HeteroTCR: A heterogeneous graph neural network-based method for predicting peptide-TCR interaction.

Identifying interactions between T-cell receptors (TCRs) and immunogenic peptides holds profound implications across diverse research domains and clinical scenarios. Unsupervised clustering models (UCMs) cannot predict peptide-TCR binding directly, while supervised predictive models (SPMs) often face challenges in identifying antigens previously unencountered by the immune system or possessing limited TCR binding repertoires. Therefore, we propose HeteroTCR, an SPM based on Heterogeneous Graph Neural Network (GNN), to accurately predict peptide-TCR binding probabilities. HeteroTCR captures within-type (TCR-TCR or peptide-peptide) similarity information and between-type (peptide-TCR) interaction insights for predictions on unseen peptides and TCRs, surpassing limitations of existing SPMs. Our evaluation shows HeteroTCR outperforms state-of-the-art models on independent datasets. Ablation studies and visual interpretation underscore the Heterogeneous GNN module's critical role in enhancing HeteroTCR's performance by capturing pivotal binding process features. We further demonstrate the robustness and reliability of HeteroTCR through validation using single-cell datasets, aligning with the expectation that pMHC-TCR complexes with higher predicted binding probabilities correspond to increased binding fractions.

VitTCR: A deep learning method for peptide recognition prediction.

This study introduces VitTCR, a predictive model based on the vision transformer (ViT) architecture, aimed at identifying interactions between T cell receptors (TCRs) and peptides, crucial for developing cancer immunotherapies and vaccines. VitTCR converts TCR-peptide interactions into numerical AtchleyMaps using Atchley factors for prediction, achieving AUROC (0.6485) and AUPR (0.6295) values. Benchmark analysis indicates VitTCR's performance is comparable to other models, with further comparative studies suggested to understand its effectiveness in varied contexts. Additionally, integrating a positional bias weight matrix (PBWM), derived from amino acid contact probabilities in structurally resolved pMHC-TCR complexes, slightly improves VitTCR's accuracy. The model's predictions show weak yet statistically significant correlations with immunological factors like T cell clonal expansion and activation percentages, underscoring the biological relevance of VitTCR's predictive capabilities. VitTCR emerges as a valuable computational tool for predicting TCR-peptide interactions, offering insights for immunotherapy and vaccine development.

Characterization of a mobilizable megaplasmid carrying multiple resistance genes from a clinical isolate of Pseudomonas aeruginosa.

Introduction: The horizontal transfer of antibiotic resistance genes mediated by plasmids seriously hinders the effectiveness of modern medical treatment, and thus has attracted widespread attention. Additionally, the co-selection mechanism of antibiotic resistance genes (ARGs) and heavy metal resistance genes (MRGs) on mobile elements may further exacerbate the horizontal transfer of resistance genes. Methods: In this study, a multidrug-resistant Pseudomonas aeruginosa strain, termed BJ86 (CHPC/NPRC1.4142), was isolated from a patient's sputum specimen. In vitro tests for antimicrobial susceptibility, conjugation, whole-genome sequencing, and bioinformatics analysis were used to explore the potential mechanisms of resistance and its spread. Results and discussion: Sequencing analysis indicates that P. aeruginosa BJ86 carries an amazing 522.5 kb-length megaplasmid, pBJ86, which contained a 93.5 kb-length multiple resistance region (MRR); 18 kinds of genes were identified as ARGs in this region, including tmexCD-oprJ, blaDIM-1, qnrVC6 that mediate resistance to multiple antibiotics and the operons mer that mediates heavy metal mercury resistance. In addition, there is also an 80 kb variable region (VR) on the plasmid pBJ86, and the genes encoding relaxase and type IV coupling protein (T4CP) were determined in this region, both of which are related to the conjugation and transfer ability of the plasmid. Bioinformatics analysis shows that many functional genes have insertion sequences and transposases on their flanks, which may have accumulated in the plasmid pBJ86 after multiple acquisition events. Conjugated transfer and in vitro tests for antimicrobial susceptibility verified the mobility and plasmid pBJ86-mediated resistance. To our knowledge, we are the first to report a mobilizable megaplasmid that simultaneously carried tmexCD-oprJ, blaDIM-1, qnrVC6, and the operons mer and can be transferred with frequencies of 6.24 × 10-7 transconjugants per donor cell.

Constructing an Interactive and Integrated Analysis and Identification Platform for Pathogenic Microorganisms to Support Surveillance Capacity.

INTRODUCTION: Whole genome sequencing (WGS) holds significant promise for epidemiological inquiries, as it enables the identification and tracking of pathogenic origins and dissemination through comprehensive genome analysis. This method is widely preferred for investigating outbreaks and monitoring pathogen activity. However, the effective utilization of microbiome sequencing data remains a challenge for clinical and public health experts. Through the National Pathogen Resource Center, we have constructed a dynamic and interactive online analysis platform to facilitate the in-depth analysis and use of pathogen genomic data, by public health and associated professionals, to support infectious disease surveillance framework building and capacity warnings. METHOD: The platform was implemented using the Java programming language, and the front-end pages were developed using the VUE framework, following the MVC (Model-View-Controller) pattern to enable interactive service functionalities for front-end data collection and back-end data computation. Cloud computing services were employed to integrate biological information analysis tools for conducting fundamental analysis on sequencing data. RESULT: The platform achieved the goal of non-programming analysis, providing an interactive visual interface that allows users to visually obtain results by setting parameters in web pages. Moreover, the platform allows users to export results in various formats to further support their research. DISCUSSION: We have established a dynamic and interactive online platform for bioinformatics analysis. By encapsulating the complex background experiments and analysis processes in a cloud-based service platform, the complex background experiments and analysis processes are presented to the end-user in a simple and interactive manner. It facilitates real-time data mining and analysis by allowing users to independently select parameters and generate analysis results at the click of a button, based on their needs, without the need for a programming foundation.

Screening of Staphylococcus aureus for Disinfection Evaluation and Transcriptome Analysis of High Tolerance to Chlorine-Containing Disinfectants.

The nonstandard use of disinfectants can lead to the disinfectant resistance of bacteria and even increase antibiotic resistance. However, compared with the study of antibiotic resistance, studies of bacterial resistance to disinfectants are relatively few in number. In this study, we explored the standard strain screening procedure for the evaluation of disinfection efficacy. Staphylococcus aureus strains with different sources and substrates were selected from the National Pathogen Resource Center of China and screened the standard strains that could evaluate the long-term bacteriostatic effect of the chlorine-containing disinfectants through the determination of the physical properties, genome-based safety evaluation, and disinfection test evaluation. In this process, one S. aureus strain was more resistant to the long-term bacteriostasis of chlorine-containing disinfectants than the other strains. This strain and the standard strain ATCC 6538 were cultured in the medium containing a low concentration of chlorine-containing disinfectant synchronously. Then, comparative transcriptome analysis was carried out to investigate the potential mechanism of a high tolerance to chlorine-containing disinfectants. The pathway of significant differential expression is related to the oxocarboxylic acid metabolic mechanism, amino acid metabolic mechanism, and pyrimidine mechanism, which may be the molecular mechanism of S. aureus evolution to adapt to chlorine-containing disinfectants. Our study established a technical process for screening and evaluating standard strains for disinfection, which also provided a reference for studying the bacterial evolution mechanism toward chlorine tolerance.

The Effect of Cryopreservation on the Survival of Nocardia farcinica and Yersinia pestis vaccine strains.

Pathogenic microorganisms are valuable biological resources, closely related to biosecurity, human health, environmental protection, and renewable energy. It is very important to properly preserve the microbial resources by methods to maintain the purity, viability, and integrity, and to avoid prolonged degradation. The present work aims to explore the cryopreservation technology of Nocardia farcinica (Gram-positive bacteria) and Yersinia pestis vaccine strains (Gram-negative bacteria). The effects of cryoprotectants (CPAs), freezing temperature, and freeze-thaw cycles on the two bacteria in the cryopreservation process were studied. The results showed that the addition of CPAs (glycerol, propylene glycol, sucrose, glucose, l-carnitine, l-proline, and skim milk) significantly enhanced the survival rates of the N. farcinica and Y. pestis vaccine strains. However, high concentrations of CPAs can produce biochemical toxicity in the two pathogens. The utilization of composite CPAs not only reduced the toxicity but also improved the survival rates of samples during cryopreservation. The optimal composite CPA for N. farcinica is 0.292 M sucrose, 0.62 M l-carnitine, and 2.82 M glycerol. The optimal composite CPA for Y. pestis is 0.62 M l-carnitine, 8.46 M glycerin, and 0.292 M sucrose. The results showed that the quality of the strains stored at -80°C and -196°C was better. For the case of freeze-thaw cycles, the two pathogens have different degrees of reduction, and the survival rate of Y. pestis decreased more than that of N. farcinica. The uniform distribution of bacteria in CPAs can form uniform nucleation sites in the solution system, which is beneficial to the cryopreservation of strains, as can be seen from the experimental results from a differential scanning calorimeter. This study may provide a reference for better preservation of precious natural biological resources of pathogenic microorganisms.

Distribution and Molecular Characteristics of Vibrio Species Isolated from Aquatic Environments in China, 2020.

To understand the characteristics of Vibrio isolates in aquatic environments in China and their public health significance, this study investigated water samples in six cities in China in 2020. A total of 88 sampling locations were included and Vibrio isolates were identified in 81 of them. A total of 143 Vibrio isolates belonging to 16 species were selected for characterization. The population structure of Vibrio species showed great differences among the six cities, indicating regional specificity. The presence of virulence genes was examined for the isolates (n = 78) of five pathogenic Vibrio species. All isolates except one (n = 77) contained at least one virulence gene and isolates belonging to the same species showed very similar virulence gene profiles. Then, 26 isolates from 12 species were examined by multilocus sequence typing and were assigned to 25 STs, of which 24 STs were new. Also, the presence of antibiotic-resistant genes was investigated for all 143 isolates and only three isolates were found to contain genes from aminoglycosides, phenicols, beta-lactams or the tetracycline family. Our results provide valuable insights into the Vibrio community in Chinese aquatic environments and can be applied as guidance for the environmental surveillance of the risk of Vibrio isolates.

Transforming Ti3C2Tx MXene's intrinsic hydrophilicity into superhydrophobicity for efficient photothermal membrane desalination.

Owing to its 100% theoretical salt rejection capability, membrane distillation (MD) has emerged as a promising seawater desalination approach to address freshwater scarcity. Ideal MD requires high vapor permeate flux established by cross-membrane temperature gradient (∆T) and excellent membrane durability. However, it's difficult to maintain constant ∆T owing to inherent heat loss at feedwater side resulting from continuous water-to-vapor transition and prevent wetting transition-induced membrane fouling and scaling. Here, we develop a Ti3C2Tx MXene-engineered membrane that imparts efficient localized photothermal effect and strong water-repellency, achieving significant boost in freshwater production rate and stability. In addition to photothermal effect that circumvents heat loss, high electrically conductive Ti3C2Tx MXene also allows for self-assembly of uniform hierarchical polymeric nanospheres on its surface via electrostatic spraying, transforming intrinsic hydrophilicity into superhydrophobicity. This interfacial engineering renders energy-efficient and hypersaline-stable photothermal membrane distillation with a high water production rate under one sun irradiation.

Access and benefit-sharing of the pathogenic microorganisms such as SARS-CoV-2.

With the outbreak of coronavirus disease 2019 (COVID-19), it is essential to share pathogens and their data information safely, transparently, and timely. At the same time, it is also worth exploring how to share the benefits of using the provided pathogenic microorganisms fairly and equitably. There are some mechanisms for the management and sharing of pathogenic microbial resources in the world, such as the World Health Organization (WHO), the United States, the Europe, and China. This paper studies these mechanisms and puts forward "PICC" principles, including public welfare principle, interests principle, classified principle, and category principle, to strengthen cooperation, improve efficiency, and maintain biosafety.

Corrigendum: Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equi.

[This corrects the article DOI: 10.3389/fcimb.2022.807610.].

Genomic Characteristics Revealed Plasmid-Mediated Pathogenicity and Ubiquitous Rifamycin Resistance of Rhodococcus equi.

Rhodococcus equi is a zoonotic pathogen that can cause fatal disease in patients who are immunocompromised. At present, the epidemiology and pathogenic mechanisms of R. equi infection are not clear. This study characterized the genomes of 53 R. equi strains from different sources. Pan-genome analysis showed that all R. equi strains contained 11481 pan genes, including 3690 core genes and 602 ~ 1079 accessory genes. Functional annotation of pan genome focused on the genes related to basic lifestyle, such as the storage and expression of metabolic and genetic information. Phylogenetic analysis based on pan-genome showed that the R. equi strains were clustered into six clades, which was not directly related to the isolation location and host source. Also, a total of 84 virulence genes were predicted in 53 R. equi strains. These virulence factors can be divided into 20 categories related to substance metabolism, secreted protein and immune escape. Meanwhile, six antibiotic resistance genes (RbpA, tetA (33), erm (46), sul1, qacEdelta 1 and aadA9) were detected, and all strains carried RbpA related to rifamycin resistance. In addition, 28 plasmids were found in the 53 R. equi strains, belonging to Type-A (n = 14), Type-B (n = 8) and Type-N (n = 6), respectively. The genetic structures of the same type of plasmid were highly similar. In conclusion, R. equi strains show different genomic characteristics, virulence-related genes, potential drug resistance and virulence plasmid structures, which may be conducive to the evolution of its pathogenesis.

Inhibiting the Leidenfrost effect above 1,000 °C for sustained thermal cooling.

The Leidenfrost effect, namely the levitation of drops on hot solids1, is known to deteriorate heat transfer at high temperature2. The Leidenfrost point can be elevated by texturing materials to favour the solid-liquid contact2-10 and by arranging channels at the surface to decouple the wetting phenomena from the vapour dynamics3. However, maximizing both the Leidenfrost point and thermal cooling across a wide range of temperatures can be mutually exclusive3,7,8. Here we report a rational design of structured thermal armours that inhibit the Leidenfrost effect up to 1,150 °C, that is, 600 °C more than previously attained, yet preserving heat transfer. Our design consists of steel pillars serving as thermal bridges, an embedded insulating membrane that wicks and spreads the liquid and U-shaped channels for vapour evacuation. The coexistence of materials with contrasting thermal and geometrical properties cooperatively transforms normally uniform temperatures into non-uniform ones, generates lateral wicking at all temperatures and enhances thermal cooling. Structured thermal armours are limited only by their melting point, rather than by a failure in the design. The material can be made flexible, and thus attached to substrates otherwise challenging to structure. Our strategy holds the potential to enable the implementation of efficient water cooling at ultra-high solid temperatures, which is, to date, an uncharted property.

The first strain of monkeypox isolated in the Chinese Mainland and preserved at the National Pathogen Resource Center of China.

On September 16, 2022, the first imported monkeypox case was reported in the Chinese Mainland. Laboratory tests including nucleic acid detection were carried out in Chongqing Nan'an Centre for Disease Control and Prevention and Chongqing Center for Disease Control and Prevention. After that, monkeypox virus was isolated by the Institute for Viral Disease Control and Prevention and preserved at the National Pathogen Resource Center on September 18, 2022. The National Pathogen Resource Center shared the basic information of monkeypox virus strain, samples, biosafety, strain imaging, RT-PCR primers, and probes sequence timely to support the prevention and control of monkeypox epidemic and facilitate the scientific research on vaccine development, drug screening and evaluation of monkeypox virus in the future.

Rapid electrochemical detection of domoic acid based on polydopamine/reduced graphene oxide coupled with in-situ imprinted polyacrylamide.

Domoic acid, namely amnesic shellfish toxin, is a highly neurotoxic substance to marine animals and humankind. To reduce the incidence of poisoning accidents, the exploitation of specific and rapid detection method for domoic acid monitoring is highly required. Herein, an electrochemical molecularly imprinted polymer (MIP) sensor based on polydopamine-reduced graphene oxide/polyacrylamide composite (PDA-rGO/PAM) was constructed successfully to detect domoic acid. The domoic acid molecule could be recognized in imprinted cavities of PAM reversibly through hydrogen bonding. PDA-rGO promoted the loading capacity of PAM and improved the charge transfer rate, which amplified the electrical signal response of the MIP sensor. The screen-printed electrode (SPE) modified with PDA-rGO/PAM displayed satisfactory response toward toxin contaminated sample at a linear range from 1 to 600 nM and a low detection limit of 0.31 nM, demonstrating the prospective application of the transducer as a portable sensing platform for the on-site detection of hazardous marine biotoxin. Moreover, benefiting from the superior specificity and stability of MIP, the fabricated sensor could be utilized to detect the domoic acid content in mussel extracts directly without complex pretreatment operation.

Cobalt Phosphide (Co2P) with Notable Electrocatalytic Activity Designed for Sensitive and Selective Enzymeless Bioanalysis of Hydrogen Peroxide.

In this work, cobalt phosphide nanoparticles (Co2P NPs) were prepared by simple and mild hydrothermal method without the use of harmful phosphorous source. The morphological structure and surface component of Co2P were characterized by transmission electron microscopy, X-ray diffraction and X-ray photoelectron spectroscopy measurements. Considering the excellent electrocatalytic reduction activity and good electrical conductivity of transition-metal phosphide, we fabricated Co2P NPs on indium tin oxide (ITO) substrate (Co2P/ITO) for H2O2 detection. The Co2P/ITO transducer displayed a rapid amperometric response less than 5 s, a broader response range from 0.001 to 10.0 mM and a low detection limit of 0.65 µM. In addition, the non-enzymatic Co2P/ITO sensor showed outstanding selectivity, reproducibility, repeatability and stability, all of which qualified the Co2P/ITO electrode for quite a reliable and promising biosensor for H2O2 sensing.

2-Deoxy-Rh2: A novel ginsenoside derivative, as dual-targeting anti-cancer agent via regulating apoptosis and glycolysis.

20(S)-Rh2 is a ginsenoside isolated from Panax ginseng, which exhibits anti-cancer activities on various human cancer cells. A novel 20(S)-Rh2 derivative, 2-Deoxy-Rh2 was synthesized and hybridized with protopanaxadiol and 2-deoxy-glucose in an attempt to enhance the anticancer activity. Through screening the antitumor effect against various cell lines by MTT assay, 2-Deoxy-Rh2 especially resulted in a concentration-dependent and time-dependent inhibition of viability in MCF-7 human breast cancer cells. Multiple methods were used to explore the cellular and molecular mechanisms of 2-Deoxy-Rh2 as a potent anti-cancer agent. In MCF-7 cells, 2-Deoxy-Rh2 triggered apoptosis, stimulated ROS production and disrupted normal mitochondrial membrane potential. Meantime, 2-Deoxy-Rh2 eff ;ectively suppressed the glucose uptake capabilities and intracellular ATP production. The cellular oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) were significantly decreased in response to 2-Deoxy-Rh2, which were carried out to assess the overall glycolytic flux and mitochondrial respiration. Docking studies and molecular dynamics simulations were performed to verify the binding mode of 2-DG and 2-Deoxy-Rh2 with hexokinase II, with results showing that 2-Deoxy-Rh2 could easily fit into the similar active site of 2-DG, finally binding to hexokinase II to suppress glycolysis. Taken together, the results suggest that 2-Deoxy-Rh2 exhibited remarkable anticancer activity based on regulating mitochondrial apoptosis pathway, dampening glycolysis and inhibiting mitochondrial respiration, which support development of 2-Deoxy-Rh2 as a potential agent for cancer therapy.

Use of optical coherence tomography angiography for assessment of microvascular changes in the macula and optic nerve head in hypertensive patients without hypertensive retinopathy.

PURPOSE: To compare optical coherence tomography angiography (OCTA) screening parameters of the macula and optic nerve head (ONH) between healthy volunteers and chronic hypertensive patients without hypertensive retinopathy. METHODS: This was an observational, cross-sectional study. Fifty-seven chronic hypertensive patients without hypertensive retinopathy (22 men and 35 women) and 40 healthy volunteers (17 men and 23 women), ranging in age from 60 to 70 years, were included in this study. Patients and volunteers were divided into three groups and one eye was selected randomly from each participant. Group A comprised patients who had a history of hypertension for >10 years (n = 35); Group B comprised patients who had a history of hypertension for 5-10 years (n = 22); and Group C comprised 40 healthy volunteers who had no history of hypertension. A 3 × 3-mm macula scan and a 4.5 × 4.5-mm ONH scan were performed in each group by OCTA using prototype AngioVue software within the AngioVue device. Vessel density (VD), foveal avascular zone (FAZ) area, choriocapillaris flow area, ONH capillary density, retinal nerve fiber layer (RNFL) thickness, and demographic information were compared among the groups. RESULTS: Macula scans showed that superficial plexus VD was significantly lower in groups A and B than in group C (P < 0.05). In addition, FAZ area was significantly larger in group A than in group C (P < 0.05). Inner retinal layer thickness was significantly thinner in groups A and B than in group C (P < 0.05). In ONH scans, RNFL thickness was significantly thinner in group A than in groups B and C (P < 0.05); it was significantly thinner in group B than in group C (P < 0.05). Inside disc capillary density and peripapillary capillary density were significantly lower (P < 0.05) and greater (P < 0.05), respectively, in groups A and B than in group C. CONCLUSIONS: Superficial plexus VD, FAZ area, capillary density, and inner retinal thickness changed significantly in hypertensive patients without hypertensive retinopathy. However, only RNFL thickness was significantly thinner in patients who had >10 years of hypertension, compared to patients who had 5-10 years of hypertension. In addition, OCTA provided a method to prospectively assess changes in retinal microvasculature and thickness, thereby avoiding further long-term retinal damage in hypertensive patients.

Supercapillary Architecture-Activated Two-Phase Boundary Layer Structures for Highly Stable and Efficient Flow Boiling Heat Transfer.

Development of smaller, faster, and more powerful electronic devices requires effective cooling strategies to efficiently remove ever-greater heat. Phase-change heat transfer such as boiling and evaporation has been widely exploited in various water-energy industries owing to its efficient heat transfer mode. Despite extensive progress, it remains challenging to achieve the physical limit of flow boiling due to highly transitional and chaotic nature of multiphase flows as well as unfavorable boundary layer structures. Herein, a new strategy that promises to approach the physical limit of flow boiling heat transfer is reported. The flow boiling device with multiple channels is characterized with the design of micropinfin fences, which fundamentally transforms the boundary layer structures and imparts significantly higher heat transfer coefficient even at high heat flux conditions, in which boiling heat transfer is usually deteriorated due to the development of dryout starting from outlet regions and severe two-phase flow instabilities. Moreover, the approaching of physical limit is achieved without elevating pressure drop.

The neuroprotective effects of novel estrogen receptor GPER1 in mouse retinal ganglion cell degeneration.

PURPOSE: To investigate the potential protective effect of novel G protein coupled estrogen receptor (GPER1) against the neurotoxicity induced by NMDA in the mouse retina. METHODS: We induce retinal ganglion cells (RGCs) toxic injury through intravitreal injection of NMDA or acute ocular hypertension (AOH) induced by anterior chamber infusion with saline. Endogenous ligand 17-ß-estradiol (E2), GPER1 agonist (G-1), and E2 with GPER1 antagonist (G-15) or classic estrogen receptor α and ß (ERα and ERß) antagonist tamoxifen (TAM) were subcutaneous administered before NMDA to identify the possible involved receptors. Immunofluorescence staining was performed to explore the survival of RGCs and Müller cell gliosis. TUNEL staining was used to evaluate the RGC apoptosis. The involved molecular pathway was detected via antibody array expression profiling. RESULTS: Activation of estrogen receptor by E2 or G-1 could significantly rescue the RGCs injury in NMDA administration. The protective effect was carried exclusively by GPER1 activation. E2 application can still mimicked the protective function when estrogen receptor α and ß (ERα and ERß) blocked by tamoxifen (TAM), while the effects was blocked by GPER1 antagonist G-15. Moreover, the TUNEL positive RGCs and GFAP expression level were both attenuated in G-1 application and the effects could be reversed by G-15. In addition, application of the PI3K/Akt antagonist LY294002 counteracted the effect of G-1. And a number of apoptosis regulatory factors decreased dramatically in the G-1 group, including Bad, Caspase 3, Caspase 7, Smad2, P-53 and TAK1. Also, similar protective effect of G-1 was spotted in acute ocular hypertension (AOH) model. CONCLUSION: Estrogen played a protective role via a novel estrogen receptor, GPER1, instead of classical receptors ERα or ERß. Activation of GPER1 attenuated RGCs apoptosis and Müller cells gliosis, indicating GPER1 as a potential treatment target in RGCs degeneration diseases.