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This document is a correction notice for an article titled "Simulated complexes formed from a set of postsynaptic proteins suggest a localized effect of a hypomorphic Shank mutation." The authors of the original article identified an error in Figure 1, where the incorrect version of the figure was accidentally replaced during proofing. The correct version of Figure 1 has been updated in this correction notice. The correction was made by Marcell Miski, Áron Weber, Krisztina Fekete-Molnár, Bence Márk Keömley-Horváth, Attila Csikász-Nagy, and Zoltán Gáspári. Springer Nature, the publisher, remains neutral with regard to jurisdictional claims and institutional affiliations. [Extracted from the article]

Background: Oral leukoplakia (OL) is the most common potentially malignant disease of the oral cavity. In recent years, studies have identified a correlation between the gut microbiota (GM) and oral cancer, in addition, inflammation-related proteins have been reported to play an important role in the development of OL. However, the causal relationship between gut microbiota and OL, as well as whether cytokines play a mediating role, remain unclear. Methods: In this Mendelian randomization (MR) study, the genome-wide association studies (GWAS) (n=18340) of the MiBioGen consortium microbiome was used as exposure data. Genetic variation data related to OL were extracted from the Finngen R9 project (513 cases of OL and 411668 controls). The 91 inflammation-related proteins obtained in the literature serve as potential mediators. Two-sample Mendelian randomization analysis was applied to infer causality using Inverse Variance Weighted (IVW), MR Egger, weighted media, simple mode and weighted mode method. Subsequently, sensitivity analysis was conducted to ensure the robustness of the MR results. In addition, we conducted reverse MR analysis to alleviate reverse causality. Finally, we used mediation analysis to determine the pathway mediated by inflammation-related proteins from the gut microbiota to OL. Results: The five bacterial taxa in the gut microbiota indicate a potential causal relationship with the development of OL. Notably, family Clostridiaceae1 was negatively correlated with the risk of OL development, while genus Dorea, genus Ruminococcus1, genus Senegalimasilia and genus Veillonella were positively associated with the risk of OL development. In addition, this study identified a potential causal relationship between interleukin-10 receptor subunit alpha (IL-10RA), interleukin-18 receptor 1(IL18-R1) and the occurrence of OL. In addition, intermediary analysis indicates that IL18-R1 mediated the pathway between the gut microbiota genus Senegalimasilia and OL. Conclusions: In summary, our research emphasize the complex relationship between gut microbiota, inflammation-related proteins and OL. The identified associations and mediating effects provide new insights into potential therapeutic approaches for targeting the gut microbiota in the management of OL, and contribute to its prevention, diagnosis and treatment. [ABSTRACT FROM AUTHOR]

SHP-1, a nonreceptor protein tyrosine phosphatase encoded by ptpn6, has been regarded as a regulatory protein of hematopoietic cell biology for years. However, there is now increasing evidence to support its role in tumors. Thus, the role of ptpn6 for prognosis and immune regulation across 33 tumors was investigated, aiming to explore its functional heterogeneity and clinical significance in pan-cancer. Differential expression of ptpn6 was found between cancer and adjacent normal tissues, and its expression was significantly correlated with the prognosis of tumor patients. In most cancers, ptpn6 expression was significantly associated with immune infiltration. This was further confirmed by ptpn6-related genes/proteins enrichment analysis. Additionally, genetic alterations in ptpn6 was observed in most cancers. As for epigenetic changes, it's phosphorylation levels significantly altered in 6 tumors, while methylation levels significantly altered in 12 tumors. Notably, the methylation levels of ptpn6 were significantly decreased in 11 tumors, accompanied by its increased expression in 8 of them, suggesting that the hypomethylation may be related to its increased expression. Our results show that ptpn6 plays a specific role in tumor immunity and exerts a pleiotropic effect in a variety of tumors. It can serve as a prognostic factor for some cancers. Especially in LGG, KIRC, UCS and TGCT, the increased expression of ptpn6 is associated with poor prognosis and high immune infiltration. This aids in understanding the role of ptpn6 in tumor biology, and can provide insight into presenting a potential biomarker for poor prognosis and immune infiltration in cancers. [ABSTRACT FROM AUTHOR]

Objective: To explore the biological function and mechanisms of CEBPB and NAT10‐mediated N4‐acetylcytidine (ac4c) modification in salivary adenoid cystic carcinoma (SACC). Materials and Methods: CEBPB and NAT10 were knocked down in SACC–LM cells by siRNA transfection and overexpressed in SACC‐83 cells by plasmid transfection. Malignant phenotypes were evaluated using CCK‐8, Transwell migration and colony formation assays. Real‐time PCR, western blotting, ChIP and acRIP were used to investigate the molecular mechanisms involved. Results: We found that CEBPB was highly expressed in SACC tissues and correlated with lung metastasis and unfavourable prognosis. Gain‐ and loss‐of‐function experiments revealed that CEBPB promoted SACC malignant phenotypes. Mechanistically, CEBPB exerted its oncogenic effect by binding to the vimentin gene promoter region to enhance its expression. Moreover, NAT10‐mediated ac4c modification led to stabilization and overexpression of CEBPB in SACC cells. We also found that NAT10, the only known human enzyme responsible for ac4C modification, promoted SACC cell migration, proliferation and colony formation. Moreover, CEBPB overexpression restored the inhibitory effect of NAT10 knockdown on malignant phenotypes. Conclusions: Our study reveals the critical role of the newly identified NAT10/CEBPB/vimentin axis in SACC malignant progression, and the findings may be applied to improve treatment for SACC. [ABSTRACT FROM AUTHOR]

One of the central issues in the understanding of early cellular evolution is the characterisation of the cenancestor. This includes the description of the chemical nature of its genome. The disagreements on this question comprise several proposals, including the possibility that AlkB-mediated methylation repair of alkylated RNA molecules may be interpreted as evidence of a cenancestral RNA genome. We present here an evolutionary analysis of the cupin-like protein superfamily based on tertiary structure-based phylogenies that includes the oxygen-dependent AlkB and its homologs. Our results suggest that the repair of methylated RNA molecules is the outcome of the enzyme substrate ambiguity, and doesn´t necessarily indicates that the last common ancestor was endowed with an RNA genome. [ABSTRACT FROM AUTHOR]

A group of three deep‐learning tools, referred to collectively as CHiMP (Crystal Hits in My Plate), were created for analysis of micrographs of protein crystallization experiments at the Diamond Light Source (DLS) synchrotron, UK. The first tool, a classification network, assigns images into categories relating to experimental outcomes. The other two tools are networks that perform both object detection and instance segmentation, resulting in masks of individual crystals in the first case and masks of crystallization droplets in addition to crystals in the second case, allowing the positions and sizes of these entities to be recorded. The creation of these tools used transfer learning, where weights from a pre‐trained deep‐learning network were used as a starting point and repurposed by further training on a relatively small set of data. Two of the tools are now integrated at the VMXi macromolecular crystallography beamline at DLS, where they have the potential to absolve the need for any user input, both for monitoring crystallization experiments and for triggering in situ data collections. The third is being integrated into the XChem fragment‐based drug‐discovery screening platform, also at DLS, to allow the automatic targeting of acoustic compound dispensing into crystallization droplets. [ABSTRACT FROM AUTHOR]

Nuclear envelope repair is a fundamental cellular response to stress, especially for cells experiencing frequent nuclear ruptures, such as cancer cells. Moreover, for chromosomally unstable cancer cells, characterized by the presence of micronuclei, the irreversible rupture of these structures constitutes a fundamental step toward cancer progression and therapy resistance. For these reasons, the study of nuclear envelope rupture and repair is of paramount importance. Nonetheless, due to the constraint imposed by the stochastic nature of rupture events, a precise characterization of the initial stage of nuclear repair remains elusive. In this study, we overcame this limitation by developing a new imaging pipeline that deterministically induces rupture while simultaneously imaging fluorescently tagged repair proteins. We provide a detailed step-by-step protocol to implement this method on any confocal microscope and applied it to study the major nuclear repair protein, barrier-to-autointegration factor (BAF). As a proof of principle, we demonstrated two different downstream analysis methods and showed how BAF is differentially recruited at sites of primary and micronuclear rupture. Additionally, we applied this method to study the recruitment at primary nuclei of the inner nuclear membrane protein LEM-domain 2 (LEMD2) and Charged Multivesicular Protein 7 (CHMP7), the scaffolding protein of the endosomal sorting complex required for transport III (ESCRT-III) membrane remodeling complex. The CHMP7-LEMD2 binding is the fundamental step allowing the recruitment of ESCRT-III, which represents the other major nuclear repair mechanism. This demonstrates the method's applicability for investigating protein dynamics at sites of nuclear and micronuclear envelope rupture and paves the way to more time-resolved studies of nuclear envelope repair. [ABSTRACT FROM AUTHOR]

Objectives: In order to investigate the impact of L-cysteine (L-Cys) on starch and protein degradation during barley germination. The amylase activities, degradation of macromolecules during germination were determined in this study. Methods: Barley was germinated in petri dish for 0 to 5 days with different levels of L-Cys (0 mM, 2.5 mM, 5 mM, 10 mM). Results: L-Cys addition increased the total limit dextrinase (LD) activities and decreased the LD inhibitor activities during whole germination stage. The activities of α-amylase, β-amylase and free LD were increased with the addition of 2.5, 5 mM L-Cys at germination days 1 to 4. Due to higher amylase in malt with the addition of L-Cys, the non-fermentable sugars were reduced and the glucose, maltotriose were improved. Furthermore, the protein degradation analysis showed that low molecular weight protein increased and middle molecular weight protein decreased obviously in wort from the malt germinated with L-Cys, demonstrating that the L-Cys promote the protein degradation. Lastly, the filtration performance of malt with the addition of L-Cys during malting was better than the control. Conclusion: In conclusion, L-Cys can promote the degradation of storage material (starch, protein) during barley germination, leading to a better green malt quality. [ABSTRACT FROM AUTHOR]

The transport of biopolymers across nanopores is an important biological process currently under investigation for the rapid analysis of DNA and proteins. While the transport of DNA is generally understood, methods to induce unfolded protein translocation have only recently been discovered (Yu et al., 2023, Sauciuc et al., 2023). Here, we found that during electroosmotically driven translocation of polypeptides, blob-like structures typically form inside nanopores, often obstructing their transport and preventing addressing individual amino acids. This is in contrast with the electrophoretic transport of DNA, where the formation of such structures has not been reported. Comparisons between different nanopore sizes and shapes and modifications by different surface chemistries allowed formulating a mechanism for blob formation. We also show that single-file transport can be achieved by using 1) nanopores that have an entry and an internal diameter smaller than the persistence length of the polymer, 2) nanopores with a nonsticky (i.e., nonaromatic) inner surface, and 3) moderate translocation velocities. These experiments provide a basis for understanding polypeptide transport under confinement and for improving the design and engineering of nanopores for protein analysis. [ABSTRACT FROM AUTHOR]

Our study investigates the impact of FGF23 overexpression on SaOS-2 cells to elucidate its role in cellular stress and morphology, contributing to the understanding of skeletal pathologies like X-linked hypophosphatemia (XLH). Using transmission electron microscopy and protein analysis (Western blot), we analyzed the rough endoplasmic reticulum (rER) and mitochondria in SaOS-2 cells with FGF23 overexpression compared to controls. We found significant morphological changes, including enlarged and elongated rER and mitochondria, with increased contact zones, suggesting enhanced interaction and adaptation to elevated protein synthesis and secretion demands. Additionally, we observed higher apoptosis rates of the cells after 24–72 h in vitro and upregulated proteins associated with ER stress and apoptosis, such as CHOP, XBP1 (spliced and unspliced), GRP94, eIF2α, and BAX. These findings indicate a robust activation of the unfolded protein response (UPR) and apoptotic pathways due to FGF23 overexpression. Our results highlight the critical role of ER and mitochondrial interactions in cellular stress responses and provide new insights into the mechanistic link between FGF23 signaling and cellular homeostasis. In conclusion, our study underscores the importance of analyzing UPR-related pathways in the development of therapeutic strategies for skeletal and systemic diseases and contributes to a broader understanding of diseases like XLH. [ABSTRACT FROM AUTHOR]

Simple Summary: Non-small cell lung cancer (NSCLC) is marked by low survival and resistance to platinum-based chemotherapy. Recent studies have emphasized the critical role of DNA repair mechanisms in NSCLC tumorigenesis and response to treatment. XPG endonuclease, a crucial component of the Nucleotide Excision Repair (NER) pathway, has emerged as a promising biomarker of clinical outcome in advanced NSCLC and its downregulation improved cisplatin efficacy by increasing DNA damage. However, so far, no study has been carried out with the purpose of identifying XPG inhibitors. This work thus aims to discover potential small-molecule inhibitors of XPG to be used in combination with cisplatin therapy to enhance its efficacy in NSCLC patients. NSCLC is marked by low survival and resistance to platinum-based chemotherapy. The XPG endonuclease has emerged as a promising biomarker for predicting the prognosis of cisplatin-treated patients and its downregulation having been reported to increase cisplatin efficacy. This study presents an integrated strategy for identifying small molecule inhibitors of XPG to improve cisplatin therapy in NSCLC. A structure-based virtual screening approach was adopted, including a structural and physicochemical analysis of the protein, and a library of small molecules with reported inhibitory activities was retrieved. This analysis identified Lys84 as a crucial residue for XPG activity by targeting its interaction with DNA. After molecular docking and virtual screening calculations, 61 small molecules were selected as potential XPG inhibitors, acquired from the ChemBridge database and then validated in H1299 cells, a NSCLC cell line exhibiting the highest ERCC5 expression. The MTS assay was performed as a first screening approach to determine whether these potential inhibitors could enhance cisplatin-induced cytotoxicity. Overall, among the eight compounds identified as the most promising, three of them revealed to significantly increase the impact of cisplatin. The inherent cytotoxicity of these compounds was further investigated in a non-tumoral lung cell line (BEAS-2B cells), which resulted in the identification of two non-cytotoxic candidates to be used in combination with cisplatin in order to improve its efficacy in NSCLC therapy. [ABSTRACT FROM AUTHOR]

The mycotoxin deoxynivalenol (DON) is frequently present in cereals at low levels, resulting in its occurrence in food and feed. DON has been proven to alter the immune response and induce inflammation in all species, with pigs exhibiting heightened sensitivity and exposure. However, no study has yet evaluated the effects of exposure to DON at the recommended levels in pig feed. In two separate trials, piglets were subjected to control feed or feed contaminated with a low level of purified DON (0.83 mg/kg feed in trial 1 and 0.85 mg/kg feed in trial 2) for either three weeks (trial 1) or two weeks (trial 2). Additionally, a group of animals exposed to 2.85 mg/kg feed of DON was included as a positive control in Trial 1. The impact of DON on porcine tissues (intestine, liver, and spleen) was evaluated through histological and qPCR analyses of immune-related genes. Additionally, biochemical analyses and acute-phase proteins were examined in plasma samples. Lesions were identified in the intestine (jejunum and ileum), the liver, and the spleen of pigs receiving diets contaminated with low and high concentrations of DON. The low level of DON also resulted in impaired expression of genes associated with intestinal barrier integrity, intestinal immune responses, and liver function. In conclusion, the results of the two trials demonstrate the impact of DON exposure even at doses below the recommended level of 0.9 mg/kg feed set by the European Union. This suggests that the current recommended level should be reconsidered to ensure the optimal health and well-being of pigs. [ABSTRACT FROM AUTHOR]

Integrating in vitro embryo production with embryonic microsurgery facilitates the generation of monozygotic twins. However, despite their potential benefits, these methods have not been widely adopted in commercial settings because of their substantial costs. Hence, there is a need to streamline the bisection procedure while ensuring efficient production of viable demi-embryos. In this study, we investigated the impact of different orientations of microsurgical incisions in relation to inner cell mass on embryonic development, morphology, viability, and expression of cell fate protein markers using a simplified microsurgery approach. Ovaries were transported from the slaughterhouse to the laboratory and aspirated to obtain oocytes that were selected and subjected to in vitro embryo production. The selected expanded blastocysts (n = 204) underwent microsurgery. The blastocysts were immobilized to facilitate incision using an adapted microblade, yielding demi-embryos (vertical incision) and viable embryonic fragments (transverse incision). The structures were then re-cultured for 12 h. Viability was assessed by measuring the re-expansion rate after re-culture, followed by immunofluorescence analysis of proteins (CDX2 and NANOG) and apoptosis analysis using terminal deoxynucleotyl transferase dUTP nick end-labeling (TUNEL). Microsurgically derived embryos exhibited remarkable plasticity, as evidenced by a slight reduction (P < 0.05) in the re-expansion rate (transverse 64.2 % and vertical 57.2 %) compared to that of the control group (blastocysts without microsurgery) (86.7 %). They also demonstrated the ability of morphological reconstitution after culturing. Despite the anticipated decrease (P < 0.05) in the total number of cells and embryo volume, microsurgery did not result in a significant increase (P > 0.05) in the number of apoptotic cells. Furthermore, microsurgery led to higher (P < 0.05) expression of markers associated with pluripotency, indicating its efficiency in preserving regenerative capacity. Moreover, microsurgery, whether followed by immunosurgery or not, made the isolation of embryonic cells easier. In conclusion, both transverse and vertical microsurgery incisions enabled the production of identical demi-embryos and served as tools for isolating embryonic cells without compromising the resumption of development and the apoptotic index. • Different microsurgical incision orientations on embryonic viability. • Cellular and molecular blastocyst reconstitution characterization. • Re-expansion rates after microsurgery demonstrate incredible embryonic plasticity. • Embryonic microsurgery is a tool for obtaining demi-embryos and embryonic cells. [ABSTRACT FROM AUTHOR]

Phenylalanine ammonia lyase (PAL) is a pivotal enzyme in the phenylalanine metabolic pathway in plants and has a crucial role in the plant's response to environmental stress. Although the PAL family has been widely studied in many plant species, limited is known about its particular role in cucumbers under stress. We investigated the physicochemical properties, gene structure, gene duplication events, conserved motifs, cis-acting elements, protein interaction networks, stress-related transcriptome data, and quantitatively validated key stress-related genes. The main results indicated that 15 PAL genes were grouped into four clades: I, II, and III when arranged in a phylogenetic tree of PAL genes in angiosperms. The analysis of the promoter sequence revealed the presence of multiple cis-acting elements related to hormones and stress responses in the cucumber PAL genes (CsPALs). The analysis of protein interaction networks suggested that CsPAL1 interacts with eight other members of the PAL family through CsELI5 and CsHISNA, and directly interacts with multiple proteins in the 4CL family. Further investigation into the expression patterns of CsPAL genes in different tissues and under various stress treatments (NaCl, Cu2+, Zn2+, PEG6000, aphids) demonstrated significant differential expression of CsPALs across cucumber tissues. In summary, our characterization of the CsPAL family offers valuable insights and provides important clues regarding the molecular mechanisms of CsPALs in managing abiotic and biotic stress interactions in cucumbers. [ABSTRACT FROM AUTHOR]

Lindera aggregata, a member belongs to the genus Lindera of Lauraceae family. Its roots and leaves have been used as traditional Chinese medicine or functional food for thousands of years. However, its mitochondrial genome has not been explored. Our aim is to sequence and assemble the mitogenome of L. aggregata to elucidate the genetic mechanism and evolutionary pathway. The results had shown that the mitogenome was extremely complex and had a unique multibranched conformation with total size of 912,473 bp. Comprehensive analysis of protein coding genes of 7 related species showed that there were 40 common genes in their mitogenome. Interestingly, positive selection had become an important factor in the evolution of ccmB, ccmFC, rps10, rps11 and rps7 genes. Furthermore, our data highlighted the repeated trend of homologous fragment migrations between chloroplast and mitochondrial organelles, and 38 homologous fragments were identified. Phylogenetic analysis identified a tree that was basically consistent with the phylogeny of Laurales species described in the APG IV system. To sum up, this study will be helpful to the study of population genetics and evolution of Lindera species. [ABSTRACT FROM AUTHOR]

Mutations in glycosylation pathways, such as N-linked glycosylation, O-linked glycosylation, and GPI anchor synthesis, lead to Congenital Disorders of Glycosylation (CDG). CDG typically present with seizures, hypotonia, and developmental delay but display large clinical variability with symptoms affecting every system in the body. This variability suggests modifier genes might influence the phenotypes. Because of the similar physiology and clinical symptoms, there are likely common genetic modifiers between CDG. Here, we use evolution as a tool to identify common modifiers between CDG and glycosylation genes. Protein glycosylation is evolutionarily conserved from yeast to mammals. Evolutionary rate covariation (ERC) identifies proteins with similar evolutionary rates that indicate shared biological functions and pathways. Using ERC, we identified strong evolutionary rate signatures between proteins in the same and different glycosylation pathways. Genome-wide analysis of proteins showing significant ERC with GPI anchor synthesis proteins revealed strong signatures with ncRNA modification proteins and DNA repair proteins. We also identified strong patterns of ERC based on cellular sub-localization of the GPI anchor synthesis enzymes. Functional testing of the highest scoring candidates validated genetic interactions and identified novel genetic modifiers of CDG genes. ERC analysis of disease genes and biological pathways allows for rapid prioritization of potential genetic modifiers, which can provide a better understanding of disease pathophysiology and novel therapeutic targets. Author summary: Congenital Disorders of Glycosylation (CDG) are a group of rare disorders resulting from impaired protein glycosylation. Glycosylation is the addition of sugar chains onto proteins and is required for proper protein function. CDG patients typically present with seizures and hypotonia. However, they can have a large amount of clinical variability, which is likely influenced by modifier genes. Modifier genes are genes that affect a phenotype without causing the disease. Using an evolutionary method that examines proteins that evolve at similar rates, we identified proteins within glycosylation pathways and among other unexpected pathways, such as ncRNA modification and DNA repair, that could be potential genetic modifiers of CDG genes. We also tested top protein pairs using the Drosophila eye as a model and identified novel genetic modifiers of CDG genes. Broadening our understanding of CDG modifiers can help us to better understand why loss of glycosylation results in specific patient symptoms and could provide new treatment targets. [ABSTRACT FROM AUTHOR]

Background Objectives Materials and Methods Results Discussion and Conclusion Testicular torsion/detorsion can cause testis loss and infertility. Aloperine is a major active alkaloid extracted from Sophora alopecuroides Linn. It has been shown to have organ‐protective effects. However, the effects of aloperine on the testis and its underlying mechanisms remain unclear.This study investigated the effect of aloperine on testicular torsion/detorsion injury in rats.Male Sprague‐Dawley rats were randomized to the sham‐operated (sham), testicular I/R (TI/R), or aloperine preconditioning (ALOPre) or postconditioning (ALOPost) groups. All rats except for the sham‐operated rats were subjected to 3 h of right spermatic cord torsion (720°, clockwise), followed by 3 h of detorsion. Aloperine (10 mg/kg) was intravenously administered before testicular torsion (ALOPre) or at the onset of testicular detorsion (ALOPost). The therapeutic efficacy of aloperine was evaluated by histological analysis, oxidative stress evaluation, inflammatory response examination, apoptosis analysis, protein analysis, and immunohistological assessment.Compared with TI/R, aloperine protected both the ipsilateral and contralateral testes against unilateral testicular I/R, as evidenced by a reduced testicular weight to body weight (TW/BW) ratio (ALOPre: p = 0.0037; ALOPost: p = 0.0021) and volume (ALOPre: p = 0.0020; ALOPost: p = 0.0009), less structural damage with better Johnsen (ALOPre: p = 0.0013; ALOPost: p = 0.0021), and Cosentino scores (ALOPre: p < 0.0001; ALOPost: p < 0.0001), increased mean seminiferous tubule diameter and mean seminiferous tubule epithelial height, decreased testicular apoptosis, and less oxidative stress and inflammatory response. In addition, aloperine significantly stimulated the phosphorylation of signal transducer and activator of transcription (STAT)‐3 in the ipsilateral testes following detorsion. Administration of Ag490 suppressed STAT‐3 phosphorylation, thereby abrogating the protective effects exerted by aloperine on the ipsilateral testis.Aloperine has a strong testicular protective effect on the ipsilateral and contralateral testes after testicular torsion/detorsion. This aloperine‐induced ipsilateral testicular protection is mediated via the STAT‐3 signaling pathway. [ABSTRACT FROM AUTHOR]

Motivation Protein embedding, which represents proteins as numerical vectors, is a crucial step in various learning-based protein annotation/classification problems, including gene ontology prediction, protein–protein interaction prediction, and protein structure prediction. However, existing protein embedding methods are often computationally expensive due to their large number of parameters, which can reach millions or even billions. The growing availability of large-scale protein datasets and the need for efficient analysis tools have created a pressing demand for efficient protein embedding methods. Results We propose a novel protein embedding approach based on multi-teacher distillation learning, which leverages the knowledge of multiple pre-trained protein embedding models to learn a compact and informative representation of proteins. Our method achieves comparable performance to state-of-the-art methods while significantly reducing computational costs and resource requirements. Specifically, our approach reduces computational time by ∼70% and maintains ±1.5% accuracy as the original large models. This makes our method well-suited for large-scale protein analysis and enables the bioinformatics community to perform protein embedding tasks more efficiently. Availability and implementation The source code of MTDP is available via https://github.com/KennthShang/MTDP [ABSTRACT FROM AUTHOR]

This study introduces the intelligent learning engine (ILE) optimization technology, a novel approach designed to revolutionize screening processes in bioinformatics, cheminformatics, and a range of other scientific fields. By focusing on the efficient and precise identification of candidates with desirable characteristics, the ILE technology marks a significant leap forward in addressing the complexities of candidate selection in drug discovery, protein classification, and beyond. The study's primary objective is to address the challenges associated with optimizing screening processes to efficiently select candidates across various fields, including drug discovery and protein classification. The methodology employed involves a detailed algorithmic process that includes dataset preparation, encoding of protein sequences, sensor nucleation, and optimization, culminating in the empirical evaluation of molecular activity indexing, homology-based modeling, and classification of proteins such as G-protein-coupled receptors. This process showcases the method's success in multiple sequence alignment, protein identification, and classification. Key results demonstrate the ILE's superior accuracy in protein classification and virtual high-throughput screening, with a notable breakthrough in drug development for assessing drug-induced long QT syndrome risks through hERG potassium channel interaction analysis. The technology showcased exceptional results in the formulation and evaluation of novel cancer drug candidates, highlighting its potential for significant advancements in pharmaceutical innovations. The findings underline the ILE optimization technology as a transformative tool in screening processes due to its proven effectiveness and broad applicability across various domains. This breakthrough contributes substantially to the fields of systems optimization and holds promise for diverse applications, enhancing the process of selecting candidate molecules with target properties and advancing drug discovery, protein classification, and modeling. [ABSTRACT FROM AUTHOR]

To predict the role of the MsICE gene family in the response to abiotic stress, in this study, bioinformatics analysis and real-time fluorescence quantitative PCR were performed. Alfalfa (Medicago sativa) is one of the most economically valuable crops globally. Inducer of CBF expression (ICE), which is part of the basic helix–loop–helix (bHLH) transcription factor (TF) family, acts as a key regulator of cold tolerance. Despite this, there is little information available about ICE genes in alfalfa. Therefore, we studied the function of ICE TFs in alfalfa. We identified 11 MsICE genes from the alfalfa genome and classified them into two groups. Analysis of the protein motif and gene structure revealed relatively high conservation among subgroups of the tightly clustered MsICE genes. Through synteny analysis, we detected duplication events in the MsICE gene family, suggesting that the ICE gene family was formed through fragment duplications. All the MsICE proteins were located in the nucleus according to subcellular localization predictions. The promoter cis-regulatory elements of MsICE genes are largely involved in light (Box 4), hormone (ABRE), and stress (MYB) responses. The MsICE01/MsICE07/MsICE09/MsICE10/MsICE11 genes contained MYB- and MYC-binding motifs, indicating an association with abiotic stress. The specific expression patterns of MsICE genes in leaves were revealed by examining their expression patterns in different tissues. These findings suggest that these genes may sense external environmental changes through leaves. Abiotic stress can cause striking upregulation of MsICE07 (PCA score: −4.03) and MsICE10 (PCA score: −4.05) expression. In this study, candidate genes associated with cold stress were identified, and subsequent molecular biological analyses allowed elucidation of the biological functions of these genes in alfalfa. This research provides a theoretical foundation for enhancing alfalfa yield and quality under cold conditions. [ABSTRACT FROM AUTHOR]

This study investigated the effects of chelidonic acid (CA) on hydrogen peroxide (H2O2) induced cellular senescence in human skin fibroblast cells (BJ). Cellular senescence is a critical mechanism that is linked to age-related diseases and chronic conditions. CA, a γ-pyrone compound known for its broad pharmacological activity, was assessed for its potential to mitigate oxidative stress and alter senescence markers. A stress-induced premature senescence (SIPS) model was designed in BJ fibroblast cells using the oxidative stress agent H2O2. After this treatment, cells were treated with CA, and the potential effect of CA on senescence was evaluated using senescence-related β-galactosidase, 4′,6-diamino-2-phenylindole (DAPI), acridine-orange staining (AO), comet assay, molecular docking assays, gene expression, and protein analysis. These results demonstrate that CA effectively reduces senescence markers, including senescence-associated β-galactosidase activity, DNA damage, lysosomal activity, and oxidative stress indicators such as malondialdehyde. Molecular docking revealed CA's potential interactions with critical proteins involved in senescence signalling pathways, suggesting mechanisms by which CA may exert its effects. Gene expression and protein analyses corroborated the observed anti-senescent effects, with CA modulating p16, p21, and pRB1 expressions and reducing oxidative stress markers. In conclusion, CA appeared to have senolytic and senomorphic potential in vitro, which could mitigate and reverse SIPS markers in BJ fibroblasts. [ABSTRACT FROM AUTHOR]

Chicken Parvovirus (ChPV) belongs to the genus Aveparvovirus and is implicated in enteric diseases like runting–stunting syndrome (RSS) in poultry. In RSS, chicken health is affected by diarrhea, depression, and increased mortality, causing significant economic losses in the poultry industry. This study aimed to characterize the ChPV genomes detected in chickens with RSS through a metagenomic approach and compare the molecular and evolutionary characteristics within the Aveparvovirus galliform1 species. The intestinal content of broiler flocks affected with RSS was submitted to viral metagenomics. The assembled prevalent genomes were identified as ChPV after sequence and phylogenetic analysis, which consistently clustered separately from Turkey Parvovirus (TuPV). The strain USP-574-A presented signs of genomic recombination. The selective pressure analysis indicated that most of the coding genes in A. galliform1 are evolving under diversifying (negative) selection. Protein modeling of ChPV and TuPV viral capsids identified high conservancy over the VP2 region. The prediction of epitopes identified several co-localized antigenic peptides from ChPV and TuPV, especially for T-cell epitopes, highlighting the immunological significance of these sites. However, most of these peptides presented host-specific variability, obeying an adaptive scenario. The results of this study show the evolutionary path of ChPV and TuPV, which are influenced by diversifying events such as genomic recombination and selective pressure, as well as by adaptation processes, and their subsequent immunological impact. [ABSTRACT FROM AUTHOR]

Background: The presence of contamination and microorganisms at any stage of processing renders a method unsafe, leading to a high risk of cross-transmission and cross-infection. Objective: The objective of this study was to assess the cleaning quality of aspirator instruments used in neurosurgical procedures. Methods: The experimental study was conducted at the materials and sterilization center, as well as the microbiology laboratory, of a philanthropic hospital in Brazil. A study protocol was implemented, which involved the analysis of 10 samples of Yasargil aspirators with varying dimensions. The samples were subjected to protein tests to detect the presence of organic matter and microbiological analysis. Descriptive statistics were used to analyze the data. Results: The results indicated that 40% of the instruments tested positive for protein after manual cleaning. Furthermore, after automated cleaning, samples showed an increased microbiological load, with Escherichia coli accounting for 20% and Klebsiella aerogenes for 10% of the identified microorganisms. Conclusion: This study provides evidence of failures in the cleaning process of healthcare products and highlights the presence of biofilm in the pipes, thereby compromising the drinking water quality standard. [ABSTRACT FROM AUTHOR]

Poly(ADP-ribose) polymerase 1 (PARP1) is a highly conserved nuclear protein in multicellular organisms that by modulating chromatin opening facilitates gene expression during development. All reported Parp1 null knockout mouse strains are viable with no developmental anomalies. It was believed that functional redundancy with other PARP family members, mainly PARP2, explains such a controversy. However, while PARP2 has similar catalytic domain to PARP1, it lacks other domains, making the absence of developmental problems in Parp1 mice knockouts unlikely. Contrary to prior assumptions, in our analysis of the best-investigated Parp1 knockout mouse strain, we identified persistent mRNA expression, albeit at reduced levels. Transcript analysis revealed an alternatively spliced Parp1 variant lacking exon 2. Subsequent protein analysis confirmed the existence of a truncated PARP1 protein in knockout mice. The decreased level of poly(ADP-ribose) (pADPr) was detected in Parp1 knockout embryonic stem (ES) cells with western blotting analysis, but immunofluorescence staining did not detect any difference in distribution or level of pADPr in nuclei of knockout ES cells. pADPr level in double Parp1 Parg mutant ES cells greatly exceeded its amount in normal and even in hypomorph Parg mutant ES cells, suggesting the presence of functionally active PARP1. Therefore, our findings challenge the conventional understanding of PARP1 depletion effects. [ABSTRACT FROM AUTHOR]

In a traditional Gaussian graphical model, data homogeneity is routinely assumed with no extra variables affecting the conditional independence. In modern genomic datasets, there is an abundance of auxiliary information, which often gets under-utilized in determining the joint dependency structure. In this article, we consider a Bayesian approach to model undirected graphs underlying heterogeneous multivariate observations with additional assistance from covariates. Building on product partition models, we propose a novel covariate-dependent Gaussian graphical model that allows graphs to vary with covariates so that observations whose covariates are similar share a similar undirected graph. To efficiently embed Gaussian graphical models into our proposed framework, we explore both Gaussian likelihood and pseudo-likelihood functions. For Gaussian likelihood, a G-Wishart distribution is used as a natural conjugate prior, and for the pseudo-likelihood, a product of Gaussian-conditionals is used. Moreover, the proposed model has large prior support and is flexible to approximate any ν-Hölder conditional variance-covariance matrices with ν ∈ (0 , 1 ] . We further show that based on the theory of fractional likelihood, the rate of posterior contraction is minimax optimal assuming the true density to be a Gaussian mixture with a known number of components. The efficacy of the approach is demonstrated via simulation studies and an analysis of a protein network for a breast cancer dataset assisted by mRNA gene expression as covariates. for this article are available online. [ABSTRACT FROM AUTHOR]

The integrity of the reconstructed human epidermis generated in vitro can be assessed using histological analyses combined with immunohistochemical staining of keratinocyte differentiation markers. Technical differences during the preparation and capture of stained images may influence the outcome of computational methods. Due to the specific nature of the analyzed material, no annotated datasets or dedicated methods are publicly available. Using a dataset with 598 unannotated images showing cross-sections of in vitro reconstructed human epidermis stained with DAB-based immunohistochemistry reaction to visualize four different keratinocyte differentiation marker proteins (filaggrin, keratin 10, Ki67, HSPA2) and counterstained with hematoxylin, we developed an unsupervised method for the detection and quantification of immunohistochemical staining. The pipeline consists of the following steps: (i) color normalization; (ii) color deconvolution; (iii) morphological operations; (iv) automatic image rotation; and (v) clustering. The most effective combination of methods includes (i) Reinhard's normalization; (ii) Ruifrok and Johnston color-deconvolution method; (iii) proposed image-rotation method based on boundary distribution of image intensity; and (iv) k-means clustering. The results of the work should enhance the performance of quantitative analyses of protein markers in reconstructed human epidermis samples and enable the comparison of their spatial distribution between different experimental conditions. [ABSTRACT FROM AUTHOR]

Lipid nanoparticles (LNPs) have successfully entered the clinic for the delivery of mRNA- and siRNA-based therapeutics, most recently as vaccines for COVID-19. Nevertheless, there is a lack of understanding regarding their in vivo behavior, in particular cell targeting. Part of this LNP tropism is based on the adherence of endogenous protein to the particle surface. This protein forms a so-called corona that can change, amongst other things, the circulation time, biodistribution and cellular uptake of these particles. The formation of this protein corona, in turn, is dependent on the nanoparticle properties (e.g., size, charge, surface chemistry and hydrophobicity) as well as the biological environment from which it is derived. With the potential of gene therapy to target virtually any disease, administration sites other than intravenous route are considered, resulting in tissue specific protein coronas. For neurological diseases, intracranial administration of LNPs results in a cerebral spinal fluid derived protein corona, possibly changing the properties of the lipid nanoparticle compared to intravenous administration. Here, the differences between plasma and CSF derived protein coronas on a clinically relevant LNP formulation were studied in vitro. Protein analysis showed that LNPs incubated in human CSF (C-LNPs) developed a protein corona composition that differed from that of LNPs incubated in plasma (P-LNPs). Lipoproteins as a whole, but in particular apolipoprotein E, represented a higher percentage of the total protein corona on C-LNPs than on P-LNPs. This resulted in improved cellular uptake of C-LNPs compared to P-LNPs, regardless of cell origin. Importantly, the higher LNP uptake did not directly translate into more efficient cargo delivery, underlining that further assessment of such mechanisms is necessary. These findings show that biofluid specific protein coronas alter LNP functionality, suggesting that the site of administration could affect LNP efficacy in vivo and needs to be considered during the development of the formulation. Schematic representation of the protein corona formation, isolation and characterization protocol. [Display omitted] • Unique protein coronas develop on the surface of lipid nanoparticles after exposure to human plasma or cerebrospinal fluid. • Biofluid specific protein coronas affect lipid nanoparticle performance and influence their uptake by cells in vitro in time. • Biofluid specific protein coronas affect lipid nanoparticle delivery efficiency of cargo siRNA to cells in vitro. • Lipid nanoparticle uptake is not a predictor for siRNA transfection efficiency in vitro • Difference in Apolipoprotein content in cerebrospinal fluid and plasma could affect lipid nanoparticle performance in vitro. [ABSTRACT FROM AUTHOR]

This work was devoted to a study of the composition of protein concentrates from amaranth grain (Amaranthus hypochondriacus L.) of variety Voronezh. Amaranth protein concentrates were obtained by alkaline extraction of proteins and neutralization of the solution followed by ultrafiltration, by separating the starch fraction with amylolytic enzymes, and by alkaline extraction of proteins and their precipitation at pH 4.5. Conditions for the extraction of proteins followed by chromatography–mass spectrometric analysis and identification were selected. It was found that proteins from amaranth grain were more effectively extracted with a buffer with urea at protein concentrations of 1.7, 1.9, and 2.9 mg/cm3 in solution, respectively, while a buffer with detergents was more effective for the extraction of low-molecular-weight proteins at protein concentrations of 4.9, 2.9, and 9.0 mg/cm3 in solution, respectively. As a result of HPLC–MS/MS analysis followed by identification and search in the UNIPROT database, it was established that the main protein of amaranth grain is 11S-globulin, which acts as a reserve protein of amaranth seeds. In amaranth concentrates, 14 unique proteins belonging only to A. hipochondriacus L. were identified, and also proteins that did not belong to this species were reliably identified. Based on the results of semiquantitative analysis of the peptide profile of amaranth grain protein concentrates, a high frequency of occurrence of the main 11S-globulin proteins was established in all samples. The frequency of occurrence of other proteins in samples obtained by different methods differed significantly due to the peculiarities of protein isolation from amaranth grain. The results obtained can be used to prepare plant protein concentrates with a given protein composition. [ABSTRACT FROM AUTHOR]

Nanoparticles are increasingly implemented in biomedical applications, including the diagnosis and treatment of disease. When exposed to complex biological media, nanoparticles spontaneously interact with their surrounding environment, leading to the surface-adsorption of small and bio- macromolecules- termed the "corona". Corona composition is governed by nanoparticle properties and incubation parameters. While the focus of most studies is on the protein signature of the nanoparticle corona, the impact of experimental protocols on nanoparticle size in the presence of complex biological media, and the impact of nanoparticle recovery from biological media has not yet been reported. Here using a non-degradable robust model, we show how centrifugation-resuspension protocols used for the isolation of nanoparticles from incubation media, incubation duration and shear flow conditions alter nanoparticle parameters including particle size, zeta potential and total protein content. Our results show significant changes in nanoparticle size following exposure to media containing protein under different flow conditions, which also altered the composition of surface-adsorbed proteins profiled by SDS-PAGE. Our in situ analysis of nanoparticle size in media containing protein using particle tracking analysis highlights that centrifugation-resuspension is disruptive to agglomerates that are spontaneously formed in protein containing media, highlighting the need for in situ analytical methods that do not alter the intermediates formed following nanoparticle exposure to biological media. Nanomedicines are mostly intended for parenteral administration, and our findings show that parameters such as shear flow can significantly alter nanoparticle physicochemical parameters. Overall, we show that the centrifugation-resuspension isolation of nanoparticles from media significantly alters particle parameters in addition to the overall protein composition of surface-adsorbed proteins. We recommend that nanoparticle characterization pipelines studying bio-nano interactions during early nanomedicine development consider biologically-relevant shear flow conditions and media composition that can significantly alter particle physical parameters and subsequent conclusions from these studies. [Display omitted] • We investigate the impact of protein corona experimental pipelines on particle colloid stability. • We show that physiologically relevant flow conditions alter nanoparticle parameters. • Using a model system, we demonstrate that more gentle separation or in situ techniques are needed for analysis of the nanoparticle protein corona. [ABSTRACT FROM AUTHOR]

Six new complexes (1–6), [Ru(η6‐p‐cymene)(FA)Cl] (1), [Ru(η6‐p‐cymene)(PA)Cl] (2), [Ru(η6‐p‐cymene)(SA)Cl] (3), [Ru(η6‐p‐cymene)(FA)PPh3]Cl (4), [Ru(η6‐p‐cymene)(PA)PPh3]Cl (5), [Ru(η6‐p‐cymene)(SA)PPh3]Cl(6), [HFA = ferulic acid, HPA = p‐coumaric acid, HSA = sinapinic acid], were synthesized and well characterized by various spectroscopic, analytical techniques and computational studies. Amongst these six complexes, complexes 4, 5, and 6 were found to be selectively cytotoxic toward melanoma (A375) cell lines and were non‐cytotoxic toward non‐cancerous cell lines (HEK 293 T). Further investigation on the probable bio‐molecular interaction mechanisms revealed that all the complexes show strong groove binding interactions with the DNA, however, complexes 3, 4 and 3, 6 show strong interaction with BSA and HSA, respectively. Through Hoechst staining it can be elucidated that complexes 4–6 cause characteristic apoptotic nuclear changes in the cells indicating apoptosis as the cell death mechanism caused by complexes 4–6. To further confirm the cell death mechanism, protein expression analysis was done through western blotting, which showed a decrease in anti‐apoptotic protein (Bcl‐xL) expression and increased pro‐apoptotic protein (PARP) expression, which confirms the cell death by apoptosis. Using DCFDA staining, we observed that complexes 4, 5, and 6 produced more ROS in the cells, which also might be the cause of cell death by the complexes. Along with that the complexes show enhanced anti‐migratory abilities depicted through wound healing assay. [ABSTRACT FROM AUTHOR]

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Profile mixture models capture distinct biochemical constraints on the amino acid substitution process at different sites in proteins. These models feature a mixture of time-reversible models with a common matrix of exchangeabilities and distinct sets of equilibrium amino acid frequencies known as profiles. Combining the exchangeability matrix with each profile generates the matrix of instantaneous rates of amino acid exchange for that profile. Currently, empirically estimated exchangeability matrices (e.g. the LG matrix) are widely used for phylogenetic inference under profile mixture models. However, these were estimated using a single profile and are unlikely optimal for profile mixture models. Here, we describe the GTRpmix model that allows maximum likelihood estimation of a common exchangeability matrix under any profile mixture model. We show that exchangeability matrices estimated under profile mixture models differ from the LG matrix, dramatically improving model fit and topological estimation accuracy for empirical test cases. Because the GTRpmix model is computationally expensive, we provide two exchangeability matrices estimated from large concatenated phylogenomic-supermatrices to be used for phylogenetic analyses. One, called Eukaryotic Linked Mixture (ELM), is designed for phylogenetic analysis of proteins encoded by nuclear genomes of eukaryotes, and the other, Eukaryotic and Archaeal Linked mixture (EAL), for reconstructing relationships between eukaryotes and Archaea. These matrices, combined with profile mixture models, fit data better and have improved topology estimation relative to the LG matrix combined with the same mixture models. Starting with version 2.3.1, IQ-TREE2 allows users to estimate linked exchangeabilities (i.e. amino acid exchange rates) under profile mixture models. [ABSTRACT FROM AUTHOR]

A nanoliter liquid chromatography–high resolution mass spectrometry-based method was developed for quantitative proteomics analysis of COVID-19 vaccines. It can be used for simultaneous qualitative and quantitative analysis of target proteins and host cell proteins (HCPs) in vaccine samples. This approach can directly provide protein information at the molecular level. Based on this, the proteomes of 15 batches of COVID-19 inactivated vaccine samples from two companies and 12 batches of COVID-19 recombinant protein vaccine samples from one company were successfully analyzed, which provided a significant amount of valuable information. Samples produced in different batches or by different companies can be systematically contrasted in this way, offering powerful supplements for existing quality standards. This strategy paves the way for profiling proteomics in complex samples and provides a novel perspective on the quality evaluation of bio-macromolecular drugs. [ABSTRACT FROM AUTHOR]

Soybean (Glycine max (L.) Merr.) is one of the important oilseed crops that is widely cultivated around the world. It has a high amount of protein content as well as other essential vitamins that are important in our daily lives. For continuous improvement, the development of novel plant species that are resistant to biotic and abiotic stress using effective genetic diversity strategies is important. In the current study, a total of 25 diverse genotypes of soybean using 21 important agro morphological traits were studied. For qualitative traits significant level of variation was found for most of the traits. For quantitative traits, the highest coefficient of variance 32.74% was found for days to flower initiation, followed by days to flower completion 29.62%, while the lowest was found for a number of pods/plants 2.96%. Based on cluster analysis, all the genotypes were separated into two groups at 25% distance and further subdivided at 75% distance, where the genotypes NARC-2 and SWAT-84 were found the most diverse. The cluster three genotypes were found to have early mature genotypes (89 ± 2.44). Based on a number of pods/plant and yield per plant, the cluster 4 genotypes were found to have a maximum number of pods/plant (98.26 ± 32.10), and (38.66 ± 6.85). Among the studied genotypes the highest grain yield (49 g) was produced by genotype C/B 28, whereas the lowest (14.56 g) was observed for C/B 7. Principal component analysis with an eigenvalue of 1.48 accounted for the total variation of 67.73%. The total seed storage proteins analysis resulted in 13 bands, and the molecular weight ranged from 15 to 170 kDa. Two-way cluster analysis was performed and all the populations were divided into two main lineages at 25% distance and further sub divided into six subgroups at distance of a 75%, where the genotypes NARC-2 and SWAT-84 were found the most diverse genotypes. These findings provide a basis for developing elite, locally adapted soybean genotypes as well as implications for understanding the diversity and relationships among these diverse Glycine max genotypes. [ABSTRACT FROM AUTHOR]

Waters polluted with Pb and Cd have a negative impact on the environment. Padina australis grows abundantly on the coast of Palang Subdistrict, Tuban, and the local community consumes it. Macroalgae as food must be free of metal contamination. This study aims to determine the impact of Pb and Cd bioaccumulation on P. australis. Sampling was conducted at two stations, including Station I, Panyuran Village, and Station II, Glodog Village. Analysis of Pb and Cd metal levels using Atomic Absorption Spectrophotometry (AAS). Analysis of protein content using the Kjeldahl method. The data obtained was analyzed with Principle Component Analysis (PCA). The results of the analysis of Pb and Cd levels in P. australis at station II, which are 0.200 ± 0.028 and 0.021 ± 0.004 mg.kg-1 higher than station I, which are 0.194 ± 0.015 and 0.010 ± 0.001 mg.kg-1. The protein content of P. australis at station I was 4.713 ± 0.508 mg.kg-1, and at station II was 5.900 ± 0.928 mg.kg-1. This shows that P. australis is still considered good for consumption even though it has been polluted and contains Pb and Cd metals. P. australis can tolerate and does not experience severe physiological damage so it has the potential as a heavy metal phytoremediator. [ABSTRACT FROM AUTHOR]

With the rapid development of NGS technology, the number of protein sequences has increased exponentially. Computational methods have been introduced in protein functional studies because the analysis of large numbers of proteins through biological experiments is costly and time-consuming. In recent years, new approaches based on deep learning have been proposed to overcome the limitations of conventional methods. Although deep learning-based methods effectively utilize features of protein function, they are limited to sequences of fixed-length and consider information from adjacent amino acids. Therefore, new protein analysis tools that extract functional features from proteins of flexible length and train models are required. We introduce DeepPI, a deep learning-based tool for analyzing proteins in large-scale database. The proposed model that utilizes Global Average Pooling is applied to proteins of flexible length and leads to reduced information loss compared to existing algorithms that use fixed sizes. The image generator converts a one-dimensional sequence into a distinct two-dimensional structure, which can extract common parts of various shapes. Finally, filtering techniques automatically detect representative data from the entire database and ensure coverage of large protein databases. We demonstrate that DeepPI has been successfully applied to large databases such as the Pfam-A database. Comparative experiments on four types of image generators illustrated the impact of structure on feature extraction. The filtering performance was verified by varying the parameter values and proved to be applicable to large databases. Compared to existing methods, DeepPI outperforms in family classification accuracy for protein function inference. [ABSTRACT FROM AUTHOR]

Group A rotaviruses (RVAs) are the most common etiological agents of severe acute diarrhea among children under 5 years old worldwide. At present, two live-attenuated RVA vaccines, LLR (G10P[15]) and RotaTeq (G1–G4, G6 P[8], P [5]), have been introduced to mainland China. Although RVA vaccines can provide homotypic and partially heterotypic protection against several strains, it is necessary to explore the genetic and antigenic variations between circulating RVAs and vaccine strains. In this study, we sequenced viral protein VP7 and VP4 outer capsid proteins of 50 RVA strains circulating in China from 2016 to 2019. The VP7 and VP4 sequences of almost all strains showed high homology to those of previously reported human strains and vaccine strains of the same genotype. However, in the presumed antigenic epitopes of the VP7 and VP4, multiple amino acid variations were found, regardless of the G and P genotypes of these strains. Moreover, all circulating G3 RVA strains in China potentially possess an extra N-linked glycosylation site compared with the G3 strain of RotaTeq. The potential N-linked glycosylation site at residues 69–71 was found in all G9 strains in China but not in the G9 strain of the Rotavac or Rotasill vaccine. These variations in antigenic sites might result in the selection of strains that escape the RVA neutralizing-antibody pressure imposed by vaccines. Furthermore, the G4 and P[6] genotypes in this study showed high homology to those of porcine strains, indicating the transmission of G4 and P [6] genotypes from pigs to humans in China. More genetic surveillance with antigenic evaluation in prevalent RVAs is necessary for developing and implementing rotavirus vaccines in China. [ABSTRACT FROM AUTHOR]

Pseudocontact shifts (PCS) generated by paramagnetic lanthanide ions deliver powerful restraints for protein structure analysis by NMR spectroscopy. We present a new lanthanide tag that generates different PCSs than that of a related tag, which differs in structure by a single oxygen atom. It is highly reactive towards cysteine and performs well in turn-on luminescence and in EPR spectroscopy. [ABSTRACT FROM AUTHOR]

Hodgkin lymphoma (HL) is a rare lymphoid neoplasm in which Hodgkin/Reed–Stenberg (HRS) cells are admixed with a population of non-neoplastic inflammatory cells and fibrosis. Dysregulated expressions of cell cycle regulators and transcription factors have been proven as one of the hallmarks of HL. In that context, SATB1 and p16 have been reported as potential regulators of HL progression and survival. However, to date, no studies have assessed the expression levels of SATB1 and p16 in HL in Croatian patients or their prognostic values. Therefore, we investigated the expression pattern of SATB1 and p16 in paraffin-embedded lymph node biopsies using standard immunohistochemistry. We found that 21% of the patients stained positive for SATB1, while 15% of the patients displayed positive staining for p16. Furthermore, we aimed to understand the prognostic value of each protein through the analysis of the overall survival (OS) and progression-free survival (PFS). SATB1 showed a significantly positive correlation with better OS and PFS, while p16 expression had no impact. Interestingly, when patients were stratified by a combination of the two studied markers, we found that patients in the SATB1+/p16- group tended to have the best prognosis in HL, according to statistical significance. In conclusion, SATB1 and p16 might be potentially useful as diagnostic and prognostic markers for HL. [ABSTRACT FROM AUTHOR]

Serial capture affinity purification (SCAP) is a powerful method to isolate a specific protein complex. When combined with cross-linking mass spectrometry and computational approaches, one can build an integrated structural model of the isolated complex. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone reader that recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to a previous SCAP analysis of the SPIN1:SPINDOC complex, histones and the H3K4me3 mark were enriched with the WDR76:SPIN1 complex. Next, interaction network analysis of copurifying proteins and microscopy analysis revealed a potential role of the WDR76:SPIN1 complex in the DNA damage response. Since we detected 149 pairs of cross-links between WDR76, SPIN1, and histones, we then built an integrated structural model of the complex where SPIN1 recognized the H3K4me3 epigenetic mark while interacting with WDR76. Finally, we used the powerful Bayesian Integrative Modeling approach as implemented in the Integrative Modeling Platform to build a model of WDR76 and SPIN1 bound to the nucleosome. [ABSTRACT FROM AUTHOR]

Background: Oculocutaneous albinism (OCA) is a genetically heterogeneous condition that is associated with reduced or absent melanin pigment in the skin, hair, and eyes, resulting in reduced vision, high sensitivity to light, and rapid and uncontrolled eye movements. To date, seventeen genes have been associated with OCA including syndromic and non-syndromic forms of the condition. Methods: Whole exome sequencing (WES) was performed to identify pathogenic variants in nine Pakistani families with OCA, with validation and segregation of candidate variants performed using Sanger sequencing. Furthermore, the pathogenicity of the identified variants was assessed using various in-silico tools and 3D protein structural analysis software. Results: WES identified biallelic variants in three genes explaining the OCA in these families, including four variants in TYR, three in OCA2, and two in HPS1, including two novel variants c.667C > T: p.(Gln223*) in TYR, and c.2009 T > C: p.(Leu670Pro) in HPS1. Conclusions: Overall, this study adds further knowledge of the genetic basis of OCA in Pakistani communities and facilitates improved management and counselling services for families suffering from severe genetic diseases in Pakistan. [ABSTRACT FROM AUTHOR]

Neuroendocrine tumors are a heterogeneous group of tumors located mainly in the gastrointestinal tract or the respiratory system. We aimed to determine the concentrations of IGF-1R, ERK2, and EGFR using the ELISA method in serum samples from patients with NETs and from a control group. Results were evaluated with the selected demographic, clinicopathological, and biochemical characteristics. The analyses performed on a group of patients (80 in the study group and 62 in the control group) showed that the concentration of EGFR in patients with neuroendocrine tumors was significantly higher (p < 0.001) compared to the control group. Additionally, a significantly higher (p < 0.001) EGFR concentration was found in GEP-NET. Our results indicate that impaired EGFR signaling pathways are important in the context of neuroendocrine tumors. The data presented are a good starting point for further analysis of these proteins. [ABSTRACT FROM AUTHOR]

Introduction: Alzheimer pathology (AD) is characterized by the deposition of amyloid beta (Aβ) and chronic neuroinflammation, with the NLRP3 inflammasome playing a significant role. This study demonstrated that the OCD drug fluvoxamine maleate (FXN) can potently ameliorate AD pathology in 5XFAD mice by promoting autophagy-mediated clearance of Aβ and inhibiting the NLRP3 inflammasome. Methods: We used mice primary astrocytes to establish the mechanism of action of FXN against NLRP3 inflammasome by using various techniques like ELISA, Western blotting, confocal microscopy, Immunofluorescence, etc. The anti-AD activity of FXN was validated in transgenic 5XFAD mice following two months of treatment. This was followed by behavior analysis, examination of inflammatory and autophagy proteins and immunohistochemistry analysis for Aβ load in the hippocampi. Results: Our data showed that FXN, at a low concentration of 78 nM, induces autophagy to inhibit NF-κB and the NLRP3 inflammasome, apart from directly inhibiting NLRP3 inflammasome in primary astrocytes. FXN activated the PRKAA2 pathway through CAMKK2 signaling, leading to autophagy induction. It inhibited the ATP-mediated NLRP3 inflammasome activation by promoting the autophagic degradation of NF-κB, resulting in the downregulation of pro-IL-1β and NLRP3. The anti-NLRP3 inflammasome effect of FXN was reversed when autophagy was inhibited by either genetic knockdown of the PRKAA2 pathway or pharmacological inhibition with bafilomycin A1. Furthermore, FXN treatment led to improved AD pathology in 5XFAD mice, resulting in significant improvements in various behavioral parameters such as working memory and neuromuscular coordination, making their behavior more similar to that of wild-type animals. FXN improved behavior in 5XFAD mice by clearing the Aβ deposits from the hippocampi and significantly reducing multiple inflammatory proteins, including NF-κB, GFAP, IBA1, IL-1β, TNF-α, and IL-6, which are associated with NF-κB and NLRP3 inflammasome in the brain. Moreover, these changes were accompanied by increased expression of autophagic proteins. Discussion: Our data suggest that FXN ameliorates AD pathology, by simultaneously targeting two key pathological features: Aβ deposits and neuroinflammation. As an already approved drug, FXN holds potential as a candidate for human studies against AD. [ABSTRACT FROM AUTHOR]

The dynamic evolution of SARS‐CoV‐2 variants necessitates ongoing advancements in therapeutic strategies. Despite the promise of monoclonal antibody (mAb) therapies like bebtelovimab, concerns persist regarding resistance mutations, particularly single‐to‐multipoint mutations in the receptor‐binding domain (RBD). Our study addresses this by employing interface‐guided computational protein design to predict potential bebtelovimab‐resistance mutations. Through extensive physicochemical analysis, mutational preferences, precision‐recall metrics, protein–protein docking, and energetic analyses, combined with all‐atom, and coarse‐grained molecular dynamics (MD) simulations, we elucidated the structural‐dynamics‐binding features of the bebtelovimab–RBD complexes. Identification of susceptible RBD residues under positive selection pressure, coupled with validation against bebtelovimab‐escape mutations, clinically reported resistance mutations, and viral genomic sequences enhances the translational significance of our findings and contributes to a better understanding of the resistance mechanisms of SARS‐CoV‐2. [ABSTRACT FROM AUTHOR]

Histone H3 lysine36 dimethylation (H3K36me2) is generally distributed in the gene body and euchromatic intergenic regions. However, we found that H3K36me2 is enriched in pericentromeric heterochromatin in some mouse cell lines.We here revealed the mechanism of heterochromatin targeting of H3K36me2. Among several H3K36 methyltransferases, NSD2 was responsible for inducing heterochromatic H3K36me2. Depletion and overexpression analyses of NSD2-associating proteins revealed that NSD2 recruitment to heterochromatin was mediated through the imitation switch (ISWI) chromatin remodeling complexes, such as BAZ1B-SMARCA5 (WICH), which directly binds to AT-rich DNA via a BAZ1B domain-containing AT-hook-like motifs. The abundance and stoichiometry of NSD2, SMARCA5, and BAZ1B could determine the localization of H3K36me2 in different cell types. In mouse embryos, H3K36me2 heterochromatin localization was observed at the two- to four-cell stages, suggesting its physiological relevance. [ABSTRACT FROM AUTHOR]

Veno-occlusive disease with immunodeficiency (VODI) syndrome is a rare genetic disorder characterized by immune system irregularities and a significant mortality rate, despite its infrequency. SP110, situated on chromosome 2q37.1, plays a pivotal role in VODI syndrome, and its association with tuberculosis has been extensively studied. The identification of SP110 mutations holds promise for accelerating the diagnosis and treatment of VODI syndrome, by providing a comprehensive panel for diagnosis and potentially leading to targeted therapies. In this case study, we examined a three-year-old girl born to a consanguineous union who was suspected of having an immunodeficiency disorder. Whole-exome sequencing (WES) and clinical assessments were conducted to screen for and confirm potentially pathogenic mutations. The detected mutation was further analyzed using bioinformatics tools to forecast its impact on protein structure. WES analysis revealed a novel deletion-insertion mutation, c.1181-1182delAGinsT, within SP110. Protein analysis indicated substantial structural modifications in the SP110 protein. This study identified a novel deletion-insertion mutation as a potential contributor to VODI syndrome by affecting the functionality of the SP110 protein. By including various mutations associated with the SP110 gene, this study aimed to expedite diagnosis by creating a comprehensive panel for VODI syndrome. [ABSTRACT FROM AUTHOR]

Proteins have evolved through mutations—amino acid substitutions—since life appeared on Earth, some 109 years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function, and structure. This study offers a new viewpoint on how the most recent findings in these areas can be used to explore the impact of mutations on protein sequence, stability, and evolvability. Preliminary results indicate that: (1) mutations can be viewed as sensitive probes to identify 'typos' in the amino-acid sequence, and also to assess the resistance of naturally occurring proteins to unwanted sequence alterations; (2) the presence of 'typos' in the amino acid sequence, rather than being an evolutionary obstacle, could promote faster evolvability and, in turn, increase the likelihood of higher protein stability; (3) the mutation site is far more important than the substituted amino acid in terms of the marginal stability changes of the protein, and (4) the unpredictability of protein evolution at the molecular level—by mutations—exists even in the absence of epistasis effects. Finally, the Darwinian concept of evolution "descent with modification" and experimental evidence endorse one of the results of this study, which suggests that some regions of any protein sequence are susceptible to mutations while others are not. This work contributes to our general understanding of protein responses to mutations and may spur significant progress in our efforts to develop methods to accurately forecast changes in protein stability, their propensity for metamorphism, and their ability to evolve. [ABSTRACT FROM AUTHOR]

Primary aldosteronism is a common clinical syndrome in hypertensive patients. Early identification and timely treatment of primary aldosteronism are of great significance to improve the prognosis of patients. Endothelial dysfunction is currently considered an important potential pathological change in primary aldosteronism. In this study, we observed that the levels of von Willebrand factor and soluble intercellular adhesion molecule-1 were significantly elevated in primary aldosteronism and were closely associated with pathological progression. Von Willebrand factor and soluble intercellular adhesion molecule-1 are important adhesion factors in blood, and their levels are directly related to blood viscosity. Meanwhile, both markers showed excellent efficacy in diagnosing primary aldosteronism in hypertensive patients. Additionally, an inverse correlation of soluble intercellular adhesion molecule-1 and primary aldosteronism with the nutritional protein levels of primary aldosteronism patients was identified, which also confirms the promising potential of von Willebrand factor and soluble intercellular adhesion molecule-1 for dynamic nutritional status assessment in primary aldosteronism. These findings are of great significance for the future clinical diagnosis and treatment of primary aldosteronism. [ABSTRACT FROM AUTHOR]

• Tandem mass tag technology was an effective technique for analyzing the expression of salt-tolerant differential proteins in purslane. • Salt-tolerance in purslane might be closely related with specific protein expression in carbohydrate metabolism pathway. • Different with salt-sensitive genotype, up-regulation of many ribosomal proteins and lipid transfer-like protein, and down-regulation of relatively few photosynthesis related proteins, might be the important reason of salt-tolerance in salt-resistant purslane genotype. Proteomics serves as a crucial method for elucidating plant stress resistance mechanisms under environmental pressures. Purslane (Portulaca oleracea), valued for its medicinal, edible, and halophytic properties, holds significant nutritional importance with diverse applications. Despite its importance, limited studies have explored the salt tolerance mechanisms in purslane. Differential protein expression in two purslane genotypes ('PL' and 'LCL') under NaCl stress were analyzed using tandem mass tag technology. The function of differentially expressed proteins was analyzed using bioinformatics tools. According to KEGG and COG analysis, carbohydrate metabolism and lipid metabolism were the most important metabolite pathways in purslane under salt stress. Compared with control, 48 up-regulated and 43 down-regulated proteins in 'PL' and 22 up-regulated and 26 down-regulated proteins in 'LCL' were found under 72 h of 200 mM NaCl stress. Six proteins were up-regulated and six down-regulated in both genotypes due to salt stress. Among them, four up-regulated proteins and two down-regulated proteins were related to carbohydrate metabolism. Specific protein expressions in carbohydrate metabolism pathway may be the vital reason of salt-tolerance in purslane. The differential protein expression in two purslane genotypes under salt stress unveiled significant up-regulation of seven proteins belonging to the ribosomal protein family, along with two non-specific lipid-transfer proteins and two lipid transfer-like proteins in the 'PL' genotype. Additionally, the down-regulation of relatively few photosynthesis-related proteins were observed in the 'PL' genotype. Differential expression of these proteins might be associated with the salt tolerance in the salt-tolerant variety. [ABSTRACT FROM AUTHOR]

Background: The natural history and pathophysiology of diverticular disease (DD) are still uncertain. An ex‐vivo human complicated DD (cDD) model has recently shown a predominant transmural oxidative imbalance. The present study aims to evaluate whether the previously described alterations may precede the symptomatic form of the disease. Methods: Colonic surgical samples obtained from patients with asymptomatic diverticulosis (DIV), complicated DD, and controls were systematically and detailed morphologically and molecularly analyzed. Therefore, histologic, histomorphometric, immunohistochemical evaluation, and gene and protein expression analysis were performed to characterize colonic muscle changes and evaluate chronic inflammation, oxidative imbalance, and hypoxia. Functional muscle activity was tested on strips and isolated cells in response to contractile and relaxant agents. Key Results: Compared with controls, DD showed a marketed increase in muscle layer thickness, smooth muscle cell syncytium disarray, and increased interstitial fibrosis; moreover, the observed features were more evident in the cDD group. These changes mainly affected longitudinal muscle and were associated with altered contraction‐relaxation dynamics and fibrogenic switch of smooth muscle cells. Chronic lymphoplasmacytic inflammation was primarily evident in the mucosa and spared the muscle. A transmural increase in carbonylated and nitrated proteins, with loss of antioxidant molecules, characterized both stages of DD, suggesting early oxidative stress probably triggered by recurrent ischemic events, more pronounced in cDD, where HIF‐1 was detected in both muscle and mucosa. Conclusion & Inferences: The different DD clinical scenarios are part of a progressive process, with oxidative imbalance representing a new target in the management of DD. [ABSTRACT FROM AUTHOR]