A chitosan/gelatin/aldehyde hyaluronic acid hydrogel coating releasing calcium ions and vancomycin in pH response to prevent the formation of bacterial biofilm

Osteomyelitis is a refractory disease of orthopedics, part of which is caused by medical implants. The main difficulties in treatment are the barrier effect after the formation of bacterial biofilm, and the difficulty in achieving sustained antibiotic intervention. In view of this situation, we studied a hydrogel coating that can release CaCl2 and vancomycin in pH-responsive manner. We used nano-TiO2 to modify Chitosan/ Gelatin/Aldehyde Hyaluronic Acid (CS/Gel/AHA) hydrogel, and combined with the dip-coating technique, prepared a coating with good mechanical strength. The hydrogel-loaded zeolitic imidazolate framework (ZIF) decomposes under acidic conditions, and the released Ca2+ act on the bacterial Bap protein to inhibit the formation of biofilm, and the released vancomycin kills free bacteria. The antibacterial coating achieved good bactericidal effect in both in vitro experiments and rat subcutaneous implant model. These results not only provide a new way to enhance the strength of hydrogels to prepare coatings, but also utilize a new approach to responsively inhibit the formation of biofilms, showing the promising application prospects of the coating in antibacterial treatment of medical implants.

Artificial chemotaxis under electrodiffusiophoresis

HYPOTHESIS

Through a large parameter space, electric fields can tune colloidal interactions and forces leading to diverse static and dynamical structures. So far, however, field-driven interactions have been limited to dipole-dipole and hydrodynamic contributions. Nonetheless, in this work, we propose that under the right conditions, electric fields can also induce interactions based on local chemical fields and diffusiophoretic flows.

EXPERIMENTS

Herein, we present a strategy to generate and measure 3D chemical gradients under electric fields. In this approach, faradaic reactions at electrodes induce global pH gradients that drive long-range transport through electrodiffusiophoresis. Simultaneously, the electric field induces local pH gradients by driving the particle's double layer far from equilibrium.

FINDINGS

As a result, while global pH gradients lead to 2D focusing away from electrodes, local pH gradients induce aggregation in the third dimension. Evidence points to a mechanism of interaction based on diffusiophoresis. Interparticle interactions display a strong dependence on surface chemistry, zeta potential and diameter of particles. Furthermore, pH gradients can be readily tuned by adjusting the voltage and frequency of the electric field. For large Péclet numbers, we observed a collective chemotactic-like collapse of particles. Remarkably, such collapse occurs without reactions at a particle's surface. By mixing particles with different sizes, we also demonstrate, through experiments and Brownian dynamics simulations, the emergence of non-reciprocal interactions, where small particles are more drawn towards large ones.

Desalting strategies for native mass spectrometry

In native mass spectrometry (MS) salts are indispensable for preserving the native structures of biomolecules, but detrimental to mass sensitivity, resolution, and accuracy. Such a conflict makes desalting in native MS more challenging, distinctive, and sample-dependent than in peptide-centric MS. This review first briefly introduces the charged residue mechanism whereby native-like gaseous protein ions are released from electrospray droplets, revealing a higher degree of salt adduction than denatured proteins. Subsequently, this review summarizes and explores the existing strategies, underlying mechanisms and future perspectives of desalting in native MS. These strategies mainly focus on buffer exchange into volatile salts (offline and online approaches), addition of solution additives (e.g., anion, supercharging reagent, solution phase chelator and amino acid), use of submicron electrospray emitters (down to 60 nm), and other potential approaches (e.g., induced and electrophoretic nanoelectrospray ionization). The strategies of online buffer exchange and using nanoscale electrospray emitters are highlighted. This review would not only be a valuable addition to the field of sample preparation in MS, but would also serve as a beginner's guide to desalting in native MS.

A novel peptide pair-based rapid fluorescent diagnostic system for malaria Plasmodium falciparum detection

Advanced diagnostic materials, such as aptamers, are required due to the scarcity of efficient diagnostic antibodies and the low sensitivity of rapid diagnostic kits at detecting the malaria parasite, Plasmodium falciparum.

METHODS

Two peptides M2.9 [(KPTAEQTESPELQSAPEN) and M2.17 (KILFNVYSPLGCTCECWV)] were designed using simple epitope prediction tools and modified against the merozoite surface antigen 2 of P. falciparum (Pf.MSP2) by 3-dimensional modeling based on binding affinity. Based on five prediction tools for hydropathy, M2.17 was selected as an appropriate capture peptide. A peptide-based fluorescence-linked immunosorbent assay (FLISA) and a peptide pair-based fluorescent immunochromatographic test strip (FICT) were developed to detect P. falciparum 3D7 (drug-sensitive) and P. falciparum K1 (multi drugs-resistant) strains.

RESULTS

Bioinformatic analysis of two peptides demonstrated the potential binding affinity with the merozoite surface protein 2 of P. falciparum (Pf.MSP2) with a positive hydropathy value. The limit of detection (LOD) of FLISA was 10 parasites/μL and of a peptide pair-linked rapid FICT system was 5 and 200 parasites/μL for P. falciparum 3D7 and K1, respectively. Compared to commercial rapid detection systems (RDTs), a peptide pair-linked FICT system exhibited a 20-fold greater efficiency in detecting P. falciparum 3D7 and specifically discriminated another protozoan spp.

CONCLUSION

A peptide pair-linked rapid diagnostic strip could be an alternative to conventional RDTs for monitoring wild-type and drug-resistant malaria parasites.

Advances in biomacromolecule-functionalized magnetic particles for phytopathogen detection

Due to the increasing crop losses caused by common and newly emerging phytopathogens, there is a pressing need for the development of rapid and reliable methods for phytopathogen detection and analysis. Leveraging advancements in biochemical engineering technologies and nanomaterial sciences, researchers have put considerable efforts on utilizing biofunctionalized magnetic micro- and nanoparticles (MPs) to develop rapid and reliable systems for phytopathogen detection. MPs facilitate the rapid, high-throughput analysis and in-field applications, while the biomacromolecules, which play key roles in the biorecognitions, interactions and signal amplification, determine the specificity, sensitivity, reliability, and portability of pathogen detection systems. The integration of MPs and biomacromolecules provides dimensionality- and composition-dependent properties, representing a novel approach to develop phytopathogen detection systems. In this review, we summarize and discuss the general properties, synthesis and characterization of MPs, and focus on biomacromolecule-functionalized MPs as well as their representative applications for phytopathogen detection and analysis reported over the past decade. Extensively studied bioreceptors, such as antibodies, phages and phage proteins, nucleic acids, and glycans that are involved in the recognitions and interactions, are covered and discussed. Additionally, the integration of MPs-based detection system with portable microfluidic devices to facilitate their in-field applications is also discussed. Overall, this review focuses on biomacromolecule-functionalized MPs and their applications for phytopathogen detection, aiming to highlight their potential in developing advanced biosensing systems for effective plant protection.

Mechanisms of levan in ameliorating hyperuricemia: Insight into levan on serum metabolites, gut microbiota, and function in hyperuricemia rats

This study aims to investigate the effects of levan on the progression of hyperuricemia (HUA) rats and elucidate its underlying mechanisms. After levan intervention, both low and high-dose groups exhibited a significant decrease in serum uric acid (UA) levels, reaching 71.0 % and 77.5 %, respectively, compared to the model group. Furthermore, levan could alleviate renal pathological damage caused by glomerular cell vacuolation, inflammatory infiltration and collagen deposition. The results of enzyme activity assay and real-time fluorescence quantitative PCR showed that levan decreased UA production by inhibiting adenosine deaminase (ADA) activity and gene expression in liver; it upregulated ATP-binding cassette subfamily G member 2 protein (ABCG2) and organic anion transporter 1 (OAT1) transporter gene expression in the kidney, promoting UA excretion. Gut microbiome analysis indicated that levan regulated gut flora dysbiosis induced by HUA, resulting in up-regulated the abundance of beneficial bacteria (Muribaculaceae, Faecalibaculum, Bifidobacterium, and Lactobacillus) and decreased conditioned pathogenic bacteria (Escherichia_Shigella and Proteus). Non-targeted metabolomics showed changes in various serum metabolites associated with glycerophospholipid metabolism, lipid metabolism, and inflammation following oral administration of levan. Therefore, levan may be a promising functional dietary supplement for regulating the gut flora and remodeling of metabolic disorders in individuals with HUA.

Intracellularly manipulable aggregation of the aggregation-induced emission luminogens

Biophotonics has seen significant advancements with the development of optical imaging techniques facilitating the noninvasive detection of biologically relevant species. Aggregation-induced emission (AIE) materials have emerged as a novel class of luminogens exhibiting enhanced luminescence or photodynamic efficiency in the aggregated state, making them ideal for biomedical applications. The intracellularly controlled aggregation of aggregate-induced emission luminogens (AIEgens) enables high-resolution imaging of intracellular targets and diagnosis of related diseases, and enables disease therapy by exploiting the novel properties of aggregates. This review provides an in-depth analysis of the strategies employed to modulate the aggregation of AIEgens, focusing on the importance of molecular modifications to improve hydrophilicity and achieve precise control over the intercellular aggregation of AIEgens. Furthermore, the representative applications of AIEgens in bioimaging, such as enzyme activity monitoring, protein tracking, organelle function monitoring, and in vivo tumor-specific therapeutics, are reviewed. Additionally, we outline the challenges and future opportunities for AIE research, emphasizing the importance of the strategies for realizing the precisely controllable aggregation of AIEgens inside cells and the need for extending AIEgens' absorption and emission wavelengths. This review aims to elucidate the rational development of responsive AIEgens for advanced biomedical applications.

Application of Proteomics Technology Based on LC-MS Combined with Western Blotting and Co-IP in Antiviral Innate Immunity

As an interferon-stimulating factor protein, STING plays a role in the response and downstream liaison in antiviral natural immunity. Upon viral invasion, the immediate response of STING protein leads to a series of changes in downstream proteins, which ultimately leads to an antiviral immune response in the form of proinflammatory cytokines and type I interferons, thus triggering an innate immune response, an adaptive immune response in vivo, and long-term protection of the host. In the field of antiviral natural immunity, it is particularly important to rigorously and sequentially probe the dynamic changes in the antiviral natural immunity connector protein STING caused by the entire anti-inflammatory and anti-pathway mechanism and the differences in upstream and downstream proteins. Traditionally, proteomics technology has been validated by detecting proteins in a 2D platform, for which it is difficult to sensitively identify changes in the nature and abundance of target proteins. With the development of mass spectrometry (MS) technology, MS-based proteomics has made important contributions to characterizing the dynamic changes in the natural immune proteome induced by viral infections. MS analytical techniques have several advantages, such as high throughput, rapidity, sensitivity, accuracy, and automation. The most common techniques for detecting complex proteomes are liquid chromatography (LC) and mass spectrometry (MS). LC-MS (Liquid Chromatography-Mass Spectrometry), which combines the physical separation capability of LC and the mass analysis capability of MS, is a powerful technique mainly used for analyzing the proteome of cells, tissues, and body fluids. To explore the combination of traditional proteomics techniques such as Western blotting, Co-IP (co-Immunoprecipitation), and the latest LC-MS methods to probe the anti-inflammatory pathway and the differential changes in upstream and downstream proteins induced by the antiviral natural immune junction protein STING.

Golden Gate Cloning of Synthetic CRISPR RNA Spacer Sequences

Prokaryotes use CRISPR-Cas systems to interfere with viruses and other mobile genetic elements. CRISPR arrays comprise repeated DNA elements and spacer sequences that can be engineered for custom target sites. These arrays are transcribed into precursor CRISPR RNAs (pre-crRNAs) that undergo maturation steps to form individual CRISPR RNAs (crRNAs). Each crRNA contains a single spacer that identifies the target cleavage site for a large variety of Cas protein effectors. Precise manipulation of spacer sequences within CRISPR arrays is crucial for advancing the functionality of CRISPR-based technologies. Here, we describe a protocol for the design and creation of a minimal, plasmid-based CRISPR array to enable the expression of specific, synthetic crRNAs. Plasmids contain entry spacer sequences with two type IIS restriction sites and Golden Gate cloning enables the efficient exchange of these spacer sequences. Factors that influence the compatibility of the CRISPR arrays with native or recombinant Cas proteins are discussed.

Metabolomic analysis reveals the potential of fucosylated chondroitin sulfate from sea cucumber in modulating metabolic homeostasis

In this study, we prepared four derivatives of fucosylated chondroitin sulfate (FCS): full-length FCS (flFCS) from Holothuria leucospilota, low molecular weight FCS (lmFCS) derived from flFCS, and their de-branched counterparts, de-branched flFCS (d-flFCS) and de-branched lmFCS (d-lmFCS) via controlled acid treatment. Following structural verification using various analytical techniques, we applied targeted metabolomics to examine the impact of FCS on nutritional efficacy and its structure-activity relationship. Analysis of 225 plasma and feces samples from 75 mice revealed a positive correlation between metabolomic shifts and increased weight gain, underscoring FCS's potential to enhance nutrient absorption and promote growth. The observed linear relationship between the levels of short-chain fatty acids in plasma and feces suggests that FCS may facilitate catabolic activities in the gastrointestinal tract. The comparative study of different FCS derivatives on mouse growth and metabolic homeostasis regulation led to the conclusion that FCS exhibits greater biological activity with a higher degree of branching and larger molecular weight.

Genome Annotation

The hallmark of genome sequencing projects is to provide genetic information on a species with functional annotations of genes and proteins. This process heavily relies on genome annotation based on homology detections from previously known genomic data. The rapid advancement of genome sequencing technologies has made genome sequencing affordable and effective in terms of the time frame for the generation of genomic data. Hence, genome sequencing has become a common practice. The annotation and characterization of newly sequenced genomes are crucial factors for the success of any biological experiment based on genomic data. The proteogenomic sector requires annotated genome further characterization of proteomic-based studies, and these are coupled with genomic and RNA-seq data. This chapter describes the genome annotation process from scratch genome sequencing to general genome annotation and specialized genome annotation using BLAST, BLAT2GO (now OMICSBOX), PANNZER, gene ontology (GO), and KEGG. It also covers different processes like repeat identification and masking, gene prediction, genome-wide annotation process, and RNA-seq protocol. It also focuses on genes of interest such as genes associated with BGCs (biosynthetic gene clusters), carbohydrate-active enzymes (CAZymes), serpins (serine protease inhibitors), membrane transporters, and toxins. Manual annotation is also a critical step for at least some groups of genes, which are often critical for the species in consideration. This chapter also briefly describes the phylogenetic and phylogenomic processes required during genome annotation.

Asparagine synthetase and G-protein coupled estrogen receptor are critical responders to nutrient supply in KRAS mutant colorectal cancer

Survival differences exist in colorectal cancer (CRC) patients by sex and disease stage. However, the potential molecular mechanism(s) are not well understood. Here we show that asparagine synthetase (ASNS) and G protein-coupled estrogen receptor-1 (GPER1) are critical sensors of nutrient depletion and linked to poorer outcomes for females with CRC. Using a 3D spheroid model of isogenic SW48 KRAS wild-type (WT) and G12A mutant (MT) cells grown under a restricted nutrient supply, we found that glutamine depletion inhibited cell growth in both cell lines, whereas ASNS and GPER1 expression were upregulated in KRAS MT versus WT. Estradiol decreased growth in KRAS WT but had no effect on MT cells. Selective GPER1 and ASNS inhibitors suppressed cell proliferation with increased caspase-3 activity of MT cells under glutamine depletion condition particularly in the presence of estradiol. In a clinical colon cancer cohort from The Cancer Genome Atlas, both high GPER1 and ASNS expression were associated with poorer overall survival for females only in advanced stage tumors. These results suggest KRAS MT cells have mechanisms in place that respond to decreased nutrient supply, typically observed in advanced tumors, by increasing the expression of ASNS and GPER1 to drive cell growth. Furthermore, KRAS MT cells are resistant to the protective effects of estradiol under nutrient deplete conditions. The findings indicate that GPER1 and ASNS expression, along with the interaction between nutrient supply and KRAS mutations shed additional light on the mechanisms underlying sex differences in metabolism and growth in CRC, and have clinical implications in the precision management of KRAS mutant CRC.

Characterization of Bacterial Membrane Fatty Acid Profiles for Biofilm Cells

When submitted to environmental stresses, bacteria can modulate its fatty acid composition of membrane phospholipids in order to optimize membrane fluidity. Characterization of bacterial membrane fatty acid profiles is thus an interesting indicator of cellular physiological state. The methodology described here aims to improve the recovering of biofilm cells for the characterization of their fatty acid profiles. The saponification reagent is directly applied on the whole biofilm before the removal of cells from the inert surface. In this way, maximum of the cells and their fatty acids can be recovered from the deepest layers of the biofilm.

Deciphering the acidophilia and acid resistance in Acetilactobacillus jinshanensis dominating baijiu fermentation through multi-omics analysis

Lactic acid bacteria (LAB) are pivotal in constructing the intricate bio-catalytic networks underlying traditional fermented foods such as Baijiu. However, LAB and their metabolic mechanisms are partially understood in Moutai flavor Baijiu fermentation. Here, we found that Acetilactobacillus jinshanensis became the· dominant species with relative abundance reaching 92%, where the acid accumulated rapidly and peaked at almost 30 g/kg in Moutai flavor Baijiu. After separation, purification, and cultivation, A. jinshanensis exhibited pronounced acidophilia and higher acid resistance compared to other LAB. Further integrated multi-omics analysis revealed that fatty acid synthesis, cell membrane integrity, pHi and redox homeostasis maintenance, protein and amide syntheses were possibly crucial acid-resistant mechanisms in A. jinshanensis. Structural proteomics indicated that the surfaces of A. jinshanensis proteases contained more positively charged amino acid residues to maintain protein stability in acidic environments. The genes HSP20 and acpP were identified as acid-resistant genes for A. jinshanensis by heterologous expression analysis. These findings not only enhance our understanding of LAB in Baijiu, providing a scientific basis for acid regulation for production process, but also offer valuable insights for studying core species in other fermentation systems.

Engineering mesoporous polydopamine-based potentiate STING pathway activation for advanced anti-biofilm therapy

The biofilm-induced "relatively immune-compromised zone" creates an immunosuppressive microenvironment that is a significant contributor to refractory infections in orthopedic endophytes. Consequently, the manipulation of immune cells to co-inhibit or co-activate signaling represents a crucial strategy for the management of biofilm. This study reports the incorporation of Mn2+ into mesoporous dopamine nanoparticles (Mnp) containing the stimulator of interferon genes (STING) pathway activator cGAMP (Mncp), and outer wrapping by M1-like macrophage cell membrane (m-Mncp). The cell membrane enhances the material's targeting ability for biofilm, allowing it to accumulate locally at the infectious focus. Furthermore, m-Mncp mechanically disrupts the biofilm through photothermal therapy and induces antigen exposure through photodynamic therapy-generated reactive oxygen species (ROS). Importantly, the modulation of immunosuppression and immune activation results in the augmentation of antigen-presenting cells (APCs) and the commencement of antigen presentation, thereby inducing biofilm-specific humoral immunity and memory responses. Additionally, this approach effectively suppresses the activation of myeloid-derived suppressor cells (MDSCs) while simultaneously boosting the activity of T cells. Our study showcases the efficacy of utilizing m-Mncp immunotherapy in conjunction with photothermal and photodynamic therapy to effectively mitigate residual and recurrent infections following the extraction of infected implants. As such, this research presents a viable alternative to traditional antibiotic treatments for biofilm that are challenging to manage.

Enhancing multiplex detection capabilities of the Cas12a/blocker DNA system

In the field of molecular diagnostics, the demand for multiplex detection, aimed at reducing overall analysis costs and streamlining procedures, is on the rise, prompting ongoing developments in various technologies. In this study, we developed a novel system, the split T7 promoter-based three-way junction-transcription, coupled with Cas12a/Blocker DNA (T3-CaB), for the multiplex detection of target nucleic acids. The T3-CaB system builds upon the foundation of the T3 system, generating numerous RNA transcripts upon encountering target nucleic acids. Subsequently, these RNA transcripts displace the blocker DNA from reporter DNA, allowing active Cas12a to engage in efficient trans-cleavage reaction on the reporter DNA, resulting in a strong fluorescence signal. Importantly, the proposed system operates at the isothermal condition (37 °C), with the entire analysis completed within 90 min. Further, the detection performance of the proposed system surpasses that of the preceding Cas12a/Blocker DNA system. Model targets, namely the 16S rRNA of Staphylococcus aureus and Escherichia coli, were selected, and a successful demonstration of multiplex detection was achieved. This technology holds promise for broadening the applicability of CRISPR/Cas-based diagnostics, especially in settings necessitating multiplex detection capabilities.

Cyclic peptides: A powerful instrument for advancing biomedical nanotechnologies and drug development

Cyclic peptides have emerged as an essential tool in the advancement of biomedical nanotechnologies, offering unique structural and functional advantages over linear peptides. This review article aims to highlight the roles of cyclic peptides in the development of biomedical fields, with a particular focus on their application in drug discovery and delivery. Cyclic peptides exhibit exceptional stability, bioavailability, and binding specificity, making them ideal candidates for therapeutic and diagnostic applications. We explore the synthesis and design strategies that enable the precise control of cyclic peptide structures, leading to enhanced performance in targeting specific cellular pathways. The article also highlights recent breakthroughs in the use of cyclic peptides for creating innovative drug delivery systems, including nanoparticle conjugates and peptide-drug conjugates, which have shown promise in improving the efficacy and safety profiles of existing traditional treatments. The integration of cyclic peptides into nanotechnological frameworks holds significant promise for addressing unmet medical needs, providing a foundation for future advancements in personalized medicine and targeted drug delivery.

Different fates of Sb(III) and Sb(V) during the formation of jarosite mediated by Acidithiobacillus ferrooxidans

Secondary iron-sulfate minerals such as jarosite, which are easily formed in acid mine drainage, play an important role in controlling metal mobility. In this work, the typical iron-oxidizing bacterium Acidithiobacillus ferrooxidans ATCC 23270 was selected to synthesize jarosite in the presence of antimony ions, during which the solution behavior, synthetic product composition, and bacterial metabolism were studied. The results show that in the presence of Sb(V), Fe2+ was rapidly oxidized to Fe3+ by A. ferrooxidans and Sb(V) had no obvious effect on the biooxidation of Fe2+ under the current experimental conditions. The presence of Sb(III) inhibited bacterial growth and Fe2+ oxidation. For the group with Sb(III), products with amorphous phases were formed 72 hr later, which were mainly ferrous sulfate and pentavalent antimony oxide, and the amorphous precursor was finally transformed into a more stable crystal phase. For the group with Sb(V), the morphology and structure of jarosite were changed in comparison with those without Sb. The biomineralization process was accompanied by the removal of 94% Sb(V) to form jarosite containing the Fe-Sb-O complex. Comparative transcriptome analysis shows differential effects of Sb(III) and Sb(V) on bacterial metabolism. The expression levels of functional genes related to cell components were much more downregulated for the group with Sb(III) but much more regulated for that with Sb(V). Notably, cytochrome c and nitrogen fixation-relevant genes for the A.f_Fe2+_Sb(III) group were enhanced significantly, indicating their role in Sb(III) resistance. This study is of great value for the development of antimony pollution control and remediation technology.

Combined biochar and wheat-derived endophytic bacteria reduces cadmium uptake in wheat grains in a metal-polluted soil

In this study, two wheat-derived cadmium (Cd)-immobilizing endophytic Pseudomonas paralactis M14 and Priestia megaterium R27 were evaluated for their effects on wheat tissue Cd uptake under hydroponic conditions. Then, the impacts of the biochar (BC), M14+R27 (MR), and BC+MR treatments on wheat Cd uptake and the mechanisms involved were investigated at the jointing, heading, and mature stages of wheat plants under field-plot conditions. A hydroponic experiment showed that the MR treatment significantly decreased the above-ground tissue Cd content compared with the M14 or R27 treatment. The BC+MR treatment reduced the grain Cd content by 51.5%-67.7% and Cd translocation factor at the mature stage of wheat plants and increased the organic matter-bound Cd content by 31%-75% in the rhizosphere soils compared with the BC or MR treatment. Compared with the BC or MR treatment, the relative abundances of the biomarkers associated with Gemmatimonas, Altererythrobacter, Gammaproteobacteria, Xanthomonadaceae, Phenylobacterium, and Nocardioides in the BC+MR-treated rhizosphere microbiome decreased and negatively correlated with the organic matter-bound Cd contents. In the BC+MR-treated root interior microbiome, the relative abundance of the biomarker belonging to Exiguobacterium increased and negatively correlated with the Cd translocation factor, while the relative abundance of the biomarker belonging to Pseudonocardiaceae decreased and positively correlated with the Cd translocation factor. Our findings suggested that the BC+MR treatment reduced Cd availability and Cd transfer through affecting the abundances of these specific biomarkers in the rhizosphere soil and root interior microbiomes, leading to decreased wheat grain Cd uptake in the contaminated soil.

Using GWAS and Machine Learning to Identify and Predict Genetic Variants Associated with Foodborne Bacteria Phenotypic Traits

One of the main challenges in food microbiology is to prevent the risk of outbreaks by avoiding the distribution of food contaminated by bacteria. This requires constant monitoring of the circulating strains throughout the food production chain. Bacterial genomes contain signatures of natural evolution and adaptive markers that can be exploited to better understand the behavior of pathogen in the food industry. The monitoring of foodborne strains can therefore be facilitated by the use of these genomic markers capable of rapidly providing essential information on isolated strains, such as the source of contamination, risk of illness, potential for biofilm formation, and tolerance or resistance to biocides. The increasing availability of large genome datasets is enhancing the understanding of the genetic basis of complex traits such as host adaptation, virulence, and persistence. Genome-wide association studies have shown very promising results in the discovery of genomic markers that can be integrated into rapid detection tools. In addition, machine learning has successfully predicted phenotypes and classified important traits. Genome-wide association and machine learning tools have therefore the potential to support decision-making circuits intending at reducing the burden of foodborne diseases. The aim of this chapter review is to provide knowledge on the use of these two methods in food microbiology and to recommend their use in the field.

Influence of critical micelle concentration of choline-based long chain fatty acid soaps on their antibacterial activity against Methicillin resistant Staphylococcus aureus

HYPOTHESIS

Antimicrobial resistance (AMR) is a pressing global health concern. ESKAPEE pathogens, such as Methicillin-resistant Staphylococcus aureus (MRSA) are notable of concern in healthcare settings due to their resistance to critical antibiotics. To combat AMR, the development of alternatives such as bacterial membrane-active agents is crucial. Fatty acids (FAs) have emerged as a sustainable, antibiotic-free solution with inherent antibacterial activity. However, long chain saturated fatty acids (LCFAs) sodium soaps exhibit poorly antibacterial properties in comparison to short chain FAs, believed to be linked to limited solubility in aqueous media.

EXPERIMENTS

We employed choline as a chaotropic organic counter-ion to enhance the solubility of LCFAs and investigated their antibacterial effects against MRSA. The optimal medium conditions for micelle formation for LCFAs was first investigated. Then, we determined the critical micelle concentration (CMC), micellar morphology, and aggregation number through surface tension measurements and small angle neutron scattering experiments. Antimicrobial activity was assessed using minimum bactericidal concentration (MBC) assays and time-kill experiments.

FINDINGS

We have identified conditions where LCFAs are effective against MRSA for the first time, providing valuable insights for developing new antibacterial agents to fight AMR. LCFAs need to be used above their Krafft temperatures and CMC to exhibit antibacterial efficacy.

Development and application of a bacteriophage cocktail for Shigella flexneri biofilm inhibition on the stainless steel surface

Food contamination and biofilm formation by Shigella in food processing facilities are major causes of acute gastrointestinal infection and mortality in humans. Bacteriophages (phages) are promising alternatives to antibiotics in controlling plankton and biofilms in food matrices. This study isolated two novel phages, S2_01 and S2_02, with lytic activity against various Shigella spp. From sewage samples. Transmission electron microscopy revealed that phages S2_01 and S2_02 belonged to the Caudovirales order. On characterizing their lytic ability, phage S2_01 initially exhibited relatively weak antibacterial activity, while phage S2_02 initially displayed rapid antibacterial activity after phage application. A combination of these phages in a 1:9 ratio was selected, as it has been suggested to elicit the most rapid and sustained lysis ability for up to 24 h. It demonstrated lytic activity against various foodborne pathogens, including six Shigella spp. The phage cocktail exhibited biofilm inhibition and disruption abilities of approximately 79.29% and 42.55%, respectively, after 24 h in a 96-well microplate. In addition, inhibition (up to 23.42%) and disruption (up to 19.89%) abilities were also observed on stainless steel surfaces, and plankton growth was also significantly suppressed. Therefore, the phage cocktail formulated in this study displays great potential as a biological control agent in improving food safety against biofilms and plankton.

Lipidic drug delivery systems are responsive to the human microbiome

In vitro and in vivo tests for therapeutic agents are typically conducted in sterile environments, but many target areas for drug delivery are home to thousands of microbial species. Here, we examine the behaviour of lipidic nanomaterials after exposure to representative strains of four bacterial species found in the gastrointestinal tract and skin. Small angle X-ray scattering measurements show that the nanostructure of monoolein cubic and inverse hexagonal phases are transformed, respectively, into inverse hexagonal and inverse micellar cubic phases upon exposure to a strain of live Staphylococcus aureus often present on skin and mucosa. Further investigation demonstrates that enzymatic hydrolysis and cell membrane lipid transfer are both likely responsible for this effect. The structural responses to S. aureus are rapid and significantly reduce the rate of drug release from monoolein-based nanomaterials. These findings are the first to demonstrate how a key species in the live human microbiome can trigger changes in the structure and drug release properties of lipidic nanomaterials. The effect appears to be strain specific, varies from patient to patient and body region to body region, and is anticipated to affect the bioapplication of monoglyceride-based formulations.

Impact of pre-exposure stress on the growth and viability of Lactobacillus acidophilus in regular, buriti pulp and orange byproduct fermented milk products

The loss of probiotics viability in yogurts and fermented milk is a significant challenge in producing yogurt and fermented milk. Thus, pre-exposure of probiotics to stress conditions can be a viable alternative to increase the probiotic viability. Moreover, the use of fruit pulp and agro-industrial residues in these products has demonstrated promising results in promoting growth and improving the viability of probiotics. Thus, this study aimed to evaluate the effects of pre-exposure to acid, oxidative and osmotic stress on the growth and viability of Lactobacillus acidophilus in yogurts and naturally fermented milk containing buriti (Mauritia flexuosa Mart.) pulp or orange byproduct. L. acidophilus was individually pre-exposed to acid, oxidative, and osmotic stress and used in the production of yogurts and fermented milk to determine both the acidification profile and growth of the cultures. Furthermore, during cold storage, the post-acidification profiles and viability of microbial cultures added to the yogurts and fermented milk were monitored. Results showed that pre-exposure to stress conditions influenced the growth parameters as the growth rate (μ) and lag phase (λ) of L. acidophilus and the starter cultures of S. thermophilus and L. delbrueckii subsp. bulgaricus. Moreover, an increase in the viability of L. acidophilus - pre-exposed to acid stress - was observed on the 21st day of storage of natural yogurts containing orange byproduct compared with non-stressful conditions. This study reports new data on the growth of probiotic cultures pre-exposed to stress conditions in products added of pulps and agro-industrial residues, which have not yet been shown in the literature.

Exploring the antibiofilm potential of chitosan nanoparticles by functional modification with chloroquine and deoxyribonuclease

Planktonic bacteria tend to form sessile community architectures to shield resident bacteria from various environmental stresses. The formed biofilm leads to the failure of conventional antimicrobial therapy. Extracellular macromolecules, including extracellular DNA (eDNA), proteins, lipids, and polysaccharides, crosslink into gel-like structures through electrostatic forces in the mature biofilm matrix. The stereo-structural integrity and chemical inertia of the extracellular polymeric matrix result in comprehensive antimicrobial resistance to antibacterial polysaccharides. Herein, an ionic gelation method was employed to functionalize cationic chitosan nanoparticles (CSNPs) with chloroquine and deoxyribonuclease. The modification involved shifting eDNA chirality through a DNA-intercalating agent, chloroquine, and hydrolyzing an eDNA scaffold with deoxyribonuclease. The antibiofilm activity was assessed against a standard Staphylococcus aureus strain and clinical subtype isolates. Functional modifications targeting eDNA improved the chitosan anti-biofilm efficiency (residual biomass decreased from 74.2 to 90.3 % to 16.7-24.6 %) by disrupting the biofilm matrix. The functional CSNPs worked as a sensitizer prodrug, contributing to a bactericidal process of chitosan itself (cell wall damage increased from 11.38-18.16 % to 55.2-61.4 %) by dispersing the biofilm-enclosed bacteria. In vivo, the bacterial burden of infected mouse joints was reduced by 4.1 lg CFU/mL. Our results indicate the potential of this chitosan-based anti-infection strategy in biofilm-related infections.

High-throughput single-cell sequencing of activated sludge microbiome

Wastewater treatment plants (WWTPs) represent one of biotechnology's largest and most critical applications, playing a pivotal role in environmental protection and public health. In WWTPs, activated sludge (AS) plays a major role in removing contaminants and pathogens from wastewater. While metagenomics has advanced our understanding of microbial communities, it still faces challenges in revealing the genomic heterogeneity of cells, uncovering the microbial dark matter, and establishing precise links between genetic elements and their host cells as a bulk method. These issues could be largely resolved by single-cell sequencing, which can offer unprecedented resolution to show the unique genetic information. Here we show the high-throughput single-cell sequencing to the AS microbiome. The single-amplified genomes (SAGs) of 15,110 individual cells were clustered into 2,454 SAG bins. We find that 27.5% of the genomes in the AS microbial community represent potential novel species, highlighting the presence of microbial dark matter. Furthermore, we identified 1,137 antibiotic resistance genes (ARGs), 10,450 plasmid fragments, and 1,343 phage contigs, with shared plasmid and phage groups broadly distributed among hosts, indicating a high frequency of horizontal gene transfer (HGT) within the AS microbiome. Complementary analysis using 1,529 metagenome-assembled genomes from the AS samples allowed for the taxonomic classification of 98 SAG bins, which were previously unclassified. Our study establishes the feasibility of single-cell sequencing in characterizing the AS microbiome, providing novel insights into its ecological dynamics, and deepening our understanding of HGT processes, particularly those involving ARGs. Additionally, this valuable tool could monitor the distribution, spread, and pathogenic hosts of ARGs both within AS environments and between AS and other environments, which will ultimately contribute to developing a health risk evaluation system for diverse environments within a One Health framework.

One-step copper deposition-induced signal amplification for multiplex bacterial infection diagnosis on a lateral flow immunoassay device

The lateral flow immunoassay (LFIA) is predominant in rapid diagnostic tests owing to its cost-effectiveness and operational simplicity. However, the conventional LFIA exhibits limited sensitivity and is susceptible to human variance for the result readout, impacting result interpretation. In this study, we introduced a novel one-step copper deposition-induced signal amplification lateral flow immunoassay (osa-LFIA) that markedly enhances the detection sensitivity for Staphylococcus aureus (protein A) and Pseudomonas aeruginosa (exotoxin A). Utilizing gold nanoparticles (AuNPs) as a catalyst, this approach employs ascorbic acid to reduce Cu2+ to Cu0, depositing on AuNPs at the test line and amplifying the signal. A user-friendly design features a three-dimensional paper structure incorporating pre-dried reagents, enabling a streamlined, efficient testing process. The osa-LFIA significantly lowers detection limits to 3 ng mL-1 for protein A and 10 ng mL-1 for exotoxin A, offering a tenfold improvement over conventional LFIA. Additionally, we developed a portable grayscale detection device, achieving less than 10% error in quantitative analysis compared to the data acquired and analyzed in the lab. This entire process, from detection to signal amplification, is completed in just 20 min. For the clinical trial, we utilized the osa-LFIA to test synovial fluid samples infected with Staphylococcus aureus. We also successfully detected different concentrations of the exotoxin A in parallel, with a recovery value of 96%-110%. Our findings demonstrate the osa-LFIA's potential as a rapid, highly sensitive, and simple-to-use diagnostic tool for detecting various pathogens, significantly advancing the field of rapid diagnostic testing.

In Vitro and In Vivo Evaluation of Virus-Induced Innate Immunity in Mouse

The innate immune system is the first line of host defense against infection by pathogenic microorganisms, among which macrophages are important innate immune cells. Macrophages are widely distributed throughout the body and recognize and eliminate viruses through pattern recognition receptors (PRRs) to sense pathogen-associated molecular patterns (PAMPs). In the present chapter, we provide detailed protocols for vesicular stomatitis virus (VSV) amplification, VSV titer detection, isolation of mouse primary peritoneal macrophages, in vitro and in vivo VSV infection, detection of interferon-beta (IFN-β) expression, and lung injury. These protocols provide efficient and typical methods to evaluate virus-induced innate immunity in vitro and in vivo.

Metagenomic perspectives on antibiotic resistance genes in tap water: The environmental characteristic, potential mobility and health threat

As an emerging environmental contaminant, antibiotic resistance genes (ARGs) in tap water have attracted great attention. Although studies have provided ARG profiles in tap water, research on their abundance levels, composition characteristics, and potential threat is still insufficient. Here, 9 household tap water samples were collected from the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) in China. Additionally, 75 sets of environmental sample data (9 types) were downloaded from the public database. Metagenomics was then performed to explore the differences in the abundance and composition of ARGs. 221 ARG subtypes consisting of 17 types were detected in tap water. Although the ARG abundance in tap water was not significantly different from that found in drinking water plants and reservoirs, their composition varied. In tap water samples, the three most abundant classes of resistance genes were multidrug, fosfomycin and MLS (macrolide-lincosamide-streptogramin) ARGs, and their corresponding subtypes ompR, fosX and macB were also the most abundant ARG subtypes. Regarding the potential mobility, vanS had the highest abundance on plasmids and viruses, but the absence of key genes rendered resistance to vancomycin ineffective. Generally, the majority of ARGs present in tap water were those that have not been assessed and are currently not listed as high-threat level ARG families based on the World Health Organization Guideline. Although the current potential threat to human health posed by ARGs in tap water is limited, with persistent transfer and accumulation, especially in pathogens, the potential danger to human health posed by ARGs should not be ignored.

Nitrogen-cycling processes under long-term compound heavy metal(loids) pressure around a gold mine: Stimulation of nitrite reduction

Mining and tailings deposition can cause serious heavy metal(loids) pollution to the surrounding soil environment. Soil microorganisms adapt their metabolism to such conditions, driving alterations in soil function. This study aims to elucidate the response patterns of nitrogen-cycling microorganisms under long-term heavy metal(loids) exposure. The results showed that the diversity and abundance of nitrogen-cycling microorganisms showed negative feedback to heavy metal(loids) concentrations. Denitrifying microorganisms were shown to be the dominant microorganisms with over 60% of relative abundance and a complex community structure including 27 phyla. Further, the key bacterial species in the denitrification process were calculated using a random forest model, where the top three key species (Pseudomonas stutzei, Sphingobium japonicum and Leifsonia rubra) were found to play a prominent role in nitrite reduction. Functional gene analysis and qPCR revealed that nirK, which is involved in nitrite reduction, significantly accumulated in the most metal-rich soil with the increase of absolute abundance of 63.86%. The experimental results confirmed that the activity of nitrite reductase (Nir) encoded by nirK in the soil was increased at high concentrations of heavy metal(loids). Partial least squares-path model identified three potential modes of nitrite reduction processes being stimulated by heavy metal(loids), the most prominent of which contributed to enhanced nirK abundance and soil Nir activity through positive stimulation of key species. The results provide new insights and preliminary evidence on the stimulation of nitrite reduction processes by heavy metal(loids).

Golden Gate Cloning of Expression Plasmids for Synthetic Small RNAs in Bacteria

Bacterial small RNAs (sRNAs) are well known for their ability to modulate gene expression at the post-transcriptional level. Their rather simple and modular organization provides the user with defined building blocks for synthetic biology approaches. In this chapter, we introduce a plasmid series for Escherichia coli and describe protocols for fast and efficient construction of synthetic sRNA expression plasmids based on Golden Gate assembly. In addition, we present the G-GArden tool, which assists with the design of oligodeoxynucleotides and overhangs for scarless assembly strategies. We propose that the presented procedures are suitable for many applications in different bacteria, which are related to E. coli and beyond.

Aggregation-induced emission luminogens for intracellular bacteria imaging and elimination

Intracellular bacterial infections are a serious threat to human health due to their ability to escape immunity and develop drug resistance. Recent attention has been devoted to identifying and ablating intracellular bacteria with fluorescence probes. Aggregation-induced emission luminogens (AIEgens) photosensitizers as fluorescence probes possess excellent photostability and rapid response, which have emerged as powerful fluorescent tools for intracellular bacterial detection and antibacterial therapy. This review is intended to highlight the current advances in AIEgens on intracellular bacteria imaging and elimination, which covers topics from intracellular AIE mechanism, intracellular bacteria imaging of AIEgens to the elimination of intracellular bacteria with AIEgens. AIEgens utilized different interactions to detect intracellular bacteria, emitting bright light due to restricted intramolecular movement to visualize intracellular bacteria. Photosensitive AIEgens generate reactive oxygen species (ROS) in the aggregate state to elimate intracellular bacteria. Moreover, the prospects and application of AIEgens in intracellular bacteria imaging and elimination are also discussed, which provides insights for the development of AIE-based diagnostic and therapeutic materials and technologies.

Dual action electrochemical bandage operated by a programmable multimodal wearable potentiostat

We have developed electrochemical bandage (e-bandage) prototypes that generate the reactive oxygen species hypochlorous acid (HOCl) or hydrogen peroxide (H2O2) for potential use to treat biofilm-infected wounds in humans. We have shown that both e-bandage-generated HOCl and H2O2 kill biofilms in vitro and in infected wounds on mice, with the former being more active in vitro. The H2O2-generating e-bandage, more so than the HOCl-generating e-bandage, was associated with improved healing of infected wounds. Here, a strategy in which H2O2 and HOCl are alternately generated-for dual action-was explored. The goal was to develop a programmable multimodal wearable potentiostat [PMWP] that can generate HOCl or H2O2, as needed. An ultralow-power microcontroller unit was developed to manage operation of the PMWP. The system was operated with a 260-mAh capacity coin battery and weighed 4.6 g, making it suitable for future small animal experiments (and ultimately, potential evaluation in humans). As assessed using electrochemical parameters, the device functioned comparably to a commercial benchtop potentiostat. To confirm antimicrobial activity, PMWP-controlled e-bandages were tested in vitro against clinical isolates of methicillin-resistant Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, Enterococcus faecium, and Candida auris. When programmed to deliver HOCl followed by H2O2, PMWP-controlled e-bandages exhibited activity against biofilms of all study isolates tested. Finally, we demonstrated the PMWP's usability in a murine wound infection model.

Induction of protective immune responses at respiratory mucosal sites

Many pathogens enter the host through mucosal sites. Thus, interfering with pathogen entry through local neutralization at mucosal sites therefore is an effective strategy for preventing disease. Mucosally administered vaccines have the potential to induce protective immune responses at mucosal sites. This manuscript delves into some of the latest developments in mucosal vaccination, particularly focusing on advancements in adjuvant technologies and the role of these adjuvants in enhancing vaccine efficacy against respiratory pathogens. It highlights the anatomical and immunological complexities of the respiratory mucosal immune system, emphasizing the significance of mucosal secretory IgA and tissue-resident memory T cells in local immune responses. We further discuss the differences between immune responses induced through traditional parenteral vaccination approaches vs. mucosal administration strategies, and explore the protective advantages offered by immunization through mucosal routes.

COVID-19 vaccination perspectives among patients with Long COVID: A qualitative study

Individuals who have Long COVID may have unique perspectives about COVID-19 vaccination due to the significant impact that COVID-19 has had on their lives. However, little is known about the specific vaccination perspectives among this patient population. The goal of our study was to improve our understanding of perspectives about COVID-19 vaccines among individuals with Long COVID. Interviews were conducted with patients receiving care at a post-COVID recovery clinic. Deductive thematic analysis was used to characterize participant perspectives according to the vaccine acceptance continuum framework, which recognizes a spectrum from vaccine acceptance to refusal. From interviews with 21 patients, we identified perspectives across the continuum of vaccine acceptance. These perspectives included acceptance of vaccines to prevent future illness, concerns about vaccine side effects on Long COVID symptoms, and refusal of vaccines due to perceived natural immunity. A limitation of our study is that these perspectives are specific to individuals receiving care at one post-COVID recovery clinic. In conclusion, our study demonstrates that some patients with Long COVID are uncertain about COVID-19 vaccines and boosters but may also be amenable to conversations that impact future vaccination acceptance. Patient perspectives should be considered when communicating recommendations for COVID-19 vaccinations to this population.

Immune imprinting: The persisting influence of the first antigenic encounter with rapidly evolving viruses

Immune imprinting is a phenomenon that stems from the fundamentals of immunological memory. Upon recurrent exposures to an evolving pathogen, the immune system must weigh the benefits of rapidly recalling established antibody repertoires with greater affinity to the initial variant or invest additional time and energy in producing de novo responses specific to the emerging variant. In this review, we delve into the mechanistic complexities of immune imprinting and its role in shaping subsequent immune responses, both de novo and recall, against rapidly evolving respiratory viruses such as influenza and coronaviruses. By exploring the duality of immune imprinting, we examine its potential to both enhance or hinder immune protection against disease, while emphasizing the role of host and viral factors. Finally, we explore how different vaccine platforms may affect immune imprinting and comment on vaccine strategies that can favor de novo variant-specific antibody responses.

Barriers and pathways to environmental surveillance of antibiotic resistance in middle- and low-income settings: a qualitative exploratory key expert study

BACKGROUND

Local and global surveillance of antibiotic resistance (ABR) has proven a challenge to implement effectively in low- and middleincome (LMI) settings. Environmental surveillance solutions are increasingly highlighted as a strategy to help overcome such problems, and thus to promote global health as well as the local management of ABR in LMI countries. While technical and scientific aspects of such solutions are being probed continuously, no study has investigated their practical feasibility.

OBJECTIVE

Explore practical barriers for environmental surveillance of ABR in LMI countries, and pathways for surveillance experts to manage these.

METHODS

To start charting this unknown territory, we conducted an explorative, qualitative interview study with key informants, applying a constructivist grounded theory approach to analyze the results.

RESULTS

Barriers were identified across infrastructural, institutional and social dimensions, and pathways to manage them were mostly counterproductive from an ABR management perspective, including avoiding entire regions, applying substandard methods and failing to include local collaborators.

CONCLUSION

The research community as well as international agencies, organizations and states have key roles and responsibilities for improving the prospects of feasible environmental ABR surveillance in LMI-settings.

Editorial: plant-microbial symbiosis toward sustainable food security

The use of plant-associated microorganisms is increasingly being investigated as a key tool for mitigating the impact of biotic and abiotic threats to crops and facilitating migration to sustainable agricultural practices. The microbiome is responsible for several functions in agroecosystems, such as the transformation of organic matter, nutrient cycling, and plant/pathogen growth regulation. As climate change and global warming are altering the dynamics of plant-microbial interactions in the ecosystem, it has become essential to perform comprehensive studies to decipher current and future microbial interactions, as their useful symbiotic mechanisms could be better exploited to achieve sustainable agriculture. This will allow for the development of effective microbial inoculants that facilitate nutrient supply for the plant at its minimal energy expense, thus increasing its resilience to biotic and abiotic stresses. This article collection aims to compile state-of-the-art research focused on the elucidation and optimization of symbiotic relationships between crops and their associated microbes. The information presented here will contribute to the development of next-generation microbial inoculants for achieving a more sustainable agriculture.

Lead toxicity in plants: mechanistic insights into toxicity, physiological responses of plants and mitigation strategies

Soil toxicity is a major environmental issue that leads to numerous harmful effects on plants and human beings. Every year a huge amount of Pb is dumped into the environment either from natural sources or anthropogenically. Being a heavy metal it is highly toxic and non-biodegradable but remains in the environment for a long time. It is considered a neurotoxic and exerts harmful effects on living beings. In the present review article, investigators have emphasized the side effects of Pb on the plants. Further, the authors have focused on the various sources of Pb in the environment. Investigators have emphasized the various responses including molecular, biochemical, and morphological of plants to the toxic levels of Pb. Further emphasis was given to the effect of elevated levels of Pb on the microbial population in the rhizospheres. Further, emphasized the various remediation strategies for the Pb removal from the soil and water sources.

A systematic review on malaria and dengue vaccines for the effective management of these mosquito borne diseases: Improving public health

Insect vector-borne diseases (VBDs) pose significant global health challenges, particularly in tropical and subtropical regions. The WHO has launched the "Global Vector Control Response (GVCR) 2017-2030" to address these diseases, emphasizing a comprehensive approach to vector control. This systematic review investigates the potential of malaria and dengue vaccines in controlling mosquito-borne VBDs, aiming to alleviate disease burdens and enhance public health. Following PRISMA 2020 guidelines, the review incorporated 39 new studies out of 934 identified records. It encompasses various studies assessing malaria and dengue vaccines, emphasizing the significance of vaccination as a preventive measure. The findings indicate variations in vaccine efficacy, duration of protection, and safety considerations for each disease, influencing public health strategies. The review underscores the urgent need for vaccines to combat the increasing burden of VBDs like malaria and dengue, advocating for ongoing research and investment in vaccine development.

Advances in understanding the interaction between Solanaceae NLR resistance proteins and the viral effector Avr

The rising prevalence of viral-induced diseases, particularly those caused by certain strains, poses a substantial risk to the genetic diversity of Solanaceae crops and the overall safety of horticultural produce. According to the "gene-for-gene" hypothesis, resistance proteins are capable of selectively identifying nontoxic effectors produced by pathogens, as they are under purview of the host's immune defenses. The sensitivity and responsiveness of Solanaceae plants to viral attacks play a crucial role in shaping the outcomes of their interactions with viruses. Pathogenic organisms, devise an array of infection tactics aimed at circumventing or neutralizing the host's immune defenses to facilitate effective invasion. The invasion often accomplishes by suppressing or disrupting the host's defensive mechanisms or immune signals, which are integral to the infection strategies of such invading pathogens. This comprehensive review delves into the myriad approaches that pathogenic viruses employ to infiltrate and overcome the sophisticated immune system of tomatoes. Furthermore, the review explores the possibility of utilizing these viral strategies to bolster the resilience of horticultural crops, presenting a hopeful direction for forthcoming progress in plant health and agricultural stability.

Genome editing in Sub-Saharan Africa: a game-changing strategy for climate change mitigation and sustainable agriculture

Sub-Saharan Africa's agricultural sector faces a multifaceted challenge due to climate change consisting of high temperatures, changing precipitation trends, alongside intensified pest and disease outbreaks. Conventional plant breeding methods have historically contributed to yield gains in Africa, and the intensifying demand for food security outpaces these improvements due to a confluence of factors, including rising urbanization, improved living standards, and population growth. To address escalating food demands amidst urbanization, rising living standards, and population growth, a paradigm shift toward more sustainable and innovative crop improvement strategies is imperative. Genome editing technologies offer a promising avenue for achieving sustained yield increases while bolstering resilience against escalating biotic and abiotic stresses associated with climate change. Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein (CRISPR/Cas) is unique due to its ubiquity, efficacy, alongside precision, making it a pivotal tool for Sub-Saharan African crop improvement. This review highlights the challenges and explores the prospect of gene editing to secure the region's future foods.

COVID-19 vaccines: Immune correlates and clinical outcomes

Severe disease due to COVID-19 has declined dramatically as a result of widespread vaccination and natural immunity in the population. With the emergence of SARS-CoV-2 variants that largely escape vaccine-elicited neutralizing antibody responses, the efficacy of the original vaccines has waned and has required vaccine updating and boosting. Nevertheless, hospitalizations and deaths due to COVID-19 have remained low. In this review, we summarize current knowledge of immune responses that contribute to population immunity and the mechanisms how vaccines attenuate COVID-19 disease severity.

The 2nd China Vaccinology Integrated Innovation & Teaching Development Conference: Promoting the construction of vaccinology discipline system

The 2nd China Vaccinology Integrated Innovation & Teaching Development Conference was held in Sun Yat-sen University, Shenzhen, 18-19, November 2023. Over 200 participants in the field of Vaccinology gathered together to address challenges and issues relevant to vaccine education and training courses, research, and public health programs in China. The conference themed "Promoting the Integrated and Innovative Development of Vaccinology through Collective Efforts." The conference was organized by the China Association of Vaccine (CAV) and hosted by Vaccinology Education Professional Committee of CAV, and School of Public Health (Shenzhen), Sun Yat-sen University. Other partners included the Medical Virology Branch of the Chinese Medical Association, the editorial committee of the Chinese Journal of Preventive Medicine, Human Vaccines & Immunotherapeutics, and the People's Medical Publishing House. The 1st conference was held in Hangzhou, in October 2020.

The anticancer mechanisms of Toxoplasma gondii rhoptry protein 16 on lung adenocarcinoma cells

Lung adenocarcinoma is the most prevalent subtype of lung cancer, which is the leading cause of cancer-related mortality worldwide. Toxoplasma gondii (T.gondii) Rhoptry protein 16 (ROP16) has been shown to quickly enter the nucleus, and through activate host cell signaling pathways by phosphorylation STAT3 and may affect the survival of tumor cells. This study constructed recombinant lentiviral expression vector of T. gondii ROP16 I/II/III and stably transfected them into A549 cells, and the effects of ROP16 on cell proliferation, cell cycle, apoptosis, invasion, and migration of A549 cells were explored by utilizing CCK-8, flow cytometry, qPCR, Western blotting, TUNEL, Transwell assay, and cell scratch assay, and these effects were confirmed in the primary human lung adenocarcinoma cells from postoperative cancer tissues of patients. The type I and III ROP16 activate STAT3 and inhibited A549 cell proliferation, regulated the expression of p21, CDK6, CyclinD1, and induced cell cycle arrest at the G1 phase. ROP16 also regulated the Bax, Bcl-2, p53, cleaved-Caspase3, and Caspase9, inducing cell apoptosis, and reduced the invasion and migration of A549 cells, while type II ROP16 protein had no such effect. Furthermore, in the regulation of ROP16 on primary lung adenocarcinoma cells, type I and III ROP16 showed the same anticancer potential. These findings confirmed the anti-lung adenocarcinoma effect of type I and III ROP16, offering fresh perspectives on the possible application of ROP16 as a target with adjuvant therapy for lung adenocarcinoma and propelling the field of precision therapy research toward parasite treatment of tumors.

Safety and immunogenicity of a modified mRNA-lipid nanoparticle vaccine candidate against COVID-19: Results from a phase 1, dose-escalation study

This phase 1, open-label, dose-escalation, multi-center study (NCT05477186) assessed the safety and immunogenicity of a booster dose of an mRNA COVID-19 vaccine (CV0501) encoding the SARS-CoV-2 Omicron BA.1 spike protein. Participants aged ≥ 18 years previously vaccinated with ≥ 2 doses of an mRNA COVID-19 vaccine received CV0501 doses ranging from 12 to 200 μg. After assessment of safety and immunogenicity of the 12 μg dose in 30 adults, 30 adults ≤ 64 years were randomized to receive either a 3 or 6 μg dose. Solicited adverse events (AEs) were collected for 7 days, unsolicited AEs for 28 days, and serious AEs (SAEs), medically attended AEs (MAAEs), and AEs of special interest (AESIs) until day (D) 181 post-vaccination. Serum neutralizing titers specific to SARS-CoV-2 BA.1, wild-type, Delta, and additional Omicron subvariants were assessed at D1, D15, D29, D91, and D181. Of 180 vaccinated participants (mean age: 49.3 years; 57.8% women), 70.6% had prior SARS-CoV-2 infection. Most solicited local (98.1%) and systemic (96.7%) AEs were of mild-to-moderate severity; the most common were injection site pain (57.5%; 33.3-73.3% across groups) and myalgia (36.9%; 13.3-56.7%). Unsolicited AEs were reported by 14.4% (6.7-26.7%) of participants (mild-to-moderate severity in 88.5% of the participants). Three participants (1.7%) reported SAEs, 16.7% (6.7-30.0%) reported MAAEs, and 8.3% (0.0-13.3%) reported AESIs (15 COVID-19 cases), none related to vaccination. Geometric means of serum neutralizing titers increased from baseline to D15 and D29 (dose-dependent), and then decreased over time. The safety and immunogenicity results supported advancement to a phase 2 trial.

A pharmacological approach to investigating effector translocation in rice-Magnaporthe oryzae interactions

Fungal pathogens deliver effector proteins into living plant cells to suppress plant immunity and control plant processes that are needed for infection. During plant infection, the devastating rice blast fungus, Magnaporthe oryzae, forms the specialized biotrophic interfacial complex (BIC), which is essential for effector translocation. Cytoplasmic effectors are first focally secreted into BICs, and subsequently packaged into dynamic membranous effector compartments (MECs), then translocated via clathrin-mediated endocytosis (CME) into the host cytoplasm. This study demonstrates that clathrin-heavy chain inhibitors endosidin-9 (ES9) and endosidin-9-17 (ES9-17) blocked the internalization of the fluorescently labeled effectors Bas1 and Pwl2 in rice cells, leading to swollen BICs lacking MECs. In contrast, ES9-17 treatment had no impact on the localization pattern of the apoplastic effector Bas4. This study provides further evidence that cytoplasmic effector translocation occurs by CME in BICs, suggesting a potential role for M. oryzae effectors in co-opting plant endocytosis.

Assessment of effectiveness and impact of universal prophylaxis with nirsevimab for prevention of hospitalizations due to respiratory syncytial virus in infants. The NIRSE-GAL study protocol

Nirsevimab has been recently licensed for universal RSV prophylaxis in infants. NIRSE-GAL is a three-year population-based study initiated in Galicia in September 2023. It aims to evaluate nirsevimab effectiveness against RSV-related hospitalizations lower respiratory tract infections (LRTI), severe RSV, all-cause LRTI, and all-cause hospitalization. NIRSE-GAL also aims to estimate nirsevimab impact on primary healthcare use in the short and mid-term, children's wheezing and asthma, and medical prescriptions for RSV. The immunization campaigns will be scheduled based on the expected start week for the RSV season and will last the whole season. Immunization will be offered to: i) infants born during the campaign (seasonal), ii) infants < 6 months at the start of the campaign (catch-up), and iii) infants with high-risk factors, aged 6-24 months at the start of the campaign (high-risk). The follow-up period will start: i) the immunization date for all immunized infants, ii) the start of the campaign, for the non-immunized catch-up or high-risk groups, or iii) the birthdate for the non-immunized seasonal group. Infants will be followed up until outcome occurrence, death, or end of study. Nirsevimab effectiveness will be estimated using Poisson and Cox regression models. Sensitivity and stratified analyses will be undertaken. The number of averted cases and the number needed to immunize will be estimated. Immunization failure and nirsevimab safety will be monitored. NIRSE-GAL was approved by the ethics committee of Galicia (CEIC 2023-377) and registered in ClinicalTrials.gov (ID: NCT06180993). Findings will be mainly shared via peer-reviewed publications and scientific conferences.

Immunogenicity and safety of concomitant administration of recombinant COVID-19 vaccine and quadrivalent inactivated influenza vaccine in Chinese adults: An open-label, randomized, controlled trial

The immunogenicity and safety of the concomitant administration of recombinant COVID-19 vaccine and quadrivalent inactivated influenza vaccine (Split Virion) (QIIV) in Chinese adults are unclear. In this open-label, randomized controlled trial, participants aged ≥ 18 years were recruited. Eligible healthy adults were randomly assigned (1:1) to receive QIIV at the same time as the first dose of COVID-19 vaccine (simultaneous-group) or 14 days after the second dose of COVID-19 vaccine (non-simultaneous-group). The primary outcome was to compare the difference in immunogenicity of QIIV (H1N1, H3N2, Yamagata, and Victoria) between the two groups. A total of 299 participants were enrolled, 149 in the simultaneous-group and 150 in the non-simultaneous-group. There were no significant differences in geometric mean titer (GMT) [H1N1: 386.4 (95%CI: 299.2-499.0) vs. 497.4 (95%CI: 377.5-655.3); H3N2: 66.9 (95%CI: 56.1-79.8) vs. 81.4 (95%CI: 67.9-97.5); Yamagata: 95.6 (95%CI: 79.0-115.8) vs. 74.3 (95%CI: 58.6-94.0); and Victoria: 48.5 (95%CI: 37.6-62.6) vs. 65.8 (95%CI: 49.0-88.4)] and seroconversion rate (H1N1: 87.5% vs. 90.1%; H3N2: 58.1% vs. 62.0%; Yamagata: 75.0% vs. 64.5%; and Victoria: 55.1% vs. 62.8%) of QIIV antibodies between the simultaneous and non-simultaneous groups. For the seroprotection rate of QIIV antibodies, a higher seroprotection rate of Yamagata antibody was observed only in the simultaneous-group than in the non-simultaneous-group [86.0% vs. 76.0%, p = .040]. In addition, no significant difference in adverse events was observed between the two groups (14.2% vs. 23.5%, p = .053). In conclusion, no immune interference or safety concerns were found for concomitant administration of COVID-19 vaccine with QIIV in adults aged ≥ 18 years.

A highly neutralizing human monoclonal antibody targeting a novel linear epitope on staphylococcal enterotoxin B

Staphylococcal Enterotoxin B (SEB), produced by Staphylococcus aureus (S. aureus), is a powerful superantigen that induces severe immune disruption and toxic shock syndrome (TSS) upon binding to MHC-II and TCR. Despite its significant impact on the pathogenesis of S. aureus, there are currently no specific therapeutic interventions available to counteract the mechanism of action exerted by this toxin. In this study, we have identified a human monoclonal antibody, named Hm0487, that specifically targets SEB by single-cell sequencing using PBMCs isolated from volunteers enrolled in a phase I clinical trial of the five-antigen S. aureus vaccine. X-ray crystallography studies revealed that Hm0487 exhibits high affinity for a linear B cell epitope in SEB (SEB138-147), which is located distantly from the site involved in the formation of the MHC-SEB-TCR ternary complex. Furthermore, in vitro studies demonstrated that Hm0487 significantly impacts the interaction of SEB with both receptors and the binding to immune cells, probably due to an allosteric effect on SEB rather than competing with receptors for binding sites. Moreover, both in vitro and in vivo studies validated that Hm0487 displayed efficient neutralizing efficacy in models of lethal shock and sepsis induced by either SEB or bacterial challenge. Our findings unveil an alternative mechanism for neutralizing the pathogenesis of SEB by Hm0487, and this antibody provides a novel strategy for mitigating both SEB-induced toxicity and S. aureus infection.