Biology Strategies Research Articles

A new flavor of synthetic yeast communities sees the light.

No organism is an island: organisms of varying taxonomic complexity, including genetic variants of a single species, can coexist in particular niches, cooperating for survival while simultaneously competing for environmental resources. In recent years, synthetic biology strategies have witnessed a surge of efforts focused on creating artificial microbial communities to tackle pressing questions about the complexity of natural systems and the interactions that underpin them. These engineered ecosystems depend on the number and nature of their members, allowing complex cell communication designs to recreate and create diverse interactions of interest. Due to its experimental simplicity, the budding yeast Saccharomyces cerevisiae has been harnessed to establish a mixture of varied cell populations with the potential to explore synthetic ecology, metabolic bioprocessing, biosensing, and pattern formation. Indeed, engineered yeast communities enable advanced molecule detection dynamics and logic operations. Here, we present a concise overview of the state-of-the-art, highlighting examples that exploit optogenetics to manipulate, through light stimulation, key yeast phenotypes at the community level, with unprecedented spatial and temporal regulation. Hence, we envision a bright future where the application of optogenetic approaches in synthetic communities (optoecology) illuminates the intricate dynamics of complex ecosystems and drives innovations in metabolic engineering strategies.

Selective inhibitors of the TrkC.T1 receptor reduce retinal inflammation and delay neuronal death in a model of retinitis pigmentosa.

The heterogeneity of receptor isoforms can cause an apparent paradox where each isoform can promote different or even opposite biological pathways. One example is the neurotrophin receptor TrkC. The trkC mRNA translates a full-length receptor tyrosine kinase (TrkC-FL) whose activation by the growth factor NT3 promotes neuronal survival. In some diseases, the trkC mRNA is spliced to a kinase-truncated isoform (TrkC.T1) whose activation by NT3 up-regulates tumor necrosis factor alpha (TNF-α) causing neurotoxicity. Since TrkC.T1 expression is significantly increased at the onset of neurodegeneration, we hypothesized that in disease TrkC.T1-mediated toxicity prevails over TrkC-FL-mediated survival. To study this, we developed small molecules that selectively antagonize NT3-driven TrkC.T1 neurotoxicity without compromising TrkC-FL survival. In a genetic mouse model of retinitis pigmentosa, therapeutic administration of TrkC.T1 antagonists prevents elevation of TNF-α and reduces photoreceptor neuronal death. This work demonstrates the importance of accounting for functional and structural heterogeneity in receptor-ligand interactions, illustrates chemical biology strategies to develop isoform-selective agents, validates TrkC.T1 as a druggable target, and expands the therapeutic concept of reducing neurotoxicity as a strategy to achieve neuroprotection.

Cyclization diversity of meroditerpenoids from endophytic fungi of medicinal plants driven by synthetic biology strategies

Abstract Background Medicinal plants rich in endophytic fungi are a significant source of natural lead compounds. Meroterpenoids, which are hybrid natural products originating from partially terpenoid pathways, exhibit impressive structural complexity and substantial potential as drug candidates. The structural diversity of meroterpenoids is largely attributed to the functional diversity of terpenoid cyclases, which generate a variety of terpenoid compounds with different ring systems. This enzymatic versatility underscores the biochemical potential of endophytic fungi and their invaluable role in drug discovery. Objective The aim of the study was to investigate the role of endophytic fungi from Paris polyphylla var. yunnanensis in facilitating diverse cyclization modifications of meroditerpenoids through four terpene cyclases (TCs) from the Pyr4 family. Methods This study utilized a recombinant strategy to successfully reconstruct four distinct TCs from endophytic fungi in the heterologous host, Aspergillus oryzae NSAR1. The structural characterization of the resulting secondary metabolites was performed using mass spectrometry and NMR techniques. Results The substitution of TCs from the endophytes Aspergillus felis 0260 and Fusarium graminearum 1962 in Aspergillus oryzae through hydrophobic intermediates 1 and 2, led to the production of meroditerpenoids sartorypyrone C (3) and a new compound, 4′-methylchevalone E (4), respectively. This study demonstrates the critical role of endophytic fungi in enhancing structural diversity. Conclusions These findings provide valuable insights into the compatibility of pathway combinations and the interchangeability of terpene cyclases derived from endophytic fungi in medicinal plants, which advanced the understanding of meroditerpenoid biosynthesis and highlighted the importance of endophytic fungi in drug discovery.

Development and evaluation of a microfluidic human testicular tissue chip: a novel in vitro platform for reproductive biology and pharmacology studies.

Organ-on-a-chip culture systems using human organ tissues provide invaluable preclinical insights into systemic functions in vitro. This study aimed to develop a novel human testicular tissue chip within a microfluidic device employing computer-aided design software and photolithography technology. Polydimethylsiloxane was used as the primary material to ensure marked gas permeability and no biotoxicity, enabling effective mimicry of the in vivo testicular microenvironment. This biochip preserved the structural integrity and cellular composition of human testicular tissue, as well as part of its functionality, over an extended period in vitro. Moreover, compared to traditional static culture methods, it more effectively maintained tissue viability and endocrine function. The chip maintained cellular components, histological morphology, and an ultrastructure similar to those in vivo. Notably, the addition of gonadotropins to the human testis tissue on the chip resulted in consistent and steady in vitro production of testosterone and inhibin B. Additionally, the chip displayed sensitivity to the reproductive toxicity of the chemotherapeutic drug busulfan. The results demonstrate the successful establishment of a novel human testicular tissue chip culture system, providing a novel in vitro approach enabling the exploration of human reproductive biology, reproductive pharmacology, toxicology, individual diagnosis, and treatment strategies.

Synthetic Biology‐Based Engineering Cells for Drug Delivery

ABSTRACTAlthough drug delivery technology has promoted the clinical translation of small molecule drugs, there is an urgent need for advanced delivery systems to overcome complex physiological barriers and the increasing development of biological drugs. This review overviews the emerging applications of synthetic biology‐based engineered cells for drug delivery. We first introduce synthetic biology strategies to engineer cells for biological drug delivery and discuss the benefits in terms of specificity, intelligence, and controllability. Furthermore, we highlight the cutting‐edge advancements at the convergence of synthetic biology and nanotechnology in drug delivery. Nanotechnology expands the engineering design and construction concepts of synthetic biology, and synthetic biology drives the development for biotechnology‐driven nanomaterial synthesis. In the future, synthetic biology‐based engineered cells may be developed to be more modular, standardized, and intelligent, leading to significant breakthroughs in the construction of advanced drug delivery systems.

ODSEI Chip: An Open 3D Microfluidic Platform for Studying Tumor Spheroid-Endothelial Interactions.

Current in vitro models of 3D tumor spheroids within the microenvironment have emerged as promising tools for understanding tumor progression and potential drug responses. However, creating spheroids with functional vasculature remains challenging in a controlled and high-throughput manner. Herein, a novel open 3D-microarray platform is presented for a spheroid-endothelium interaction (ODSEI) chip, capable of arraying more than 1000 spheroids on top of the vasculature, compartmentalized for single spheroid-level analysis of drug resistance, and allows for the extraction of specific spheroids for further analysis. As proof of concept, the crosstalk between breast cancer spheroids and vasculature is monitored, validating the roles of endothelial cells in acquired tamoxifen resistance. Cancer spheroids exhibited reduced sensitivity to tamoxifen in the presence of vasculature. Further analysis through single-cell RNA sequencing of extracted spheroids and protein arrays elucidated gene expression profiles and cytokines associated with acquired tamoxifen resistance, particularly involving the TNF-α pathway via NF-κB and mTOR signaling. By targeting the highly expressed cytokines (IL-8, TIMP1) identified, tamoxifen resistance in cancer spheroid can be effectively reversed. In summary, the ODSEI chip allows to study spheroid and endothelial interaction in various contexts, leading to improved insights into tumor biology and therapeutic strategies.

Study of the SPL gene family and miR156-SPL module in Populus tomentosa: Potential roles in juvenile-to-adult phase transition and reproductive phase.

Populus tomentosa, a deciduous tree species distinguished by its significant economic and ecological value, enjoys a wide-ranging natural distribution. However, its long juvenile period severely restricts the advancement of breeding work. The SPL gene family, a distinctive class of transcription factors exclusive to the plant kingdom, is critical in various processes of plant growth and development. The miR156-SPL molecular module stands as an indispensable regulatory mechanism in the transition from the vegetative juvenile phase to the adult phase in plants. Consequently, this research endeavored a methodical and exhaustive exploration of the SPL gene family within the P.tomentosa species, synergistically integrating the miR156 family into the analysis. A total of 56 PtSPL genes were identified and subjected to a comprehensive analysis of their gene structure, conserved motifs, collinearity relationships, chromosomal localization, and promoter cis-acting elements. Further analysis of gene expression profiles confirmed the pivotal role of PtSPLs in the reproductive phase and tissue development of P. tomentosa. In addition, 11 members of miR156 in P. tomentosa were identified and their sequences analyzed, elucidating the miR156-SPL regulatory network. The target relationship between miR156k and PtSPLs was further validated by detecting the expression levels of PtSPLs in transgenic poplars overexpressing 35S::MIR156k. This comprehensive study lays a robust theoretical foundation for the continued exploration and application of the SPL genes in P. tomentosa, opening avenues for future research and potential advancements in plant biology and breeding strategies.

Current Approaches for Genetic Manipulation of Streptomyces spp.-Key Bacteria for Biotechnology and Environment.

Organisms from the genus Streptomyces feature actinobacteria with complex developmental cycles and a great ability to produce a variety of natural products. These soil bacteria produce more than 2/3 of antibiotics used in medicine, and a large variety of bioactive compounds for industrial, medical and agricultural use. Although Streptomyces spp. have been studied for decades, the engineering of these bacteria remains challenging, and the available genetic tools are rather limited. Furthermore, most biosynthetic gene clusters in these bacteria are silent and require strategies to activate them and exploit their production potential. In order to explore, understand and manipulate the capabilities of Streptomyces spp. as a key bacterial for biotechnology, synthetic biology strategies emerged as a valuable component of Streptomyces research. Recent advancements in strategies for genetic manipulation of Streptomyces involving proposals of a large variety of synthetic components for the genetic toolbox, as well as new approaches for genome mining, assembly of genetic constructs and their delivery into the cell, allowed facilitation of the turnaround time of strain engineering and efficient production of new natural products at an industrial scale, but still have strain- and design-dependent limitations. A new perspective offered recently by technical advances in DNA sequencing, analysis and editing proposed strategies to overcome strain- and construct-specific difficulties in the engineering of Streptomyces. In this review, challenges and recent developments of approaches for Streptomyces engineering are discussed, an overview of novel synthetic biology strategies is provided and examples of successful application of new technologies in molecular genetic engineering of Streptomyces are highlighted.

Mechanistic understanding of pH as a driving force in cancer therapeutics.

The development of pH-directed nanoparticles for tumor targeting represents a significant advancement in cancer biology and therapeutic strategies. These innovative materials have the ability to interact with the unique acidic microenvironment of tumors. They enhance drug delivery, increase therapeutic efficacy, and reduce systemic toxicity. The acidic conditions within tumors trigger the release of drugs from pH-responsive nanoparticles, ensuring targeted and controlled delivery directly to cancer cells while minimizing damage to healthy tissues. This review comprehensively explores the design, synthesis, and application of pH-stabilized nanoparticles in cancer therapy. It delves into the mechanisms of pH-responsive behavior, such as the use of pH-sensitive polymers and cleavable linkages that respond to the acidic tumor environment. Current strategies for nanoparticle stabilization, including surface coating, core-shell nanostructures, and hybrid nanoparticles, are discussed in detail, highlighting how these approaches enhance the stability and functionality of the nanoparticles in biological systems. Recent advancements in nanoparticle-based drug delivery systems are examined, showcasing multi-functional nanoparticles that combine therapeutic and diagnostic functions, as well as those designed for combination therapy to overcome drug resistance. This review identifies future directions in the field, such as the need for improved stability and biocompatibility, controlled and predictable drug release, and overcoming regulatory and manufacturing hurdles. Herein, we have highlighted the transformative potential of pH-stabilized nanoparticles in cancer therapy, offering a pathway towards more effective and targeted cancer treatments.

Recent advances in synthetic biology toolkits and metabolic engineering of Ralstonia eutropha H16 for production of value-added chemicals.

Ralstonia eutropha H16, a facultative chemolithoautotrophic Gram-negative bacterium, demonstrates remarkable metabolic flexibility by utilizing either diverse organic substrates or CO2 as the sole carbon source, with H2 serving as the electron donor under aerobic conditions. The capacity of carbon and energy metabolism of R. eutropha H16 enabled development of synthetic biology technologies and strategies to engineer its metabolism for biosynthesis of value-added chemicals. This review firstly outlines the development of synthetic biology tools tailored for R. eutropha H16, including construction of expression vectors, regulatory elements, and transformation techniques. The availability of comprehensive omics data (i.e., transcriptomic, proteomic, and metabolomic) combined with the fully annotated genome sequence provides a robust genetic framework for advanced metabolic engineering. These advancements facilitate efficient reprogramming metabolic network of R. eutropha. The potential of R. eutropha as a versatile microbial platform for industrial biotechnology is further underscored by its ability to utilize a wide range of carbon sources for the production of value-added chemicals through both autotrophic and heterotrophic pathways. The integration of state-of-the-art genetic and genomic engineering tools and strategies with high cell-density fermentation processes enables engineered R. eutropha as promising microbial cell factories for optimizing carbon fluxes and expanding the portfolio of bio-based products.

In vivo self-assembled siRNAs within small extracellular vesicles attenuate LRRK2-induced neurodegeneration in Parkinson's disease models.

Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene play an important role in Parkinson's disease (PD) pathogenesis, and downregulation of LRRK2 has become a promising therapy for PD. Here, we developed a synthetic biology strategy for the self-assembly and delivery of small interfering RNAs (siRNAs) of LRRK2 into the substantia nigra via small extracellular vesicles (sEVs) using a genetic circuit (in the form of naked DNA plasmid) to attenuate PD-like phenotypes in mouse model. We generated the genetic circuit encoding both a neuron-targeting rabies virus glycoprotein (RVG) tag and a LRRK2 siRNA under the control of a cytomegalovirus (CMV) promoter, and assessed its therapeutic effects using LRRK2R1441G mouse models of PD. After intravenous injection, the genetic circuit was taken up by the host liver to reprogram liver cells to produce and self-assemble LRRK2 siRNAs into sEVs, and then the sEV-enclosed LRRK2 siRNAs were further transferred by the endogenous circulating system of sEVs and guided by the RVG tag to the substantia nigra. Intravenous injection of this genetic circuit reduced total and phosphorylated LRRK2 levels in the substantia nigra, and attenuated PD-like phenotypes in two mouse models by rescuing LRRK2R1441G-induced dopaminergic neurodegeneration and reducing microgliosis. This study provides an efficient therapeutic strategy to attenuate LRRK2-induced neurodegeneration and neuroinflammation in PD mouse models, and may open a new avenue to safely deliver siRNA into brain after peripheral intravenous injection and facilitate PD treatment.

Constructing High-Yielding Serratia marcescens for (-)-α-Bisabolol Production Based on the Exogenous Haloarchaeal MVA Pathway and Endogenous Molecular Chaperones.

(-)-α-Bisabolol exhibits analgesic, anti-inflammatory, and skin-soothing properties and is widely applied in the cosmetic and pharmaceutical industries. The use of plant essential oil distillation or chemical synthesis to produce (-)-α-bisabolol is both inefficient and unsustainable. Currently, the microbial production of (-)-α-bisabolol mainly relies on Escherichia coli and Saccharomyces cerevisiae as chassis strains; however, high concentrations of (-)-α-bisabolol have certain toxicity to the strain. This study uses synthetic biology and metabolic engineering strategies to redesign a solvent-tolerant Serratia marcescens for the efficient production of (-)-α-bisabolol. By introducing the Haloarchaea-type mevalonate (MVA) pathway and the (-)-α-bisabolol biosynthesis pathway, we successfully constructed a strain capable of producing (-)-α-bisabolol. The coexpression of the chaperone protein DnaK/J significantly enhanced the soluble expression of the (-)-α-bisabolol synthase, resulting in a 10% increase in (-)-α-bisabolol titer. Furthermore, knockout of the PhoA gene, which reduced the formation of the byproduct farnesol (FOH), further increased the (-)-α-bisabolol titer to 3.21 g/L. In a 5 L bioreactor, S. marcescens achieved a final (-)-α-bisabolol titer of 30.2 g/L, representing the highest titer reported to date. This research provides guidance for the production of (-)-α-bisabolol in nonmodel microorganisms without the requirement for induction.

Mitophagy in Doxorubicin-Induced Cardiotoxicity: Insights into Molecular Biology and Novel Therapeutic Strategies.

Doxorubicin is a chemotherapeutic drug utilized for solid tumors and hematologic malignancies, but its clinical application is hampered by life-threatening cardiotoxicity, including cardiac dilation and heart failure. Mitophagy, a cargo-specific form of autophagy, is specifically used to eliminate damaged mitochondria in autophagosomes through hydrolytic degradation following fusion with lysosomes. Recent advances have unveiled a major role for defective mitophagy in the etiology of DOX-induced cardiotoxicity. Moreover, specific interventions targeting this mechanism to preserve mitochondrial function have emerged as potential therapeutic strategies to attenuate DOX-induced cardiotoxicity. However, clinical translation is challenging because of the unclear mechanisms of action and the potential for pharmacological adverse effects. This review aims to offer fresh perspectives on the role of mitophagy in the development of DOX-induced cardiotoxicity and investigate potential therapeutic strategies that focus on this mechanism to improve clinical management.

Synthesis of Polymers via Cancer Cell Metabolism-Mediated Controlled Radical Polymerization and Application in Engineering of Cell Surface.

In this study, we present a novel chemical biology strategy that leverages the reductive metabolic pathways of cancer cells to develop a new approach for synthesizing polymers in nonstrictly anaerobic conditions. This method utilizes the reductive metabolism of cancer cells to reduce Cu(II) to Cu(I), enabling Cu(I)-catalyzed controlled radical polymerization with poly(ethylene glycol) methyl ether methacrylate (MAPEGOMe) monomer, producing polymers with low dispersity (1.28-1.38). Furthermore, we found that this method could use MAPEGOMe as a monomer to in situ form a polymer layer on the initiator-modified cell surface, achieving a cell surface engineering modification. This study reveals the broad application value and potential of cancer cell metabolism-mediated controlled radical polymerization in the fields of chemical biology and polymer science.

New insights on an old friend: AroA linked to iron-dependent outer membrane stability.

Salmonella is a common causative agent of infectious intestinal and systemic disease and has been extensively studied for several decades. Yet, much of Salmonella pathogenicity remains a mystery due in part to the highly complex virulence and adaptation strategies at the pathogen's disposal. One of the more influential tools within the field, an attenuated aroA-deficient Salmonella strain, has been used for many years to probe the host immune response that would otherwise be impossible with a fully virulent strain. Now, new work by Rooke et al. (J. L. Rooke, E. C. A. Goodall, K. Pullela, R. Da Costa, et al., mBio 15:e03319-23, 2024, https://doi.org/10.1128/mbio.03319-23) utilizes in-depth transposon-directed insertion-site sequencing to elucidate the contribution of genes to Salmonella fitness within isogenic wild-type and aroA-deficient strains. Specifically, Rooke et al. demonstrate that the deletion of the aroA gene leads to iron-dependent membrane instability, raising several exciting new ideas surrounding Salmonella biology and therapeutic strategies.

Bibliometric analysis of dendritic cell-cytokine induced killers cell therapy

Objective: Dendritic cell-cytokine induced killers (DC-CIK) immunotherapy involves co-culturing dendritic cells (DCs) and cytokine-induced killer (CIK) cells to generate activated immune cells for reinfusion into patients, directly killing tumor cells while enhancing the body's immune response, aiming to inhibit tumor growth and recurrence. Here, we conducted a comprehensive bibliometric analysis of DC-CIK immunotherapy, to provide insights into the current state of DC-CIK therapy research and guide future directions in this promising immunotherapeutic approach. Methods: Data were collected from the Web of Science Core Collection (WOSCC) using the search terms "Dendritic cell-cytokine induced killers cell therapy" and "Immune cell therapy" for the period from 1997 to 2024. Bibliometric analysis was performed using VOSviewer to examine publication trends, citation networks, thematic focuses, and global collaboration networks. Results: The number of publications on DC-CIK therapy has shown a significant increase over the years, peaking in 2014 and fluctuating since then. China leads in the number of publications, followed by the United States. Sun Yat-sen University is the most prolific institution, and Ying Mu and Anqi Zhang are the most productive authors. Frontiers in immunology is the most productive journal, publishing 15 papers on DC-CIK therapy. Keyword analysis revealed a focus on cancer biology, immune modulation, and therapeutic strategies, with a particular emphasis on co-culture techniques, cytokines, immune checkpoint inhibitors, and genetic engineering. Conclusion: DC-CIK therapy represents a significant advancement in cancer treatment, integrating the unique properties of DCs and CIK cells to enhance anti-tumor immunity. Despite its promise, challenges remain in optimizing clinical efficacy and addressing translational hurdles. Future research should focus on refining co-culture strategies, improving therapeutic outcomes, and ensuring the safe and accessible application of DC-CIK therapy in clinical settings.

An independent biosynthetic route to frame a xanthanolide-type sesquiterpene lactone in Asteraceae.

Xanthanolides, also described as seco-guaianolides, are unique sesquiterpene lactones (STLs) with diverse bioactivities. Most of xanthanolides are 12,8-olides based on the position of their lactone ring. The biosynthetic pathway leading to xanthanolides has hitherto been elusive, especially how nature creates the xanthane skeleton is a long-standing question. This study reports the elucidation of a complete biosynthetic pathway to the important 12,8-xanthanolide 8-epi-xanthatin. The xanthane-type backbone is directly derived from the central precursor germacrene-type sesquiterpene, germacrene A acid, via oxidative rearrangement, catalyzed by an unusual cytochrome P450. Subsequently, a 12,8-lactone ring is formed within this xanthane-type backbone resulting in xanthanolides. The biosynthetic pathway for xanthanolides contrasts with the previously unified biosynthetic route for diverse 12,6-guaianolides, in which a 12,6-lactone ring formation precedes the transformation of a germacrene-type skeleton into a guaiane-type structure. The discovery of the full biosynthetic pathway of 8-epi-xanthantin opens new opportunities for producing xanthanolides in microbial organisms using synthetic biology strategies.

Chromosome-level genome assembly of a stored-product psocid, Liposcelis tricolor (Psocodea: Liposcelididae)

Liposcelis tricolor (Psocoptera: Liposcelididae) is a significant pest affecting stored products globally. However, due to the lack of a detailed genomic reference, the mechanisms of sex determination, stress resistance, and potential control methods for this booklouse remain poorly understood. In this study, the chromosome-level genome of L. tricolor was assembled by employing Illumina, Nanopore, and Hi-C sequencing technologies. The final genome size was determined to be 229.33 Mb, anchored to 9 pseudo-chromosomes. BUSCO analysis showed that 99.2% of complete BUSCOs were identified, suggesting the high completeness of the genome. A total of 91.49 Mb of repetitive sequences, accounting for 38.84% of the total genome, were annotated, and 15,647 protein-coding genes were predicted, with 88.17% functionally annotated. Additionally, we identified 25 typical sex-determining genes based on the genomic data. This high-quality genome assembly provides a crucial foundation for advancing our comprehension of the molecular biology, genetics, and potential control strategies for psocid L. tricolor.

Insights on the genetics, molecular biology and management strategies on emerging false smut pathogenesis in rice

Insights on the genetics, molecular biology and management strategies on emerging false smut pathogenesis in rice

The changing landscape of nonobstructive azoospermia.

This article aims to describe new developments in the field of nonobstructive azoospermia biology, diagnostics, biomarkers, and therapeutic strategies. Recent studies have investigated the molecular underpinnings of cellular dysfunction that is contributing to spermatogenic dysfunction and findings suggest abnormalities across both somatic and germ cells. Biomarkers to predict the chances of sperm retrieval are being explored utilizing cell free (cf) DNA and RNA from various body fluids, in addition to a full range of transcripts and epigenetics within seminal fluid. Various approaches are being explored to optimize sperm identification from surgical specimens including microfluidic and machine learning approaches. Finally, approaches to regenerating sperm production from males with nonobstructive azoospermia are evolving to include various 3-dimensional culture techniques with integration of computational modeling. The landscape of nonobstructive azoospermia biomarkers, molecular underpinnings, technological approaches to more reliably identify sperm and novel regenerative therapeutic strategies are likely to transform the field of male reproduction in years to come.