Effects of multiple metals exposure on abnormal liver function: The mediating role of low-density lipoprotein cholesterol.

Equilibration of metal metabolism is critical for normal liver function. Most epidemiological studies have only concentrated on the influence of limited metals. However, the single and synergistic impact of multiple-metal exposures on abnormal liver function (ALF) are still unknown. A cross-sectional study involving 1493 Chinese adults residing in Shenzhen was conducted. Plasma concentrations of 13 metals, including essential metals (calcium, copper, cobalt, iron, magnesium, manganese, molybdenum, zinc, and selenium) and toxic metals (aluminum, cadmium, arsenic, and thallium) were detected by the inductively coupled plasma spectrometry (ICP-MS). ALF was ascertained as any observed abnormality from albumin, alanine transaminase, aspartate transaminase, γ-glutamyl transpeptidase, and direct bilirubin. Diverse statistical methods were used to evaluate the single and mixture effect of metals, as well as the dose-response relationships with ALF risk, respectively. Mediation analysis was conducted to evaluate the role of blood lipids in the relation of metal exposure with ALF. The average age of subjects was 59.7 years, and 56.7 % were females. Logistic regression and the least absolute shrinkage and selection operator (LASSO) penalized regression model consistently suggested that increased levels of arsenic, aluminum, manganese, and cadmium were related to elevated risk of ALF; while magnesium and zinc showed protective effects on ALF (all p-trend < 0.05). The grouped weighted quantile sum (GWQS) regression revealed that the WQS index of essential metals and toxic metals showed significantly negative or positive relationship with ALF, respectively. Aluminum, arsenic, cadmium, and manganese showed linear whilst magnesium and zinc showed non-linear dose-response relationships with ALF risk. Mediation analysis showed that LDL-c mediated 4.41 % and 14.74 % of the relationship of plasma cadmium and manganese with ALF, respectively. In summary, plasma aluminum, arsenic, manganese, cadmium, magnesium, and zinc related with ALF, and LDL-c might underlie the pathogenesis of ALF associated with cadmium and manganese exposure. This study may provide critical public health significances in liver injury prevention and scientific evidence for the establishment of environmental standard.

Deep Learning-Based Bioactive Therapeutic Peptide Generation and Screening.

Many bioactive peptides demonstrated therapeutic effects over complicated diseases, such as antiviral, antibacterial, anticancer, etc. It is possible to generate a large number of potentially bioactive peptides using deep learning in a manner analogous to the generation of de novo chemical compounds using the acquired bioactive peptides as a training set. Such generative techniques would be significant for drug development since peptides are much easier and cheaper to synthesize than compounds. Despite the limited availability of deep learning-based peptide-generating models, we have built an LSTM model (called LSTM_Pep) to generate de novo peptides and fine-tuned the model to generate de novo peptides with specific prospective therapeutic benefits. Remarkably, the Antimicrobial Peptide Database has been effectively utilized to generate various kinds of potential active de novo peptides. We proposed a pipeline for screening those generated peptides for a given target and used the main protease of SARS-COV-2 as a proof-of-concept. Moreover, we have developed a deep learning-based protein-peptide prediction model (DeepPep) for rapid screening of the generated peptides for the given targets. Together with the generating model, we have demonstrated that iteratively fine-tuning training, generating, and screening peptides for higher-predicted binding affinity peptides can be achieved. Our work sheds light on developing deep learning-based methods and pipelines to effectively generate and obtain bioactive peptides with a specific therapeutic effect and showcases how artificial intelligence can help discover de novo bioactive peptides that can bind to a particular target.

DeepBindBC: A practical deep learning method for identifying native-like protein-ligand complexes in virtual screening.

Identifying native-like protein-ligand complexes (PLCs) from an abundance of docking decoys is critical for large-scale virtual drug screening in early-stage drug discovery lead searching efforts. Providing reliable prediction is still a challenge for most current affinity predicting models because of a lack of non-binding data during model training, lost critical physical-chemical features, and difficulties in learning abstract information with limited neural layers. In this work, we proposed a deep learning model, DeepBindBC, for classifying putative ligands as binding or non-binding. Our model incorporates information on non-binding interactions, making it more suitable for real applications. ResNet model architecture and more detailed atom type representation guarantee implicit features can be learned more accurately. Here, we show that DeepBindBC outperforms Autodock Vina, Pafnucy, and DLSCORE for three DUD.E testing sets. Moreover, DeepBindBC identified a novel human pancreatic α-amylase binder validated by a fluorescence spectral experiment (Ka = 1.0 × 105 M). Furthermore, DeepBindBC can be used as a core component of a hybrid virtual screening pipeline that incorporating many other complementary methods, such as DFCNN, Autodock Vina docking, and pocket molecular dynamics simulation. Additionally, an online web server based on the model is available at http://cbblab.siat.ac.cn/DeepBindBC/index.php for the user's convenience. Our model and the web server provide alternative tools in the early steps of drug discovery by providing accurate identification of native-like PLCs.

[Studies on thermal denaturation of peanut allergen Ara h1 and its interaction with reducing sugars].

The thermal denaturation of peanut allergen Ara h1, its interaction with reducing sugars and the corresponding changes in allergenicity were investigated by circular dichroism (CD), fluorescence and ELISA method comprehensively. The experimental results indicate that the secondary structure of Ara h1 changes significantly along with decreasing alpha-helical structure and its allergenicity with the temperature higher than 85 degrees C, and that both xylose and fructose can stabilize Ara h1 protein structure through interacting with Ara h1 protein and decrease its allergenicity obviously. This study should be helpful to the further understanding of sensitization mechanism of food allergy and be useful for the guidance on reasonable manufacturing of peanut foods.

Modulating the allergenicity and functional properties of peanut protein by covalent conjugation with polyphenols.

Peanut protein is a common food allergen. Our previous study demonstrated that the allergenicity of Ara h1 declines after covalent conjugation with polyphenols in vitro; however, how polyphenols affect the structure, function, and allergenicity of peanut protein extract (PPE) after covalent conjugating needs clarifying. Here, we assessed how the structure, function, and allergenicity of PPE changed after covalent conjugation with epigallocatechin-3-gallate (PPE-EGCG) and chlorogenic acid (PPE-CA). PPE covalently conjugated with EGCG and CA using the alkali treatment method. Multi-spectroscopy showed that the structure of PPE-EGCG/CA conjugate changed, becoming less folded. In contrast, the functional properties of PPE significantly improved. The allergenicity of PPE-EGCG/CA significantly declined in vitro and in vivo experiments. Our findings confirm that covalent conjugation of PPE with EGCG and CA reduces the allergenicity and improves the functional properties of PPE by changing the structure of the protein.

Bile Acid Profile Influences Digestion Resistance and Antigenicity of Soybean 7S Protein.

Soybean 7S storage protein (ß-conglycinin) is the most important allergen, exhibits resistance in gastrointestinal (GI) digestion, and causes allergies in humans and animals. A previous study has demonstrated that 7S proteins contained innate amyloid aggregates, but the fate of these specific protein aggregates in intestinal digestion and correlation to allergenicity are unclear. In this study, via a modified INFOGEST static in vitro digestion and IgE binding test, we illustrate that the survived amyloid aggregates of soybean 7S protein in GI digestion might be dominant IgE epitopes of soybean protein in humans. The impact of conjugated primary bile acid salt (BS) profile on digestion resistance and immunogenicity of soybean protein is assessed, regarding the binding affinity of BS to protein aggregates with consideration of the BS composition and the physiologically relevant colloidal structure. The results show that chenodeoxycholate-containing colloidal structures exhibit high affinity and unfolding capacity to protein amyloid aggregates, promoting proteolysis by pancreatic enzymes and thus mitigating the antigenicity of soybean protein. This study presents a novel understanding of bile acid profile and colloidal structure influence on the digestibility and antigenicity of dietary proteins. It should be helpful to design in vitro digestion protocol and accurately replicate physiologically relevant digestion conditions.

Aggravation of food allergy symptoms by treatment with acrylamide in a mouse model.

Acrylamide (AA) forms during the thermal processing of food, but adversely affects human health. As the consumption of heat-processed foods increases, the potentially harmful effect of AA on food allergies needs to be clarified. Here, we investigated how AA affects the allergenicity of OVA in vivo using a mouse model of orally induced OVA allergy. AA enhanced OVA-induced food allergic response by increasing IgE, IgG, IgG1, histamine, and MCP-1. AA promoted the Th2 cell response to modulate the imbalance in Th1/Th2. Furthermore, AA reduced the expression of intestinal tight junction proteins, and disrupted the permeability of the intestine, which impaired the intestinal epithelial barrier, resulting in more OVA crossing it. These actions aggravated the allergic reaction of OVA. In conclusion, this study confirmed the potentially harmful effect of AA on food allergy.

Application of Grafting Method in Resistance Identification of Sweet Potato Virus Disease and Resistance Evaluation of Elite Sweet Potato [Ipomoea batatas (L.) Lam] Varieties.

Sweet potato virus disease (SPVD) is one of the main virus diseases in sweet potato [Ipomoea batatas (L.) Lam] that seriously affects the yield of sweet potato. Therefore, the establishment of a simple, rapid and effective method to detect SPVD is of great significance for the early warning and prevention of this disease. In this study, the experiment was carried out in two years to compare the grafting method and side grafting method for three sweet potato varieties, and the optimal grafting method was selected. After grafting with seedlings infected with SPVD, the symptomatic diagnosis and serological detection were performed in 86 host varieties, and the differences in SPVD resistance were determined by fluorescence quantitative PCR (qRT-PCR) and nitrocellulose membrane enzyme-linked immunosorbent assay (NCM-ELISA). The results showed that the survival rate of grafting by insertion method was significantly higher than that by side grafting method, and the disease resistance of different varieties to sweet potato virus disease was tested. The detection method established in this study can provide theoretical basis for identification and screening of resistant sweet potato varieties.

IbInvInh2, a novel invertase inhibitor in sweet potato, regulates starch content through post-translational regulation of vacuolar invertase IbßFRUCT2.

As a key enzyme in the starch and sugar metabolic pathways in sweet potato (Ipomoea batatas (L.) Lam.), the vacuolar invertase (EC 3.2.1.26) IbßFRUCT2 is involved in partitioning and modulating the starch and sugar components of the storage root. However, the post-translational regulation of its invertase activity remains unclear. In this study, we identified three invertase inhibitors, IbInvInh1, IbInvInh2, and IbInvInh3, as potential interaction partners of IbßFRUCT2. All were found to act as vacuolar invertase inhibitors (VIFs) and belonged to the plant invertase/pectin methyl esterase inhibitor superfamily. Among the three VIFs, IbInvInh2 is a novel VIF in sweet potato and was confirmed to be an inhibitor of IbßFRUCT2. The N-terminal domain of IbßFRUCT2 and the Thr39 and Leu198 sites of IbInvInh2 were predicted to be engaged in their interactions. The transgenic expression of IbInvInh2 in Arabidopsis thaliana plants reduced the starch content of leaves, while its expression in the Ibßfruct2-expressing Arabidopsis plants increased the starch content of leaves, suggesting that the post-translational inhibition of IbßFRUCT2 activity by IbInvInh2 contributes to the regulation of the plant starch content. Taken together, our findings reveal a novel VIF in sweet potato and provide insights into the potential regulatory roles of the VIFs and invertase-VIF interaction in starch metabolism. These insights lay the foundation for using VIFs to improve the starch properties of crops.

Regulatory and functional divergence among members of Ibßfruct2, a sweet potato vacuolar invertase gene controlling starch and glucose content.

Sweet potato [Ipomoea batatas (L.) Lam.] is an important food and industrial crop. Its storage root is rich in starch, which is present in the form of granules and represents the principal storage carbohydrate in plants. Starch content is an important trait of sweet potato controlling the quality and yield of industrial products. Vacuolar invertase encoding gene Ibßfruct2 was supposed to be a key regulator of starch content in sweet potato, but its function and regulation were unclear. In this study, three Ibßfruct2 gene members were detected. Their promoters displayed differences in sequence, activity, and cis-regulatory elements and might interact with different transcription factors, indicating that the three Ibßfruct2 family members are governed by different regulatory mechanisms at the transcription level. Among them, we found that only Ibßfruct2-1 show a high expression level and promoter activity, and encodes a protein with invertase activity, and the conserved domains and three conserved motifs NDPNG, RDP, and WEC are critical to this activity. Only two and six amino acid residue variations were detected in sequences of proteins encoded by Ibßfruct2-2 and Ibßfruct2-3, respectively, compared with Ibßfruct2-1; although not within key motifs, these variations affected protein structure and affinities for the catalytic substrate, resulting in functional deficiency and low activity. Heterologous expression of Ibßfruct2-1 in Arabidopsis decreased starch content but increased glucose content in leaves, indicating Ibßfruct2-1 was a negative regulator of starch content. These findings represent an important advance in understanding the regulatory and functional divergence among duplicated genes in sweet potato, and provide critical information for functional studies and utilization of these genes in genetic improvement.

Purification, Immunological Identification, and Characterization of the Novel Silkworm Pupae Allergen Bombyx mori Lipoprotein 3 (Bomb m 6).

Allergic reactions caused by silkworm pupae greatly limit their utilization, and studies suggest that silkworm pupae proteins of 25-30 kDa may be the principal allergens. To further understand these allergens, we attempted to purify a protein of about 30 kDa by ammonium sulfate salting, pH-graded precipitation, and ion-exchange chromatography. The protein was identified by mass spectrometry and characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), western blot, enzyme-linked immunosorbent assays, circular dichroism, and fluorescence spectroscopy analyses. We identified the purified protein as Bombyx mori lipoprotein 3 (Bmlp3), which has high IgE reactivity and is a novel uncharacterized allergen that we named Bomb m 6 according to the WHO/IUIS Allergen Nomenclature Sub-Committee. This allergen is stable against heat, acids, bases, and digestion. In conclusion, we successfully purified and characterized a novel silkworm pupa allergen, which may inform the diagnosis and treatment of silkworm pupa allergies.

Validation of Deep Learning-Based DFCNN in Extremely Large-Scale Virtual Screening and Application in Trypsin I Protease Inhibitor Discovery.

Computational methods with affordable computational resources are highly desirable for identifying active drug leads from millions of compounds. This requires a model that is both highly efficient and relatively accurate, which cannot be achieved by most of the current methods. In real virtual screening (VS) application scenarios, the desired method should perform much better in selecting active compounds by prediction than by random chance. Here, we systematically evaluate the performance of our previously developed DFCNN model in large-scale virtual screening, and the results show our method has approximately 22 times the success rate compared to the random chance on average with a score cutoff of 0.99. Of the 102 test cases, 10 cases have more than 98 times the success rate of a random guess. Interestingly, in three cases, the prediction success rate is 99 times that of a random guess by a score cutoff of 0.99. This indicates that in most situations after our extremely large-scale VS, the dataset can be reduced 20 to 100 times for the next step of virtual screening based on docking or MD simulation. Furthermore, we have employed an experimental method to verify our computational method by finding several activity inhibitors for Trypsin I Protease. In addition, we also show its proof-of-concept application in de novo drug screening. The results indicate the massive potential of this method in the first step of the real drug development workflow. Moreover, DFCNN only takes about 0.0000225s for one protein-compound prediction on average with 80 Intel CPU cores (2.00 GHz) and 60 GB RAM, which is at least tens of thousands of times faster than AutoDock Vina or Schrödinger high-throughput virtual screening. Additionally, an online webserver based on DFCNN for large-scale screening is available at http://cbblab.siat.ac.cn/DFCNN/index.php for the convenience of the users.

A new method to reduce allergenicity by improving the functional properties of soybean 7S protein through covalent modification with polyphenols.

The 7S fraction contains several major allergens of soybean protein. Here, the effects of covalent modification by chlorogenic acid (CHA) and (-)-epigallo-catechin 3-gallate (EGCG) on the allergenicity and functional properties of soybean 7S protein were investigated. Conjugation with EGCG and CHA resulted in the formation of cross-linked protein polymers and changes to the structures of the protein, which might mask or destroy the epitopes on it. In vitro analysis revealed that modification by polyphenols noticeably reduced IgE binding activity and histamine release. In vivo analysis showed that modification led to milder anaphylactic shock symptoms and minor damage of the intestine in mice, with reducing IgG, IgE, IgG1, mMCP-1, and histamine levels. The allergic response was also suppressed by the repression of IFN-γ, IL-4, and IL-5 and the up-regulation of IL-10 and TGF-ß in the conjugate groups. Furthermore, modification enhanced antioxidant, emulsion, foaming capacity, and foam stability of the protein.

Functional and Allergenic Properties Assessment of Conalbumin (Ovotransferrin) after Oxidation.

Conalbumin (CA) is an iron-binding egg protein that has various bioactivities and causes major allergenicity in humans. This study investigated how oxidation affects the multiple functional properties of CA. The lipid peroxidation method was used to prepare treated CA [2,2'-azobis (2-amidinopropane) dihydrochloride (AAPH)-CA and acrolein-CA] complexes. CA induced structural changes through oxidation. These changes enhanced the digestibility, rate of endocytosis in dendritic cells, and emulsifying and foaming properties of CA. ELISA and immunoblot analysis showed that the complexes reduced the IgE-binding ability of CA through lipid oxidation. KU812 cell assays showed that modification by AAPH and acrolein caused the release of IL-4 and histamine to decline. In conclusion, oxidation treatment modified the functional and structural properties of CA, reducing allergenicity during processing and preservation.

Effect of Silkworm Pupa Protein Hydrolysates on Proliferation of Gastric Cancer Cells In Vitro.

The proliferation inhibition effects of the hydrolysates from silkworm pupa proteins on MGC-803 gastric cancer cells were investigated in this study. The specific morphological changes (cell membrane, cell nucleus and cytoskeleton) of cells were measured. In vitro, the proliferation of MGC-803 cells was inhibited by silkworm pupa protein hydrolysates (SPPHs) in a dose-dependent manner. The flow cytometry analysis showed that the blocking effect of SPPHs on the MGC-803 cells was mainly in the G0/G1-phase. The morphological changes, disintegration of the cytoskeleton and retardant cell cycles were probably related to the activation of apoptosis. Thus, SPPHs could be promising as a chemopreventive agent due to their ability to promote apoptosis of tumor cells.

[Spectroscopic studies on the relationship between heat treatment process and immunogenicity of beta-lactoglobulin in milk].

The thermal denaturation of beta-lactoglobulin of milk was investigated by using DSC, circular dichroism spectra, and fluorescence spectra systematically. And its corresponding immunogenicity was tested with ELISA experiments. In addition, bioinformatics methods were also used to explain the spectral characteristics and its corresponding immunogenic change, analyze the conformational changes of the protein during thermal denaturation, and discuss the relationship between conformational change of beta-lactoglobulin caused by heat and immunogenic change. Results from this study should be useful to the establishment of a spectral method examining the extent of thermal denaturation of the food allergen, and be helpful to the understanding of the mechanism of immunogenic change of food allergen treated by heat.

Changes in structure and allergenicity of shrimp tropomyosin by dietary polyphenols treatment.

Here, the potential allergenicity of shrimp tropomyosin (TM) after conjugation with chlorogenic acid (CA) and (-)-epigallo-catechin 3-gallate (EGCG) was assessed. Conformational structures of TM-polyphenol complexes were detected using SDS-PAGE, circular dichroism (CD), and fluorescence. Potential allergenicity was assessed by immunological methods, a rat basophil leukemia cell model (RBL-2H3), and in vivo assays. Indirect ELISA showed that TM-polyphenol complexes caused a conformational change to TM structure, with decreased IgG/IgE binding capacity significantly fewer inflammatory mediators were released with EGCG-TM and CA-TM in a mediator-releasing RBL-2H3 cell line. Mice model showed low allergenicity to serum levels of TM-specific antibody and T-cell cytokine production. EGCG-TM and CA-TM might reduce the potential allergenicity of shrimp TM, which could be used to produce hypoallergenic food in the food industry.

Nutritional, functional, and allergenic properties of silkworm pupae.

Edible insects are a food source that has high nutritional value. Domestic silkworm pupae are an important by-product of sericulture and have a long history as food and feed ingredients in East Asia. Silkworm pupae are a good source of protein, lipids, minerals, and vitamins and are considered a good source of nutrients for humans. Silkworm pupae are a valuable insect source of substances used in healthcare products, medicines, food additives, and animal feed. Because silkworm pupae are being increasingly used in the human diet, potential allergic reactions to the substances they contain must be elucidated. Here, we present an overview of the benefits of silkworm pupae. First, we describe their nutritional value. Second, we report their functional properties and applications, focusing on their potential use in the food and pharmaceutical industries. Finally, we consider the current state of research regarding silkworm pupae-induced allergies.

Enzymatic and Nonenzymatic Conjugates of Lactoferrin and (-)-Epigallocatechin Gallate: Formation, Structure, Functionality, and Allergenicity.

The impact of covalent attachment of (-)-epigallocatechin gallate (EGCG) to lactoferrin (LF) on the structure, morphology, functionality, and allergenicity of the protein was studied. These polyphenol-protein conjugates were formed using various enzymatic (laccase- and tyrosinase-catalyzed oxidation) and nonenzymatic (free radical grafting and alkali treatment) methods. The preparation conditions for forming the enzymatic conjugates were optimized by exploring the influence of order-of-addition effects: protein, polyphenols, and enzymes. The total phenol content of the LF-EGCG conjugates was quantified using the Folin-Ciocalteu method. The nature of the conjugates formed was determined using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Fourier transform infrared (FTIR) spectroscopy analyses. These studies showed that enzymatic cross-linking was a highly effective means of forming LF-EGCG conjugates. Analysis of these conjugates using various spectroscopic methods showed that conjugation to EGCG changed the molecular structure of LF. Atomic force microscopy showed that the four covalent cross-linking methods affected the size and morphology of these LF-EGCG conjugates formed. The antioxidant activity and emulsifying stability of LF were significantly improved by conjugation to EGCG. Finally, an enzyme-linked immunosorbent assay (ELISA) and a western blot assay indicated that conjugation of EGCG reduced the binding capacity of LF to immunoglobulin E (IgE) and immunoglobulin G (IgG), which is consistent with a decrease in allergenicity. Overall, this study suggests that LF-EGCG conjugates formed using enzymatic or nonenzymatic methods have potential applications as functional ingredients in foods.

A Genetically Encoded Bioluminescent System for Fast and Highly Sensitive Detection of Antibodies with a Bright Green Fluorescent Protein.

A method for fast and highly sensitive detection of antibodies in serum would greatly facilitate the early diagnosis of disease and infection and dose optimization of therapeutic antibody. Bioluminescence detection with LUMABS (renamed mNeonG-LUMABS, where mNeonG is short for mNeonGreen) sensors based on bioluminescence resonance energy transfer (BRET) between blue-emitting luciferase Nluc and green fluorescent protein (FP) mNeonGreen has been demonstrated to enable fast detection of antibodies directly in serum with reasonable sensitivity. However, some mNeonG-LUMABS sensors exhibit low sensitivity, and thus, sensitivity improvement remains imperative. Here, we report a bright green FP, Clover4, obtained by structure-guided mutagenesis of green FP Clover. Despite similar brightness and fluorescence spectra of Clover and mNeonGreen, Clover4-LUMABS sensors exhibit a largely increased dynamic range (maximum 20-fold) and much lower limit of detection (LOD) (maximum 5.6-fold), most likely because Clover4 is positioned in a more parallel orientation to Nluc in LUMABS. Due to modular design, Clover4-LUMABS offers a general BRET system for fast and highly sensitive antibody detection in serum.