Search Results (43)

The intestine–liver–muscle axis plays an essential role in drug and nutrient absorption, metabolism, and energy balance. Yet in vitro models capable of recapitulating this inter-organ communication remain limited. Here, we present a pump-free, 3D-printed multi-organ-on-a-chip device that enables dynamic co-culture of Caco-2 intestinal epithelial cells, HepG2 hepatocytes, and primary human skeletal myoblasts (HSkMs) under gravity-driven oscillatory flow. The device consists of five interconnected chambers designed to accommodate Transwell cell culture inserts for intestine and muscle compartments and hydrogel-embedded hepatocyte spheroids in the central hepatic compartment. The device was fabricated by low-cost fused deposition modeling (FDM) using acrylonitrile butadiene styrene (ABS) polymers. Under dynamic rocking, oscillatory perfusion promoted inter-organ communication without the need for external pumps or complex tubing. Biological assessments revealed that dynamic co-culture significantly enhanced the characteristics of skeletal muscle, as indicated by increased myosin heavy chain expression and elevated lactate production, while HepG2 spheroids exhibited improved hepatic function with higher albumin expression compared with monoculture. Additionally, Caco-2 cells maintained stable tight junctions and transepithelial electrical resistance, demonstrating preserved intestinal barrier integrity under dynamic flow. These results establish the device as a versatile, accessible 3D-printed platform for modeling the intestine–liver–muscle axis and investigating metabolic cross-talk in drug discovery and disease modeling. Full article

Whole genome doubling (WGD) triggers profound genomic and epigenetic reorganization, yet the functional dynamics of DNA methylation during this process remain incompletely resolved. Here, we integrate whole genome bisulfite sequencing (WGBS) and three-dimensional chromatin interaction data to display methylation landscapes in autotetraploid Arabidopsis thaliana. Our analysis reveals evolutionarily conserved spatial patterning of DNA methylation after WGD, with centromeric enrichment and telomeric depletion. Chromosome-level profiling identifies Chromosome 2 as the most highly methylated across CG, CHG, and CHH contexts, while Chromosome 1 shows the lowest methylation. Subcontext methylation analysis uncovers increases in methylation levels in autotetraploid Arabidopsis thaliana, most pronounced in the CHH context, yet global distribution patterns remain stable. Comparative methylation profiling around genes and transposable elements (TEs) reveals elevated CHH methylation in autotetraploid gene bodies and flanking regions, whereas TE bodies exhibit minimal changes despite minor flanking hypermethylation. Strikingly, 8% of chromatin compartments were restructured, and B-B interactions weakened in autotetraploid, while DNA methylation remained stable across shifting A/B compartments. Our findings suggest that DNA methylation serves as a resilient epigenetic modification during WGD, even if 3D chromatin architecture undergoes reorganization upon WGD in some degree. Full article

Background: Mucosal immunity plays a pivotal role in preventing infections with SARS-CoV-2. While COVID-19 mRNA vaccines induce robust systemic immune responses in patients with inflammatory bowel disease (IBD), little is known about their efficacy in the mucosal immune compartment. In this sub-investigation of the ongoing STAR-SIGN study, we present the first analysis of mucosal immunity elicited by XBB.1.5 mRNA vaccines in immunocompromised patients with IBD. Methods: IgG and IgA antibodies targeting the receptor-binding domain of the SARS-CoV-2 JN.1 variant were quantified longitudinally in the saliva of IBD patients using the multiplex immunoassay MultiCoV-Ab. Antibody levels were quantified before and 2–4 weeks after vaccination with XBB.1.5 mRNA vaccines. All patients previously received three doses with original COVID-19 vaccines. Results: Mucosal IgG antibodies were readily induced by XBB.1.5 mRNA vaccines (p = 0.0013 comparing pre- and post-vaccination levels). However, mucosal IgA levels were comparable before and after vaccination (p = 0.8233). Consequently, mucosal IgG and IgA antibody levels correlated only moderately before and after immunization (pre-vaccination: r = 0.5294; p = 0.0239; post-vaccination: r = 0.4863; p = 0.0407). Contrary to a previous report in healthy individuals, vaccination did not induce serum IgA in patients with IBD (p = 0.5841 comparing pre- and post-vaccination levels). These data suggest that COVID-19 mRNA vaccines fail to elicit mucosal IgA in patients with IBD. Conclusions: Since mucosal IgA plays a pivotal role in infection control, the lack of IgA induction indicates that patients lack sufficient protection against SARS-CoV-2 infections which warrants the development of mucosal COVID-19 vaccines. Full article

Background/Objectives. Central nervous system (CNS)-related diseases such as Alzheimer’s and Parkinson’s, Attention Deficit Hyperactive Disorder (ADHD), stroke, epilepsy, and migraines are leading causes of morbidity and disability worldwide. New solutions for drug delivery are increasingly needed. In this context, three-dimensional (3D) printing technology has introduced innovative alternatives to produce more efficient medicines with diverse features, patterns, and consistencies, particularly oral medications. Even though research in this area is growing rapidly, no study has thoroughly analyzed 3D printing oral drug delivery progress for the CNS. To fill this gap this study pursues to determine a technological landscape in this field. Methods. For this aim, a Competitive Technology Intelligence (CTI) methodology was applied, examining 747 publications from 1 January 2019 to 20 May 2024 published in the Scopus database. Results. The main advances identified comprise six categories: 3D printing techniques, characteristics and applications, materials, design factors, user acceptance, and quality processes. FDM was identified as the main technique for pharmaceutical use. The main applications include pills, polypills, caplets, gel caps, multitablets, orodispersible films, and tablets, featuring external patterns and internal structures with one or more active substances. Insights show that the most utilized materials are thermoplastic polymers like PLA, PVA, PCL, ABS, and HIPS. A novel design factor involves release patterns using compartments of varying thicknesses and volumes in the core. Additionally, advances in specialized software have enabled the creation of highly complex designs. In the user acceptance category, oral drugs dosages are tailored to the specific needs and preferences of neurological patients. Finally, for the quality aspect, the precision in Active Pharmaceutical Ingredient (API) dosage and controlled-release mechanisms are critical, given the narrow margin between therapeutic doses and toxicity for CNS diseases. Conclusions. Revealing these advancements in 3D printing for oral drug delivery allows researchers, academics, and decision-makers to identify opportunities and allocate resources efficiently, promising enhanced oral medicaments for the health and well-being of individuals suffering from CNS disorders. Full article

Background: The African hedgehog (Atelerix albiventris) exhibits specialized skin differentiation leading to spine formation, yet its regulatory mechanisms remain unclear. Transposable elements (TEs), particularly LINEs (long interspersed nuclear elements) and SINEs (short interspersed nuclear elements), are known to influence genome organization and gene regulation. Objectives: Given the high proportion of SINEs in the hedgehog genome, this study aims to characterize the distribution, evolutionary dynamics, and potential regulatory roles of LINEs and SINEs, focusing on their associations with chromatin architecture, DNA methylation, and gene expression. Methods: We analyzed LINE and SINE distribution using HiFi sequencing and classified TE families through phylogenetic reconstruction. Hi-C data were used to explore TE interactions with chromatin architecture, while whole-genome 5mCpG methylation was inferred from PacBio HiFi reads of muscle tissue using a deep-learning-based approach. RNA-seq data from skin tissues were analyzed to assess TE expression and potential associations with genes linked to spine development. Results: SINEs form distinct genomic blocks in GC-rich and highly methylated regions, whereas LINEs are enriched in AT-rich, hypomethylated regions. LINEs and SINEs are associated differently with A/B compartments, with SINEs in euchromatin and LINEs in heterochromatin. Methylation analysis suggests that younger TEs tend to have higher methylation levels, and expression analysis indicates that some differentially expressed TEs may be linked to genes involved in epidermal and skeletal development. Conclusions: This study provides a genome-wide perspective on LINE and SINE distribution, methylation patterns, and potential regulatory roles in A. albiventris. While not establishing a direct causal link, the findings suggest that TEs may influence gene expression associated with spine development, offering a basis for future functional studies. Full article

Background: The parenteral administration of antivenoms is the mainstay in snakebite envenoming therapy. The standardized protocol does not exist, but it is agreed that the intravenous (i.v.) route is more effective than the others, especially the intramuscular (i.m.) route, based on the monitoring of venom/antivenom pharmacokinetics in the systemic circulation. Recent evidence suggests that the lymphatic system may be crucial in abolishing venom action. Methods: A preclinical study was performed to determine the optimal administration route with emphasis on venom/antivenom interplay in both the blood and lymph of experimentally envenomed sheep. Timed level measurements were used to compare the antivenom effect on the decrement of venom quantities in both relevant body compartments. Hematological and coagulation parameters, as well as proportions of developed anti-antivenom IgGs, were evaluated. Results: The i.m. antivenom resulted in faster and greater lymphatic absorption and complete neutralization of the venom, whereas the i.v. antivenom only slowed its absorption. The total amount of venom reaching the lymph (AUC_0-t) was two times lower after i.m. administration. In the systemic circulation, i.m. antivenom had a lower peak concentration (c_max) and a longer time to reach it (t_max). However, the total venom exposure was three times lower than with i.v. antivenom. Irrespective of the treatment approach, both groups showed improvement in blood disorders with no significant difference in humoral response against equine F(ab’)₂ fragments. Conclusions: I.m. administration proved to be a viable option for the snakebite management. Full article

Data on the diffusion and migration characteristics of rare earth metal ions in fluoride molten salt systems are crucial for optimizing the electrolytic preparation of rare earth metals and alloys. This study investigated the solubility, conductivity, and density of the (LiF-CaF₂)_eut. system saturated with Nd₂O₃ using the isothermal saturation method, conductivity cell constant variation, and the Archimedes method, respectively. Employing the Hittorf method’s principles, a three-compartment electrolyzer was designed to determine the mobility number of dissolved Nd* (III) ions in the saturated (LiF-CaF₂)_eut.-Nd₂O₃ system. The radial distribution function was computed via ab initio molecular dynamics, and the self-diffusion coefficient of ions in the system was analyzed. Utilizing the Nernst–Einstein equation, the diffusion coefficient of Nd* (III) ions was calculated. The solubility, conductivity, and density of the saturated (LiF-CaF₂)_eut.-Nd₂O₃ system exhibit linear variation within 1173–1473 K. The mobility number of solvated Nd* (III) ions increases linearly with temperature, displaying nonlinear variation with potential within 3.5–4.5 V, and gradually decreases after reaching a maximum of 4.0–4.25 V. The radial distribution function reveals the highest diffusion and mobility barriers for Nd* (III) ions, with solvated O* (II) ions presenting the most significant hindrance. The Nd* (III) ion diffusion coefficients linearly increase with temperature (1123–1373 K) under specific potential conditions (3.5–4.5 V) but exhibit nonlinear changes with potential (3.5–4.5 V) under fixed temperature conditions (1123–1373 K), then decrease after peaking within 4.0–4.5 V. The diffusion coefficients of Nd* (III) ions are sensitive to potential changes. Full article

Background: Schwann cells (SCs) and their plasticity contribute to the peripheral nervous system’s capacity for nerve regeneration after injury. The Egr2/Krox20 promoter antisense RNA (Egr2-AS) recruits chromatin remodeling complexes to inhibit Egr2 transcription following peripheral nerve injury. Methods: RNA-seq and ATAC-seq were performed on control cells, Lenti-GFP-transduced cells, and cells overexpressing Egr2-AS (Lenti-AS). Egr2 AS-RNA was cloned into the pLVX-DsRed-Express2-N1 lentiviral expression vector (Clontech, Mountain View, CA, USA), and the levels of AS-RNA expression were determined. Ezh2 and Wdr5 were immunoprecipitated from rat SCs and RT-qPCR was performed against AS-Egr2 RNA. ChIP followed by DNA purification columns was used to perform qPCR for relevant promoters. Hi-C, HiC-DC+, R, Bioconductor, and TOBIAS were used for significant and differential loop analysis, identifications of COREs and CORE-promotor loops, comparisons of TF activity at promoter sites, and identification of site-specific TF footprints. OnTAD was used to detect TADs, and Juicer was used to identify A/B compartments. Results: Here we show that a Neuregulin-ErbB2/3 signaling axis mediates binding of the Egr2-AS to YY1^Ser184 and regulates its expression. Egr2-AS modulates the chromatin accessibility of Schwann cells and interacts with two distinct histone modification complexes. It binds to EZH2 and WDR5 and enables targeting of H3K27me3 and H3K4me3 to promoters of Egr2 and C-JUN, respectively. Expression of the Egr2-AS results in reorganization of the global chromatin landscape and quantitative changes in the loop formation and contact frequency at domain boundaries exhibiting enrichment for AP-1 genes. In addition, the Egr2-AS induces changes in the hierarchical TADs and increases transcription factor binding scores on an inter-TAD loop between a super-enhancer regulatory hub and the promoter of mTOR. Conclusions: Our results show that Neuregulin-ErbB2/3-YY1 regulates the expression of Egr2-AS, which mediates remodeling of the chromatin landscape in Schwann cells. Full article

Biological barriers remain a major obstacle for the development of innovative therapeutics. Depending on a disease’s pathophysiology, the involved tissues, cell populations, and cellular components, drugs often have to overcome several biological barriers to reach their target cells and become effective in a specific cellular compartment. Human biological barriers are incredibly diverse and include multiple layers of protection and obstruction. Importantly, biological barriers are not only found at the organ/tissue level, but also include cellular structures such as the outer plasma membrane, the endolysosomal machinery, and the nuclear envelope. Nowadays, clinicians have access to a broad arsenal of therapeutics ranging from chemically synthesized small molecules, biologicals including recombinant proteins (such as monoclonal antibodies and hormones), nucleic-acid-based therapeutics, and antibody-drug conjugates (ADCs), to modern viral-vector-mediated gene therapy. In the past decade, the therapeutic landscape has been changing rapidly, giving rise to a multitude of innovative therapy approaches. In 2018, the FDA approval of patisiran paved the way for small interfering RNAs (siRNAs) to become a novel class of nucleic-acid-based therapeutics, which—upon effective drug delivery to their target cells—allow to elegantly regulate the post-transcriptional gene expression. The recent approvals of valoctocogene roxaparvovec and etranacogene dezaparvovec for the treatment of hemophilia A and B, respectively, mark the breakthrough of viral-vector-based gene therapy as a new tool to cure disease. A multitude of highly innovative medicines and drug delivery methods including mRNA-based cancer vaccines and exosome-targeted therapy is on the verge of entering the market and changing the treatment landscape for a broad range of conditions. In this review, we provide insights into three different disease entities, which are clinically, scientifically, and socioeconomically impactful and have given rise to many technological advancements: acquired immunodeficiency syndrome (AIDS) as a predominant infectious disease, pancreatic carcinoma as one of the most lethal solid cancers, and hemophilia A/B as a hereditary genetic disorder. Our primary objective is to highlight the overarching principles of biological barriers that can be identified across different disease areas. Our second goal is to showcase which therapeutic approaches designed to cross disease-specific biological barriers have been promising in effectively treating disease. In this context, we will exemplify how the right selection of the drug category and delivery vehicle, mode of administration, and therapeutic target(s) can help overcome various biological barriers to prevent, treat, and cure disease. Full article

Canopy gaps and their associated processes play an important role in shaping forest structure and dynamics. Understanding the information about canopy gaps allows forest managers to assess the potential for regeneration and plan interventions to enhance regeneration success. Traditional field surveys for canopy gaps are time consuming and often inaccurate. In this study, canopy gaps were detected using unmanned aerial vehicle (UAV) imagery of two sub-compartments of an uneven-aged mixed forest in northern Japan. We compared the performance of U-Net and ResU-Net (U-Net combined with ResNet101) deep learning models using RGB, canopy height model (CHM), and fused RGB-CHM data from UAV imagery. Our results showed that the ResU-Net model, particularly when pre-trained on ImageNet (ResU-Net_2), achieved the highest F1-scores—0.77 in Sub-compartment 42B and 0.79 in Sub-compartment 16AB—outperforming the U-Net model (0.52 and 0.63) and the non-pre-trained ResU-Net model (ResU-Net_1) (0.70 and 0.72). ResU-Net_2 also achieved superior overall accuracy values of 0.96 and 0.97, outperforming previous methods that used UAV datasets with varying methodologies for canopy gap detection. These findings underscore the effectiveness of the ResU-Net_2 model in detecting canopy gaps in uneven-aged mixed forests. Furthermore, when these trained models were applied as transfer models to detect gaps specifically caused by selection harvesting using pre- and post-UAV imagery, they showed considerable potential, achieving moderate F1-scores of 0.54 and 0.56, even with a limited training dataset. Overall, our study demonstrates that combining UAV imagery with deep learning techniques, particularly pre-trained models, significantly improves canopy gap detection accuracy and provides valuable insights for forest management and future research. Full article

This study investigates how grapevines (Vitis vinifera L.) respond to shading induced by artificial nets, focusing on physiological and metabolic changes. Through a multidisciplinary approach, grapevines’ adaptations to shading are presented via biochemical analyses and hyperspectral data that are then combined with systems biology techniques. In the study, conducted in a ‘Moscatel Galego Branco’ vineyard in Portugal’s Douro Wine Region during post-veraison, shading was applied and predawn leaf water potential (${\Psi }_{pd}$) was then measured to assess water stress. Biochemical analyses and hyperspectral data were integrated to explore adaptations to shading, revealing higher chlorophyll levels (chlorophyll a-b 117.39% higher) and increased Reactive Oxygen Species (ROS) levels in unshaded vines (52.10% higher). Using a self-learning artificial intelligence algorithm (SL-AI), simulations highlighted ROS’s role in stress response and accurately predicted chlorophyll a (R²: 0.92, MAPE: 24.39%), chlorophyll b (R²: 0.96, MAPE: 17.61%), and ROS levels (R²: 0.76, MAPE: 52.17%). In silico simulations employing flux balance analysis (FBA) elucidated distinct metabolic phenotypes between shaded and unshaded vines across cellular compartments. Integrating these findings provides a systems biology approach for understanding grapevine responses to environmental stressors. The leveraging of advanced omics technologies and precise metabolic models holds immense potential for untangling grapevine metabolism and optimizing viticultural practices for enhanced productivity and quality. Full article

Heterosis plays a significant role in enhancing variety, boosting yield, and raising economic value in crops, but the molecular mechanism is still unclear. We analyzed the transcriptomes and 3D genomes of a hybrid (F₁) and its parents (w30 and 082). The analysis of the expression revealed a total of 485 specially expressed genes (SEGs), 173 differentially expressed genes (DEGs) above the parental expression level, more actively expressed genes, and up-regulated DEGs in the F₁. Further study revealed that the DEGs detected in the F₁ and its parents were mainly involved in the response to auxin, plant hormone signal transduction, DNA metabolic process, purine metabolism, starch, and sucrose metabolism, which suggested that these biological processes may play a crucial role in the heterosis of Brassica rapa. The analysis of 3D genome data revealed that hybrid F₁ plants tend to contain more transcriptionally active A chromatin compartments after hybridization. Supplementaryly, the F₁ had a smaller TAD (topologically associated domain) genome length, but the number was the highest, and the expression change in activated TAD was higher than that of repressed TAD. More specific TAD boundaries were detected between the parents and F₁. Subsequently, 140 DEGs with genomic structural variants were selected as potential candidate genes. We found two DEGs with consistent expression changes in A/B compartments and TADs. Our findings suggested that genomic structural variants, such as TADs and A/B chromatin compartments, may affect gene expression and contribute to heterosis in Brassica rapa. This study provides further insight into the molecular mechanism of heterosis in Brassica rapa. Full article

The system of the four different human blood groups is based on the oligosaccharide antigens A or B, which are located on the surface of blood cells and other cells including endothelial cells, attached to the membrane proteins or lipids. After transfusion, the presence of these antigens on the apical surface of endothelial cells could induce an immunological reaction against the host. The final oligosaccharide sequence of AgA consists of Gal-GlcNAc-Gal (GalNAc)-Fuc. AgB contains Gal-GlcNAc-Gal (Gal)-Fuc. These antigens are synthesised in the Golgi complex (GC) using unique Golgi glycosylation enzymes (GGEs). People with AgA also synthesise antibodies against AgB (group A [II]). People with AgB synthesise antibodies against AgA (group B [III]). People expressing AgA together with AgB (group AB [IV]) do not have these antibodies, while people who do not express these antigens (group O [0; I]) synthesise antibodies against both antigens. Consequently, the antibodies are synthesised against antigens that apparently do not exist in the body. Here, we compared the prediction power of the main hypotheses explaining the formation of these antibodies, namely, the concept of natural antibodies, the gut bacteria-derived antibody hypothesis, and the antibodies formed as a result of glycosylation mistakes or de-sialylation of polysaccharide chains. We assume that when the GC is overloaded with lipids, other less specialised GGEs could make mistakes and synthesise the antigens of these blood groups. Alternatively, under these conditions, the chylomicrons formed in the enterocytes may, under this overload, linger in the post-Golgi compartment, which is temporarily connected to the endosomes. These compartments contain neuraminidases that can cleave off sialic acid, unmasking these blood antigens located below the acid and inducing the production of antibodies. Full article

Na-K-2Cl cotransporter 1 (NKCC1) regulates chloride influx in neurons and thereby GABA_A receptor activity in normal and pathological conditions. Here, we characterized in hippocampal neurons the membrane expression, distribution and dynamics of exogenous NKCC1a and NKCC1b isoforms and compared them to those of the chloride extruder K-Cl cotransporter 2 (KCC2). We found that NKCC1a and NKCC1b behave quite similarly. NKCC1a/1b but not KCC2 are present along the axon initial segment where they are confined. Moreover, NKCC1a/1b are detected in the somato-dendritic compartment at a lower level than KCC2, where they form fewer, smaller and less compact clusters at perisynaptic and extrasynaptic sites. Interestingly, ~60% of dendritic clusters of NKCC1a/1b are colocalized with KCC2. They are larger and brighter than those devoid of KCC2, suggesting a particular NKCC1a/1b-KCC2 relationship. In agreement with the reduced dendritic clustering of NKCC1a/1b compared with that of KCC2, NKCC1a/1b are more mobile on the dendrite than KCC2, suggesting weaker cytoskeletal interaction. NKCC1a/b are confined to endocytic zones, where they spend more time than KCC2. However, they spend less time in these compartments than at the synapses, suggesting that they can rapidly leave endocytic zones to increase the membrane pool, which can happen in pathological conditions. Thus, NKCC1a/b have different membrane dynamics and clustering from KCC2, which helps to explain their low level in the neuronal membrane, while allowing a rapid increase in the membrane pool under pathological conditions. Full article

Drug development in recent years is increasingly focused on developing personalized treatments based on blocking molecules selective for therapeutic targets specifically present in individual patients. In this perspective, the specificity of therapeutic targets and blocking agents plays a crucial role. Monoclonal antibodies (mAbs) and their surrogates are increasingly used in this context thanks to their ability to bind therapeutic targets and to inhibit their activity or to transport bioactive molecules into the compartments in which the targets are expressed. Small antibody-like molecules, such as Fabs, are often used in certain clinical settings where small size and better tissue penetration are required. In the wake of this research trend, we developed a murine mAb (3D1) neutralizing the activity of Nodal, an oncofetal protein that is attracting an ever-increasing interest as a selective therapeutic target for several cancer types. Here, we report the preparation of a recombinant Fab of 3D1 that has been humanized through a computational approach starting from the sequence of the murine antibody. The Fab has been expressed in bacterial cells (1 mg/L bacterial culture), biochemically characterized in terms of stability and binding properties by circular dichroism and bio-layer interferometry techniques and tested in vitro on Nodal-positive cancer cells. Full article