Biosensors (Basel). 2025 Mar 8;15(3):175. doi: 10.3390/bios15030175.

ABSTRACT

Reporter systems are widely used to study biomolecular interactions and processes in vivo, representing one of the basic tools used to characterize synthetic regulatory circuits. Here, we developed a method that enables the monitoring of RNA-protein interactions through a reporter system in bacteria with high temporal resolution. For this, we used a Real-Time Protein Expression Assay (RT-PEA) technology for real-time monitoring of a fluorescent reporter protein, while having bacteria growing on solid media. Experimental results were analyzed by fitting a three-variable Gompertz growth model. To validate the method, the interactions between a set of RNA sequences and the RNA-binding protein (RBP) Musashi-1 (MSI1) were evaluated, as well as the allosteric modulation of the interaction by a small molecule (oleic acid). This new approach proved to be suitable to quantitatively characterize RNA-RBP interactions, thereby expanding the toolbox to study molecular interactions in living bacteria, including allosteric modulation, with special relevance for systems that are not suitable to be studied in liquid media.

PMID:40136972 | DOI:10.3390/bios15030175

Curr Oncol. 2025 Mar 19;32(3):179. doi: 10.3390/curroncol32030179.

ABSTRACT

Little is known about patient perspectives regarding consent for obtaining extra research-specific bone marrow (BM) samples during the diagnostic procedure for acute leukemia (AL). This study aimed to better understand patient experiences with consenting to provide these samples and identify potential areas for practice improvement. Semi-structured interviews were conducted with patients treated for AL, 4-6 years prior to the interviews, and healthcare professionals involved with obtaining patient consent and sample collection. A total of 17 patients (14 agreed to provide a sample and 3 did not have a sample in the biobank) and 5 healthcare professionals were interviewed, achieving data saturation. Patients supported increasing public knowledge about research and noted the importance of friends and family in providing emotional support and retaining information. Despite time pressure and anxiety, the decision to donate a research sample did not require much deliberation. Proximal factors informing decisions included impact on patient health and family and anticipated, procedure-associated pain; distal factors included altruism and trust in healthcare professionals. Key information included expected pain and management, the purpose of research samples, and sample security and privacy. Our findings suggest that BM research sample collection may be facilitated through optimizing the environment where information is provided and the type of information provided, including pain management options and the value of the samples for current and future research.

PMID:40136383 | DOI:10.3390/curroncol32030179

Plant Cell Environ. 2025 Mar 26. doi: 10.1111/pce.15488. Online ahead of print.

ABSTRACT

The antioxidative enzyme monodehydroascorbate reductase (MDHAR) is represented by five genes in Arabidopsis, including four that encode cytosolic and peroxisomal proteins. The in planta importance of these specific isoforms during oxidative stress remain to be characterised. T-DNA mutants for MDAR genes encoding cytosolic and peroxisomal isoforms were studied. To examine their roles in conditions of intracellular oxidative stress, mutants were crossed with a cat2 line lacking the major leaf catalase. Enzyme assays in mdar mutants and of recombinant MDHARs suggest that peroxisomal MDHAR1 and cytosolic MDHAR2 are major players in leaf NADH- and NADPH-dependent activities, respectively. All mutants showed a wild-type phenotype when grown in standard conditions. In the cat2 background, loss of peroxisomal MDHAR functions decreased growth whereas loss of the cytosolic MDHAR2 function had no effect on growth but annulled a large part of transcriptomic and phenotypic responses to oxidative stress. The effects of the mdar2 mutation included decreased salicylic acid accumulation and enhanced glutathione oxidation, and were reverted by complementation with the MDAR2 sequence. Together, the data show that the cytosolic MDHAR2 is dispensable in optimal conditions but essential to promote biotic defence responses triggered by oxidative stress.

PMID:40136012 | DOI:10.1111/pce.15488

J Biomol Struct Dyn. 2025 Mar 26:1-26. doi: 10.1080/07391102.2025.2480259. Online ahead of print.

ABSTRACT

Triple-negative breast cancer (TNBC), characterized by the absence of Estrogen Receptor (ER), Progesterone Receptor (PR), and amplified HER2, represents an aggressive subtype devoid of targeted therapies, contributing to heightened mortality rates. Matairesinol (MAT) has demonstrated anti-cancer, anti-inflammatory, immunomodulatory, anti-migratory, and antiangiogenic activities. This study investigates MAT's therapeutic potential for TNBC, employing network pharmacology, molecular docking, and molecular dynamics simulations. Through the integration of MAT and TNBC targets from public databases, we identified 47 potential therapeutic targets. Top 10 hub targets, including HIF1A, ESR1, AKT1, EGFR, HSP90AA1, Src, ERBB2, IGF1, ANXA5, and MAPK1, were revealed through protein-protein interaction analysis. Biological enrichments, encompassing GO and KEGG pathway analyses, unveiled insights into functional roles and associated pathways. The Compound-Targets-Pathways-Disease (C-T-P-D) network illustrated relationships between MAT, its targets, and pertinent pathways. Exploring protein-protein interactions with STRING, followed by validation and supplementation using the GeneMANIA-based functional association (GMFA) method and David web wizard, emphasized the MAPK signaling pathway as a more potential target of MAT against TNBC. The biological significance of these findings underscores MAT's potential as a multi-target inhibitor within multiple signaling pathways related to TNBC, showcasing its efficacy against TNBC. Molecular docking and dynamics simulations substantiated the interaction between MAT and the identified hub targets. In conclusion, our in-silico analysis proposes that MAT could mediate a multi-target and multi-pathway anti-TNBC effect with the MAPK pathway as its novel target pathway. These insights into the potential therapeutic mechanisms of MAT offer valuable directions for further research and the development of interventions against TNBC.

PMID:40135676 | DOI:10.1080/07391102.2025.2480259

J Am Chem Soc. 2025 Mar 26. doi: 10.1021/jacs.5c01526. Online ahead of print.

ABSTRACT

The dynamics of membranes are integral to regulating biological pathways in living systems, particularly in mediating intra- and extracellular communication between membraneless and membranized nano- and microcompartments. Mimicking these dynamics using biomimetic cell structures deepens our understanding of biologically driven processes, including morphological transformations, communication, and molecular sequestration within distinct environments (e.g., (membraneless) organelles, cytoplasm, cells, and the extracellular matrix). In this context, the demembranization of membranized coacervates represents a promising approach to endow them with additional functionalities and dynamic reconfiguration capabilities in response to external or biological stimuli. This versatility broadens their applicability in synthetic biology, systems biology, and biotechnology. Here, we present a strategy for controlled demembranization of membranized coacervate droplets. The membranized coacervates are created by coating membraneless coacervates with terpolymer-based nanoparticles to form a solid-like membrane. The addition of an anionic polysaccharide then triggers the demembranization process arising from electrostatic competition with the membrane components, resulting in polysaccharide-containing demembranized coacervate droplets. This membranization/demembranization process not only allows for the controlled structural reconfiguration of the coacervate entities but also varies their permeability toward (biological) (macro)molecules and nano- and microscale objects. Additionally, integrating an additional polymersome layer in this process facilitates the creation of bilayer and ″Janus-like″ membranized coacervates, advancing the development of coacervate protocells with hierarchical and asymmetric membrane structures. Our work highlights the control over both membranization and demembranization processes of coacervate protocells, establishing a platform for creating advanced protein-containing synthetic protocells with dynamic and diverse (membrane(less)) architectures.

PMID:40135632 | DOI:10.1021/jacs.5c01526

J Am Chem Soc. 2025 Mar 26. doi: 10.1021/jacs.4c14474. Online ahead of print.

ABSTRACT

Ribonucleic acids (RNA) are commonly formulated into lipid nanoparticles (LNP) for in vivo use, but challenges exist with systemic delivery and low in vivo expression efficiency. Inspired by ribonucleoprotein complexes in cells, we created synthetic ribonucleocarbohydrate (RNC) complexes based on cyclodextrin nanoparticles with ferrocenyl fluorocarbons capable of carrying mRNA and additional small-molecule drug payloads, facilitating lysosomal escape and immune stimulation all in the same nanoparticle. We show that this strategy results in highly efficient myeloid cell targeting (dendritic cells and MHC expressing macrophages) and protein expression following systemic administration. The RNC platform should have broad applications in vaccine development, immunosuppression, and immunostimulation for various diseases.

PMID:40135499 | DOI:10.1021/jacs.4c14474

Trends Biochem Sci. 2025 Mar 24:S0968-0004(25)00048-9. doi: 10.1016/j.tibs.2025.02.006. Online ahead of print.

ABSTRACT

Deaminases belonging to the AID/APOBEC family are known as ssDNA and mRNA mutators involved in innate/adaptive immunity, mRNA editing, genome stabilization by restricting retrotransposons, and carcinogenesis. Recent studies suggest that the repertoire of AID/APOBEC targets is more diverse than previously thought and imply a broader biological impact of these proteins.

PMID:40133172 | DOI:10.1016/j.tibs.2025.02.006

Dev Cell. 2025 Mar 18:S1534-5807(25)00120-0. doi: 10.1016/j.devcel.2025.02.015. Online ahead of print.

ABSTRACT

A population of putative mesendoderm progenitors that can contribute cellular descendants to both mesoderm and endoderm lineages is identified in the gastrulating mouse embryo. These progenitor cells are localized to the posterior epiblast, primitive streak, and nascent mesoderm of mid-streak- (E7.0) to late-streak-stage (E7.5) embryos. Lineage tracing in vivo identified that putative mesendoderm progenitors contribute descendants to the definitive endoderm and the axial mesendoderm of E7.75 embryos and to the endoderm of the foregut and hindgut of the E8.5-8.75 embryos. Differentiation of mouse epiblast stem cells identified that the choice between endoderm and mesoderm cell fates depends on the timing of Mixl1 activation upon exit from pluripotency. The knowledge gained on the spatiotemporal distribution of mesendoderm progenitors and the molecular drivers underpinning the divergence of cell lineages in these progenitors enriches our mechanistic understanding of the allocation of the tissue progenitors to germ layer derivatives in early development.

PMID:40132585 | DOI:10.1016/j.devcel.2025.02.015

Cell Rep Methods. 2025 Mar 24;5(3):101009. doi: 10.1016/j.crmeth.2025.101009.

ABSTRACT

We demonstrate a cybernetic approach to control the composition of a P. putida and E. coli co-culture that does not rely on genetic engineering to interface cells with computers. We first show how composition information can be extracted from different bioreactor measurements and then combined with a system model using an extended Kalman filter to generate accurate estimates of a noisy system. We then demonstrate that adjusting the culture temperature can drive the composition due to the species' different optimal temperatures. Using a proportional-integral control algorithm, we are able to track dynamic references with real-time noise rejection and independence from starting conditions such as inoculation ratio. We stabilize the co-culture for 7 days (∼250 generations) with the experiment ending before the cells could adapt out of the control. This cybernetic framework is broadly applicable, with different microbes' unique characteristics enabling robust control over diverse co-cultures.

PMID:40132542 | DOI:10.1016/j.crmeth.2025.101009

PLoS One. 2025 Mar 25;20(3):e0320219. doi: 10.1371/journal.pone.0320219. eCollection 2025.

ABSTRACT

Neuroinflammation is a key feature of human neurodisease including neuropathy and neurodegenerative disease and is driven by the activation microglia, immune cells of the nervous system. During activation microglia release pro-inflammatory cytokines as well as reactive oxygen species (ROS) that can drive local neuronal and glial damage. Phytocannabinoids are an important class of naturally occurring compounds found in the cannabis plant (Cannabis sativa) that interact with the body's endocannabinoid receptor system. Cannabidiol (CBD) is a prototype phytocannabinoid with anti-inflammatory properties observed in cells and animal models. We measured ROS in human microglia (HMC3) cells using CellROX, a fluorescent dynamic ROS indicator. We tested the effect of CBD on ROS level in the presence of three known immune activators: lipopolysaccharide (LPS), amyloid beta (Aβ42), and human immunodeficiency virus (HIV) glycoprotein (GP120). Confocal microscopy images within microglia were coupled to a deep learning model using a convolutional neural network (CNN) to predict ROS responses. Our study demonstrates a deep learning platform that can be used in the assessment of CBD effect in immune cells using ROS image measure.

PMID:40131976 | DOI:10.1371/journal.pone.0320219

STAR Protoc. 2025 Mar 24;6(2):103712. doi: 10.1016/j.xpro.2025.103712. Online ahead of print.

ABSTRACT

In Alzheimer's disease, there is an imbalance in neurotransmitter release and altered neuronal activation. Here, we present a protocol approach to analyze neuronal activity by combining local field potential (LFP) recording with microdialysis within the same animal. We describe steps for measuring glutamate and GABA levels following hippocampal amyloid-beta oligomer (Aβo) injections in rats. We then detail procedures for assembling the electrode and cannula, surgical implantation and simultaneous in vivo LFP recording, interstitial fluid collection, and Aβo injections.

PMID:40131934 | DOI:10.1016/j.xpro.2025.103712

PLoS One. 2025 Mar 25;20(3):e0320910. doi: 10.1371/journal.pone.0320910. eCollection 2025.

ABSTRACT

[This corrects the article DOI: 10.1371/journal.pone.0314754.].

PMID:40131880 | DOI:10.1371/journal.pone.0320910

Acta Biotheor. 2025 Mar 25;73(2):6. doi: 10.1007/s10441-025-09495-3.

ABSTRACT

To bring clarity, the term 'information' is resolved into three distinct meanings: physical pattern, statistical relations and knowledge about things. In parallel, three kinds of 'causation' are resolved: the action of physical force constrained by physical pattern (efficient cause), cybernetic (formal cause) and statistical inference. Cybernetic causation is an expression of fundamental (necessary) logical relations, statistical inference is phenomenological, but physical information and causation are proposed as what actually happens in the physical world. Examples of the latter are given to illustrate the underlying material dynamics in a range of biological systems from the appearance of 'synergistic information' among multiple variables (mainly in neuroscience); positional information in multicellular development; and the organisational structure of ecological communities, especially incorporating niche construction theory. A rigorous treatment of multi-level causation is provided as well as an explanation of the causal power of non-physical information structure, especially of interaction networks. The focus on physical information as particular pattern, echoing the insights of Howard Pattee, provides a more physically grounded view of emergence, downward causation and the concept of 'closure to efficient causation', all now prevalent in the organisational approach to biology.

PMID:40131488 | DOI:10.1007/s10441-025-09495-3

J Biomech Eng. 2025 Mar 25:1-53. doi: 10.1115/1.4068290. Online ahead of print.

ABSTRACT

Multiscale coupling between cell scale biology and tissue-scale mechanics is a promising approach for modeling disease growth. In such models, tissue-level growth and remodeling (G&R) is driven by cell-level signaling pathways and systems biology models, where each model operates at different scales. Herein, we generate multiscale G&R models to capture the associated multiscale connections. At the cell-scale, we consider systems biology models in the form of systems of ordinary differential equations (ODEs) and partial differential equations (PDEs) representing the reactions between the biochemicals causing the growth based on mass-action or logic-based Hill-type kinetics. At the tissue-scale, we employ kinematic growth in continuum frameworks. Two illustrative test problems (a tissue graft and aneurysm growth) are examined with various chemical signaling networks, boundary conditions, and mechano-chemical coupling strategies. We extend two open-source software frameworks - FEBio and FEniCS - to disseminate examples of multiscale growth and remodeling simulations. One-way and two-way coupling between the systems biology and the growth models are compared and the effect of biochemical diffusivity and ODE vs. PDE based systems biology modeling on the G&R results are studied. The results show that growth patterns emerge from reactions between biochemicals, the choice between ODEs and PDEs systems biology modeling, and the coupling strategy. Cross-verification confirms that results for FEBio and FEniCS are nearly identical. We hope that these open-source tools will support reproducibility and education within the biomechanics community.

PMID:40131342 | DOI:10.1115/1.4068290

Minerva Pediatr (Torino). 2025 Mar 25. doi: 10.23736/S2724-5276.24.07715-2. Online ahead of print.

ABSTRACT

Immunoglobulin A (IgA) vasculitis (IgAV, also known as Henoch-Schoenlein purpura, HSP) is a small vessel vasculitis, most commonly presenting in childhood. In most, it has a straightforward, self-limiting disease course, however some children may develop kidney involvement (IgAV-N) which occurs 4-12 weeks following disease onset and remains the biggest contributor to long-term morbidity. Therefore, children undergo a six-month period of kidney monitoring to identify nephritis via surrogate markers including urinalysis and blood pressure measurements. On-going efforts aim at earlier identification and prevention of nephritis during the window of opportunity between disease onset and established nephritis. By identifying those at highest risk of developing poorer kidney outcomes, the number of children developing chronic kidney disease stage 5 (CKD5) as a result of IgAV-N may be reduced. This review summarizes the latest scientific evidence that support the use of novel biomarkers which may allow nephritis to be identified earlier compared to traditional markers, as well as the risk stratification of children with established IgAV-N. These biomarkers may also enhance the evolving understanding of underlying inflammatory pathways. Promising novel urinary markers of early nephritis include angiotensinogen, Gd-IgA1, various complement proteins, and MCP-1, and serum markers such as α-SMA, C-Met, PTX-3, MMP-9, MRP 8/14, and adiponectin may help identify those at risk of developing CKD5. Prospective, longitudinal, international validation studies are required to investigate these markers further, including exploration of implementation into clinical practice.

PMID:40131233 | DOI:10.23736/S2724-5276.24.07715-2

mBio. 2025 Mar 25:e0045025. doi: 10.1128/mbio.00450-25. Online ahead of print.

ABSTRACT

DNA viruses at once elicit and commandeer host pathways, including DNA repair pathways, for virus replication. Despite encoding its own DNA polymerase and processivity factor, human cytomegalovirus (HCMV) recruits the cellular processivity factor, proliferating cell nuclear antigen (PCNA) and specialized host DNA polymerases involved in translesion synthesis (TLS) to replication compartments (RCs) where viral DNA (vDNA) is synthesized. While the recruitment of TLS polymerases is important for viral genome stability, the role of PCNA is poorly understood. PCNA function in DNA repair is regulated by monoubiquitination (mUb) or SUMOylation of PCNA at lysine 164 (K164). We find that mUb-PCNA increases over the course of infection, and modification of K164 is required for PCNA-mediated restriction of virus replication. mUb-PCNA plays important known roles in recruiting TLS polymerases to DNA, which we have shown are important for viral genome integrity and diversity, represented by structural variants and single nucleotide variants (SNVs), respectively. We find that PCNA drives SNVs on vDNA similar to Y-family TLS polymerases, but this did not require modification at K164. Unlike TLS polymerases, depeletion of PCNA did not result in large-scale rearrangements on vDNA. These striking results suggest separable PCNA-dependent and -independent functions of TLS polymerases on vDNA. By extension, these results imply roles for TLS polymerase beyond their canonical function in TLS in host biology. These findings highlight PCNA as a complex restriction factor for HCMV infection, likely with multiple distinct roles, and provide new insights into the PCNA-mediated regulation of DNA synthesis and repair in viral infection.IMPORTANCEGenome synthesis is a critical step of virus life cycles and a major target of antiviral drugs. Human cytomegalovirus (HCMV), like other herpesviruses, encodes machinery sufficient for viral DNA synthesis and relies on host factors for efficient replication. We have shown that host DNA repair factors play important roles in HCMV replication, but our understanding of this is incomplete. Building on previous findings that specialized host DNA polymerases contribute to HCMV genome integrity and diversity, we sought to determine the importance of proliferating cell nuclear antigen (PCNA), the central polymerase regulator. PCNA is associated with nascent viral DNA and restricts HCMV replication. While PCNA is dispensable for genome integrity, it contributes to genome diversity. Our findings suggest that host polymerases function on viral genomes by separable PCNA-dependent and -independent mechanisms. Through revealing complex roles for PCNA in HCMV replication, this study expands the repertoire of host DNA synthesis and repair proteins hijacked by this ubiquitous herpesvirus.

PMID:40130902 | DOI:10.1128/mbio.00450-25

J Virol. 2025 Mar 25:e0201824. doi: 10.1128/jvi.02018-24. Online ahead of print.

ABSTRACT

PRO 140, a humanized anti-HIV monoclonal antibody targeting the cell coreceptor CCR5, is currently under clinical trials, but it only affects CCR5-tropic viruses. In this study, we have engineered two tandem fusion proteins (2P23-PRO140SC and 2P23-PRO140-Fc) with bifunctional activity by adding short fusion-inhibitory peptide 2P23 to the single-chain fragment variable (scFv) of PRO 140 (PRO140SC) with or without the Fc domain of human IgG4. We first demonstrated that 2P23-PRO140SC and 2P23-PRO140-Fc could efficiently bind to the cell membranes through CCR5 anchoring, which did not affect the expression level of CCR5 on the cell surface. We then verified that the addition of 2P23 peptide to PRO140SC enabled a very potent activity against CXCR4-tropic HIV-1 isolates. As expected, the bispecific fusion proteins exhibited highly potent activities in inhibiting divergent HIV-1 subtypes and viral mutants that were resistant to the fusion inhibitors 2P23 and T20, and they displayed relatively low in vitro cytotoxicity. Furthermore, both the fusion proteins had robust in vivo anti-HIV activities in rats, with 2P23-PRO140-Fc much better than 2P23-PRO140SC. In conclusion, our studies have provided bispecific HIV-1 inhibitors that overcome the drawbacks of PRO 140 antibody and offered novel tools for studying the mechanisms of HIV-1 infection.IMPORTANCEGiven that HIV-1 evolves with high variability and drug resistance, the development of novel antivirals is important. CCR5-directed antibody PRO 140 is currently under clinical trials, but it only inhibits CCR5-tropic HIV-1 isolates. The designed fusion proteins by adding a minimum fusion-inhibitory peptide to PRO 140 enable dramatically increased activities in inhibiting both CCR5-tropic and CXCR4-tropic viruses, thus offering novel antiviral agents with a bispecific functionality that can overcome the drawbacks of PRO 140 antibody.

PMID:40130879 | DOI:10.1128/jvi.02018-24

Plant Cell Environ. 2025 Mar 25. doi: 10.1111/pce.15493. Online ahead of print.

ABSTRACT

In most angiosperms, female gametogenesis originates from a specifically selected haploid megaspore, as three out of the four megaspores produced by meiosis degenerate without undergoing further division or differentiation. The remaining megaspore acquires functional megaspore (FM) identity, becoming the FM, which is essential for plant reproductive development. However, the molecular mechanisms governing FM development (or megaspore degeneration) remain largely unexplored, with current studies focusing on only a limited number of genes or regulatory networks. To date, no comprehensive review has systematically introduced advances in this field. This review aims to highlight recent progress in understanding FM development, discuss its critical role in female reproductive development and prospect the mechanism of FM development in environmental adaptation. By offering new insights, this review enriches existing knowledge of FM development and provides fresh perspectives for future research in plant reproduction and its adaptation to the environment.

PMID:40130504 | DOI:10.1111/pce.15493

Front Bioinform. 2025 Mar 10;5:1572937. doi: 10.3389/fbinf.2025.1572937. eCollection 2025.

ABSTRACT

Genomic and metagenomic sequence data provides an unprecedented ability to re-examine findings, offering a transformative potential for advancing research, developing computational tools, enhancing clinical applications, and fostering scientific collaboration. However, effective and ethical reuse of genomics data is hampered by numerous technical and social challenges. The International Microbiome and Multi'Omics Standards Alliance (IMMSA, https://www.microbialstandards.org/) and the Genomic Standards Consortium (GSC, https://gensc.org) hosted a 5-part seminar series "A Year of Data Reuse" in 2024 to explore challenges and opportunities of data reuse and reproducibility across disparate domains of the genomic sciences. Addressing these challenges will require a multifaceted approach, including common metadata reporting, clear communication, standardized protocols, improved data management infrastructure, ethical guidelines, and collaborative policies that prioritize transparency and accessibility. We offer strategies to enable responsible and technically feasible data reuse, recognition of data reproducibility challenges, and emphasizing the importance of cross-disciplinary efforts in the pursuit of open science and data-driven innovation.

PMID:40130011 | PMC:PMC11931119 | DOI:10.3389/fbinf.2025.1572937

Front Plant Sci. 2025 Mar 10;16:1570346. doi: 10.3389/fpls.2025.1570346. eCollection 2025.

NO ABSTRACT

PMID:40129746 | PMC:PMC11931147 | DOI:10.3389/fpls.2025.1570346