Major royal-jelly proteins intake modulates immune functions and gut microbiota in mice

In this study,we investigated the effects of major royal jelly proteins(MRJPs)on the estrogen,gut microbiota,and immunological responses in mice.Mice given 250 or 500 mg/kg,not 125 mg/kg of MRJPs,enhanced the proliferation of splenocytes in response to mitogens.The splenocytes and mesenteric lymphocytes activated by T-cell mitogens(Con A and anti-CD3/CD28 antibodies)released high levels of IL-2 but low levels of IFN-γand IL-17A.The release of IL-4 was unaffected by MRJPs.Additionally,splenocytes and mesenteric lymphocytes activated by LPS were prevented by MRJPs at the same dose as that required for producing IL-1βand IL-6,two pro-inflammatory cytokines.The production of IL-1β,IL-6,and IFN-γwas negatively associated with estrogen levels,which were higher in the MRJP-treated animals than in the control group.Analysis of the gut microbiota revealed that feeding mice 250 mg/kg of MRJPs maintained the stability of the natural intestinal microflora of mice.Additionally,the LEf Se analysis identified biomarkers in the MRJP-treated mice,including Prevotella,Bacillales,Enterobacteriales,Gammaproteobacteria,Candidatus_Arthromitus,and Shigella.Our results showed that MRJPs are important components of royal jelly that modulate host immunity and hormone levels and help maintain gut microbiota stability.

Essential proteins identification method based on four-order distances and subcellular localization information

Essential proteins are inseparable in cell growth and survival. The study of essential proteins is important for understanding cellular functions and biological mechanisms. Therefore, various computable methods have been proposed to identify essential proteins. Unfortunately, most methods based on network topology only consider the interactions between a protein and its neighboring proteins, and not the interactions with its higher-order distance proteins. In this paper, we propose the DSEP algorithm in which we integrated network topology properties and subcellular localization information in protein–protein interaction(PPI) networks based on four-order distances, and then used random walks to identify the essential proteins. We also propose a method to calculate the finite-order distance of the network, which can greatly reduce the time complexity of our algorithm. We conducted a comprehensive comparison of the DSEP algorithm with 11 existing classical algorithms to identify essential proteins with multiple evaluation methods. The results show that DSEP is superior to these 11 methods.

Interplay between the glymphatic system and neurotoxic proteins in Parkinson’s disease and related disorders:current knowledge and future directions

Parkinson’s disease is a common neurodegenerative disorder that is associated with abnormal aggregation and accumulation of neurotoxic proteins,includingα-synuclein,amyloid-β,and tau,in addition to the impaired elimination of these neurotoxic protein.Atypical parkinsonism,which has the same clinical presentation and neuropathology as Parkinson’s disease,expands the disease landscape within the continuum of Parkinson’s disease and related disorders.The glymphatic system is a waste clearance system in the brain,which is responsible for eliminating the neurotoxic proteins from the interstitial fluid.Impairment of the glymphatic system has been proposed as a significant contributor to the development and progression of neurodegenerative disease,as it exacerbates the aggregation of neurotoxic proteins and deteriorates neuronal damage.Therefore,impairment of the glymphatic system could be considered as the final common pathway to neurodegeneration.Previous evidence has provided initial insights into the potential effect of the impaired glymphatic system on Parkinson’s disease and related disorders;however,many unanswered questions remain.This review aims to provide a comprehensive summary of the growing literature on the glymphatic system in Parkinson’s disease and related disorders.The focus of this review is on identifying the manifestations and mechanisms of interplay between the glymphatic system and neurotoxic proteins,including loss of polarization of aquaporin-4 in astrocytic endfeet,sleep and circadian rhythms,neuroinflammation,astrogliosis,and gliosis.This review further delves into the underlying pathophysiology of the glymphatic system in Parkinson’s disease and related disorders,and the potential implications of targeting the glymphatic system as a novel and promising therapeutic strategy.

Exploration of cyclooxygenase-2 inhibitory peptides from walnut dreg proteins based on in silico and in vitro analysis

Walnut dreg protein hydrolysates(WDPHs)exhibit a variety of biological activities,however,the cyclooxygenase-2(COX-2)inhibitory peptide of WDPHs remain unclear.The aim of this study was to rapidly screen for such peptides in WDPHs through a combination of in silico and in vitro analysis.In total,1262 peptide sequences were observed by nano liquid chromatography/tandem mass spectrometry(nano LC-MS/MS)and 4 novel COX-2 inhibitory peptides(AGFP,FPGA,LFPD,and VGFP)were identified.Enzyme kinetic data indicated that AGFP,FPGA,and LFPD displayed mixed-type COX-2 inhibition,whereas VGFP was a non-competitive inhibitor.This is mainly because the peptides form hydrogen bonds and hydrophobic interactions with residues in the COX-2 active site.These results demonstrate that computer analysis combined with in vitro evaluation allows for rapid screening of COX-2 inhibitory peptides in walnut protein dregs.

Prognosis value of heat-shock proteins in esophageal and esophagogastric cancer:A systematic review and meta-analysis

BACKGROUND Heat shock proteins(HSPs)are molecular chaperones that play an important role in cellular protection against stress events and have been reported to be overex-pressed in many cancers.The prognostic significance of HSPs and their regulatory factors,such as heat shock factor 1(HSF1)and CHIP,are poorly understood.AIM To investigate the relationship between HSP expression and prognosis in esophageal and esophagogastric cancer.METHODS A systematic review was conducted in accordance with PRISMA recommend-ations(PROSPERO:CRD42022370653),on Embase,PubMed,Cochrane,and LILACS.Cohort,case-control,and cross-sectional studies of patients with eso-phagus or esophagogastric cancer were included.HSP-positive patients were compared with HSP-negative,and the endpoints analyzed were lymph node metastasis,tumor depth,distant metastasis,and overall survival(OS).HSPs were stratified according to the HSP family,and the summary risk difference(RD)was calculated using a random-effect model.RESULTS The final selection comprised 27 studies,including esophageal squamous cell carcinoma(21),esophagogastric adenocarcinoma(5),and mixed neoplasms(1).The pooled sample size was 3465 patients.HSP40 and 60 were associated with a higher 3-year OS[HSP40:RD=0.22;95%confidence interval(CI):0.09-0.35;HSP60:RD=0.33;95%CI:0.17-0.50],while HSF1 was associated with a poor 3-year OS(RD=-0.22;95%CI:-0.32 to-0.12).The other HSP families were not associated with long-term survival.HSF1 was associated with a higher probability of lymph node metastasis(RD=-0.16;95%CI:-0.29 to-0.04).HSP40 was associated with a lower probability of lymph node dissemination(RD=0.18;95%CI:0.03-0.33).The expression of other HSP families was not significantly related to tumor depth and lymph node or distant metastasis.CONCLUSION The expression levels of certain families of HSP,such as HSP40 and 60 and HSF1,are associated with long-term survival and lymph node dissemination in patients with esophageal and esophagogastric cancer.

Research Progress on Plant Anti-Freeze Proteins

Plant antifreeze proteins(AFPs)are special proteins that can protect plant cells from ice crystal damage in low-temperature environments,and they play a crucial role in the process of plants adapting to cold environ-ments.Proteins with these characteristics have been found infish living in cold regions,as well as many plants and insects.Although research on plant AFPs started relatively late,their application prospects are broad,leading to the attention of many researchers to the isolation,cloning,and genetic improvement of plant AFP genes.Studies have found that the distribution of AFPs in different species seems to be the result of independent evolu-tionary events.Unlike the AFPs found infish and insects,plant AFPs have multiple hydrophilic ice-binding domains,and their recrystallization inhibition activity is about 10–100 times that offish and insect AFPs.Although different plant AFPs have the characteristics of low TH and high RI,their DNA and amino acid sequences are completely different,with small homology.With in-depth research and analysis of the character-istics and mechanisms of plant AFPs,not only has our understanding of plant antifreeze mechanisms been enriched,but it can also be used to improve crop varieties and enhance their freezing tolerance,yield,and quality through genetic engineering.In addition,the study of plant AFPs also contributes to our understanding of freezing resistance mechanisms in other organisms and provides new research directions for thefield of biotech-nology.Therefore,based on the analysis of relevant literature,this article will delve into the concepts,character-istics,research methods,and mechanisms of plant AFPs,summarize the latest research progress and application prospects of AFPs in plant,and provide prospects for the future development of AFP gene research.

Hmo1:A versatile member of the high mobility group box family of chromosomal architecture proteins

Eukaryotic chromatin consisting of nucleosomes connected by linker DNA is organized into higher order structures,which is facilitated by linker histone H1.Formation of chromatin compacts and protects the genome,but also hinders DNA transactions.Cells have evolved mechanisms to modify/remodel chromatin resulting in chromatin states suitable for genome functions.The high mobility group box(HMGB)proteins are non-histone chromatin architectural factors characterized by one or more HMGB motifs that bind DNA in a sequence nonspecific fashion.They play a major role in chromatin dynamics.The Saccharomyces cerevisiae(yeast hereafter)HMGB protein Hmo1 contains two HMGB motifs.However,unlike a canonical HMGB protein that has an acidic C-terminus,Hmo1 ends with a lysine rich,basic,C-terminus,resembling linker histone H1.Hmo1 exhibits characteristics of both HMGB proteins and linker histones in its multiple functions.For instance,Hmo1 promotes transcription by RNA polymerases I and II like canonical HMGB proteins but makes chromatin more compact/stable like linker histones.Recent studies have demonstrated that Hmo1 destabilizes/disrupts nucleosome similarly as other HMGB proteins in vitro and acts to maintain a common topological architecture of genes in yeast genome.This minireview reviews the functions of Hmo1 and the underlying mechanisms,highlighting recent discoveries.

Analysis and Review of Downregulated Actin Cytoskeletal Proteins in Non-Small Cell Lung Cancer

Actin, a highly conserved protein, plays a dominant role in Non-small cell lung cancer (NSCLC). Late diagnosis and the aggressive nature of NSCLC pose a significant threat. Studying the clinic pathological properties of NSCLC proteins is a potential alternative for developing treatment strategies. Towards this, 35 downregulated actin cytoskeletal proteins on NSCLC prognosis and treatment were studied by examining their protein-protein interactions, gene ontology enrichment terms, and signaling pathways. Using PubMed, various proteins in NSCLC were identified. The protein-protein interactions and functional associations of these proteins were examined using the STRING database. The focal adhesion signaling pathway was selected from all available KEGG and Wiki pathways because of its role in regulating gene expression, facilitating cell movement and reproduction, and significantly impacting NSCLC. The protein-protein interaction network of the 35 downregulated actin cytoskeleton proteins revealed that ACTG1, ACTR2, ACTR3, ANXA2, ARPC4, FLNA, TLN1, CALD1, MYL6, MYH9, MYH10, TPM1, TPM3, TPM4, PFN1, IQGAP1, MSN, and ZXY exhibited the highest number of interactions. Whereas HSPB1, CTNNA1, KRT17, KRT7, FLNB, SEPT2, and TUBA1B displayed medium interactions, while UTRN, TUBA1B, and DUSP23 had relatively fewer interactions. It was discovered that focal adhesions are critical in connecting membrane receptors with the actin cytoskeleton. In addition, protein kinases, phosphatases, and adapter proteins were identified as key signaling molecules in this process, greatly influencing cell shape, motility, and gene expression. Our analysis shows that the focal adhesion pathway plays a crucial role in NSCLC and is essential for developing effective treatment strategies and improving patient outcomes.

CRISPR/Cas9-mediated NlInR2 mutants:Analyses of residual mRNA and truncated proteins

CRISPR/Cas9 technology is a powerful genome manipulation tool in insects.However,little is known about whether mRNA and protein of a target gene are completely cleared in homozygous mutants.This study generated homozygous mutants of the insulin receptor gene 2(NlInR2)in the brown planthopper(Nilaparvata lugens)using CRISPR/Cas9 genome editing.Both frameshift mutants,E5_D17 and E6_I7,differentiated towards long wings,but there were differences in wing morphology,with E5_D17 showing wing deformities.Subsequent investigations revealed the presence of residual expression of NlInR2 mRNA in both mutants,as well as the occurrence of spliceosomes featuring exon skipping splicing in E5_D17.Additionally,the E5_D17 exhibited the detection of N-terminally truncated NlInR2 protein.RNA interference experiments indicated that the knockdown of NlInR2 expression in the E5_D17 mutant line increased the proportion of wing deformities from 11.1 to 65.6%,suggesting that the residual NlInR2 mRNA of the E5_D17 mutant might have retained some genetic functions.Our results imply that systematic characterization of residual protein expression or function in CRISPR/Cas9-generated mutant lines is necessary for phenotypic interpretation.

The DUF579 proteins GhIRX15s regulate cotton fiber development by interacting with proteins involved in xylan synthesis

Cotton provides the most abundant natural fiber for the textile industry.The mature cotton fiber largely consists of secondary cell walls with the highest proportion of cellulose and a small amount of hemicellulose and lignin.To dissect the roles of hemicellulosic polysaccharides during fiber development,four IRREGULAR XYLEM 15(IRX15)genes,GhIRX15-1/-2/-3/-4,were functionally characterized in cotton.These genes encode DUF579 domain-containing proteins,which are homologs of AtIRX15 involved in xylan biosynthesis.The four GhIRX15 genes were predominantly expressed during fiber secondary wall thickening,and the encoded proteins were localized to the Golgi apparatus.Each GhIRX15 gene could restore the xylan deficient phenotype in the Arabidopsis irx15irx15l double mutant.Silencing of GhIRX15s in cotton resulted in shorter mature fibers with a thinner cell wall and reduced cellulose content as compared to the wild type.Intriguingly,GhIRX15-2 and GhIRX15-4 formed homodimers and heterodimers.In addition,the GhIRX15s showed physical interaction with glycosyltransferases GhGT43C,GhGT47A and GhGT47B,which are responsible for synthesis of the xylan backbone and reducing end sequence.Moreover,the GhIRX15s can form heterocomplexes with enzymes involved in xylan modification and side chain synthesis,such as GhGUX1/2,GhGXM1/2 and GhTBL1.These findings suggest that GhIRX15s participate in fiber xylan biosynthesis and modulate fiber development via forming large multiprotein complexes.

Changes in milk fat globule membrane proteins along lactation stage of Laoshan dairy goat

The milk fat globule membrane(MFGM)is a complex structure with numerous functions,and its composition is affected by many factors.There have been few systematic investigations on goat MFGM proteome profiling during lactation.Individual milk samples from 15 healthy dairy goats were obtained at six lactation time points for investigation of the MFGM proteome using both data-independent acquisition(DIA)and data-dependent acquisition(DDA)proteomics techniques combined with multivariate statistical analysis.Using the DIA method,890 variably abundant MFGM proteins were discovered throughout the lactation cycle.From 1 to 240 d,butyrophilin subfamily 1 member A1,lipoprotein lipase,perilipin-2,and adipose triglyceride lipase were upregulated,while APOE,complement C3,clusterin,and IgG were downregulated.Furthermore,from 1 to 90 d,annexin A1,annexin A2,and antithrombin-ll were downregulated,then upregulated by d 240.Albumin had a high degree of connectedness,indicating that it was a key protein,according to protein-protein interaction research.Overall,our findings gave new insights into the biological features of MFGM protein in goat milk throughout lactation,which may aid in the creation of specialized MFGM products and infant formula.

Characterization of physicochemical and immunogenic properties of allergenic proteins altered by food processing:a review

Food allergens are mainly naturally-occurring proteins with immunoglobulin E(IgE)-binding epitopes.Understanding the structural and immunogenic characteristics of allergenic proteins is essential in assessing whether and how food processing techniques reduce allergenicity.We here discuss the impacts of food processing technologies on the modification of physicochemical,structural,and immunogenic properties of allergenic proteins.Detection techniques for characterizing changes in these properties of food allergens are summarized.Food processing helps to reduce allergenicity by aggregating or denaturing proteins,which masks,modifies,or destroys antigenic epitopes,whereas,it cannot eliminate allergenicity completely,and sometimes even improves allergenicity by exposing new epitopes.Moreover,most food processing techniques have been tested on purified food allergens rather than food products due to potential interference of other food components.We provide guidance for further development of processing operations that can decrease the allergenicity of allergenic food proteins without negatively impacting the nutritional profile.

Paired box proteins as diagnostic biomarkers for endocervical adenocarcinoma

In this editorial,we commented on the article by Akers et al published in the recent issue of the World Journal of Clinical Cases.We focused specifically on the role of the transcription factor paired box protein 8(PAX8)belonging to the family PAX in the carcinogenesis of a gynecologic tumor,endocervical adenocarcinoma,arising from the tissue of mesonephric origin,and the potential diagnostic value for the same type of neoplasms.The global vaccination program of human papillomavirus(HPV)has dramatically reduced the incidence of cervical cancer,including cases of adenocarcinoma.The type of adenoid epithelial origin has a lower frequency of HPV detection but tends to be more aggressive and fatal.Cases of endocervical adenocarcinoma occurring in females of menopause age have been described in the 2023 volume of the World Journal of Clinical Cases and in our study recently published in Oncol Lett.The histopathological findings and immunohistochemical assays showed that the lesions had glandular morphology,and the specimens in these two reports were immunohistochemically positive for the transcription factor PAX8,albeit that they had opposing expression profiles of tumor suppressor p16 and estrogen receptor and the presence of the HPV genome.The presence of a mucin protein,MUC 5AC,as revealed in both studies suggested target molecules for the diagnosis of mucinous adenoid type of uterine tumor and other histological origins.The clinical outcome was unfavorable due to metastasis and recurrence.This prompted the improvement of the antitumor modality,with the introduction of precise targeting therapy.Mucin has now been reported to be the therapeutic target for adenocarcinomas.

Analysis of quality-related proteins in golden pompano(Trachinotus ovatus)fillets with modified atmosphere packaging under superchilling storage

Here,we aimed to study the changes in proteome of golden pompano fillets during post-mortem storage.Tandem mass tags(TMT)-labeled quantitative proteomic strategy was applied to investigate the relationships between protein changes and quality characteristics of modified atmosphere packaging(MAP)fillets during superchilling(-3°C)storage.Scanning electron microscopy was used to show that the muscle histology microstructure of fillets was damaged to varying degrees,and low-field nuclear magnetic resonance was used to find that the immobilized water and free water in the muscle of fillets changed significantly.Total sulfhydryl content,TCA-soluble peptides and Ca2+-ATPase activity also showed that the fillet protein had a deterioration by oxidation and denaturation.The Fresh(FS),MAP,and air packaging(AP)groups were set.Total of 150 proteins were identified as differential abundant proteins(DAPs)in MAP/FS,while 209 DAPs were in AP/FS group.The KEGG pathway analysis indicated that most DAPs were involved in binding proteins and protein turnover.Correlation analysis found that 52 DAPs were correlated with quality traits.Among them,8 highly correlated DAPs are expected to be used as potential quality markers for protein oxidation and water-holding capacity.These results provide a further understanding of the muscle deterioration mechanism of packaging golden pompano fillets during superchilling.

Solid-state NMR studies of proteins in condensed phases

Some proteins perform their biological functions by changing their material states through liquid-liquid phase separation.Upon phase separation,the protein condenses into a concentrated liquid phase and sometimes into a gel phase,changing its dynamic properties and intermolecular interactions,thereby regulating cellular functions.Although the biological significance of this phenomenon has been widely recognized by researchers,there is still a lack of a comprehensive understanding of the structural and dynamic properties of the protein in the condensed phase.In this phase,molecules usually contain domains with varied dynamic properties and undergo intermediate exchanges.Magic angle spinning(MAS)solid-state NMR(SSNMR)experiments are very powerful in studying rigid protein polymers such as amyloid.The incorporation of solution-like experiments into SSNMR and the development of J-coupling based MAS SSNMR techniques extend its ability to study partially mobile segments of proteins in a condensed liquid or gel phase which are not visible by solution NMR or dipolar-coupling based SSNMR.Therefore,it has been applied in studying protein condensation and has provided very important information that is hard to obtain by other techniques.

Systematic Analysis of Post-Translational Modifications for Increased Longevity of Biotherapeutic Proteins

Protein-based therapeutics (PPTs) are drugs used to treat a variety of different conditions in the human body by alleviating enzymatic deficiencies, augmenting other proteins and drugs, modulating signal pathways, and more. However, many PPTs struggle from a short half-life due to degradation caused by irreversible protein aggregation in the bloodstream. Currently, the most researched strategies for improving the efficiency and longevity of PPTs are post-translational modifications (PTMs). The goal of our research was to determine which type of PTM increases longevity the most for each of three commonly-used therapeutic proteins by comparing the docking scores (DS) and binding free energies (BFE) from protein aggregation and reception simulations. DS and BFE values were used to create a quantitative index that outputs a relative number from −1 to 1 to show reduced performance, no change, or increased performance. Results showed that methylation was the most beneficial for insulin (p < 0.1) and human growth hormone (p < 0.0001), and both phosphorylation and methylation were somewhat optimal for erythropoietin (p < 0.1 and p < 0.0001, respectively). Acetylation consistently provided the worst benefits with the most negative indices, while methylation had the most positive indices throughout. However, PTM efficacy varied between PPTs, supporting previous studies regarding how each PTM can confer different benefits based on the unique structures of recipient proteins.

Altered expression of nuclear matrix proteins in etoposide induced apoptosis in HL-60 cells

The events of cell death and the expression of nuclear matrix protein (NMP) have been investigated in a promyelocytic leukemic cell line HL-60 induced with etoposide. By means of TUNEL assay, the nuclei displayed a characteristic morphology change, and the amount of apoptotic cells increased early and reached maximun about 39% after treatment with etoposide for 2 h. Nucleosomal DNA fragmentation was observed after treatment for 4 h. The morphological change of HL-60 cells, thus, occurred earlier than the appearance of DNA ladder. Total nuclear matrix proteins were analyzed by 2-dimensional gel electrophoresis. Differential expression of 59 nuclear matrix proteins was found in 4 h etoposide treated cells. Western blotting was then performed on three nuclear matrix acssociated proteins, PML, HSC70 and NuMA. The expression of the suppressor PML protein and heat shock protein HSC70 were significantly upregulated after etoposide treatment, while NuMA, a nuclear mitotic apparatus protein, was down regulated. These results demonstrate that significant biochemical alterations in nuclear matrix proteins take place during the apoptotic process.

Selected dietary plant-based proteins for growth and health response of Nile tilapia Oreochromis niloticus

Tilapia culture is one of the largest sectors of global aquaculture.Among the different species of tilapia,Nile tilapia(Oreochromis niloticus)is perhaps the top cultured species.The production of Nile tilapia has been continually increasing throughout the years resulting in genetic deterioration.Several tilapia strains with better growth performance and adaptive capability to survive in different culture conditions have been developed to alleviate the crisis.Increased demand for Nile tilapia implies higher farming cost.Plant-based proteins are utilized as partial or complete fishmeal replacements to reduce feed cost.However,these proteins can adversely affect and alter growth and feed performance,carcass composition and indices,and gut and hepatic health.This review discusses the use of seven plant-based proteins:namely,soybean,copra,pea,corn,palm kernel,microalgae,and seaweed as a Nile tilapia aquafeed.Different processing methods are employed to produce several types of plant-based proteins.Processed plant-protein types,when utilized as an aquafeed ingredient,vary in its effect on the performance,hemato-immunological parameters,and gut and hepatic health of Nile tilapia.Studies have shown that Nile tilapia can effectively maximize plant-based protein diets based on the preparation method,type of plant source,amino acid supplementation,and inclusion levels of the plant proteins.These readily available crops should be considered as primary protein sources for aquaculture.Hindrances to the use of plant-based proteins as a main dietary protein are limiting amino acids,presence of anti-nutritional factors,and the competition between its demand as human food and as animal feed.

Kidney stone matrix proteins:Role in stone formation

Stone formation is induced by an increased level of urine crystallization promoters and reduced levels of its inhibitors.Crystallization inhibitors include citrate,magnesium,zinc,and organic compounds such as glycosaminoglycans.In the urine,there are various proteins,such as uromodulin(Tamm-Horsfall protein),calgranulin,osteopontin,bikunin,and nephrocalcin,that are present in the stone matrix.The presence of several carboxyl groups in these macromolecules reduces calcium oxalate monohydrate crystal adhesion to the urinary epithelium and could potentially protect against lithiasis.Proteins are the most abundant component of kidney stone matrix,and their presence may reflect the process of stone formation.Many recent studies have explored the proteomics of urinary stones.Among the stone matrix proteins,the most frequently identified were uromodulin,S100 proteins(calgranulins A and B),osteopontin,and several other proteins typically engaged in inflammation and immune response.The normal level and structure of these macromolecules may constitute protection against calcium salt formation.Paradoxically,most of them may act as both promoters and inhibitors depending on circumstances.Many of these proteins have other functions in modulating oxidative stress,immune function,and inflammation that could also influence stone formation.Yet,the role of these kidney stone matrix proteins needs to be established through more studies comparing urinary stone proteomics between stone formers and non-stone formers.

AG-GATCN:A novel method for predicting essential proteins

Essential proteins play an important role in disease diagnosis and drug development.Many methods have been devoted to the essential protein prediction by using some kinds of biological information.However,they either ignore the noise presented in the biological information itself or the noise generated during feature extraction.To overcome these problems,in this paper,we propose a novel method for predicting essential proteins called attention gate-graph attention network and temporal convolutional network(AG-GATCN).In AG-GATCN method,we use improved temporal convolutional network(TCN)to extract features from gene expression sequence.To address the noise in the gene expression sequence itself and the noise generated after the dilated causal convolution,we introduce attention mechanism and gating mechanism in TCN.In addition,we use graph attention network(GAT)to extract protein–protein interaction(PPI)network features,in which we construct the feature matrix by introducing node2vec technique and 7 centrality metrics,and to solve the GAT oversmoothing problem,we introduce gated tanh unit(GTU)in GAT.Finally,two types of features are integrated by us to predict essential proteins.Compared with the existing methods for predicting essential proteins,the experimental results show that AG-GATCN achieves better performance.