Irreversible Attachment Research Articles

Impact of Nutrient Starvation on Biofilm Formation in Pseudomonas aeruginosa: An Analysis of Growth, Adhesion, and Spatial Distribution.

Objectives: This study investigates the impact of nutrient availability on the growth, adhesion, and biofilm formation of Pseudomonas aeruginosa ATCC 27853 under static conditions. Methods: Bacterial behaviour was evaluated in nutrient-rich Luria-Bertani (LB) broth and nutrient-limited M9 media, specifically lacking carbon (M9-C), nitrogen (M9-N), or phosphorus (M9-P). Bacterial adhesion was analysed microscopically during the transition from reversible to irreversible attachment (up to 120 min) and during biofilm production/maturation stages (up to 72 h). Results: Results demonstrated that LB and M9 media supported bacterial growth, whereas nutrient-starved conditions halted growth, with M9-C and M9-N inducing stationary phases and M9-P leading to cell death. Fractal analysis was employed to characterise the spatial distribution and complexity of bacterial adhesion patterns, revealing that nutrient-limited conditions affected both adhesion density and biofilm architecture, particularly in M9-C. In addition, live/dead staining confirmed a higher proportion of dead cells in M9-P over time (at 48 and 72 h). Conclusions: This study highlights how nutrient starvation influences biofilm formation and bacterial dispersion, offering insights into the survival strategies of P. aeruginosa in resource-limited environments. These findings should contribute to a better understanding of biofilm dynamics, with implications for managing biofilm-related infections and industrial biofouling.

Nanoparticle transport in partially saturated porous media: Attachment at fluid interfaces

Like the solid-water interface (SWI), air-water and oil-water interfaces (AWI and OWI) also act as collectors for nano-sized particles in porous media. The attachment of hydrophobic nanoparticles, which is often favorable and irreversible, is of particular interest because the transport and retention of such particles is closely linked to the fate of nanoplastics in unsaturated subsurface environments and the success of nanoremediation practices. Here, we show how a pore-network model (PNM) can be used to upscale the kinetics and extent of irreversible nanoparticle attachment at a single fluid-fluid interface under conditions of advection and dispersion in a sphere packing. By focusing on a trapped (immobile) non-wetting phase, we highlight a fundamental difference between the single-collector contact efficiency of AWI/OWI and SWI. Namely, AWI/OWI collectors, which are largely by-passed by the flowing aqueous phase, are exposed to a hydrodynamic environment dominated by diffusion. This difference has profound implications for the modelling of nanoparticle transport in porous media at the continuum (Darcy) scale. This study reveals the potential of pore network modelling as an essential complement to continuum models for upscaling the behavior of nanocolloids in porous media.

Antibiotic susceptibility and biofilm forming ability of Staphylococcus aureus isolated from Jordanian patients with diabetic foot ulcer.

Microbial biofilm is characterized by the irreversible attachment of planktonic cells to a surface and is usually associated with high antimicrobial resistance with worsening the wound healing. The objective of the study was to determine the prevalence of Staphylococcus aureus in diabetic foot ulcers (DFUs) of diabetic patients and to investigate antibiotic susceptibility patterns of these isolates. In addition to screen biofilm forming ability of isolated S. aureus. A total of 112 non-healing wound swabs of diabetic foot patients were collected and cultured on different culture media to identify and characterize 98 isolates. The S. aureus isolates were examined for their antibiotic susceptibility to different antimicrobial agents. Furthermore, S. aureus isolates were evaluated for their biofilm production capability using the Tissue Culture Plate Method (TPC). The level of icaA gene expression was determined by RT-PCR. The results of this study showed that these non-healing wounds yield positive cultures, with an average of 1.67 organisms per sample. The isolates showed highest resistance against oxacillin (95.2%) and lowest resistance against linezolid (3.7%). All isolates were biofilm producers and a significant association with the icaA gene expression level was recorded. This study showed that S. aureus isolates have a great ability to produce biofilms that are associated with the chronicity of wounds in diabetic patients. Routine screening for biofilm formers in chronic wounds and their antibiotic susceptibility testing will help in early treatment and prevent any other complications.

Facilitated transport of ferrihydrite with phosphate under saturated flow conditions

With increasing phosphate (P) entering the environment during agricultural application, the subsurface flow of particular P has been recently discussed as a vital P transport pathway. Iron (oxyhydr)oxide colloid-facilitated P transport is critical for iron and P biogeochemical processes in the subsurface. This study investigated the ferrihydrite colloid-facilitated P transport through adsorption and column experiments under different P concentrations and three pH conditions. Increased P loading on ferrihydrite colloids decreased the transport of ferrihydrite colloids (< 8.0%) under acid conditions through pore straining and irreversible attachment. Under neutral and alkaline conditions, ferrihydrite colloids exhibited more negative surfaces and smaller diameters with increasing P, which further enhanced ferrihydrite colloid transport (maximum to 95.6%). Ferrihydrite colloid-facilitated P transport was limited under acid conditions, and it was 10% - 57% enhancement under neutral and alkaline conditions with increasing P adsorption. Under neutral conditions, ferrihydrite colloid-facilitated P transport was strongest (maximum to 68.84%) because of its stronger ferrihydrite colloid transport than under acid conditions and larger P adsorption capacity than under alkaline conditions. Our findings indicate that the facilitated transport of ferrihydrite colloids in the presence of P may be appreciable in iron and phosphate-rich soil and subsurface systems, which is essential for evaluating the fate of iron and iron-facilitated P and potential environmental risks of P transport in the subsurface.

Nanobubble transport in porous media: Towards agro- and environmental applications

Nanobubbles have been increasingly used in various applications involving porous media, such as groundwater remediation and irrigation. However, the fundamental scientific knowledge regarding the interactions between nanobubbles and the media is still limited. The interactions can be repulsive, attractive, or inert, and can involve reversible or irreversible attachment as well as destructive mechanisms. Specifically, the stability and mobility of nanobubbles in porous media is expected to be dependent on the dynamic conditions and the physicochemical properties of the porous media, solutions, and nanobubbles themselves. In this study, we investigated how changes in solution chemistry (pH, ionic strength, and valence) and media characteristics (size and wettability) affect the size and concentration of nanobubbles under dynamic conditions using column experiments. Quartz crystal microbalance with dissipation monitoring provided a deeper understanding of irreversible and elastic nanobubbles’ interactions with silica-coated surfaces. Our findings suggest that nanobubbles are less mobile in solutions of higher ionic strength and valence, acidic pH and smaller porous media sizes, while the wettability of porous media has a negligible influence on the retention of nanobubbles. Overall, our findings provide insights into the underlying mechanisms of nanobubble interactions and suggest potential strategies to optimize their delivery in various applications.

Wet steam method for reducing attached cells of Salmonella and Listeria monocytogenes on Hass avocado

The consumption of avocados and their products has been linked to outbreaks of illness caused by Salmonella enterica and Listeria monocytogenes. These pathogens have been isolated from avocados collected from farms and markets. After contact with the avocado epicarp, the cells of Salmonella and L. monocytogenes can become loosely attached (LA) by suspension in a film of water and attraction by electrostatic forces, or strongly attached (SA) by physical and irreversible attachment mechanisms. Attached cells may have greater resistance to agents used to decontaminate the fruit. The effect of applying wet steam (WS) to the epicarp of Hass avocados on the reduction LA and SA counts of Salmonella and L. monocytogenes was evaluated as a function of the exposure time. The inoculated avocados were washed and exposed to WS for 30, 45, and 60 s inside a treatment chamber. Salmonella was found to be more susceptible to WS than L. monocytogenes. The efficacy of steam in reducing LA and SA cell numbers was similar for both pathogens. Steaming avocados for 60 s reduced LA Salmonella and L. monocytogenes cells by 4.6 and 4.8 log CFU/avocado, whereas SA cells were decreased by 5.2 and 4.4 log CFU/avocado, respectively.•Steaming the avocados for 60 s produced the greatest reduction in loosely and strongly attached cells for both pathogens.•Wet steam treatment efficiently eliminated the loosely and strongly attached cells of both pathogens.•The Listeria monocytogenes attached cells showed greater resistance to steam treatment than Salmonella.

Mechanistic insights into manganese oxide impacting the oxidation and transport of Cr(III) immobilized by nano-zero valent charged ion particles in water-saturated porous media

The presence of manganese oxide (MnO2) could influence the stability of green-synthesized nano-zero valent iron (nZVI@GT) associated with trivalent chromium (Cr(III)) after its excess application in the in situ remediation of hexachromium (Cr(VI)) contaminated soil. The research findings revealed that the co-transport of the remaining nZVI@GT with Cr(III) was substantially inhibited by high δ-MnO2 concentrations due to the formation of hetero-aggregates between nZVI@GT and δ-MnO2, resulting in an increased irreversible attachment parameter at second-site in a two-site kinetic attachment model. Simultaneously, the Cr(III) complex immobilized on nZVI@GT could be oxidized leading to high levels of Cr(VI) leaching at high δ-MnO2 concentrations. During this process, Mn(IV) was converted to Mn(III)/Mn(II). Subsequently, leachate containing a partial amount of Cr(VI) preferentially adsorbed onto the nZVI@GT surface, enhancing the dispersion of the nZVI@GT and δ-MnO2 agglomerates. Thereafter, nZVI@GT transportability was enhanced with a decreased second-site attachment parameter and the flow content of dissolved Cr(VI) was increased to double, also increasing the potential risk of Cr(VI) being carried by nZVI@GT to underground water systems. This study provides theoretical support for preserving the long-term stability of nZVI@GT after the in situ remediation of heavy metal-contaminated sites in the presence of δ-MnO2.

Recent advancement on water filtration membranes: Navigating biofouling challenges

This study investigates the field of antifouling membranes for water filtration and desalination applications, specifically focusing on two-dimensional materials. The study examines the importance of these membranes in the context of climate change and its effects on coastal ecosystems. The occurrence of biofouling in seawater desalination membranes is closely connected to intricate processes influenced by factors such as water quality, microbial communities, hydrodynamics, and membrane properties. Microorganism adhesion initiates the process, which then advances into irreversible attachment and the creation of biofilm. Detached pieces contribute to the perpetuation of fouling. Biofouling is caused by a variety of biomaterials and organics, including bacteria, extracellular polymeric substances (EPS), proteins, and humic compounds. Innovative methods such as surface alterations using two-dimensional materials like graphene and graphene oxide, as well as the use of biofouling-resistant materials, provide promising possibilities. These materials have antifouling characteristics, making them environmentally beneficial options that reduce the need for chemical cleaning. Their application improves the water treatment process by preventing fouling and enhancing membrane performance. Real-world research applications can enhance and optimize these tactics to effectively reduce biofouling in seawater desalination systems, hence improving efficiency and sustainability. This is particularly important in light of climate change and its impact on coastal ecosystems. The findings obtained from the literature review emphasise the utmost significance of tackling biofouling in the face of a changing environment, particularly with regard to microorganisms. Important factors to consider are the selection of coating materials, the implementation of environmentally friendly cleaning solutions made from natural chemicals, and the improvement of pretreatment systems. Green cleaning agents are important eco-friendly alternatives to typical biocides, as they possess antibacterial, antifungal, and antifouling capabilities. Given the existence of climate change, these observations serve as a basis for promoting environmentally friendly methods in water treatment technology.

Spectroscopic and Microscopic Characterization of Microbial Biofouling on Aircraft Fuel Tanks.

Avoiding microbial contamination and biofilm formation on the surfaces of aircraft fuel tanks is a major challenge in the aviation industry. The inevitable presence of water in fuel systems and nutrients provided by the fuel makes an ideal environment for bacteria, fungi, and yeast to grow. Understanding how microbes grow on different fuel tank materials is the first step to control biofilm formation in aviation fuel systems. In this study, biofilms of Pseudomonas putida, a model Gram-negative bacterium previously found in aircraft fuel tanks, were characterized on aluminum 7075-T6 surfaces, which is an alloy used by the aviation industry due to favorable properties including high strength and fatigue resistance. Scanning electron microscopy (SEM) coupled with energy-dispersive X-ray (EDX) showed that extracellular polymeric substances (EPS) produced by P. putida were important components of biofilms with a likely role in biofilm stability and adhesion to the surfaces. EDX analysis showed that the proportion of phosphorus with respect to nitrogen is higher in the EPS than in the bacterial cells. Additionally, different morphologies in biofilm formation were observed in the fuel phase compared to the water phase. Micro-Fourier transform infrared spectroscopy (micro-FTIR) analysis suggested that phosphoryl and carboxyl functional groups are fundamental for the irreversible attachment between the EPS of bacteria and the aluminum surface, by the formation of hydrogen bonds and inner-sphere complexes between the macromolecules and the aluminum surface. Based on the hypothesis that nucleic acids (particularly DNA) are an important component of EPS in P. putida biofilms, the impact of degrading extracellular DNA was tested. Treatment with the enzyme DNase I affected both water and fuel phase biofilms─with the cell structure disrupted in the aqueous phase, but cells remained attached to the aluminum coupons.

In Situ Measurements of Dynamic Bacteria Transport and Attachment in Heterogeneous Sand-Packed Columns.

Prevention, mitigation, and regulation of bacterial contaminants in groundwater require a fundamental understanding of the mechanisms of transport and attachment in complex geological materials. Discrepancies in bacterial transport behaviors observed between field studies and laboratory experiments indicate an incomplete understanding of dynamic bacterial transport and immobilization processes in realistic heterogeneous geologic systems. Here, we develop a new experimental approach for in situ quantification of dynamic bacterial transport and attachment distribution in geologic media that relies on radiolabelingEscherichia coliwith positron-emitting radioisotopes and quantifying transport with three-dimensional (3D) positron emission tomography (PET) imaging. Our results indicate that the highest bacterial attachment occurred at the interfaces between sand layers oriented orthogonal to the direction of flow. The predicted bacterial attachment from a 3D numerical model matched the experimental PET results, highlighting that the experimentally observed bacterial transport behavior can be accurately captured with a distribution of a first-order irreversible attachment model. This is the first demonstration of the direct measurement of attachment coefficient distributions from bacterial transport experiments in geologic media and provides a transformational approach to better understand bacterial transport mechanisms, improve model parametrization, and accurately predict how local geologic conditions can influence bacterial fate and transport in groundwater.

Factors Influencing Pseudomonas aeruginosa Initial Adhesion and Evolution at the Dodecane-Water Interface.

Bacterial adhesion and evolution at the oil-water interface are important for a broad range of applications such as food manufacturing and microbial-enhanced oil recovery, etc. However, our understanding on bacterial interfacial adhesion and evolution, particularly at the single-cell level, is still far from complete. In this work, by employing Pseudomonas aeruginosa PAO1 at the dodecane-water interface as a model system, we have studied the effects of different factors on bacterial interfacial adhesion and the dynamic evolution of bacterial interfacial behavior at the single-cell level. The results show that PAO1 cells displayed a chemotactic behavior toward dodecane. Among the tested factors, bacterial initial interfacial attachment showed a negative correlation with the secreted cell-surface associated lipopolysaccharide and Psl while a positive correlation with type IV pili. Adding nonbiological surfactant Pluronic F-127, as expected, greatly reduced the cell interfacial adhesion. More importantly, the dynamics analysis of cell attachment/detachment at the dodecane-water interface over a long-time scale revealed a reversible to irreversible attachment transition of cells. This transition is accompanied with the interface aging resulting from bacterial activities, which led to an increase of the interfacial viscoelasticity with time and finally the formation of the gel-like interface. Further analysis demonstrated the important role of exopolysaccharides in the latter process. Our findings provide more details of bacterial oil-water interfacial behavior at the single-cell level and may shed light on developing new strategies for controlling bacterial colonization at the oil-water interface.

Evidence for the Type IV Pilus Retraction Motor PilT as a Component of the Surface Sensing System in Pseudomonas aeruginosa.

Biofilm formation begins when bacteria contacting a surface induce cellular changes to become better adapted for surface growth. One of the first changes to occur for Pseudomonas aeruginosa after surface contact is an increase in the nucleotide second messenger 3',5'-cyclic AMP (cAMP). It has been demonstrated that this increase in intracellular cAMP is dependent on functional type IV pili (T4P) relaying a signal to the Pil-Chp system, but the mechanism by which this signal is transduced remains poorly understood. Here, we investigate the role of the type IV pilus retraction motor PilT in sensing a surface and relaying that signal to cAMP production. We show that mutations in PilT, and in particular those impacting the ATPase activity of this motor protein, reduce surface-dependent cAMP production. We identify a novel interaction between PilT and PilJ, a member of the Pil-Chp system, and propose a new model whereby P. aeruginosa uses its PilT retraction motor to sense a surface and to relay that signal via PilJ to increased production of cAMP. We discuss these findings in light of current T4P-dependent surface sensing models for P. aeruginosa. IMPORTANCE T4P are cellular appendages that allow P. aeruginosa to sense a surface, leading to the production of cAMP. This second messenger not only activates virulence pathways but leads to further surface adaptation and irreversible attachment of cells. Here, we demonstrate the importance of the retraction motor PilT in surface sensing. We also present a new surface sensing model in P. aeruginosa whereby the T4P retraction motor PilT senses and transmits the surface signal, likely via its ATPase domain and interaction with PilJ, to mediate production of the second messenger cAMP.

Anti-Bacterial Adhesion on Abiotic and Biotic Surfaces of the Exopolysaccharide from the Marine Bacillus licheniformis B3-15

The eradication of bacterial biofilm represents a crucial strategy to prevent a clinical problem associated with microbial persistent infection. In this study we evaluated the ability of the exopolysaccharide (EPS) B3-15, produced by the marine Bacillus licheniformis B3-15, to prevent the adhesion and biofilm formation of Pseudomonas aeruginosa ATCC 27853 and Staphylococcus aureus ATCC 29213 on polystyrene and polyvinyl chloride surfaces. The EPS was added at different times (0, 2, 4 and 8 h), corresponding to the initial, reversible and irreversible attachment, and after the biofilm development (24 or 48 h). The EPS (300 µg/mL) impaired the initial phase, preventing bacterial adhesion even when added after 2 h of incubation, but had no effects on mature biofilms. Without exerting any antibiotic activity, the antibiofilm mechanisms of the EPS were related to the modification of the (i) abiotic surface properties, (ii) cell-surface charges and hydrophobicity, and iii) cell-to-cell aggregation. The addition of EPS downregulated the expression of genes (lecA and pslA of P. aeruginosa and clfA of S. aureus) involved in the bacterial adhesion. Moreover, the EPS reduced the adhesion of P. aeruginosa (five logs-scale) and S. aureus (one log) on human nasal epithelial cells. The EPS could represent a promising tool for the prevention of biofilm-related infections.

A Bis(imidazole)-based cysteine labeling tool for metalloprotein assembly

Precise metal-protein coordination by design remains a considerable challenge. Polydentate, high-metal-affinity protein modifications, both chemical and recombinant, can enable metal localization. However, these constructs are often bulky, conformationally and stereochemically ill-defined, or coordinately saturated. Here, we expand the biomolecular metal-coordination toolbox with the irreversible attachment to cysteine of bis(1-methylimidazol-2-yl)ethene (“BMIE”), which generates a compact imidazole-based metal-coordinating ligand. Conjugate additions of small-molecule thiols (thiocresol and N-Boc-Cys) with BMIE confirm general thiol reactivity. The BMIE adducts are shown to complex the divalent metal ions Cu++ and Zn++ in bidentate (N2) and tridentate (N2S*) coordination geometries. Cysteine-targeted BMIE modification (>90% yield at pH 8.0) of a model protein, the S203C variant of carboxypeptidase G2 (CPG2), measured with ESI-MS, confirms its utility as a site-selective bioconjugation method. ICP-MS analysis confirms mono-metallation of the BMIE-modified CPG2 protein with Zn++, Cu++, and Co++. EPR characterization of the BMIE-modified CPG2 protein reveals the structural details of the site selective 1:1 BMIE-Cu++ coordination and symmetric tetragonal geometry under physiological conditions and in the presence of various competing and exchangeable ligands (H2O/HO−, tris, and phenanthroline). An X-ray protein crystal structure of BMIE-modified CPG2-S203C demonstrates that the BMIE modification is minimally disruptive to the overall protein structure, including the carboxypeptidase active sites, although Zn++ metalation could not be conclusively discerned at the resolution obtained. The carboxypeptidase catalytic activity of BMIE-modified CPG2-S203C was also assayed and found to be minimally affected. These features, combined with ease of attachment, define the new BMIE-based ligation as a versatile metalloprotein design tool, and enable future catalytic and structural applications.

Review on the Role of Biofilm Formation in Bacterial Pathogenesis

Biofilms are defined as a accumulation of microorganisms living in a self-assembled matrix of polymeric substances that adheres to a variety of surfaces. Depending on the interaction between the surface and constituent cells, biofilms can be monolayer or multilayer. Initial attachment, irreversible attachment, micro colony growth, biofilm maturation, and biofilm dispersal are the five steps of the biofilm formation process. The processes that contribute tobiofilm formation are a dynamic and complicated process. Biofilm Formation Causes many bacteria have the ability to transition between planktonic and biofilm forms. The biofilm state appears to be a natural and prevalent condition of bacteria. Biofilm-forming bacteria are important for animal health. The risk of infection in animal species is likely to be higher than in humans. Because of the differences in animal housing and living conditions. Microorganisms capable of generating biofilms include P. aeruginosa, S. epidermidis, E. colispp, S. aureus, E. cloacae, and K. pneumonia. Bacterial pathogenesis of biofilms occurs frequently on medical devices and bits of dead tissue, such as sequestra of dead bone; nevertheless, they canals of or nonliving tissues. Biofilms in bacterial infections can improve the pathogenicity of the organism while also protecting it from external treatment. UV radiation, pH stress, chemical exposure, phagocytosis, dehydration, and antibiotics are all threats to cells that biofilms protect them. The Role of Signaling in Biofilm Formation is the bond between environmental stimuli and the bacteria’ reciprocation of the relevant signaling is required for the formation of a biofilm. Two-component systems and Quorum sensing can both be induced by these sensing systems. Tissue culture plate, cong red agar, and bioluminescent assay are some of the laboratory tests used to diagnose biofilm. The emergence and spread of antibiotic resistance among bacteria is one of the world’s most serious health issues. One of the implications of the bacterial biofilm communities that lead to persistent illnesses is antibiotic resistance.

Exchangeable HaloTag Ligands for Super-Resolution Fluorescence Microscopy.

The specific and covalent labeling of the protein HaloTag with fluorescent probes in living cells makes it a powerful tool for bioimaging. However, the irreversible attachment of the probe to HaloTag precludes imaging applications that require transient binding of the probe and comes with the risk of irreversible photobleaching. Here, we introduce exchangeable ligands for fluorescence labeling of HaloTag (xHTLs) that reversibly bind to HaloTag and that can be coupled to rhodamines of different colors. In stimulated emission depletion (STED) microscopy, probe exchange of xHTLs allows imaging with reduced photobleaching as compared to covalent HaloTag labeling. Transient binding of fluorogenic xHTLs to HaloTag fusion proteins enables points accumulation for imaging in nanoscale topography (PAINT) and MINFLUX microscopy. We furthermore introduce pairs of xHTLs and HaloTag mutants for dual-color PAINT and STED microscopy. xHTLs thus open up new possibilities in imaging across microscopy platforms for a widely used labeling approach.

Development of a classification model and an immune-related network based on ferroptosis in periodontitis.

Periodontitis is an immunoinflammatory disease characterized by irreversible periodontal attachment loss and bone destruction. Ferroptosis is a kind of immunogenic cell death that depends on the participation of iron ions and is involved in various inflammatory and immune processes. However, information regarding the relationship between ferroptosis and immunomodulation processes in periodontitis is extremely limited. The purpose of this study was to investigate the correlation between ferroptosis and immune responses in periodontitis. Gene expression profiles of gingivae were collected from the Gene Expression Omnibus data portal. After detecting differentially expressed ferroptosis-related genes (FRGs), we used univariate logistic regression analysis followed by logistic least absolute shrinkage and selection operator (LASSO) regression to establish a ferroptosis-related classification model in an attempt to accurately distinguish periodontitis gingival tissues from healthy samples. The infiltration level of immunocytes in periodontitis was then assessed through single-sample gene-set enrichment analysis. Subsequently, we screened out immune-related genes by weighted correlation network analysis and protein-protein interaction (PPI) analysis and constructed an immune-related network based on FRGs and immune-related genes. A total of 24 differentially expressed FRGs were detected, and an 8-FRG combined signature constituted the classification model. The established model showed outstanding discriminating ability according to the results of receiver operating characteristic (ROC) curve analysis. In addition, the periodontitis samples had a higher degree of immunocyte infiltration. Activated B cells had the strongest positive correlation while macrophages had a strong negative correlation with certain FRGs, and we found that XBP1, ALOX5 and their interacting genes might be crucial genes in the immune-related network. The FRG-based classification model had a satisfactory determination ability, which could bring new insights into the pathogenesis of periodontitis. Those genes in the immune-related network, especially hub genes along with XBP1 and ALOX5, would have the potential to serve as promising targets of immunomodulatory treatments for periodontitis.

Strategies for controlling biofilm formation in food industry

Foodborne pathogen poses a threat to the food industries as many outbreaks have been found to be associated with biofilm formation. The formation of biofilm is a self-protection growth pattern of bacteria, which increases post-processing contamination and risk to public health. It is difficult to eliminate the biofilm in the food industries, since the biofilm cells have a barrier preventing or lessening the contact with environmental stresses, antimicrobial agents and the host immune system. Bacterial biofilm formation is a complex process, including initial attachment stage, irreversible attachment stage, biofilm development stage, biofilm maturation stage, and biofilm dispersion stage. The genetic mechanism, substratum and bacterial cell surface properties involve in the biofilm formation. The biofilm inhibition methods studied are physical treatment, chemical and biochemical treatment. The potential green and safe biochemical method attracts more attention, especially, the novel strategies using the safe biochemical agents (essential oils, enzymes, biosurfactants, others) constantly emerged. The review emphasized on effective strategies for inhibiting biofilm formation in different stages (initial irreversible attachment, formation, and maturation) by use of biochemical agents, aiming to provide new insight into biofilm control in food industry thus improving food quality and safety.

Molecular regulation of conditioning film formation and quorum quenching in sulfate reducing bacteria.

Sensing surface topography, an upsurge of signaling biomolecules, and upholding cellular homeostasis are the rate-limiting spatio-temporal events in microbial attachment and biofilm formation. Initially, a set of highly specialized proteins, viz. conditioning protein, directs the irreversible attachment of the microbes. Later signaling molecules, viz. autoinducer, take over the cellular communication phenomenon, resulting in a mature microbial biofilm. The mandatory release of conditioning proteins and autoinducers corroborated the existence of two independent mechanisms operating sequentially for biofilm development. However, both these mechanisms are significantly affected by the availability of the cofactor, e.g., Copper (Cu). Generally, the Cu concentration beyond threshold levels is detrimental to the anaerobes except for a few species of sulfate-reducing bacteria (SRB). Remarkably SRB has developed intricate ways to resist and thrive in the presence of Cu by activating numerous genes responsible for modifying the presence of more toxic Cu(I) to Cu(II) within the periplasm, followed by their export through the outer membrane. Therefore, the determinants of Cu toxicity, sequestration, and transportation are reconnoitered for their contribution towards microbial adaptations and biofilm formation. The mechanistic details revealing Cu as a quorum quencher (QQ) are provided in addition to the three pathways involved in the dissolution of cellular communications. This review articulates the Machine Learning based data curing and data processing for designing novel anti-biofilm peptides and for an in-depth understanding of QQ mechanisms. A pioneering data set has been mined and presented on the functional properties of the QQ homolog in Oleidesulfovibrio alaskensis G20 and residues regulating the multicopper oxidase properties in SRB.

(Invited) The Evolution of Inorganic Nanocrystals for Bioimaging

The first applications of luminescent nanocrystals to bioimaging were semiconductor quantum dots with optoelectronic properties that largely mirror those of organics and proteins, but with substantially increased stability and brightness that have enabled single molecule and other challenging imaging applications. Building on this success, newer nanocrystals have been engineered with optical properties unlike anything found in traditional probes, including perfect photostability,1,2 anti-Stokes emission a billion-fold more efficient than 2-photon excitation,3 and most recently, photon avalanches hosted within nanostructures.4 Avalanches are steeply nonlinear events in which outsized responses arise from a series of minute inputs. With light, photon avalanching (PA) had been observed only in bulk materials and aggregates, often at cryogenic temperatures, preventing its application to bioimaging. We recently reported the realization of PA at room temperature in sub-30 nm Tm3+-doped NaYF4 upconverting nanoparticles (UCNPs) and demonstrated their use in high-resolution imaging at wavelengths that fall within NIR spectral windows of maximal biological transparency. Avalanching nanoparticles (ANPs) can be pumped by either continuous-wave or pulsed lasers and exhibit all of the defining features of PA: clear excitation power thresholds, exceptionally long rise time at threshold, and a dominant excited-state absorption that is >10,000 times larger than ground-state absorption. Beyond the avalanching threshold, ANP emission scales with up to the 31st power of pump intensity, an extreme nonlinearity caused by the induced positive optical feedback within each nanocrystal. This enables sub-70 nm spatial resolution using only simple scanning confocal microscopy and before any computational data analysis. NaYF4 ANPs with 8-20% Tm3+content can be excited at either 1064 or 1450 nm, with avalanching emission at 800 nm. Pairing the steep nonlinearity of ANPs with existing superresolution techniques and computational methods allows for imaging with higher resolution and at ca. 100-fold lower excitation intensities than is possible with other probes. For application of ANPs to live-cell imaging, we have developed synthetic chemistry-free methods for conjugating engineered antibodies to NP-surface SpyCatcher proteins,5 which bind and spontaneously form covalent isopeptide bonds with cognate SpyTag peptides. This enables controlled and irreversible attachment of antibodies to nanoparticle surfaces, for specific targeting of cell-surface receptors in quantitative live-cell study of their distribution, trafficking, and physiology. Wu, S. et al. Non-blinking and photostable upconverted luminescence from single lanthanide-doped nanocrystals. Proc. Natl. Acad. Sci. 106, 10917–10921 (2009).Fernandez-Bravo, A. et al. Continuous-wave upconverting nanoparticle microlasers. Nat. Nanotechnol. 13, 572–577 (2018).Tian, B. et al. Low irradiance multiphoton imaging with alloyed lanthanide nanocrystals. Nat. Commun. 9, 3082 (2018).Lee, C. et al. Giant nonlinear optical responses from photon-avalanching nanoparticles. Nature 589, 230–235 (2021).Pedroso, C. C. S. et al. Immunotargeting of nanocrystals by SpyCatcher conjugation of engineered antibodies. ACS Nano 15, 18374–18384 (2021). Figure 1