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Soybean is a crucial source of food, protein, and oil worldwide that is facing challenges from biotic stresses. Infestation of Tetranychus urticae Koch (Acari: Tetranychidae) stands out as detrimentally affecting plant growth and grain production. Understanding soybean responses to T. urticae infestation is pivotal for unravelling the dynamics of mite–plant interactions. We evaluated the physiological and molecular responses of soybean plants to mite infestation after 5 and 21 days.We employed visual/microscopy observations of leaf damage, H2O2 accumulation, and lipid peroxidation. Additionally, the impact of mite infestation on shoot length/dry weight, chlorophyll concentration, and development stages was analysed. Proteomic analysis identified differentially abundant proteins (DAPs) after early (5 days) and late (21 days) infestation. Furthermore, GO, KEGG, and protein–protein interaction analyses were performed to understand effects on metabolic pathways.Throughout the analysed period, symptoms of leaf damage, H2O2 accumulation, and lipid peroxidation consistently increased. Mite infestation reduced shoot length/dry weight, chlorophyll concentration, and development stage duration. Proteomics revealed 185 and 266 DAPs after early and late mite infestation, respectively, indicating a complex remodelling of metabolic pathways. Photorespiration, chlorophyll synthesis, amino acid metabolism, and Krebs cycle/energy production were impacted after both early and late infestation. Additionally, specific metabolic pathways were modified only after early or late infestation.This study underscores the detrimental effects of mite infestation on soybean physiology and metabolism. DAPs offer potential in breeding programs for enhanced resistance. Overall, this research highlights the complex nature of soybean response to mite infestation, providing insights for intervention and breeding strategies. [ABSTRACT FROM AUTHOR]

The study aims to investigate the differences in protein expressions in Xizang's (Tibetan) middle-to-long distance runners after the transition from high altitude to low altitude and reveal the molecular mechanisms underlying their enhanced middle-to-long distance running performance. In the study, eleven subjects were selected from native Tibetan middle-to-long distance runners to participate in an 8-week pre-competition exercise training program consisting of a 6-week training stage in Kangding City at an altitude of 2 560 meters (m) and a subsequent 2-week training stage in Leshan City at an altitude of 360 m. Blood samples were collected twice from the runners before beginning altitude exercise training in Kangding and after going to sea level - Leshan City. Using a label-free quantitative method, peptides in the samples were analyzed by mass spectrometry. Proteomic analysis was performed to identify differentially expressed proteins and predict their biological functions. A total of 846 proteins were identified in the 21 samples, including 719 quantified proteins. In total, 49 significantly differentially expressed proteins (p < 0.05) were identified, including twenty-eight 0.2-fold up-regulated proteins or twenty-one 0.17-fold down-regulated proteins. The up-regulated proteins, including cystic fibrosis transmembrane conductance regulator (CFTR) and carbonic anhydrase I (CAI), were of particular interest due to their role in regulating the oxygen saturation in deep tissues. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these proteins were mainly involved in regulating actin cytoskeleton, local adhesion, biotin absorption and metabolism, immune system, cancer, and membrane transport processes. In conclusion, Tibetan middle-to-long distance runners who resided in high-altitude areas benefited from repeated plateau-plain alternate training mode during the pre-competition period. The training mode induced positive changes in peripheral blood plasma proteins (CFTR and CAI), the biomarkers associated with aerobic capacity. Among the 11 runners, one female athlete won the gold medal in the 3 000-m running event in this competition, demonstrating that the plateau-plain alternate training mode could enhance the aerobic capacity of athletes. [ABSTRACT FROM AUTHOR]

Patulin (PAT) is a significant mycotoxin contaminant of fruit and fruit products. Hannaella sinensis is an antagonistic yeast that controls postharvest diseases and mycotoxins in crops and is potentially valuable for ensuring food safety. Our previous studies have shown that H. sinensis can effectively degrade PAT. The possible physiological mechanisms of yeast have been previously reported, however, the molecular mechanism of PAT degradation by the yeast needs to be explored in depth. Therefore, our current work aimed to use transcriptomic and proteomic techniques to unravel the molecular mechanisms by which PAT degradation occurs in H. sinensis. The results showed that transcriptomic studies of H. sinensis in PAT culture identified 951 differentially expressed genes, of which 194 were up-regulated, and 757 were down-regulated. These genes could be used to induce the ability of H. sinensis to resist stress, promote the synthesis of drug-resistant substances and maintain the integrity of cell membranes. Besides, proteomic analyses revealed that PAT treatment enhances multiple aspects of H. sinensis, including protein processing, cell growth, reproduction, catalase, cell wall synthesis, and more. Our study helps to understand the possible mechanisms of PAT degradation and PAT stress response at the transcription and protein expression levels in H. sinensis. [ABSTRACT FROM AUTHOR]

Introduction: Numerous studies have reported the beneficial effects of silicon (Si) in alleviating biotic or abiotic stresses in many plant species. However, the role of Si in Fabaceae facing environmental stress is poorly documented. The aim of this study is to investigate the effect of Si on physiological traits and nodulation efficiency in Trifolium incarnatum L. Methods: Si was supplied (1.7 mM in the form of Na2SiO3) plants inoculated with Rhizobium leguminosarum bv trifolii and plant physiological traits and nodule ionomic and molecular traits were monitored over 25 days. Results: Si supply promoted shoot biomass, the quantity of both Si and N in roots and shoots, and the number, biomass and density of nodules and their nitrogenase abundance which contribute to better dinitrogen (N2) fixation. Ionomic analysis of nodules revealed that Si supply increased the amount of several macroelements (potassium, phosphorus and sulfur) and microelements (copper, zinc and molybdenum) known to improve nodulation efficiency and N2 fixation. Finally, comparative proteomic analysis (+Si versus -Si) of nodules highlighted that Si modulated the proteome of both symbionts with 989 and 212 differentially accumulated proteins (DAPs) in the infected host root cells and their symbiont bacteria, respectively. Discussion: Among the DAPs, the roles of those involved in nodulation and N2 fixation are discussed. For the first time, this study provides new insights into the effects of Si on both nodular partners and paves the way for a better understanding of the impact of Si on improving nodule function, and more specifically, on the nodules' N2-fixing capacity. [ABSTRACT FROM AUTHOR]

Background: Human induced pluripotent stem cells represent a scalable source of youthful tissue progenitors and secretomes for regenerative therapies. The aim of our study was to investigate the potential of conditioned medium (CM) from hiPSC-mesenchymal progenitors (hiPSC-MPs) to stimulate osteogenic differentiation of human bone marrow-derived mesenchymal stromal cells (MSCs). We also investigated whether prolonged cultivation or osteogenic pre-differentiation of hiPSC-MPs could enhance the stimulatory activity of CM. Methods: MSCs were isolated from 13 donors (age 20–90 years). CM derived from hiPSC-MPs was added to the MSC cultures and the effects on proliferation and osteogenic differentiation were examined after 14 days and 6 weeks. The stimulatory activity of hiPSC-MP-CM was compared with the activity of MSC-derived CM and with the activity of CM prepared from hiPSC-MPs pre-cultured in growth or osteogenic medium for 14 days. Comparative proteomic analysis of CM was performed to gain insight into the molecular components responsible for the stimulatory activity. Results: Primary bone marrow-derived MSC exhibited variability, with a tendency towards lower proliferation and tri-lineage differentiation in older donors. hiPSC-MP-CM increased the proliferation and alkaline phosphatase activity of MSC from several adult/aged donors after 14 days of continuous supplementation under osteogenic conditions. However, CM supplementation failed to improve the mineralization of MSC pellets after 6 weeks under osteogenic conditions. hiPSC-MP-CM showed greater enhancement of proliferation and ALP activity than CM derived from bone marrow-derived MSCs. Moreover, 14-day cultivation but not osteogenic pre-differentiation of hiPSC-MPs strongly enhanced CM stimulatory activity. Quantitative proteomic analysis of d14-CM revealed a distinct profile of components that formed a highly interconnected associations network with two clusters, one functionally associated with binding and organization of actin/cytoskeletal components and the other with structural constituents of the extracellular matrix, collagen, and growth factor binding. Several hub proteins were identified that were reported to have functions in cell-extracellular matrix interaction, osteogenic differentiation and development. Conclusions: Our data show that hiPSC-MP-CM enhances early osteogenic differentiation of human bone marrow-derived MSCs and that prolonged cultivation of hiPSC-MPs enhances CM-stimulatory activity. Proteomic analysis of the upregulated protein components provides the basis for further optimization of hiPSC-MP-CM for bone regenerative therapies. [ABSTRACT FROM AUTHOR]

• SHSY-5Y cells exposed to Aβo showed increased oxidative stress and apoptosis. • LC-MS/MS identified 80 confirmed AD-related proteins and 43 novel candidates. • AD-related proteins VGF, LTF, PARP1, and MAOA, were identified using NeuroPro. • Less-studied proteins MYH9, CISD1, and SNRNP70 were also identified. • These shortlisted proteins hold promise for early AD diagnosis and treatment. Alzheimer's disease (AD) remains a pressing global health concern, necessitating comprehensive investigations into its underlying molecular mechanisms. While the late-stage pathophysiology of this disease is well understood, it is crucial to examine the role of amyloid beta oligomers (Aβo), which form in the brain during the early stages of disease development. These toxic oligomers could affect neuronal viability and generate oxidative stress in the brain. In this study, we exposed SHSY-5Y cells to Aβo. The increase in intracellular reactive oxygen species and apoptosis observed in Aβo-treated cells mimics the early stages of AD. Comprehensive proteomic profiling identified 2966 differentially expressed proteins, with 123 significantly modulated. Utilizing the NeuroPro database, we identified 80 confirmed AD-related proteins and 43 novel candidates. Seven AD-related proteins with a NeuroPro score ≥ 5 were shortlisted. Furthermore, these proteins are found to be associated with Aβ plaques in AD brains. VGF, LTF, PARP1, and MAOA have been implicated in various mechanisms underlying AD, including synaptic plasticity, iron homeostasis, DNA repair, and neurotransmitter degradation. Our study also revealed the involvement of less-explored proteins like MYH9, CISD1, and SNRNP70, which play critical roles in cytoskeletal dynamics, mitochondrial function, and RNA splicing, respectively. These findings underscore the complex pathophysiology of AD, highlighting potential biomarkers and therapeutic targets for early intervention. The present study advances the understanding of Aβo-induced oxidative stress and neuronal damage, providing a foundation for future research into early-stage AD diagnosis and subsequent treatment strategies. [ABSTRACT FROM AUTHOR]

Introduction: Metagenomic research has allowed the identification of numerous viruses present in the human body. Viruses may significantly increase the likelihood of developing intrauterine fetal growth restriction (FGR). The goal of this study was to examine and compare the virome of normal and FGR placentas using proteomic techniques. Methods: The study group of 18 women with late FGR was compared with 18 control patients with physiological pregnancy and eutrophic fetus. Proteins from the collected afterbirth placentas were isolated and examined using liquid chromatography linked to a mass spectrometer. Results: In this study, a group of 107 viral proteins were detected compared to 346 in the controls. In total, 41 proteins were common in both groups. In total, 64 proteins occurred only in the study group and indicated the presence of bacterial phages: E. coli, Bacillus, Mediterranenean, Edwardsiella, Propionibacterium, Salmonella, Paenibaciilus and amoebae Mimiviridae, Acanthamoeba polyphaga, Mimivivirus, Pandoravirdae, Miroviridae, Pepper plant virus golden mosaic virus, pol proteins of HIV-1 virus, and proteins of Pandoravirdae, Microviridae, and heat shock proteins of the virus Faustoviridae. Out of 297 proteins found only in the control group, only 2 viral proteins occurred statistically significantly more frequently: 1/hypothetical protein [uncultured Mediterranean phage uvMED] and VP4 [Gokushovirus WZ-2015a]. Discussion: The detection of certain viral proteins exclusively in the control group suggests that they may play a protective role. Likewise, the proteins identified only in the study group could indicate a potentially pathogenic function. A virome study may be used to identify an early infection, evaluate its progress, and possible association with fetal growth restriction. Utilizing this technology, an individualized patient therapy is forthcoming, e.g., vaccines. [ABSTRACT FROM AUTHOR]

Background: The effects of heat acclimation (HA) on the hypothalamus after exertional heatstroke (EHS) and the specific mechanism have not been fully elucidated, and this study aimed to address these questions. Methods: In the present study, rats were randomly assigned to the control, EHS, HA, or HA + EHS groups (n = 9). Hematoxylin and eosin (H&E) staining was used to examine pathology. Tandem mass tag (TMT)-based proteomic analysis was utilized to explore the impact of HA on the protein expression profile of the hypothalamus after EHS. Bioinformatics analysis was used to predict the functions of the differentially expressed proteins. The differential proteins were validated by western blotting. An enzyme-linked immunosorbent assay was used to measure the expression levels of inflammatory cytokines in the serum. Results: The H&E staining (n = 5) results revealed that there were less structural changes in hypothalamus in the HA + EHS group compared with the EHS group. Proteomic analysis (n = 4) revealed that proinflammatory proteins such as argininosuccinate synthetase (ASS1), high mobility group protein B2 (HMGB2) and vimentin were evidently downregulated in the HA + EHS group. The levels of interleukin (IL)-1β, IL-1, and IL-8 were decreased in the serum samples (n = 3) from HA + EHS rats. Conclusions: HA may alleviate hypothalamic damage caused by heat attack by inhibiting inflammatory activities, and ASS1, HMGB2 and vimentin could be candidate factors involved in the exact mechanism. [ABSTRACT FROM AUTHOR]

Cerebral ischemia–reperfusion injury significantly contributes to global morbidity and mortality. Loganin is a natural product with various neuroprotective effects; however, it lacks targeted specificity for particular cells or receptors, which may result in reduced therapeutic efficacy and an increased risk of side effects. To address the limitations of loganin, we developed LA-1, a novel compound incorporating an Arg-Gly-Asp (RGD) peptide to target integrin receptor αvβ3, enhancing brain-targeting efficacy. LA-1 exhibited optimal nanoscale properties, significantly improved cell viability, reduced ROS production, and enhanced survival rates in vitro. In vivo, LA-1 decreased infarct sizes, improved neurological function, and reduced oxidative stress and neuroinflammation. Proteomic analysis showed LA-1 modulates PI3K/Akt and Nrf2/HO-1 pathways, providing targeted neuroprotection. These findings suggest LA-1's potential for clinical applications in treating cerebral ischemia–reperfusion injury. [ABSTRACT FROM AUTHOR]

Background: Staphylococcus aureus is the predominant pathogen isolated in diabetic foot infections. Recently, the skin commensal bacterium, Helcococcus kunzii, was found to modulate the virulence of this pathogen in an in vivo model. This study aims to elucidate the molecular mechanisms underlying the interaction between these two bacterial species, using a proteomic approach. Results: Our results reveal that H. kunzii can coexist and proliferate alongside S. aureus in a Chronic Wound Media (CWM), thereby mimicking an in vitro chronic wound environment. We noted that the secreted proteome of H. kunzii induced a transcriptional effect on S. aureus virulence, resulting in a decrease in the expression level of agrA, a gene involved in quorum sensing. The observed effect could be ascribed to specific proteins secreted by H. kunzii including polysaccharide deacetylase, peptidoglycan DD-metalloendopeptidase, glyceraldehyde-3-phosphate dehydrogenase, trypsin-like peptidase, and an extracellular solute-binding protein. These proteins potentially interact with the agr system, influencing S. aureus virulence. Additionally, the virulence of S. aureus was notably affected by modifications in iron-related pathways and components of cell wall architecture in the presence of H. kunzii. Furthermore, the overall metabolism of S. aureus was reduced when cocultured with H. kunzii. Conclusion: Future research will focus on elucidating the role of these excreted factors in modulating virulence. [ABSTRACT FROM AUTHOR]

This study aims to obtain overall information about all proteins formed in body fluids, cells, or tissues at a certain time and to analyze the mechanism of cell responses to various types of stress and drugs. Single black garlic (SBG) has the potential to be a pharmacological agent. However, the safety of using single black garlic is still unknown, so a material toxicity test is needed. This research is a laboratory experimental research with a post-test-only control group design. An oral acute toxicity test was used. Observation time was 14 days and consisted of four treatments, negative control, SBG dose 2000 mg/kgbw (P1), 3000 mg/kgbw (P2), and 5000 mg/kgbw (P3). Post-treatment protein analysis was done using the SDS-PAGE electrophoresis method. Observations of clinical symptoms of SBG at doses of 2000 mg/kgbw, 3000 mg/kgbw, and 5000 mg/kgbw showed no clinical symptoms in mice, both motor activity and pupils were still normal, no convulsions (seizures), lacrimation, paralysis or death were seen in mice. Observations on plasma proteins showed differences in protein between the treatments at the SBG dose of 2000 mg/kgbw with the SBG dose of 3000 mg/kgbw and 5000 mg/kgbw, but the four treatments have the same type of protein in the protein band with a molecular weight of 25 kDa. So, it can be concluded that SBG doses of 2000 mg/kgbw, 3000 mg/kgbw, and 5000mg/kgbw are not toxic tomice but can stimulate the expression of certain proteins. [ABSTRACT FROM AUTHOR]

The polyketide antibiotic 2,4-diacetylphloroglucinol (DAPG) is a phenolic secondary metabolite produced by Pseudomonas spp. that serves as a biocontrol agent. DAPG is known to inhibit root growth and seed germination in plants. However, the effects of DAPG on leaf growth have not been elucidated yet. In this study, we found that applying DAPG at concentration above 30 µM suppresses the development of Arabidopsis leaves. Using an integrated proteomic analysis approach, we investigated the physio-molecular responses of Arabidopsis leaves under 10–100 µM DAPG treatment. Two-dimensional electrophoresis (2-DE)-based proteomic analysis identified 46 differentially expressed spots with at least a twofold change, corresponding to 37 proteins involved in stress and defense, metabolism, photosynthesis, and carbohydrate metabolism processes. Furthermore, we found that the expressions of stress and defense-related proteins were upregulated in response to DAPG, while those of photosynthesis-related proteins were downregulated. Additionally, RT-PCR result showed that the identified DAPG-responsive proteins in the proteomic analysis were similarly regulated at the transcriptional level. Collectively, our findings provide insights into the molecular mechanism of the response to DAPG in Arabidopsis leaves. [ABSTRACT FROM AUTHOR]

Abstract New insights into cellular interactions and key biomolecules involved in lung cancer (LC) bone metastasis could offer remarkable therapeutic benefits. Using a panel of four LC cells, we investigated LC-bone interaction by exposing differentiating osteoclasts (OCs) to LC cells (LC-OC interaction) directly in a co-culture setting or indirectly via treatment with LC secretomes (conditioned media or exosomes). LC-OC interaction facilitated the production of large-sized OCs (nuclei > 10) coupled with extensive bone resorption pits. Proteomic analysis of LC exosomes identified galectin-3-binding protein (Gal3bp) as a potential biomarker which was released primarily by most of LC-derived exosomes. The facilitation of OC differentiation and function by LC-exosomal Gal3bp was supported by the application of recombinant Gal3bp and anti-Gal3bp in OC treatment. Further, our results exhibited a dysregulation of crucial OC markers (TRAF6, p-SAPK/JNK, p-44/42 MAPK, NFAT2 and CD9) during LC-OC interaction that possibly contributed to the facilitation of osteoclastogenesis. Simulation of bone metastasis via intratibial injection of LC cells revealed Gal3bp’s possible roles in enhancing OC activation leading to osseous tissue resorption. Overall, this work implicated LC-exosomal Gal3bp in osteolytic metastasis of LC which warrants further studies to assess its potential prognostic and therapeutic relevance.

Abstract Background Staphylococcus aureus is the predominant pathogen isolated in diabetic foot infections. Recently, the skin commensal bacterium, Helcococcus kunzii, was found to modulate the virulence of this pathogen in an in vivo model. This study aims to elucidate the molecular mechanisms underlying the interaction between these two bacterial species, using a proteomic approach. Results Our results reveal that H. kunzii can coexist and proliferate alongside S. aureus in a Chronic Wound Media (CWM), thereby mimicking an in vitro chronic wound environment. We noted that the secreted proteome of H. kunzii induced a transcriptional effect on S. aureus virulence, resulting in a decrease in the expression level of agrA, a gene involved in quorum sensing. The observed effect could be ascribed to specific proteins secreted by H. kunzii including polysaccharide deacetylase, peptidoglycan DD-metalloendopeptidase, glyceraldehyde-3-phosphate dehydrogenase, trypsin-like peptidase, and an extracellular solute-binding protein. These proteins potentially interact with the agr system, influencing S. aureus virulence. Additionally, the virulence of S. aureus was notably affected by modifications in iron-related pathways and components of cell wall architecture in the presence of H. kunzii. Furthermore, the overall metabolism of S. aureus was reduced when cocultured with H. kunzii. Conclusion Future research will focus on elucidating the role of these excreted factors in modulating virulence.

The proximal tubule (PT) is a nephron segment that is responsible for the majority of solute and water reabsorption in the kidney. Each of its sub-segments have specialized functions; however, little is known about the genes and proteins that determine the oxidative phosphorylation capacity of the PT sub-segments. This information is critical to understanding kidney function and will provide a comprehensive landscape of renal cell adaptations to injury, physiologic stressors, and development. This study analyzed three immortalized murine renal cell lines (PT S1, S2, and S3 segments) for protein content and compared them to a murine fibroblast cell line. All three proximal tubule cell lines generate ATP predominantly by oxidative phosphorylation while the fibroblast cell line is glycolytic. The proteomic data demonstrates that the most significant difference in proteomic signatures between the cell lines are proteins known to be localized in the nucleus followed by mitochondrial proteins. Mitochondrial metabolic substrate utilization assays were performed using the proximal tubule cell lines to determine substrate utilization kinetics thereby providing a physiologic context to the proteomic dataset. This data will allow researchers to study differences in nephron-specific cell lines, between epithelial and fibroblast cells, and between actively respiring cells and glycolytic cells. SIGNIFICANCE: Proteomic analysis of proteins expressed in immortalized murine renal proximal tubule cells was compared to a murine fibroblast cell line proteome. The proximal tubule segment specific cell lines: S1, S2 and S3 are all grown under conditions whereby the cells generate ATP by oxidative phosphorylation while the fibroblast cell line utilizes anaerobic glycolysis for ATP generation. The proteomic studies allow for the following queries: 1) comparisons between the proximal tubule segment specific cell lines, 2) comparisons between polarized epithelia and fibroblasts, 3) comparison between cells employing oxidative phosphorylation versus anaerobic glycolysis and 4) comparisons between cells grown on clear versus opaque membrane supports. The data finds major differences in nuclear protein expression and mitochondrial proteins. This proteomic data set will be an important baseline dataset for investigators who need immortalized renal proximal tubule epithelial cells for their research.

This study investigates the biochemical and proteomic responses of Penaeus indicus post-larvae (PL) to sublethal copper exposure. Significant reductions in total carbohydrates, proteins, lipids, and energy levels were observed in exposed PL, indicating oxidative stress and disruptions in metabolic pathways. These disturbances led to protein damage, lipid peroxidation, and impaired cellular respiration, ultimately compromising organismal health. Proteomic analysis, performed using one-dimensional SDS-PAGE and two-dimensional gel electrophoresis, revealed differential expression of several key proteins, including guanylate cyclase, thioredoxin, nuclear autoantigenic sperm, nucleoside diphosphatase, ferritin, cyclin-T, Vasa-like protein, aspartate racemase, hemocyanin, prohibitin-2, argonaute, variant transformer-2, and ubiquitin-activating enzyme. These proteins are implicated in oxidative stress response, cell cycle regulation, and cellular defense mechanisms. In addition to highlighting the potential of these proteins as biomarkers for evaluating copper pollution in aquatic ecosystems, the work emphasizes the importance of proteomic analysis in interpreting cellular responses to environmental pollutants. These findings have implications for environmental monitoring and management as well as a deeper understanding of the physiological and biochemical responses of marine invertebrates to environmental stresses, particularly copper toxicity. [ABSTRACT FROM AUTHOR]

Acanthosyris paulo-alvinii G.M. Barroso (cacao killer) is a woody and hemiparasitic species, endemic to Southern Bahia, Brazil, presents chemical properties of unknown nature that promote the death of Theobroma cacao L. plants as a result of the hemiparasitism of its roots by haustoria. The objective of the present study was to identify possible anatomical, physiological, biochemical, and molecular changes that could elucidate the death of the host when exposed to hemiparasitism. The two species were grown alone and together in plastic water boxes of 350 L containing soil. At 30 days after application of treatments (DAAT), the host began to show symptoms characteristic of hemiparasitism, such as chlorosis and leaf necrotic spots. Structural differences were observed in leaf mesophyll cells, root tissue, and the haustorium of the hemiparasite, both in the presence and absence of the T. cacao host. The hemiparasitism did not affect host leaf gas exchange but reduced the production of flavonoids in the leaves. Furthermore, 27% of the proteins were associated with energy metabolism and carbohydrate metabolism, indicating a probable response to stress and, consequently, positive feedback for its benefit since it tries to use metabolism for their nutrition, which may further increase their demand. Enzymatic and non-enzymatic antioxidative metabolism in the T. cacao hemiparasitized by cacao killer were not sufficient to eliminate the reactive oxygen species excess. Oxidative stress associated with greater energy consumption in the T. cacao hemiparasitized by cacao killer interfered in cell homeostasis, resulting in lipid peroxidation of cell membranes, followed by programmed cell death and, consequently, the death of the host plant at 40 DAAT. [ABSTRACT FROM AUTHOR]

Abstract The intricate causes of Alzheimer's disease (AD) hinder effective, lasting treatment. Although the dietary modulation of the brain–gut axis was explored for AD therapy, the exact mechanism remains unclear. This study suggested that 140 days of the whey protein hydrolysate (WPH) intake could attenuate the AD pathologic symptoms in APP/PS1 transgenic mice via a bidirectional action of the gut microbe–SCFA (short‐chain fatty acid)–brain axis. Behavioral tests demonstrated that high‐dose WPH (WPH‐H, 100 mg/kg body weight [bw]) improved passive and recognition memory in mice. Furthermore, WPH‐H significantly reduced amyloid beta 1–42 (Aβ1–42) levels in serum (p

Abstract Background Drought stress restricts the growth, distribution and productivity of alfalfa (Medicago sativa L.). In order to study the response differences of alfalfa cultivars to drought stress, we previously carried out physiological and molecular comparative analysis on two alfalfa varieties with contrasting drought resistance (relatively drought-tolerant Longdong and drought-sensitive Algonquin). However, the differences in proteomic factors of the two varieties in response to drought stress still need to be further studied. Therefore, TMT-based quantitative proteomic analysis was performed using leaf tissues of the two alfalfa cultivars to identify and uncover differentially abundant proteins (DAPs). Results In total, 677 DAPs were identified in Algonquin and 277 in Longdong under drought stress. Subsequently, we conducted various bioinformatics analysis on these DAPs, including subcellular location, functional classification and biological pathway enrichment. The first two main COG functional categories of DAPs in both alfalfa varieties after drought stress were ‘Translation, ribosomal structure and biogenesis’ and ‘Posttranslational modification, protein turnover, chaperones’. According to KEGG database, the DAPs of the two alfalfa cultivars after drought treatment were differentially enriched in different biological pathways. The DAPs from Algonquin were enriched in ‘photosynthesis’ and ‘ribosome’. The pathways of ‘linoleic acid metabolism’, ‘protein processing in endoplasmic reticulum’ and ‘RNA transport’ in Longdong were significantly enriched. Finally, we found significant differences in DAP enrichment and expression patterns between Longdong and Algonquin in glycolysis/glycogenesis, TCA cycle, photosynthesis, protein biosynthesis, flavonoid and isoflavonoid biosynthesis, and plant-pathogen interaction pathway after drought treatment. Conclusions The differences of DAPs involved in various metabolic pathways may explain the differences in the resistance of the two varieties to drought stress. These DAPs can be used as candidate proteins for molecular breeding of alfalfa to cultivate new germplasm with more drought tolerance to adapt to unfavorable environments.

Background: Postoperative Intestinal Adhesions (PIAs) remain a significant complication of abdominal surgery that can cause pain, infertility, and a potentially lethal bowel obstruction. Kangnian (KN) decoction, a Traditional Chinese Medicine prescription, has been shown to be effective in treating PIAs. Nevertheless, its underlying mechanisms remain unclear. Objective: This study aims to explore the therapeutic effects of KN decoction in a PIA rat model, as well as its potential mechanisms via metabolomics and proteomics analyses. Materials and methods: 60 rats were randomly assigned to six groups: Normal Control (NC), PIA model, Dexamethasone, KN-Low, KN-Medium, and KN-High. The PIA model was created by abdominal surgery under anesthesia. Pathological damage was evaluated through H&E staining and adhesion grading of affected tissues. The levels of serumcytokines (IL-1β, IL-6, TNF-α, and TGF-1), Connective Tissue Growth Factor (CTGF), andMotilin (MTL) in adherent intestinal tissueswere detected using ELISA kits. Untargeted metabolomics was used to investigate potential metabolic pathways of the KN decoction intervention in intestinal adhesions and to screen for differential biomarkers. The label-free quantitative proteomics technique was employed to detect Differentially Expressed Proteins and for biological function and pathway enrichment analyses. Results: In PIA rats, KN decoction significantly improved the pathological injury associated with intestinal adhesions and effectively regulated the blood inflammation indicators. Furthermore, KN presented a favorable anti-fibrotic and protective effect against abdominal adhesions, effectively modifying gastrointestinal motility disorders in PIA rats. We identified 58 variables as potential biomarkers and discovered seven main pathological pathways that may be associated with PIAs. Proteomics analysis revealed 75 DEPs that were primarily involved in Valine, leucine, and isoleucine degradation, the MAPK signaling pathway, and retrograde endocannabinoid signaling. Conclusion: This study proved that KN reduces intestinal mucosal injury, downregulates inflammatory factors, and alleviates intestinal adhesions, thus protecting the intestinal barrier function in PIA rats. The combination of proteomics and metabolomics provided a feasible approach for unraveling the therapeutic mechanism of KN decoction in PIAs. [ABSTRACT FROM AUTHOR]

Previous studies have revealed that ammonia nitrogen has several adverse effects on clam Ruditapes philippinarum. However, knowledge is lacking regarding the related proteins involved in the toxicological responses, which is vital to elucidate the underlying mechanism of ammonia nitrogen. In this study, clams R. philippinarum were exposed to ammonia nitrogen for 21 d at two environmentally relevant concentrations. The tandem mass tags approach (TMT) was applied to assay the differentially expressed proteins (DEPs) in clam gill tissues on the 3rd and 21st day. Finally, a total of 7 263 proteins were identified. Bioinformatics analyses revealed that clam protein profiles changed in dose- and time-dependent manner after ammonia nitrogen exposure. We inferred that the clams may face heavy challenges after ammonia exposure, such as unbalanced gender ratio, lysosomal disease, energy lack, neurological disorders, altered glutamine metabolism, increased lipid synthesis, and impaired immunity. Variation profiles of enzyme activities of glutaminase and glutamine synthase provided direct evidence to verify the related inference from proteome data. Most of the inferred toxic effects merit further study. This study identified important proteins related to ammonia nitrogen toxicity in the clam and indicated the severe stress of marine ammonia pollution on the healthy development of mollusc aquaculture. [ABSTRACT FROM AUTHOR]

Ischemic stroke (IS) and subsequent neuropsychiatric disorders are among the leading causes of disability worldwide. Several strategies have been previously proposed to utilize exosomes for assessing the risk of IS-related diseases. The aim of this work was to evaluate serum exosomal proteins in IS patients during the chronic post-stroke period and to search for their associations with the development of post-stroke mild cognitive impairment (MCI). Comparative quantitative proteomic analysis of serum exosomes of patients without post-stroke MCI (19 patients mean age 52.0 ± 8.1 years) and patients with post-stroke MCI (11 patients, mean age 64.8 ± 5.6 years) revealed significant differences in the levels of 62 proteins out of 186 identified. Increased levels of the proteins associated with immune system and decreased levels of the proteins involved in lipid metabolism were observed in the patients with MCI compared to the patients without MCI in the chronic post-stroke period. The obtained data suggest that the higher level of immune system activation in the patients during a relatively long period after IS may be one of the risk factors for the development of post-stroke cognitive disorders and suggest participation of exosomal transport in these processes. [ABSTRACT FROM AUTHOR]

Membrane vesicles (MVs) are produced by species across all domains of life and have diverse physiological functions as well as promising applications. While the mechanisms for vesiculation in Gram‐negative bacteria are well‐established, the genetic determinants and regulatory factors responsible for MV biogenesis in Gram‐positive bacteria remain largely unknown. Here, we demonstrate that a Q225P substitution in the alternative sigma factor B (SigB) triggers MV production in Staphylococcus aureus strain Newman by hindering the specific binding of SigB to the asp23 promoter, thereby repressing expression of alkaline shock protein 23 (Asp23). Isogenic deletion of asp23 also promotes MV formation in Newman, confirming the critical roles played by sigB and asp23 in modulating S. aureus vesiculation. While bacterial growth and cytoplasmic membrane fluidity are not impaired, mutation of asp23 weakens the cell wall and enhances autolysis, consistent with decreased expression of alpha‐type psm and lrgAB that modulate murein hydrolase activity. TEM and proteomic analysis show that Newman and asp23 deletion mutant generate MVs with nearly identical morphology and composition, but virulence‐associated factors are significantly enriched in MVs from the asp23 mutant. Overall, this study reveals novel genetic determinants underlying S. aureus vesiculation and advances the understanding of the physiology of MV biogenesis in S. aureus. [ABSTRACT FROM AUTHOR]

Methicillin-resistant Staphylococcus aureus (MRSA) is a highly threatening foodborne pathogen capable of causing severe organ and life-threatening diseases. Over the past years, various commercial antibiotics have been used to treat MRSA infections. However, these commercial antibiotics have not yielded efficient results and also cause other side effects; therefore, there is a need for the development of effective alternatives to replace these commercial antibiotics. Suberanilic acid, an amide alkaloid obtained from the endophytic fungus Pestalotiopsis trachycarpicola DCL44, has been identified as a significant antimicrobial agent. However, its antibiotic properties on multi-drug-resistant bacteria such as MRSA have not been fully explored. Therefore, to investigate the potential antimicrobial mechanism of suberanilic acid against MRSA, a quantitative proteomics approach using tandem mass tagging (TMT) was used. The results obtained in the study revealed that suberanilic acid targets multiple pathways in MRSA, including disruption of ribosome synthesis, inhibition of membrane translocation for nutrient uptake (ABC transporter system), and causing dysregulation of carbohydrate and amino acid energy metabolism. These results provide new insights into the mechanism of action of suberanilic acid against MRSA and offer technical support and a theoretical basis for the development of novel food antimicrobial agents derived from endophytic fungal origin. [ABSTRACT FROM AUTHOR]

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the accumulation of amyloid-β, leading to N-methyl-D-aspartate (NMDA) receptor-dependent synaptic depression, spine elimination, and memory deficits. Glycine transporter type 1 (GlyT1) modulates glutamatergic neurotransmission via NMDA receptors (NMDAR), presenting a potential alternative therapeutic approach for AD. This study investigates the neuroprotective potential of GlyT1 inhibition in an amyloid-β-induced AD mouse model. C57BL/6 mice were treated with N-[3-([1,1-Biphenyl]-4-yloxy)-3-(4-fluorophenyl)propyl]-N-methylglycine (NFPS), a GlyT1 inhibitor, 24 h prior to intrahippocampal injection of amyloid-β. NFPS pretreatment prevented amyloid-β-induced cognitive deficits in short-term and long-term memory, evidenced by novel object recognition and spatial memory tasks. Moreover, NFPS pretreatment curbed microglial activation, astrocytic reactivity, and subsequent neuronal damage from amyloid-β injection. An extensive label-free quantitative UPLC-MSE proteomic analysis was performed on the hippocampi of mice treated with NFPS. In proteomics, KEGG enrichment analysis revealed increased in dopaminergic synapse, purine-containing compound biosynthetic process and long-term potentiation, and a reduction in Glucose catabolic process and glycolytic process pathways. The western blot analysis confirmed that NFPS treatment elevated BDNF levels, correlating with enhanced TRKB phosphorylation and mTOR activation. Moreover, NFPS treatment reduced the GluN2B expression after 6 h, which was associated with an increase on CaMKIV and CREB phosphorylation. Collectively, these findings demonstrate that GlyT1 inhibition by NFPS activates diverse neuroprotective pathways, enhancing long-term potentiation signaling and countering amyloid-β-induced hippocampal damage. [ABSTRACT FROM AUTHOR]

Hunting strategies in the Paleolithic period represent a significant and complex challenge, influencing the lifestyles of early human populations dependent on the seasonal activity of herds. Varying seasonally, a composition of a herd caused changes in the speed of animals movements, their aggressiveness, hides and the fatness and flavor of their meat. The morphological criteria for determining grazer sex and age have long been established in zooarchaeology. However, many traits associated with bison sex are poorly defined for archeozoological collections due to the fragmented and scattered nature of the bone remains. The objective of presented study was to demonstrate the potential utility of proteomic tooth enamel analysis detecting the AmelX and AmelY peptide fragments for prey-sex determination in cases where morphological criteria did not work. In the study, the tooth enamel samples from 18 animals were analyzed, including eight modern specimens of known sex, and ten Pleistocene specimens of unknown sex from four different Paleolithic sites. A blind test conducted for the modern collection yielded a 100% accuracy. This outcome prompted the development of the criteria for sex determination in the bison based on proteomic analysis of tooth enamel. [ABSTRACT FROM AUTHOR]

Acanthamoeba is a ubiquitous genus of amoebae that can trigger a severe and progressive ocular disease known as Acanthamoeba Keratitis (AK). Furthermore, current treatment protocols are based on the combination of different compounds that are not fully effective. Therefore, an urgent need to find new compounds to treat Acanthamoeba infections is clear. In the present study, we evaluated staurosporine as a potential treatment for Acanthamoeba keratitis using mouse cornea as an ex vivo model, and a comparative proteomic analysis was conducted to elucidate a mechanism of action. The obtained results indicate that staurosporine altered the conformation of actin and tubulin in treated trophozoites of A. castellanii. In addition, proteomic analysis of treated trophozoites revealed that this molecule induced overexpression and a downregulation of proteins related to key functions for Acanthamoeba infection pathways. Additionally, the ex vivo assay used validated this model for the study of the pathogenesis and therapies of AK. Finally, staurosporine eliminated the entire amoebic population and prevented the adhesion and infection of amoebae to the epithelium of treated mouse corneas. [ABSTRACT FROM AUTHOR]

The recent discovery of disease caused by Nucleospora braziliensis in Nile tilapia (Oreochromis niloticus) is important as it has highlighted the high prevalence of infection and associated mortality in cultured fish. Thus, this study conducted an experimental infection of this microsporidium to evaluate pathological alterations and conduct proteomic analysis. For pathological observation, samples of brain, eyes, gall bladder, gut, heart, kidney, liver, muscle, skin, spleen, and stomach tissue, were collected, and liquid chromatography–mass spectrometry (LC-MS/MS) was performed for proteomic analysis. The most prevalent lesions were brownish color of the liver, gill filament fusion, gut ischemia, hemorrhage of the lips and fins, hepatomegaly, spleen atrophy, splenomegaly, and stomach congestion. The most common microscopic lesions were degeneration, hemorrhage, and inflammation in the brain, gills, gut, kidney, liver, muscle, spleen, and stomach. The digested peptides were identified by LC-MS/MS and the intersection of each group showed that in the spleen there were 121 exclusive proteins in the infected sample and 252 in the control, while in the kidney, 129 proteins were identified in the infected specimen compared to 83 in the control. In conclusion, this study demonstrates the proteome profile of O. niloticus kidney and spleen tissue in response to infection with N. braziliensis. [ABSTRACT FROM AUTHOR]

Background: Drought stress restricts the growth, distribution and productivity of alfalfa (Medicago sativa L.). In order to study the response differences of alfalfa cultivars to drought stress, we previously carried out physiological and molecular comparative analysis on two alfalfa varieties with contrasting drought resistance (relatively drought-tolerant Longdong and drought-sensitive Algonquin). However, the differences in proteomic factors of the two varieties in response to drought stress still need to be further studied. Therefore, TMT-based quantitative proteomic analysis was performed using leaf tissues of the two alfalfa cultivars to identify and uncover differentially abundant proteins (DAPs). Results: In total, 677 DAPs were identified in Algonquin and 277 in Longdong under drought stress. Subsequently, we conducted various bioinformatics analysis on these DAPs, including subcellular location, functional classification and biological pathway enrichment. The first two main COG functional categories of DAPs in both alfalfa varieties after drought stress were ‘Translation, ribosomal structure and biogenesis’ and ‘Posttranslational modification, protein turnover, chaperones’. According to KEGG database, the DAPs of the two alfalfa cultivars after drought treatment were differentially enriched in different biological pathways. The DAPs from Algonquin were enriched in ‘photosynthesis’ and ‘ribosome’. The pathways of ‘linoleic acid metabolism’, ‘protein processing in endoplasmic reticulum’ and ‘RNA transport’ in Longdong were significantly enriched. Finally, we found significant differences in DAP enrichment and expression patterns between Longdong and Algonquin in glycolysis/glycogenesis, TCA cycle, photosynthesis, protein biosynthesis, flavonoid and isoflavonoid biosynthesis, and plant-pathogen interaction pathway after drought treatment. Conclusions: The differences of DAPs involved in various metabolic pathways may explain the differences in the resistance of the two varieties to drought stress. These DAPs can be used as candidate proteins for molecular breeding of alfalfa to cultivate new germplasm with more drought tolerance to adapt to unfavorable environments. [ABSTRACT FROM AUTHOR]

Nanoparticles play a crucial role in the field of nanotechnology, offering different properties due to their surface area attributed to their small size. Among them, silver nanoparticles (AgNPs) have attracted significant attention due to their antimicrobial properties, with applications that date back from ancient medicinal practices to contemporary commercial products containing ions or silver nanoparticles. AgNPs possess broad-spectrum biocidal potential against bacteria, fungi, viruses, and Mycobacterium, in addition to exhibiting synergistic effects when combined with certain antibiotics. The mechanisms underlying its antimicrobial action include the generation of oxygen-reactive species, damage to DNA, rupture of bacterial cell membranes and inhibition of protein synthesis. Recent studies have highlighted the effectiveness of AgNPs against various clinically relevant bacterial strains through their potential to combat antibioticresistant pathogens. This review investigates the proteomic mechanisms by which AgNPs exert their antimicrobial effects, with a special focus on their activity against planktonic bacteria and in biofilms. Furthermore, it discusses the biomedical applications of AgNPs and their potential non-preparation of antibiotic formulations, also addressing the issue of resistance to antibiotics. [ABSTRACT FROM AUTHOR]

Sham control groups are essential in experimental animal studies to reduce the influence of surgical intervention. The intraluminal filament procedure is one of the most common models of middle cerebral artery occlusion (MCAO) used in the study of brain ischemia. However, a sham group is usually not included in the experimental design of these studies. In this study, we aimed to evaluate the relevance of the sham group by analyzing and comparing the brain protein profiles of the sham and MCAO groups. In the sham group, 98 dysregulated proteins were detected, compared to 171 in the ischemic group. Moreover, a comparative study of protein profiles revealed the existence of a pool of 57 proteins that appeared to be dysregulated in both sham and ischemic animals. These results indicated that the surgical procedure required for the intraluminal occlusion of the middle cerebral artery (MCA) induces changes in brain protein expression that are not associated with ischemic lesions. This study highlights the importance of including sham control groups in the experimental design, to ensure that surgical intervention does not affect the therapeutic target under study. [ABSTRACT FROM AUTHOR]

Liver fibrosis, a consequence of chronic liver damage or inflammation, is characterized by the excessive buildup of extracellular matrix components. This progressive condition significantly raises the risk of severe liver diseases like cirrhosis and hepatocellular carcinoma. The lack of approved therapeutics underscores the urgent need for novel anti-fibrotic drugs. Hepatic stellate cells (HSCs), key players in fibrogenesis, are promising targets for drug discovery. This study investigated the anti-fibrotic potential of Citrus hystrix DC. (KL) and its bioactive compound, β-citronellol (β-CIT), in a human HSC cell line (LX-2). Cells exposed to TGF-β1 to induce fibrogenesis were co-treated with crude KL extract and β-CIT. Gene expression was analyzed by real-time qRT-PCR to assess fibrosis-associated genes (ACTA2, COL1A1, TIMP1, SMAD2). The release of matrix metalloproteinase 9 (MMP-9) was measured by ELISA. Proteomic analysis and molecular docking identified potential signaling proteins and modeled protein–ligand interactions. The results showed that both crude KL extract and β-CIT suppressed HSC activation genes and MMP-9 levels. The MAPK signaling pathway emerged as a potential target of β-CIT. This study demonstrates the ability of KL extract and β-CIT to inhibit HSC activation during TGF-β1-induced fibrogenesis, suggesting a promising role of β-CIT in anti-hepatic fibrosis therapies. [ABSTRACT FROM AUTHOR]

Despite advances in the genomic classification of breast cancer, current clinical tests and treatment decisions are commonly based on protein-level information. Nowadays breast cancer clinical treatment selection is based on the immunohistochemical (IHC) determination of four protein biomarkers: Estrogen Receptor 1 (ESR1), Progesterone Receptor (PGR), Human Epidermal Growth Factor Receptor 2 (HER2), and proliferation marker Ki-67. The prognostic correlation of tumor-infiltrating T cells has been widely studied in breast cancer, but tumor-infiltrating B cells have not received so much attention. We aimed to find a correlation between immunohistochemical results and a proteomic approach in measuring the expression of proteins isolated from B-cell lymphocytes in peripheral blood samples. Shotgun proteomic analysis was chosen for its key advantage over other proteomic methods, which is its comprehensive and untargeted approach to analyzing proteins. This approach facilitates better characterization of disease-associated changes at the protein level. We identified 18 proteins in B cell lymphocytes with a significant fold change of more than 2, which have promising potential to serve as breast cancer biomarkers in the future. [ABSTRACT FROM AUTHOR]

Exosomes are a subclass of extracellular vesicles shown to promote the cancer growth and support metastatic progression. The proteomic analysis of neuroblastoma-derived exosomes has revealed proteins involved in cell migration, proliferation, metastasis, and in the modulation of tumor microenvironment - thus contributing to the tumor development and an aggressive metastatic phenotype. This review gives an overview of the current understanding of the exosomal proteins in neuroblastoma and of their potential as diagnostic/prognostic biomarker of disease and therapeutics. [ABSTRACT FROM AUTHOR]

Chinese hamster ovary (CHO) cells are among the most common cell lines used for therapeutic protein production. Membrane fouling during bioreactor harvesting is a major limitation for the downstream purification of therapeutic proteins. Host cell proteins (HCP) are the most challenging impurities during downstream purification processes. The present work focuses on identification of HCP foulants during CHO bioreactor harvesting using reverse asymmetrical commercial membrane BioOptimal™ MF‐SL. In order to investigate foulants and fouling behavior during cell clarification, for the first time a novel backwash process was developed to effectively elute almost all the HCP and DNA from the fouled membrane filter. The isoelectric points (pIs) and molecular weights (MWs) of major HCP in the bioreactor harvest and fouled on the membrane were successfully characterized using two‐dimensional gel electrophoresis (2D SDS‐PAGE). In addition, a total of 8 HCP were identified using matrix‐assisted laser desorption/ionization‐mass spectroscopy (MALDI‐MS). The majority of these HCP are enzymes or associated with exosomes, both of which can form submicron‐sized particles which could lead to the plugging of the filters. [ABSTRACT FROM AUTHOR]

Introduction: Kidney transplantation significantly improves the lives of those with end-stage kidney disease, offering best alternative to dialysis. However, transplant success is threatened by the acute and chronic rejection mechanisms due to complex immune responses against the new organ. Areas covered: The ongoing research into biomarkers holds promise for revolutionizing the early detection and monitoring of the graft health. Liquid biopsy techniques offer a new avenue, with several diagnostic, predictive, and prognostic biomarkers showing promise in detecting and monitoring kidney diseases and an early and chronic allograft rejection. Expert opinion: Evaluating the protein composition related to kidney transplant results could lead to identifying biomarkers that provide insights into the graft functionality. Non-invasive proteomic biomarkers can drastically enhance clinical outcomes and change the way how kidney transplants are evaluated for patients and physicians if they succeed in this transition. Hence, the advancement in proteomic technologies, leads toward a significant improvement in understanding of the protein markers and molecular mechanisms linked to the outcomes of kidney transplants. However, the road from discovery to the use of such proteins in clinical practice is long, with a need for continuous validation and beyond the singular research team with comprehensive infrastructure and across research groups collaboration. [ABSTRACT FROM AUTHOR]

ABSTRACTCellulose fibers from ramie is a kind of functional biological material with multipurpose in the textile industry, which called as “China grass.” The degumming of ramie fibers performed with Bacillus subtilis were regulated by response regulator CitT from CitS/CitT two-component system through specifically functioning on the degradation of component pectin. In this study, comparative proteomic analysis was executed to obtain insights into the sensitivity by which the metabolic network induced by the absence of CitT protein, and to further explore the regulatory mechanism during bio-degumming process of ramie fibers. Results showed that 29 differentially expressed proteins were detected from original strain and mutant strain, which were mainly involved in transmembrane transport system, two-component system, and amino acid metabolism. This study demonstrated that the lack of CitT protein could result in the down-regulation of enzymes in histidine biosynthesis pathway, and the up-regulation of enzyme in arginine degradation pathway. This study is the first time to reveal comprehensive information about the regulatory function of CitT protein in bio-degumming of ramie fibers, and may provide important scientific and technological basis for targeted constructing engineering strains in degumming of ramie fibers.

IntroductionNumerous studies have reported the beneficial effects of silicon (Si) in alleviating biotic or abiotic stresses in many plant species. However, the role of Si in Fabaceae facing environmental stress is poorly documented. The aim of this study is to investigate the effect of Si on physiological traits and nodulation efficiency in Trifolium incarnatum L.MethodsSi was supplied (1.7 mM in the form of Na2SiO3) plants inoculated with Rhizobium leguminosarum bv trifolii and plant physiological traits and nodule ionomic and molecular traits were monitored over 25 days.ResultsSi supply promoted shoot biomass, the quantity of both Si and N in roots and shoots, and the number, biomass and density of nodules and their nitrogenase abundance which contribute to better dinitrogen (N2) fixation. Ionomic analysis of nodules revealed that Si supply increased the amount of several macroelements (potassium, phosphorus and sulfur) and microelements (copper, zinc and molybdenum) known to improve nodulation efficiency and N2 fixation. Finally, comparative proteomic analysis (+Si versus -Si) of nodules highlighted that Si modulated the proteome of both symbionts with 989 and 212 differentially accumulated proteins (DAPs) in the infected host root cells and their symbiont bacteria, respectively.DiscussionAmong the DAPs, the roles of those involved in nodulation and N2 fixation are discussed. For the first time, this study provides new insights into the effects of Si on both nodular partners and paves the way for a better understanding of the impact of Si on improving nodule function, and more specifically, on the nodules’ N2-fixing capacity.

ContextRecent insights into type 2 inflammation have led to the development of monoclonal antibody therapies for severe asthma and chronic rhinosinusitis with nasal polyps (CRSwNP). Despite add-on therapy with a monoclonal antibody, some individuals remain uncontrolled in terms of upper and/or lower airway symptoms, prompting an exploration of the efficacy of combining biological therapies and their impact on inflammatory pathways.ObjectivesIn this article, we present a distinctive case of a patient with CRSwNP, severe eosinophilic asthma, and uncontrolled upper airway symptoms, who experienced substantial clinical and local inflammatory improvements through dual monoclonal antibody therapy.MethodsWe provide a detailed case description and analysis of the patient's nasal tissue and secretions to gain insights into the local nasal inflammation under this unique therapeutic approach.ResultsThe addition of an anti-IL-4Rα antibody led to an improvement in upper airway symptoms and a reduction in both eosinophilic and neutrophilic inflammation, despite prior anti-IL-5 therapy. These effects were consistently observed in both polyp tissue and nasal secretions.ConclusionOur patient, with CRSwNP, severe eosinophilic asthma, and uncontrolled upper airway symptoms, experienced substantial improvement with dual monoclonal antibody therapy, without major complications or side effects.

One of the most common diseases of the organ of vision, characterized by a loss of homeostasis of the tear film, with a violation of the stability of the tear film and its hyperosmolarity, is the dry eye syndrome (DES). The article presents a review of modern scientific literature, reflecting the prevalence and main factors of the pathogenesis of DES, as well as evaluating the prospects for the use of proteomic mapping, which provides significant assistance in studying the patterns of development and progression of the disease. The methodological foundations of tear collection for research are considered in detail, and current data on changes in the biochemical composition of tear fluid in DES are analyzed.

Abstract Background The ricefield eel Monopterus albus undergoes a natural sex change from female to male during its life cycle, and previous studies have shown the potential mechanisms of this transition at the transcriptional and protein levels. However, the changes in protein levels have not been fully explored, especially in the intersexual stage. Results In the present study, the protein expression patterns in the gonadal tissues from five different periods, the ovary (OV), early intersexual stage gonad (IE), middle intersexual stage gonad (IM), late intersexual stage gonad (IL), and testis (TE), were determined by untargeted proteomics sequencing. A total of 5125 proteins and 394 differentially expressed proteins (DEPs) were detected in the gonadal tissues. Of the 394 DEPs, there were 136 between the OV and IE groups, 20 between the IM and IE groups, 179 between the IL and IM groups, and 59 between the TE and IL groups. Three candidate proteins, insulin-like growth factor 2 mRNA-binding protein 3 isoform X1 (Igf2bp3), triosephosphate isomerase (Tpi), and Cu-Zn superoxide dismutase isoform X1 [(Cu-Zn) Sod1], were validated by western blotting to verify the reliability of the data. Furthermore, metal metabolite-related proteins were enriched in the IL vs. IM groups and TE vs. IL groups, which had close relationships with sex change, including Cu2+-, Ca2+-, Zn2+- and Fe2+/Fe3+-related proteins. Analysis of the combined transcriptome data revealed consistent protein/mRNA expression trends for two metal metabolite-related proteins/genes [LOC109953912 and calcium Binding Protein 39 Like (cab39l)]. Notably, we detected significantly higher levels of Cu2+ during the sex change process, suggesting that Cu2+ is a male-related metal metabolite that may have an important function in male reproductive development. Conclusions In summary, we analyzed the protein profiles of ricefield eel gonadal tissues in five sexual stages (OV, IE, IM, IL, and TE) and verified the plausibility of the data. After preforming the functional enrichment of metal metabolite-related DEPs, we detected the contents of the metal metabolites Zn2+, Cu2+, Ca2+, and Fe2+/Fe3+ at these five stages and screened for (Cu-Zn) Sod1 and Mmp-9 as possible key proteins in the sex reversal process.

Meiping Chen,1,2 Yijun Ge,1,3 Wen Zhang,1 Ping Wu,4 Chao Cao1 1Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, People’s Republic of China; 2Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, People’s Republic of China; 3Department of Respiratory and Critical Care Medicine, Ninghai First Hospital, Ningbo, 315600, People’s Republic of China; 4National Facility for Protein in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, CAS, Shanghai, 201210, People’s Republic of ChinaCorrespondence: Chao Cao, The First Affiliated Hospital of Ningbo University, 59 Liuting Road, Ningbo, 315010, People’s Republic of China, Tel +86-574-87089878, Fax +86-0574-8729-1583, Email caocdoctor@163.comPurpose: Little research has explored the proteomic characteristics of nasal lavage fluid from asthmatic patients. This study aims to investigate whether differentially expressed proteins (DEPs) in nasal lavage fluid can serve as a biomarker to differentiate asthma patients from healthy controls (HCs) and to discern between individuals with well controlled and poorly controlled asthma.Patients and Methods: We enrolled patients with allergic rhinitis (AR), asthma, or both conditions, and HCs in this study. We recorded patients’ demographic and medical history data and administered asthma quality of life questionnaire (AQLQ) and asthma control questionnaire (ACQ). Nasal fluid samples were collected, followed by protein measurements, and proteomic analysis utilizing the data-independent acquisition (DIA) method.Results: Twenty-four with asthma, 27 with combined asthma+ AR, 25 with AR, and 12 HCs were enrolled. Four proteins, superoxide dismutase 2 (SOD2), serpin B7 (SERPINB7), kallikrein-13 (KLK13), and bleomycin hydrolase (BLMH) were significantly upregulated in nasal lavage fluid samples of asthma without AR, compared to HCs (Fold change ≥ 2.0, false-discovery rate [FDR] < 0.05). Conversely, 56 proteins including secretoglobin family 2A member 1 (SCGB2A1) were significantly downregulated (fold change ≥ 2.0, FDR < 0.05). Furthermore, 96.49% of DEPs including peptidase inhibitor 3 (PI3) and C-X-C motif chemokine 17 (CXCL17) were upregulated in poorly controlled asthma patients without AR relative those with well- or partly controlled asthma (fold change ≥ 1.5, FDR < 0.05). Search tool for the retrieval of interacting genes/proteins (STRING) analysis showed that PI3, with 18 connections, may be pivotal in asthma control.Conclusion: The study revealed significant alteration in the nasal lavage proteome in asthma without AR patients. Moreover, our results indicated a potential association between the expression of proteome in the upper airway and the level of asthma control. Specifically, PI3 appears to be a key role in the regulation of asthma without AR. Keywords: allergy, proteomic analysis, nasal lavage fluid, asthma control

The discovery and investigation of new natural compounds with antimicrobial activity are new potential strategies to reduce the spread of antimicrobial resistance. The presented study reveals, for the first time, the promising antibacterial potential of two fractions from Cornu aspersum mucus with an MW < 20 kDa and an MW > 20 kDa against five bacterial pathogens—Bacillus cereus 1085, Propionibacterium acnes 1897, Salmonella enterica 8691, Enterococcus faecalis 3915, and Enterococcus faecium 8754. Using de novo sequencing, 16 novel peptides with potential antibacterial activity were identified in a fraction with an MW < 20 kDa. Some bioactive compounds in a mucus fraction with an MW > 20 kDa were determined via a proteomic analysis on 12% sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS–PAGE) and bioinformatics. High homology with proteins and glycoproteins was found, with potential antibacterial activity in mucus proteins named aspernin, hemocyanins, H-lectins, and L-amino acid oxidase-like protein, as well as mucins (mucin-5AC, mucin-5B, mucin-2, and mucin-17). We hypothesize that the synergy between the bioactive components determined in the composition of the fraction > 20 kDa are responsible for the high antibacterial activity against the tested pathogens in concentrations between 32 and 128 µg/mL, which is comparable to vancomycin, but without cytotoxic effects on model eukaryotic cells of Saccharomyces cerevisiae. Additionally, a positive effect, by reducing the levels of intracellular oxidative damage and increasing antioxidant capacity, on S. cerevisiae cells was found for both mucus extract fractions of C. aspersum. These findings may serve as a basis for further studies to develop a new antibacterial agent preventing the development of antibiotic resistance. [ABSTRACT FROM AUTHOR]

Mesenchymal stromal/stem cells (MSCs) are a heterogeneous population of multipotent cells that can be obtained from various tissues, such as dental pulp, adipose tissue, bone marrow and placenta. MSCs have gained importance in the field of regenerative medicine because of their promising role in cell therapy and their regulatory abilities in tissue repair and regeneration. However, a better characterization of these cells and their products is necessary to further potentiate their clinical application. In this study, we used unbiased high-resolution mass spectrometry-based proteomic analysis to investigate the impact of distinct priming strategies, such as hypoxia and IFN-γ treatment, on the composition and therapeutic functionality of the secretome produced by MSCs derived from the amniotic membrane of the human placenta (hAMSCs). Our investigation revealed that both types of priming improved the therapeutic efficacy of hAMSCs, and these improvements were related to the secretion of functional factors present in the conditioned medium (CM) and exosomes (EXOs), which play crucial roles in mediating the paracrine effects of MSCs. In particular, hypoxia was able to induce a pro-angiogenic, innate immune responseactivating, and tissue-regenerative hAMSC phenotype, as highlighted by the elevated production of regulatory factors such as VEGFA, PDGFRB, ANGPTL4, ENG, GRO-γ, IL8, and GRO-α. IFN-γ priming, instead, led to an immunosuppressive profile in hAMSCs, as indicated by increased levels of TGFB1, ANXA1, THBS1, HOMER2, GRN, TOLLIP and MCP-1. Functional assays validated the increased angiogenic properties of hypoxic hAMSCs and the enhanced immunosuppressive activity of IFN-γ-treated hAMSCs. This study extends beyond the direct priming effects on hAMSCs, demonstrating that hypoxia and IFN-γ can influence the functional characteristics of hAMSC-derived secretomes, which, in turn, orchestrate the production of functional factors by peripheral blood cells. This research provides valuable insights into the optimization of MSC-based therapies by systematically assessing and comparing the priming type-specific functional features of hAMSCs. These findings highlight new strategies for enhancing the therapeutic efficacy of MSCs, particularly in the context of multifactorial diseases, paving the way for the use of hAMSC-derived products in clinical practice. [ABSTRACT FROM AUTHOR]

The dietary approach to stop hypertension (DASH) diet combines the antihypertensive effect of a low sodium and high potassium diet. In particular, the potassium component of the diet acts as a switch in the distal convoluted tubule to reduce sodium reabsorption, similar to a diuretic but without the side effects. Previous trials to understand the mechanism of the DASH diet were based on animal models and did not characterize changes in human ion channel protein abundance. More recently, protein cargo of urinary extracellular vesicles (uEVs) has been shown to mirror tissue content and physiological changes within the kidney. We designed an inpatient open label nutritional study transitioning hypertensive volunteers from an American style diet to DASH diet to examine physiological changes in adults with stage 1 hypertension otherwise untreated (Sacks FM, Svetkey LP, Vollmer WM, Appel LJ, Bray GA, Harsha D, Obarzanek E, Conlin PR, Miller ER 3rd, Simons-Morton DG, Karanja N, Lin PH; DASH-Sodium Collaborative Research Group. N Engl J Med 344: 3–10, 2001). Urine samples from this study were used for proteomic characterization of a large range of pure uEVs (small to large) to reveal kidney epithelium changes in response to the DASH diet. These samples were collected from nine volunteers at three time points, and mass spectrometry identified 1,800 proteins from all 27 samples. We demonstrated an increase in total SLC12A3 [sodium-chloride cotransporter (NCC)] abundance and a decrease in aquaporin-2 (AQP2) in uEVs with this mass spectrometry analysis, immunoblotting revealed a significant increase in the proportion of activated (phosphorylated) NCC to total NCC and a decrease in AQP2 from day 5 to day11. This data demonstrates that the human kidney's response to nutritional interventions may be captured noninvasively by uEV protein abundance changes. Future studies need to confirm these findings in a larger cohort and focus on which factor drove the changes in NCC and AQP2, to which degree NCC and AQP2 contributed to the antihypertensive effect and address if some uEVs function also as a waste pathway for functionally inactive proteins rather than mirroring protein changes. NEW & NOTEWORTHY: Numerous studies link DASH diet to lower blood pressure, but its mechanism is unclear. Urinary extracellular vesicles (uEVs) offer noninvasive insights, potentially replacing tissue sampling. Transitioning to DASH diet alters kidney transporters in our stage 1 hypertension cohort: AQP2 decreases, NCC increases in uEVs. This aligns with increased urine volume, reduced sodium reabsorption, and blood pressure decline. Our data highlight uEV protein changes as diet markers, suggesting some uEVs may function as waste pathways. We analyzed larger EVs alongside small EVs, and NCC in immunoblots across its molecular weight range. [ABSTRACT FROM AUTHOR]

Background: Human dermal fibroblasts secrete diverse proteins that regulate wound repair and tissue regeneration. Methods: In this study, dermal fibroblast‐conditioned medium (DFCM) proteins potentially regulating nerve restoration were bioinformatically selected among the 337 protein lists identified by quantitative liquid chromatography‐tandem mass spectrometry. Using these proteins, protein–protein interaction network analysis was conducted. In addition, the roles of DFCM proteins were reviewed according to their protein classifications. Results: Gene Ontology protein classification categorized these 57 DFCM proteins into various classes, including protein‐binding activity modulator (N = 11), cytoskeletal protein (N = 8), extracellular matrix protein (N = 6), metabolite interconversion enzyme (N = 5), chaperone (N = 4), scaffold/adapter protein (N = 4), calcium‐binding protein (N = 3), cell adhesion molecule (N = 2), intercellular signal molecule (N = 2), protein modifying enzyme (N = 2), transfer/carrier protein (N = 2), membrane traffic protein (N = 1), translational protein (N = 1), and unclassified proteins (N = 6). Further protein–protein interaction network analysis of 57 proteins revealed significant interactions among the proteins that varied according to the settings of confidence score. Conclusions: Our bioinformatic analysis demonstrated that DFCM contains many secretory proteins that form significant protein–protein interaction networks crucial for regulating nerve restoration. These findings underscore DFCM proteins' critical roles in various nerve restoration stages during the wound repair process. [ABSTRACT FROM AUTHOR]

Rheumatoid arthritis (RA) is an autoimmune disease characterized by progressive joint destruction. Early diagnosis and treatment, before joint deformation or destruction occurs, are crucial. Identifying novel biomarkers for RA in saliva could potentially enable early detection of the disease, prior to its onset. We conducted a comprehensive proteomic analysis of salivary proteins in a mouse model of RA. Proteins were identified using western blotting and enzyme-linked immunosorbent assay in the serum, saliva, and ankle joints of DBA/1JJmsSlc mice, a model of RA. Ankle joints and submandibular glands were stained with hematoxylin and eosin and immunostained, and the results were compared with those of control mice. Citrullinated alpha-1 antitrypsin (A1AT, 46 kDa) was commonly detected in the saliva, serum, and ankle joints of mice with severe RA and was confirmed through proteomic analysis. Western blotting showed a band corresponding to 46 kDa in the serum, saliva, and ankle joints. Immunostaining of the ankle joints with the A1AT antibody showed a strong positive signal in the synovium. In DBA/1JJmsSlc mice, cyclic citrullinated peptide antibodies and A1AT may be involved in citrullination and contribute to the development and severity of RA, making them valuable treatment targets requiring further study. • New biomarkers are needed for early diagnosis of rheumatoid arthritis (RA). • We analyzed serum, saliva, and ankle joint proteins from mice with rheumatoid arthritis (DBA mice) to find diagnostic markers for RA. • Citrullinated A1AT was commonly detected in serum, saliva and ankle joints of mice with RA severe group. • Suggesting that A1AT may be involved in the pathogenesis and severity of RA. [ABSTRACT FROM AUTHOR]