Placenta. 2025 Jul 26;169:94-106. doi: 10.1016/j.placenta.2025.07.085. Online ahead of print.

ABSTRACT

BACKGROUND: Preeclampsia (PE) is a hypertensive pregnancy syndrome with significant clinical and pathological diversity, linked to distinct etiological subclasses. One etiological subclass of PE, characterized by increased inflammation at the maternal-fetal interface (I-PE), is strongly associated with preterm birth and fetal growth restriction, though its specific pathophysiology remains poorly understood. Inflammatory signals can induce iron overload, leading to ferroptosis-a programmed cell death process. Dysregulation of systemic and placental iron metabolism has been described in PE when considered as a single clinical entity, but previous studies have not accounted for distinct underlying etiologies. This study investigates the role of ferroptosis signaling in placental dysfunction across different PE subclasses.

METHODS: Histological analysis assessed placental iron accumulation and ferritin protein expression. Placental gene expression was evaluated for ferroptosis-related genes (FRGs) using gene set enrichment analysis (GSEA) on placenta samples from healthy controls and three previously described PE subclasses. Digital cytometry estimated cell type-specific expression of FRGs across these subclasses.

RESULTS: Significant placenta iron accumulation and reduced ferritin expression were found exclusively in I-PE subclass. GSEA showed enrichment of FRGs across various functional categories, including regulators, markers, suppressors, and unclassified FRGs in the placentas from I-PE. Digital cytometry indicated disrupted FRG expression in trophoblasts and mesodermal stromal cells in these placentas, consistent with histologically observed iron accumulation.

CONCLUSION: Placental iron accumulation and disrupted ferroptosis signaling in I-PE subclass suggests a novel mechanism of placental dysfunction unique to this subclass. Further research is needed to explore how regulating ferroptosis could aid in managing I-PE.

PMID:40738047 | DOI:10.1016/j.placenta.2025.07.085

Phytomedicine. 2025 Jul 23;146:157095. doi: 10.1016/j.phymed.2025.157095. Online ahead of print.

ABSTRACT

BACKGROUND: Sophora flos (SF) is a medicinal plant with a rich history. Its principal bioactive constituents are flavonoids, which are known for their remarkable anti-inflammatory and antioxidant properties. Nevertheless, a thorough investigation of its potential regulatory mechanisms in the context of treating inflammatory bowel disease (IBD) is lacking.

PURPOSE: This study comprehensively assessed the pharmacological effects of Sophora flos extract (SFE) both in vitro and in vivo, with a specific focus on its efficacy against IBD and the underlying mechanisms involved.

METHODS: UHPLC-LTQ-ESI-Orbitrap-MS was used to analyze the chemical composition of SFE. Mouse colitis models were induced with dextran sulfate sodium (DSS). SFE therapeutic efficacy was assessed by colon length, disease activity index (DAI) and histopathology score. Changes in inflammatory cytokines, tight junction proteins and the macrophage phenotype after SFE treatment were assessed. Furthermore, the anti-inflammatory, antioxidant and regulatory effects of SFE on the macrophage phenotype were evaluated in lipopolysaccharide (LPS)-stimulated RAW 264.7 cells. Using systems biology methodologies, we predicted potential targets and signaling pathways and validated them through experiments.

RESULTS: UPLC‒LTQ‒Orbitrap‒MS analysis revealed 59 compounds in SFE, and the most abundant of these compounds was rutin. Animal studies demonstrated that SFE treatment improved colon length, DAI, and colon inflammation while decreasing proinflammatory cytokine expression and increasing the expression of anti-inflammatory cytokines and tight junction proteins. Immunofluorescence revealed that SFE treatment inhibited M1 macrophage polarization and promoted M2 macrophage polarization. Cellular experiments revealed that SFE treatment reduced ROS levels and modulated the release of inflammatory mediators and the balance of M1/M2 macrophage polarization. Network pharmacology analyses revealed that SF comprises eight principal components and interacts with 123 potential targets involved in IBD treatment, which are intricately associated with signaling pathways such as the PI3K/Akt, mTOR, and TNF pathways. Molecular docking results confirmed that PIK3CA, AKT1, PIK3R1 and TNF had high affinities for the main active components of SF, with the strongest affinity for rutin. Western blot and Q-PCR experiments revealed that PI3K/Akt/mTOR and TNFα expression were increased after LPS or DSS induction, and SFE or rutin treatment reversed these changes.

CONCLUSION: This study integrates UPLC‒MS phytochemical profiling, network pharmacology, and experimental validation to elucidate the anti-IBD mechanisms of SFE. We identified 59 bioactive compounds in SFE and demonstrated their efficacy via the inhibition of PI3K/Akt/mTOR and TNFα signaling. Notably, this work is the first to reveal that SFE alleviates IBD by restoring intestinal barrier integrity and rebalancing M1/M2 macrophage polarization. Molecular docking/dynamics confirmed the high affinity of rutin for core targets (PIK3CA, AKT1, and TNF). These findings establish SFE as a multitarget IBD therapeutic, synergizing traditional use with mechanistic validation through integrative omics and experimental approaches.

PMID:40737847 | DOI:10.1016/j.phymed.2025.157095

Plant Physiol Biochem. 2025 Jul 26;228:110264. doi: 10.1016/j.plaphy.2025.110264. Online ahead of print.

ABSTRACT

Drought stress reduces plant growth and yield of crops. Common bean (Phaseolus vulgaris L.) establishes symbiosis with rhizobia, ensuring an adequate nitrogen supply without fertilizers. However, the relationship with rhizobia is constrained by limited water availability which inhibits both nitrogen fixation and plant growth. In addition, physiological and molecular responses of common bean to drought are conditioned by the form of nitrogen assimilated. Therefore, understanding the molecular mechanism(s) triggered in common bean under water-deficit conditions is relevant to identify the best strategies to resist drought stress. With the objective of understanding the molecular responses of roots and nodules from common bean to water-deficit stress, plants cultivated under N2-fixation or nitrate fertilization were exposed to ten days of water deprivation. Afterwards, transcriptomic analysis was performed in roots, while metabolome profiling was carried out in roots and nodules. Physiological results showed that under water-deficit, N2-fixing plants increased their root biomass more than nitrate-fertilized plants. Furthermore, water-deficit stress induced more transcriptional changes in nitrate-fertilized plants than in N2-fixing plants, including a larger number of transcription factors in these plants compared with the N2-fixing plants. On the other hand, roots from N2-fixing plants accumulated more metabolites with potential protective functions such as allantoin, proline, raffinose, abscisic acid, and flavonoids in response to water-deficit stress than plants fertilized with nitrate, indicating that symbiosis might facilitate a faster and more efficient response to water-deficit stress. Moreover, common bean nodules exposed to water-deficit stress accumulated proline and erythritol, but reduced their content of maltose, pyruvic acid and allantoin compared to their respective controls. Taken collectively, these findings suggest that, despite the inhibition of nodule activity, N2-fixing plants respond better to water-deficit stress than nitrate-fertilized plants.

PMID:40737754 | DOI:10.1016/j.plaphy.2025.110264

ACS Synth Biol. 2025 Jul 30. doi: 10.1021/acssynbio.4c00867. Online ahead of print.

ABSTRACT

Human milk oligosaccharides (HMOs) are the third most abundant solid component in human breast milk, playing vital roles in promoting infant growth, supporting immune system development, and preventing infections. Due to these benefits, HMOs are increasingly being incorporated into infant formula, making their low-cost, large-scale production a pressing need. Recent advances in biosynthesis have focused on developing efficient production methods, particularly using genetically engineered Escherichia coli and other microbial hosts. This review begins by outlining the biological significance and structural complexity of HMOs, followed by an analysis of the limitations associated with traditional chemical and enzymatic synthesis approaches. The review then highlights the advantages of metabolic engineering in industrial microbes, such as reduced costs by eliminating the need for enzyme purification and leveraging native cellular pathways for sugar nucleotide biosynthesis. It further explores the construction of synthetic pathways for various HMOs in microbial systems, detailing metabolic engineering strategies including modular pathway design, cofactor optimization, glycosyltransferase and transporter engineering, and the spatial organization of enzymes through self-assembly techniques. Finally, the review addresses current challenges and future directions in the field. These include promoter engineering, further optimization of glycosyltransferases and transporters, balancing product synthesis with cell growth, and the integration of omics technologies and metabolic flux analysis. Overall, this review provides a comprehensive overview of HMO biosynthesis, emphasizing the integration of traditional metabolic engineering with synthetic and systems biology. This multilevel dynamic regulation approach is key to enabling the efficient and sustainable microbial production of HMOs.

PMID:40737581 | DOI:10.1021/acssynbio.4c00867

Toxicol Sci. 2025 Jul 30:kfaf110. doi: 10.1093/toxsci/kfaf110. Online ahead of print.

ABSTRACT

Alcohol-associated liver disease (ALD) remains a leading contributor to global morbidity and mortality. Chronic ethanol intake drives hepatocellular damage through multiple mechanisms, such as acetaldehyde-induced cytotoxicity, dysregulated lipid metabolism, oxidative stress, and inflammation. Per- and polyfluoroalkyl substances (PFAS) have emerged as major environmental contaminants, characterized by their persistence, bioaccumulation, and capacity to disrupt hepatic function. PFAS share pathogenic pathways with ALD, including interference with mitochondrial function, oxidative stress induction, and steatosis promotion via altered lipid homeostasis. As exposure to PFAS becomes increasingly widespread and the burden of ALD continues to rise, understanding their potential synergistic impact on liver function is crucial. This review synthesizes current findings on the central mechanisms of ALD pathology, summarizes the hepatotoxic effects of PFAS, and explores their converging roles in exacerbating liver injury. Key pathways of interest include shared disruption of fatty acid oxidation, additive oxidative stress, and immunomodulation. The potential for concurrent exposure in high-risk populations (such as occupational groups with elevated PFAS exposure and higher-than-average alcohol use) warrants concern, particularly given these people often face more limited healthcare access. By identifying mechanistic convergences, this review underscores the need for targeted studies that address how common co-exposures to PFAS and alcohol may intensify liver pathology, the value of a systems biology approach for future investigations, and the importance of implementing strategies to mitigate these synergistic hazards.

PMID:40737496 | DOI:10.1093/toxsci/kfaf110

Sci Adv. 2025 Aug;11(31):eads2310. doi: 10.1126/sciadv.ads2310. Epub 2025 Jul 30.

ABSTRACT

Coordinated growth of multiple tissues is fundamental to shaping our body, but the underlying mechanisms remain underexplored. In zebrafish embryos, midline tissues composed of the notochord, floorplate, and hypochord elongate synchronously with their lengths aligned. We show that floorplate and hypochord cells collectively migrate posteriorly along the nascent notochord extracellular matrix as it extends posteriorly, maintaining the tripartite configuration. Fibroblast growth factor-mediated migration in a spatially graded manner causes cell stretching, which triggers Yap-dependent proliferation and controls floorplate and hypochord growth. Supported by mathematical modeling, we further suggest that their growth is fine-tuned by mechanical tethering to the notochord via cadherin 2 at the posterior end. We propose that the notochord instructs and sustains the tripartite formation via leader-follower formation control, a strategy from engineering that spatially organizes multiple agents to coordinate the growth of the midline tissues.

PMID:40737421 | DOI:10.1126/sciadv.ads2310

ACS Synth Biol. 2025 Jul 30. doi: 10.1021/acssynbio.5c00051. Online ahead of print.

ABSTRACT

Achieving precise control over quantitative developmental phenotypes is a key objective in plant biology. Recent advances in synthetic biology have enabled tools to reprogram entire developmental pathways; however, the complexity of designing synthetic genetic programs and the inherent interactions between various signaling processes remains a critical challenge. Here, we leverage Type-B response regulators to modulate the expression of genes involved in cytokinin-dependent growth and development processes. We rationally engineered these regulators to modulate their transcriptional activity (i.e., repression or activation) and potency while reducing their sensitivity to cytokinin. By localizing the expression of these engineered transcription factors using tissue-specific promoters, we can predictably tune cytokinin-regulated traits. As a proof of principle, we deployed this synthetic system in Arabidopsis thaliana to either decrease or increase the number of lateral roots. The simplicity and modularity of our approach makes it an ideal system for controlling other developmental phenotypes of agronomic interest in plants.

PMID:40737362 | DOI:10.1021/acssynbio.5c00051

PLoS Biol. 2025 Jul 30;23(7):e3003318. doi: 10.1371/journal.pbio.3003318. Online ahead of print.

ABSTRACT

The ventricular zone (VZ) harbors the largest neurogenic niche in the adult mammalian brain and is consisted of neural stem cells (NSCs) and multiciliated ependymal cells (EPCs). Previous lineage tracing studies showed that both NSCs and EPCs were derived from radial glial cells (RGCs). However, the transcriptomic dynamics and the molecular mechanisms guiding the cell fate commitment during the differentiation remain poorly understood. In this study, we analyzed the developing VZ of mice at single-cell resolution and identified three distinct cellular states of RGCs: bipotent glial progenitor cells (bGPCs), neonatal NSC-neuroblasts (nNSC-NBs) and neonatal EPCs (nEPCs). The differentiation from bGPCs to nNSC-NBs and nEPCs forms a continuous bifurcating trajectory. Analysis along the NSC branch unveiled a novel intermediate state of cells expressing oligodendrocyte precursor cell (OPC) and neuroblast (NB) marker genes simultaneously. Several transcription factors (TFs) were found to be essential for the EPC-lineage differentiation. Notably, we uncovered that TFEB can tune NSC/EPC bifurcation, independent of its canonical function as a master regulator of the lysosome biogenesis. TFEB activation prevents the overproduction of EPCs by cooperating with LHX2 to balance the expressions of many multicilia-related genes while promotes the differentiation into NSC-NBs. Our results resolve the dynamic repertoire of divergent RGCs during VZ development and offer novel insights into the potential application of TFEB-targeted clinical drugs in VZ-related disorders, such as hydrocephalus and neurodegenerative diseases (NDDs).

PMID:40737354 | DOI:10.1371/journal.pbio.3003318

Brief Bioinform. 2025 Jul 2;26(4):bbaf387. doi: 10.1093/bib/bbaf387.

ABSTRACT

In the last two decades, numerous in silico methods have been developed for drug repurposing, to accelerate and reduce the risks about early drug development. Particularly, following Connectivity Map, dozens of distinct data-driven methods have been implemented to find candidates from the comparison of differential transcriptomic signatures. Interestingly, there have been multiple proposals to integrate available knowledge using systems biology databases and adapted algorithms from the network biology research field. Despite their similarities, these methods have been formulated inconsistently over the years, even if some of them are fundamentally similar. The aim of this review is to reconcile these integrative methods, focusing on elucidating their common structures while underlining the specificities of their strategies. To achieve this, we classified those methods into two main categories, provided schematic workflow representations, and presented a homogenized formulation for each.

PMID:40736744 | DOI:10.1093/bib/bbaf387

Cell Mol Life Sci. 2025 Jul 30;82(1):293. doi: 10.1007/s00018-025-05822-6.

ABSTRACT

The prevalence of the Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important transition in the epidemic of coronavirus disease 2019 (COVID-19). Compared with other SARS-CoV-2 variants, Omicron and its subvariants exhibit decreased pathogenicity, thus contributing to the moderation of the epidemic. However, the mechanism underlying such changes is not fully understood. NSP5 is a SARS-CoV-2-encoded protease that counteracts antiviral immunity, and the P132H mutation of NSP5 is present exclusively in Omicron and its subvariants. In this study, we found that this mutation solely relieved cytopathogenicity and reduced the viral replication during SARS-CoV-2 infection. Further studies suggested that P132H blocked the NSP5-mediated degradation of MAVS by impairing the K136-linked ubiquitination of MAVS, thus restoring the IFN-β activation inhibited by NSP5. Structural analysis in silico suggested that P132H disrupted multiple hydrogen bonds between NSP5 and UbcH5b, an E2 ubiquitin-conjugating enzyme required for K136 ubiquitination. In summary, our results provide a potential mechanism explaining the decreased pathogenicity of the Omicron variant of SARS-CoV-2.

PMID:40736574 | DOI:10.1007/s00018-025-05822-6

Endocr Metab Immune Disord Drug Targets. 2025 Jul 28. doi: 10.2174/0118715303364014250713045734. Online ahead of print.

ABSTRACT

AIM: Observational studies have suggested an association between celiac disease and thyroid dysfunction, but their causal relationship has not yet been established.

METHODS: Summary statistics for celiac disease were retrieved from the FinnGen Consortium, thyroid hormone and antibody data were obtained from the ThyroidOmics Consortium, and genetic variants associated with hyperthyroidism and hypothyroidism were sourced from the UK Biobank. MR statistical analyses used the inverse variance weighted algorithm, followed by various sensitivity analyses and reliability evaluations.

RESULTS: Genetic proxied celiac disease was significantly associated with increased free thyroxine (FT4) and thyroid peroxidase antibody (TPOAb) levels and decreased free triiodothyronine (FT3)/FT4 ratio, whereas the causality of this common enteropathy on thyroid stimulating hormone (TSH), FT3, total triiodothyronine (TT3), and TT3/FT4 ratio (and vice versa) is unfounded. Moreover, the findings of MR analysis tend to favor the causality of celiac disease for hyperthyroidism, but not hypothyroidism.

CONCLUSION: By leveraging large GWAS consortia datasets, our MR study indicates that the genetic liability to celiac disease is suggestively detrimental to the homeostasis of FT4 and TPOAb levels and FT3/FT4 ratio. Our findings provide caution regarding the risk of hyperthyroidism but not hypothyroidism for individuals suffering from celiac disease.

PMID:40735990 | DOI:10.2174/0118715303364014250713045734

Mol Ecol. 2025 Jul 29:e70057. doi: 10.1111/mec.70057. Online ahead of print.

ABSTRACT

Urbanisation presents unique environmental pressures that drive rapid evolutionary adaptations, particularly in species inhabiting fragmented and anthropogenised landscapes. In this study, we investigate the genomic differentiation between urban and non-urban populations of Anolis carolinensis, focusing on two main aspects: (1) the effect of habitat fragmentation on inbreeding and mutational load and (2) genomic adaptation to the urban habitat. We found that urban populations can exhibit a reduced mutational load, which is a direct consequence of systemic inbreeding. Using genome-wide scans of selection and analyses of genetic diversity, we identify key genomic regions exhibiting significant divergence between urban and non-urban populations. These regions are enriched for genes associated with immunity, behaviour and development, suggesting that urban adaptation is polygenic and involves traits related to stress response, locomotion and thermoregulation. Scans for association with the urban environment reveal a large genomic region in chromosome 2 encompassing the HOXC gene cluster. We also detect a signal of both association and increased differentiation on chromosome 1 in a region previously identified as a candidate for convergent adaptation in another Anolis species, A. cristatellus. Although evidence for convergent evolution at the gene level remains limited, potential signatures of urban adaptation in loci involved in immune response, locomotion and behaviour support the hypothesis that urban environments exert similar selective pressures across species. These results provide evidence for redundancy and polygenic adaptation and highlight the complexity of urban evolution. Future work with denser population sampling and time-series data will be essential to confirm the role of urban selective pressures and track the genetic dynamics of urban populations over time.

PMID:40734377 | DOI:10.1111/mec.70057

Mol Ther. 2025 Jul 28:S1525-0016(25)00577-5. doi: 10.1016/j.ymthe.2025.07.041. Online ahead of print.

ABSTRACT

Spinal cord injury (SCI) disrupts communication between the brain and the spinal circuits, resulting in severe motor, sensory, and autonomic dysfunctions. Transplantation of neural progenitor cells (NPC) has been demonstrated to provide multiple benefits; however, limited graft survival and neuronal differentiation must be overcome to achieve improved results. Here, we explore the optogenetic modulation of rat spinal cord-derived NPC expressing channelrhodopsin-2 (ChR2), through AAV9-mediated transduction, transplanted into the sub-acute stage after SCI. Daily blue-light stimulation and ChR2-dependent activation control of the modified NPC significantly enhanced locomotor skills, run speed, sustained walking coordination, and body stability in a rat SCI model. Engrafted rat NPC-ChR2 reduces astrocytic reactivity and the injured area volume; preserves a higher number of descending propriospinal neurons above the injury; and a higher innervation of 5-HT fibers to ChAT-positive motoneurons below the injury, and the increased VGlut2 expression suggests an enhanced excitatory synaptic activity. Overall, sustained activation of rat NPC post-transplantation offers a promising strategy for improved locomotor recovery following SCI.

PMID:40734274 | DOI:10.1016/j.ymthe.2025.07.041

Carbohydr Polym. 2025 Oct 15;366:123840. doi: 10.1016/j.carbpol.2025.123840. Epub 2025 Jun 6.

ABSTRACT

Polymer-based nanoparticle systems are gaining increasing attention in drug delivery due to their stability, biocompatibility, and controlled release capabilities. Understanding the self-assembly behavior of polysaccharides is crucial for designing effective nanocarriers, yet the conditions governing their organization remain poorly explored. In this study, we employed a combined in silico and in vitro approach to investigate the self-assembly mechanisms of levan and leverage this knowledge to develop a surfactant-free, bioinspired drug delivery system. Molecular simulations revealed that self-assembly is strongly influenced by pH, with alkaline conditions promoting compact, organized structures and acidic conditions leading to disordered arrangements. Guided by these findings, levan nanoparticles were synthesized both with and without the addition of the commonly used non-ionic surfactants Pluronic F-127 and Tween-80 and under optimal conditions, surfactant-free formulations demonstrated high encapsulation efficiency (∼80-92 %), enhanced stability, and controlled release of oleuropein (OLE), a bioactive polyphenol with poor gastrointestinal bioavailability. In vitro release studies demonstrated sustained OLE delivery over 24 h, with diffusion-controlled kinetics in intestinal conditions. Antioxidant activity assays confirmed that OLE retained its radical-scavenging properties post-encapsulation. Furthermore, cytocompatibility tests using fibroblast and colon cancer cell lines demonstrated that levan nanoparticles were non-toxic and supported cell viability.

PMID:40733757 | DOI:10.1016/j.carbpol.2025.123840

Vaccines (Basel). 2025 Jul 13;13(7):750. doi: 10.3390/vaccines13070750.

ABSTRACT

Background: Hemodialysis patients, due to impaired kidney function and compromised immune responses, face increased risks from SARS-CoV-2. Anti-nucleocapsid IgG (anti-IgG N) antibodies are a commonly used marker to assess prior infection in the general population; however, their efficacy for hemodialysis patients remains unclear. Methods: A retrospective study of 361 hemodialysis patients evaluated anti-IgG N antibodies for detecting prior SARS-CoV-2 infection. Antibody levels were measured using a chemiluminescence immunoassay (CLIA) over the four time points. Boxplots illustrated antibody distribution across sampling stages and infection status. Logistic regression and receiver operating characteristic (ROC) curve analysis determined diagnostic accuracy, sensitivity, specificity, and optimal cutoff values. Results: Among the 361 hemodialysis patients, 36 (10.0%) had SARS-CoV-2 infection. Sex distribution showed a trend toward significance (p = 0.05). Boxplot analysis showed that anti-IgG N levels remained low in non-infected patients but increased in infected patients, peaking at the third sampling. Anti-IgG N demonstrated high diagnostic accuracy (AUC: 0.973-0.865) but declined over time (p = 0.00525). The optimal cutoff at C1 was 0.01 AU/mL (sensitivity 1.00, specificity 0.94). Adjusted models had lower predictive value. Conclusions: Anti-IgG N antibodies showed high diagnostic accuracy for detecting prior SARS-CoV-2 infection in hemodialysis patients, though performance declined over time. These findings highlight the need for tailored diagnostic strategies in this vulnerable population.

PMID:40733727 | DOI:10.3390/vaccines13070750

Plants (Basel). 2025 Jul 14;14(14):2176. doi: 10.3390/plants14142176.

ABSTRACT

Bulgarian botanical gardens harbor more than 3600 plant species from across the world. Some of them are well-known plants widely used by humans, others are underutilized crops or little-known exotic species. The latter group constitutes a rich reservoir of plant resources whose potential to bring benefits to society is still untapped. The aim of this review is to describe the diversity of species and their potentially valuable secondary metabolites in three of the largest Bulgarian botanical gardens, with a focus on underutilized crops and medicinal plants that are typical of Bulgaria. With this, we aim to pave the way for future research on the most promising of these plants. The report includes currently available ethnobotanical data on the properties and composition of their bioactive components, known culinary or therapeutic uses, and nutritional profiles. We also outline the vast potential of these plants in providing healthy diets, as well as for performing future groundbreaking biomedical research. Finally, we present the approach that will be used to screen extracts from these plants for biological activity.

PMID:40733413 | DOI:10.3390/plants14142176

Molecules. 2025 Jul 11;30(14):2941. doi: 10.3390/molecules30142941.

ABSTRACT

We present a detailed examination of the absorption coefficients in the THz region for different water models using different types of potentials: the non-polarizable SPC/E, the Drude-polarizable SWM4-NDP and OPC3-pol, IPOL-0.13 and the multipole AMOEBA14 water. The primary focus is on understanding the interplay between permanent and induced dipole moments and their influence on the THz spectrum. Although the induced dipoles strongly contribute to the peak at 200 cm-1, merely increasing the induced dipole moments does not improve the agreement with experiments. We aim to investigate the behavior of the intensity at 200 cm-1 depending on the water model. Furthermore, we dissect the THz spectra of the water models into distinct contributions to gain more insight into the inter- and intramolecular interactions. Intermolecular interactions significantly contribute to the low-frequency peak, while the peak observed at 600 cm-1 can be adequately attributed to intramolecular dipole-dipole interactions.

PMID:40733210 | DOI:10.3390/molecules30142941

Nutrients. 2025 Jul 17;17(14):2348. doi: 10.3390/nu17142348.

ABSTRACT

Background/Objectives: Childhood stunting remains a critical public health issue in low- and middle-income countries. Despite Malaysia's economic growth, there is limited large-scale evidence on the determinants of stunting among children from infancy to primary school age. This cross-sectional study, part of South East Asian Nutrition Surveys II (SEANUTS II), aimed to determine sociodemographic and environmental risk factors for stunting among 2989 children aged 0.5-12 years. Methods: Children were recruited from four regions in Peninsular Malaysia (Central, East Coast, 2022-2030Northern, Southern). Standing height or recumbent length was measured, and stunting was classified based on WHO criteria (height-for-age Z-score below -2 standard deviations). Parents reported information on socioeconomic status, sanitation facilities, and hygiene practices. Multivariate binary logistic regression was used to determine the determinants of stunting. Results: Stunting prevalence was 8.9%, with infants (aOR = 2.92, 95%CI:1.14-7.52) and young children (aOR = 2.92, 95%CI:1.80-4.76) having higher odds than school-aged children. Key biological predictors included low birth weight (aOR = 2.41; 95%CI:1.40-4.13) and maternal height <150 cm (aOR = 2.24; 95%CI:1.36-3.70). Chinese (aOR = 0.56; 95%CI:0.35-0.88) and Indian children (aOR = 0.16; 95%CI:0.05-0.52) had a lower risk of stunting compared to Malays. Conclusions: This study highlights the ongoing challenge of childhood stunting in Malaysia, with age, birth weight, ethnicity, and maternal height identified as key determinants. These findings call for early identification of at-risk households and targeted support, especially through education and financial aid to foster healthy child growth.

PMID:40732975 | DOI:10.3390/nu17142348

Microorganisms. 2025 Jul 9;13(7):1622. doi: 10.3390/microorganisms13071622.

ABSTRACT

Verticillium wilt, caused by Verticillium dahliae, poses a significant threat to olive trees (Olea europaea L.). The isolation of endophytic Streptomyces strains from olive roots has led to the discovery of several strains showing strong antifungal activity against V. dahliae, as demonstrated through in vitro and small-scale soil experiments. Molecular analyses confirmed that strain OE54 belongs to Streptomyces iranensis. The main antifungal compound identified in this strain was rapamycin. Rapamycin displayed potent antifungal effects, notably inhibiting conidiospore germination (IC50 = 87.36 μg/mL) and the hyphal growth of V. dahliae, with a minimum inhibitory concentration (MIC50) of 3.91 ng/mL. Additionally, a second rapamycin-producing strain, OE57T, was isolated. Phenotypic and genotypic analyses indicated that OE57T represents a new species, which is proposed to be named Streptomyces lacaronensis sp. nov., with OE57T designated as the type strain (=DSM 118741T; CECT 31164T). The discovery of two endophytic rapamycin-producing Streptomyces strains residing within olive roots is especially notable, given the rarity of rapamycin production among microorganisms. These findings highlight the potential of rapamycin-producing Streptomyces strains in developing biofertilizers to manage V. dahliae and reduce the impact of Verticillium wilt on olive trees and other crops.

PMID:40732131 | DOI:10.3390/microorganisms13071622

Genome Biol. 2025 Jul 29;26(1):228. doi: 10.1186/s13059-025-03673-9.

ABSTRACT

Standardized analysis pipelines contribute to making data bioinformatics research compliant with the paradigm of Findability, Accessibility, Interoperability, and Reusability (FAIR), and facilitate collaboration. Nextflow and Snakemake, two popular command-line solutions, are increasingly adopted by users, complementing GUI-based platforms such as Galaxy. We report recent developments of the nf-core framework with the new Nextflow Domain-Specific Language (DSL2). An extensive library of modules and subworkflows enables research communities to adopt common standards progressively, as resources and needs allow. We present an overview of some of the research communities built around nf-core and showcase its adoption by six EuroFAANG farmed animal research consortia.

PMID:40731283 | DOI:10.1186/s13059-025-03673-9