Methods Mol Biol. 2025;2912:191-204. doi: 10.1007/978-1-0716-4454-6_17.

ABSTRACT

Full-length viral genome sequencing is key for virus distribution profiling, new virus discovery, and understanding virus populations across different samples. Circular DNA Enrichment Sequencing (CIDER-Seq) allows unbiased enrichment and long-read sequencing of circular DNA viruses. CIDER-Seq produces single-read full-length virus genomes, combining PCR-free enrichment with Single Molecule Real-Time sequencing and de-concatenation algorithm. CIDER-Seq data analysis package, using the DeConcat algorithm, processes PacBio sequencing data into intact circular DNA sequences, generating fully annotated and highly accurate circular DNA virus genome sequences.

PMID:40064783 | DOI:10.1007/978-1-0716-4454-6_17

J Prev Alzheimers Dis. 2025 Mar 9:100129. doi: 10.1016/j.tjpad.2025.100129. Online ahead of print.

ABSTRACT

BACKGROUND: Type 2 diabetes (T2D) is commonly co-morbid with Alzheimer's disease (AD). However, it remains unclear whether T2D itself or the antidiabetic drug metformin contributes to the progression of AD.

OBJECTIVE: This study aimed to investigate the overall and independent effects of T2D and metformin use on the risk of AD.

METHODS: Summary genome-wide association study datasets were utilized for the Mendelian randomization (MR) and multivariable MR (MVMR) analyses, including ones for T2D (N = 455,017), metformin (N = 456,276), and AD (N = 453,733). Additionally, using the proportional imbalance method, we analyzed AD-related adverse drug events in the FDA Adverse Event Reporting System (FAERS) database (covering Q1 2004 to Q2 2024).

RESULTS: Our two-sample MR analysis indicated that T2D is not associated with the risk of AD (OR: 1.03, CI: 0.99-1.08, P = 0.128). However, while not statistically significant, genetic signature for metformin exposure demonstrated a trend toward an increased risk of AD (OR: 1.05, CI: 1.00-1.09, P = 0.053). Interestingly, in MVMR analysis, which evaluates independent effects of T2D and metformin exposure on T2D, we found a robust association of T2D with a decrease in the risk of AD (OR: 0.82, CI: 0.68-0.98, P = 0.031), while the use of metformin was associated with a higher risk of AD (OR: 1.26, CI: 1.06-1.50, P = 9.45E-3). In the FAERS database, a total of 228,283 metformin-related adverse event reports from 67,742 cases were found. For metformin as the target drug and AD as the target adverse event, signal analysis reported 29 cases of AD (ROR: 0.83, 95 % CI: 0.58-1.19, P = 0.3126).

CONCLUSIONS: Our study reveals the opposite independent causal effects of T2D and metformin exposure on AD. These findings highlight the importance of assessing AD risk when prescribing metformin to patients with T2D.

PMID:40064559 | DOI:10.1016/j.tjpad.2025.100129

Proc Natl Acad Sci U S A. 2025 Mar 18;122(11):e2424470122. doi: 10.1073/pnas.2424470122. Epub 2025 Mar 10.

ABSTRACT

The cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel whose dysfunction leads to intracellular accumulation of chloride ions, dehydration of cell surfaces, and subsequent damage to airway and ductal organs. Beyond its function as a chloride channel, interactions between CFTR, epithelium sodium channel, and solute carrier (SLC) transporter family membrane proteins and cytoplasmic proteins, including calmodulin and Na+/H+ exchanger regulatory factor-1 (NHERF-1), coregulate ion homeostasis. CFTR has also been observed to form mesoscale membrane clusters. However, the contributions of multivalent protein and lipid interactions to cluster formation are not well understood. Using a combination of computational modeling and biochemical reconstitution assays, we demonstrate that multivalent interactions with CFTR protein binding partners, calcium, and membrane cholesterol can induce mesoscale CFTR cluster formation on model membranes. Phosphorylation of the intracellular domains of CFTR also promotes mesoscale cluster formation in the absence of calcium, indicating that multiple mechanisms can contribute to CFTR cluster formation. Our findings reveal that coupling of multivalent protein and lipid interactions promotes CFTR cluster formation consistent with membrane-associated biological phase separation.

PMID:40063811 | DOI:10.1073/pnas.2424470122

Microb Genom. 2025 Mar;11(3). doi: 10.1099/mgen.0.001365.

ABSTRACT

Diabetes mellitus is a complex metabolic disorder and one of the fastest-growing global public health concerns. The gut microbiota is implicated in the pathophysiology of various diseases, including diabetes. This study utilized 16S rRNA metagenomic data from a volunteer citizen science initiative to investigate microbial markers associated with diabetes status (positive or negative) and type (type 1 or type 2 diabetes mellitus) using supervised machine learning (ML) models. The diversity of the microbiome varied according to diabetes status and type. Differential microbial signatures between diabetes types and negative group revealed an increased presence of Brucellaceae, Ruminococcaceae, Clostridiaceae, Micrococcaceae, Barnesiellaceae and Fusobacteriaceae in subjects with diabetes type 1, and Veillonellaceae, Streptococcaceae and the order Gammaproteobacteria in subjects with diabetes type 2. The decision tree, elastic net, random forest (RF) and support vector machine with radial kernel ML algorithms were trained to screen and type diabetes based on microbial profiles of 76 subjects with type 1 diabetes, 366 subjects with type 2 diabetes and 250 subjects without diabetes. Using the 1000 most variable features, tree-based models were the highest-performing algorithms. The RF screening models achieved the best performance, with an average area under the receiver operating characteristic curve (AUC) of 0.76, although all models lacked sensitivity. Reducing the dataset to 500 features produced an AUC of 0.77 with sensitivity increasing by 74% from 0.46 to 0.80. Model performance improved for the classification of negative-status and type 2 diabetes. Diabetes type models performed best with 500 features, but the metric performed poorly across all model iterations. ML has the potential to facilitate early diagnosis of diabetes based on microbial profiles of the gut microbiome.

PMID:40063675 | DOI:10.1099/mgen.0.001365

J Vis Exp. 2025 Feb 21;(216). doi: 10.3791/67911.

ABSTRACT

Mitochondrial membrane potential (MMP, ΔΨm) is critical for mitochondrial functions, including ATP synthesis, ion transport, reactive oxygen species (ROS) generation, and the import of proteins encoded by the nucleus. Existing methods for measuring ΔΨm typically use lipophilic cation dyes, such as Rhodamine 800 and tetramethylrhodamine methyl ester (TMRM), but these are limited by low specificity and are not well-suited for in vivo applications. To address these limitations, we have developed a novel protocol utilizing genetically encoded voltage indicators (GEVIs). Genetically encoded voltage indicators (GEVIs), which generate fluorescent signals in response to membrane potential changes, have demonstrated significant potential for monitoring plasma membrane and neuronal potentials. However, their application to mitochondrial membranes remains unexplored. Here, we developed protein-based mitochondrial-targeted GEVIs capable of detecting ΔΨm fluctuations in cells and the motor cortex of living animals. The mitochondrial potential indicator (MPI)offers a non-invasive approach to study ΔΨm dynamics in real-time, providing a method to investigate mitochondrial function under both normal and pathological conditions.

PMID:40063520 | DOI:10.3791/67911

Clin Exp Med. 2025 Mar 10;25(1):79. doi: 10.1007/s10238-025-01577-3.

ABSTRACT

High-altitude pulmonary hypertension (HAPH) is characterized by an increase in pulmonary artery pressure due to prolonged exposure to hypoxic environment at high altitudes. The development of HAPH involves various factors such as pressure changes, inflammation, oxidative stress, gene regulation, and signal transduction. The pathophysiological mechanisms of this condition operate at molecular, cellular, and genetic levels. Diagnosis of HAPH often relies on echocardiography, cardiac catheterization, and other methods to assess pulmonary artery pressure and its impact on cardiac function. Treatment options for HAPH encompass both nondrug and drug therapies. While advancements have been made in understanding the pathological mechanisms through research on animal models and clinical trials, there are still limitations to be addressed. Future research should focus on exploring molecular targets, personalized medicine, long-term management strategies, and interdisciplinary approaches. By leveraging advanced technologies like systems biology, omics technology, big data, and artificial intelligence, a comprehensive analysis of HAPH pathogenesis can lead to the identification of new treatment targets and strategies, ultimately enhancing patient quality of life and prognosis. Furthermore, research on health monitoring and preventive measures for populations living at high altitudes should be intensified to reduce the incidence and mortality of HAPH.

PMID:40063280 | DOI:10.1007/s10238-025-01577-3

Liver Int. 2025 Apr;45(4):e70058. doi: 10.1111/liv.70058.

ABSTRACT

BACKGROUND: This study utilised the Global Burden of Disease data (2010-2021) to analyse the rates and trends in point prevalence, annual incidence and years lived with disability (YLDs) for major chronic liver diseases, such as hepatitis B, hepatitis C, metabolic dysfunction-associated liver disease, cirrhosis and other chronic liver diseases.

METHODS: Age-standardised rates per 100,000 population for prevalence, annual incidence and YLDs were compared across regions and countries, as well as the socio-demographic index (SDI). Trends were expressed as percentage changes (PC) and estimates were reported with uncertainty intervals (UI).

RESULTS: Globally, in 2021, the age-standardised rates per 100,000 population for the prevalence of hepatitis B, hepatitis C, MASLD and cirrhosis and other chronic liver diseases were 3583.6 (95%UI 3293.6-3887.7), 1717.8 (1385.5-2075.3), 15018.1 (13756.5-16361.4) and 20302.6 (18845.2-21791.9) respectively. From 2010 to 2021, the PC in age-standardised prevalence rates were-20.4% for hepatitis B, -5.1% for hepatitis C, +11.2% for MASLD and + 2.6% for cirrhosis and other chronic liver diseases. Over the same period, the PC in age-standardized incidence rates were -24.7%, -6.8%, +3.2%, and +3.0%, respectively. Generally, negative associations, but with fluctuations, were found between age-standardised prevalence rates for hepatitis B, hepatitis C, cirrhosis and other chronic liver diseases and the SDI at a global level. However, MASLD prevalence peaked at moderate SDI levels.

CONCLUSIONS: The global burden of chronic liver diseases remains substantial. Hepatitis B and C have decreased in prevalence and incidence in the last decade, while MASLD, cirrhosis and other chronic liver diseases have increased, necessitating targeted public health strategies and resource allocation.

PMID:40062742 | DOI:10.1111/liv.70058

iScience. 2025 Jan 23;28(3):111873. doi: 10.1016/j.isci.2025.111873. eCollection 2025 Mar 21.

ABSTRACT

The COVID-19 pandemic was the most dramatic in the newest history with nearly 7 million deaths and global impact on mankind. Here, we report binding index of 305 human leukocyte antigen (HLA) class I molecules from 18,771 unique haplotypes of 28,104 individuals to 821 peptides experimentally observed from spike protein receptor binding domain (RBD) of five main SARS-CoV-2 strains hydrolyzed by human proteasomes with constitutive and immune catalytic phenotypes. Our data read that mutations in the human angiotensin-converting enzyme 2 (hACE2)-binding region RBD496-513 of Omicron B.1.1.529 strain results in a dramatic increase of proteasome-mediated release of two public HLA class I epitopes. Global population analysis of HLA class I haplotypes, specific to these peptides, demonstrated decreased mortality of human populations enriched in these haplotypes from COVID-19 after but not before December, 2021, when Omicron became dominant SARS-CoV-2 strain. Noteworthy, currently circulating BA.2.86 and JN.1 strains contain same amino acid substitutions at key proteasomal cleavage sites, thus preserving identified core epitopes.

PMID:40060909 | PMC:PMC11889684 | DOI:10.1016/j.isci.2025.111873

iScience. 2025 Feb 4;28(3):111876. doi: 10.1016/j.isci.2025.111876. eCollection 2025 Mar 21.

ABSTRACT

T cell-redirecting bispecific antibodies (bsAbs) to treat advanced stage solid tumors are gaining interest after recent clinical successes. The immune checkpoint human leukocyte antigen G (HLA-G) is expressed in several tumor types while in normal tissues expression is limited. Here, we describe JNJ-78306358, a T cell-redirecting bispecific antibody (bsAb) to treat advanced stage solid tumors. JNJ-78306358 binds with high affinity to the α3 subunit of HLA-G on cancer cells and with purposely engineered weaker affinity to CD3ε on T cells. JNJ-78306358 induced potent T cell-mediated cytotoxicity of HLA-G-expressing solid tumors in vitro and in vivo. JNJ-78306358 also blocked the interaction of HLA-G with its receptors in vitro, indicating that immune checkpoint blocking may contribute to its anti-tumor activity. These results suggest that T cell-redirection against HLA-G could be a potent and effective treatment for a wide range of solid tumor indications.

PMID:40060890 | PMC:PMC11889666 | DOI:10.1016/j.isci.2025.111876

bioRxiv [Preprint]. 2025 Feb 28:2025.02.24.639810. doi: 10.1101/2025.02.24.639810.

ABSTRACT

Biological sex plays a crucial role in the outcomes of cardiac health and therapies. Sex hormones are known to strongly influence cardiac remodeling through intracellular signaling pathways, yet their underlying mechanisms remain unclear. To address this need, we developed and validated a logic-based systems biology model of cardiomyocyte hypertrophy that, for the first time, incorporates the effects of both estradiol (E2) and testosterone (T) alongside well-established hypertrophic stimuli (Strain, angiotensin II (AngII), and endothelin-1 (ET-1)). We qualitatively validated the model to literature data with 84% agreement. Quantitative validation was done by simulating the impact of the inputs (E2, T, Strain, AngII, and ET-1) on cardiac hypertrophy, captured as change in CellArea. We perturbed the validated model to examine the differential response to hypertrophy and identify changes in influential and sensitive downstream nodes for a male, pre-menopausal female, and post-menopausal female condition. Our results suggest that T has a greater impact on hypertrophy than E2. This model increases our understanding of the mechanisms through which sex hormones influence cardiac hypertrophy and can aid with developing more effective cardiac therapies for all patients.

AUTHOR SUMMARY: Differences between female and male hearts extend far beyond size and structure. Sex hormones estradiol and testosterone play key roles in sex-specific cardiac remodeling via intracellular pathways. Understanding how these sex hormones impact cardiac remodeling is critical for developing more effective, sex-specific approaches to cardiovascular care. Logic-based systems biology models have proven useful in quantifying and analyzing complex and intricate intracellular signaling network dynamics in various cell types. We leverage this method to develop a model of cardiomyocyte hypertrophy, which, for the first time, includes the effect of both estradiol and testosterone. Considering the combined influence of these hormones is important because both women and men have varying concentrations of these hormones throughout their lives. The model was developed and validated based on previously published studies. We then investigated differences in cardiomyocyte hypertrophy in pre- and post-menopausal women and men.

PMID:40060665 | PMC:PMC11888296 | DOI:10.1101/2025.02.24.639810

bioRxiv [Preprint]. 2025 Feb 27:2025.02.21.639501. doi: 10.1101/2025.02.21.639501.

ABSTRACT

Matrix metalloproteinases (MMPs) are a family of proteases that drive degradation of extracellular matrix (ECM) across many tissues. MMP activity is antagonized by tissue inhibitors of metalloproteinases (TIMPs), resulting in a complex multivariate system with many MMP isoforms and TIMP isoforms interacting across a network of biochemical reactions - each with their own distinct kinetic rates. This system complexity makes it very difficult to identify which specific molecules are most responsible for driving ECM turnover in vivo and therefore the most promising therapeutic targets. To help elucidate the specific roles of various MMP and TIMP isoforms, we present a computational systems biology model of collagen turnover capturing all possible interactions between type I collagen, four different MMP isoforms (MMP-1, -2, -8, and -9), and three different TIMP isoforms (TIMP-1, -2, and -4). We used dye-quenched fluorescent collagen to monitor the degradation of collagen in the presence of various MMP+TIMP cocktails, and we then used these experimental data to fit hypothetical reaction system topologies in order to investigate their respective accuracies. We determined kinetic rate constants for this system and used post-myocardial infarct time courses of collagen, MMP, and TIMP levels to perform a parameter sensitivity analysis across the model reaction rates and predict which molecules and interactions are the important regulators of ECM in the infarcted heart. Notably, the model suggested that MMP degradation and inactivation terms were more important for driving collagen levels than TIMP interaction terms. In sum, this work highlights the need for systems-level analyses to distinguish the roles of various biomolecules operating with a complex system, prioritizes therapeutic targets for post-infarct cardiac remodeling, and presents a computational framework that can be applied to many other collagen-rich tissues.

PMID:40060515 | PMC:PMC11888197 | DOI:10.1101/2025.02.21.639501

3 Biotech. 2025 Apr;15(4):76. doi: 10.1007/s13205-025-04248-y. Epub 2025 Mar 6.

ABSTRACT

Heavy metal toxicity hinders plant growth and development by inducing oxidative stress, decreasing biomass, impairing photosynthesis, and potentially leading to plant death. The inherent defense mechanisms employed by plants, including metal sequestration into vacuoles, phytochelation, cell wall metal adsorption and an enhanced antioxidant system can be improved via various approaches to mitigate heavy metal toxicity. This review primarily outlines plants direct and indirect responses to HM stress and the tolerance mechanisms by which plants combat the toxic effects of metals and metalloids to understand the effective management of HMs and metalloids in the soil system. Furthermore, this review highlights measures to mitigate metal and metalloid toxicity and improve metal tolerance through various physio-biochemical, biological, and molecular approaches. This review also provides a comprehensive account of all the mitigative approaches by comparing physio-biochemical, biological and molecular approaches. Finally, we compared all the mitigative approaches used in monocotyledonous and dicotyledonous to increase their metal tolerance. Although many studies have compared monocot and dicot plants based on metal toxicity and tolerance effects, comparisons of these mitigative approaches have not been explored.

PMID:40060292 | PMC:PMC11885775 | DOI:10.1007/s13205-025-04248-y

MedComm (2020). 2025 Mar 6;6(3):e70101. doi: 10.1002/mco2.70101. eCollection 2025 Mar.

ABSTRACT

Neutrophil extracellular traps (NETs) are unique fibrous structures released by neutrophils in response to various pathogens, exhibiting both anti-inflammatory and proinflammatory effects. In autoimmune conditions, NETs serve as crucial self-antigens triggering inflammatory cascades by activating the inflammasome and complement systems, disrupting self-tolerance mechanisms and accelerating autoimmune responses. Furthermore, NETs play a pivotal role in modulating immune cell activation, affecting adaptive immune responses. This review outlines the intricate relationship between NETs and various diseases, including inflammatory arthritis, systemic autoimmune diseases, Behçet's disease, systemic lupus erythematosus, autoimmune kidney diseases, autoimmune skin conditions, systemic sclerosis, systemic vasculitis, and gouty arthritis. It highlights the potential of targeting NETs as a therapeutic strategy in autoimmune diseases. By examining the dynamic balance between NET formation and clearance in autoimmune conditions, this review offers critical insights and a theoretical foundation for future research on NET-related mechanisms. Advances in systems biology, flow cytometry, and single-cell multiomics sequencing have provided valuable tools for exploring the molecular mechanisms of neutrophils and NETs. These advancements have renewed focus on the role of neutrophils and NETs in autoimmune diseases, offering promising avenues for further investigation into their clinical implications.

PMID:40060194 | PMC:PMC11885892 | DOI:10.1002/mco2.70101

aBIOTECH. 2025 Jan 23;6(1):116-132. doi: 10.1007/s42994-024-00194-0. eCollection 2025 Mar.

ABSTRACT

Plant metabolites are crucial for the growth, development, environmental adaptation, and nutritional quality of plants. Plant metabolomics, a key branch of systems biology, involves the comprehensive analysis and interpretation of the composition, variation, and functions of these metabolites. Advances in technology have transformed plant metabolomics into a sophisticated process involving sample collection, metabolite extraction, high-throughput analysis, data processing, and multidimensional statistical analysis. In today's era of big data, the field is witnessing an explosion in data acquisition, offering insight into the complexity and dynamics of plant metabolism. Moreover, multiple omics strategies can be integrated to reveal interactions and regulatory networks across different molecular levels, deepening our understanding of plant biological processes. In this review, we highlight recent advances and challenges in plant metabolomics, emphasizing the roles for this technique in improving crop varieties, enhancing nutritional value, and increasing stress resistance. We also explore the scientific foundations of plant metabolomics and its applications in medicine, and ecological conservation.

PMID:40060186 | PMC:PMC11889285 | DOI:10.1007/s42994-024-00194-0

Front Microbiol. 2025 Feb 21;15:1462941. doi: 10.3389/fmicb.2024.1462941. eCollection 2024.

ABSTRACT

Permafrost thaw increases the bioavailability of ancient organic matter, facilitating microbial metabolism of volatile organic compounds (VOCs), carbon dioxide, and methane (CH4). The formation of thermokarst (thaw) lakes in icy, organic-rich Yedoma permafrost leads to high CH4 emissions, and subsurface microbes that have the potential to be biogeochemical drivers of organic carbon turnover in these systems. However, to better characterize and quantify rates of permafrost changes, methods that further clarify the relationship between subsurface biogeochemical processes and microbial dynamics are needed. In this study, we investigated four sites (two well-drained thermokarst mounds, a drained thermokarst lake, and the terrestrial margin of a recently formed thermokarst lake) to determine whether biogenic VOCs (1) can be effectively collected during winter, and (2) whether winter sampling provides more biologically significant VOCs correlated with subsurface microbial metabolic potential. During the cold season (March 2023), we drilled boreholes at the four sites and collected cores to simultaneously characterize microbial populations and captured VOCs. VOC analysis of these sites revealed "fingerprints" that were distinct and unique to each site. Total VOCs from the boreholes included > 400 unique VOC features, including > 40 potentially biogenic VOCs related to microbial metabolism. Subsurface microbial community composition was distinct across sites; for example, methanogenic archaea were far more abundant at the thermokarst site characterized by high annual CH4 emissions. The results obtained from this method strongly suggest that ∼10% of VOCs are potentially biogenic, and that biogenic VOCs can be mapped to subsurface microbial metabolisms. By better revealing the relationship between subsurface biogeochemical processes and microbial dynamics, this work advances our ability to monitor and predict subsurface carbon turnover in Arctic soils.

PMID:40059907 | PMC:PMC11885255 | DOI:10.3389/fmicb.2024.1462941

J Exp Bot. 2025 Mar 10:eraf100. doi: 10.1093/jxb/eraf100. Online ahead of print.

ABSTRACT

Hydrogen sulfide (H2S) is increasingly recognized as a crucial signaling molecule in plants, playing key roles in regulating physiological processes and enhancing stress tolerance. This review provides an updated summary of H2S signaling in plant stress responses, discussing its uptake from external environmental sources, its endogenous biosynthesis, and its broader functions in stress adaptation. We summarize the impact of H2S on plants under various stress conditions and review the mechanisms through which it mediates signaling functions, with a particular focus on H2S-mediated protein persulfidation. Additionally, we provide an overview of the current understanding of protein persulfidation in regulating physiological processes and stress responses in plants, offering both a general discussion of its effects under different stress conditions and specific examples to highlight its significance. Finally, we review recent proteomic studies on protein persulfidation in plants, comparing the identified persulfidated proteins across studies and highlighting shared biological processes and pathways. This review aims to consolidate the current understanding of H2S signaling and its roles mediated by protein persulfidation in plants, while also offering insights to inspire future research in this rapidly evolving field.

PMID:40059712 | DOI:10.1093/jxb/eraf100

Genetics. 2025 Mar 10:iyaf025. doi: 10.1093/genetics/iyaf025. Online ahead of print.

ABSTRACT

Tissue-regulated alternative exons are dictated by the interplay between cis-elements and trans-regulatory factors such as RNA binding proteins. Despite extensive research on splicing regulation, the full repertoire of these cis and trans features and their evolutionary dynamics across species are yet to be fully characterized. Members of the CUG-binding protein and ETR-like family (CELF) of RNA binding proteins are known to play a key role in the regulation of tissue-biased splicing patterns, and when mutated, these proteins have been implicated in a number of neurological and muscular disorders. In this study, we sought to characterize specific mechanisms that drive tissue-specific splicing in vivo of a model switch-like exon regulated by the neuronal-enriched CELF ortholog in C. elegans, UNC-75. Using sequence alignments, we identified deeply conserved intronic UNC-75 binding motifs overlapping the 5' splice site and upstream of the 3' splice site, flanking a strongly neural-repressed alternative exon in the Zonula Occludens gene zoo-1. We confirmed that loss of UNC-75 or mutations in either of these cis-elements lead to substantial de-repression of the alternative exon in neurons. Moreover, mis-expression of UNC-75 in muscle cells is sufficient to induce the neuron-like robust skipping of this alternative exon. Lastly, we demonstrate that overlapping an UNC-75 motif within a heterologous 5' splice site leads to increased skipping of the adjacent alternative exon in an unrelated splicing event. Together, we have demonstrated that a specific configuration and combination of cis elements bound by this important family of RNA binding proteins can achieve robust splicing outcomes in vivo.

PMID:40059624 | DOI:10.1093/genetics/iyaf025

Small Methods. 2025 Mar 9:e2500136. doi: 10.1002/smtd.202500136. Online ahead of print.

ABSTRACT

Mechanical strain substantially influences tissue shape and function in various contexts from embryonic development to disease progression. Disruptions in these processes can result in congenital abnormalities and short-circuit mechanotransduction pathways. Manipulating strain in live tissues is crucial for understanding its impact on cellular and subcellular activities, unraveling the interplay between mechanics and cells. Existing tools, such as optogenetic modulation of strain, are limited to small strains over limited distances and durations. Here, a high-strain stretcher system, the TissueTractor, is introduced to enable simultaneous high-resolution spatiotemporal imaging of live cells and tissues under strain applications varying from 0% to over 100%. We use the system with organotypic explants from Xenopus laevis embryos, where applied tension reveals cellular strain heterogeneity and remodeling of intracellular keratin filaments. To highlight the device's adaptability, the TissueTractor is also used to study two other mechanically sensitive cell types with distinct physiological roles: human umbilical vein endothelial cells and mouse neonatal cardiomyocytes, revealing cell morphological changes under significant strain. The results underscore the potential of the TissueTractor for investigating mechanical cues that regulate tissue dynamics and morphogenesis.

PMID:40059484 | DOI:10.1002/smtd.202500136

Brain Behav Immun. 2025 Mar 7:S0889-1591(25)00099-6. doi: 10.1016/j.bbi.2025.03.013. Online ahead of print.

ABSTRACT

BACKGROUND: Individuals raised in an urban environment (URBANs) show an exaggerated inflammatory response to the Trier Social Stress Test (TSST) compared with individuals raised in a rural environment. The underlying mechanisms are unclear but may relate to childhood animal contact. As an exaggerated immune (re)activity plays a causal role in the pathogenesis of stress-associated disorders, these findings might explain the higher prevalence of stress-associated disorders in urban vs. rural areas.

METHODS: We recruited physically and emotionally healthy male URBANs, raised in a city with more than 40,000 residents either in the absence (noPETs) or presence (PETs) of household pets. Participants were individually exposed to the TSST, and before and after the TSST, blood and saliva were collected for assessment of different stress-related parameters. An additional saliva sample before the TSST was collected for salivary microbiome analysis. Heart rate (HR) and HR variability (HRV) were recorded continuously. Mental and physical health status, early-life and perceived life stress, current animal contact, and subjective strain induced by TSST exposure were assessed using validated questionnaires.

RESULTS: Here we show that adult healthy male URBANs raised in the absence (noPETs) vs. presence (PETs) of household pets still reported less animal contact during adulthood and were characterized by deficits in their immunoregulatory and intestinal barrier function, which under basal conditions did not translate into a chronic low-grade inflammatory state. This was different under acute psychosocial stress conditions. Exposure to the TSST resulted in a facilitated mobilization of particularly neutrophil granulocytes in noPETs vs. PETs, accompanied by an enhanced pro- and compromised anti-inflammatory systemic stress response.

CONCLUSION: Together, the presence of pets seems to reduce the risk for URBANs to develop stress-associated disorders later in life (i.e., primary prevention) by facilitating immunoregulatory and barrier functions, in turn preventing an overshooting immune activation in response to acute stressors and chronic low-grade inflammation in response to repeated/chronic stressors.

PMID:40058670 | DOI:10.1016/j.bbi.2025.03.013

BMB Rep. 2025 Mar 5:6350. Online ahead of print.

ABSTRACT

Abscisic acid (ABA) is a key phytohormone that regulates multiple biological processes in plants, including seed germination, seedling growth, and abiotic stress response. ABA enhances drought tolerance by promoting stomatal closure, thereby improving crop productivity under unfavorable stress conditions. Extensive research efforts have focused on understanding ABA signaling more clearly for its potential application in agriculture. The accumulation and stability of signaling components involved in the efficient transduction of downstream ABA signaling are affected by both transcriptional regulation and post-translational modifications. Ubiquitination is a representative post-translational modification that regulates protein stability, and E3 ubiquitin ligase is a key enzyme that determines target substrates for ubiquitination. To date, many E3 ligases functioning as a monomeric form such as RING-, HECT- and Ubox-types have been known to participate in the ABA signaling process. In this review, we summarize the current understanding of ABA-related monomeric E3 ligases, their regulation, and mode of action in Arabidopsis, which will help develop a detailed and integrated understanding of the ABA signaling process in Arabidopsis.

PMID:40058874