Search Results (7,948)

Resource-limited settings continue to face challenges in the identification of COVID-19, bacterial pneumonia, viral pneumonia, and normal lung conditions because of the overlap of CT appearance and inter-observer variability. We justify a hybrid architecture of deep learning which combines hand-designed descriptors (Histogram of Oriented Gradients, Local Binary Patterns) and a 20-layer Convolutional Neural Network with dual self-attention. Handcrafted features were then trained with Support Vector Machines, and ensemble averaging was used to integrate the results with the CNN. The confidence level of 0.7 was used to mark suspicious cases to be reviewed manually. On a balanced dataset of 14,000 chest CT scans (3500 per class), the model was trained and cross-validated five-fold on a patient-wise basis. It had 97.43% test accuracy and a macro F1-score of 0.97, which was statistically significant compared to standalone CNN (92.0%), ResNet-50 (90.0%), multiscale CNN (94.5%), and ensemble CNN (96.0%). A further 2–3% enhancement was added by the self-attention module that targets the diagnostically salient lung regions. The predictions that were below the confidence limit amounted to only 5 percent, which indicated reliability and clinical usefulness. The framework provides an interpretable and scalable method of diagnosing multiclass lung disease, especially applicable to be deployed in healthcare settings with limited resources. The further development of the work will involve the multi-center validation, optimization of the model, and greater interpretability to be used in the real world. Full article

Transport emissions are a major source of urban polycyclic aromatic hydrocarbons (PAHs), posing risks to human health. While plant leaves and their epiphytic microbes contribute to PAH degradation, how plant traits and environmental factors affect this process remains unclear. This study examined 20 tree species in Beijing’s traffic corridors to explore PAH enrichment on leaves and the structure of phyllospheric bacterial communities. Results show that leaf area, morphology, and sampling height significantly influenced bacterial community assembly. Normalized Stochasticity Ratio (NST) analysis indicated that deterministic processes dominate on medium-sized leaves (11.8–40.1 cm²), simple leaves, and those below 2.3 m or above 3 m in height, whereas stochastic factors prevail on nano leaves, compound leaves, and leaves at low-position (<2.3 m). Although low-molecular-weight PAHs (2–4 rings) were predominant in leaves, Mantel tests revealed significant positive correlations between bacterial communities and high molecular weight PAHs (4–6 rings), such as benz(a)anthracene, benzo[e]pyrene, and picene. Spearman analysis identified 10 dominant bacterial taxa with PAH degradation potential, including Kocuria rosea, Serratia symbiotica, Massilia sp. WG5, and seven unclassified species from Hymenobacter, Sphingomonas, Roseomonas, Curtobacterium, and Deinococcus. Functional Annotation of Prokaryotic Taxa(FAPROTAX) prediction further associated 14 species across six genera, including Acinetobacter, Nocardioides, Gordonia, Rhodococcus, Clostridium_sensu_stricto_18, and Geobacter, with PAH degradation function. This work clarifies the composition and function of phyllospheric PAH-degrading bacteria in an urban traffic environment, offering a theoretical basis for enhancing degradation via bacterial consortia, biosurfactants, and optimized plant selection. Full article

The selection of an optimal antifoam is critical for efficient fermentation, as industrial agents often have detrimental side effects like growth inhibition, while some can enhance productivity. We studied the efficacy of novel silicone–polyol antifoam emulsions for use in fermentation as defoamers. Except for agent 3L10, all antifoams tested did not show inhibition on six bacterial and one fungal culture. Interestingly, agent 3L10 strongly inhibited Gram-positive bacteria (especially Corynebacterium glutamicum) but not Gram-negative strains. A comprehensive evaluation protocol—combining chemical design, cytotoxicity screening across diverse microorganisms, the determination of minimum effective concentrations (MECs), and validation in model bioreactor fermentations—was established. Through this process, 6T80 was identified as a promising antifoam agent for fermentation. It exhibited a low MEC, high emulsion stability, and no cytotoxicity and did not impair growth or recombinant protein production in Bacillus subtilis or Pseudomonas putida fermentations. This study concludes that agent 6T80 is suitable for further application in processes involving Gram-negative and certain Gram-positive hosts. The developed methodology enables the targeted selection of highly efficient and biocompatible antifoams for specific biotechnological processes. Full article

Δ¹-Pyrroline-5-carboxylate reductase (EC 1.5.1.2; called ProC in most bacteria) is an enzyme of central metabolism that catalyzes the last step of the proline biosynthetic pathways, namely the NADPH-dependent reduction of pyrroline-5-carboxylate (P5C) to L-proline (L-Pro). The enzyme, however, is also active towards other substrates, and these reactions might have physiological relevance. Herein, the substrate versatility of ProC from Escherichia coli was explored as follows. We initially characterized the reverse reaction carried out by ProC, i.e., the formation of P5C from L-Pro. This reaction was easily measurable at pH 10, allowing the determination of the kinetic parameters. Under the same conditions, we then tested the ability of ProC to oxidize a number of L-Pro analogs, confirming that ProC reacts most effectively with analogs containing a simple five-membered ring such as L-thioproline (THP) and 3,4-dehydro-L-proline (DHP). Larger substrates such as L-pipecolate (PIP) reacted with lower efficiency, and the four-membered ring analog, L-azetidine-2-carboxylate (A2C) showed no detectable reactivity and behaved as a weak inhibitor of the ProC reaction. To interpret these results, we built a structural model of ProC and employed this model for a docking analysis of L-Pro and of its analogs. This approach highlighted the presence of a peculiar “three-point interaction”, in which the L-Pro carboxylate and amino groups form hydrogen bonds with conserved residues in the binding site, while the substrate ring stacks with the nicotinamide ring of NADP⁺. The L-Pro analogs tried to preserve as much as possible these critical interactions for a correct positioning and a favorable binding. The possibility of an inherent multifunctionality of ProC was further explored by examining the genomic context of the proC gene in a large number of bacterial species. Full article

This study compares the chemical composition, antimicrobial effects, and antibiotic-potentiating capacity of three Lauraceae essential oils (EO): Cryptocarya agathophylla (CAEO), Litsea cubeba (LCEO), and Laurus nobilis (LNEO). Gas chromatography–mass spectrometry (GC–MS) analysis revealed distinct chemotypes: CAEO and LCEO were dominated by oxygenated monoterpenes, while LNEO contained the highest levels of monoterpene hydrocarbons. Antibacterial testing against nine bacterial strains showed strain-dependent growth suppression trends, while true minimum inhibitory concentrations (MICs) were reached only in selected cases. EO–ampicillin interactions were evaluated using MIC-based checkerboard criteria, whereas OD-derived inhibition parameters were used exclusively to describe sub-MIC potentiation trends. In combination assays, LNEO exhibited the most pronounced potentiating effects against Streptococcus pyogenes, Shigella flexneri, and Haemophilus influenzae, while CAEO and LCEO showed moderate or strain-dependent enhancement. Hierarchical clustering highlighted distinct oil- and strain-specific interaction profiles. Overall, although CAEO displayed stronger intrinsic antibacterial effects when tested alone, LNEO emerged as the most effective potentiator of ampicillin activity in a strain-dependent manner. The effects of the major compounds identified in the Lauraceae EO were assessed in silico against protein targets of some microorganisms using the AutoDock software. The docking scores revealed binding affinities of the bioactive compounds towards Dpr protein (4.3–5.8 kcal/mol), DNA gyrase (4.7–7.1 kcal/mol), mono- diacylglycerol lipase (4.4–6.2 kcal/mol), CYP51 (5.8–8.0 kcal/mol), phage-encoded quorum sensing anti-activator (5.8–8.0 kcal/mol) and Chondroitin ABC lyase I (4.8–6.3 kcal/mol). Two (2) hit compounds (α-Citral, β-Citral) were finely defined by strong hydrophobic and hydrophilic interactions with the bacterial and fungal protein targets, respectively. Full article

Rice blast and bacterial blight are two major diseases that seriously threaten rice production. Developing rice germplasm with enhanced resistance to multiple diseases while maintaining favorable agronomic traits is essential for sustainable breeding. In this study, two rice landraces from Motuo County, Xizang Autonomous Region, China, Benglinba and Gare, were used to simultaneously edit OsERF922 and Xa41 using a structurally optimized dual-target CRISPR/Cas9 vector, pRGEB32-2T. A total of 32 and 28 T₀ transgenic plants were generated in the Benglinba and Gare backgrounds, respectively. Targeted mutagenesis generated eight homozygous oserf922 mutants and three homozygous xa41 mutants in Benglinba, and four and five homozygous mutants in Gare. Twelve double homozygous mutant lines (nine Benglinba and three Gare) were selected for further analysis. Disease resistance assays showed that these double mutants exhibited significantly enhanced resistance to the rice blast fungus strain GDYJ7 and the bacterial blight pathogen strain GDXO-1, with markedly reduced lesion size or lesion length compared with wild-type plants (p < 0.001, Student’s t-test). Importantly, three independent T-DNA-free double mutant lines from each genetic background displayed no significant differences from their corresponding wild types in major agronomic traits, including plant height, effective panicle number, panicle length, seed-setting rate, or thousand-grain weight (p > 0.05). Grain quality parameters, such as brown rice rate, milled rice rate, amylose content, and gel consistency, were also unaffected. Overall, this study generated rice materials with enhanced resistance to rice blast and bacterial blight while maintaining elite agronomic and quality traits, providing valuable germplasm resources and a feasible strategy for the precise improvement of disease resistance in rice landraces from Xizang Autonomous Region. Full article

Vultures are extraordinarily adapted to feed on carrion, providing them with a constant microbiologically hostile environment. This peculiar ecological position has influenced the evolution of their gut microbiota, potentially conferring its uncommon antimicrobial traits and resistance to stress. In this study, we report on the isolation and comprehensive characterization of a lactic acid bacterium strain, identified as Ligilactobacillus agilis, from vulture feces via 16S rRNA gene sequencing. This strain exhibited potent antagonistic activity against several clinically relevant bacterial pathogens, including Salmonella enterica Typhimurium (25.26 ± 0.26 mm), Escherichia coli (23.5 ± 0.88 mm), Staphylococcus aureus (23.1 ± 1.8 mm), and Listeria monocytogenes (24.88 ± 0.61 mm), as demonstrated by agar well diffusion assays. Remarkably, it also demonstrated considerable resilience in simulated gastrointestinal conditions, with survival rates of 52.5 ± 7.4% in artificial gastric juice and 61.1 ± 3.7% in intestinal fluids. Antimicrobial susceptibility profiling confirmed its sensitivity to a broad range of commonly used antibiotics, including gentamicin, streptomycin, clindamycin, and penicillin. Whole-genome sequencing further revealed a complete repertoire of core genes associated with genetic information processing, robust carbohydrate metabolism, and nutrient assimilation, underscoring its adaptability and probiotic potential. It is important to note that the analysis of the assembled genome against VFDB did not show the presence of any known virulence factor according to the given criteria, which is preliminary evidence of safety-related aspects that are to be followed with the help of guideline-based analyses. Taken together, the unique ecological origin and in vitro inhibitory activity against the tested pathogens, gastrointestinal robustness, genomic features, and safety credentials position this L. agilis strain as a promising probiotic candidate for mitigating enteric infections in animal production systems, warranting further functional validation and in vivo efficacy studies. Full article

Drought is one of the most limiting abiotic stresses for agricultural production, especially in horticultural crops grown in arid and semi-arid areas. In the present study, we evaluated the potential of bacterial isolates obtained from coastal environments in Chile to improve drought tolerance in Lagenaria siceraria, a plant species increasingly used as a rootstock for cucurbit cropping. Rhizosphere bacteria were isolated from Sicyos baderoa, the only native cucurbit species of the Chilean coast, from which four isolates with plant growth-promoting traits, such as indole-3-acetic acid production, phosphorus solubilization, nitrogen fixation, and siderophore production, were selected. These isolates were inoculated on two L. siceraria genotypes, Illapel and Osorno, under both normal irrigation and water deficit conditions. The results showed that Peribacillus frigoritolerans showed a clearer positive effect on biomass and net photosynthesis under water deficit in the Illapel genotype, increasing shoot biomass by up to ~75% and restoring net photosynthetic rates by up to ~260% relative to non-inoculated drought-stressed plants. In contrast, responses associated with Staphylococcus succinus and those observed in the Osorno genotype were mainly expressed as trait- and tissue-specific adjustments, consistent with a more stabilizing response rather than broad growth stimulation. Additionally, malondialdehyde levels were reduced by up to ~25%, while free proline accumulation increased by more than 100% under water deficit. In contrast, total phenolic compounds showed more variable responses, indicating genotype- and strain-specific adjustment of antioxidant metabolism. Overall, the observed responses were heterogeneous and strongly dependent on the specific strain–genotype–trait combination and, therefore, should be interpreted as preliminary evidence supporting the potential value of native rhizobacteria for improving early drought-related traits in cucurbit rootstocks. Among the tested strains, Peribacillus frigoritolerans emerged as the most promising candidate for enhancing early drought tolerance in responsive genotypes such as Illapel, while highlighting the need for follow-up studies under replicated nursery and field conditions, including grafted plants, multiple drought intensities and combined inoculant strategies. Full article

In this work, we demonstrate precise control over laser-induced periodic surface structures (LIPSS) on stainless steel (SS) using femtosecond (fs) laser processing to suppress bacterial adhesion. We systematically compare the antifouling behavior of laser-textured surfaces with distinct pattern directionalities—linear and circular. Fs laser irradiation with linear polarization produces directional and anisotropic LIPSS, which progressively evolve into more complex hierarchical surface textures as processing conditions vary. In contrast, fs laser irradiation with circular polarization yields isotropic surface morphologies. Despite these morphological differences, the surface wettability remains nearly constant, with contact angles confined to a narrow range of 32.6–36.9°. Bacterial adhesion tests using Escherichia coli reveal that surfaces patterned with anisotropic features generated by linear polarization—particularly at an incident power of 30 mW—exhibit enhanced antifouling performance compared to isotropic counterparts. These results indicate that antifouling efficacy is governed not only by surface wettability but also by the spatial organization and anisotropy of the LIPSS. This study highlights the critical role of polarization-controlled fs laser processing in tailoring surface architectures and provides a rational strategy for designing bio-resistant metallic surfaces. Full article

Background/Objectives: Multidrug-resistant (MDR) strains of Streptococcus suis are increasingly prevalent and present significant challenges in clinical management. Given that the development of new antibiotics is a resource-intensive process and time-consuming, there is an urgent need for alternative therapeutic strategies to address resistance in the short term. One promising approach is the use of combination therapy, which involves pairing potent antibiotics with agents that may be less effective on their own, to enhance therapeutic efficacy and potentially overcome resistance mechanisms. This study aimed to investigate the in vitro antibacterial activity of combining two classes of antibiotics with distinct mechanisms of action—cell wall synthesis inhibitors and protein synthesis inhibitors—against MDR S. suis strains isolated from diseased pigs. Methods: A total of 36 MDR S. suis strains were tested using a microbroth dilution checkerboard assay to determine the minimum inhibitory concentration (MIC) of four cell wall synthesis inhibitors —amoxicillin/clavulanic acid (AMC), ampicillin (AMP), penicillin G (PEN), and vancomycin (VAN)— in combination with four protein synthesis inhibitors —gentamicin (GEN), neomycin (NEO), tilmicosin (TMS), and tylosin (TYL). Time–kill curve assays were conducted to evaluate the in vitro bactericidal activity of synergistic antibiotic combinations (PEN–GEN and AMP–NEO) against Beta-lactam-resistant and Beta-lactam-susceptible MDR S. suis strains. Results: Checkerboard analysis revealed that penicillin-gentamicin combination exhibited the most effective synergistic activity against the MDR S. suis strains (10/19, 52.6%), with ∑FIC values of 0.25–1.06 and MIC reductions from resistant to susceptible levels. Time-kill assays further confirmed the synergistic bactericidal effect of the combination, demonstrating complete bacterial clearance within 6–9 h, markedly rapid bacterial killing compared to monotherapy. Conclusions: This study demonstrates that antibiotic combinations, particularly Beta-lactams combined with aminoglycosides, show synergistic activity against pig-isolated S. suis MDR strains. The PEN-GEN combination exhibited strong synergistic and bactericidal effects, supporting combination therapy as a potential strategy to address antimicrobial resistance. Further evaluation in diverse strain backgrounds and prudent antibiotic use are essential to confirm efficacy and limit the emergence of antibiotic resistance. Full article

UV-C LED systems have emerged as a chemical-free alternative to hydrogen peroxide (H₂O₂) mist-based technologies. This study assesses the sporicidal efficacy of a UV-C LED HLD system under clinically relevant conditions using performance qualification (PQ) and compares its outcomes with two established H₂O₂ mist devices. The effectiveness of Lumicare ONE^® UV-C LED system and two H₂O₂ mist systems (trophon^® EPR and trophon^®2) in achieving a 6 log₁₀ reduction was evaluated using Geobacillus stearothermophilus spores as challenge test. Tests were conducted under three conditions: bare-metal non-flamed, bare-metal flamed, and packaged (glassine or Tyvek^®), with indicators positioned at both upper and lower chamber locations. AOAC 966.04 carrier tests using bacterial spores were also performed to confirm log-reduction performance. Under clinically representative bare-metal conditions, both non-flamed and flamed, Lumicare ONE achieved complete sporicidal efficacy at all chamber positions, matching the performance of the H₂O₂ mist systems. Under non-relevant (packaged) conditions, only the H₂O₂ systems passed the test, which is consistent with packaging materials that allowed H₂O₂ penetration, but blocked UV-C. AOAC carrier testing confirmed > 6 log₁₀ reductions following a 90 s UV-C cycle. Overall, when evaluated using appropriate PQ criteria, the UV-C LED system delivered efficacy equivalent to H₂O₂ systems while providing a fast and chemical-free HLD option for semi-critical probes. Full article

Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by barrier dysfunction and susceptibility to Staphylococcus aureus colonization. Biofilm formation modifies antibiotic resistance and the host immune response. This longitudinal study analyzed antimicrobial susceptibility and biofilm formation in 136 S. aureus isolates obtained over 18 months from lesional, nonlesional, and nasal samples of 26 pediatric patients with moderate-to-severe AD. Antimicrobial susceptibility testing was determined by the disk diffusion method, and biofilm production was quantified using a crystal violet microtiter assay. Clinical parameters, including disease severity, treatment response, and the administration of dilute bleach baths, were evaluated in relation to bacterial characteristics. Overall, 60.2% of isolates exhibited moderate-to-strong biofilm production, significantly associated with severe AD at baseline (p = 0.01), lack of clinical improvement (p = 0.04), and persistent moderate-to-severe disease (p = 0.01). Resistance rates for penicillin, gentamicin, clindamycin, and erythromycin exceeded 15%. Isolates from patients using dilute bleach baths showed greater resistance to ciprofloxacin (p < 0.0001) and exhibited constitutive or inducible macrolide–lincosamide–streptogramin B (MLS_B) resistance, with ermA detected in 80% of inducible cases. In conclusion, S. aureus biofilm formation is linked to disease severity and treatment failure in pediatric AD, underscoring the importance of culture-guided, targeted therapeutic strategies. Full article

SARS-CoV-2 main protease (M^pro) is essential for viral polyprotein processing and represents a prime target for antiviral drug discovery. However, most available screening strategies rely on computational predictions or cell-free biochemical approaches that provide limited functional context and often require specialized instrumentation, while mammalian cell-based models remain costly and require high biosafety levels. Accordingly, there remains a shortage of simple, rapid, and biosafe functional screening tools suitable for early-stage prioritization of potential M^pro inhibitors, particularly those derived from natural sources and in urgent situations such as the COVID-19 pandemic. In this study, a bacterial colorimetric reporter assay was developed that directly links SARS-CoV-2 M^pro activity to β-galactosidase function in Escherichia coli. To the best of our knowledge, the developed assay represents the first bacterial colorimetric model for functional detection of SARS-CoV-2 M^pro inhibition based on a phenotypic readout. The assay enables the rapid visual detection of protease inhibition on X-gal-containing medium and provides a cost-effective and biosafe platform for prioritizing candidate inhibitors, under standard laboratory conditions, prior to further validation. Due to its bacterial expression context, this assay is intended for functional screening to provide the most promising candidate compounds and/or extracts for subsequent biochemical or mammalian cell-based validation; it is not intended to determine quantitative potency or to replace further validation approaches. It should be noted that the selective compound uptake in E. coli restricts the range of chemical compositions that can be evaluated using this method. Therefore, proof-of-concept application was demonstrated using pomegranate juice, a representative natural inhibitor source, rather than most currently known specific M^pro inhibitors. In addition, other plant-derived preparations, including rhubarb, grape, and red/black currant juices, were tested demonstrating the assay’s applicability to diverse natural matrices. Full article

This study reports the incidental collection and exploratory analysis of a biofilm sample obtained from a water distribution pipeline in the Central Province of Sri Lanka, which had been in continuous service for approximately 50 years. Access to the pipe interior was achieved during a repair operation, providing a rare opportunity to directly sample an aged pipeline under the typical operating conditions of a tropical, developing country. An exploratory research design was adopted to examine the bacterial community composition and was explicitly framed as hypothesis-generating rather than testing predefined hypotheses. Bacterial community composition was analyzed using high-throughput MiSeq sequencing. At the genus level, the community was strongly enriched with Clostridium sensu stricto lineages, notably type 1 (relative abundance of 9.19%), type 12 (8.58%), and type 9 (3.09%). Several other genera, Nitrospira (4.94%), Bacillus (4.60%), Methyloligobacillus (3.75%), Hyphomicrobium (2.14%), and Haliangium (1.82%), occurred at moderate abundances, raising their potential consequences on biological and chemical water quality issues. Given the exploratory nature of the study, these findings represent site-specific biofilm characteristics in an aging drinking water distribution line in Sri Lanka. Although limited to a single biofilm sample, this study provides empirical observations from a rarely accessible environment and identifies knowledge gaps to guide future comprehensive investigations into biofilm dynamics, microbial ecology, and infrastructure management in tropical water distribution systems. Full article

The bacterial microbiome in aquaria plays an essential role in system stability by metabolizing toxic compounds like ammonia. This study monitored microbiome changes in seven zoo aquatic systems during their first year to assess responses to external influences. Over one year (October 2021–October 2022), water and swab samples were collected from one seawater tank and six filtration systems at regular intervals. Bacterial cultivation included total bacterial counts. Metagenomic analysis was performed on samples corresponding to environmental events using Oxford Nanopore sequencing. Taxonomical analysis at the phylum and genus levels used EPI2ME software. Diversity analyses and statistical tests were performed using R. Total bacterial counts increased steadily after inoculation and stabilized by the end of the collection period. Diversity analysis revealed significant differences within and between freshwater and saltwater tanks. Each aquarium exhibited a distinct bacterial community with frequent compositional changes. Despite environmental conditions and maintenance interventions and resulting disturbances that affected the microbiome, the overall nitrifying capacity remained unaffected. Nitrifying taxa emerged as potential indicators for environmental effects. Combined with investigations of ecological function, next-generation sequencing could facilitate the development of aquarium management protocols, ultimately improving fish welfare. Full article