Phosphatidic acid-regulated SOS2 controls sodium and potassium homeostasis in Arabidopsis under salt stress.

The maintenance of sodium/potassium (Na+ /K+ ) homeostasis in plant cells is essential for salt tolerance. Plants export excess Na+ out of cells mainly through the Salt Overly Sensitive (SOS) pathway, activated by a calcium signal; however, it is unknown whether other signals regulate the SOS pathway and how K+ uptake is regulated under salt stress. Phosphatidic acid (PA) is emerging as a lipid signaling molecule that modulates cellular processes in development and the response to stimuli. Here, we show that PA binds to the residue Lys57 in SOS2, a core member of the SOS pathway, under salt stress, promoting the activity and plasma membrane localization of SOS2, which activates the Na+ /H+ antiporter SOS1 to promote the Na+ efflux. In addition, we reveal that PA promotes the phosphorylation of SOS3-like calcium-binding protein 8 (SCaBP8) by SOS2 under salt stress, which attenuates the SCaBP8-mediated inhibition of Arabidopsis K+ transporter 1 (AKT1), an inward-rectifying K+ channel. These findings suggest that PA regulates the SOS pathway and AKT1 activity under salt stress, promoting Na+ efflux and K+ influx to maintain Na+ /K+ homeostasis.

Sialic acids as attachment factors in mosquitoes mediating Japanese encephalitis virus infection.

The role of Culex mosquitoes in the transmission of Japanese encephalitis virus (JEV) is crucial, yet the mechanisms of JEV infection in these vectors remain unclear. Previous research has indicated that various host factors participate in JEV infection. Herein, we present evidence that mosquito sialic acids enhance JEV infection both in vivo and in vitro. By treating mosquitoes and C6/36 cells with neuraminidase or lectin, the function of sialic acids is effectively blocked, resulting in significant inhibition of JEV infection. Furthermore, knockdown of the sialic acid biosynthesis genes in Culex mosquitoes also leads to a reduction in JEV infection. Moreover, our research revealed that sialic acids play a role in the attachment of JEV to mosquito cells, but not in its internalization. To further explore the mechanisms underlying the promotion of JEV attachment by sialic acids, we conducted immunoprecipitation experiments to confirm the direct binding of sialic acids to the last α-helix in JEV envelope protein domain III. Overall, our study contributes to a molecular comprehension of the interaction between mosquitoes and JEV and offers potential strategies for preventing the dissemination of flavivirus in natural environments.IMPORTANCEIn this study, we aimed to investigate the impact of glycoconjugate sialic acids on mosquito infection with Japanese encephalitis virus (JEV). Our findings demonstrate that sialic acids play a crucial role in enhancing JEV infection by facilitating the attachment of the virus to the cell membrane. Furthermore, our investigation revealed that sialic acids directly bind to the final α-helix in the JEV envelope protein domain III, thereby accelerating virus adsorption. Collectively, our results highlight the significance of mosquito sialic acids in JEV infection within vectors, contributing to a better understanding of the interaction between mosquitoes and JEV.

AraPathogen2.0: An Improved Prediction of Plant-Pathogen Protein-Protein Interactions Empowered by the Natural Language Processing Technique.

Plant-pathogen protein-protein interactions (PPIs) play crucial roles in the arm race between plants and pathogens. Therefore, the identification of these interspecies PPIs is very important for the mechanistic understanding of pathogen infection and plant immunity. Computational prediction methods can complement experimental efforts, but their predictive performance still needs to be improved. Motivated by the rapid development of natural language processing and its successful applications in the field of protein bioinformatics, here we present an improved XGBoost-based plant-pathogen PPI predictor (i.e., AraPathogen2.0), in which sequence encodings from the pretrained protein language model ESM2 and Arabidopsis PPI network-related node representations from the graph embedding technique struc2vec are used as input. Stringent benchmark experiments showed that AraPathogen2.0 could achieve a better performance than its precedent version, especially for processing the test data set with novel proteins unseen in the training data.

Deep learning-assisted prediction of protein-protein interactions in Arabidopsis thaliana.

Currently, the experimentally identified interactome of Arabidopsis (Arabidopsis thaliana) is still far from complete, suggesting that computational prediction methods can complement experimental techniques. Motivated by the prosperity and success of deep learning algorithms and natural language processing techniques, we introduce an integrative deep learning framework, DeepAraPPI, allowing us to predict protein-protein interactions (PPIs) of Arabidopsis utilizing sequence, domain and Gene Ontology (GO) information. Our current DeepAraPPI comprises: (i) a word2vec encoding-based Siamese recurrent convolutional neural network (RCNN) model; (ii) a Domain2vec encoding-based multiple-layer perceptron (MLP) model; and (iii) a GO2vec encoding-based MLP model. Finally, DeepAraPPI combines the prediction results of the three individual predictors through a logistic regression model. Compiling high-quality positive and negative training and test samples by applying strict filtering strategies, DeepAraPPI shows superior performance compared with existing state-of-the-art Arabidopsis PPI prediction methods. DeepAraPPI also provides better cross-species predictive ability in rice (Oryza sativa) than traditional machine learning methods, although the overall performance in cross-species prediction remains to be improved. DeepAraPPI is freely accessible at http://zzdlab.com/deeparappi/. In the meantime, we have also made the source code and data sets of DeepAraPPI available at https://github.com/zjy1125/DeepAraPPI.

Manipulating ZmEXPA4 expression ameliorates the drought-induced prolonged anthesis and silking interval in maize.

Drought poses a major environmental threat to maize (Zea mays) production worldwide. Since maize is a monoecious plant, maize grain yield is dependent on the synchronous development of male and female inflorescences. When a drought episode occurs during flowering, however, an asynchronism occurs in the anthesis and silking interval (ASI) that results in significant yield losses. The underlying mechanism responsible for this asynchronism is still unclear. Here, we obtained a comprehensive development-drought transcriptome atlas of maize ears. Genes that function in cell expansion and growth were highly repressed by drought in 50 mm ears. Notably, an association study using a natural-variation population of maize revealed a significant relationship between the level of α-expansin4 (ZmEXPA4) expression and drought-induced increases in ASI. Furthermore, genetic manipulation of ZmEXPA4 expression using a drought-inducible promoter in developing maize ears reduced the ASI under drought conditions. These findings provide important insights into the molecular mechanism underlying the increase in ASI in maize ears subjected to drought and provide a promising strategy that can be used for trait improvement.

A CRISPR/Cas12a-powered gold/nickel foam surface-enhanced Raman spectroscopy biosensor for nucleic acid specific detection in foods.

Food is a necessary source of energy, but it also serves as a pathway for transmitting infectious pathogens, making food safety a matter of great concern. Rapid, accurate, and specific detection methods for foodborne viruses are crucial. Surface-Enhanced Raman Scattering (SERS), due to its superior sensitivity and characteristic fingerprint spectra, holds enormous potential. However, due to the limitations of SERS, it requires specific conditions to achieve specificity. In order to enhance the specificity and accuracy of nucleic acid detection based on SERS, we have developed a CRISPR-Cas12a-mediated SERS technique to identify target DNA, harnessing the targeting recognition capability of CRISPR-Cas12a and ultra-sensitive SERS tags and successfully addressing SERS' lack of specific detection capability. This system includes a gold/nickel foam substrate (Au-NFs) and a reporter (ssDNA-ROX). The phenomenon of colloidal gold/silver nano-aggregation due to magnesium ions, which is commonly encountered in CRISPR-SERS, was simultaneously solved using AuNFs. The qualitative and quantitative analysis of target DNA in drinking water was performed by monitoring the intensity change of ROX Raman reporter molecules. The results showed that the sensor detected DNA within 30 min and the limit of detection (LOD) was 8.23 fM. This is expected to become one of the alternative methods for nucleic acid detection for its rapid detection and high specificity.

Characterization and function analysis of cathepsin C in Marsupenaeusjaponicus.

Cathepsin C is a cysteine protease widely found in invertebrates and vertebrates, and has the important physiological role participating in proteolysis in vivo and activating various functional proteases in immune/inflammatory cells in the animals. In order to study the role of cathepsin C in the disease resistance of shrimp, we cloned cathepsin C gene (MjcathC) from Marsupenaeus japonicus, analyzed its expression patterns in various tissues, performed MjcathC-knockdown, and finally challenged experimental shrimps with Vibrio alginolyticus and WSSV. The results have shown the full length of MjcathC is 1782 bp, containing an open reading frame of 1350 bp encoding 449 amino acids. Homology analysis revealed that the predicted amino acid sequence of MjcathC shared respectively 88.42 %, 87.36 % and 87.58 % similarity with Penaeus monodon, Fenneropenaeus penicillatus and Litopenaeus vannamei. The expression levels of MjcathC in various tissues of healthy M. japonicus are the highest in the liver, followed by the gills and heart, and the lowest in the stomach. The expression levels of MjcathC were significantly up-regulated in all examined tissues of shrimp challenged with WSSV or V. alginolyticus. After knockdown-MjcathC using RNAi technology in M. japonicus, the expression levels of lectin and heat shock protein 70 in MjcathC-knockdown shrimp were significantly down-regulated, and the mortality of MjcathC-knockdown shrimp challenged by WSSV and V. alginolyticus significantly increased. Knockdown of the MjcathC reduced the resistance of M. japonicus to WSSV and V. alginolyticus. The above results have indicated that cathepsin C may play an important role in the antibacterial and antiviral innate immunity of M. japonicus.

More Is Better: Dual-Acceptor Engineering for Constructing Second Near-Infrared Aggregation-Induced Emission Luminogens to Boost Multimodal Phototheranostics.

The manipulation of electron donor/acceptor (D/A) shows an endless impetus for innovating optical materials. Currently, there is booming development in electron donor design, while research on electron acceptor engineering has received limited attention. Inspired by the philosophical idea of "more is different", two systems with D'-D-A-D-D' (1A system) and D'-D-A-A-D-D' (2A system) structures based on acceptor engineering were designed and studied. It was demonstrated that the 1A system presented a weak aggregation-induced emission (AIE) to aggregation-caused quenching (ACQ) phenomenon, along with the increased acceptor electrophilicity and planarity. In sharp contrast, the 2A system with one more acceptor exhibited an opposite ACQ-to-AIE transformation. Interestingly, the fluorophore with a more electron-deficient A-A moiety in the 2A system displayed superior AIE activity. More importantly, all compounds in the 2A system showed significantly higher molar absorptivity (ε) in comparison to their counterparts in the 1A system. Thanks to the highest ε, near-infrared-II (NIR-II, 1000-1700 nm) emission, desirable AIE property, favorable reactive oxygen species (ROS) generation, and high photothermal conversion efficiency, a representative member of the 2A system handily performed in fluorescence-photoacoustic-photothermal multimodal imaging-guided photodynamic-photothermal collaborative therapy for efficient tumor elimination. Meanwhile, the NIR-II fluorescence imaging of blood vessels and lymph nodes in living mice was also accomplished. This study provides the first evidence that the dual-connected acceptor tactic could be a new molecular design direction for the AIE effect, resulting in high ε, aggregation-intensified NIR-II fluorescence emission, and improved ROS and heat generation capacities of phototheranostic agents.

Non-invasive diagnosis of primary Sjögren's syndrome using ultrasonography and transcriptome biomarkers.

Diagnosing primary Sjögren's syndrome (pSS) is difficult due to clinical heterogeneity and the absence of non-invasive specific biomarkers. To develop non-invasive pSS diagnosis methods that integrate classic clinical indexes, major salivary gland ultrasonography (SGUS), and gene expression profiles shared by labial gland and peripheral blood, we conducted a study on a cohort of 358 subjects. We identified differentially expressed genes (DEGs) in glands and blood that were enriched in defense response to virus and type I interferon production pathways. Four upregulated DEGs common in glands and blood were identified as hub genes based on the protein-protein interaction networks. A random forest model was trained using features, including SGUS, anti-SSA/Ro60, keratoconjunctivitis sicca tests, and gene expression levels of MX1 and RSAD2. The model achieved comparable pSS diagnosis accuracy to the golden standard method based on labial gland biopsy. Our findings implicate this novel model as a promising diagnosis technique of pSS.

Current status and future perspectives of computational studies on human-virus protein-protein interactions.

The protein-protein interactions (PPIs) between human and viruses mediate viral infection and host immunity processes. Therefore, the study of human-virus PPIs can help us understand the principles of human-virus relationships and can thus guide the development of highly effective drugs to break the transmission of viral infectious diseases. Recent years have witnessed the rapid accumulation of experimentally identified human-virus PPI data, which provides an unprecedented opportunity for bioinformatics studies revolving around human-virus PPIs. In this article, we provide a comprehensive overview of computational studies on human-virus PPIs, especially focusing on the method development for human-virus PPI predictions. We briefly introduce the experimental detection methods and existing database resources of human-virus PPIs, and then discuss the research progress in the development of computational prediction methods. In particular, we elaborate the machine learning-based prediction methods and highlight the need to embrace state-of-the-art deep-learning algorithms and new feature engineering techniques (e.g. the protein embedding technique derived from natural language processing). To further advance the understanding in this research topic, we also outline the practical applications of the human-virus interactome in fundamental biological discovery and new antiviral therapy development.

HVIDB: a comprehensive database for human-virus protein-protein interactions.

While leading to millions of people's deaths every year the treatment of viral infectious diseases remains a huge public health challenge.Therefore, an in-depth understanding of human-virus protein-protein interactions (PPIs) as the molecular interface between a virus and its host cell is of paramount importance to obtain new insights into the pathogenesis of viral infections and development of antiviral therapeutic treatments. However, current human-virus PPI database resources are incomplete, lack annotation and usually do not provide the opportunity to computationally predict human-virus PPIs. Here, we present the Human-Virus Interaction DataBase (HVIDB, http://zzdlab.com/hvidb/) that provides comprehensively annotated human-virus PPI data as well as seamlessly integrates online PPI prediction tools. Currently, HVIDB highlights 48 643 experimentally verified human-virus PPIs covering 35 virus families, 6633 virally targeted host complexes, 3572 host dependency/restriction factors as well as 911 experimentally verified/predicted 3D complex structures of human-virus PPIs. Furthermore, our database resource provides tissue-specific expression profiles of 6790 human genes that are targeted by viruses and 129 Gene Expression Omnibus series of differentially expressed genes post-viral infections. Based on these multifaceted and annotated data, our database allows the users to easily obtain reliable information about PPIs of various human viruses and conduct an in-depth analysis of their inherent biological significance. In particular, HVIDB also integrates well-performing machine learning models to predict interactions between the human host and viral proteins that are based on (i) sequence embedding techniques, (ii) interolog mapping and (iii) domain-domain interaction inference. We anticipate that HVIDB will serve as a one-stop knowledge base to further guide hypothesis-driven experimental efforts to investigate human-virus relationships.

A novel perlucin-like protein (PLP) protects Litopenaeus vannamei against Vibrio harveyi infection.

C-type lectins (CTLs), as pattern recognition receptors (PRRs), play an important role in the innate immunity of Litopenaeus vannamei. In this study, a novel CTL, named perlucin-like protein (PLP), was identified from L. vannamei, which shared homology sequences of PLP from Penaeus monodon. PLP from L. vannamei was expressed in the hepatopancreas, eyestalk, muscle and brain and could be activated in the tissues (hepatopancreas, muscle, gill and intestine) after infection with the pathogen Vibrio harveyi. Bacteria (Vibrio alginolyticus, V. parahaemolyticus, V. harveyi, Streptococcus agalactiae and Bacillus subtilis) could be bound and agglutinated by the PLP recombinant protein in a Ca2+-dependent manner. Moreover, PLP could stabilise the expression of the immune-related genes (ALF, SOD, HSP70, Toll4 and IMD) and apoptosis gene (Caspase2). The RNAi of PLP could remarkably affect the expression of antioxidant gene, antimicrobial peptide genes, other CTLs, apoptosis genes, Toll signaling pathways, and IMD signaling pathways. Moreover, PLP reduced the bacterial load in the hepatopancreas. These results suggested that PLP was involved in the innate immune response against V. harveyi infection by recognising bacterial pathogens and activating the expression of immune-related and apoptosis genes.

Involvement of Nrf2 in the immune regulation of Litopenaeus vannamei against Vibrio harveyi infection.

NF-E2-related factor-like-2 (Nrf2) is a transcription factor that belongs to the Cap'n'Collar transcription factor family and plays a role in regulating inflammation, autophagy, metabolism, proteostasis, and cancer prevention. However, its influence on Vibrio spp infection in L. vannamei remains uncertain. In this study, the effects of Nrf2 on the immune response in Vibrio spp infection was determined by RT-PCR and histopathological analysis. The results showed that RNAi of Nrf2 significantly decreased the expression of antioxidant-related genes (CAT, SOD and GST; p < 0.05), and significantly up-regulated inflammation-related genes (IMD, pro-PO, P38, Toll, Hsp70, NFκB and RAB6A; p < 0.05) and the apoptosis gene (caspase3). Under the infection of V. harveyi, histopathological analysis showed that after RNAi of Nrf2, the hepatopancreas of shrimp has an abnormal arrangement of hepatic tubules and vacuolization of hepatocyte; The basement membrane is peeled off and the epithelial cells are massively necrotic. Compared with the RNAi of Nrf2 group, the tissue damage in the SFN group was much lessened, and there were fewer apoptosis signals in the TUNEL assay. In conclusion, this experiment indicated that Nrf2 is involved in the regulation of inflammatory response, oxidative stress,and apoptosis induced by V. harveyi in L. vannamei.

A novel C-type lectin for Litopenaeus vannamei involved in the innate immune response against Vibrio infection.

C-type lectins (CTLs), as a member of pattern recognition receptors, play a vital role in the innate immune response of invertebrates to eliminate micro-invaders. In this study, a novel CTL of Litopenaeus vannamei, namely, LvCTL7, was successfully cloned, with an open reading frame of 501 bp and a capability to encode 166 amino acids. Blast analysis showed that the amino acid sequence similarity between LvCTL7 and MjCTL7 (Marsupenaeus japonicus) was 57.14%. LvCTL7 was mainly expressed in hepatopancreas, muscle, gill and eyestalk. Vibrio harveyi can significantly affect LvCTL7 expression level in hepatopancreases, gills, intestines and muscles (p < 0.05). LvCTL7 recombinant protein can bind to Gram-positive bacteria (Bacillus subtilis) and Gram-negative bacteria (Vibrio parahaemolyticus and V. harveyi). It can cause the agglutination of V. alginolyticus and V. harveyi, but it had no effect on Streptococcus agalactiae and B. subtilis. The expression levels of SOD, CAT, HSP 70, Toll 2, IMD and ALF genes in the challenge group added with LvCTL7 protein were more stable than those in the direct challenge group (p < 0.05). Moreover, knockdown of LvCTL7 by double-stranded RNA interference downregulated the expression levels of genes (ALF, IMD and LvCTL5) that protect against bacterial infection (p < 0.05). These results indicated that LvCTL7 had microbial agglutination and immunoregulatory activity, and it was involved in the innate immune response against Vibrio infection in L. vannamei.

Heme Oxygenase-1 Is Involved in the Repair of Oxidative Damage Induced by Oxidized Fish Oil in Litopenaeus vannamei by Sulforaphane.

Heme oxygenase-1 (HO-1), which could be highly induced under the stimulation of oxidative stress, functions in reducing the damage caused by oxidative stress, and sulforaphane (SFN) is an antioxidant. This study aims to investigate whether HO-1 is involved in the repair of oxidative damage induced by oxidized fish oil (OFO) in Litopenaeus vannamei by sulforaphane (SFN). The oxidative stress model of L. vannamei was established by feeding OFO feed (OFO accounts for 6%), and they were divided into the following four groups: control group (injected with dsRNA-EGFP and fed with common feed), dsRNA-HO-1 group (dsRNA-HO-1, common feed), dsRNA-HO-1 + SFN group (dsRNA-HO-1, supplement 50 mg kg-1 SFN feed), and SFN group (dsRNA-EGFP, supplement 50 mg kg-1 SFN feed). The results showed that the expression level of HO-1 in the dsRNA-HO-1 + SFN group was significantly increased compared with the dsRNA-HO-1 group (p < 0.05). The activities of SOD in muscle and GPX in hepatopancreas and serum of the dsRNA-HO-1 group were significantly lower than those of the control group, and MDA content in the dsRNA-HO-1 group was the highest among the four groups. However, SFN treatment increased the activities of GPX and SOD in hepatopancreas, muscle, and serum and significantly reduced the content of MDA (p < 0.05). SFN activated HO-1, upregulated the expression of antioxidant-related genes (CAT, SOD, GST, GPX, Trx, HIF-1α, Nrf2, prx 2, Hsp 70), and autophagy genes (ATG 3, ATG 5), and stabilized the expression of apoptosis genes (caspase 2, caspase 3) in the hepatopancreas (p < 0.05). In addition, knocking down HO-1 aggravated the vacuolation of hepatopancreas and increased the apoptosis of hepatopancreas, while the supplement of SFN could repair the vacuolation of hepatopancreas and reduce the apoptosis signal. In summary, HO-1 is involved in the repair of the oxidative damage induced by OFO in L. vannamei by SFN.

Immune-enhancing effects of Astragalus polysaccharides and Ganoderma lucidum polysaccharides on Vibrio harveyi flgJ DNA vaccine in grouper.

Astragalus polysaccharides (APS) and Ganoderma lucidum polysaccharides (GLP) have been shown to possess strong immunoregulatory properties in aquatic animals. In this study, the fragment containing Vibrio harveyi flgJ gene was ligated into pcDNA3.1(+) vector and pcDNA3.1(+)-flgJ was constructed as DNA vaccine. APS and GLP were used as DNA vaccine adjuvants to evaluate the immunoregulatory effect by intramuscular injection to pearl gentian grouper (♀Epinephelus fuscoguttatus × â™‚E. lanceolatus). The results showed that pcDNA3.1(+)-flgJ combined with APS or GLP could significantly up-regulate the innate and adaptive immune response in fish, including serum-specific antibody titres, catalase and lysozyme activities. At the same time, DNA vaccine combined with APS or GLP significantly up-regulated the expression levels of CD8α, IgM, IL-1ß, MHC-Iα, MyD88 and TLR3 genes in thymus, head kidney, spleen and liver of pearl gentian grouper in comparison with those of the pFlgJ group. After 42 days post-vaccination, V. harveyi was used to challenge pearl gentian grouper by intraperitoneal injection. The relative percentage of survival (RPS) of pFlgJ, pFlgJ +APS, pFlgJ +GLP and pFlgJ+APS+GLP groups were 69%, 81%, 77% and 88%, respectively. These results suggested APS and GLP were potential adjuvants for DNA vaccine against V. harveyi infection in pearl gentian grouper.

Economic values of reproductive and growth traits in Chinese Yiling sheep.

This study aimed to calculate the economic value (EV) of reproductive and growth traits for Yiling sheep. A bio-economic model was developed to assess the economic value of litter size (LS), litter size at weaning (LSW), age at first lambing (AFL), lambing interval (LI), birth weight (BW), weaning weight (WW), and 6-month body weight (6MW). The sensitivity of the economic value of traits to changes in market prices was also analyzed. In this study, the trait with the highest EV was LSW (427.97 ¥), followed by LS (419.96 ¥), BW (52.13 ¥), 6MW (14.46 ¥), WW (11.03 ¥), AFL (-0.51 ¥), and LI (-9.09 ¥). LS was the most important trait in the production system with a relative economic weight of 22.81%, followed by 6MW and LSW with relative economic weights of 18.98% and 19.01%, respectively. All traits assessed, except AFL and LI, had positive economic values, indicating that genetic improvement of these traits would have a positive impact on profitability. The results of the sensitivity analysis showed that the economic value of AFL was not sensitive to price changes. All growth traits were unaffected by price changes in labor and medical costs. In addition, the LS, LSW, LI, WW, and 6MW were sensitive to changes in liveweight and feed prices. Generally, as feed prices increased, the economic value of all traits except LI and BW decreased. Except for LI and BW, the economic value of all traits increased due to the rise in liveweight prices. This suggested that liveweight and feed prices significantly affect the profitability of the production system.

Transfer learning via multi-scale convolutional neural layers for human-virus protein-protein interaction prediction.

MOTIVATION: To complement experimental efforts, machine learning-based computational methods are playing an increasingly important role to predict human-virus protein-protein interactions (PPIs). Furthermore, transfer learning can effectively apply prior knowledge obtained from a large source dataset/task to a small target dataset/task, improving prediction performance. RESULTS: To predict interactions between human and viral proteins, we combine evolutionary sequence profile features with a Siamese convolutional neural network (CNN) architecture and a multi-layer perceptron. Our architecture outperforms various feature encodings-based machine learning and state-of-the-art prediction methods. As our main contribution, we introduce two transfer learning methods (i.e. 'frozen' type and 'fine-tuning' type) that reliably predict interactions in a target human-virus domain based on training in a source human-virus domain, by retraining CNN layers. Finally, we utilize the 'frozen' type transfer learning approach to predict human-SARS-CoV-2 PPIs, indicating that our predictions are topologically and functionally similar to experimentally known interactions. AVAILABILITY AND IMPLEMENTATION: The source codes and datasets are available at https://github.com/XiaodiYangCAU/TransPPI/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Glutathione-Responsive Chemodynamic Therapy of Manganese(III/IV) Cluster Nanoparticles Enhanced by Electrochemical Stimulation via Oxidative Stress Pathway.

Escalating the level of reactive oxygen species (ROS) in a tumor microenvironment is one of the effective strategies to improve the efficacy of anticancer therapy. In this work, manganese cluster nanoparticles (Mn12) encapsulated with heparin (Mn12-heparin) were developed as a chemodynamic therapeutic agent for cancer treatment by raising ROS levels in tumor cells via cascade reactions. The manganese cluster is a cluster of mixed valence (III/IV) with acetate as the ligand. The cluster is readily subject to reduction by glutathione (GSH) to release Mn(II), which reacts with H2O2 to generate hydroxyl radicals via a Fenton-like pathway. The generation of hydroxyl radicals could be enhanced by the stimulation of an external alternative electric field during which GSH acts as an electron mediator to enhance the release of Mn(II) from the cluster. The relatively high levels of both H2O2 and GSH and the acidic environment in tumor cells strengthen its specificity when the manganese cluster system is employed to suppress or eliminate tumors. Both in vitro and in vivo results suggest that, in addition to the cytotoxicity imposed by the raised ROS level due to the presence of Mn(II) species, the depletion of endogenous GSH leads indirectly to the inhibition of glutathione peroxidase 4 (GPX4), consequently raising the lipid peroxidation (LPO) level to cause ferroptosis. The apoptosis and ferroptosis jointly render the manganese-based agent potent efficacy with tumor-targeting specificity in antitumor treatment under electric stimulation.

Effect of sub-lethal ammonia and nitrite stress on autophagy and apoptosis in hepatopancreas of Pacific whiteleg shrimp Litopenaeusvannamei.

Oxidative stress caused by ammonia and nitrite, affect the health and growth of aquaculture animals, results in oxidative damages. However, the toxic mechanism and pathogenesis of ammonia and nitrite to aquatic invertebrates are not completely clear. The present study was conducted to investigate the effects of sub-lethal ammonia and nitrite on autophagy and apoptosis in hepatopancreas of Pacific whiteleg shrimp Litopenaeus vannamei. Shrimps were exposed to sub-lethal ammonia (20 mg/L) and nitrite (20 mg/L) for 72 h, respectively. Hepatopancreas was collected for investigating the autophagy and apoptosis under stress conditions. The results showed that ammonia stress could induce up-regulated of autophagy (ATG3, ATG4, ATG10 and ATG12) and apoptosis (Caspase3 and P53) genes transcription. Nitrite stress could also induce up-regulated of autophagy (ATG3, ATG4, ATG5 and ATG10) and apoptosis (Caspase3) genes transcription. The expression of the autophagy related genes increased at first and then decreased with increasing exposure time. The atrophy, lysis, vacuolation of cell and other tissue damages in hepatopancreas were observed after 72h exposure to ammonia and nitrite. The results indicated that ammonia and nitrite stress could induce autophagy and apoptosis, and results in oxidative damage.