABSTRACT FROM AUTHOR]

The document discusses the synthesis of bioactive natural products using engineered plants and microorganisms, highlighting the potential pharmaceutical and health benefits of compounds like artemisinin, ginsenosides, and Ganoderic triterpenes. Various research articles explore the biosynthesis pathways, extraction methods, and industrial-scale production of these natural products, emphasizing the importance of interdisciplinary tools like synthetic biology for further advancements. While significant progress has been made, there is still untapped potential in developing bioactive natural products through engineered plants and microorganisms, calling for continued collaboration between academia and industry to drive technological innovation and market expansion in related industries. [Extracted from the article]

The document discusses the advancements in drug discovery and the application of new technologies, particularly focusing on the integration of artificial intelligence, proteomics, metabolomics, next-generation sequencing, and nanotechnology. It highlights the challenges faced in translating these innovations into clinical success, such as the scarcity of biological data and the complexity of synthetic biology. The Special Issue presents groundbreaking studies showcasing novel methodologies and compounds in drug discovery, with applications ranging from viral infection treatment to cancer therapy, aiming to provide valuable resources for researchers in the field. [Extracted from the article]

This review collects the synthetic modifications performed on andrographolide, a natural molecule derived from Andrographis paniculata, for oncology applications. Various pharmacomodulations were carried out, and the products were tested on different cancer cell lines. The impact of these modifications was analyzed with the aim of mapping the positions essential for activity to facilitate future research in this field. However, this study makes it clear that, in addition to structural modifications of the molecule, which can result in varying degrees of effectiveness in targeting interactions, the lipophilic capacity of the structures obtained through hemisynthesis is of significant importance. [ABSTRACT FROM AUTHOR]

This document, titled "Research on Plant Genomics and Breeding 2.0," discusses recent advancements in plant genomics and breeding. The article highlights various research approaches, such as genome-wide association studies (GWAS), transcriptome sequencing, genome research, molecular marker-assisted breeding, and gene family studies. These studies have identified key genes involved in nitrogen utilization, salt tolerance, and anthocyanin biosynthesis pathways in different plant species. The findings contribute to our understanding of plant biology and regulatory networks, providing valuable information for crop breeding. The authors also mention the potential for future advancements in biotechnology to further enhance our understanding of crop genetics and streamline breeding methods. [Extracted from the article]

Circular RNAs (circRNAs) have emerged as pivotal regulators of gene expression with diverse roles in various biological processes. In recent years, research into circRNAs' involvement in bone biology has gained significant attention, unveiling their potential as novel regulators and biomarkers in bone-related disorders and diseases. CircRNAs, characterized by their closed-loop structure, exhibit stability and resistance to degradation, underscoring their functional significance. In bone tissue, circRNAs are involved in critical processes such as osteogenic differentiation, osteoclastogenesis, and bone remodeling through intricate molecular mechanisms including microRNA regulation. Dysregulated circRNAs are associated with various bone disorders, suggesting their potential as diagnostic and prognostic biomarkers. The therapeutic targeting of these circRNAs holds promise for addressing bone-related conditions, offering new perspectives for precision medicine. Thus, circRNAs constitute integral components of bone regulatory networks, impacting both physiological bone homeostasis and pathological conditions. This review provides a comprehensive overview of circRNAs in bone biology, emphasizing their regulatory mechanisms, functional implications, and therapeutic potential. [ABSTRACT FROM AUTHOR]

Aroma, an important quality characteristic of plant fruits, is produced by volatile organic compounds (VOCs), mainly terpenes, aldehydes, alcohols, esters, ketones, and other secondary metabolites, in plant cells. There are significant differences in the VOC profile of various fruits. The main pathways involved in the synthesis of VOCs are the terpenoid, phenylalanine, and fatty acid biosynthesis pathways, which involve several key enzyme-encoding genes, transcription factors (TFs), and epigenetic factors. This paper reviews the main synthetic pathways of the main volatile components in fruit, summarizes studies on the regulation of aroma formation by key genes and TFs, summarizes the factors affecting the fruit aroma formation, describes relevant studies on the improvement of fruit flavor quality, and finally proposes potential challenges and prospects for future research directions. This study provides a theoretical basis for the further precise control of fruit aroma quality and variety improvement. [ABSTRACT FROM AUTHOR]

Simple Summary: Pseudomonas putida KT2440 is an attractive platform for bioremediation with versatile growth substrate and tolerance capabilities. The limited research on the salt tolerance of strain KT2440 hinders its application in bioremediation in high-salinity environments, where the composition of pollutants becomes increasingly complex and wastewater salinity often remains high. Therefore, the salt tolerance of strain KT2440 was explored in this work. By analyzing transcriptomic data from the high-salinity minimal salts medium, we identified key salt-tolerance genes and used them to improve the salt tolerance of strain KT2440 under 4% w/v NaCl. With co-expression of salt-tolerant genes, the maximum salt tolerance of strain KT2440 increased to 5% w/v NaCl. Further addition of compatible solutes increased the salt tolerance of the strain to 6% w/v NaCl. The engineered strain KT2440 could degrade common pollutants under 4% w/v NaCl in 48 h, and could be a promising platform for bioremediation in high-salinity environments. Pseudomonas putida KT2440 is a popular platform for bioremediation due to its robust tolerance to environmental stress and strong biodegradation capacity. Limited research on the salt tolerance of P. putida KT2440 has hindered its application. In this study, the strain KT2440 was tested to tolerate a maximum of 4% w/v NaCl cultured with minimal salts medium. Transcriptomic data in a high-salinity environment showed significant expression changes in genes in membrane components, redox processes, chemotaxis, and cellular catabolic processes. betB-encoding betaine-aldehyde dehydrogenase was identified from the transcriptome data to overexpress and enhance growth profile of the strain KT2440 in minimal salts medium containing 4% w/v NaCl. Meanwhile, screening for exogenous salt-tolerant genes revealed that the Na+/H+ antiporter EcnhaA from Escherichia coli significantly increased the growth of the strain KT2440 in 4% w/v NaCl. Then, co-expression of EcnhaA and betB (KT2440-EcnhaA-betB) increased the maximum salt tolerance of strain KT2440 to 5% w/v NaCl. Further addition of betaine and proline improved the salt tolerance of the engineered strain to 6% w/v NaCl. Finally, the engineered strain KT2440-EcnhaA-betB was able to degrade 56.70% of benzoic acid and 95.64% of protocatechuic acid in minimal salt medium containing 4% w/v NaCl in 48 h, while no biodegradation was observed in the normal strain KT2440 in the same conditions. However, the strain KT2440-EcnhaA-betB failed to degrade catechol in minimal salt medium containing 3% w/v NaCl. This study illustrated the improvement in the salt tolerance performance of Pseudomonas putida KT2440 and the feasibility of engineered strain KT2440 as a potential salt-tolerant bioremediation platform. [ABSTRACT FROM AUTHOR]

This document provides an overview of the 2023 Physical Virology Gordon Research Conference, which aimed to advance scientific knowledge and foster collaboration in the field of physical virology. The conference brought together researchers from various disciplines and emphasized the importance of diversity, equity, and inclusivity. The program included sessions on viral lifecycles, virus-host interactions, and the development of antiviral agents and nanotechnology platforms. The conference highlighted the biomedical significance of physical virology in developing vaccines and strategies to combat infectious diseases. The document also includes a list of speakers and topics discussed at the conference, as well as acknowledgments and gratitude to participants and funders. [Extracted from the article]

Genome engineered B-cells are being developed for chronic, systemic in vivo protein replacement therapies and for localized, tumor cell-actuated anticancer therapeutics. For continuous systemic engineered protein production, expression may be driven by constitutively active promoters. For actuated payload delivery, B-cell conditional expression could be based on transgene alternate splicing or heterologous promotors activated after engineered B-cell receptor (BCR) stimulation. This study used a bioinformatics-based approach to identify putative BCR-stimulated gene promoters. Gene expression data at four timepoints (60, 90, 210, and 390 min) following in vitro BCR stimulation using an anti-IgM antibody in B-cells from six healthy donors were analyzed using R (4.2.2). Differentially upregulated genes were stringently defined as those with adjusted p-value < 0.01 and a log2FoldChange > 1.5. The most upregulated and statistically significant genes were further analyzed to find those with the lowest unstimulated B-cell expression. Of the 46 significantly upregulated genes at 390 min post-BCR stimulation, 6 had average unstimulated expression below the median unstimulated expression at 390 min for all 54,675 gene probes. This bioinformatics-based identification of 6 relatively quiescent genes at baseline that are upregulated by BCR-stimulation ("on-switch") provides a set of promising promotors for inclusion in future transgene designs and engineered B-cell therapeutics development. [ABSTRACT FROM AUTHOR]

The sophisticated, elegant protein-polymers designed by nature can serve as inspiration to redesign and biomanufacture protein-based materials using synthetic biology. Historically, petro-based polymeric materials have dominated industrial activities, consequently transforming our way of living. While this benefits humans, the fabrication and disposal of these materials causes environmental sustainability challenges. Fortunately, protein-based biopolymers can compete with and potentially surpass the performance of petro-based polymers because they can be biologically produced and degraded in an environmentally friendly fashion. This paper reviews four groups of protein-based polymers, including fibrous proteins (collagen, silk fibroin, fibrillin, and keratin), elastomeric proteins (elastin, resilin, and wheat glutenin), adhesive/matrix proteins (spongin and conchiolin), and cyanophycin. We discuss the connection between protein sequence, structure, function, and biomimetic applications. Protein engineering techniques, such as directed evolution and rational design, can be used to improve the functionality of natural protein-based materials. For example, the inclusion of specific protein domains, particularly those observed in structural proteins, such as silk and collagen, enables the creation of novel biomimetic materials with exceptional mechanical properties and adaptability. This review also discusses recent advancements in the production and application of new protein-based materials through the approach of synthetic biology combined biomimetics, providing insight for future research and development of cutting-edge bio-inspired products. Protein-based polymers that utilize nature's designs as a base, then modified by advancements at the intersection of biology and engineering, may provide mankind with more sustainable products. [ABSTRACT FROM AUTHOR]

Komagataella phaffii (formerly Pichia pastoris) is a methylotrophic yeast widely used in laboratories around the world to produce recombinant proteins. Given its advantageous features, it has also gained much interest in the context of modern biotechnology. In this review, we present the utilization of K. phaffii as a platform to produce several products of economic interest such as biopharmaceuticals, renewable chemicals, fuels, biomaterials, and food/feed products. Finally, we present synthetic biology approaches currently used for strain engineering, aiming at the production of new bioproducts. [ABSTRACT FROM AUTHOR]

Recombinant protein expression is a fundamental aspect of both synthetic biology and biotechnology as well as a field unto itself. Microalgae, with their eukaryotic cellular machinery, high lipid content, cost-effective cultivation conditions, safety profile for human consumption, and environmentally friendly attributes, are a promising system for protein expression or metabolic engineering for sustainable chemical production. Amongst the incredible diversity of microalgae species, Chlorella spp. are heavily studied due to their high growth efficiency, potential for low-cost cultivation, and well-characterized scale-up process for large-scale cultivation. This review aims to comprehensively examine the ongoing advancements in the bioengineering of Chlorella spp. for recombinant protein production and its biotechnological applications. This includes genetic elements such as promoters, terminators, reporters and markers, enhancers, and tags successfully used in Chlorella spp. [ABSTRACT FROM AUTHOR]

Pseudomonas chlororaphis ATCC 9446 is a non-pathogenic bacterium associated with the rhizosphere. It is commonly used as a biocontrol agent against agricultural pests. This organism can grow on a variety of carbon sources, has a robust secondary metabolism, and produces secondary metabolites with antimicrobial properties. This makes it an alternative host organism for synthetic biology applications. However, as a novel host there is a need for well-characterized molecular tools that allow fine control of gene expression and exploration of its metabolic potential. In this work we developed and characterized expression vectors for P. chlororaphis. We used two different promoters: the exogenously induced lac-IPTG promoter, and LuxR-C6-AHL, which we evaluated for its auto-inducible capacities, as well as using an external addition of C6-AHL. The expression response of these vectors to the inducer concentration was characterized by detecting a reporter fluorescent protein (YFP: yellow fluorescent protein). Furthermore, the violacein production operon was evaluated as a model heterologous pathway. We tested violacein production in shake flasks and a 3 L fermenter, showing that P. chlororaphis possesses a vigorous aromatic amino acid metabolism and was able to produce 1 g/L of violacein in a simple batch reactor experiment with minimal medium using only glucose as the carbon source. We compared the experimental results with the predictions of a modified genome scale model. The presented results show the potential of P. chlororaphis as a novel host organism for synthetic biology applications. [ABSTRACT FROM AUTHOR]

Antibiotic resistance poses a significant threat to global public health due to complex interactions between bacterial genetic factors and external influences such as antibiotic misuse. Artificial intelligence (AI) offers innovative strategies to address this crisis. For example, AI can analyze genomic data to detect resistance markers early on, enabling early interventions. In addition, AI-powered decision support systems can optimize antibiotic use by recommending the most effective treatments based on patient data and local resistance patterns. AI can accelerate drug discovery by predicting the efficacy of new compounds and identifying potential antibacterial agents. Although progress has been made, challenges persist, including data quality, model interpretability, and real-world implementation. A multidisciplinary approach that integrates AI with other emerging technologies, such as synthetic biology and nanomedicine, could pave the way for effective prevention and mitigation of antimicrobial resistance, preserving the efficacy of antibiotics for future generations. [ABSTRACT FROM AUTHOR]

Hydroxytyrosol (HT), a plant-derived phenolic compound, is recognized for its potent antioxidant capabilities alongside a spectrum of pharmacological benefits, including anti-inflammatory, anti-cancer, anti-bacterial, and anti-viral properties. These attributes have propelled HT into the spotlight as a premier nutraceutical and food additive, heralding a new era in health and wellness applications. Traditional methods for HT production, encompassing physico-chemical techniques and plant extraction, are increasingly being supplanted by biotechnological approaches. These modern methodologies offer several advantages, notably environmental sustainability, safety, and cost-effectiveness, which align with current demands for green and efficient production processes. This review delves into the biosynthetic pathways of HT, highlighting the enzymatic steps involved and the pivotal role of genetic and metabolic engineering in enhancing HT yield. It also surveys the latest progress in the biotechnological synthesis of HT, examining innovative strategies that leverage both genetically modified and non-modified organisms. Furthermore, this review explores the burgeoning potential of HT as a nutraceutical, underscoring its diverse applications and the implications for human health. Through a detailed examination of both the biosynthesis and biotechnological advances in HT production, this review contributes valuable insights to the field, charting a course towards the sustainable and scalable production of this multifaceted compound. [ABSTRACT FROM AUTHOR]

Recent years have seen a surge in research focused on NAD+ decline and potential interventions, and despite significant progress, new discoveries continue to highlight the complexity of NAD+ biology. Nicotinamide mononucleotide (NMN), a well-established NAD+ precursor, has garnered considerable interest due to its capacity to elevate NAD+ levels and induce promising health benefits in preclinical models. Clinical trials investigating NMN supplementation have yielded variable outcomes while shedding light on the intricacies of NMN metabolism and revealing the critical roles played by gut microbiota and specific cellular uptake pathways. Individual variability in factors such as lifestyle, health conditions, genetics, and gut microbiome composition likely contributes to the observed discrepancies in clinical trial results. Preliminary evidence suggests that NMN's effects may be context-dependent, varying based on a person's physiological state. Understanding these nuances is critical for definitively assessing the impact of manipulating NAD+ levels through NMN supplementation. Here, we review NMN metabolism, focusing on current knowledge, pinpointing key areas where further research is needed, and outlining future directions to advance our understanding of its potential clinical significance. [ABSTRACT FROM AUTHOR]

Oxidation–reduction post-translational modifications (redox-PTMs) are chemical alterations to amino acids of proteins. Redox-PTMs participate in the regulation of protein conformation, localization and function, acting as signalling effectors that impact many essential biochemical processes in the cells. Crucially, the dysregulation of redox-PTMs of proteins has been implicated in the pathophysiology of numerous human diseases, including neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease. This review aims to highlight the current gaps in knowledge in the field of redox-PTMs biology and to explore new methodological advances in proteomics and computational modelling that will pave the way for a better understanding of the role and therapeutic potential of redox-PTMs of proteins in neurodegenerative diseases. Here, we summarize the main types of redox-PTMs of proteins while providing examples of their occurrence in neurodegenerative diseases and an overview of the state-of-the-art methods used for their detection. We explore the potential of novel computational modelling approaches as essential tools to obtain insights into the precise role of redox-PTMs in regulating protein structure and function. We also discuss the complex crosstalk between various PTMs that occur in living cells. Finally, we argue that redox-PTMs of proteins could be used in the future as diagnosis and prognosis biomarkers for neurodegenerative diseases. [ABSTRACT FROM AUTHOR]