bims-biopma 2025-06-08 papers

bims-biopma

Biomed News

on Bioprogrammable materials

Issue of 2025–06–08
ten papers selected by
Shrikrishnan Sankaran, Leibniz-Institut für Neue Materialien

Construction of stable niches for denitrifiers using 3D bioprinting for efficient nitrogen removal.
Anisotropic Growth of Filamentous Fungi in Wood Hydrogel Composites Increases Mechanical Properties.
A review of low-cost production of polyhydroxyalkanoates: Strategies, challenges, and perspectives.
Angiogenesis in rheumatoid Arthritis: Pathological characterization, pathogenic mechanisms, and nano-targeted therapeutic strategies.
Recent Advances in Microalgae Robots for Biomedical Applications.
Standardized Quorum Sensing Tools for Gram-Negative Bacteria.
Synergistic Genetic and Chemical Engineering of Probiotics for Enhanced Intestinal Microbiota Regulation and Ulcerative Colitis Treatment.
Engineering microbial carbon metabolism for sustainable resource utilization.
Prospects of Synthetic Biology-Based Approaches in the Enhanced Production of Pyocyanin in Pseudomonas aeruginosa MCCB 117 as the Drug of Choice in Aquaculture.
When good guides go bad: empirical evaluation of all unique cas9 targets in E. coli reveal widespread functionality and rules for gRNA biological design.

Water Res. 2025 May 27. pii: S0043-1354(25)00824-3. [Epub ahead of print]282 123916

Construction of stable niches for denitrifiers using 3D bioprinting for efficient nitrogen removal.

Yinuo Liu, Tianyang Zhao, Yichen Wu, Jiaojiao Niu, Chunfang Chao, Yingxin Zhao.

  The denitrification process is the core of biological nitrogen removal technology, but its efficacy is limited by the fragile ecological niches of denitrifying bacteria. This study successfully created three-dimensional (3D) denitrification living materials by the controllable and biocompatible 3D bioprinting technology, enabling the construction of artificial 3D microscale structures that facilitate microenvironments for the efficient dynamic reactions of denitrifying bacteria. By developing the double network structure of sodium alginate-gelatin, the bioink with easy extrusion and robust mechanical properties was obtained. Subsequently, the denitrifying bacteria were arranged in three dimensions through a 3D bioprinting platform, and the living materials characterized by precisely controlled three-dimensional morphology and excellent dynamic metabolism were created. The results further indicated that the stable denitrifying bacterial niches were successfully established within 3D living materials, resulting in a significant improvement in the denitrification performance. Additionally, the 3D living materials still maintained high bacterial activity at the low temperatures, showing their potential for repeated use and tolerance to adverse conditions. This study demonstrated the potential of 3D bioprinting technology in constructing living materials with ideal bacterial niches for efficient wastewater treatment, thereby offering novel avenues for addressing the water pollution concerns.

Keywords:  3D bioprinting; Living materials; denitrification niche; high bacterial activity; wastewater treatment

DOI:  https://doi.org/10.1016/j.watres.2025.123916
ACS Appl Bio Mater. 2025 Jun 06.

Anisotropic Growth of Filamentous Fungi in Wood Hydrogel Composites Increases Mechanical Properties.

Ciatta Wobill, Ziyu Zhang, Peter Fischer, Patrick A Rühs.

  There is a rising demand for sustainable, biodegradable, and robust materials in response to growing environmental concerns. Here, we propose using delignified wood as a scaffold for fungal proliferation to obtain wood-fungi composites. The delignification process preserves the fiber directionality inherent to natural wood, enabling fungi to grow along these fibers, enhancing the composites' mechanical properties, and promoting anisotropic fungal growth. The delignified wood was used as a scaffold for the growth of Aspergillus oryzae and Rhizopus oligosporus. Both wood-fungi composites exhibited a higher mechanical strength after fungal proliferation. We used balsa, poplar, and spruce as wood to demonstrate the effects of varying wood architectures. Even though the tensile strengths of all three wood scaffolds were not significantly different, wood scaffolds with lower densities promoted fungal growth. Increasing agar and glucose concentrations were found to significantly enhance tensile strength and Young's modulus. The tensile strength and Young's modulus of wood scaffolds increased from 101 kPa to nearly 103 kPa and 10-3 GPa to nearly 10-1 GPa, respectively. These results highlight the versatile nature of delignified wood as a platform for fungal growth. It offers tunable properties that can be optimized for various applications in composite manufacturing.

Keywords:  anisotropy; composite material; delignified wood; engineered living materials; mycelium; tensile test

DOI:  https://doi.org/10.1021/acsabm.5c00374
Bioresour Technol. 2025 May 31. pii: S0960-8524(25)00711-4. [Epub ahead of print]433 132745

A review of low-cost production of polyhydroxyalkanoates: Strategies, challenges, and perspectives.

Jian Yao, Xin-Yu Xiao, Meng Wang, Quan Zhang, Yating Chen, Min Gou, Zi-Yuan Xia, Yue-Qin Tang.

  In light of the growing severity of plastic pollution and the fossil resource crisis, replacing conventional fossil-based plastics with bio-based and biodegradable "green plastics" is imperative. Polyhydroxyalkanoates (PHAs), which are synthesized by microorganisms, are considered to be the most promising candidates due to their good biodegradability and material properties. However, their widespread commercial adoption is hindered by their high production costs. To develop low-cost PHA synthesis processes, it is necessary to fully evaluate the successes and the limitations of current technologies. This review summarizes recent advancements in reducing PHA production costs, focusing on the development of low-cost carbon sources, strain engineering, extremophilic PHA fermentation, and mixed microbial cultures (MMCs) fermentation. Among low-cost carbon sources, lignocellulosic biomass, owing to its abundant availability, shows greater potential for driving economically viable, large-scale PHA production. However, current pure-culture fermentation processes face challenges such as low carbon conversion efficiency and susceptibility to inhibitors when utilizing lignocellulosic feedstocks. Strain engineering offers promising solutions to these challenges through strategies such as ribosome-binding site optimization, promoter optimization, metabolic engineering, and cell morphology engineering. In contrast to pure-culture fermentation, MMCs-based fermentation, which operates in open environments, demonstrates superior economic feasibility. Future research should focus on refining protocols for MMCs enrichment and establishing continuous, high-efficiency PHA production systems tailored to industrial requirements. Additionally, the PHA recovery protocols need to be optimized to minimize the chemical usage for economic viability and environmental sustainability.

Keywords:  Cost reduction; Lignocellulosic biomass; Mixed microbial culture; Polyhydroxyalkanoates; Pure culture; Synthetic biology

DOI:  https://doi.org/10.1016/j.biortech.2025.132745
Bioact Mater. 2025 Aug;50 603-639

Angiogenesis in rheumatoid Arthritis: Pathological characterization, pathogenic mechanisms, and nano-targeted therapeutic strategies.

Fang Zhao, Zeyu Hu, Gejing Li, Min Liu, Qiong Huang, Kelong Ai, Xiong Cai.

  Angiogenesis is critical from early development through the progression of life-threatening diseases. In rheumatoid arthritis (RA), angiogenesis is markedly heightened and undergoes aberrant changes that exacerbate the progression of synovitis. However, the intricate mechanisms underlying these changes remain poorly understood. Despite the development of numerous anti-angiogenic agents, their clinical efficacy is often compromised by adverse effects and the emergence of adaptive resistance, leading to disease relapse or progression. Nanomedicine has gained significant attention owing to its excellent biocompatibility, precise biological targeting, and enhanced therapeutic outcomes. Anti-angiogenic nanoagents have shown transformative potential in treating cancer and retinal diseases. Nevertheless, a comprehensive review addressing the fundamental mechanisms of anti-angiogenic nanoagents in RA has yet to be undertaken. Herein, this review provides an in-depth description of the unique structural and functional aspects of pathological angiogenesis in RA and its negative consequences. The mechanisms of pro-angiogenic mediators contributing to RA angiogenesis are further explored. Subsequently, biological activities of nanomedicines for the treatment of RA are summarized. Finally, the cutting-edge developments in the anti-angiogenic nanoagents of RA engineered based on these mechanisms and bioactivities are outlined. A helpful introduction to anti-angiogenic strategies for treatment of RA, which may offer novel perspectives for the development of nanoagents, is opening a new horizon in the fight against RA.

Keywords:  Angiogenesis; Nanoagents; Pro-angiogenic factor; Rheumatoid arthritis

DOI:  https://doi.org/10.1016/j.bioactmat.2025.04.026
ACS Biomater Sci Eng. 2025 Jun 03.

Recent Advances in Microalgae Robots for Biomedical Applications.

Tianming He, Yang Liu, Zheng Yang, Shaobo Zhai, Yuchuan Wu, Xiaolu Shi, Shunli Chu.

  Microalgae robots are an emerging biohybrid microrobot that combines the biological properties of microalgae with microrobot technology and shows a wide range of applications in the medical field. In recent years, it has been found that microalgae are ideal biodriven carriers as they have good binding sites and unique properties such as motility, light responsiveness, and oxygen production. The natural substances inside microalgae also have certain medical value and can act synergistically with the exogenous drugs carried. This study provides an in-depth summary of the progress of research and application of microalgae robots in biomedicine over the past 3 years, with a view of providing new ideas for the fabrication and medical application of microalgae robots. This review first introduces the structure and properties of microalgae, which is the basis for the design of microalgae robots; second, it summarizes the formation and movement of microalgae robots, which are formed by functionalizing the surface of microalgae to form microalgae robots with various functions and driven to move in a directional manner by their own targeting ability and external means; the last and most important is it introduces the current research status of microalgae robot applications in drug delivery, targeted treatment of tumors and gastrointestinal inflammation, medical imaging, tissue regeneration, and other fields, as well as their advantages in terms of environmental friendliness, and the future prospects of microalgae robots in the field of biomedicine are also demonstrated.

Keywords:  algae microrobots; biohybrid robots; drug delivery; healing of wound

DOI:  https://doi.org/10.1021/acsbiomaterials.5c00248
ACS Synth Biol. 2025 Jun 06.

Standardized Quorum Sensing Tools for Gram-Negative Bacteria.

Paula Múgica-Galán, Jesús Miró-Bueno, Ángeles Hueso-Gil, Pablo Japón, Ángel Goñi-Moreno.

  Engineering synthetic consortia to perform distributed functions requires robust quorum sensing (QS) systems to facilitate communication between cells. However, the current QS toolbox lacks standardized implementations, which are particularly valuable for use in bacteria beyond the model species Escherichia coli. We developed a set of three QS systems encompassing both sender and receiver modules, constructed using backbones from the SEVA (Standard European Vector Architecture) plasmid collection. This increases versatility, allowing plasmid features like the origin of replication or antibiotic marker to be easily swapped. The systems were characterized using the synthetic biology chassis Pseudomonas putida. We first tested individual modules, then combined sender and receiver modules in the same host, and finally assessed the performance across separate cells to evaluate consortia dynamics. Alongside the QS set, we provide mathematical models and rate parameters to support the design efforts. Together, these tools advance the engineering of robust and predictable multicellular functions.

Keywords:  bacteria; cell−cell communication; distributed computation; genetic tools; quorum sensing; standards

DOI:  https://doi.org/10.1021/acssynbio.5c00036
Adv Mater. 2025 Jun 01. e2417050

Synergistic Genetic and Chemical Engineering of Probiotics for Enhanced Intestinal Microbiota Regulation and Ulcerative Colitis Treatment.

Jiani Jiang, Yi Ma, Liang Zhou, Wenfang Han, Ying Liang, Jiangyan Dong, Yuqin Ding, Wen Li, Qi Lei, Jiangtao Li, Wei Zhu, Qinlu Lin.

  Live bacterial therapeutics (LBT) hold significant promise for treating ulcerative colitis (UC) by utilizing engineered microorganisms to restore mucosal barrier function, modulate microbiota imbalances, and enhance immunity. However, challenges such as low bacterial survival under harsh gastrointestinal conditions, difficulties in achieving long-term colonization, and unclear therapeutic targets limit their effectiveness. To address these issues, a novel approach is proposed that integrates genetic and chemical engineering for intestinal flora regulation in UC treatment. This strategy employs bacterial programmability and gene editing to produce bactericidal agents that dynamically modulate the intestinal microecology and utilize controlled chemical modifications to enhance bacterial resistance. Using Escherichia coli Nissle 1917 (EcN) as a model, a polyelectrolyte composite coating is developed that significantly increased bacterial survival in the gastrointestinal tract-40-fold in the stomach and 74-fold in the small intestine. Additionally, EcN::mcmA is engineered to overproduce iron-carrier microcins (MccM) with a "Trojan horse" mechanism to target and disrupt pathogenic bacteria. In a dextran sulfate sodium (DSS)-induced mouse UC model, EcN::mcmA@P/O treatment effectively reduced inflammation and improved intestinal flora regulation, presenting a promising and potentially safer long-term solution for UC.

Keywords:  chemical modification; engineered probiotics; intestinal flora; live bacterial therapeutics; ulcerative colitis

DOI:  https://doi.org/10.1002/adma.202417050
Biotechnol Adv. 2025 Jun 02. pii: S0734-9750(25)00108-9. [Epub ahead of print] 108622

Engineering microbial carbon metabolism for sustainable resource utilization.

Xin Meng, Cong Gao, Guipeng Hu, Xiaomin Li, Liming Liu, Jing Wu.

  Concerns over the depletion of fossil resources prompt us to consider the development of green and energy-saving resources. One alternative to fossil fuels is the microbial biosynthesis of chemicals using renewable carbon sources through metabolic engineering. In this review, we provide a broad and high-level overview of various research efforts to address the challenges of utilizing sustainable carbon sources, including glucose, lignocellulose, and one‑carbon (C1) compounds, through synthetic biology. We emphasize these endeavors can accelerate the development of microbial industrial application. Additionally, we discuss the prospects of using multi-omics sequencing, machine learning, and artificial intelligence to guide strain engineering for improving the utilization of sustainable carbon sources and prospects for reducing their costs.

Keywords:  C1 compounds; Carbon substrate utilization; Co-utilization of xylose and glucose; Microbial cell factories; Synthetic biology

DOI:  https://doi.org/10.1016/j.biotechadv.2025.108622
Curr Microbiol. 2025 Jun 03. 82(7): 322

Prospects of Synthetic Biology-Based Approaches in the Enhanced Production of Pyocyanin in Pseudomonas aeruginosa MCCB 117 as the Drug of Choice in Aquaculture.

Jini Jimmy, Jayesh Puthumana, Valsamma Joseph, I S Bright Singh.

Pyocyanin, the nitrogen-containing heterocyclic phenazine compound produced by Pseudomonas aeruginosa, has been proven to be a potential drug of choice against vibriosis in sustainable aquaculture production systems. Considering the cost of production and the fact that pyocyanin is produced in very small quantities in nature genetic improvement of bacterial strains for enhanced production of pyocyanin is a requirement. In-depth studies on the key biomolecules behind the biosynthesis of pyocyanin in P.aeruginosa has been conducted previously, however, gene level manipulations of the pyocyanin biosynthetic pathway has to be experimented enhancing the yield in P.aeruginosa. In this review, we look in to the molecular mechanism behind pyocyanin production in P. aeruginosa and an attempt has been made to investigate the growing scope of microbial synthetic biology in pyocyanin biosynthesis. In the present scenario where, synthetic biology-based tools are gaining much importance, this review throws light to building up a platform for synthetic biology-based production of pyocyanin.

DOI: https://doi.org/10.1007/s00284-025-04279-x
bioRxiv. 2025 May 31. pii: 2025.05.23.651106. [Epub ahead of print]

When good guides go bad: empirical evaluation of all unique cas9 targets in E. coli reveal widespread functionality and rules for gRNA biological design.

Elise K Phillips, Riley Harrison, S'Khaja Charles, Dawn Klingeman, Timothy D Wiser, Carrie A Eckert, William G Alexander.

The Cas9 nuclease has become central to modern methods and technologies in synthetic biology, largely due to the ease in which it can be targeted to specific DNA loci via guide RNAs (gRNAs). Reports vary widely on the actual specificity of this targeting, with some studies observing 60% of gRNAs possessing no activity against the genome, while there is a general assumption in the E. coli community that inactive gRNAs are rare. To resolve these contradictions, we evaluated the activity of nearly 500,000 unique gRNAs in the E. coli K12 MG1655 genome. We show that the overwhelming majority of unique gRNAs are functional (at least 93%) while only 0.3% are nonfunctional. These nonfunctional gRNAs tend to exhibit strong spacer self-interaction, leading to the development of a simple set of gRNA design rules for bacteria. Finally, this work provides the greater microbial synthetic biology community a set of nearly half a million sgRNA spacers that have been empirically evaluated in vivo which will expedite future biological engineering projects.

DOI: https://doi.org/10.1101/2025.05.23.651106