Abstract: PIEZO1 are Ca2+-permeable mechanogated channels that play a crucial role in numerous fundamental cellular responses. Ca2+ influx via PIEZO1 could control the activity of various Ca2+-dependent molecules within the cells, thus activating Ca2+-dependent signaling processes and reactions. Previously we have demonstrated Ca2+-mediated coupling between PIEZO1 and KCa channels in the plasma membrane of transformed mouse fibroblasts, where Ca2+ influx through PIEZO1 stimulates the activity of functionally co-localized KCa channels. Importantly, the selective PIEZO1 activator, Yoda1, inhibited transformed fibroblast migration, induced F-actin assembly and stress fiber formation. However, the impact of PIEZO1-KCa channel coupling to the observed effects remains unknown. Here, we performed the molecular identification of KCa channels in transformed mouse fibroblasts. Importantly, TRAM-34, a specific KCa3.1 channel blocker, abrogated the effect of Yoda1 on F-actin organization and fibroblast motility. We could conclude that KCa3.1 channels in the plasma membrane are primary downstream effectors and critical contributors to the decrease in transformed fibroblast migration and F-actin assembly caused by selective PIEZO1 activation.

Abstract: Gene expression is inherently stochastic, and promoter switching–induced transcriptional bursting generates substantial cell-to-cell variability in mRNA abundance. Such variability is commonly characterized by the mean and variance; however, these low-order statistics fail to capture the geometric features of mRNA copy number distributions and may obscure mechanistic differences in promoter dynamics. In this work, we analyze a two-state stochastic gene transcription model and derive explicit analytical expressions for higher-order moments of mRNA abundance. We show that skewness and kurtosis provide mechanistically informative signatures of transcriptional bursting, explicitly depending on promoter switching kinetics and burst size. In particular, positive skewness increases with slower promoter switching and larger burst sizes, even when the mean expression level is fixed, while elevated kurtosis distinguishes burst-dominated, low-expression regimes from Gaussian-like high-expression regimes. Our results demonstrate that distinct promoter dynamics can produce identical mean expression levels and variances while exhibiting markedly different skewness and kurtosis. Incorporating higher-order statistics, therefore, extends conventional mean–variance analyses and enables improved discrimination between competing stochastic gene expression mechanisms in single-cell data.

Abstract: Macrophages differentiated with macrophage colony-stimulating factor (M-CSF) (M-Mac) are widely used as an experimental model. Interleukin 27 (IL-27)-polarized M-Mac (27M-Mac) suppress HIV replication; however, the effects of IL-27 polarization on granulocyte-macrophage colony-stimulating factor (GM-CSF)-induced macrophages (GM-Mac) remain less investigation. Here, we compare multiple functional properties and gene expression profiles of 27M-Mac and IL-27-polarized GM-Mac (27GM-Mac). M-Mac and GM-Mac were generated from monocytes of healthy donors and subsequently treated with IL-27 for three-day. HIV replication in 27M-Mac, GM-Mac, and 27GM-Mac was suppressed to nearly 10 % of that in M-Mac; however, single-cell RNA sequencing showed that M-Mac clustered with GM-Mac, and 27M-Mac clustered with 27GM-Mac. Expression of CD38 and secretion of CXCL9 and C1q were significantly increased in 27M-Mac and 27GM-Mac compared with M-Mac and GM-Mac. Although CD16 and CD64 expression increased in 27M-Mac and 27GM-Mac relative to their respective controls, phagocytic activity in 27M-Mac and 27GM-Mac was 30% of that in M-Mac. Autophagy was induced 3.7-fold more strongly in 27M-Mac than in M-Mac, reaching levels comparable to those in GM-Mac and 27GM-Mac. Collectively, these findings indicate that IL-27 polarizes M-Mac and GM-Mac toward transcriptionally and functionally similar subtypes, providing insight into the role of IL-27 in macrophage polarization and plasticity.

Abstract: Tight junction (TJ) proteins such as Junctional Adhesion Molecule-A (JAM-A), claudins, and occludin play increasingly recognised roles in cancer biology beyond their structural functions, influencing tumour proliferation, invasion, metastasis and therapy resistance. Understanding how these proteins modulate tumour progression in vivo requires models that are both physiologically relevant and ethically viable. The Chick Chorioallantoic Membrane (CAM) Xenograft model has emerged as a powerful and cost-effective in vivo system that aligns with the 3Rs (Replacement, Reduction, and Refinement), offering unique advantages such as vascular accessibility, rapid tumour growth kinetics and im-munotolerance. This review explores how the CAM model can be leveraged to study the mechanistic role of TJ proteins in tumour-stroma interactions, angiogenesis, extracellular matrix (ECM) remodelling and mechanotransduction, including the YAP/TAZ pathway. While limitations remain, particularly with respect to immune modelling and long-term studies, recent advances in imaging, genetic manipulation and integration of pa-tient-derived xenografts (PDXs) are expanding the model’s translational relevance. Standardising methodologies and embracing new molecular tools will further elevate the utility of this approach as a complementary platform to traditional rodent models, with significant promise for TJ-focused cancer research and therapeutic innovation.

Abstract: The TGF-β superfamily, including BMP and TGF-β pathways, regulates fundamental cellular processes such as fate specification, tissue patterning, and stem cell homeostasis across metazoans. The BMP pathway across these diverse animal systems share a conserved intracellular SMAD signaling architecture. The quantitative dynamics of SMAD signaling and regulatory strategies governing pathway activity show a wide range of variation across developmental and stem-cell systems. In this review, we summarize insights from six major biological contexts — Drosophila embryo, germline stem cells, and the larval and pupal wing discs; the Danio rerio (zebrafish) embryo; and human pluripotent stem cells (hPSCs) — to compare how BMP and TGF-β signals are measured, manipulated, modeled, and integrated. We begin by outlining the canonical TGF-β/BMP signaling pathway and gradient formation across these species. We then compare the mechanism that shapes these signaling profiles from ligand diffusion, extracellular modulation and intracellular feedback through genetic, chemical, and mechanical perturbations. Finally, we highlight how endogenous pathway activity is measured through quantitative imaging of the pSmad/pMad activity, and how this approach contributes to the development of a full range of mechanistic and computational models across the presented systems. These insights reveal unifying design principles and performance objectives that govern BMP–SMAD signaling across species and cell types.

Abstract: Retinoic acid receptor (RARg) mRNA is expressed spatially and temporally during mouse embryogenesis and largely within stem and progenitor cells, indicating a role in organ formation. RARg agonism promoted the maintenance of hematopoietic stem cells, and blocked stem cell development as shown for hematopoiesis, zebrafish development, and chondrogenesis. Transgene expression enhanced the generation of induced pluripotent stem cells, indicating a role in ground state pluripotency. RARg is oncogenic in acute myeloid leukemia, cholangiocarcinoma and colorectal, head and neck, hepatocellular, ovarian, pancreatic, prostate, and renal cancers. RARg agonism or overexpression enhanced the proliferation of cancer cells. Conversely, antagonism or inhibition of all-trans retinoic acid synthesis led to the death of cancer cells including cancer stem cells. The pathways regulated by RARg, via canonical activation and repression of gene expression, include Wnt/b-catenin and Notch signaling. RARg also acts as a co-factor to Smad3 and reduced or enhanced TGFb driven and Smad3-mediated events when liganded and non-liganded, respectively. Collectively the findings support the view that RARg plays a crucial role to control stem and progenitor cell behavior.

Abstract:

Adeno-Associated Viruses (AAVs) and nanoparticles have been used to deliver DNA or RNA to target cells for gene therapy technologies. These vectors are also useful for DNA- or RNA-based vaccines. Although AAVs and nanoparticles are promising technologies, two major technical problems remain. One problem is that the commonly used AAVs have a low efficiency to penetrate the blood-brain-barrier (BBB) and the blood-retina-barrier (BRB). Consequently, gene delivery to the nervous system has limitations. Another problem is that AAVs induce immune reactions that cause serious side effects. To avoid immune reactions, the AAV dose must be reduced to lower levels that may result in insufficient gene delivery. To overcome these problems, researchers searched for effective peptide sequences by modifying viral capsid proteins. As a result, Cell Penetrating Penta-Peptides (CPP5s) have been shown to be effective in improving the BBB/BRB penetration of AAV and the suppression immune reactions against AAV. CPP5s were originally developed from peptide sequences of Bax (a pro-apoptotic protein) binding domain of Ku70 (a DNA repair protein) and from negative control cell penetrating peptides without Bax-binding activity. This article will discuss the background science of CPP5 and the future direction of the use of CPP5 for AAV- and nanoparticle-mediated gene delivery to the nervous system as well as other organs.

Abstract: Adult stem cells are crucial for the regeneration of organs, such as hair follicles and skin, but the molecular pathways underlying their origin remain incompletely understood. The dermal papilla (DP), a mesenchymal component of the hair follicle, demonstrates significant plasticity and stem cell potential in vitro. DP cells are crucial for hair growth, but their inductive capacity is temporarily suppressed during the catagen phase or permanently lost in culture, leading to cellular senescence. This study examined the molecular signatures associated with DP cell plasticity and the capacity to maintain signals essential for initiating new hair follicle cycles. By culturing DP explants and propagating young cells, three DP cell populations were generated, each representing progressive loss of hair induction and increased senescence. Global gene expression analysis and data mining, combined with gene interactive networks, revealed a transient upregulation of wound healing and stem cell markers in pre-senescent DP cells. This upregulation coincides with the signatures characterising hair follicle regression, suggesting that dynamic changes in gene expression are closely linked to the plasticity and regenerative potential of DP cells. These findings indicate that the reprogramming window in DP cells could be leveraged for hair growth and skin rejuvenation strategies.

Abstract: Programmable organoids are emerging as a powerful new class of engineered developmental systems in which genetic circuits, epigenetic memory architectures, synthetic organizers, and closed-loop control frameworks converge to enable precise regulation of morphogenesis. Traditional organoids rely on spontaneous self-organization, but this intrinsic variability limits reproducibility, causal inference, and translational relevance. Recent advances in CRISPR-based transcriptional and epigenetic engineering, optogenetic and chemogenetic patterning technologies, reaction–diffusion design, and real-time biosensing now allow developmental trajectories to be scripted with increasing precision. This review synthesizes these developments into a unified framework spanning genetic circuit construction, epigenetic programming, synthetic morphogenesis, multi-scale sensing, adaptive regulation, and AI-guided design. Applications across human developmental biology, disease modeling, and regenerative medicine are highlighted, alongside the technical, biosafety, and ethical considerations associated with building increasingly autonomous, self-regulating developmental systems. Collectively, these advances establish programmable organoids as a foundation for developmental synthetic biology and outline a roadmap toward fully engineered human developmental architectures.

Abstract: Tubule-derived pro-fibrotic mediators are central for the development of kidney fibrosis. We previously showed that fibrotic stimuli activate and elevate GEF-H1 (ARHGEF2) in tubular cells, leading to RhoA-dependent fibrotic reprogramming. In search of new mechanisms of GEF-H1 regulation, in this study we used immunoprecipitation and proximity ligation assay to show interaction between GEF-H1 and Myotonic Dystrophy Kinase-related Cdc42-binding kinase (MRCK)α in tubular cells. MRCKα silencing elevated GEF-H1 activity, and induced GEF-H1-dependent RhoA activation, stress fibre formation and myosin light chain phosphorylation. MRCKα depletion also elevated phospho-cofilin levels in a RhoA-dependent manner. The fibrogenic cytokine TGFβ1 rapidly increased binding between GEF-H1 and MRCKα, while MRCKα silencing augmented TGFβ1-induced GEF-H1 activation, suggesting a negative feedback loop. An mRNA array detecting fibrogenic genes revealed increase in a subset of basal and TGFβ1-induced genes following MRCKα depletion. MRCKα silencing promoted nuclear translocation of the profibrotic transcriptional co-activator Myocardin-Related Transcription Factor (MRTF), and MRTF-A+B depletion prevented increase in ACTA2 (α-smooth muscle actin), a key marker of fibrotic reprogramming. Finally, total MRCKα mRNA was reduced in a murine kidney fibrosis model, and immunohistochemistry revealed a drop in tubular MRCKα. Taken together, we identified MRCKα as a new suppressor of GEF-H1/RhoA/MRTF signaling. Reduced MRCKα expression in kidney fibrosis may promote tubular fibrotic gene expression.

Abstract: Pregnant women undergo a myriad of physiological changes during this stage, including important hormonal variations. Pregnancy gingivitis is a condition that affects up to 30% to 100% of women, is related to hormonal modifications, and could play an important role in gestational gut colonization and immunological training in the newborn. Nonetheless, oral health is not always considered part of routine prenatal care. In this study, we collected saliva samples of pregnant women with and without pregnancy gingivitis and analyzed the oral microbiota through 16S sequencing. In addition, meconium from the infants of participating women was also analyzed. The oral microbiota of pregnant women with and without pregnancy gingivitis did not show significant diversity differences. However, significant differences in microbiome composition were observed. In addition, it appears that microbiome composition of the offspring of mothers with gingivitis may also differ from that of mothers without gingivitis, although the number of available samples did not allow definite conclusions. As such, a larger cohort and deeper sequencing methods are needed to demonstrate the differences in the oral microbiota of pregnant women with and without gingivitis and to explore the possibility of bacterial translocation from the maternal gingiva to the fetal gut.

Abstract:

The unicellular ciliate Paramecium caudatum undergoes a developmental transition from asexual binary fission to sexual reproduction during its mature stage. This transition is triggered by mating interactions between cells of complementary mating types, leading to aggregate formation, mating pairs, and the meiotic division of micronuclei. Although calcium-driven EF-hand kinases have been implicated as mating type proteins, the spatiotemporal dynamics of calcium signaling during conjugation have not been comprehensively characterized. In this study, we established a behavioral assay to isolate committed cells from aggregates immediately after mating onset, and developed an experimental system to monitor intracellular calcium fluctuations specifically expressed in these cells. By combining Ca²⁺/EGTA buffering and microinjection approaches, we manipulated extracellular and intracellular calcium levels and confirmed the continuous requirement of calcium ions for conjugation-specific functions. Two significant findings emerged. First, we identified, for the first time, a calcium atlas covering the entire cell, with ascending centers localized in the anterior, oral apparatus, and posterior regions. The calcium/Indo-1-AM fluorescence peaked at six h after mating initiation and declined gradually, but persisted until conjugation was completed at ~48 h. Second, we demonstrated that distinct intracellular calcium thresholds are required for each stage of mating, including maintenance of mating activity, commitment of micronuclei to meiosis, and two-stepwise formation of mating pairs. These thresholds function as regulatory checkpoints that coordinate subcellular localization and stage synchronization. Collectively, our findings highlight calcium ions as pivotal regulators of conjugation in Paramecium and propose a novel framework, the Paramecium calcium atlas, for understanding the cellular and molecular mechanisms underlying sexual reproduction in ciliates.

Abstract: Background: The escalating global burden of complex chronic diseases and severe mental health challenges represents a significant limitation of reductionist healthcare paradigms. We propose that health is not merely the absence of disease, but rather a dynamic state of coherence across three integrated domains: biological, psychological, and noetic (consciousness-related). This review evaluates emerging technologies and interventions designed to restore this tripartite coherence. Objective: To systematically synthesize and critically evaluate the scientific evidence for technologies and interventions aligned with the ReGEN framework's seven pillars: Light, Water, Frequency, Energy, Breath, Intention, and Food. Methods: Following PRISMA guidelines, we conducted a systematic literature search across PubMed, IEEE Xplore, PsycINFO, and Cochrane Library (2010-2024). Included studies were evaluated against five criteria: biophysical plausibility, evidence quality, biomarker correlates, safety profile, and transdisciplinary alignment. Technologies were graded (A-D) based on evidence strength. Results: From 2,148 identified records, 215 studies met inclusion criteria after systematic screening. Our analysis identified a "Foundational Triad" of interventions with the strongest mechanistic plausibility and evidence base: Photobiomodulation (Light Pillar, Grade A), Coherent Breathing (Breath Pillar, Grade A), and Focused Intention (Intention Pillar, Grade B). These pillars demonstrate significant combined potential for initiating systemic healing cascades. Technologies targeting the Frequency and Energy pillars showed more preliminary evidence (Grade B-C), requiring further rigorous validation. Conclusion: The ReGEN framework provides a thorough transdisciplinary taxonomy for classifying and evaluating coherence-enhancing technologies. Convergent evidence across multiple scientific disciplines supports the complementary application of photobiomodulation, coherent breathing, and focused intention as a potent, non-invasive approach for restoring systemic coherence. This synthesis outlines a verification protocol via a Tripartite Coherence Index and identifies critical research priorities for advancing this emerging paradigm.

Abstract: We propose the Informational Field Consciousness Theory (IFCT), an integrative framework combining information physics, quantum biology, and neuroscience to address the Hard Problem of Consciousness. Central to our thesis is the hypothesis that DNA functions as a fractal antenna capable of coupling with a fundamental informational field (IF), with neural networks serving as processors that filter and render conscious experience. We present empirical evidence from recent studies on DNA’s electromagnetic properties, biophoton emission, and quantum coherence in biological systems. Critically, we argue that the inability of synthetic biology to design functional DNA de novo - despite successfully replicating existing sequences - suggests undiscovered principles governing DNA’s role beyond genetic information storage, potentially including antenna/receiver properties optimized through evolution. We propose testable experimental protocols to distinguish our framework from purely materialist emergence theories and discuss implications for artificial consciousness, ethics, and the nature of life itself.

Abstract: The current manuscript is meant to introduce how piezo2 channelopathy may play a critical role in (epi)genetics, when it comes to development, growth and aging initiation from a neurocentric view. Accordingly, it demonstrates how the principality of excitatory Piezo2 ion channel may not only reflected in Piezo cross-frequency coupling, transcription activation, ultradian event sensing and modulation, but might also fine-modulates emergent entropic force from gravity and (epi)genetics, hence underscoring its principality not only in proprioception. The implicated Piezo ion channels, especially Piezo2, have cellular, inter-cellular, compartmental and systemic effect through a Piezo system, however the underlying backbone ultrafast (glutamatergic proprioceptive Piezo2) system may carry the principality. Syndecans as co-functioning accessory ligand of Piezo2 may serve the non-linear dynamics of the ultrafast non-linear time-delay system in order to quantum tunnel/synchronize protons in an ultrafast fashion into the suggested anticipatory coupled hippocampal chaotic system. The co-function of the intrinsically disordered intracellular domain of Piezo2 and the intrinsically disordered ectodomain of syndecans may posit the critical structure in this proposed ultrafast non-linear dynamics that may be impaired due to Piezo2 channeloapthy, leading to altered response to postural perturbations, consequently might cause an increased the risk of non-contact injuries. Proton affinity switch on proprioceptive glutamatergic terminals may not only induce acquired Piezo2 channeloapthy and resultant switch to glutamate-based signaling, but may miswire protons as well through the lipoxygenase pathway. This proton miswiring may also inhibit fine-regulation of excitatory AMPA information processing in neuronal synapsis. After all, acquired Piezo2 channelopathy may posit such an initiatingcritical primary damage that impacts development, growth and aging through (epi)genetics, however quantum (gravity) theory is needed for translation.

Abstract: Background/Objectives: Neutrophils express the receptor for advanced glycation end products (RAGE), but its role in the responses of neutrophils to bacteria is not well understood. Methods: Human peripheral neutrophils were isolated from blood of healthy donors. Fluorescent-based techniques and spectroscopy were used to assess calcium flux, ROS/RNS formation and phagocytic activity. Cellular expression of the PAGE-antigen was studied using immunofluorescence microscopy and flow cytometry. ELISA was used to quantify sRAGE in the culture medium. Results: We studied human peripheral neutrophils interacting with gram-negative bacteria S. typhimurium and asked how RAGE controls the neutrophil cellular responses. Blocking RAGE with the specific inhibitor FPS-ZM1 reduced bacteria-induced calcium signals, reactive oxygen species, nitric oxide production, and phagocytosis. We also found that neutrophil adhesion and stimulation by bacteria, lipopolysaccharide, or fMLP caused rapid release of soluble RAGE (sRAGE) into the cell environment. Immunofluorescence and flow cytometry showed low RAGE at the plasma membrane but abundant intracellular RAGE, which decreased on activation. Conclusions: Our data support a dual role of RAGE in neutrophils as both a membrane sensor and a secreted regulator.

Abstract: Pathological USH2A mutations cause Usher Syndrome type II, characterized by progres-sive retinitis pigmentosa and hearing and balance impairment. This study aims to inves-tigate the cellular mechanisms underlying USH2A-related retinal degeneration using hu-man induced pluripotent stem cell (hiPSC)-derived retinal organoids. The introduction of a homozygous nonsense mutation in the USH2A hotspot exon-13 resulted in normal photoreceptor development, but loss of ciliary localization of usherin long form B and its interacting proteins, ADGRV1 and whirlin. Notably, single-cell RNA sequencing revealed unexpected significant changes in Müller glial cells (MGCs), with disruptions in the translation, innate immune response, and endolysosomal system. These findings suggest that, while photoreceptor cells are mildly affected by the exon-13 USH2A mutation, MGCs exhibit major dysfunction, potentially contributing to the disease progression and there-fore shedding light on potential alternative therapeutic targets.

Abstract: The growing use of computed tomography (CT) in medicine requires a better understanding of how low-dose radiation affects human stem cells. This study investigated the long-term consequences of CT-level radiation on the secretory profile of human adipose-derived mesenchymal stem cells (AD-MSCs). AD-MSCs were exposed to radiation regimens simulating a single or multiple head CT scans, or to a single 2 Gy therapeutic dose, and their secretion of 41 cytokines, chemokines, and growth factors was monitored during long-term culture. At the early passage, AD-MSCs receiving a single 2 Gy dose showed a coordinated increase in several lymphocyte-regulating cytokines compared to cells exposed to multiple CT scans. However, these initial differences were not sustained. Long-term culturing led to a progressive and widespread decrease in the secretion of 26 cytokines, chemokines, and growth factors across all groups. By the latest passage, all irradiated cells showed a generalized reduction in secretory function compared to non-irradiated controls. These findings demonstrate that while different radiation regimens trigger distinct immediate responses, long-term culture results in a broad decline of the AD-MSCs secretome, which is accentuated by prior radiation exposure. This underscores the importance of assessing long-term consequences to fully evaluate the functional impact of diagnostic radiation on stem cells.

Abstract: This study examined how ultrasonic frequency changes droplet size and affects the delivery of nanoparticles through airway mucus. A simple nebulizer system was tested at 1.7 MHz and 2.5 MHz using fluorescent nanoparticles in a mouse model. At 2.5 MHz, the average droplet size decreased from 4.5 µm to 2.1 µm, which increased total lung deposition by 38% and extended mucus penetration by about 25 µm. Fluorescence imaging showed that the higher frequency produced a more uniform spread and higher drug level in the alveolar region. These findings show that adjusting ultrasonic frequency can improve droplet control and nanoparticle movement in the lungs. This approach offers a useful way to improve inhaled drug delivery and may also support future aerosol treatments for long-term lung diseases.

Abstract: This study used a PDMS microfluidic chip to study how nanoparticle size and surface wettability affect their movement in airway mucus. Artificial mucus with 3% mucin was used to test nanoparticles ranging from 50 nm to 300 nm in size and with contact angles between 40° and 90°. When the particle size was smaller than 150 nm and the contact angle was below 60°, the diffusion coefficient increased about 2.7 times, and the retention time in mucus dropped by nearly 45%. A simple regression model combining particle size and contact angle showed strong agreement with experimental data ( ), allowing clear prediction of transport efficiency. Unlike earlier static or single-factor tests, this microfluidic system provided a stable and repeatable environment close to airway conditions. The results offer practical guidance for designing nanoparticles that can cross mucus barriers and improve inhaled drug delivery. Future work should test real human mucus and include ciliary movement to verify the model under physiological conditions.