Metabolic and protein expression responses of Shewanella baltica in golden pomfret broths to slightly acidic electrolysed water.

Shewanella baltica is a specific spoilage organism of golden pomfret. This study aims to explore the antibacterial mechanism of slightly acidic electrolysed water (SAEW) against S. baltica (strains ABa4, ABe2 and BBe1) in golden pomfret broths by metabolomics, proteomics and bioinformatics analyses. S. baltica was decreased by at least 3.94 log CFU/mL after SAEW treatment, and strain ABa4 had the highest resistance. Under SAEW stress, amino acids and organic acids in S. baltica decreased, and nucleotide related compounds degraded. Furthermore, 100 differentially expressed proteins (DEPs) were identified. Most DEPs of strains ABe2 and BBe1 were down-regulated, while some DEPs of strain ABa4 were up-regulated, especially those oxidative stress related proteins. These results suggest that the modes of SAEW against S. baltica can be traced to the inhibition of amino acid, carbon, nucleotide and sulphur metabolisms, and the loss of functional proteins for temperature regulation, translation, motility and protein folding.

Proteomic insights from extracellular vesicles into the molecular mechanisms of health effects induced by Per- and polyfluoroalkyl substances.

Per- and polyfluoroalkyl substances (PFASs) can induce a range of adverse health effects, with the precise molecular mechanisms remaining elusive. Extracellular vesicles (EVs) have demonstrated their potential to elucidate unknown molecular mechanisms. Building upon the close alignment of their biological functions with the observed health effects of PFASs, this study innovatively focuses on proteomic insights from EVs into the molecular mechanisms underlying the systemic health effects of PFASs. Through rat exposure experiments and proteomics technology, it not only demonstrated the occurrence of PFASs in EVs but also revealed the alterations in the serum EVs and the expression of their protein cargos following mixed exposure to PFASs, leading to changes in related pathways. These changes encompass various biological processes, including proteasome activity, immune response, cytoskeletal organization, oxidative stress, cell signaling, and nervous system function. Particularly noteworthy is the uncovering of the activation of the proteasome pathway, highlighting significant key contributing proteins. These novel findings provide a new perspective for exploring the molecular mechanism underlying the systemic health effects of PFASs and offer reliable screening for potential biomarkers. Additionally, comparisons with serum confirmed the potential of serum EVs as biological responders and measurable endpoints for evaluating PFASs-induced toxicity.

Application of Proteomics Technology Based on LC-MS Combined with Western Blotting and Co-IP in Antiviral Innate Immunity.

As an interferon-stimulating factor protein, STING plays a role in the response and downstream liaison in antiviral natural immunity. Upon viral invasion, the immediate response of STING protein leads to a series of changes in downstream proteins, which ultimately leads to an antiviral immune response in the form of proinflammatory cytokines and type I interferons, thus triggering an innate immune response, an adaptive immune response in vivo, and long-term protection of the host. In the field of antiviral natural immunity, it is particularly important to rigorously and sequentially probe the dynamic changes in the antiviral natural immunity connector protein STING caused by the entire anti-inflammatory and anti-pathway mechanism and the differences in upstream and downstream proteins. Traditionally, proteomics technology has been validated by detecting proteins in a 2D platform, for which it is difficult to sensitively identify changes in the nature and abundance of target proteins. With the development of mass spectrometry (MS) technology, MS-based proteomics has made important contributions to characterizing the dynamic changes in the natural immune proteome induced by viral infections. MS analytical techniques have several advantages, such as high throughput, rapidity, sensitivity, accuracy, and automation. The most common techniques for detecting complex proteomes are liquid chromatography (LC) and mass spectrometry (MS). LC-MS (Liquid Chromatography-Mass Spectrometry), which combines the physical separation capability of LC and the mass analysis capability of MS, is a powerful technique mainly used for analyzing the proteome of cells, tissues, and body fluids. To explore the combination of traditional proteomics techniques such as Western blotting, Co-IP (co-Immunoprecipitation), and the latest LC-MS methods to probe the anti-inflammatory pathway and the differential changes in upstream and downstream proteins induced by the antiviral natural immune junction protein STING.

Protein profile of purified plasma- and aqueous humor-derived extracellular vesicles from patients with ocular toxoplasmosis

ABSTRACT Purpose: To characterize the extracellular vesicle protein cargo in the aqueous humor and plasma of patients with ocular toxoplasmosis. Methods: Aqueous humor and plasma were collected from six patients with active ocular toxoplasmosis and six patients with cataract. Extracellular vesicles were isolated, and western blotting and mass spectrometry were performed for protein analysis. Results: All plasma samples from patients with ocular toxoplasmosis and cataract were positive for the tetraspanins CD63 and TSG101. However, the aqueous humor from patients with ocular toxoplasmosis was positive only for CD63. Sixty-seven new unreported proteins were identified in the aqueous humor and plasma of patients with the ocular toxoplasmosis and cataract. Of the 67 proteins, 10 and 7 were found only in the cataract and ocular toxoplasmosis groups, respectively. In general, these proteins were involved in immune system activation and retina homeostasis and were related to infections and retina-associated diseases. Conclusion: The distinct protein signatures between ocular toxoplasmosis and cataract may be helpful in the differential diagnosis of ocular toxoplasmosis. However, more studies are needed to better understand the role of these proteins in the pathogenesis of ocular toxoplasmosis.

Actin cytoskeleton and plasma membrane aquaporins are involved in different drought response of Arabidopsis rhd2 and der1 root hair mutants.

Actin cytoskeleton and reactive oxygen species are principal determinants of root hair polarity and tip growth. Loss of function in RESPIRATORY BURST OXIDASE HOMOLOG C/ROOT HAIR DEFECTIVE 2 (AtRBOHC/RHD2), an NADPH oxidase emitting superoxide to the apoplast, and in ACTIN 2, a vegetative actin isovariant, in rhd2-1 and der1-3 mutants, respectively, lead to similar defects in root hair formation and elongation Since early endosome-mediated polar localization of AtRBOHC/RHD2 depends on actin cytoskeleton, comparing the proteome-wide consequences of both mutations might be of eminent interest. Therefore, we employed a differential proteomic analysis of Arabidopsis rhd2-1 and der1-3 mutants. Both mutants exhibited substantial alterations in abundances of stress-related proteins. Notably, plasma membrane (PM)-localized PIP aquaporins showed contrasting abundance patterns in the mutants compared to wild-types. Drought-responsive proteins were mostly downregulated in rhd2-1 but upregulated in der1-3. Proteomic data suggest that opposite to der1-3, altered vesicular transport in rhd2-1 mutant likely contributes to the deregulation of PM-localized proteins, including PIPs. Moreover, lattice light sheet microscopy revealed reduced actin dynamics in rhd2-1 roots, a finding contrasting with previous reports on der1-3 mutant. Phenotypic experiments demonstrated a drought stress susceptibility in rhd2-1 and resistance in der1-3. Thus, mutations in AtRBOHC/RHD2 and ACTIN2 cause similar root hair defects, but they differently affect the actin cytoskeleton and vesicular transport. Reduced actin dynamics in rhd2-1 mutant is accompanied by alteration of vesicular transport proteins abundance, likely leading to altered protein delivery to PM, including aquaporins, thereby significantly affecting drought stress responses.

Proteomic biomarkers of long-term lung function decline in textile workers: a 35-year longitudinal study.

BACKGROUND: Occupational exposures contribute significantly to obstructive lung disease among textile workers. However, biomarkers associated with such declines are not available. OBJECTIVES: We conducted a large-scale proteomic study to explore protein biomarkers potentially associated with long-term lung function decline. METHODS: Shanghai Textile Workers Cohort was established in 1981 with 35 years of follow-up, assessing textile workers' lung functions every five years. Quantitative serum proteomics was performed on all 453 workers at 2016 survey. We employed four distinct models to examine the association between forced expiratory volume in one second (FEV1) and proteins, and consolidated the findings using an aggregated Cauchy association test. Furthermore, proteomic data of UK Biobank (UKB) was used to explore the associations of potential protein markers and decline of FEV1, and the interactions of these proteins were examined through STRING database. Associations were also externally validated using two-sample Mendelian randomizations (MR). RESULTS: 15 of 907 analyzed proteins displayed potential associations with long-term FEV1 decline, including two hemoglobin subunits: hemoglobin subunit beta (HBB, FDR-qACAT = 0.040), alpha globin chain (HBA2, FDR-qACAT = 0.045), and four immunoglobulin subunits: immunoglobulin kappa variable 3-7 (IGKV3-7, FDR-qACAT = 0.003), immunoglobulin heavy chain variable region (IgH, FDR-qACAT = 0.011). Five proteins were significantly associated with the rate of decline of FEV1 in UKB, in which RAB6A, LRRN1, and BSG were also found to be associated with proteins identified in Shanghai Textile Workers Cohort using STRING database. MR indicated bidirectional associations between HBB and FEV1 (P < 0.05), while different immunoglobulin subunits exhibited varying associations with FEV1. IMPACT STATEMENT: We performed a large-scale proteomic study of the longest-follow-up pulmonary function cohort of textile workers to date. We discovered multiple novel proteins associated with long-term decline of FEV1 that have potential for identifying new biomarkers associated with long-term lung function decline among occupational populations, and may identify individuals at risk, as well as potential pharmaceutical targets for early intervention.

Two-Dimensional Layered Nano-MoS2 Induces Earthworm Immune Cell Apoptosis by Regulating Lysosomal Maintenance and Function: Toward Unbiased Screening and Validation of Suspicious Pathways.

Molybdenum-based nanosheets (NSMoS2) are increasingly applied in various fields and undergoing relevant risk evaluations on subjectively hypothesized toxicity pathways. However, risk assessment should be unbiased and focus on appropriate end points to avoid biased prescreening. Here, we developed an adverse biological outcome screening strategy based on nontargeted functional protein profiles in earthworm (Eisenia fetida) immune cells exposed to NSMoS2 and their ionic counterpart (Na2MoO4). Through this framework, the apoptosis-related processes with distinct mechanisms were rapidly identified and thoroughly validated phenotypically. Specifically, upon exposure to 50 µg Mo/mL Na2MoO4, cellular signaling and energy homeostasis were disrupted within the transcription-translation biological chain. The autophagic pathway was activated, which, together with energy deprivation, phenotypically induced significant autophagy that ultimately led to apoptosis. In contrast, NSMoS2, tested at the same concentration, caused a reprogramming of apoptotic gene and protein expressions. Transcriptome plasticity facilitated the endocytic-adaptive transcriptional profile characterized by cytoskeleton remodeling and lysosome organization/movement under NSMoS2 exposure. Subcellular dynamics further revealed NSMoS2-induced lysosomal damage with a time-sensitive physiological window, ultimately mediating apoptosis. These findings provide a mechanistic and visual understanding of the distinct risk profile of NSMoS2 compared to molybdate, highlighting the importance of integrating nontargeted screening and phenotypic validation in early risk warning.

Mechanisms of Polyethylene Terephthalate Pellet Fragmentation into Nanoplastics and Assimilable Carbons by Wastewater Comamonas.

Comamonadaceae bacteria are enriched on poly(ethylene terephthalate) (PET) microplastics in wastewaters and urban rivers, but the PET-degrading mechanisms remain unclear. Here, we investigated these mechanisms with Comamonas testosteroniKF-1, a wastewater isolate, by combining microscopy, spectroscopy, proteomics, protein modeling, and genetic engineering. Compared to minor dents on PET films, scanning electron microscopy revealed significant fragmentation of PET pellets, resulting in a 3.5-fold increase in the abundance of small nanoparticles (<100 nm) during 30-day cultivation. Infrared spectroscopy captured primarily hydrolytic cleavage in the fragmented pellet particles. Solution analysis further demonstrated double hydrolysis of a PET oligomer, bis(2-hydroxyethyl) terephthalate, to the bioavailable monomer terephthalate. Supplementation with acetate, a common wastewater co-substrate, promoted cell growth and PET fragmentation. Of the multiple hydrolases encoded in the genome, intracellular proteomics detected only one, which was found in both acetate-only and PET-only conditions. Homology modeling of this hydrolase structure illustrated substrate binding analogous to reported PET hydrolases, despite dissimilar sequences. Mutants lacking this hydrolase gene were incapable of PET oligomer hydrolysis and had a 21% decrease in PET fragmentation; re-insertion of the gene restored both functions. Thus, we have identified constitutive production of a key PET-degrading hydrolase in wastewater Comamonas, which could be exploited for plastic bioconversion.

Vinpocetine Ameliorates Neuronal Injury After Cold-Induced Traumatic Brain Injury in Mice.

Traumatic brain injury (TBI), also known as intracranial injury, is a common condition with the highest incidence rate among neurodegenerative disorders and poses a significant public health burden. Various methods are used in the treatment of TBI, but the effects of cold-induced traumatic brain injury have not been thoroughly studied. In this context, vinpocetine (VPN), derived from Vinca minor, exhibits notable anti-inflammatory and antioxidant properties. VPN is known for its neuroprotective role and is generally utilized for treating various neurodegenerative disorders. However, the function of VPN after cold-induced TBI needs to be studied in more detail. This study aims to investigate the neuroprotective effects of VPN at varying doses (5 mg/kg or 10 mg/kg) after cold-induced TBI. C57BL/6 mice were sacrificed 2 or 28 days after cold-induced TBI. Results indicate that VPN administration significantly reduces brain infarct volume, brain swelling, blood-brain barrier disruption, and DNA fragmentation in a dose-dependent manner. Additionally, VPN enhances neuronal survival in the ipsilesional cortex. In the long term, VPN treatment (5 mg/kg/day or 10 mg/kg/day, initiated 48 h post-TBI) improved locomotor activity, cell proliferation, neurogenesis, and decreased whole brain atrophy, specifically motor cortex atrophy. We performed liquid chromatography-tandem mass spectrometry (LC-MS/MS) to elucidate the underlying mechanisms to profile proteins and signaling pathways influenced by prolonged VPN treatment post-TBI. Notably, we found that 192 different proteins were significantly altered by VPN treatment, which is a matter of further investigation for the development of therapeutic targets. Our study has shown that VPN may have a neuroprotective role in cold-induced TBI.

Comprehensive Proteomic Analysis of Dysferlinopathy Unveiling Molecular Mechanisms and Biomarkers Linked to Pathological Progression.

AIMS: Previous proteomics studies in dysferlinopathy muscle have been limited in scope, often utilizing 2D-electrophoresis and yielding only a small number of differential expression calls. To address this gap, this study aimed to employ high-resolution proteomics to explore the proteomic landscapes of dysferlinopathy and analyze the correlation between muscle pathological changes and alterations in protein expression in muscle biopsies. METHODS: We conducted a comprehensive approach to investigate the proteomic profile and disease-associated changes in the muscle tissue proteome from 15 patients with dysferlinopathy, exhibiting varying degrees of dystrophic pathology, alongside age-matched controls. Our methodology encompasses tandem mass tag (TMT)-labeled liquid chromatography-mass spectrometry (LC-MS/MS)-based proteomics, protein-protein interaction (PPI) network analysis, weighted gene co-expression network analysis, and differential expression analysis. Subsequently, we examined the correlation between the expression of key proteins and the clinical characteristics of the patients to identify pathogenic targets associated with DYSF mutations in dysferlinopathy. RESULTS: A total of 1600 differentially expressed proteins were identified, with 1321 showing high expression levels and 279 expressed at lower levels. Our investigation yields a molecular profile delineating the altered protein networks in dysferlinopathy-afflicted skeletal muscle, uncovering dysregulation across numerous cellular pathways and molecular processes, including mRNA metabolic processes, regulated exocytosis, immune response, muscle system processes, energy metabolic processes, and calcium transmembrane transport. Moreover, we observe significant associations between the protein expression of ANXA1, ANXA2, ANXA4, ANXA5, LMNA, PYGM, and the extent of histopathologic changes in muscle biopsies from patients with dysferlinopathy, validated through immunoblotting and immunofluorescence assays. CONCLUSIONS: Through the aggregation of expression data from dysferlinopathy-impacted muscles exhibiting a range of pathological alterations, we identified multiple key proteins associated with the dystrophic pathology of patients with dysferlinopathy. These findings provide novel insights into the pathogenesis of dysferlinopathy and propose promising targets for future therapeutic endeavors.

The ROSMAP project: aging and neurodegenerative diseases through omic sciences.

The Religious Order Study and Memory and Aging Project (ROSMAP) is an initiative that integrates two longitudinal cohort studies, which have been collecting clinicopathological and molecular data since the early 1990s. This extensive dataset includes a wide array of omic data, revealing the complex interactions between molecular levels in neurodegenerative diseases (ND) and aging. Neurodegenerative diseases (ND) are frequently associated with morbidity and cognitive decline in older adults. Omics research, in conjunction with clinical variables, is crucial for advancing our understanding of the diagnosis and treatment of neurodegenerative diseases. This summary reviews the extensive omics research-encompassing genomics, transcriptomics, proteomics, metabolomics, epigenomics, and multiomics-conducted through the ROSMAP study. It highlights the significant advancements in understanding the mechanisms underlying neurodegenerative diseases, with a particular focus on Alzheimer's disease.

Identifying new biomarkers and potential therapeutic targets for breast cancer through the integration of human plasma proteomics: a Mendelian randomization study and colocalization analysis.

Background: The proteome is a crucial reservoir of targets for cancer treatment. While some targeted therapies have been developed, there are still significant challenges in early diagnosis and treatment, highlighting the need to identify new biomarkers and therapeutic targets for breast cancer. Therefore, we conducted a comprehensive proteome-wide Mendelian randomization (MR) study to identify novel biomarkers and potential therapeutic targets for breast cancer. Methods: Protein quantitative trait locus (pQTL) data were extracted from two published plasma proteome-wide association studies. Genetic variants associated with breast cancer were obtained from the Breast Cancer Association Consortium, which included 133,384 cases and 113,789 controls, and the Finnish cohort study, comprising 18,786 cases and 182,927 controls. We employed summary-based MR and colocalization methods to identify potential drug targets for breast cancer, which were subsequently validated using a two-sample MR approach. Finally, a protein-protein interaction (PPI) network was constructed to detect interactions between the identified proteins and existing cancer drug targets. Results: Gene-predicted levels of ten proteins were associated with breast cancer risk. Decreased levels of CASP8, DDX58, CPNE1, ULK3, PARK7, and BTN2A1, as well as increased levels of TNFRSF9, TNXB, DNPH1, and TLR1, were linked to an elevated risk of breast cancer. Among these, CASP8 and DDX58 were supported by tier-one evidence, while CPNE1, ULK3, PARK7, and TNFRSF9 received tier-two evidence support. The remaining proteins, TNXB, BTN2A1, DNPH1, and TLR1, were supported by tier-three evidence. CASP8, DDX58, CPNE1, ULK3, PARK7, and TNFRSF9 have already been identified as targets in drug development and potential therapeutic targets for breast cancer treatment. Additionally, ULK3 showed promise as a prognostic biomarker for breast cancer. Conclusions: The present study identified several novel potential drug targets and biomarkers for breast cancer, providing new insights into its diagnosis and treatment. The integration of PPI and druggability evaluations enhances the prioritization of these therapeutic targets, paving the way for future drug development efforts.

Recent advances in proteomic analysis to study carotid artery plaques.

Objective: We sought to identify differentially expressed proteins in serum, plasma, and plaque samples of patients with carotid atherosclerotic lesions. Methods: We performed a systematic review of the proteomic profile of serum, plasma, and plaque samples of patients with carotid artery disease. We included full-length peer-reviewed studies of adult humans and reported them using PRISMA guidelines. The quality of the design and content of the articles included in the review was assessed using the Newcastle-Ottawa scale. Results: We included six peer-reviewed articles reporting protein expression in serum, plasma, or plaque samples from patients with carotid atherosclerosis. Three were single-center cross-sectional studies, two were single-center case-control studies, and one was a single-center cohort study. Thirty-six proteins were found to be expressed differentially when comparing samples from healthy subjects and individuals with diseased carotid vessels and between patients with symptomatic and asymptomatic carotid artery atherosclerotic lesions. Some of these were shown to be related to inflammatory or anti-inflammatory pathways in atherogenesis. CD5L and S100A12 were both found to be upregulated in patients with unstable plaque, the former owing to its anti-inflammatory properties and the latter for its pro-oxidant effects in atherosclerosis. ACTB is involved in cellular structure and integrity and was found to be downregulated in patients with ruptured carotid plaques. Conclusions: Atherosclerotic carotid disease places the patient at increased risk of ischemic neurological events. Proteomics may help to understand their pathophysiological processes and can identify differential protein expression in blood samples from healthy subjects and patients with carotid artery plaques. This patient-centered approach will allow for the timely identification of individuals at higher risk of experiencing stroke.

Combined proteomics and metabolomics analysis reveal the effect of a training course on the immune function of Chinese elite short-track speed skaters.

INTRODUCTION: The aim of this study was to combine proteomics and metabolomics to evaluate the immune system of short-track speed skaters (STSS) before and after a training course. Our research focused on changes in urinary proteins and metabolites that have the potential to serve as indicators for training load. METHODS: Urine samples were collected from 21 elite STSS (13 male and 8 female) of the China National Team before and immediately after one training course. First-beat sports sensor was used to monitor the training load. Proteomic detection was performed using a Thermo UltiMate 3000 ultra high performence chromatography nano liquid chromatograph and an Orbitrap Exploris 480 mass spectrometer. MSstats (R package) was used for the statistical evaluation of significant differences in proteins from the samples. Two filtration criteria (fold change [FC] > 2 and p < 0.05) were used to identify the differential expressed proteins. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis for differential proteins was performed to identify the pathways involved. Nontargeted metabolomic detection was performed using ultra performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS_) with an ACQUITY 2D UPLC plus Q Exactive (QE) hybrid Quadrupole-Orbitrap mass spectrometer. Differential metabolites were identified using non-parametric statistical methods (Wilcox's rank test). Two filtration criteria (FC > 1.2 and p < 0.05) were used to identify differential metabolites. Combined analysis of proteomic and metabolomics were performed on the "Wu Kong" platform. Correlation analysis was performed using Spearman's rank correlation coefficient. RESULTS: (1) The most upregulated proteins were immune-related proteins, including complement proteins (C9, C4-B, and C9) and immunoglobulins (IgA, IgM, and IgG). The most downregulated proteins were osteopontin (OPN) and CD44 in urine. The correlation analysis showed that the content of OPN and CD44 (the receptor for OPN) in urine were significantly negatively correlated with the upregulated immune-related proteins. The content of OPN and CD44 is sex-dependent and negatively correlated with the training load. (2) The most upregulated metabolites included lactate, cortisol, inosine, glutamine, argininosuccinate (the precursor for arginine synthesis), 3-methyl-2-oxobutyrate (the catabolite of valine), 3-methyl-2-oxovalerate (the catabolite of isoleucine), and 4-methyl-2-oxopentanoate (the catabolite of leucine), which is sex-dependent and negatively correlated with OPN and CD44. (3) The joint analysis revealed five main related pathways, including the immune and innate immune systems. The enriched immune-related proteins included complements, immunoglobulins, and protein catabolism-related proteins. The enriched immune-related metabolites included cAMP, N-acetylgalactosamine, and glutamate. (4) There is a significant negative correlation between the content of OPN and CD44 in urine and the training load. CONCLUSION: One training course can lead to the activation of the immune system and a sex-dependent decrease in the content of OPN and CD44. Training load has a significant and negative correlation with the content of OPN and CD44, suggesting that OPN and CD44 could be potential indicators for training load.

Curcumol derivatives exhibit ameliorating effects on lipopolysaccharide-induced acute lung injury: Synthesis, biological evaluation, structure-activity relationship and action mechanism.

Acute lung injury (ALI) is an intricate clinical disease marked by high mortality and a sudden start. Currently, although there are no specific therapeutics for ALI, the administration of anti-inflammatory drugs is a promising treatment strategy. Curcumol, a terpenoid natural product, has demonstrated significant anti-inflammatory activity. Herein, we designed and synthesised 42 curcumol derivatives using curcumol as the core scaffold. These derivatives underwent in vitro screening for anti-inflammatory activity, and their structure-activity relationship was assessed. Among them, derivative 2 exhibited potent anti-inflammatory potential, inhibiting the expression of inflammatory markers at the nanomolar level. In addition, its water solubility was considerably improved, thereby laying the foundation for enhanced druggability. Derivative 2 also ameliorated lipopolysaccharide (LPS)-induced ALI and reduced pulmonary inflammation at a dose of 5 mg/kg. Proteomics analysis revealed that the anti-inflammatory effect of this compound primarily involved the mTOR signalling pathway. Furthermore, molecular docking and cellular thermal shift assays indicated that GSK3ß is a critical target of action of derivative 2, as verified via western blotting. These findings suggest that derivative 2 can be a lead therapeutic compound for ALI, with GSK3ß emerging as a promising novel target for the development of specific anti-ALI drugs.

Salinity-Induced Photorespiration in Populus Vascular Tissues Facilitate Nitrogen Reallocation.

Adaptation to abiotic stress is critical for the survival of perennial tree species. Salinity affects plant growth and productivity by interfering with major biosynthetic processes. Detrimental effects of salinity may vary between different plant tissues and cell types. However, spatial molecular mechanisms controlling plant responses to salinity stress are not yet thoroughly understood in perennial trees. We used laser capture microdissection in clones of Populus tremula x alba to isolate palisade and vascular cells of intermediary leaf from plants exposed to 150 mM NaCl for 10 days, followed by a recovery period. Cell-specific changes in proteins and metabolites were determined. Salinity induced a vascular-specific accumulation of proteins associated with photorespiration, and the accumulation of serine, 3-phosphoglycerate and NH4 + suggesting changes in N metabolism. Accumulation of the GLUTAMINE SYNTHETASE 2 protein, and increased GS1.1 gene expression, indicated that NH4 + produced in photorespiration was assimilated to glutamine, the main amino acid translocated in Populus trees. Further analysis of total soluble proteins in stems and roots showed the accumulation of bark storage proteins induced by the salinity treatments. Collectively, our results suggest that the salt-induced photorespiration in vascular cells mediates N-reallocation in Populus, an essential process for the adaptation of trees to adverse conditions.

Data-Independent Acquisition Proteome Technology for Analysis of Antifungal and Anti-aflatoxigenic Properties of Eugenol to Aspergillus flavus.

Several toxicogenic Aspergilli, such as Aspergillus flavus and A. parasiticus, could biosynthesize aflatoxin B1 (AFB1) and other mycotoxins. Chemical fungicides are commonly used to control fungal contamination, but chemical residues may pose significant risks to human health and environmental stability. Consequently, natural antifungal and aflatoxin-inhibiting agents could be sustainable alternatives. Eugenol has been used as an inhibitor of aflatoxins (AFs), which is a common essential oil. Nevertheless, the definite mechanism by which eugenol exerts its inhibitory effect on Aspergillus remains unclear. This research demonstrates that eugenol significantly suppressed fungi growth and AF production as the dose increased (40.9 to 100%). With the proteomics approach, the inhibition pathway of eugenol was investigated. The production of proteins involved in cell wall integrity was notably reduced under eugenol treatment, indicating that eugenol destroys the cell wall integrity of A. flavus. Furthermore, exposure to eugenol downregulated several fungal developmental regulators and subsequently inhibited A. flavus development. Energy metabolism in A. flavus is closely related to its secondary metabolism. Under eugenol treatment, the synthesis of proteins relevant to the pentose phosphate pathway was significantly enhanced, leading to a decrease in the availability of acetyl-CoA, a precursor for AF biosynthesis. Simultaneously, the valine, leucine, and isoleucine biosynthesis pathways were enhanced, further reducing the content of acetyl-CoA. This might be the primary factor in the inhibition of AF biosynthesis by eugenol. Ribosome biogenesis was the most dysregulated pathway based on KEGG data, indicating that eugenol disturbed ribosome biogenesis and affected its normal function in A. flavus. In conclusion, eugenol inhibits the cellular integrity, energy metabolism, and protein synthesis and then suppresses A. flavus development and AF biosynthesis, which provides a clearer grasp of the inhibitory mechanism meaningful for A. flavus and AF contamination control.

Circulating Proteins Associated with Anti-IL6 Receptor Therapeutic Resistance in the Sera of Patients with Severe COVID-19.

Circulating proteomes provide a snapshot of the physiological state of a human organism responding to pathogenic challenges and drug interventions. The outcomes of patients with COVID-19 and acute respiratory distress syndrome triggered by the SARS-CoV2 virus remain uncertain. Tocilizumab is an anti-interleukin-6 treatment that exerts encouraging clinical activity by controlling the cytokine storm and improving respiratory distress in patients with COVID-19. We investigate the biological determinants of therapeutic outcomes after tocilizumab treatment. Overall, 28 patients hospitalized due to severe COVID-19 who were treated with tocilizumab intravenously were included in this study. Sera were collected before and after tocilizumab, and the patient's outcome was evaluated until day 30 post-tocilizumab infusion for favorable therapeutic response to tocilizumab and mortality. Hyperreaction monitoring measurements by liquid chromatography-mass spectrometry-based proteomic analysis with data-independent acquisition quantified 510 proteins and 7019 peptides in the serum of patients. Alterations in the serum proteome reflect COVID-19 outcomes in patients treated with tocilizumab. Our results suggested that circulating proteins associated with the most significant prognostic impact belonged to the complement system, platelet degranulation, acute-phase proteins, and the Fc-epsilon receptor signaling pathway. Among these, upregulation of the complement system by activation of the classical pathway was associated with poor response to tocilizumab, and upregulation of Fc-epsilon receptor signaling was associated with lower mortality.

Plasma Proteomic Insights for Identification of Novel Predictors and Potential Drug Targets in Atrial Fibrillation: A Prospective Cohort Study and Mendelian Randomization Analysis.

BACKGROUND: Currently, there are no reliable methods for predicting and preventing atrial fibrillation (AF) in its early stages. This study aimed to identify plasma proteins associated with AF to discover biomarkers and potential drug targets. METHODS: The UK Biobank Pharma Proteomics Project examined 2923 circulating proteins using the Olink platform, forming the basis of this prospective cohort study. The UK Biobank Pharma Proteomics Project included a randomly selected discovery cohort and the consortium-selected replication cohort. The study's end point was incident AF, identified using International Classification of Diseases, Tenth Revision codes. The association between plasma proteins and incident AF was evaluated using Cox proportional hazard models in both cohorts. Proteins present in both cohorts underwent Mendelian randomization analysis to delineate causal connections, utilizing cis-protein quantitative trait loci as genetic tools. The predictive efficacy of the identified proteins for AF was assessed using the area under the receiver operating characteristic curve, and their druggability was explored. RESULTS: Data from 53 032 participants were included in this study. Incident AF cases were identified in the discovery cohort (1894; 5.5%) within a median follow-up of 14.5 years and in the replication cohort (451; 10.6%) within a median follow-up of 14.4 years. Twenty-one proteins linked to AF were identified in both cohorts. Specifically, COL4A1 (collagen IV α-1; odds ratio, 1.11 [95% CI, 1.04-1.19]; false discovery rate, 0.016) and RET (proto-oncogene tyrosine-protein kinase receptor Ret; odds ratio, 0.96 [95% CI, 0.94-0.98]; false discovery rate, 0.013) demonstrated a causal link with AF, and RET is druggable. COL4A1 improved the short- and long-term predictive performance of established AF models, as evidenced by significant enhancements in the area under the receiver operating characteristic, integrated discrimination improvement, and net reclassification index, all with P values below 0.05. CONCLUSIONS: COL4A1 and RET are associated with the development of AF. RET is identified as a potential drug target for AF prevention, while COL4A1 serves as a biomarker for AF prediction. Future studies are needed to evaluate the effectiveness of targeting these proteins to reduce AF risk.

Novel Serum Markers that Distinguish Behcet's Disease from Idiopathic Recurrent Aphthous Stomatitis.

BACKGROUND: Behcet's disease (BD) is a rare and recurrent autoinflammatory disorder characterized by systemic vasculitis, frequently manifested as recurrent aphthous stomatitis (RAS). We aim to identify specific serum proteins to discriminate between BD and idiopathicRAS. METHOD: Peripheral blood was collected from 12 BD patients, 12 idiopathic RAS patients, and 21 healthy volunteers. The serum samples underwent Tandem Mass Tag-based mass spectrometry analysis. Differentially expressed proteins (DEPs) were identified for KEGG pathway enrichment, Gene Ontology (GO), and protein-protein interaction (PPI) analyses. ELISA was utilized to verify two BD-specific DEPs in another cohort consisting of 18 BD patients, 18 idiopathic RAS patients, and 18 controls. RESULTS: Compared with RAS serum, BD serum showed 242 DEPs. 49 proteins were differentially expressed in BD but not RAS serum compared to healthy controls. KEGG pathway and GO analyses revealed that DEPs in BD and RAS have similar biological functions and cellular distributions, featuring a significant association with pathways regulating blood coagulation and immune response. When comparing DEPs between BD and RAS, several keratins emerged as markers that distinguish RAS from BD. We also identified multiple DEPs in BD but not RAS patients. PPI analysis uncovered that lipoprotein metabolism regulators serve as hub proteins, indicating their potentially essential roles in BD pathology. In addition, ELISA results confirmed the elevated LRG1 and SOD3 levels in BD, but not RAS patients, compared to healthy donors. CONCLUSION: Our data uncovered novel serum proteins that distinguish BD from RAS, which may potentially be useful in BD diagnosis and treatment.