Rapid nanomolar detection of cocaine in biofluids by electrochemical aptamer-based sensor with low-temperature effect for drugged driving screening.

Cocaine is one of the most abused illicit drugs, and its abuse damages the central nervous system and can even lead directly to death. Therefore, the development of simple, rapid and highly sensitive detection methods is crucial for the prevention and control of drug abuse, traffic accidents and crime. In this work, an electrochemical aptamer-based (EAB) sensor based on the low-temperature enhancement effect was developed for the direct determination of cocaine in bio-samples. The signal gain of the sensor at 10 °C was greatly improved compared to room temperature, owing to the improved affinity between the aptamer and the target. Additionally, the electroactive area of the gold electrode used to fabricate the EAB sensor was increased 20 times by a simple electrochemical roughening method. The porous electrode possesses more efficient electron transfer and better antifouling properties after roughening. These improvements enabled the sensor to achieve rapid detection of cocaine in complex bio-samples. The low detection limits (LOD) of cocaine in undiluted urine, 50% serum and 50% saliva were 70 nM, 30 nM and 10 nM, respectively, which are below the concentration threshold in drugged driving screening. The aptasensor was simple to construct and reusable, which offers potential for drugged driving screening in the real world.

Construction of charge-reversible coordination-crosslinked spherical nucleic acids to deliver dual anti-cancer genes and ferroptosis payloads.

Spherical nucleic acids (SNAs) are nanostructures with the DNA arranged radially on the surface, thus allowing specific binding with cancer cells expressing high levels of scavenger receptor-A to enhance cellular uptake. However, conventional carriers for SNAs are cytotoxic, not degradable and difficult to deliver multiple payloads. In this study, we developed charge-reversible coordination-crosslinked SNAs to deliver dual anti-cancer genes and ferroptosis payload for anti-cancer purposes. To this end, we modified poly(lactic acid) (PLA) with functionalized side chains to allow its binding with antisense oligonucleotides (ASOs) and siRNA, annealed two single-stranded RNAs to obtain double-stranded RNA, and introduced a polyethylene glycol (PEG) shell to enhance the circulation time. Additionally, the ferroptosis payload imidazole was coordinated with iron ions as a core-crosslinked group to enhance the stability of SNAs and efficiency to kill cancer cells. We demonstrated that this novel nanocomplex efficiently internalized and killed CT-26 cells in vitro. In vivo data confirmed that the dual gene delivery system successfully targeted CT-26 tumors in tumor-bearing BALB/c mice, and exhibited strong tumor suppression ability, without inducing adverse toxic effects. Taken together, our dual gene therapy system offered an enhanced anti-tumor solution by simultaneously delivering dual anti-cancer genes and ferroptosis payload in tumor microenvironment.

Network Pharmacology, Molecular Docking Analysis and Experiment Validations on Molecular Targets and Mechanisms of the Dispel-Scar Ointment in Scar Treatment.

ETHNOPHARMACOLOGICAL RELEVANCE: Dispel-Scar Ointment is used in Traditional Chinese Medicine to treat scarred tissue and increasing evidence has shown that DSO has potent therapeutic; however, its exact mechanism remains unexplored. AIM OF THE STUDY: This study explored the molecular mechanisms of action of DSO in scarring using network pharmacology, molecular docking, and experimental validation. MATERIALS AND METHODS: Public databases were used to predict the bioactive ingredients and putative targets of DSO against scars. A compounds-targets network was constructed using the Cytoscape software. Enrichment analysis was performed using ClueGo and FunRich to specify the biological functions and associated pathways of hub targets. Molecular docking was used to verify the correlation between the major active components and hub targets, visualised using PyMol 2.3. Experimental validations were conducted to elucidate the influence of DSO on keloid fibroblast cells using the CCK-8, wound-scratch, cell reactive oxygen species, and western blot assays. Results：Network pharmacological analysis of DSO for scar treatment identified 146 ingredients and 1078 gene targets. Major targets included, prostaglandin-endoperoxide synthase 2 matrix metallopeptidases, and nitric oxide synthase 2. ClueGo analysis revealed 29 pathways (p<0.05) and FunRich 345 pathways (p<0.05), mainly toll-like receptor, TGF-ß, interleukin-4/13, glypican, and tumour necrosis factor-related apoptosis-inducing ligand pathways. Molecular docking showed MMP2-flavoxanthin, MMP9-luteolin and MMP-9-kaempferol bound best to DSO. DSO could inhibit the proliferation and migration of scar fibroblasts and promote their apoptosis in a concentration-dependent manner. DSO also decreased TGF-ß1, -ßR2, pSMAD2, pSMAD3, SMAD4, CoL1a1, and MMP2 expression. CONCLUSIONS: Network pharmacology, molecular docking, and experimental validation showed DSO's potential in treating scars. It may inhibit scars via the TGF-ß1/SMADs/MMPs signalling pathway, providing a basis for DSO's scar treatment application.

Multiple valence states of Fe boosting SERS activity of Fe3O4 nanoparticles and enabling effective SERS-MRI bimodal cancer imaging.

Developing novel nanoparticle-based bioprobes utilized in clinical settings with imaging resolutions ranging from cell to tissue levels is a major challenge for tumor diagnosis and treatment. Herein, an optimized strategy for designing a Fe3O4-based bioprobe for dual-modal cancer imaging based on surface-enhanced Raman scattering (SERS) and magnetic resonance imaging (MRI) is introduced. Excellent SERS activity of ultrasmall Fe3O4 nanoparticles (NPs) was discovered, and a 5 × 10-9 M limit of detection for crystal violet molecules was successfully obtained. The high-efficiency interfacial photon-induced charge transfer in Fe3O4 NPs was promoted by multiple electronic energy levels ascribed to the multiple valence states of Fe, which was observed using ultraviolet-visible diffuse reflectance spectroscopy. Density functional theory calculations were utilized to reveal that the narrow band gap and high electron density of states of ultrasmall Fe3O4 NPs significantly boosted the vibronic coupling resonances in the SERS system upon illumination. The subtypes of cancer cells were accurately recognized via high-resolution SERS imaging in vitro using the prepared Fe3O4-based bioprobe with high sensitivity and good specificity. Notably, Fe3O4-based bioprobes simultaneously exhibited T1 -weighted MRI contrast enhancement with an active targeting capability for tumors in vivo. To the best of our knowledge, this is the first report on the use of pure semiconductor-based SERS-MRI dual-modal nanoprobes in tumor imaging in vivo and in vitro, which has been previously realized only using semiconductor-metal complex materials. The non-metallic materials with SERS-MRI dual-modal imaging established in this report are a promising cancer diagnostic platform, which not only showed excellent performance in early tumor diagnosis but also possesses great potential for image-guided tumor treatment.

Generation of transgenic fish cell line with α-lactalbumin nanocarriers co-delivering Tol2 transposase mRNA and plasmids.

Fish cells, such as grass carp (Ctenopharyngodon idella) kidney (CIK) cells, are harder to transfect than mammalian cells. There is a need for an efficient gene delivery system for fish cells. Here, we used CIK cell line as a model to develop a strategy to enhance RNA and plasmid DNA transfection efficiency using a nanocarrier generated from α-lactalbumin (α-NC). α-NC absorbed nucleic acid cargo efficiently and exhibited low cytotoxicity. Plasmid transfection was more efficient with α-NC than with liposomal transfection reagents. We used α-NC to co-transfect Tol2 transposase mRNA and a plasmid containing Cas9 and GFP, generating a stable transgenic CIK cell line. Genome and RNA sequencing revealed that the Cas9 and GFP fragments were successfully inserted into the genome of CIK cells and efficiently transcribed. In this study, we established an efficient transfection system for fish cells using α-NC, simplifying the process of generating stable transgenic fish cell lines.

Overcoming treatment resistance in cholangiocarcinoma: current strategies, challenges, and prospects.

Significant advancements in our understanding and clinical treatment of cholangiocarcinoma (CCA) have been achieved over the past 5 years. Groundbreaking studies have illuminated the immune landscape and pathological characteristics of the tumor microenvironment in CCA. The development of immune- and metabolism-based classification systems has enabled a nuanced exploration of the tumor microenvironment and the origins of CCA, facilitating a detailed understanding of tumor progression modulation. Despite these insights, targeted therapies have not yet yielded satisfactory clinical results, highlighting the urgent need for innovative therapeutic strategies. This review delineates the complexity and heterogeneity of CCA, examines the current landscape of therapeutic strategies and clinical trials, and delves into the resistance mechanisms underlying targeted therapies. Finally, from a single-cell and spatial transcriptomic perspective, we address the challenge of therapy resistance, discussing emerging mechanisms and potential strategies to overcome this barrier and enhance treatment efficacy.

Physical Reservoir Computing Using van der Waals Ferroelectrics for Acoustic Keyword Spotting.

Acoustic keyword spotting (KWS) plays a pivotal role in the voice-activated systems of artificial intelligence (AI), allowing for hands-free interactions between humans and smart devices through information retrieval of the voice commands. The cloud computing technology integrated with the artificial neural networks has been employed to execute the KWS tasks, which however suffers from propagation delay and the risk of privacy breach. Here, we report a single-node reservoir computing (RC) system based on the CuInP2S6 (CIPS)/graphene heterostructure planar device for implementing the KWS task with low computation cost. Through deliberately tuning the Schottky barrier height at the ferroelectric CIPS interfaces for the thermionic injection and transport of the electrons, the typical nonlinear current response and fading memory characteristics are achieved in the device. Additionally, the device exhibits diverse synaptic plasticity with an excellent separation capability of the temporal information. We construct a RC system through employing the ferroelectric device as the physical node to spot the acoustic keywords, i.e., the natural numbers from 1 to 9 based on simulation, in which the system demonstrates outstanding performance with high accuracy rate (>94.6%) and recall rate (>92.0%). Our work promises physical RC in single-node configuration as a prospective computing platform to process the acoustic keywords, promoting its applications in the artificial auditory system at the edge.

Cold-hot Janus electrochemical aptamer-based sensor for calibration-free determination of biomolecules.

Real-time, high-frequency measurements of pharmaceuticals, metabolites, exogenous antigens, and other biomolecules in biological samples can provide critical information for health management and clinical diagnosis. Electrochemical aptamer-based (EAB) sensor is a promising analytical technique capable of achieving these goals. However, the issues of insufficient sensitivity, frequent calibration and lack of adapted portable electrochemical device limit its practical application in immediate detection. In response we have fabricated an on-chip-integrated, cold-hot Janus EAB (J-EAB) sensor based on the thermoelectric coolers (TECs). Attributed to the Peltier effect, the enhanced/suppressed current response can be generated simultaneously on cold/hot sides of the J-EAB sensor. The ratio of the current responses on the cold and hot sides was used as the detection signal, enabling rapid on-site, calibration-free determination of small molecules (procaine) as well as macromolecules (SARS-CoV-2 spike protein) in single step, with detection limits of 1 µM and 10 nM, respectively. We have further demonstrated that the J-EAB sensor is effective in improving the ease and usability of the actual detection process, and is expected to provide a universal, low-cost, fast and easy potential analytical tool for other clinically important biomarkers, drugs or pharmaceutical small molecules.

CD122 is an activation marker ensuring proper proliferation of T cells in teleost.

As one of subunits for interleukin-2 receptor (IL-2R), CD122 can bind to IL-2 and then activate downstream signal transduction to participate in adaptive immune response. Although CD122 has been identified and investigated from several teleost species, studies on its function at T-cell level are still scarce for lack of specific antibodies. In this study, a typical CD122 in Nile tilapia (Oreochromis niloticus) was characterized by bioinformatics analysis, cloned to produce retrovirus infected NIH/3T3 cells for mouse immunization. After cell fusion and screening, we successfully developed a mouse anti-tilapia CD122 monoclonal antibody (mAb), which could specifically recognize CD122 and identify CD122-producing T cells of tilapia. Using the mAb to detect, CD122 was found to widely distribute in immune-related tissues, and significantly elevate post Edwardsiella piscicida infection or T-cell activation. More importantly, the expansion of CD122+ T cells and up-regulation of CD122 occurred both in total T cells and T-cell subsets during T-cell activation upon in vitro stimulation or in vivo infection. These results indicate that CD122 can be used as a T-cell activation marker in tilapia. Notably, CD122 mAb blocking blunted the activation of MAPK/Erk and mTORC1 pathways, and inhibited T-cell proliferation, suggesting a critical role of CD122 in ensuring proper proliferation of tilapia T cells. Therefore, this study enriches the knowledge of T-cell responses in fish and provides new evidence for understanding the evolution of lymphocyte-mediated adaptive immunity.

Initialization-Free and Magnetic Field-Free Spin-Orbit p-Bits with Backhopping-like Magnetization Switching for Probabilistic Applications.

Probabilistic bits (p-bits) with thermal- and spin torque-induced nondeterministic magnetization switching are promising candidates for performing probabilistic computing. Previously reported spin torque p-bits include volatile low-energy barrier nanomagnets (LBNMs) with spontaneously fluctuating magnetizations and initialization-necessary nonvolatile magnets. However, initialization-free nonvolatile spin torque p-bits are still lacking. Here, we demonstrate moderately thermal stable spin-orbit torque (SOT) p-bits with non-consecutively deposited Pt//Pt/Co/Pt stacks. Backhopping-like (BH) magnetization switching with a wide range current-tunable probability of final up and down magnetization states from 0% to 100% was achieved, regardless of the initial magnetization state, which was attributed to the interplay of SOT and thermal contributions. Integer factorization using such BH-SOT p-bits in zero magnetic field was demonstrated at times that are significantly shorter than those of existing nonvolatile STT or volatile LBNMs p-bits. Our realization of initialization-free and magnetic field-free moderately thermally stable BH-SOT p-bits opens up a new perspective for probabilistic spintronic applications.

Phenotyping of FGF12AV52H mutation in mouse implies a complex FGF12 network.

Pathogenic missense mutation of the FGF12 gene is responsible for a variable disease phenotypic spectrum. Disease-specific therapies require precise dissection of the relationship between different mutations and phenotypes. The lack of a proper animal model hinders the investigation of related diseases, such as early-onset epileptic encephalopathy. Here, an FGF12AV52H mouse model was generated using CRISPR/Cas9 technology, which altered the A isoform without affecting the B isoform. The FGF12AV52H mice exhibited seizure susceptibility, while no spontaneous seizures were observed. The increased excitability in dorsal hippocampal CA3 neurons was confirmed by patch-clamp recordings. Furthermore, immunostaining showed that the balance of excitatory/inhibitory neurons in the hippocampus of the FGF12AV52H mice was perturbed. The increases in inhibitory SOM+ neurons and excitatory CaMKII+ neurons were heterogeneous. Moreover, the locomotion, anxiety levels, risk assessment behavior, social behavior, and cognition of the FGF12AV52H mice were investigated by elevated plus maze, open field, three-chamber sociability, and novel object tests, respectively. Cognition deficit, impaired risk assessment, and social behavior with normal social indexes were observed, implying complex consequences of V52H FGF12A in mice. Together, these data suggest that the function of FGF12A in neurons can be immediate or long-term and involves modulation of ion channels and the differentiation and maturation of neurons. The FGF12AV52H mouse model increases the understanding of the function of FGF12A, and it is of great importance for revealing the complex network of the FGF12 gene in physiological and pathological processes.

Novel extracellular lipase gene Lip1728 influences nutrient-dependent performance bacterial quorum sensing of Burkholderia pyrrocinia WZ10-3.

Quorum sensing (QS) is a cellular communication mechanism in which bacteria secrete and recognize signaling molecules to regulate group behavior. Lipases provide energy for bacterial cell growth but it is unknown whether they influence nutrient-dependent QS by hydrolyzing substrate. A high-yield lipase-producing strain, Burkholderia pyrrocinia WZ10-3, was previously identified in our laboratory, but the composition of its crude enzymes was not elucidated. Here, we identified a key extracellular lipase, Lip1728, in WZ10-3, which accounts for 99 % of the extracellular lipase activity. Lip1728 prefers to hydrolyze triglycerides at sn-1,3 positions, with pNP-C16 being its optimal substrate. Lip1728 exhibited activity at pH 5.0-10.0 and regardless of the presence of metal ions. It had strong resistance to sodium dodecyl sulfate and short-chain alcohols and was activated by phenylmethanesulfonylfluoride (PMSF). Lip1728 knockout significantly affected lipid metabolism and biofilm formation in the presence of olive oil. Finally, oleic acid, a hydrolysate of Lip1728, influenced the production of the signal molecule N-acyl homoserine lactone (AHL) and biofilm formation by downregulating the AHL synthetase gene pyrI. In conclusion, Lip1728, as a key extracellular lipase in B. pyrrocinia WZ10-3, exhibits superior properties that make it suitable for biodiesel production and plays a crucial role in QS.

TopMarker: Computational screening biomarkers of hepatocellular carcinoma from transcriptome and interactome based on differential network topological parameters.

Identifying diagnostic biomarkers for cancer is crucial in the field of personalized medicine. The available transcriptome and interactome provide unprecedented opportunities and challenges for biomarker screening. From a systematic perspective, network-based medicine methods provide alternative approaches to organizing the available high-throughput omics data for deciphering molecular interactions and their associations with phenotypic states. In this work, we propose a bioinformatics strategy named TopMarker for discovering diagnostic biomarkers by comparing the network topology differences in control and disease samples. Specifically, we build up gene-gene interaction networks in the two states of control and disease respectively. The network rewiring status across the two networks results in differential network topologies reflecting dynamics and changes in normal samples when compared with those in disease. Thus, we identify the potential biomarker genes with differential network topological parameters between the control and disease gene networks. For a proof-of-concept study, we introduce the computational pipeline of biomarker discovery in hepatocellular carcinoma (HCC). We prove the effectiveness of the proposed TopMarker method using these candidate biomarkers in classifying HCC samples and validate its signature capability across numerous independent datasets. We also compare the discriminant power of biomarker genes identified by TopMarker with those identified by other baseline methods. The higher classification performances and functional implications indicate the advantages of our proposed method for discovering biomarkers from differential network topology.

Enhancement of lipid synthesis by the transcription factor Asg1 in Saitozyma podzolica zwy-2-3 under dissolved oxygen stress.

Microbial oils have been of considerable interest as food additives and biofuel resources due to high lipid contents, but lipid accumulation of oleaginous microorganisms can be induced by environmental stresses, such as dissolved oxygen (DO), which limit large-scale lipid production. Here, DO stress gave rise to the endogenous nitric oxide (NO) level to mediate S-nitrosylation of SpAsg1, regulating the lipid accumulation in Saitozyma podzolica zwy-2-3. Notably, qRT-PCR, yeast one-hybrid, dual-luciferase reporter assays, and metabolomics analysis exhibited that overexpression of SpAsg1 promoted lipid synthesis by directly regulation of glucose metabolism, enhancing glucose uptake, ATP and NADPH contents under DO stress. Meanwhile, SpAsg1 improved the antioxidant capacity to reduce the intracellular reactive oxygen species (ROS) and NO levels. Overall, we systematically investigated the regulation of SpAsg1 on lipid metabolism of S. podzolica zwy-2-3 under DO stress, which sheds light on further studies for alleviating oxygen limitation of lipid production in microbial industry.

The Dimensionality of Hydrogen Bond Networks Induces Diverse Physical Properties of Peptide Crystals.

Short peptides are attractive building blocks for the fabrication of self-assembled materials with significant biological, chemical, and physical properties. The microscopic and macroscopic properties of assemblies are usually closely related to the dimensionality of formed hydrogen bond networks. Here, two completely different supramolecular architectures connected by distinct hydrogen bond networks were obtained by simply adding a hydroxyl group to switch from cyclo-tryptophan-alanine (cyclo-WA) to cyclo-tryptophan-serine (cyclo-WS). While hydroxyl-bearing cyclo-WS molecules provided an additional hydrogen bond donor that links to adjacent molecules, forming a rigid three-dimensional network, cyclo-WA arranged into a water-mediated zipper-like structure with a softer two-dimensional layer template. This subtle alteration resulted in a 14-fold enhancement of Young's modulus values in cyclo-WS compared to cyclo-WA. Both cyclo-dipeptides exhibit biocompatibility, high fluorescence, and piezoelectricity. The demonstrated role of dimensionality of hydrogen bond networks opens new avenues for rational design of materials with precise morphologies and customizable properties for bioelectronic applications.

Combined effects of TiO2 nanoparticle and fipronil co-exposure on microbiota in mouse intestine.

Oral exposure to nanoparticles (NPs) may affect intestinal microbiota, and this effect may be further changed by co-contaminates. In the present study, we investigated the combined effects of TiO2 NPs and fipronil (FPN) on microbiota in mouse intestines. Mice were intragastric exposed to 5.74 mg/kg TiO2 NPs, 2.5 mg/kg FPN, or both of them, once a day, for 30 days. The results showed that individual exposure to TiO2 NPs or FPN decreased body weight and induced pathological changes in intestines. The exposure was also associated with increased cleaved caspase-3 protein, oxidative stress and decreased tight junction protein expression. Furthermore, the levels of diamine oxidase (DAO), lipopolysaccharide (LPS) and inflammatory cytokines in serum were also elevated, indicating increased intestinal barrier permeability. As expected, both TiO2 NPs and FPN decreased the diversity and altered the composition of microbiota. However, the observed effects were not further enhanced after the co-exposure to TiO2 NPs and FPN, except that Romboutsia was only significantly increased after the co-exposure to TiO2 NPs + FPN. We concluded that oral exposure to TiO2 NPs and FPN showed minimal synergistic effects on microbiota in mouse intestine.

Global insights from local actions: a case study on enhancing flood disaster management efficiency in China's Greater Bay Area.

This study examines the flood disaster management network within the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) from 2015 to 2021, identifying government department involvement and influence shifts. Key findings indicate a decrease in the centrality of the Public Security Office and Department of Transportation, suggesting a strategic shift toward more specialized, technology-driven disaster management. Conversely, the Science Bureau's increased engagement, from 8.43% to 12.84%, highlights a policy shift toward scientific research and technological innovation in managing flood risks. The analysis reveals underutilized communication between the Central Committee, the Poverty Alleviation Office, and the Publicity Department, highlighting opportunities for improved integration in disaster management and public communication strategies. To address these issues, the study suggests strengthening inter-departmental collaboration to leverage technological advancements in disaster management. It also recommends integrating flood disaster management with poverty alleviation initiatives to support affected populations comprehensively. Increasing the involvement of the Publicity Department is crucial for improving timely and transparent communication of flood-related data to the public. The conclusions advocate for an adaptive, strategically planned network approach to flood disaster management in the GBA, aiming to bolster responsiveness and preparedness for future flood events.

Exploring the nematicidal mechanisms and control efficiencies of oxalic acid producing Aspergillus tubingensis WF01 against root-knot nematodes.

Background and aims: Root-knot nematodes (RKN; Meloidogyne spp.) are among the highly prevalent and significantly detrimental pathogens that cause severe economic and yield losses in crops. Currently, control of RKN primarily relies on the application of chemical nematicides but it has environmental and public health concerns, which open new doors for alternative methods in the form of biological control. Methods: In this study, we investigated the nematicidal and attractive activities of an endophytic strain WF01 against Meloidogyne incognita in concentration-dependent experiments. The active nematicidal metabolite was extracted in the WF01 crude extract through the Sephadex column, and its structure was identified by nuclear magnetic resonance and mass spectrometry data. Results: The strain WF01 was identified as Aspergillus tubingensis based on morphological and molecular characteristics. The nematicidal and attractive metabolite of A. tubingensis WF01 was identified as oxalic acid (OA), which showed solid nematicidal activity against M. incognita, having LC50 of 27.48 µg ml-1. The Nsy-1 of AWC and Odr-7 of AWA were the primary neuron genes for Caenorhabditis elegans to detect OA. Under greenhouse, WF01 broth and 200 µg ml-1 OA could effectively suppress the disease caused by M. incognita on tomatoes respectively with control efficiency (CE) of 62.5% and 70.83%, and promote plant growth. In the field, WF01-WP and 8% OA-WP formulations showed moderate CEs of 51.25%-61.47% against RKN in tomato and tobacco. The combined application of WF01 and OA resulted in excellent CEs of 66.83% and 69.34% toward RKN in tomato and tobacco, respectively. Furthermore, the application of WF01 broth or OA significantly suppressed the infection of J2s in tomatoes by upregulating the expression levels of the genes (PAL, C4H, HCT, and F5H) related to lignin synthesis, and strengthened root lignification. Conclusion: Altogether, our results demonstrated that A. tubingensis WF01 exhibited multiple weapons to control RKN mediated by producing OA to lure and kill RKN in a concentration-dependent manner and strengthen root lignification. This fungus could serve as an environmental bio-nematicide for managing the diseases caused by RKN.

deepAMPNet: a novel antimicrobial peptide predictor employing AlphaFold2 predicted structures and a bi-directional long short-term memory protein language model.

Background: Global public health is seriously threatened by the escalating issue of antimicrobial resistance (AMR). Antimicrobial peptides (AMPs), pivotal components of the innate immune system, have emerged as a potent solution to AMR due to their therapeutic potential. Employing computational methodologies for the prompt recognition of these antimicrobial peptides indeed unlocks fresh perspectives, thereby potentially revolutionizing antimicrobial drug development. Methods: In this study, we have developed a model named as deepAMPNet. This model, which leverages graph neural networks, excels at the swift identification of AMPs. It employs structures of antimicrobial peptides predicted by AlphaFold2, encodes residue-level features through a bi-directional long short-term memory (Bi-LSTM) protein language model, and constructs adjacency matrices anchored on amino acids' contact maps. Results: In a comparative study with other state-of-the-art AMP predictors on two external independent test datasets, deepAMPNet outperformed in accuracy. Furthermore, in terms of commonly accepted evaluation matrices such as AUC, Mcc, sensitivity, and specificity, deepAMPNet achieved the highest or highly comparable performances against other predictors. Conclusion: deepAMPNet interweaves both structural and sequence information of AMPs, stands as a high-performance identification model that propels the evolution and design in antimicrobial peptide pharmaceuticals. The data and code utilized in this study can be accessed at https://github.com/Iseeu233/deepAMPNet.

A "Dual-Key-and-Lock" MRI Contrast Agent with T1-T2 Switchable Function for Accurate Diagnosis of Tumors.

Extremely small iron oxide nanoparticle (ESIONP)-based stimuli-responsive switchable MRI contrast agents (CAs) show great promise for accurate detection of tumors due to their outstanding advantages of high specificity and low background signal. However, currently developed ESIONP-based switchable CAs often suffer single-biomarker-induced responses, which lack absolute specificity to pathological tissues, potentially diminishing diagnostic accuracy. In this study, weak acidity and hypoxia, two of the most remarkable characteristics of tumors, are introduced as dual biomarker stimuli to construct an ESIONP-based switchable MRI CA (DKL-CA), with its signal switch controlled by a "dual-key-and-lock" strategy. Only when DKL-CA is exposed to a coexisting weakly acidic and hypoxic environment can monodispersed ESIONPs form nanoclusters, thereby realizing a switch from the T1 to T2 contrast. Moreover, DKL-CA exhibits favorable biosafety and the capacity for precise tumor diagnosis in tumor-bearing mice. Overall, DKL-CA paves the way for designing highly accurate ESIONP-based MRI CAs for tumor diagnosis.