Synthetic Biology - Science topic

Abstract: This study presents a comprehensive approach to synthetic genome design aimed at enhancing microbial biomanufacturing performance. The framework integrates CRISPR-based gene editing (using CHOPCHOP), sequence assembly with Geneious, and metabolic pathway modeling using Python's COBRApy library. We simulate and validate biofuel yield under...

The reconstitution of a cell nucleus in a lipid bilayer‐enclosed synthetic cell makes great strides in bottom‐up synthetic biology. In this study, a method for assembling a nucleus in giant unilamellar vesicles (GUVs) is proposed. To induce reconstitution of the nucleus, the interphase egg extract of African clawed frogs Xenopus laevis is utilized,...

Background Chuangxinmycin (CM) is an old antibiotic from Actinoplanes tsinanensis CPCC, 200056, characterized by a dihydrothiopyrano[4,3,2-cd]indole scaffold and potent activity against Mycobacterium tuberculosis. Its congener norchuangxinmycin (NCM), which lacks antibacterial activity against various bacteria, unexpectedly retains antitubercular a...

Background Engineered cells provide versatile tools for precise, tunable drug delivery, especially when synthetic stimulus-responsive gene circuits are incorporated. In many complex disease conditions, endogenous pathologic signals such as inflammation can vary dynamically over different time scales. For example, in autoimmune conditions such as rh...

Problem statement: Revolution of genetic-chip with AI for smarter for mutation detection and ultra-secure genomic data 3 SUMMARY The union between AI and genetic chip technology, together with synthetic biology, is simply changing the whole ecosystem of genomics by enabling fast, precise, and large-scale genetic analysis. DNA microarrays, or geneti...

Paenibacillus polymyxa is a multifaceted bacterium with widespread applications in agriculture, environmental management, medicine, and industry. In agricultural settings, it plays a crucial role in soil enhancement, plant growth promotion, and natural pathogen control, reducing the need for chemical interventions. Additionally, P. polymyxa exhibit...

Bio-based bacterial concrete is a sustainable alternative to conventional concrete in the construction industry. It covers various topics, including production processes, benefits, challenges, and performance evaluations. The roles of bacterial species in calcium carbonate precipitation are explored, along with strategies such as encapsulation, bio...

Terpenes are among the most diverse kinds of natural products because of their remarkable chemical variety. Numerous biological characteristics of terpenoids have been documented, including their antibacterial, antifungal, antiviral, antihyperglycemic, anti-inflammatory, and antiparasitic effects, as well as their cancer chemopreventive benefits. A...

Limited access to vital medicinal compounds and low yields in their natural extraction are the two major drawbacks of the current pharmaceutical industry, for which the plant metabolites act as sustainable, promising solutions, as they have diverse therapeutic properties and are eco-friendly. Their natural biosynthesis often has limitations like yi...

Synthetic genetic circuits that harness programmable protein modules and artificial transcription factors (ATF) to devise event-triggerable cascaded pathways represent an essential class of tools for studying cell biology. Fine-tuning the general structural functionality of ATFs is important for constructing orthogonal and composable transcriptiona...

There is a growing interest in establishing yeast as a cell factory for terpenoid production. Given the hydrophobicity of many terpenoids, expanding the intracellular storage pool is an effective strategy to improve titers. In this study, the storage capacity was enhanced by increasing yeast cell size through the knockout of EST1 and SSN8. The infl...

The integration of Machine Learning Operations (MLOps) in synthetic biology and patient-centered drug logistics presents unprecedented opportunities for innovation, efficiency, and personalization in healthcare. However, these benefits are contingent on robust security and compliance frameworks due to the sensitive nature of biological data and pat...

Sonogenetics is developing into a powerful tool in synthetic biology. The coupling of ultrasound with genetically engineered effectors enables non-invasive and precise control of cellular and molecular processes. Building on established techniques such as optogenetics, it overcomes the limits of tissue penetration and invasiveness, making it a prom...

Background Sclareol, a diterpene alcohol derived from Salvia sclarea, is primarily used in the synthesis of ambrox, an alternative to the expensive spice ambergris. However, commercial production of sclareol from plant extraction is costly and environmentally problematic, limiting its scalability. Recent advances in synthetic biology have enabled t...

The authenticity and integrity of synthetic genomic materials containing valuable intellectual property are essential for advancing scientific knowledge and enhancing biosafety. Nevertheless, existing DNA tags and watermarks have limited efficacy due to low mutation tolerance and inadequate digital encoding capacity. Here, we present “Genome Signat...

Hidden hunger, caused by chronic micronutrient deficiencies, affects billions of people worldwide and remains a critical public health issue despite progress in food production. Biofortification offers a promising solution by enhancing nutrient levels within plant tissues through traditional breeding or advanced biotechnologies. Recent advancements...

Biobots (Biorobots), engineered living systems, are poised to revolutionize the fields of medicine, biotechnology and environmental science. They can be created from either normal living cells and/or post-mortem cells. This short paper shades light into the fundamental concepts, design principles and diverse applications of biobots. The state-of-th...

Centrality measures are crucial for network analysis, offering insights into node importance within complex networks. However, their accuracy is often affected by observational errors and incomplete data. This study investigates how sampling biases systematically impact centrality measures. We simulate six types of biased down-sampling, transitioni...

La biología sintética es una disciplina emergente y altamente promisoria, aunque la investigación en el campo se concentra en países desarrollados. En este marco, la presente investigación mapea el campo de la biología sintética en Chile con el objetivo de describir las redes de colaboración, las características de los investigadores y líneas temát...

Conventional approaches to heterologous gene expression rely on codon optimization, which is limited to swapping synonymous codons and often fails to capture deeper adaptive changes. In contrast, naturally evolved orthologous genes between species often differ by more than just synonymous substitutions - they can include non-synonymous mutations, i...

This paper presents a comprehensive framework for investigating IQ enhancement via a continuum of interventions ranging from current methods-such as noninvasive behavioral techniques, pharmacological enhancers, and gene modification-to emerging approaches (advanced gene editing, epigenetic interventions) and speculative future technologies (nanotec...

We employ a unified framework for computing the information capacity of biological signaling systems using Fisher Information. By deriving closed-form or easily computable information capacity formulas, we quantify how well different signaling models, including binomial, multinomial, Poisson, Gaussian, and Gamma distributions, can discriminate amon...

Carbohydrates including sugar acids are commonly used as carbon sources in microbial biotechnology. These sugar acids are themselves desirable and often overlooked targets for biobased production since they find applications in a broad range of industries, examples include food, construction, medical, textile, and polymer industries. Different stag...

Lutein is a high value-added product in microalgae. There are several strategies to improve its production, including isolation and selection of high-lutein producing algal strains; strain improvement by metabolic engineering, synthetic biology, or adaptive evolution; and metabolic regulation. In this study, an integrated approach was developed to...

The rapid advancements in synthetic biology have enabled the de novo synthesis of various viral genomes, raising concerns about the potential risks associated with artificially engineered viruses. Notable examples, such as the laboratory synthesis of poliovirus and horsepox virus, have demonstrated the feasibility of reconstructing infectious agent...

The increasing burden of environmental pollutants from industrial waste, plastic accumulation, and toxic chemical spills necessitates innovative and sustainable remediation strategies. Synthetic biology offers a powerful means to address this issue by enabling the design of microbes capable of degrading and neutralizing harmful substances. Howev...

This study presents the use of metal‐phenolic networks (MPNs) for the removable membranization of peptide‐based condensates, providing a powerful strategy for stabilizing and protecting condensates from chemically harmful agents. It is demonstrated that the redox‐active properties of MPNs allow for controlled membrane formation and disassembly, off...

This coursebook offers an expansive exploration of bioethics, an interdisciplinary field examining ethical, social, and legal dilemmas in medicine, life sciences, and beyond. It challenges conventional boundaries, embracing Van Rensselaer Potter’s vision of bioethics as a global, holistic ethics of life—integrating human health, environmental consi...

Despite recent significant advances in the controlled assembly of protocell units into complex 3D architectures, the development of prototissues capable of mimicking the sophisticated energy transduction processes fundamental to living tissues remains a critical unmet challenge in bottom‐up synthetic biology. Here a synthetic approach is described...

Biomolecular integral feedback controllers offer precise regulation of molecular species copy numbers, making them valuable for synthetic biology applications. Antithetic integral feedback controllers, in particular, can be effective in low-copy-number regimes with stochastic dynamics. In this work, we introduce a modified variant of this controlle...

Gene, cell, and RNA therapies have revolutionized modern medicine, offering curative potential for genetic disorders, cancers, autoimmune diseases, and degenerative conditions. Gene therapy involves the delivery or modification of genetic material to correct disease-causing mutations, with recent advances in gene replacement (introducing the functi...

DnATA is a DNA-based data storage platform designed to address the growing need for sustainable and durable data archiving. Our system uses a computational pipeline to convert digital files into DNA sequences, which are then stored and replicated inside bacterial cells. Leveraging natural bacterial replication reduces reliance on energy-intensive,...

Protein synthesis in natural cells involves intricate interactions between chemical environments, protein-protein interactions, and protein machinery. Replicating such interactions in artificial and cell-free environments can control the precision of protein synthesis, elucidate complex cellular mechanisms, create synthetic cells, and discover new...

Synthetic biology is a versatile technology with applications in the environment, medicine, food, energy, and services. Given its direct and indirect impacts on human health, the environment, and food development, sex/gender-integrated research is essential. However, this study is the first to systematically compare public perceptions of synthetic...

Abstract: This research paper explores the transformative integration of artificial intelligence (AI) and biotechnology in advancing sustainable agriculture and ensuring global food security. It examines how AI-driven tools such as machine learning, remote sensing, and precision analytics, alongside biotechnological innovations like CRISPR gene edi...

Accurate and autonomous transportation of micro-objects and biological cells can enable significant advances in a wide variety of research disciplines. Here, we present a novel, vision-based, model-free microrobotic pushing algorithm for the autonomous manipulation of micro objects and biological cells. The algorithm adjusts the axis of a rotating...

The increasing burden of environmental pollutants from industrial waste, plastic accumulation, and toxic chemical spills necessitates innovative and sustainable remediation strategies. Synthetic biology offers a powerful means to address this issue by enabling the design of microbes capable of degrading and neutralizing harmful substances. However,...

Advanced bioengineering is often described as a transformative field with the potential to reshape aspects of society and environments. However, it remains largely unfamiliar to publics, compounded by its highly abstract and complex technical details. Increasingly, there have been calls for public engagement that grounds the field in concrete, real...

There is an urgent need to develop a more efficacious anti-tuberculosis vaccine as the current live-attenuated vaccine strain BCG fails to prevent pulmonary infection in adults. Our long-term goal is to test whether increasing the immunogenicity of BCG will improve vaccine effectiveness while maintaining its proven safety profile. In this study, we...

Hi everyone! If you want to know the latest hottest research in synthetic biology and biomaterials, join this meeting this summer! Keynote speakers are Pamela Silver and Martin Fussenegger. We have several other fantastic speakers, too. Now we wait for YOU to submit your abstract for a short talk.

Classical strategies against bacterial infections are based on antibiotics. However, the emergence of multidrug resistant bacterial strains requires exploring new avenues for innovative concepts to combat infections. Synthetic Biology offers tools to design cell-based sensor/actuator systems that detect and counteract infections early, i. e. in sta...

The increasing demand for renewable energy has resulted in significant advancements in biofuel production, offering a sustainable alternative to fossil fuels. Biofuels are created from biological materials, including crops, agricultural waste, and microorganisms, and are classified into four generations based on their sources and production methods...

Microalgae are a promising solution for mitigating climate change due to their ability to capture greenhouse gases and produce renewable materials. However, their effective application is often hindered by barriers that necessitate advances in genetic engineering to improve photosynthesis and productivity. One major obstacle is the microalgal cell...

This preprint introduces a speculative yet structured theoretical framework bridging quantum mechanics and synthetic biology. It explores how principles such as bipartition, quantum entanglement, and von Neumann entropy may underlie coherence and symmetry in genetic systems. By analyzing palindromic DNA sequences, genetic oscillators, and biobricks...

The interdisciplinary development of synthetic biology and material sciences propels medicine into a new era. For cancer therapy, living biotherapeutics integrating functional living bacteria with nanomedicine are particularly interesting. The current study developed a living biotherapeutic platform integrating oxygen‐self‐supplying cyanobacteria w...

Zur (zinc uptake regulator), a member of the Fur (ferric uptake regulator) family of transcriptional regulators, plays multifaceted roles by regulating the gene expressions, such as modulating zinc ion uptake by regulating the znuABC gene cluster and influencing bacterial motility by modulating genes associated with flagella or pili. The photosynth...

The ubiquitous presence of microplastics (MP) in different environments has been well documented. Microplastic contamination has rapidly become a serious environmental issue, threatening marine ecosystems and human health. MP has been reported to accumulate organic pollutants associated with various microbial communities. The MP hazard is specifica...

Mass spectrometry is one of the most effective analytical methods for unknown compound identification. By comparing observed m/z spectra with a database of experimentally determined spectra, this process identifies compound(s) in any given sample. Unknown sample identification is thus limited to whatever has been experimentally determined. To addre...

Industrial wastewater, petroleum pollution and plastic contamination are significant threats to global marine biosecurity because of their toxic, mutagenic and persistent nature¹. The use of microorganisms in bioremediation has been constrained by the complexity of organic pollutants and limited tolerance to saline stress². In this study, we used s...

Lignocellulose, as Earth’s most abundant renewable biomass, represents a crucial resource for the production of biofuels and biochemicals, it is of great significance for sustainable development. Microbial degradation offers a promising pathway for transforming lignocellulose into valuable products. This review explores the diversity and classifica...

Cargo‐filled protein cages are powerful tools in biotechnology with demonstrated potential as catalytic nanoreactors and vehicles for targeted drug delivery. While endogenous biomolecules can be packaged into protein cages during their expression and self‐assembly inside cells, synthetic cargo molecules are typically incompatible with live cells an...

The human microbiome plays a critical role in health and disease, with recent innovations in microbiome research offering groundbreaking insights that could reshape the future of healthcare. This study explored emerging methodologies, such as long-read sequencing, culturomics, synthetic biology, machine learning, and AI-driven diagnostics, that are...

This study introduces a novel bacterial‐based molecular communication (BBMC) model for nanoscale information exchange, harnessing the chemotactic behavior of Escherichia coli (E. coli). A comprehensive 3D simulation framework is developed to analyze the impact of key parameters diffusion coefficient (D), chemoattractant release rate (Q), receiver (...

DNA cloning methods are fundamental tools in molecular biology, synthetic biology, and genetic engineering that enable precise DNA manipulation for various scientific and biotechnological applications. This review systematically summarizes the major restriction-free overlapping sequence cloning (RFOSC) techniques currently used in synthetic biology...

The design of regulatory elements is pivotal in gene and cell therapy, where DNA sequences are engineered to drive elevated and cell-type specific expression. However, the systematic assessment of synthetic DNA sequences without robust metrics and easy-to-use software remains challenging. Here, we introduce Polygraph, a Python framework that evalua...

The utilisation of biocatalysts in biotechnological applications often necessitates their heterologous expression in suitable host organisms. However, the range of standardised microbial hosts for recombinant protein production remains limited, with most being mesophilic and suboptimal for certain protein types. Although the thermophilic bacterium...

Metagenomic approaches have revolutionised the discovery of novel enzymes with biotechnological potential from unexplored environments. Here, we report the identification and comprehensive characterisation of a novel salicylaldehyde dehydrogenase (SALD AP ) from an alpine soil metagenome. Phylogenetic analysis revealed that SALD AP is the first exp...

Light is a critical environmental factor that governs the growth and development of plants. Plants have specialised photoreceptor proteins, which allow them to sense both quality and quantity of light and drive a wide range of responses critical for optimising growth, resource use and adaptation to changes in environment. Understanding the role of...

Escherichia coli (E. coli) repair of iron center protein (also known as YtfE) is a nonheme diiron protein that plays a pivotal role in bacterial responses to nitrosative stress, particularly in nitrite reduction and nitric oxide metabolism. Although previous studies have explored its potential as a nitrite reductase, the detailed catalytic mechanis...

Nicotinamide cofactor biomimetics (NCBs) serve as low-cost alternatives to the expensive NAD(P) ⁺ /NAD(P)H, holding significant potential for applications in oxidoreductases. In this study, an alcohol dehydrogenase ( Sp ADH2) from Sphingobium sp. SYK-6 was identified for the utilization of synthetic NCBs. Sp ADH2 exhibited a catalytic activity of 1...

Guiding biological systems toward desired states, such as morphogenetic outcomes, remains a fundamental challenge with far-reaching implications for medicine and synthetic biology. While large language models (LLMs) have enabled natural language as an interface for interpretable control in AI systems, their use as mediators for steering biological...

The human gut microbiome is a complex ecosystem that plays a vital role in maintaining health and contributing to the pathogenesis of various diseases. This review proposes a transformative approach that involves engineering artificial microbial consortia—precisely designed communities of microorganisms—for personalized modulation of the gut microb...

Synthetic biology has enabled the development of biosensors to detect intestinal inflammation, yet few target the clinically validated biomarker of intestinal inflammation calprotectin with both diagnostic and therapeutic capabilities. Here, an optimized calprotectin biosensor is presented that leverages a zinc uptake regulator (Zur) controlled pro...

DNA methylation has fundamental implications for vertebrate genome evolution by influencing the mutational landscape, particularly at CpG dinucleotides. Methylation‐induced mutations drive a genome‐wide depletion of CpG sites, creating a dinucleotide composition bias across the genome. Examination of the standard genetic code reveals CpG to be the...

RNA design consists of discovering a nucleotide sequence that folds into a target secondary structure. It is useful for synthetic biology, medicine, and nanotechnology. We propose Montparnasse, a Multi Objective Generalized Nested Rollout Policy Adaptation with Limited Repetition (MOGNRPALR) RNA design algorithm. It solves the Eterna benchmark.

Synthetic biology enables the precise control of bacterial population dynamics through engineered genetic circuits, paving the way for innovative therapeutic and biosensing applications. Here, we present genetic circuit design that leverages AHL (acyl-homoserine lactone)-based quorum sensing and a transcriptional cascade regulated by an external in...

Droplet manipulation technologies play a critical role in many aspects of biochemical research, including in complex reaction assays useful for drug delivery, for building artificial cells, and in synthetic biology. While advancements have been made in manipulating liquid droplets, the capability to freely and dynamically manipulate solid objects a...

The fabrication of cytomimetic materials capable of orchestrated and adaptive functions remains a significant challenge in bottom-up synthetic biology. Inspired by the cell/matrix integration of living bone, here we covalently tether distributed single populations of alkaline phosphatase-containing inorganic protocells (colloidosomes) onto a crossl...

Microbial secondary metabolites, synthesized by biosynthetic gene clusters (BGCs), play critical roles in ecological interactions and offer vast potential for biotechnological and pharmaceutical applications. Despite advances in computational BGC detection, current methods face challenges, including time-consuming sequence alignments, dependence on...

Non-conventional yeasts exhibit exceptional genetic and functional diversity, serving as a largely untapped repertoire for biotechnological applications. Beyond the conventional yeast Saccharomyces cerevisiae, non-conventional yeasts are naturally more multifaceted, possessing the ability to utilize renewable and low-cost carbon sources while exhib...

Large serine integrases catalyse the insertion (integration) and excision of bacteriophage genomes into and from the genomes of their bacterial hosts via site-specific recombination. The recombination reaction is notable for its striking directionality: integrase recognises and efficiently recombines a ∼50-bp attachment site in the phage DNA ( attP...

Protein engineering is a pivotal aspect of synthetic biology, involving the modification of amino acids within existing protein sequences to achieve novel or enhanced functionalities and physical properties. Accurate prediction of protein variant effects requires a thorough understanding of protein sequence, structure, and function. Deep learning m...

Although the multi-disciplinarity of public policy studies is often captured by the notion of "policy sciences," the most influential approaches, research designs, and dominant empirical outputs primarily emerge from the disciplines of political science and economics. This has relegated other policy sciences to the periphery of public policy discou...

Resumen Ejecutivo Este estudio revisa cómo la ingeniería genética de plantas confiere tolerancia a la sequía para restauración de ecosistemas áridos terrestres y explora su aplicación en la terraformación de Marte. Integra avances moleculares (vía ABA, osmoprotectores, factores de transcripción, zinc-finger, CRISPR/Cas9), casos de campo (trigo HB4®...

Seed quality directly affects crop yields, germination rates, and plant vigour, so it is essential to agricultural productivity and food security. Conventional techniques for improving seed quality, like hybridization, selective breeding, and seed treatment, have advanced agriculture but have drawbacks in terms of accuracy, efficiency, and resistan...

Cottonseed is a valuable source of edible oil and protein, but its utilization is limited by high gossypol content. In this study, we engineered cotton (Gossypium hirsutum) to biosynthesize astaxanthin through both single‐gene (CrBKT) and multi‐gene (CrBKT, ZmPSY1, PaCrtI, HpCrtZ) expression strategies. Transgenic cotton plants exhibited significan...

Caffeic acid, a plant-derived phenolic compound, has attracted much attention in the fields of medicines and cosmetics due to its remarkable physiological activities including antioxidant, anti-inflammation, antibacteria, antivirus and hemostasis. However, traditional plant extraction and chemical synthesis methods exist some problems such as high...

This report explores how obelisk RNAs, their Oblin proteins, and synthetic derivatives could be harnessed as novel oral therapies via the buccal (oral mucosal) route. We discuss potential therapeutic strategies, including immune modulation, microbiome modulation, anti-inflammatory and regenerative medicine applications, and the mechanisms and chall...

Soil salinity is a critical global challenge that severely impairs crop productivity and soil health by disrupting water uptake, nutrient acquisition, and ionic balance in plants, thereby posing a significant threat to food security. This review underscores innovative strategies to mitigate salinity stress, focusing on the pivotal role of halotoler...

Cell-based immunotherapies, including CAR-T, CAR-NK, and TCR-T therapies, represent a transformative approach to cancer treatment by offering precise targeting of tumor cells. Despite their success in hematologic malignancies, these therapies encounter significant challenges in treating solid tumors, such as antigen heterogeneity, immunosuppressive...

RNA is a dynamic biomolecule with its function largely determined by its folding into complex structures. During the folding process, an RNA traverses through a series of intermediate structural states, with each transition occurring at variable rates that collectively influence the time required to reach the functional form. Understanding these fo...

Citation: Halawa, M.; ElSayed, R.M.R.; Aderibigbe, T.; Newman, P.M.; Reid, B.E.; Carabetta, V.J. Biosimilars Targeting Pathogens: A Comprehensive Review of Their Role in Bacterial, Fungal, Parasitic, and Viral Infections. Pharmaceutics 2025, 17, 581. https://doi. Abstract: Biosimilars represent medicinal products that exhibit a high degree of simil...

Acetylation introduces acetyl groups to substrates, thus altering their chemical reactivity and stability, and plays a crucial role in natural product biosynthesis by driving structural diversification and functional optimization. Emerging evidence now highlights cryptic acetylations as transient modifications that guide sequential reactions, enabl...

Over the last 40 years, several studies have provided evidence demonstrating that viral vectors can result in effective gene targeting/insertions in a host's genome. The traditional approaches of gene knock-down,-out, or-in involve an intensive transgenesis process that is plagued by extensive timescales. Plant viruses have the potential to target...

This paper analyzes the present landscape and challenges of basic research and innovation management in frontier biotechnologies. In recent years, cutting-edge biotechnologies such as gene editing, synthetic biology, and brain-computer interfaces have flourished and become the focus of global technological competition. By systematically combing and...

Wickerhamomyces ciferrii: a non-conventional yeast with significant industrial potential for tetraacetyl phytosphingosine (TAPS), remains underutilized due to the lack of a comprehensive genetic toolbox. In this study, we developed a modular genetic system tailored for Wickerhamomyces ciferrii to enable strain engineering and metabolic pathway opti...