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At least 19 recordsLinked to original sources

PubMed2026

Comparison of VCV and PCV-VG modes on diaphragmatic function in diabetic patients undergoing laparoscopic colorectal surgery: a prospective randomized controlled study.

BACKGROUND: Diabetic patients are prone to induce diaphragmatic weakness, which can lead to postoperative pulmonary complications (PPCs). The optimal mechanical ventilation mode may potentially improve postoperative diaphragmatic function. This study evaluates the effects of two ventilation modes under driving pressure-guided ventilation strategy on diaphragmatic function, as assessed by diaphragm thickening fraction (DTF) and diaphragm excursion (DE), in diabetic patients following laparoscopic colorectal surgery. METHODS: Eighty patients diagnosed with Type II diabetes scheduled for elective laparoscopic colorectal surgery, were randomly allocated to either the pressure-controlled volume-guaranteed ventilation (PCV-VG) group (Group P) or the volume-controlled ventilation (VCV) group (Group V) during surgery. The primary outcome was diaphragmatic function assessed during both tidal breathing and maximal inspiratory effort after surgery. Secondary outcomes included intraoperative mechanical power, PPCs, and other complications. RESULTS: A total of eighty patients were included in the final analysis. The averaged area under the curve (AUC) for mechanical power during ventilation was significantly lower in Group P than in Group V (p = 0.002). PCV-VG significantly improved both DE and DTF within the first two days post-surgery (AUCDEtidal: p = 0.088, AUCDTFtidal: p = 0.004, AUCDEmax: p = 0.029, AUCDTFmax: p = 0.017). Postoperative diaphragmatic weakness was less frequent in Group P than in Group V (p = 0.019). However, there was no difference in the incidence of PPCs between the two groups (p = 0.155). CONCLUSION: PCV-VG mode can reduce intraoperative mechanical power, better preserve postoperative diaphragmatic function. However, these improvements did not translate into clinical benefits, as evidenced by the lack of reduction in the incidence of PPCs.

Humans↗

PubMedDate not supplied

[Mechanism determining the variability of the immunologic specificity spectrum of antibodies and other immunoglobulins (theory)].

An analysis of the theories of immunity-the germ line theory, the translocations and recombinations theory, the somatic mutation theory, and the reverse translation theory advanced earlier shows that their postulates afford no answer to any of the central questions of immunology, such as: 1) The origin of genetic information which codes the entire multimillion totality of immunologically different antibodies and antigen-recognizing receptors of the immunological system B and T cells. 2) The causes of sharp differences in both, the resolving power and mechanisms of recognition of antigenic determinant by antibodies and B cell receptors, on the one hand, and of macromolecular antigens as such by antigen-recognizing receptors of T cells, on the other 3) The essence of the mechanisms by means of which the T cell receptors recognize and distinguish the macro-molecular antigens as such. A new theory is advanced which in terms of the principle of cross stereocomplementarycity determining the regularities of mutual specific recognition by polynucleotides and polypeptides coded by them and also on the basis of some biophysical, virological phenomena explains the physico-chemical and genetic basis of immunological phenomena mentioned above.

Antibody Specificity↗

PubMed2024

Genome-wide association study of the common retinal disorder epiretinal membrane: Significant risk loci in each of three American populations.

Epiretinal membrane (ERM) is a common retinal condition characterized by the presence of fibrocellular tissue on the retinal surface, often with visual distortion and loss of visual acuity. We studied European American (EUR), African American (AFR), and Latino (admixed American, AMR) ERM participants in the Million Veteran Program (MVP) for genome-wide association analysis-a total of 38,232 case individuals and 557,988 control individuals. We completed a genome-wide association study (GWAS) in each population separately, and then results were meta-analyzed. Genome-wide significant (GWS) associations were observed in all three populations studied: 31 risk loci in EUR subjects, 3 in AFR, and 2 in AMR, with 48 in trans-ancestry meta-analysis. Many results replicated in the FinnGen sample. Several GWS variants associate to alterations in gene expression in the macula. ERM showed significant genetic correlation to multiple traits. Pathway enrichment analyses implicated collagen and collagen-adjacent mechanisms, among others. This well-powered ERM GWAS identified novel genetic associations that point to biological mechanisms for ERM.

Humans↗

PubMed2025

Genomic plasticity drives olfactory adaptation in a pest fly.

Preference shifts in insects are often driven by changes in the olfactory system, yet the underlying mechanisms remain unclear. The worldwide pest Drosophila suzukii, which oviposits in ripe rather than overripe fruits, provides a powerful model to study these mechanisms and their behavioral consequences. Here, we show that this shift is linked to functional remodeling in four olfactory receptor neurons: ab2B, ab3A, ab4B, and ab10A. While ab3A and ab10A exhibit tuning changes shared with the non-pest relative D. biarmipes, ab2B and ab4B display species-specific adaptations in D. suzukii. These changes result not only from receptor sequence divergence but also from novel innovations: receptor co-expression in ab3A and partitioned expression of Or67a paralogs in ab2B and ab10A. Together, these findings show how genomic plasticity in chemosensory gene families enables rapid sensory adaptation and niche transition.

Journal Article↗

PubMed2026

From molecular responses to environmental monitoring: advances and translational gaps in omics approaches in fish environmental toxicology.

Fish occupy a central position in aquatic ecosystems and serve as important bioindicators for environmental monitoring, as well as powerful translational models for understanding toxic mechanisms conserved across higher vertebrates. In recent years, omics techniques have proven to be powerful tools to address complex environmental questions that conventional toxicology methods cannot answer. Despite this potential, a critical translational gap remains between molecular findings and their use in ecological risk assessment frameworks. This review critically synthesizes advances across omics techniques including epigenomics, transcriptomics, metabolomics and proteomics and their integration. Special emphasis is placed on methodological considerations and practical aspects of these techniques in fish environmental toxicology and environmental monitoring. Evidence from single-omics studies suggests conserved biomarker signatures across species while characterizing complex phenomena like non-monotonic dose-response relationships, mixture toxicity and transgenerational and stereoselective effects with implications for population level monitoring. Multi-omics studies, especially those involving triple omics, further enhance mechanistic resolution by reconstructing adverse outcome pathways. We further evaluate using case studies when additional molecular layers provide critical insight and when they offer limited advantage, a strategic distinction with direct implications in environmental monitoring programmes. Finally, current limitations and future directions that will ultimately bridge the translational gap and hold promise for advancing mechanistic ecotoxicology and predictive environmental monitoring are discussed.

Animals↗

PubMed2025

Functional phenotyping of genomic variants using joint multiomic single-cell DNA-RNA sequencing.

Genetic variants (both coding and noncoding) can impact gene function and expression, driving disease mechanisms such as cancer progression. The systematic study of endogenous genetic variants is hindered by inefficient precision editing tools, combined with technical limitations in confidently linking genotypes to gene expression at single-cell resolution. We developed single-cell DNA-RNA sequencing (SDR-seq) to simultaneously profile up to 480 genomic DNA loci and genes in thousands of single cells, enabling accurate determination of coding and noncoding variant zygosity alongside associated gene expression changes. Using SDR-seq, we associate coding and noncoding variants with distinct gene expression in human induced pluripotent stem cells. Furthermore, we demonstrate that in primary B cell lymphoma samples, cells with a higher mutational burden exhibit elevated B cell receptor signaling and tumorigenic gene expression. SDR-seq provides a powerful platform to dissect regulatory mechanisms encoded by genetic variants, advancing our understanding of gene expression regulation and its implications for disease.

Humans↗

PubMed2026

Development of a human iPSC and patient phenotyping resource for preclinical investigations of neurodevelopmental disorders.

In this manuscript, we report the development of a comprehensive resource designed to harness the transformative potential of patient-derived induced pluripotent stem cells (iPSCs) to advance the study of neurodevelopmental disorders (NDDs). Using CRISPR-Cas-mediated genome editing, the Human Neuron Core generated a repository comprising 29 isogenic iPSC pairs, two sex-matched parental control iPSC pairs, and one unmatched patient line representing six monogenic NDDs: Tuberous Sclerosis Complex, PTEN Hamartoma Tumor Syndrome, KCNQ2 Developmental and Epileptic Encephalopathy, FOXG1 Syndrome, Phelan-McDermid Syndrome, and SETBP1 Haploinsufficiency Disorder. In parallel, detailed clinical phenotyping data were collected to enable comparison of cellular phenotypes with clinical severity in future studies. This integrated collection of genetically defined iPSC lines and associated clinical data provides a powerful platform for investigating disease mechanisms and advancing iPSC-based drug discovery for NDDs.

Humans↗

PubMed2026

Quantitative interactome mapping of skeletal muscle insulin resistance.

Protein-protein interactions (PPIs) are dynamic and critical to adaptive homeostasis. While there have been massive efforts to catalogue proteome-wide PPIs, global quantification of changes remains a challenge. Here, we integrate dynamic protein correlation profiling - mass spectrometry (PCP-MS) and quantitative cross linking-mass spectrometry (qXL-MS) using multiplexed stable isotope labelling to characterise global PPI remodelling following the development of chronic skeletal muscle insulin resistance (IR) with or without acute insulin stimulation. We quantify >7,000 unique PPIs amongst 5,346 proteins and show changes in the interactome network dominate the proteome response. Our data show the dysregulation of protein processing in the endoplasmic/sarcoplasmic reticulum involving changes in PPIs with protein chaperones and disulfide isomerases is a major hallmark of skeletal muscle IR. Mechanistically, we show the dysregulation of PPIs with Protein-Disulfide Isomerase 6 (PDIA6) regulates cysteine oxidation and insulin sensitivity. Taken together, we show in vivo quantitative interactome mapping is a powerful approach to understand disease mechanisms and provide new insights into protein network re-organisations with IR.

Insulin Resistance↗

PubMed2025

Expanded Chromatin Accessibility Mapping Explains Genetic Variation Associated with Complex Traits in Liver.

Genome-wide association studies (GWAS) have identified thousands of loci associated with a variety of common, complex human traits. Recent efforts have focused on characterizing chromatin accessibility to discover regulatory elements that modify the expression of nearby genes, suggesting that trait associations are mediated through changes in gene regulation. Genetic variants associated with differences in chromatin accessibility, known as chromatin accessibility quantitative trait loci (caQTLs), are established contributors to gene expression differences, providing mechanistic hypotheses for signals identified by GWAS. Using the assay for transposase-accessible chromatin with sequencing (ATAC-seq), we assessed chromatin accessibility in 189 diverse human liver samples, identifying over two million accessible chromatin regions enriched for gene regulatory features and, in 175 of these samples, over 14,000 caQTLs. Focusing subsequently on liver-relevant complex traits, we obtained publicly available blood lipids GWAS data and identified 157 loci where caQTLs, expression quantitative trait loci (eQTLs), and GWAS signals colocalized. This generated specific molecular hypotheses about regulatory elements, affected genes, and, in some cases, implicated transcription factors. Finally, we enumerated the set of blood lipid trait signals that lack an obvious proposed mechanism beyond catalogs of liver caQTLs and eQTLs. After integrating 10 multi-omic QTL regulatory mechanism datasets whilst considering limitations in statistical power, we found that approximately 20% of blood lipid GWAS signals lacked a statistical link to a proposed mechanism. Our results demonstrate the value of integrating multiple genomic datasets to improve understanding of GWAS signals, while emphasizing the need for additional experimental approaches to fully characterize complex trait associations.

Journal Article↗

PubMed2026

Development of a rapid antiviral screening assay based on GFP reporter virus of bovine enterovirus.

In recent years, bovine enterovirus (BEV) has been increasingly associated with diarrhea in cattle in China, posing new challenges for disease control in the cattle industry. However, the mechanisms underlying BEV pathogenesis and virulence remain poorly understood. Infectious cDNA clones provide a powerful tool for dissecting viral replication and pathogenic mechanisms. In this study, we generated a full-length infectious cDNA clone of the BEV-F isolate HB19-1. Three overlapping fragments spanning the complete viral genome were amplified by RT-PCR and assembled downstream of a cytomegalovirus (CMV) promoter placed immediately upstream of the 5' untranslated region (5'UTR). To establish a reporter virus system, the green fluorescent protein (GFP) gene was inserted between the 5'UTR and the N terminus of VP4, followed by a 2A cleavage sequence (IKTAG) at the C terminus of GFP. The recombinant rHB19-GFP virus was successfully rescued. Growth curve analysis demonstrated that rHB19-GFP exhibited slower replication kinetics at early time points relative to the parental HB19-1 virus, with no significant difference in their peak viral titers. This GFP-expressing reporter virus enables convenient monitoring of BEV replication and provides a useful platform for antiviral screening. Using this system, we found that 5-(N-Ethyl-N-isopropyl)amiloride (EIPA) inhibited BEV replication, suggesting its potential as an antiviral candidate. Overall, the rHB19-GFP infectious clone developed here offers a practical tool for studying BEV biology and for identifying antiviral compounds against BEV.

Animals↗

PubMed2026

Uncovering the early and conserved molecular mechanisms of root nitrogen foraging in model and crops.

BACKGROUND: Nitrogen (N) foraging, the ability of plants to promote preferential root growth in N-rich patches of soil, is fundamental to the competitiveness and wellbeing of plants. A unique “split-root” system, where a heterogenous N environment stimulates root foraging, provides a powerful experimental model to study the mechanisms underlying root foraging in model (Arabidopsis) and/or crop plants. RESULTS: We used the split-root set up to capture early molecular events involved in systemic N-signaling after exposure to a heterogeneous N signal, through time-course transcriptomic analysis across shoots and roots of Arabidopsis. We found that a histone methyltransferase, SET DOMAIN GROUP 8 (SDG8), is necessary for root N-foraging, suggesting a previously unknown role for chromatin regulation in mediating the preferential root growth response to colonize N-rich patches. To determine if the underlying molecular mechanism is conserved in evolution, we compared the root foraging behavior from model-to-crop (Arabidopsis, tomato and maize). Our analysis showed the model and crop species shared a root N-foraging growth response, with some variation among specific genotypes. Interestingly, we observed both shared and distinct transcriptional responses to heterogenous N environments among these three species. CONCLUSIONS: Our study has generated insights into the molecular basis of root N-foraging, with the potential to improve nutrient use efficiency in crop plants in a heterogeneous field environment.

Crops, Agricultural↗

PubMed2026

Yorkie/Scalloped-OVOL-Rac1 axis controls insect wing development by promoting cell proliferation.

The regulation of organ size is a fundamental question in developmental biology, and insect wings provide a powerful model for elucidating the genetic mechanisms underlying morphogenesis. Although the conserved Hippo signaling pathway plays a central role in controlling tissue growth, its precise regulatory network during wing development remains incompletely understood. Here, we identify the zinc finger transcription factor OVOL as a critical mediator of Hippo signaling in insect wing development. We indicate that OVOL is essential for normal wing formation in both Locusta migratoria and Drosophila melanogaster, regulating cell proliferation and trichome patterning. Through transcriptomic analysis and functional validation, we further identify the small GTPase Rac1 as a key downstream effector of OVOL that promotes proliferative growth. Moreover, we find that OVOL expression is directly activated by the Yorkie/Scalloped (Yki/Sd) complex, the core transcriptional effector of the Hippo pathway, without forming a feedback loop. This regulation is mediated through a specific Sd-binding motif (GATAA) within the OVOL promoter. Importantly, Yki/Sd-induced Rac1 expression is dependent on OVOL. Collectively, our findings establish the Yorkie/Sd-OVOL-Rac1 pathway that governs insect wing development by promoting cell proliferation, providing mechanistic insights into organ size regulation in animals.

Cell proliferation↗

PubMed2026

Proteomics in environmental pollution research: Advances, challenges, and future directions.

Environmental proteomics has emerged as a powerful approach for elucidating the molecular mechanisms underlying pollutant-induced biological effects. Although this field has developed rapidly, the systematic review of recent proteomics applications in environmental pollution research remains limited. This review explored the emerging roles of toxicoproteomics in biomarker discovery and mechanistic elucidation, as well as ecotoxicoproteomics in ecological risk assessment and bioremediation strategies. Here, we review the field, highlighting recent trends such as the integration of proteomics with genomics, transcriptomics, and metabolomics to provide a comprehensive view of biological responses to environmental stressors. We further discuss the growing application of artificial intelligence in improving proteomics data interpretation and accelerating biomarker discovery. In addition, recent technological advances in environmental proteomics are highlighted, including next-generation tissue microarray proteomics, nanoscale proteomics, single-cell proteomics, and spatial proteomics. Despite its potential, proteomics faces challenges, such as high operational costs, computational complexity in analysis, and technical limitations in low-abundance protein detection. We propose that the convergence of proteomics with artificial intelligence and multi-omics approaches offers promising solutions to these challenges, enhancing the practical application of proteomics in environmental monitoring and risk assessment.

Proteomics↗

PubMed2025

A rare genetic variant confers resistance to neurodegeneration across multiple neurological disorders by augmenting selective autophagy.

The study of disease modifiers is a powerful way to identify patho-mechanisms associated with disease. Using the strong genetic traits of Huntington's disease (HD), we identified a rare, single-nucleotide polymorphism (SNP) in WDFY3 associated with a delayed age of onset of up to 23 years. Remarkably, the introduction of the orthologous SNP into mice recapitulates this neuroprotection, significantly delaying neuropathological and behavioral dysfunction in two models of HD. The SNP increases expression of the protein autophagy-linked Fab1, YOTB, Vac1, and EEA1 (FYVE) protein (Alfy), an autophagy adaptor protein for the clearance of aggregated proteins, whose ectopic overexpression is sufficient to capture the neuroprotective effects of the variant. Increasing Alfy expression protects not only against HD but also against the toxicity due to phospho-α-synuclein and AT8-positive accumulation. By combining human and mouse genetics, we have uncovered a pathway that protects against multiple proteinopathies, revealing a much-sought-after, shared therapeutic target across a broad range of neurodegenerative diseases.

Animals↗

PubMed2025

Global maintenance of histone post-translational modifications during the transition into anoxia in embryos of the annual killifish Austrofundulus limnaeus.

Many organisms have adapted to survive anoxic or hypoxic environments, but the epigenetic responses involved in this successful stress response are not well described in most species. Embryos of the annual killifish Austrofundulus limnaeus have the greatest tolerance to anoxia of all vertebrates, making them a powerful model to study the cellular mechanisms necessary for anoxia tolerance. However, the global histone landscape of this species has never been quantified or explored in relation to stress tolerance. Liquid chromatography-mass spectrometry and a Python bioinformatics workflow were used to identify histones and their post-translational modifications. This pipeline resulted in the detection of 252 unique biologically relevant histone post-translational modifications (hPTMs) (unimod + residue). These PTMs represent 16 types of biologically relevant hPTMs present during both anoxia and normoxia in Wourms' stage 36 embryos. This hPTM library presents an exciting opportunity to study histone modifications across development and in response to environmental stressors. No significant changes in PTM or histone abundance were observed between anoxic and normoxic embryos, suggesting that 24 h of anoxia is not sufficient to induce epigenetic or histone isoform changes at the organismal level. This result is inconsistent with data presented for similar stresses in mammalian cells and thus stabilization of the hPTM landscape may be an adaptation that supports anoxia tolerance.

anoxia↗

PubMed2026

Music therapy in artificial insemination by husband: Effects on psychological distress and clinical pregnancy rate.

BACKGROUND: Infertility treatment can be psychologically burdensome. Evidence on music listening during artificial insemination by husband (AIH) remains limited. We evaluated whether a standardized periprocedural music intervention reduced psychological distress and explored its association with clinical pregnancy. METHODS: In this single-center, open-label randomized trial, 254 women undergoing AIH were allocated 1:1 to routine care or routine care plus two 30-minute music-listening sessions, immediately before and after AIH. The prespecified primary outcome was the continuous 21-item Depression Anxiety Stress Scales (DASS-21) score at follow-up; clinical pregnancy was secondary. DASS-21 was completed at baseline and at day 35 after AIH. Clinical pregnancy was assessed by ultrasonography at days 30 to 35. RESULTS: Continuous DASS-21 anxiety, depression, and stress scores did not differ between groups after adjustment for baseline scores (all P ≥ .868). Absolute postintervention differences were 0.01 point or less for anxiety and depression and 0.08 point for stress, indicating neither statistical nor clinically meaningful improvement. Clinical pregnancy occurred in 34/127 participants (26.77%) in the intervention group and 14/127 (11.02%) in the control group (exploratory secondary outcome; P = .001). CONCLUSION: The intervention did not improve the primary psychological outcome. The higher clinical pregnancy rate is hypothesis-generating because the trial was not powered for pregnancy, the proposed psychological mechanism was not demonstrated, and nonspecific attention and other unmeasured factors cannot be excluded. Replication using an attention-matched control, immediate state-anxiety and physiological measures, participant-preference assessment, and live-birth follow-up is required.

Humans↗

PubMed2026

Altered ECM deposition and cell adhesion signaling in a human cortical organoid model of fragile X syndrome.

Fragile X Syndrome (FXS) is the most common inherited intellectual disability, and the most common monogenic cause of autism spectrum disorder (ASD). It is caused by epigenetic silencing of the FMR1 gene leading to the loss of FMRP, an RNA-binding protein that regulates local mRNA translation in neuronal dendrites, crucial for synapse development. Three-dimensional (3D) brain organoid models derived through in vitro differentiation of pluripotent stem cells offer a powerful tool to dissect the underlying mechanisms of neurodevelopmental disorders. Here, we generated human FXS and control organoids using isogenic human embryonic stem cell clones with and without the FXS mutation. Our results show that mature FXS cortical brain organoids can be derived by inhibiting the TGFβ and Wnt pathways. Moreover, expression analyses including immunofluorescence, qRT-PCR, proteomics and western blotting reveal altered levels of neuronal markers and ECM deposition along with modulated downstream signaling molecules. Interestingly, in silico analysis of proteomics revealed several altered pathways, such as cell adhesion, regulation of neurogenesis and cell cycle that are implicated in FXS. Collectively, our unique FXS-organoids derived from isogenic hESC lines may serve as a model for studying the pathology of FXS disorder and for developing therapeutical intervention.

Humans↗

PubMed2025

A spectral framework to map QTLs affecting joint differential networks of gene co-expression.

Studying the mechanisms underlying the genotype-phenotype association is crucial in genetics. Gene expression studies have deepened our understanding of the genotype  →  expression  →  phenotype mechanisms. However, traditional expression quantitative trait loci (eQTL) methods often overlook the critical role of gene co-expression networks in translating genotype into phenotype. This gap highlights the need for more powerful statistical methods to analyze genotype  →  network  →  phenotype mechanism. Here, we develop a network-based method, called spectral network quantitative trait loci analysis (snQTL), to map quantitative trait loci affecting gene co-expression networks. Our approach tests the association between genotypes and joint differential networks of gene co-expression via a tensor-based spectral statistics, thereby overcoming the ubiquitous multiple testing challenges in existing methods. We demonstrate the effectiveness of snQTL in the analysis of three-spined stickleback (Gasterosteus aculeatus) data. Compared to conventional methods, our method snQTL uncovers chromosomal regions affecting gene co-expression networks, including one strong candidate gene that would have been missed by traditional eQTL analyses. Our framework suggests the limitation of current approaches and offers a powerful network-based tool for functional loci discoveries.

Quantitative Trait Loci↗