During the metamorphosis of anuran amphibians, the tail resorption process is a necessary and crucial change. One subject that has received relatively little or no attention is the expression patterns of proteins and metabolites in the different tail portions during metamorphosis, especially in highland amphibians. The mechanisms of tail resorption in three portions (the tip, middle and root) of the tail were investigated in N. pleskei G43 tadpole based on two omics (proteomic and metabolomic). Integrin αVβ3 was found to be high expressed in the distal portion of the tail, which could improve the sensitiveness to thyroid hormones in the distal portion of the tail. Muscle regression displayed a spatial pattern with stronger regression in distal and weaker one in proximal portion. Probably, this stronger regression was mainly performed by the proteases of proteasome from the active translation by ribosomes. The suicide model and murder model coexisted in the tail resorption. Meanwhile, fatty acids, amino acids, pyrimidine, and purine which derived from the breakdown of tissues can be used as building blocks or energy source for successful metamorphosis. Our data improved a better comprehension of the tail resorption mechanisms underlying the metamorphism of N. pleskei tadpole through identifying important participating proteins and metabolites.

UNASSIGNED: Community-acquired acute kidney injury (CA-AKI) is a sudden structural damage and loss of kidney function in otherwise healthy individuals outside of hospital settings having high morbidity and mortality rates worldwide. Long-term sequelae of AKI involve an associated risk of progression to chronic kidney disease (CKD). Serum creatinine (SCr), the currently used clinical parameter for diagnosing AKI, varies greatly with age, gender, diet, and muscle mass. In the present study, we investigated the difference in urinary proteomic profile of subjects that recovered (R) and incompletely recovered (IR) from CA-AKI, 4 months after hospital discharge.
UNASSIGNED: Study subjects were recruited from ongoing study of CA-AKI cohort. Patients with either sex or age > 18 years with no underline CKD were enrolled at the time of hospital discharge. Incomplete recovery from CA-AKI was defined as eGFR < 60 mL/min/1.73 m2 or dialysis dependence at 4 months after discharge. Second-morning urine samples were collected, and proteome analysis was performed with LC-MS/MS. Data were analyzed by Proteome Discoverer platform 2.2 (Thermo Scientific) using statistical and various bioinformatics tools for abundance of protein, cellular component, protein class and biological process were analyzed in the recovered and incompletely recovered groups.
UNASSIGNED: A total of 28 subjects (14 in each group) were enrolled. Collectively, 2019 peptides and proteins with 30 high-abundance proteins in the incompletely recovered group (R/IR <0.5, abundance ratio adj. p-value <0.05) and 11 high-abundance proteins in the incompletely recovered group (R/IR >2.0, abundance ratio adj. p-value <0.05) were identified. Tissue specificity analysis, GO enrichment analysis, and pathway enrichment analysis revealed significant proteins in both the groups that are part of different pathways and might be playing crucial role in renal recovery during the 4-month span after hospital discharge.
UNASSIGNED: In conclusion, this study helped in identifying potential proteins and associated pathways that are either upregulated or downregulated at the time of hospital discharge in incompletely recovered CA-AKI patients that can be further investigated to check for their exact role in the disease progression or repair.

BACKGROUND: The present study explored the proinflammatory impact of Enterococcus faecalis membrane vesicles (MVs) derived from culture medium at pH 7.4 and 9.0.
METHODS: E. faecalis MVs were obtained by centrifugation and purified by size exclusion chromatography. Proteomic analyses were carried out on E. faecalis MVs to investigate their components. THP-1 macrophages were exposed to E. faecalis MVs, and the inflammatory cytokines and proteins were evaluated using ELISA and immunoblotting. The inflammatory cytokines in the serum of mice with intraperitoneal injection of E. faecalis MVs were evaluated by ELISA, and immunophenotyping of spleen cells was investigated with flow cytometry.
RESULTS: Proteomic analysis revealed 196 proteins in E. faecalis MVs obtained under neutral and alkali conditions, 110 proteins were upregulated and 79 proteins were downregulated by alkaline pH. E. faecalis MVs induced secretion of inflammatory factors interleukin (IL)-1β, IL-6 and tumor necrosis factor-α in a concentration-dependent manner. Immunoblotting revealed that E. faecalis MVs increased expression of pro-IL-1β, nuclear factor-κBp65, and Toll-like receptor 2. In vivo studies demonstrated that E. faecalis MVs significantly promoted secretion of IL-1β in mouse serum, while inflammatory cells were activated in the spleen. E. faecalis MVs obtained at pH 9.0 showed stronger proinflammatory effects than those obtained under neutral pH.
CONCLUSIONS: E. faecalis produce MVs that carry specific proteins associated with virulence factors, and these MVs can promote inflammation in vitro and in vivo. E. faecalis MVs obtained under alkaline conditions have a stronger proinflammatory effect.

The functionality of electroactive biofilms (EABs) is profoundly influenced by the proteomic dynamics within microbial communities, particularly through the participation of proteins in electron transfer. This study explored the impact of electrode surface orientation, measured by varying oblique angles, on the performance of EABs in bioelectrochemical systems (BES). Utilizing quantitative proteomics, results indicated that a slightly oblique angle (45°) optimized the spatial arrangement of microbial cells, enhancing electron transport efficiency compared to other angles tested. Specifically, the 45° orientation resulted in a 2.36-fold increase in the abundance of c-type cytochromes compared to the 90°. Additionally, Geobacter, showed a relative abundance of 83.25 % at 45°, correlating with a peak current density of 1.87 ± 0.04 A/m2. These microbial and proteomic adaptations highlighted the intricate balance between microbial behavior and the physical environment, which could be tuned to optimize operations. The findings provided new insights into the design and enhancement of BES.

Transformation represents one of the most important pathways for the horizontal transfer of antibiotic resistance genes (ARGs), which enables competent bacteria to acquire extracellular ARGs from the surrounding environment. Both heavy metals and irradiation have been demonstrated to influence the bacterial transformation process. However, the impact of ubiquitously occurring radioactive heavy metals on the transformation of ARGs remains largely unknown. Here, we showed that a representative radioactive nuclide, uranium (U), at environmental concentrations (0.005-5 mg/L), improved the transformation frequency of resistant plasmid pUC19 into Escherichia coli by 0.10-0.85-fold in a concentration-dependent manner. The enhanced ARGs transformation ability under U stress was demonstrated to be associated with reactive oxygen species (ROS) overproduction, membrane damage, and up-regulation of genes related to DNA uptake and recombination. Membrane permeability and ROS production were the predominant direct and indirect factors affecting transformation ability, respectively. Our findings provide valuable insight into the underlying mechanisms of the impacts of U on the ARGs transformation process and highlight concerns about the exacerbated spread of ARGs in radioactive heavy metal-contaminated ecosystems, especially in areas with nuclear activity or accidents.

An important determinant for oral squamous cell carcinoma (OSCC) onset and outcome is the composition of the tumor microenvironment (TME). Thus, the study of the interactions occurring among cancer cells, immune cells, and cancer-associated fibroblasts within the TME could facilitate the understanding of the mechanisms underlying OSCC development and progression, as well as of its sensitivity or resistance to the therapy. In this context, it must be highlighted that the characterization of TME proteins is enabled by proteomic methodologies, particularly mass spectrometry (MS). Aiming to identify TME protein markers employable for diagnosing and prognosticating OSCC, we have retrieved a total of 119 articles spanning 2001 to 2023, of which 17 have passed the selection process, satisfying all its criteria. We have found a total of 570 proteins detected by MS-based proteomics in the TME of OSCC; among them, 542 are identified by a single study, while 28 are cited by two or more studies. These 28 proteins participate in extracellular matrix remodeling and/or energy metabolism. Here, we propose them as markers that could be used to characterize the TME of OSCC for diagnostic/prognostic purposes. Noteworthy, most of the 28 individuated proteins share one feature: being modulated by the hypoxia that is present in the proliferating OSCC mass.

Monkeypox virus (MPXV) is a cross-kingdom pathogen infecting both humans and wildlife, which poses a significant health risk to the public. Although MPXV attracts broad attention, there is a lack of adequate studies to elucidate pathogenic mechanisms associated with viral infections. In this study, a high-throughput RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach was used to explore the transcriptional and metabolic responses of MPXV A23 protein to HEK293T cells. The protein-protein interactions and signaling pathways were conducted by GO and KEGG analyses. The localization of A23 protein in HEK293T cells was detected by immunofluorescence. A total of 648 differentially expressed genes (DEGs) were identified in cells by RNA-Seq, including 314 upregulated genes and 334 downregulated genes. Additionally, liquid chromatography-tandem mass spectrometry (LC-MS/MS) detected 115 cellular proteins that interact with the A23 proteins. Transcriptomic sequencing analysis revealed that transfection of MPXV A23 protein modulated genes primarily associated with cellular apoptosis and DNA damage repair. Proteomic analysis indicated that this protein primarily interacted with host ribosomal proteins and histones. Following the identification of the nuclear localization sequence RKKR within the A23 protein, a truncated mutant A23ΔRKKR was constructed to investigate the subcellular localization of A23 protein. The wild-type A23 protein exhibits a significantly higher nuclear-to-cytoplasmic ratio, exceeding 1.5, in contrast to the mutant A23ΔRKKR, which has a ratio of approximately 1. Immunofluorescence assays showed that the A23 protein was mainly localized in the nucleus. The integration of transcriptomics and proteomics analysis provides a comprehensive understanding of the interaction between MPXV A23 protein and the host. Our findings highlight the potential role of this enzyme in suppressing host antiviral immune responses and modulating host gene expression.

Ram sperm undergo a sequence of physiological and biochemical changes collectively termed as capacitation to perform oocyte fertilization. However, the protein changes induced by capacitation remain in need of further exploration. Thus, the present study investigated the comparative proteomic profiling in ram spermatozoa under non-capacitating (NC) and capacitating (CAP) conditions in vitro using a liquid chromatography-tandem mass spectrometry combined with tandem mass tag labeling strategy. As a results, 2050 proteins were identified and quantified; 348 of them were differentially abundant, with 280 of the proteins upregulated and 68 of the proteins downregulated between the CAP and NC spermatozoa, respectively. Functional enrichment analysis indicated that the differentially abundant proteins Prune Exopolyphosphatase 1, Galactose-1-Phosphate Uridylyltransferase, and ATP Citrate Lyase were strictly related to energy production and conversion, and Phosphoglycolate phosphatase, Glucosamine-6-Phosphate Deaminase 1 and 2 were related to metabolism, RNA processing, and vesicular transport pathways. Furthermore, the networks of protein-protein interaction indicated a strong interaction among these differential proteins in annotated pathways such as ubiquitin and transport metabolism. Our findings indicate that capacitation progress might be regulated through different pathways, providing insights into mechanisms involved in ram sperm capacitation and fertility.

Colostrum intake is a crucial determinant of survival in newborn rabbits. Neonates rely entirely on passive immunity transfer from their mothers while suckling colostrum. The goal of this study was to explore the protein differences of rabbit milk during different lactation periods. Our findings showed that the daily milk yield exhibited an increasing trend from the 2nd to the 21st day of lactation. A data-independent acquisition proteomics approach identified a total of 2011 proteins. Significantly, different abundances were found for 525 proteins in the colostrum and the mature milk samples. Eleven differentially abundant proteins (DAPs) were examined using parallel reaction monitoring, which verified the reliability of the proteomic data. Gene Ontology analysis revealed that these DAPs were primarily associated with glycosyltransferase activity, macromolecule transmembrane transporter activity, and regulation of acute inflammatory response. The dominant metabolic pathways of the DAPs involve the complement and coagulation cascades. A protein-protein interaction analysis identified apolipoprotein B, apolipoprotein A1, triose phosphate isomerase 1, and albumin as the hub proteins responsible for distinguishing differences between biological properties in rabbit colostrum and mature milk. These findings enhance our comprehension of the rabbit milk proteome, particularly in expanding our knowledge regarding the requirements of neonatal rabbits.

Increasing the age of bulls results in a decrease in reproductive function, including a reduction in sperm quality, which plays a vital role in determining the fertility of bulls. Through a proteomic approach, this research aims to analyze the influence of age factors on various proteomes contained in bull sperm. Frozen semen samples from Simmental Bulls were categorized into three age groups: two, four, and ≥10 years old. Subsequently, the post-thaw sperm cells obtained were separated based on molecular weight using 1D-SDS-PAGE. Peptides extracted from the bands produced in each age group were subjected to LC-MS/MS analysis. A total of 72 protein types were identified, with 45 being detected in the 4-year-old group and 41 expressed in both the 2 and ≥10-year-old groups. The results provided insights into proteins\' role in sperm metabolism across all age groups. Specifically, the 2-year-old group exhibited the expression of proteins associated with acrosome assembly and spermatid development (SPACA1). In contrast, those in the 4-year-old group were linked to motility (PEBP4) and sperm decapacitation factor (PEBP1). Proteins expressed in the 2 and -year-old groups were discovered to be involved in fertilization processes (TEX101). In contrast, the ≥10-year-old age group was associated with hyperactive movement related to capacitation (Tubulin). In conclusion, age influenced the differences observed in the proteomic profile of post-thaw Simmental bull sperm using the 1D-SDS-PAGE tandem LC-MS/MS approach.