AttnPep: A Self-Attention-Based Deep Learning Method for Peptide Identification in Shotgun Proteomics.

In shotgun proteomics, the proteome search engine analyzes mass spectra obtained by experiments, and then a peptide-spectra match (PSM) is reported for each spectrum. However, most of the PSMs identified are incorrect, and therefore various postprocessing software have been developed for reranking the peptide identifications. Yet these methods suffer from issues such as dependency on distribution, reliance on shallow models, and limited effectiveness. In this work, we propose AttnPep, a deep learning model for rescoring PSM scores that utilizes the Self-Attention module. This module helps the neural network focus on features relevant to the classification of PSMs and ignore irrelevant features. This allows AttnPep to analyze the output of different search engines and improve PSM discrimination accuracy. We considered a PSM to be correct if it achieves a q-value <0.01 and compared AttnPep with existing mainstream software PeptideProphet, Percolator, and proteoTorch. The results indicated that AttnPep found an average increase in correct PSMs of 9.29% relative to the other methods. Additionally, AttnPep was able to better distinguish between correct and incorrect PSMs and found more synthetic peptides in the complex SWATH data set.

Akkermansia muciniphila Ameliorates Alcoholic Liver Disease in Experimental Mice by Regulating Serum Metabolism and Improving Gut Dysbiosis.

Alcoholic liver disease (ALD) represents a significant global health concern, yet the available treatment options remain limited. Numerous studies have shown that gut microbiota is a critical target for the treatment of ALD. Additionally, there is increasing evidence that host metabolism also plays a crucial role in the development of ALD. Akkermansia muciniphila has been demonstrated to ameliorate experimental ALD through its modulatory effects on the intestinal vascular barrier, enhancement of mucus layer thickness, and promotion of intestinal tight junction proteins. Nevertheless, there is a dearth of studies investigating the impact of A. muciniphila on host metabolism and gut microbiota. Here, C57BL/6 mice were utilized to establish a modified NIAAA model in order to investigate the impact of the oral administration of A. muciniphila during the development of ALD. Furthermore, we employed targeted metabolomics to analyze the serum metabolomic profiles of the mice and 2bRAD-M sequencing to comprehensively examine the underlying mechanisms of the efficacy of A. muciniphila on ALD. Our results illustrated that the oral administration of A. muciniphila alleviated alcohol-induced liver injury in conjunction with encouraged serum levels of ornithine and diminished the elevation of oxalic acid levels induced by alcohol intake. In addition, A. muciniphila also inhibited the proliferation of harmful bacteria, such as Escherichia coli and Helicobacter hepaticus, induced by alcohol consumption while promoting the growth of butyrate-producing and commensal bacteria, including Paramuribaculum intestinale and Bacteroides ovatus. In conclusion, this study suggests that A. muciniphila restores ALD by regulating the gut microbiota, and this corrective effect is associated with alterations in the serum metabolism. Our research supplies a theoretical basis for developing A. muciniphila as an innovative generation of probiotic for preventing and managing ALD.

SUnet: A multi-organ segmentation network based on multiple attention.

Organ segmentation in abdominal or thoracic computed tomography (CT) images plays a crucial role in medical diagnosis as it enables doctors to locate and evaluate organ abnormalities quickly, thereby guiding surgical planning, and aiding treatment decision-making. This paper proposes a novel and efficient medical image segmentation method called SUnet for multi-organ segmentation in the abdomen and thorax. SUnet is a fully attention-based neural network. Firstly, an efficient spatial reduction attention (ESRA) module is introduced not only to extract image features better, but also to reduce overall model parameters, and to alleviate overfitting. Secondly, SUnet's multiple attention-based feature fusion module enables effective cross-scale feature integration. Additionally, an enhanced attention gate (EAG) module is considered by using grouped convolution and residual connections, providing richer semantic features. We evaluate the performance of the proposed model on synapse multiple organ segmentation dataset and automated cardiac diagnostic challenge dataset. SUnet achieves an average Dice of 84.29% and 92.25% on these two datasets, respectively, outperforming other models of similar complexity and size, and achieving state-of-the-art results.

Gene function and cell surface protein association analysis based on single-cell multiomics data.

Single-cell transcriptomics provides researchers with a powerful tool to resolve the transcriptome heterogeneity of individual cells. However, this method falls short in revealing cellular heterogeneity at the protein level. Previous single-cell multiomics studies have focused on data integration rather than exploiting the full potential of multiomics data. Here we introduce a new analysis framework, gene function and protein association (GFPA), that mines reliable associations between gene function and cell surface protein from single-cell multimodal data. Applying GFPA to human peripheral blood mononuclear cells (PBMCs), we observe an association of epithelial mesenchymal transition (EMT) with the CD99 protein in CD4 T cells, which is consistent with previous findings. Our results show that GFPA is reliable across multiple cell subtypes and PBMC samples. The GFPA python packages and detailed tutorials are freely available at https://github.com/studentiz/GFPA.

Fufang Fanshiliu Decoction Revealed the Antidiabetic Effect through Modulating Inflammatory Response and Gut Microbiota Composition.

Background: Diabetes mellitus brings serious threats and financial burdens to human beings worldwide. Fufang Fanshiliu decoction (FFSLD), a traditional Chinese medicine formula showing great antidiabetic effects, has been used in clinics for many years. Objective: This study aims to explore the underlying therapeutic mechanisms of FFSLD in Type II diabetes mellitus (T2DM). Methods: Sprague-Dawley rats induced by high-fat diet feeding combined with streptozotocin injection were used to establish the T2DM model. All rats were randomly divided into 6 groups: control, model, metformin, high dosage, middle dosage, and low dosage of FFSLD. After 4 weeks of treatment, serum, intestinal mucosa, and fecal samples were collected for further analysis. ELISA was used to detect the diabetic-related serum indicators and proinflammation cytokines. Gene or protein expressions of mitogen-activated protein kinase (MAPK), interleukin 1 beta (IL-1ß), transforming growth factor-beta (TGF-ß), and tumor necrosis factor-alpha (TNF-α) in intestinal mucosa were analyzed by quantitative real-time polymerase chain reaction (RT-PCR) or western blot. 16s rRNA gene sequencing was used to detect the changes of gut microbiome in these groups. Intestinal gut microbiota (GM) composition was further analyzed according to the sequencing libraries. Results: FFSLD effectively recovered the diabetic-related biochemical indexes by reducing fasting blood glucose (FBG), total cholesterol (TC), triglyceride (TG), low-density lipoprotein cholesterol (LDL-C), insulin, and increasing high-density lipoprotein cholesterol (HDL-C). Furthermore, FFSLD significantly ameliorated the abnormal levels of proinflammation cytokines including IL-1ß, IL-6, TNF-α, and TGF-ß. In addition, the GM compositions of rats in control, model, and FFSLD treated groups were different. FFSLD significantly increased the relative abundance of Lactobacillus, Akkermansia, and Proteus, and reduced the relative abundance of Alistipes, Desulfovibrio, and Helicobacter. Moreover, these changed bacteria were closely related to the diabetic-related serum indicators and proinflammatory cytokines. Conclusion: These results suggest that FFSLD alleviates diabetic symptoms in T2DM rats through regulating GM composition and inhibiting inflammatory response, which clarify the therapeutic mechanism of FFSLD on T2DM and provide a theoretical basis for its further clinical application.

Correlation of Adiponectin Gene Polymorphisms rs266729 and rs3774261 With Risk of Nonalcoholic Fatty Liver Disease: A Systematic Review and Meta-Analysis.

Background: Increasing evidence has suggested an association of adiponectin gene polymorphisms rs1501299, rs2241766, rs266729 and rs3774261 with risk of nonalcoholic fatty liver disease (NAFLD). This correlation has been extensively meta-analyzed for the first two polymorphisms, but not the second two. Methods: The PubMed, EMBASE, Google Scholar, and China National Knowledge Infrastructure databases were searched for relevant literature. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated. Results: A total of 10 case-control studies on rs266729 (2,619 cases and 1,962 controls) and 3 case-control studies on rs3774261 (562 cases and 793 controls) were included. Meta-analysis showed that rs266729 was associated with significantly higher NAFLD risk based on the following five models: allelic, OR 1.72, 95% CI 1.34-2.21, P < 0.001; recessive, OR 2.35, 95% CI 1.86-2.95, P < 0.001; dominant, OR 1.84, 95% CI 1.34-2.53, P < 0.001; homozygous, OR 2.69, 95% CI 1.84-3.92, P < 0.001; and heterozygous, OR 1.72, 95% CI 1.28-2.32, P < 0.001. This association between rs266729 and NAFLD risk remained significant for all five models among studies with Asian, Chinese and Caucasian samples. The rs2241766 polymorphism was associated with significantly higher NAFLD risk according to the recessive model (OR 1.87, 95% CI 1.15-3.04, P = 0.01). Conclusion: Polymorphisms rs266729 and rs3774261 in the adiponectin gene may be risk factors for NAFLD. These findings may pave the way for novel therapeutic strategies, but they should be verified in large, well-designed studies.

Activation of NLRP3 Inflammasome Complexes by Beta-Tricalcium Phosphate Particles and Stimulation of Immune Cell Migration in vivo.

Beta-tricalcium phosphate (ß-TCP) serves as a bone substitute in clinical practice because it is resorbable, biocompatible, osteointegrative, and osteoconductive. Particles of ß-TCP are also inflammatory mediators although the mechanism of this function has not been fully elucidated. Regardless, the ability of ß-TCP to stimulate the immune system might be useful for immunomodulation. The present study aimed to determine the effects of ß-TCP particles on NLR family pyrin domain containing 3 (NLRP3) inflammasome complexes. We found that ß-TCP activates NLRP3 inflammasomes, and increases interleukin (IL)-1ß production in primary cultured mouse dendritic cells (DCs) and macrophages, and human THP-1 cells in caspase-1 dependent manner. In THP-1 cells, ß-TCP increased also IL-18 production, and NLRP3 inflammasome activation by ß-TCP depended on phagocytosis, potassium efflux, and reactive oxygen species (ROS) generation. We also investigated the effects of ß-TCP in wild-type and NLRP3-deficient mice in vivo. Immune cell migration around subcutaneously injected ß-TCP particles was reduced in NLRP3-deficient mice. These findings suggest that the effects of ß-TCP particles in vivo are at least partly mediated by NLRP3 inflammasome complexes.

Enterovirus D68 Protease 2Apro Targets TRAF3 To Subvert Host Innate Immune Responses.

Human enterovirus D68 (EV-D68) has received considerable attention recently as a global reemergent pathogen because it causes severe respiratory tract infections and acute flaccid myelitis (AFM). The nonstructural protein 2A protease (2Apro) of EVs, which functions in the cleavage of host proteins, comprises a pivotal part of the viral immune evasion process. However, the pathogenic mechanism of EV-D68 is not fully understood. In this study, we found that EV-D68 inhibited antiviral type I interferon responses by cleaving tumor necrosis factor receptor-associated factor 3 (TRAF3), which is the key factor for type I interferon production. EV-D68 inhibited Sendai virus (SEV)-induced interferon regulatory factor 3 (IRF3) activation and beta interferon (IFN-ß) expression in HeLa and HEK293T cells. Furthermore, we demonstrated that EV-D68 and 2Apro were able to cleave the C-terminal region of TRAF3 in HeLa and HEK293T cells, respectively. A cysteine-to-alanine substitution at amino acid 107 (C107A) in the 2Apro protease resulted in the loss of cleavage activity to TRAF3, and mutation of glycine at amino acid 462 to alanine (G462A) in TRAF3 conferred resistance to 2Apro These results suggest that control of TRAF3 by 2Apro may be a mechanism EV-D68 utilizes to subvert host innate immune responses.IMPORTANCE Human enterovirus 68 (EV-D68) has received considerable attention recently as a global reemergent pathogen because it causes severe respiratory tract infections and acute flaccid myelitis. The nonstructural protein 2A protease (2Apro) of EV, which functions in cleavage of host proteins, comprises an essential part of the viral immune evasion process. However, the pathogenic mechanism of EV-D68 is not fully understood. Here, we show for the first time that EV-D68 inhibited antiviral type I interferon responses by cleaving tumor necrosis factor receptor-associated factor 3 (TRAF3). Furthermore, we identified the key cleavage site in TRAF3. Our study may suggest a new mechanism by which the 2Apro of EV facilitates subversion of host innate immune responses. These findings increase our understanding of EV-D68 infection and may help identify new antiviral targets against EV-D68.

A novel electrochemical sensing platform for detection of dopamine based on gold nanobipyramid/multi-walled carbon nanotube hybrids.

Dopamine homeostasis is an important clinical diagnostic index, because an abnormal level in the human body is closely related to certain serious diseases. Herein, a novel electrochemical sensing platform based on gold nanobipyramid/multi-walled carbon nanotube hybrids (AuNBP/MWCNTs) is developed to detect dopamine in human fluids. Using field emission scanning electron microscopy, it is observed that AuNBPs of about 60 nm with two pyramids are well dispersed on the surface of MWCNTs. Energy-dispersive X-ray spectrometry, X-ray diffraction and X-ray photoelectron spectroscopy confirm that AuNBPs are self-assembled onto the surface of MWCNTs to form the hybrids. Cyclic voltammetry reveals that the AuNBP/MWCNTs exhibit good electrocatalytic activity toward dopamine oxidation owing to the synergistic effects of AuNBPs and MWCNTs. In addition, both cyclic voltammetry and differential pulse voltammetry display three well-resolved and distinct oxidation peaks on the AuNBP/MWCNT-modified glassy carbon electrode. Based on AuNBP/MWCNTs, the newly developed electrochemical sensor is used to detect dopamine in the presence of ascorbic acid and uric acid over a wide linear range from 50 nM to 2.7 mM and a low detection limit of 15 nM (at S/N = 3). The electrochemical sensor can also be applied for the quantitative analysis of dopamine in real samples. Graphical abstract A novel electrochemical sensing platform based on gold nanobipyramid/multi-walled carbon nanotube hybrids (AuNBP/MWCNTs) was proposed to detect dopamine in the presence of ascorbic acid and uric acid.

Typical Stress Granule Proteins Interact with the 3' Untranslated Region of Enterovirus D68 To Inhibit Viral Replication.

Stress granules (SGs) are formed in the cytoplasm under environmental stress, including viral infection. Human enterovirus D68 (EV-D68) is a highly pathogenic virus which can cause serious respiratory and neurological diseases. At present, there is no effective drug or vaccine against EV-D68 infection, and the relationship between EV-D68 infection and SGs is poorly understood. This study revealed the biological function of SGs in EV-D68 infection. Our results suggest that EV-D68 infection induced the accumulation of SG marker proteins Ras GTPase-activated protein-binding protein 1 (G3BP1), T cell intracellular antigen 1 (TIA1), and human antigen R (HUR) in the cytoplasm of infected host cells during early infection but inhibited their accumulation during the late stage. Simultaneously, we revealed that EV-D68 infection induces HUR, TIA1, and G3BP1 colocalization, which marks the formation of typical SGs dependent on protein kinase R (PKR) and eIF2α phosphorylation. In addition, we found that TIA1, HUR, and G3BP1 were capable of targeting the 3' untranslated regions (UTRs) of EV-D68 RNA to inhibit viral replication. However, the formation of SGs in response to arsenite (Ars) gradually decreased as the infection progressed, and G3BP1 was cleaved in the late stage as a strategy to antagonize SGs. Our findings have important implications in understanding the mechanism of interaction between EV-D68 and the host while providing a potential target for the development of antiviral drugs.IMPORTANCE EV-D68 is a serious threat to human health, and there are currently no effective treatments or vaccines. SGs play an important role in cellular innate immunity as a target with antiviral effects. This manuscript describes the formation of SGs induced by EV-D68 early infection but inhibited during the late stage of infection. Moreover, TIA1, HUR, and G3BP1 can chelate a specific site of the 3' UTR of EV-D68 to inhibit viral replication, and this interaction is sequence and complex dependent. However, this inhibition can be antagonized by overexpression of the minireplicon. These findings increase our understanding of EV-D68 infection and may help identify new antiviral targets that can inhibit viral replication and limit the pathogenesis of EV-D68.

Effects of beta-tricalcium phosphate particles on primary cultured murine dendritic cells and macrophages.

Beta-tricalcium phosphate (ß-TCP) is widely used for bone substitution in clinical practice. Particles of calcium phosphate ceramics including ß-TCP act as an inflammation mediators, which is an unfavorable characteristic for a bone substituent or a prosthetic coating material. It is thought that the stimulatory effect of ß-TCP on the immune system could be utilized as an immunomodulator. Here, in vitro effects of ß-TCP on primary cultured murine dendritic cells (DCs) and macrophages were investigated. ß-TCP particles enhanced expression of costimulatory surface molecules, including CD86, CD80, and CD40 in DCs, CD86 in macrophages, and MHC class II and class I molecules in DCs. DEC205 and CCR7 were up-regulated in ß-TCP-treated DCs. Production of cytokines and chemokines, including CCL2, CCL3, CXCL2, and M-CSF, significantly increased in DCs; CCL2, CCL3, CCL4, CCL5, CXCL2, and IL-11ra were up-regulated in macrophages. The results of the functional assays revealed that ß-TCP caused a prominent reduction in antigen uptake by DCs, and that conditioned medium from DCs treated with ß-TCP facilitated the migration of splenocytes in the transwell migration assay. Thus, ß-TCP induced phenotypical and functional maturation/activation of DCs and macrophages; these stimulating effects may contribute to the observed in vivo effect where ß-TCP induced extensive migration of immune cells. When compared to lipopolysaccharide (LPS), an authentic TLR ligand, the stimulatory effect of ß-TCP on the immune systems is mild to moderate; however, it may have some advantages as a novel immunomodulator. This is the first report on the direct in vitro effects of ß-TCP against bone marrow-derived DCs and macrophages.

Characterization of beta-tricalcium phosphate as a novel immunomodulator.

Calcium phosphate (CaP) ceramics including hydroxyapatite (HA) and beta-tricalcium phosphate (ß-TCP) have been widely used for bone substitution in orthopedic, maxillofacial and dental surgery, as well as in tumor resections. CaP particles are also known to cause inflammatory responses, which are thought to be an unfavorable characteristic of prosthetic coating materials. On the other hand, the immunostimulatory effect of ß-TCP induces an anti-tumor effect in xenograft tumor models in athymic mice. To date, in depth analysis of the biological effects of ß-TCP has not been studied in mice. In the present study, in vivo biological effects of ß-TCP were investigated by subcutaneously injecting ß-TCP particles into mice. This induced extensive migration of immune cells to the area surrounding the injection. In addition, we found that in vitro treatment with ß-TCP in murine monocyte/macrophage cells (J774A.1) induced up-regulation of surface expression of CD86, and increased production of TNF-α, MIP-1α, and sICAM-1. Furthermore, conditioned medium from J774A.1 cells treated with ß-TCP facilitated migration of murine splenocytes in a transwell migration assay. These findings clarify that ß-TCP induces an immunostimulatory effect in mice, and suggest a potential for ß-TCP as a novel adjuvant for cancer therapy.

Flt3 ligand enhances anti-tumor effects of antibody therapeutics.

Fms-like tyrosine kinase 3 ligand ([Flt3 ligand], FL) stimulates proliferation and development of a wide range of hematopoietic cells including hematopoietic stem cells and myeloid and lymphoid progenitor cells. FL also has been shown to have anti-tumor effects in a variety of in vivo tumor models. In this study, the effect of FL against tumor growth was investigated in the COLO-205 human colon tumor xenograft model. FL was delivered in vivo by the "hydrodynamics-based gene delivery of naked DNA" method. In this experimental setting, FL and/or the therapeutic antibody anti-carcinoembryonic antigen (CEA) monoclonal antibody was administered. FL alone or anti-CEA antibody alone induced significant growth inhibition; furthermore, FL plus antibody treatment produced synergistic anti-tumor effects. This study is the first demonstration of a synergistic anti-tumor effect between FL and antibody therapeutics.

Locally applied TCP inhibits tumor growth via possible activation of macrophages.

The aim of this study was to investigate whether beta-tricalcium phosphate (TCP) inhibits cancer growth, because TCP, a widely used bone replacement material, is known to attract immune cells. Human colon cancer (WiDr) cells were subcutaneously injected on the backs of nude mice, and tumor growth was observed. Seven days after the injection, five animals were implanted with TCP at the tumor sites, five animals were treated by a direct application of 0.12 mg cisplatin at the sites, and four animals were not treated, as a control. Tumor size on the 43rd day of implantation was 1173 mm(3) in the TCP group and was smaller than that in the control, 1621 mm(3). This inhibition was comparable to that with cisplatin. Furthermore, tumor-growing rate in the TCP group was significantly lower than that in the control group. Histopathological examination of the tumors showed migration of macrophages only in the TCP group, with TCP particles remaining at the implantation loci. There were no between-group differences in neutrophil infiltration and angiogenesis. In another series of in vitro experiments, a concentration-dependent increase in luminol chemiluminescence was observed in isolated human peripheral neutrophils incubated with TCP, and the chemiluminescence due to phagocytosis of opsonized zymosan in the presence of TCP occurred with a lower level of TCP than when the chemiluminescence was due to TCP alone. These results suggest that subcutaneously implanted TCP inhibits tumor growth of implanted WiDr cells, and that the activation by TCP of macrophages plays a role in that inhibition.

Seeking for senile-related gene expression in cerebral tissue of senescence-accelerated mouse.

1. A better understanding of the molecular effect on aging in the brain may help reveal important aspects of organism aging, as well as the processes that lead to aging-related brain dysfunction. In this study, the aging-specific expression genes of the murine cerebrum were investigated by using the technique of DDRT-PCR in two senescence-accelerated mouse strains, SAMP10/Ta and SAMR1TA. 2. Through comparing gene expression profile among the age, 2, 4, 12, and 18 month of the SAMP10/Ta strain, four differential fragments have been found, and comparing gene expression profile between the two mouse strains, 24 fragments have been detected, 7 and 17 of them belong to SAMP10/Ta and SAMR1TA, respectively. 3. Sequencing analysis indicated that most of those fragments are homologous with some of certain gene cDNA that are related with senile. The data obtained from this study suggest that many genes are involved in the senile process and accelerate senescence phenotypic pathologies in SAMP10/Ta.

Structure and characterization of hamster IL-12 p35 and p40.

Complementary DNAs coding for two subunits of hamster interleukin-12 (IL-12), p35 and p40, were cloned from a hamster dendritic cell (DC) cDNA library. The cloning demonstrated that hamster IL-12 consisted of a p35 subunit with 216 amino acid (aa) residues and a p40 subunit with 327 aa. Structural comparison of hamster p35 and p40 at the protein level showed the highest homologies with each counterpart of sigmodon (hispid cotton rat). The gene expressions of hamster IL-12 p35 and p40 in bone marrow (BM) cells cultured in the presence of mouse granulocyte macrophage-colony-stimulating factor (mGM-CSF) and IL-4 were up-regulated during culture. Immunoblot analysis of 293 cells transfected with hamster p35 and p40 expression vectors suggested the presence of a covalently linked p35/p40 heterodimer. Furthermore, supernatant from the 293 cells transfected with both expression vectors induced the up-regulation of interferon-gamma (IFN-gamma) mRNA in hamster splenocytes, indicating that the p35/p40 heterodimer IL-12 protein present in the supernatant was functional. These results suggest that the vectors containing hamster IL-12 cDNA might be suitable tools for developing an immunotherapeutic approach against experimental cancer in a hamster model.

Hamster DEC-205, its primary structure, tissue and cellular distribution.

DEC-205, a putative antigen uptake receptor, belongs to a family of transmembrane C-type lectins. This molecule is known to be one of the most authentic markers for the lineage of dendritic cells. In the present study, we determined the primary structure, tissue distribution and cellular localization of hamster DEC-205. The multi-domain structure of mouse and human DEC-205 was completely conserved in hamster with the overall identity of approximately 80%. DEC-205 transcripts were detected in the thymus and bone marrow cells cultured in the presence of mouse granulocyte macrophage colony-stimulating factor and interleukin-4 in which the DEC-205 expression was up-regulated in the course of cultures. Hamster DEC-205 was mainly detected on cell membrane and shown to mediate the uptake of flourescein isothiocyanate-conjugated ovalbumin. DEC-205 is a highly conserved molecule across the species suggesting its fundamental role in the immune system.