The effect of organic solvents on selected microorganisms and model liposome membrane

Efficacy assessment of different cryoprotectants for preserving the viability of Enterobacterales strains at - 20 °C

The preservation of microorganisms is pivotal in microbiological practice. Currently, cryopreservation is assumed to be an effective and inexpensive approach for the storage of microorganisms, including bacteria. The key point of cryopreservation is optimal cryoprotectant selection. In the present study, different cryoprotectant compositions were tested for long-term storage of 15 Enterobacterales bacterial strains at - 20 °C. The survival rates of the bacterial strains were evaluated in four different cryoprotectant solutions containing 70% glycerin only (cryoprotectants 1 and 4), 10% dimethyl sulfoxide (DMSO) with 70% glycerin (cryoprotectant 2), and 10% DMSO (cryoprotectant 3). In addition, cryoprotectants 1 and 2 contained peptone and yeast extract as nutritional supplements. The general survival rates of the bacterial strains were evaluated after 12 months of storage. After 12 months, the survival rates of the different cryoprotectants were as follows: cryoprotectant 1-88.87%; cryoprotectant 2-84.85%; cryoprotectant 3-83.50%; and cryoprotectant 4-44.81%. Thus, the composition of cryoprotectant 1 (70% glycerin with nutrient supplements) was optimal for preserving 15 tested strains of the order Enterobacterales. Despite these findings, the biochemical properties of the tested strains changed after cryopreservation for 12 months in the presence of 1 or 3 cryoprotectants. Alterations in the biochemical profile could be related to changes in environmental conditions and cold adaptation. We assume that the composition of cryoprotectant 1 can be optimal for storing the order Enterobacterales at - 20 °C. However, further investigations are needed to elucidate the problem of cryopreservation and to support our assumption.

Toward the apoplast metabolome: Establishing a leaf apoplast collection approach suitable for metabolomics analysis

The leaf apoplast contains several compounds that play important roles in the regulation of different physiological processes in plants. However, this compartment has been neglected in several experimental and modelling studies, which is mostly associated to the difficulty to collect apoplast washing fluid (AWF) in sufficient amount for metabolomics analysis and as free as possible from symplastic contamination. Here, we established an approach based in an infiltration-centrifugation technique that use little leaf material but allows sufficient AWF collection for gas chromatography mass spectrometry (GC-MS)-based metabolomics analysis in both tobacco and Arabidopsis. Up to 54 metabolites were annotated in leaf and apoplast samples from both species using either 20% (v/v) methanol (20% MeOH) or distilled deionized water (ddH2O) as infiltration fluids. The use of 20% MeOH increased the yield of the AWF collected but also the level of symplastic contamination, especially in Arabidopsis. We propose a correction factor and recommend the use of multiple markers such as MDH activity, protein content and conductivity measurements to verify the level of symplastic contamination in MeOH-based protocols. Neither the concentration of sugars nor the level of primary metabolites differed between apoplast samples extracted with ddH2O or 20% MeOH. This indicates that ddH2O can be preferentially used, given that it is a non-toxic and highly accessible infiltration fluid. The infiltration-centrifugation-based approach established here uses little leaf material and ddH2O as infiltration fluid, being suitable for GC-MS-based metabolomics analysis in tobacco and Arabidopsis, with great possibility to be extended for other plant species and tissues.

Biocatalytic approach for the synthesis of chiral alcohols for the development of pharmaceutical intermediates and other industrial applications: A review

Biocatalysis has emerged as a strong tool for the synthesis of active pharmaceutical ingredients (APIs). In the early twentieth century, whole cell biocatalysis was used to develop the first industrial biocatalytic processes, and the precise work of enzymes was unknown. Biocatalysis has evolved over the years into an essential tool for modern, cost-effective, and sustainable pharmaceutical manufacturing. Meanwhile, advances in directed evolution enable the rapid production of process-stable enzymes with broad substrate scope and high selectivity. Large-scale synthetic pathways incorporating biocatalytic critical steps towards >130 APIs of authorized pharmaceuticals and drug prospects are compared in terms of steps, reaction conditions, and scale with the corresponding chemical procedures. This review is designed on the functional group developed during the reaction forming alcohol functional groups. Some important biocatalyst sources, techniques, and challenges are described. A few APIs and their utilization in pharmaceutical drugs are explained here in this review. Biocatalysis has provided shorter, more efficient, and more sustainable alternative pathways toward existing small molecule APIs. Furthermore, non-pharmaceutical applications of biocatalysts are also mentioned and discussed. Finally, this review includes the future outlook and challenges of biocatalysis. In conclusion, Further research and development of promising enzymes are required before they can be used in industry.

Modulation of bacterial membranes and cellular macromolecules by dimethyl sulfoxide: A dose-dependent study providing novel insights

Using Escherichia coli as a model, this manuscript delves into the intricate interactions between dimethyl sulfoxide (DMSO) and membranes, cellular macromolecules, and the effects on various aspects of bacterial physiology. Given DMSO's wide-ranging use as a solvent in microbiology, we investigate the impacts of both non-growth inhibitory (1.0 % and 2.5 % v/v) and slightly growth-inhibitory (5.0 % v/v) concentrations of DMSO. The results demonstrate that DMSO causes alterations in bacterial membrane potential, influences the electrochemical characteristics of the cell surface, and exerts substantial effects on the composition and structure of cellular biomolecules. Genome-wide gene expression data from DMSO-treated E. coli was used to further investigate and bolster the results. The findings of this study provide valuable insights into the complex relationship between DMSO and biological systems, with potential implications in drug delivery and cellular manipulation. However, it is essential to exercise caution when utilizing DMSO to enhance the solubility and delivery of bioactive compounds, as even at low concentrations, DMSO exerts non-inert effects on cellular macromolecules and processes.

Scalable manufacture of therapeutic mesenchymal stromal cell products on customizable microcarriers in vertical wheel bioreactors that improve direct visualization, product harvest, and cost

BACKGROUND AIMS

Human mesenchymal stromal cells (hMSCs) and their secreted products show great promise for treatment of musculoskeletal injury and inflammatory or immune diseases. However, the path to clinical utilization is hampered by donor-tissue variation and the inability to manufacture clinically relevant yields of cells or their products in a cost-effective manner. Previously we described a method to produce chemically and mechanically customizable gelatin methacryloyl (GelMA) microcarriers for culture of hMSCs. Herein, we demonstrate scalable GelMA microcarrier-mediated expansion of induced pluripotent stem cell (iPSC)-derived hMSCs (ihMSCs) in 500 mL and 3L vertical wheel bioreactors, offering several advantages over conventional microcarrier and monolayer-based expansion strategies.

METHODS

Human mesenchymal stromal cells derived from induced pluripotent cells were cultured on custom-made spherical gelatin methacryloyl microcarriers in single-use vertical wheel bioreactors (PBS Biotech). Cell-laden microcarriers were visualized using confocal microscopy and elastic light scattering methodologies. Cells were assayed for viability and differentiation potential in vitro by standard methods. Osteogenic cell matrix derived from cells was tested in vitro for osteogenic healing using a rodent calvarial defect assay. Immune modulation was assayed with an in vivo peritonitis model using Zymozan A.

RESULTS

The optical properties of GelMA microcarriers permit noninvasive visualization of cells with elastic light scattering modalities, and harvest of product is streamlined by microcarrier digestion. At volumes above 500 mL, the process is significantly more cost-effective than monolayer culture. Osteogenic cell matrix derived from ihMSCs expanded on GelMA microcarriers exhibited enhanced in vivo bone regenerative capacity when compared to bone morphogenic protein 2, and the ihMSCs exhibited superior immunosuppressive properties in vivo when compared to monolayer-generated ihMSCs.

CONCLUSIONS

These results indicate that the cell expansion strategy described here represents a superior approach for efficient generation, monitoring and harvest of therapeutic MSCs and their products.

A guide to the use of bioassays in exploration of natural resources

Bioassays are the main tool to decipher bioactivities from natural resources thus their selection and quality are critical for optimal bioprospecting. They are used both in the early stages of compounds isolation/purification/identification, and in later stages to evaluate their safety and efficacy. In this review, we provide a comprehensive overview of the most common bioassays used in the discovery and development of new bioactive compounds with a focus on marine bioresources. We present a comprehensive list of practical considerations for selecting appropriate bioassays and discuss in detail the bioassays typically used to explore antimicrobial, antibiofilm, cytotoxic, antiviral, antioxidant, and anti-ageing potential. The concept of quality control and bioassay validation are introduced, followed by safety considerations, which are critical to advancing bioactive compounds to a higher stage of development. We conclude by providing an application-oriented view focused on the development of pharmaceuticals, food supplements, and cosmetics, the industrial pipelines where currently known marine natural products hold most potential. We highlight the importance of gaining reliable bioassay results, as these serve as a starting point for application-based development and further testing, as well as for consideration by regulatory authorities.

Oxidative stress changes interactions between 2 bacterial species from competitive to facilitative

Knowing how species interact within microbial communities is crucial to predicting and controlling community dynamics, but interactions can depend on environmental conditions. The stress-gradient hypothesis (SGH) predicts that species are more likely to facilitate each other in harsher environments. Even if the SGH gives some intuition, quantitative modeling of the context-dependency of interactions requires understanding the mechanisms behind the SGH. In this study, we show with both experiments and a theoretical analysis that varying the concentration of a single compound, linoleic acid (LA), modifies the interaction between 2 bacterial species, Agrobacterium tumefaciens and Comamonas testosteroni, from competitive at a low concentration, to facilitative at higher concentrations where LA becomes toxic for one of the 2 species. We demonstrate that the mechanism behind facilitation is that one species is able to reduce reactive oxygen species (ROS) that are produced spontaneously at higher concentrations of LA, allowing for short-term rescue of the species that is sensitive to ROS and longer coexistence in serial transfers. In our system, competition and facilitation between species can occur simultaneously, and changing the concentration of a single compound can alter the balance between the two.

Effect of various concentrations of common organic solvents on the growth and proliferation ability of Candida glabrata and their permissible limits for addition in drug susceptibility testing

Objectives

Dimethyl sulfoxide (DMSO), acetone, ethanol, and methanol are organic solvents commonly used for dissolving drugs in antimicrobial susceptibility testing. However, these solvents have certain antimicrobial activity. Currently, standardized criteria for the selection and dosage of drug solvents in drug susceptibility testing research are lacking. The study aims to provide experimental evidence for the selection and addition limit of drug solvents for the in vitro antifungal susceptibility test of Candida glabrata (C. glabrata).

Methods

According to the recommendation of the Clinical and Laboratory Standards Institute (CLSI) M27-A3, a 0.5 McFarland C. glabrata suspension was prepared and then diluted 1:1,000. Next, a gradient dilution method was used to prepare 20%, 10%, 5%, and 2.5% DMSO/acetone/ethanol/methanol. The mixture was plated onto a 96-well plate and incubated at a constant temperature of 35 °C for 48 h. The inhibitory effects of DMSO, acetone, ethanol, and methanol on C. glabrata growth and proliferation were analyzed by measuring optical density values at 600 nm (OD600 values).

Results

After 48 h incubation, the OD600 values of C. glabrata decreased to different extents in the presence of the four common organic solvents. The decrease in the OD600 values was greater with increasing concentrations within the experimental concentration range. When DMSO and acetone concentrations were higher than 2.5% (containing 2.5%) and methanol and ethanol concentrations were higher than 5.0% (containing 5.0%), the differences were statistically significant compared with the growth control wells without any organic solvent (P < 0.05).

Conclusion

All four organic solvents could inhibit C. glabrata growth and proliferation. When used as solvents for drug sensitivity testing in C. glabrata, the concentrations of DMSO, acetone, ethanol, and methanol should be below 2.5%, 2.5%, 5%, and 5%, respectively.

Fermentation of biodiesel-derived crude glycerol to 1,3-propanediol with bio-wastes as support matrices: Polynomial prediction model

Biodiesel production from used cooking oil is sustainable alternative, for bio-energy production. The process generates residual crude glycerol (RCG) as the major energy-rich waste which can be used to produce various bio-based chemicals like 1,3-propanediol (1,3-PDO) through biotechnological interventions. This RCG contains several impurities like methanol, soap, organic materials, salts non-transesterified fatty acids and metals in varied concentrations. These impurities significantly affect yield and productivity of the bio-process due to their marked microbial toxicity. In this work, previously isolated Clostridium butyricum L4 was immobilized on various abundantly available cheap bio-wastes (like rice straw, activated carbon and corn cob) to explore advantages offered and improve tolerance to various feed impurities. Amongst these, shredded rice straw was found most suitable candidate for immobilization and results in maximum improvement in 1,3-PDO production (18.4%) with highest porosity (89.28%), lowest bulk density (194.48Kg/m3), and highest cellular biofilm density (CFU/g-8.4 ×1010) amongst the three matrices. For practical purposes, recyclability was evaluated and it was concluded that even after reusing for five successive cycles the production retained to ∼82.4%. Subsequently, polynomial model was developed using 30 runs central composite factorial design experiments having coefficient of regression (R²) as 0.9520, in order to predict yields under different immobilization conditions for 1,3-PDO production. Plackett-Burman was employed (Accuracy= 99.17%) to screen significant toxic impurities. Based on statistical analysis six impurities were found to be significantly influential on PDO production in adverse manner. With negative coefficient of estimate (COE) varying in decreasing order: Linoleic acid >Oleic acid >Stearic acid >NaCl>K2SO4 >KCl. The study illustrates practical application for repurposing waste glycerol generated from biodiesel plants, thus developing improved agnostic process along with yield production models.

Effects of Larrea nitida nanodispersions on the growth inhibition of phytopathogens

Larrea nitida Cav. (Zygophyllaceae) is a plant endemic to Argentina and Chile, and its extract has been studied over the last years due to the presence of antimicrobial agents that can be used to control the growth of some pathogens in agriculture. However, the extract is highly hydrophobic, which strongly affects its fungicidal activity in aqueous media. In this sense, the solid dispersion technique was used to produce L. nitida extract nanodispersions with polyethylene glycol (PLE) and with polyethylene glycol and zinc acetate (PZLE). In order to further evaluate the activity of the extract in PLE and PZLE, blank nanodispersions containing only polyethylene glycol (PEG) and zinc acetate (PZ) without the addition of the extract were also produced. The fungicidal activity of the water-soluble nanoparticles was evaluated at different concentrations (0.037-0.110 g.mL-1). In general, the nanoparticles were successfully produced on a nanometric size and presented a significant inhibitory activity on the growth of the pathogens Fusarium oxysporum and Fusarium verticillioides in aqueous media. Compared to PLE, PZLE presented increased fungistatic activity, possibly due to their increased solubility in water. Even though their application in agriculture should be further investigated, the nanodispersions present great potential to be applied as a green biotechnological tool.

Evaluating Biofilm Inhibitory Potential in Fish Pathogen, Aeromonas hydrophila by Agricultural Waste Extracts and Assessment of Aerolysin Inhibitors Using In Silico Approach

Aeromonas hydrophila, an opportunistic bacteria, causes several devastating diseases in humans and animals, particularly aquatic species. Antibiotics have been constrained by the rise of antibiotic resistance caused by drug overuse. Therefore, new strategies are required to prevent appropriate antibiotic inability from antibiotic-resistant strains. Aerolysin is essential for A. hydrophila pathogenesis and has been proposed as a potential target for inventing drugs with anti-virulence properties. It is a unique method of disease prevention in fish to block the quorum-sensing mechanism of A. hydrophila. In SEM analysis, the crude solvent extracts of both groundnut shells and black gram pods exhibited a reduction of aerolysin formation and biofilm matrix formation by blocking the QS in A. hydrophila. Morphological changes were identified in the extracts treated bacterial cells. Furthermore, in previous studies, 34 ligands were identified with potential antibacterial metabolites from agricultural wastes, groundnut shells, and black gram pods using a literature survey. Twelve potent metabolites showed interactions between aerolysin and metabolites during molecular docking analysis, in that H-Pyran-4-one-2,3 dihydro-3,5 dihydroxy-6-methyl (-5.3 kcal/mol) and 2-Hexyldecanoic acid (-5.2 kcal/mol) showed promising results with potential hydrogen bond interactions with aerolysin. These metabolites showed a better binding affinity with aerolysin for 100 ns in molecular simulation dynamics. These findings point to a novel strategy for developing drugs using metabolites from agricultural wastes that may be feasible pharmacological solutions for treating A. hydrophila infections for the betterment of aquaculture.

Solvent tolerant enzymes in extremophiles: Adaptations and applications

Non-aqueous enzymology has always drawn attention due to the wide range of unique possibilities in biocatalysis. In general, the enzymes do not or insignificantly catalyze substrate in the presence of solvents. This is due to the interfering interactions of the solvents between enzyme and water molecules at the interface. Therefore, information about solvent-stable enzymes is scarce. Yet, solvent-stable enzymes prove quite valuable in the present day biotechnology. The enzymatic hydrolysis of the substrates in solvents synthesizes commercially valuable products, such as peptides, esters, and other transesterification products. Extremophiles, the most valuable yet not extensively explored candidates, can be an excellent source to investigate this avenue. Due to inherent structural attributes, many extremozymes can catalyze and maintain stability in organic solvents. In the present review, we aim to consolidate information about the solvent-stable enzymes from various extremophilic microorganisms. Further, it would be interesting to learn about the mechanism adapted by these microorganisms to sustain solvent stress. Various approaches to protein engineering are used to enhance catalytic flexibility and stability and broaden biocatalysis's prospects under non-aqueous conditions. It also describes strategies to achieve optimal immobilization with minimum inhibition of the catalysis. The proposed review would significantly aid our understanding of non-aqueous enzymology.

Improving ethanol tolerance of ethyl carbamate hydrolase by diphasic high pressure molecular dynamic simulations

Ethyl carbamate (EC) is mainly found in fermented foods and fermented alcoholic beverages, which could cause carcinogenic potential to humans. Reducing EC is one of the key research priorities to address security of fermented foods. Enzymatic degradation of EC with EC hydrolase in food is the most reliable and efficient method. However, poor tolerance to ethanol severely hinders application of EC hydrolase. In this study, the mutants of EC hydrolase were screened by diphasic high pressure molecular dynamic simulations (dHP-MD). The best variant with remarkable improvement in specific activity and was H68A/K70R/S325N, whose specific activity was approximately 3.42-fold higher than WT, and relative enzyme activity under 20% (v/v) was 5.02-fold higher than WT. Moreover, the triple mutant increased its stability by acquiring more hydration shell and forming extra hydrogen bonds. Furthermore, the ability of degrading EC of the immobilized triple mutant was both detected in mock wine and under certain reaction conditions. The stability of immobilized triple mutant and WT were both improved, and immobilized triple mutant degraded nearly twice as much EC as that of immobilized WT. Overall, dHP-MD was proved to effectively improve enzyme activity and ethanol tolerance for extent application at industrial scale.

Qualification of Human Liver Microsomes for Antibacterial Activity Screening of Drug Metabolites

Microsomes are commonly used to perform in vitro drug metabolism, predominantly to form phase I drug metabolites. Pooled microsomes from multiple donors can contain microorganisms from underlying microbial diseases. Exposure to microbes can also occur during extraction if aseptic processing is compromised. Although microbial presence does not affect the metabolic activity of microsomes, presence of unwanted microorganisms can cause interference if the downstream application of microsomal drug metabolites is screening for antibacterial activity. In this work, traditional biochemical tests and advanced proteomics-based identification techniques were used to identify two gram-negative bacteria in pooled human liver microsomes. Several decontamination procedures were assessed to eradicate these two bacteria from the microsomes without affecting its metabolic capacity, and organic extraction was found to be the most convenient and efficient approach to decontaminate microsomes and screen drug metabolites for antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA).

Microscopy-Based Multiwell Assay to Characterize Disturbed Bacterial Morphogenesis Upon Antibiotic Action

The urgent need of new antimicrobial agents to combat life-threatening bacterial infections demands the identification and characterization of novel compounds that interfere with new and unprecedented target pathways or structures in multiresistant bacteria. Here, bacterial cell division has emerged as a new and promising target pathway for antibiotic intervention. Compounds, which inhibit division, commonly induce a characteristic filamentation phenotype of rod-shaped bacteria, such as Bacillus subtilis. Hence, this filamentation phenotype can be used to identify and characterize novel compounds that primarily target bacterial cell division. Since novel compounds of both synthetic and natural product origin are often available in small amounts only, thereby limiting the number of assays during mode of action studies, we here describe a semiautomated, microscopy-based approach that requires only small volumes of compounds to allow for the real-time observation of their effects on living bacteria, such as filamentation or cell lysis, in high-throughput 96-well-based formats. We provide a detailed workflow for the initial characterization of multiple compounds at once and further tools for the initial, microscopy-based characterization of their antibacterial mode of action.

Membrane-Binding Biomolecules Influence the Rate of Vesicle Exchange between Bacteria

The exchange of bacterial extracellular vesicles facilitates molecular exchange between cells, including the horizontal transfer of genetic material. Given the implications of such transfer events on cell physiology and adaptation, some bacterial cells have likely evolved mechanisms to regulate vesicle exchange. Past work has identified mechanisms that influence the formation of extracellular vesicles, including the production of small molecules that modulate membrane structure; however, whether these mechanisms also modulate vesicle uptake and have an overall impact on the rate of vesicle exchange is unknown. Here, we show that membrane-binding molecules produced by microbes influence both the formation and uptake of extracellular vesicles and have the overall impact of increasing the vesicle exchange rate within a bacterial coculture. In effect, production of compounds that increase vesicle exchange rates encourage gene exchange between neighboring cells. The ability of several membrane-binding compounds to increase vesicle exchange was demonstrated. Three of these compounds, nisin, colistin, and polymyxin B, are antimicrobial peptides added at sub-inhibitory concentrations. These results suggest that a potential function of exogenous compounds that bind to membranes may be the regulation of vesicle exchange between cells. IMPORTANCE The exchange of bacterial extracellular vesicles is one route of gene transfer between bacteria, although it was unclear if bacteria developed strategies to modulate the rate of gene transfer within vesicles. In eukaryotes, there are many examples of specialized molecules that have evolved to facilitate the production, loading, and uptake of vesicles. Recent work with bacteria has shown that some small molecules influence membrane curvature and induce vesicle formation. Here, we show that similar compounds facilitate vesicle uptake, thereby increasing the overall rate of vesicle exchange within bacterial populations. The addition of membrane-binding compounds, several of them antibiotics at subinhibitory concentrations, to a bacterial coculture increased the rate of horizontal gene transfer via vesicle exchange.

Cow's microbiome from antepartum to postpartum: A long-term study covering two physiological challenges

Little is known about the interplay between the ruminant microbiome and the host during challenging events. This long-term study investigated the ruminal and duodenal microbiome and metabolites during calving as an individual challenge and a lipopolysaccharide-induced systemic inflammation as a standardized challenge. Strong inter- and intra-individual microbiome changes were noted during the entire trial period of 168 days and between the 12 sampling time points. Bifidobacterium increased significantly at 3 days after calving. Both challenges increased the intestinal abundance of fiber-associated taxa, e.g., Butyrivibrio and unclassified Ruminococcaceae. NMR analyses of rumen and duodenum samples identified up to 60 metabolites out of which fatty and amino acids, amines, and urea varied in concentrations triggered by the two challenges. Correlation analyses between these parameters indicated a close connection and dependency of the microbiome with its host. It turns out that the combination of phylogenetic with metabolite information supports the understanding of the true scenario in the forestomach system. The individual stages of the production cycle in dairy cows reveal specific criteria for the interaction pattern between microbial functions and host responses.

Bioactivities and Microbial Quality of Lycium Fruits (Goji) Extracts Derived by Various Solvents and Green Extraction Methods

Goji berries, known for their health-promoting properties, are increasingly consumed around the world, often in the form of naturally- or freeze-dried fruits, further unprocessed. The aim of the study was to obtain dried goji berries extracts, characterized by high bioactivity and safety in terms of microbial contamination for the consumer. In the study, various solvents (water, ethanol, acetone, ethyl lactate, sunflower oil) and green extraction methods (heating and ultrasound-assisted extraction (UAE)) were used. In goji extracts, antioxidant activity and carotenoids content as bioactivity indicators, as well as total number of microorganisms were determined. Boiling of powdered dried goji fruits in water resulted in extracts with the best features, i.e., with high antioxidant properties (2.75−4.06 μmol of Trolox equivalent (TE)/mL), moderate to high content of carotenoids (0.67−1.86 mg/mL), and a reduced number of microorganisms compared with fruits. Extracts in 50% ethanol and 50% acetone were characterized primarily by very high antioxidant activity (3.09−4.90 μmol TE/mL). The high content of carotenoids (0.98−3.79 mg/mL) and high microbial quality (<10 CFU/g) were obtained by extraction in ethyl lactate by the UAE method. The results could be useful in the development of functional food based on goji berry ingredients.

Skin microbiota of oxazolone-induced contact hypersensitivity mouse model

Contact allergy is a common skin allergy, which can be studied utilising contact hypersensitivity (CHS) animal model. However, it is not clear, whether CHS is a suitable model to investigate skin microbiota interactions. We characterised the effect of contact dermatitis on the skin microbiota and studied the biological effects of oxazolone (OXA) -induced inflammation on skin thickness, immune cell numbers and changes of the microbiota in CHS mouse model (n = 72) for 28 days. Through 16S rRNA gene sequencing we defined the composition of bacterial communities and associations of bacteria with inflammation. We observed that the vehicle solution of acetone and olive oil induced bacterial community changes on day 1, and OXA-induced changes were observed mainly on day 7. Many of the notably enriched bacteria present in the OXA-challenged positive group represented the genus Faecalibaculum which were most likely derived from the cage environment. Additionally, skin inflammation correlated negatively with Streptococcus, which is considered a native skin bacterium, and positively with Muribacter muris, which is typical in oral environment. Skin inflammation favoured colonisation of cage-derived faecal bacteria, and additionally mouse grooming transferred oral bacteria on the skin. Due to the observed changes, we conclude that CHS model could be used for certain skin microbiome-related research set-ups. However, since vehicle exposure can alter the skin microbiome as such, future studies should include considerations such as careful control sampling and statistical tests to account for potential confounding factors.

Selection of green carrier solvent for the effective creation of bio-inspired liquid formulation and anti-fungal potency evaluation

Existing pesticide formulation solvents generate volatile organic compounds (VOCs), are combustible, and are classed as hazardous air pollutants (HAPs), meaning they are detrimental to users and phytotoxic to crops. Green solvents are required in formulations due to regulations, health, and environmental concerns. In emulsifiable concentration (EC) formulations, the "green chemistry" movement has led to the use of less harmful solvents. After a detailed and comparative fungal growth inhibition assessment, the least harmful carrier solvent among four regularly used organic solvents [dimethyl sulfoxide (DMSO), dimethylformamide (DMF), aromatic hydrocarbon (C9), and methyl oleate] was chosen in this study. We employed methyl oleate (cis-9-Octadecenoic acid methyl ester) as a bio-based green reserver (60%) to create effective bioinspired EC formulations (30%) of Pongamia pinnata L extract utilising emulsifier blends (10 percent) based on the known toxicity order (DMF > DMSO > C₉ > methyl oleate). EC1 outperformed the other thirteen formulations (EC1-EC13) in terms of emulsion stability, cold test, accelerated storage stability, flash point, and other metrics, proving its suitability for commercial production. Using four therapeutically appropriate concentrations of agricultural usage, in-vitro fungicidal effects against Alternaria solani and Phytophthora spp. were examined.A. solani (EC₅₀ = 0.08 percent) showed the greatest growth suppression (87.4 percent) at the maximum dosage (1 percent), followed by Phytophthora sp. (71.1 percent) (EC₅₀ = 0.49 percent). The study proved its utility in the production of environmentally acceptable green solvent-based herbal formulations as a long-term crop protection alternative to harmful chemical pesticides.

Adaptation and Resistance: How Bacteroides thetaiotaomicron Copes with the Bisphenol A Substitute Bisphenol F

Bisphenols are used in the process of polymerization of polycarbonate plastics and epoxy resins. Bisphenols can easily migrate out of plastic products and enter the gastrointestinal system. By increasing colonic inflammation in mice, disrupting the intestinal bacterial community structure and altering the microbial membrane transport system in zebrafish, bisphenols seem to interfere with the gut microbiome. The highly abundant human commensal bacterium Bacteroides thetaiotaomicron was exposed to bisphenols (Bisphenol A (BPA), Bisphenol F (BPF), Bisphenol S (BPS)), to examine the mode of action, in particular of BPF. All chemicals caused a concentration-dependent growth inhibition and the half-maximal effective concentration (EC50) corresponded to their individual logP values, a measure of their hydrophobicity. B. thetaiotaomicron exposed to BPF decreased membrane fluidity with increasing BPF concentrations. Physiological changes including an increase of acetate concentrations were observed. On the proteome level, a higher abundance of several ATP synthase subunits and multidrug efflux pumps suggested an increased energy demand for adaptive mechanisms after BPF exposure. Defense mechanisms were also implicated by a pathway analysis that identified a higher abundance of members of resistance pathways/strategies to cope with xenobiotics (i.e., antibiotics). Here, we present further insights into the mode of action of bisphenols in a human commensal gut bacterium regarding growth inhibition, and the physiological and functional state of the cell. These results, combined with microbiota-directed effects, could lead to a better understanding of host health disturbances and disease development based on xenobiotic uptake.

Plasmonic colloidal Au nanoparticles in DMSO: a facile synthesis and characterisation

We report a new pathway for the synthesis of plasmonic gold nanoparticles (Au NPs) in a bio-compatible medium. A modified room temperature approach based on the standard Turkevich synthesis, using sodium citrate as a reducing and stabilizing agent, results in a highly stable colloidal suspension of Au NPs in dimethyl sulfoxide (DMSO). The mean NP size of about 15 nm with a fairly low size distribution is revealed by scanning electron microscopy. The stability test through UV-vis absorption spectroscopy indicates no sign of aggregation for months. The Au NPs are also characterized by X-ray photoelectron, Raman scattering, and FTIR spectroscopies. The stabilisation mechanism of the Au NPs in DMSO is concluded to be similar to that of NPs synthesized in water. The Au NPs obtained in this work are applicable as SERS substrates, as proved by common analytes. In terms of bio-applications, they do not possess such side-effects as pronounced antibacterial activity, based on the tests performed on non-pathogenic Gram-positive or Gram-negative bacteria.

Direct production of polyhydroxybutyrate and alginate from crude glycerol by Azotobacter vinelandii using atmospheric nitrogen

While biodiesel is drawing attention as an eco-friendly fuel, the use of crude glycerol, a byproduct of the fuel production process, has increasingly become a concern to be addressed. Here we show the development of a low-cost fermentation technology using an atmospheric nitrogen-fixing bacterium to recycle crude glycerol into functional biopolymers. Azotobacter vinelandii showed substantial growth on tap water-diluted crude glycerol without any pretreatment. The number of viable A. vinelandii cells increased over 1000-fold under optimal growth conditions. Most of the glycerol content (~ 0.2%) in the crude glycerol medium was completely depleted within 48 h of culture. Useful polymers, such as polyhydroxybutyrate and alginate, were also produced. Polyhydroxybutyrate productivity was increased ten-fold by blocking the alginate synthesis pathway. Although there are few examples of using crude glycerol directly as a carbon source for microbial fermentation, there are no reports on the use of crude glycerol without the addition of a nitrogen source. This study demonstrated that it is possible to develop a technology to produce industrially useful polymers from crude glycerol through energy-saving and energy-efficient fermentation using the atmospheric nitrogen-fixing microorganism A. vinelandii.

A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling

While a range of methods for stool collection exist, many require complicated, self-directed protocols and stool transfer. In this study, we introduce and validate a novel, wipe-based approach to fecal sample collection and stabilization for metagenomics analysis. A total of 72 samples were collected across four different preservation types: freezing at -20°C, room temperature storage, a commercial DNA preservation kit, and a dissolvable wipe used with DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) solution. These samples were sequenced and analyzed for taxonomic abundance metrics, bacterial metabolic pathway classification, and diversity analysis. Overall, the DESS wipe results validated the use of a wipe-based capture method to collect stool samples for microbiome analysis, showing an R2 of 0.96 for species across all kingdoms, as well as exhibiting a maintenance of Shannon diversity (3.1-3.3) and species richness (151-159) compared to frozen samples. Moreover, DESS showed comparable performance to the commercially available preservation kit (R2 of 0.98), and samples consistently clustered by subject across each method. These data support that the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens.

Gram-negative bacteria act as a reservoir for aminoglycoside antibiotics that interact with host factors to enhance bacterial killing in a mouse model of pneumonia

In vitro exposure of multiple Gram-negative bacteria to an aminoglycoside (AG) antibiotic has previously been demonstrated to result in bacterial alterations that interact with host factors to suppress Gram-negative pneumonia. However, the mechanisms resulting in suppression are not known. Here, the hypothesis that Gram-negative bacteria bind and retain AGs, which are introduced into the lung and interact with host defenses to affect bacterial killing, was tested. Following in vitro exposure of one of several, pathogenic Gram-negative bacteria to the AG antibiotics kanamycin or gentamicin, AGs were detected in bacterial cell pellets (up to 208 μg/mL). Using inhibitors of AG binding and internalization, the bacterial outer membrane was implicated as the predominant kanamycin and gentamicin reservoir. Following intranasal administration of gentamicin-bound bacteria or gentamicin solution at the time of infection with live, AG-naïve bacteria, gentamicin was detected in the lungs of infected mice (up to 8 μg/g). Co-inoculation with gentamicin-bound bacteria resulted in killing of AG-naïve bacteria by up to 3-log₁₀, mirroring the effects of intranasal gentamicin treatment. In vitro killing of AG-naïve bacteria mediated by kanamycin-bound bacteria required the presence of detergents or pulmonary surfactant, suggesting that increased bacterial killing inside the murine lung is facilitated by the detergent component of pulmonary surfactant. These findings demonstrate that Gram-negative bacteria bind and retain AGs that can interact with host-derived pulmonary surfactant to enhance bacterial killing in the lung. This may help explain why AGs appear to have unique efficacy in the lung and might expand their clinical utility.

Extraction of Bioactive Metabolites from Achillea millefolium L. with Choline Chloride Based Natural Deep Eutectic Solvents: A Study of the Antioxidant and Antimicrobial Activity

In this study, the extraction efficiency of natural deep eutectic solvents (NADES) based on choline chloride as a hydrogen bond acceptor (HBA) and five different hydrogen bond donors (HBD; lactic acid, 1,4-butanediol, 1,2-propanediol, fructose and urea) was evaluated for the first time for the isolation of valuable bioactive compounds from Achillea millefolium L. The phytochemical profiles of NADES extracts obtained after ultrasound-assisted extraction were evaluated both spectrophotometrically (total phenolic content (TPC) and antioxidant assays) and chromatographically (UHPLC-MS and HPLC-UV). The results were compared with those obtained with 80% ethanol, 80% methanol, and water. The highest TPC value was found in the lactic acid-based NADES (ChCl-LA), which correlated with the highest antioxidant activity determined by the FRAP analysis. On the other hand, the highest antiradical potential against ABTS+• was determined for urea-based NADES. Phenolic acids (chlorogenic acid and dicaffeoylquinic acid isomers), flavones (luteolin and apigenin), and their corresponding glucosides were determined as the dominant individual phenolic compounds in all extracts. The antibacterial and antifungal properties of the extracts obtained against four bacterial cultures and two yeasts were evaluated using two methods: the agar dilution method to obtain the minimum inhibitory concentration (MIC) and the minimum bactericidal or fungicidal concentration (MBC or MFC), and the disc diffusion method. ChCl-LA had the lowest MIC and MBC/MFC with respect to all microorganisms, with an MIC ranging from 0.05 mg mL−1 to 0.8 mg mL−1, while the water extract had the weakest inhibitory activity with MIC and MBC/MFC higher than 3.2 mg mL−1.

Quality Evaluation of Drinks Based on Liposome Shape Changes Induced by Flavor Molecules

The flavors of ethyl caproate and isoamyl acetate and their precursors are crucial in sake brewing for fermentation and evaluation of the corresponding quality of drinks. However, the quality evaluation of drinks containing these flavors is challenging. Therefore, sake quality was evaluated via dynamic membrane transformation on cell-sized liposomes while adding flavor-containing solutions. Flavor varieties have been reported to influence dynamic shape change patterns. This study reports the observed difference in the dynamic shape change of each flavor. Based on these results, proper quality evaluation of drinks is expected.

Boosting the acetol production in methanotrophic biocatalyst Methylomonas sp. DH-1 by the coupling activity of heteroexpressed novel protein PmoD with endogenous particulate methane monooxygenase

BACKGROUND

Methylacidiphilum sp. IT6 has been validated its C3 substrate assimilation pathway via acetol as a key intermediate using the PmoCAB3, a homolog of the particulate methane monooxygenase (pMMO). From the transcriptomic data, the contribution of PmoD of strain IT6 in acetone oxidation was questioned. Methylomonas sp. DH-1, a type I methanotroph containing pmo operon without the existence of its pmoD, has been deployed as a biocatalyst for the gas-to-liquid bioconversion of methane and propane to methanol and acetone. Thus, Methylomonas sp. DH-1 is a suitable host for investigation. The PmoD-expressed Methylomonas sp. DH-1 can also be deployed for acetol production, a well-known intermediate for various industrial applications. Microbial production of acetol is a sustainable approach attracted attention so far.

RESULTS

In this study, bioinformatics analyses elucidated that novel protein PmoD is a C-terminal transmembrane-helix membrane with the proposed function as a transport protein. Furthermore, the whole-cell biocatalyst was constructed in Methylomonas sp. DH-1 by co-expression the PmoD of Methylacidiphilum sp. IT6 with the endogenous pMMO to enable acetone oxidation. Under optimal conditions, the maximum accumulation, and specific productivity of acetol were 18.291 mM (1.35 g/L) and 0.317 mmol/g cell/h, respectively. The results showed the first coupling activity of pMMO with a heterologous protein PmoD, validated the involvement of PmoD in acetone oxidation, and demonstrated an unprecedented production of acetol from acetone in type I methanotrophic biocatalyst. From the data achieved in batch cultivation conditions, an assimilation pathway of acetone via acetol as the key intermediate was also proposed.

CONCLUSION

Using bioinformatics tools, the protein PmoD has been elucidated as the membrane protein with the proposed function as a transport protein. Furthermore, results from the assays of PmoD-heteroexpressed Methylomonas sp. DH-1 as a whole-cell biocatalyst validated the coupling activity of PmoD with pMMO to convert acetone to acetol, which also unlocks the potential of this recombinant biocatalyst for acetol production. The proposed acetone-assimilated pathway in the recombinant Methylomonas sp. DH-1, once validated, can extend the metabolic flexibility of Methylomonas sp. DH-1.

Cometabolic degradation mechanism and microbial network response of methanotrophic consortia to chlorinated hydrocarbon solvents

The cometabolism mechanism of chlorinated hydrocarbon solvents (CHSs) in mixed consortia remains largely unknown. CHS biodegradation characteristics and microbial networks in methanotrophic consortia were studied for the first time. The results showed that all CHSs can efficiently be degraded via cometabolism with a maximum degradation rate of 4.8 mg/(h·gcell). Chloroalkane and chloroethylene were more easily degraded than chlorobenzenes by methanotrophic consortia, especially nonfully chlorinated aliphatic hydrocarbons, which were converted to Cl- with a production rate of 0.29-0.36 mg/(h·gcell). In addition, the microecological response results indicated that Methylocystaceae (49.0%), Methylomonas (65.3%) and Methylosarcina (41.9%) may be the major functional degraders in methanotrophic consortia. Furthermore, the results of the microbial correlation network suggested that interactive relationships constructed by type I methanotrophs and heterotrophs determined biodegradability. Additionally, PICRUSt analysis showed that CHSs could increase the relative abundance of CHS degradation genes and reduce the relative abundance of methane oxidation genes, which was in good agreement with the experimental results.

Methanol Dehydrogenases as a Key Biocatalysts for Synthetic Methylotrophy

One-carbon (C1) chemicals are potential building blocks for cheap and sustainable re-sources such as methane, methanol, formaldehyde, formate, carbon monoxide, and more. These resources have the potential to be made into raw materials for various products used in our daily life or precursors for pharmaceuticals through biological and chemical processes. Among the soluble C1 substrates, methanol is regarded as a biorenewable platform feedstock because nearly all bioresources can be converted into methanol through syngas. Synthetic methylotrophy can be exploited to produce fuels and chemicals using methanol as a feedstock that integrates natural or artificial methanol assimilation pathways in platform microorganisms. In the methanol utilization in methylotrophy, methanol dehydrogenase (Mdh) is a primary enzyme that converts methanol to formaldehyde. The discovery of new Mdhs and engineering of present Mdhs have been attempted to develop synthetic methylotrophic bacteria. In this review, we describe Mdhs, including in terms of their enzyme properties and engineering for desired activity. In addition, we specifically focus on the application of various Mdhs for synthetic methylotrophy.

Optimized protocols for assessing libraries of poorly soluble sortase A inhibitors for antibacterial activity against medically-relevant bacteria, toxicity and enzyme inhibition

Increasing antimicrobial resistance is a major global health concern. Conventional antibiotics apply selection pressures, which promote the accumulation of resistant microbes. Anti-virulence strategies, in contrast, are less potent antimicrobials, but are less likely to select for resistance, can be combined with existing antibiotics to improve their activity, and in some cases can overcome antimicrobial resistance towards other antimicrobials. Sortase A inhibitors (SrtAIs) represent an exciting example of this class; however, many reported examples demonstrate poor water solubility, which complicates their biological assessment and activity. This includes reports that use antimicrobial concentrations of organic solvents or conditions that fail to solubilise these compounds for minimal inhibitory concentration (MIC) assessments. Herein, we report the first study to optimise screening processes for a library of prospective SrtAIs (trans-chalcone (TC), berberine (BR), curcumin (CUR), and quercetin (QC)), including comparative assessment of the effects of various co-solvent concentrations, along with comparative assessment of their antimicrobial activities against multiple disease relevant bacterial strains (methicillin-sensitive and resistant S. aureus, E. coli, and P. aeruginosa), inhibition of the sortase A enzyme, and toxicity towards mammalian cells (HEK-293), using these optimised conditions. Optimal solubility with minimal effect on bacterial viability was observed in the presence of 5% (v/v) dimethyl sulfoxide (DMSO)-Mueller-Hinton Broth. Three antimicrobial susceptibility tests (broth microdilution, agar dilution, and disk diffusion) were assessed for their ability to accurately determine minimal inhibitory concentration (MIC) data for each SrtAI. Broth microdilution and agar dilution were both effective; however, the broth microdilution assay required the addition of a colorimetric metabolic indicator (resazurin) to enable simple and reliable MIC determination due to the development of precipitants over time. In contrast, disk diffusion did not provide reliable zone of inhibition data. Identical MIC data was observed with methicillin-sensitive and -resistant S. aureus (MRSA; ATCC43300), with lower potency activity against E. coli and P. aeruginosa. Under these conditions, TC and CUR demonstrated significant toxicity towards human embryonic kidney (HEK-293) cells, with QC showing less toxicity and BR limited-to-no toxicity at its MIC. Overall, the findings of this work provide optimised processes, which will prove useful for the study of other poorly soluble antimicrobial agents and SrtAIs. The obtained data suggests that BR should be considered in preference to the other SrtAIs for the development of new antimicrobial formulations, based on its superior antimicrobial and SrtA inhibition potency, and greatly reduced toxicity.

Evaluating acute toxicity in enriched nitrifying cultures: Lessons learned

Toxicological batch assays are essential to assess a compound's acute effect on microorganisms. This methodology is frequently employed to evaluate the effect of contaminants in sensitive microbial communities from wastewater treatment plants (WWTPs), such as autotrophic nitrifying populations. However, despite nitrifying batch assays being commonly mentioned in the literature, their experimental design criteria are rarely reported or overlooked. Here, we found that slight deviations in culture preparations and conditions impacted bacterial community performance and could skew assay results. From pre-experimental trials and experience, we determined how mishandling and treatment of cultures could affect nitrification activity. While media and biomass preparations are needed to establish baseline conditions (e.g., biomass washing), we found extensive centrifugation selectively destabilised nitrification activities. Further, it is paramount that the air supply is adjusted to minimise nitrite build-up in the culture and maintain suitable aeration levels without sparging ammonia. DMSO and acetone up to 0.03% (v/v) were suitable organic solvents with minimal impact on nitrification activity. In the nitrification assays with allylthiourea (ATU), dilute cultures exhibited more significant inhibition than concentrated cultures. So there were biomass-related effects; however, these differences minimally impacted the EC₅₀ values. Using different nutrient-media compositions had a minimal effect; however, switching mineral media for the toxicity test from the original cultivation media is not recommended because it reduced the original biomass nitrification capacity. Our results demonstrated that these factors substantially impact the performance of the nitrifying inoculum used in acute bioassays, and consequently, affect the response of AOB-NOB populations during the toxicant exposure. These are not highlighted in operation standards, and unfortunately, they can have significant consequential impacts on the determinations of toxicological endpoints. Moreover, the practical procedures tested here could support other authors in developing testing methodologies, adding quality checks in the experimental framework with minimal waste of time and resources.

On-Slide Heat Sterilization Enables Mass Spectrometry Imaging of Tissue Infected with High-Threat Pathogens Outside of Biocontainment: A Study Directed at Mycobacterium tuberculosis

Mass spectrometry imaging investigations of tissues infected with agents that require high-security biocontainment, such as Mycobacterium tuberculosis, have been limited due to incompatible sterilization techniques. Here we describe an on-slide heat sterilization method that enables mass spectrometry imaging investigations of pharmaceuticals, lipids, and metabolites in infected tissue samples outside of biocontainment. An evaluation of different temperatures and incubation times determined that 100 °C for 1 h was essential to sterilize 5 times the bacterial burden observed in tuberculosis (TB) cavity sections. Laser-capture microdissection combined with liquid chromatography with tandem mass spectrometry quantitation, in addition to mass spectrometry imaging, showed that no degradation was observed following the on-slide heat sterilization protocol for a variety of drug classes covering a range of physicochemical properties. Utilizing the tissue mimetic model, we demonstrated that the detection of lipid and metabolite ions was not impacted by heat sterilization and that, for several metabolites, the on-slide heat sterilization method improved the sensitivity when compared to control samples. An application of the on-slide heat sterilization to M. tuberculosis infected tissue enabled the first detection and spatial distribution of lipids indicative of a lysosomal storage disease phenotype within TB granuloma macrophages, in addition to the differential distribution of metabolites central to the fatty acid oxidation pathway. These initial investigations detected a pronounced heterogeneity within the cellular regions and necrotic cores of individual TB granulomas and across different evolving granulomas. This study provides the framework for mass spectrometry imaging investigations of high-threat pathogens outside of biocontainment.

Evaluation of the Antimicrobial Effect of Thymoquinone against Different Dental Pathogens: An In Vitro Study

This study aimed to evaluate the antimicrobial effect of Thymoquinone (TQ) on four different oral microorganisms. Minimum Bactericidal Concentration (MBC), Minimum Inhibition Concentration (MIC), Broth microdilution, and Well diffusion tests were used to determine the optimum antimicrobial concentrations of TQ against Streptococcus salivarius, Streptococcus oralis, Streptococcus mutans, and Staphylococcus aureus over 1, 3, 6, 12 and 24 h. Chlorhexidine 0.12% was selected as a positive control. The inhibitory effect of TQ on bacterial growth was most noticeable with S. salivarius, while the least affected was S. aureus. TQ’s MBC and MIC for S. oralis and S. aureus were comparable 2 mg/mL and 3 mg/mL, respectively. S. salivarius was most resistant to TQ and displayed a value of 5 mg/mL and 4 mg/mL for MIC and MBC, respectively. The viable count of different strains after exposure to TQ’s MBC values was most noticeable with S. aureus followed by S. oralis and S. mutans, while S. salivarius was least affected. This study emphasized the promising antimicrobial effect of TQ against the four main oral microorganisms. It has a potential preventive effect against dental caries as well as other oral diseases.

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.

Toward Intracellular Bioconjugation Using Transition-Metal-Free Techniques

Bioconjugation is the chemical strategy of covalent modification of biomolecules, using either an external reagent or other biomolecules. Since its inception in the twentieth century, the technique has grown by leaps and bounds, and has a variety of applications in chemical biology. However, it is yet to reach its full potential in the study of biochemical processes in live cells, mainly because the bioconjugation strategies conflict with cellular processes. This has mostly been overcome by using transition metal catalysts, but the presence of metal centers limit them to in vitro use, or to the cell surface. These hurdles can potentially be circumvented by using metal-free strategies. However, the very modifications that are necessary to make such metal-free reactions proceed effectively may impact their biocompatibility. This is because biological processes are easily perturbed and greatly depend on the prevailing inter- and intracellular environment. With this taken into consideration, this review analyzes the applicability of the transition-metal-free strategies reported in this decade to the study of biochemical processes in vivo.

The function of peptide-mimetic anionic groups and salt bridges in the antimicrobial activity and conformation of cationic amphiphilic copolymers

Herein we report the synthesis of ternary statistical methacrylate copolymers comprising cationic ammonium (amino-ethyl methacrylate: AEMA), carboxylic acid (propanoic acid methacrylate: PAMA) and hydrophobic (ethyl methacrylate: EMA) side chain monomers, to study the functional role of anionic groups on their antimicrobial and hemolytic activities as well as the conformation of polymer chains. The hydrophobic monomer EMA was maintained at 40 mol% in all the polymers, with different percentages of cationic ammonium (AEMA) and anionic carboxylate (PAMA) side chains, resulting in different total net charge for the polymers. The antimicrobial and hemolytic activities of the copolymer were determined by the net charge of +3 or larger, suggesting that there was no distinct effect of the anionic carboxylate groups on the antimicrobial and hemolytic activities of the copolymers. However, the pH titration and atomic molecular dynamics simulations suggest that anionic groups may play a strong role in controlling the polymer conformation. This was achieved via formation of salt bridges between cationic and anionic groups, transiently crosslinking the polymer chain allowing dynamic switching between compact and extended conformations. These results suggest that inclusion of functional groups in general, other than the canonical hydrophobic and cationic groups in antimicrobial agents, may have broader implications in acquiring functional structures required for adequate antimicrobial activity. In order to explain the implications, we propose a molecular model in which formation of intra-chain, transient salt bridges, due to the presence of both anionic and cationic groups along the polymer, may function as "adhesives" which facilitate compact packing of the polymer chain to enable functional group interaction but without rigidly locking down the overall polymer structure, which may adversely affect their functional roles.

Transcriptomic and Metabolomic Responses to Carbon and Nitrogen Sources in Methylomicrobium album BG8

Methanotrophs use methane as their sole carbon and energy source and represent an attractive platform for converting single-carbon feedstocks into value-added compounds. Optimizing these species for biotechnological applications involves choosing an optimal growth substrate based on an understanding of cellular responses to different nutrients. Although many studies of methanotrophs have examined growth rate, yield, and central carbon flux in cultures grown with different carbon and nitrogen sources, few studies have examined more global cellular responses to different media. Here, we evaluated global transcriptomic and metabolomic profiles of Methylomicrobium album BG8 when grown with methane or methanol as the carbon source and nitrate or ammonium as the nitrogen source. We identified five key physiological changes during growth on methanol: M. album BG8 cultures upregulated transcripts for the Entner-Doudoroff and pentose phosphate pathways for sugar catabolism, produced more ribosomes, remodeled the phospholipid membrane, activated various stress response systems, and upregulated glutathione-dependent formaldehyde detoxification. When using ammonium, M. album BG8 upregulated hydroxylamine dehydrogenase (haoAB) and overall central metabolic activity, whereas when using nitrate, cultures upregulated genes for nitrate assimilation and conversion. Overall, we identified several nutrient source-specific responses that could provide a valuable basis for future research on the biotechnological optimization of these species. IMPORTANCE Methanotrophs are gaining increasing interest for their biotechnological potential to convert single-carbon compounds into value-added products such as industrial chemicals, fuels, and bioplastics. Optimizing these species for biotechnological applications requires a detailed understanding of how cellular activity and metabolism vary across different growth substrates. Although each of the two most commonly used carbon sources (methane or methanol) and nitrogen sources (ammonium or nitrate) in methanotroph growth media have well-described advantages and disadvantages in an industrial context, their effects on global cellular activity remain poorly characterized. Here, we comprehensively describe the transcriptomic and metabolomic changes that characterize the growth of an industrially promising methanotroph strain on multiple combinations of carbon and nitrogen sources. Our results represent a more holistic evaluation of cellular activity than previous studies of core metabolic pathways and provide a valuable basis for the future biotechnological optimization of these species.

Cytotoxicity and Microbicidal Activity of Commonly Used Organic Solvents: A Comparative Study and Application to a Standardized Extract from Vaccinium macrocarpon

The cytotoxicity and microbicidal capacity of seven organic solvents commonly applied for studying plant extracts and bioactive compounds were systematically investigated based on international standards. Four cell lines of normal (CCL-1, HaCaT) or tumor (A-375, A-431) tissue origin, seven bacterial and one fungal strain were used. The impact of the least toxic solvents in the determination of in vitro cytotoxicity was evaluated using a standardized extract from Vaccinium macrocarpon containing 54.2% v/v proanthocyanidins (CystiCran^®). The solvents ethanol, methoxyethanol and polyethylene glycol were the least cytotoxic to all cell lines, with a maximum tolerated concentration (MTC) between 1 and 2% v/v. Ethanol, methanol and polyethylene glycol were mostly suitable for antimicrobial susceptibility testing, with minimum inhibitory concentrations (MICs) ≥ 25% v/v. The MTC values of the solvents dimethyl sulfoxide, dimethoxyethane and dimethylformamide varied from 0.03% to 1.09% v/v. The MICs of dimethyl sulfoxide, methoxyethanol and dimethoxyethane were in the range of 3.125–25% v/v. The cytotoxic effects of CystiCran^® on eukaryotic cell lines were directly proportional to the superimposed effect of the solvents used. The results of this study can be useful for selecting the appropriate solvents for in vitro estimation of the cytotoxic and growth inhibitory effects of bioactive molecules in eukaryotic and prokaryotic cells.

Recent developments in microfluidic synthesis of artificial cell-like polymersomes and liposomes for functional bioreactors

Recent advances in droplet microfluidics have led to the fabrication of versatile vesicles with a structure that mimics the cellular membrane. These artificial cell-like vesicles including polymersomes and liposomes effectively enclose an aqueous core with well-defined size and composition from the surrounding environment to implement various biological reactions, serving as a diverse functional reactor. The advantage of realizing various biological phenomena within a compartment separated by a membrane that resembles a natural cell membrane is actively explored in the fields of synthetic biology as well as biomedical applications including drug delivery, biosensors, and bioreactors, to name a few. In this Perspective, we first summarize various methods utilized in producing these polymersomes and liposomes. Moreover, we will highlight some of the recent advances in the design of these artificial cell-like vesicles for functional bioreactors and discuss the current issues and future perspectives.

Effect of high levels of CO2 and O2 on membrane fatty acid profile and membrane physiology of meat spoilage bacteria

The membrane is the major protective barrier separating the cell from the environment and is thus important for bacteria to survive environmental stress. This study investigates changes in membrane lipid compositions and membrane physiology of meat spoiling bacteria in response to high CO2 (30%) and O2 (70%) concentrations, as commonly used for modified atmosphere packaging of meat. Therefore, the fatty acid profile as well as membrane fluidity, permeability and cell surface were determined and correlated to the genomic settings of five meat spoiling bacteria Brochothrix (B.) thermosphacta, Carnobacterium (C.) divergens, C. maltaromaticum, Leuconostoc (L.) gelidum subsp. gelidum and L. gelidum subsp. gasicomitatum cultivated under different gas atmospheres. We identified different genomic potentials for fatty acid adaptations, which were in accordance with actual measured changes in the fatty acid composition for each species in response to CO2 and/or O2, e.g., an increase in saturated, iso and cyclopropane fatty acids. Even though fatty acid changes were species-specific, the general physiological responses were similar, comprising a decreased membrane permeability and fluidity. Thus, we concluded that meat spoiling bacteria facilitate a change in membrane fatty acids upon exposure to O2 and CO2, what leads to alteration of membrane fluidity and permeability. The observed adaptations might contribute to the resistance of meat spoilers against detrimental effects of the gases O2 and CO2 and thus help to explain their ability to grow under different modified atmospheres. Furthermore, this study provides fundamental knowledge regarding the impact of fatty acid changes on important membrane properties of bacteria.

Disinfection Treatments of Disposable Respirators Influencing the Bactericidal/Bacteria Removal Efficiency, Filtration Performance, and Structural Integrity

In the outbreak of COVID-19, the extended wear of single-use, disposable respirators was inevitable due to limited supplies. As a respirator is front-line protection against particulate matter, including bioaerosol and droplets, a comprehensive understanding for the reuse strategy is needed. In this study, eight different disinfection methods commonly applied for the reuse of respirators were compared for their influence on the filtration and bactericidal/bacteria removal performance, with in-depth discussion on the cause of effects. Treatments including oven-dry, ultraviolet irradiation (UV), microwaving, laundering with and without detergent, and immersion in hypochlorite, isopropanol, and ethanol were performed to respirators. Immersion in ethanol or isopropanol was effective for inactivation and removal of bacteria, yet such a treatment significantly deteriorated the filtration efficiency in about 20-28%, dissipating the surface charges. Laundering, while effective in removing the attached bacteria, triggered physical damage, leading to a possible reduction of filtration performance. A short-term oven-dry, UV irradiation, and microwaving mostly preserved the filtration performance, yet the drawback lied in the incomplete bactericidal efficiency. This study would contribute to the public health and safety by providing scientific background on the effect of disinfection treatment methods for respirators.

Porphyrin and phthalocyanine photosensitizers designed for targeted photodynamic therapy of colorectal cancer

Colorectal cancer is of particular concern due to its high mortality rate count. Recent investigations on targeted phototherapy involving novel photosensitizers and drug-delivery systems have provided promising results and realistic prospects for a successful medical treatment. New research trends have been focused particularly on development of advanced molecular systems offering effective photoactive species which could be selectively delivered directly into the affected cells. Porphyrins and phthalocyanines have been considered extremely attractive for this purpose due to their molecular versatility, excellent photochemical properties and multifunctional nature. In this review it has been demonstrated that such macrocyclic compounds may effectively contribute to the inhibition of the growth of colon cancer cells and eventually to their photonecrosis. Purposely designed and tailored porphyrin and phthalocyanine derivatives in combination with smart drug-carriers have proved suitable for photodynamic therapy (PDT) and related antitumor treatments. This survey comprises a choice of potentially applicable ideas developed since 2010 involving 9 different tumor cell lines and featuring 32 photosensitizers.