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One of the key issues of recent research on the dispersion inside complex urban environments is the ability to predict dosage-based parameters from the puff release of an airborne material from a point source in the atmospheric boundary layer inside the built-up area. The present work addresses the question of whether the computational fluid dynamics (CFD)-Reynolds-averaged Navier-Stokes (RANS) methodology can be used to predict ensemble-average dosage-based parameters that are related with the puff dispersion. RANS simulations with the ADREA-HF code were, therefore, performed, where a single puff was released in each case. The present method is validated against the data sets from two wind-tunnel experiments. In each experiment, more than 200 puffs were released from which ensemble-averaged dosage-based parameters were calculated and compared to the model's predictions. The performance of the model was evaluated using scatter plots and three validation metrics: fractional bias, normalized mean square error, and factor of two. The model presented a better performance for the temporal parameters (i.e., ensemble-average times of puff arrival, peak, leaving, duration, ascent, and descent) than for the ensemble-average dosage and peak concentration. The majority of the obtained values of validation metrics were inside established acceptance limits. Based on the obtained model performance indices, the CFD-RANS methodology as implemented in the code ADREA-HF is able to predict the ensemble-average temporal quantities related to transient emissions of airborne material in urban areas within the range of the model performance acceptance criteria established in the literature. The CFD-RANS methodology as implemented in the code ADREA-HF is also able to predict the ensemble-average dosage, but the dosage results should be treated with some caution; as in one case, the observed ensemble-average dosage was under-estimated slightly more than the acceptance criteria. Ensemble-average peak concentration was systematically underpredicted by the model to a degree higher than the allowable by the acceptance criteria, in 1 of the 2 wind-tunnel experiments. The model performance depended on the positions of the examined sensors in relation to the emission source and the buildings configuration. The work presented in this paper was carried out (partly) within the scope of COST Action ES1006 'Evaluation, improvement, and guidance for the use of local-scale emergency prediction and response tools for airborne hazards in built environments'. [ABSTRACT FROM AUTHOR]

One of the key issues of recent research on the dispersion inside complex urban environments is the ability to predict individual exposure (maximum dosages) of an airborne material which is released continuously from a point source. The present work addresses the question whether the computational fluid dynamics (CFD)–Reynolds-averaged Navier–Stokes (RANS) methodology can be used to predict individual exposure for various exposure times. This is feasible by providing the two RANS concentration moments (mean and variance) and a turbulent time scale to a deterministic model. The whole effort is focused on the prediction of individual exposure inside a complex real urban area. The capabilities of the proposed methodology are validated against wind-tunnel data (CUTE experiment). The present simulations were performed ‘blindly’, i.e. the modeller had limited information for the inlet boundary conditions and the results were kept unknown until the end of the COST Action ES1006. Thus, a high uncertainty of the results was expected. The general performance of the methodology due to this ‘blind’ strategy is good. The validation metrics fulfil the acceptance criteria. The effect of the grid and the turbulence model on the model performance is examined. [ABSTRACT FROM PUBLISHER]

Abstract Background The present study represents a genome-wide transcriptomic analysis of the response of the model streptomycete Streptomyces coelicolor A3(2) M145 to fermentor culture in Modified Evans Media limited, respectively, for nitrogen, phosphate and carbon undertaken as part of the ActinoGEN consortium to provide a publicly available reference microarray dataset. Findings A microarray dataset using samples from two replicate cultures for each nutrient limitation was generated. In this report our analysis has focused on the genes which are significantly differentially expressed, as determined by Rank Products Analysis, between samples from matched time points correlated by growth phase for the three pairs of differently limited culture datasets. With a few exceptions, genes are only significantly differentially expressed between the N6/N7 time points and their corresponding time points in the C and P-limited cultures, with the vast majority of the differentially expressed genes being more highly expressed in the N-limited cultures. Our analysis of these genes indicated expression of several members of the GlnR regulon are induced upon nitrogen limitation, as assayed for by [NH4+] measurements, and we are able to identify several additional genes not present in the GlnR regulon whose expression is induced in response to nitrogen limitation. We also note SCO3327 which encodes a small protein (32 amino acid residues) unusually rich in the basic amino acids lysine (31.25%) and arginine (25%) is significantly differentially expressed in the nitrogen limited cultures. Additionally, we investigate the expression of known members of the GlnR regulon and the relationship between gene organization and expression for the SCO2486-SCO2487 and SCO5583-SCO5585 operons. Conclusions We provide a list of genes whose expression is differentially expressed in low nitrogen culture conditions, including a putative nitrogen storage protein encoded by SCO3327. Our list includes several genes whose expression patterns are similar to up-regulated members of the GlnR regulon and are induced in response to nitrogen limitation. These genes represent likely targets for future studies into the nitrogen starvation response in Streptomyces coelicolor.

Microbes are ubiquitous and provide numerous services to humans and our planet. However, a query arises as to whether these microbial services are valued by the general public especially after unprecedented conditions like the COVID-19 pandemic. In this context a survey was conducted to investigate the concept of microbe in Greece. Thematic analysis of 672 anonymous responses (age range 4-75yo) received for the open-ended prompt "What is the first thing that comes to mind when you hear the word microbe?" revealed five thematic categories: Negative emotions, Fuzzy associations, Biology, Entities and Health. Almost 80% of responses fell under "Biology" and "Health" and the general pattern of answers was the same across all age groups. Microbes took a variety of forms in the minds of respondents, however, the concept of "microbe" seems to be more unshaped at younger ages (4-11yo), as revealed in children's language choices. Overall, the often-negative perception of microorganisms seems to be confirmed in this study. Although this research was limited to participants from Greece, it remains relevant to other countries around the world as well. We discuss the reasons behind this negative perception and offer suggestions for reversing it., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)

The Microbiology Society Education and Outreach Network (EON) recently hosted the Teaching Symposium at the Microbiology Society Annual Conference, sponsored by Access Microbiology . The presence of the Symposium as an established parallel session within the wider Annual Conference reflects the importance of high-quality, contemporary microbiology education and outreach delivered in an enthusiastic and inclusive manner. At the 2023 Symposium, a variety of pedagogical research projects in higher education learning, teaching and assessment, as well as public engagement projects, were showcased through invited talks, offered talks, flash talks and posters. The event was attended by up to 70 delegates. Several themes were noted throughout the day: engaging with Gen Z (Generation Z, those born between 1996 and 2010), active learning, art in science and engaging with non-higher education (HE) audiences. Inclusivity was a key driver in the organization of the Symposium; the room was set up to encourage discussion and participants could ask questions using an online platform as well as speaking in the room. We now encourage all speakers to consider publishing their work as a peer-reviewed article for further dissemination and impact., Competing Interests: Georgios Efthimiou is Pedagogy Editor of Access Microbiology., (© 2023 The Authors.)

Multi-strain probiotics are widely regarded as effective products for improving gut microbiota stability and host health, providing advantages over single-strain probiotics. However, in general, it is unclear to what extent different strains would cooperate or compete for resources, and how the establishment of a common biofilm microenvironment could influence their interactions. In this work, we develop an integrative experimental and computational approach to comprehensively assess the metabolic functionality and interactions of probiotics across growth conditions. Our approach combines co-culture assays with genome-scale modelling of metabolism and multivariate data analysis, thus exploiting complementary data- and knowledge-driven systems biology techniques. To show the advantages of the proposed approach, we apply it to the study of the interactions between two widely used probiotic strains of Lactobacillus reuteri and Saccharomyces boulardii, characterising their production potential for compounds that can be beneficial to human health. Our results show that these strains can establish a mixed cooperative-antagonistic interaction best explained by competition for shared resources, with an increased individual exchange but an often decreased net production of amino acids and short-chain fatty acids. Overall, our work provides a strategy that can be used to explore microbial metabolic fingerprints of biotechnological interest, capable of capturing multifaceted equilibria even in simple microbial consortia., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

The nature and airborne dispersion of the underestimated biological agents, monitoring, analysis and transmission among the human occupants into building environment is a major challenge of today. Those agents play a crucial role in ensuring comfortable, healthy and risk-free conditions into indoor working and leaving spaces. It is known that ventilation systems influence strongly the transmission of indoor air pollutants, with scarce information although to have been reported for biological agents until 2019. The biological agents' source release and the trajectory of airborne transmission are both important in terms of optimising the design of the heating, ventilation and air conditioning systems of the future. In addition, modelling via computational fluid dynamics (CFD) will become a more valuable tool in foreseeing risks and tackle hazards when pollutants and biological agents released into closed spaces. Promising results on the prediction of their dispersion routes and concentration levels, as well as the selection of the appropriate ventilation strategy, provide crucial information on risk minimisation of the airborne transmission among humans. Under this context, the present multidisciplinary review considers four interrelated aspects of the dispersion of biological agents in closed spaces, (a) the nature and airborne transmission route of the examined agents, (b) the biological origin and health effects of the major microbial pathogens on the human respiratory system, (c) the role of heating, ventilation and air-conditioning systems in the airborne transmission and (d) the associated computer modelling approaches. This adopted methodology allows the discussion of the existing findings, on-going research, identification of the main research gaps and future directions from a multidisciplinary point of view which will be helpful for substantial innovations in the field., Competing Interests: Conflict of interestThe authors declare no competing interests., (© The Author(s), under exclusive licence to Springer Nature B.V. 2022, Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

How we teach science and engage with the public, particularly in fast moving subjects such as microbiology, are constantly being reflected upon, improved and innovated. This has led to a significant increase of pedagogy publications by microbiology educators in higher education that have had a positive impact on teaching quality, student retention, progression and course satisfaction as well as how science is communicated with the public. In this paper we describe the different types of pedagogical manuscripts that biological scientists could write and the benefits that derive from doing so. We provide a glossary of terms often seen in educational literature. Project design and qualitative and quantitative research methodologies are discussed, highlighting ethical and General Data Protection Regulation (GDPR) considerations. Suggestions are made regarding how to network with colleagues who are also keen on writing pedagogical papers as well as examples of good practice. Lastly, a handy how-to-start guide aims to help with first steps. We hope that this paper will be a useful survival manual for colleagues who wish to engage in exciting pedagogical research in the field of microbiology and the broader biological sciences., Competing Interests: The authors declare that they have no conflicts of interest., (© 2022 The Authors.)

Probiotics are bacterial strains that are known to provide host health benefits. Limosilactobacillus reuteri is a well-documented lactic acid bacterium that has been cultured from numerous human sites. The strain investigated was L. reuteri DSM 20016, which has been found to produce useful metabolites. The strain was explored using genomic and proteomic tools, manual searches, and databases, including KEGG, STRING, BLAST Sequence Similarity Search, and UniProt. This study located over 200 key genes that were involved in human health benefit pathways. L. reuteri DSM 20016 has metabolic pathways to produce acetate, propionate, and lactate, and there is evidence of a pathway for butanoate production through a FASII mechanism. The bacterium produces histamine through the hdc operon, which may be able to suppress proinflammatory TNF, and the bacterium also has the ability to synthesize folate and riboflavin, although whether they are secreted is yet to be explored. The strain can bind to human Caco2 cells through srtA, mapA/cnb, msrB, and fbpA and can compete against enteric bacteria using reuterin, which is an antimicrobial that induces oxidative stress. The atlas could be used for designing metabolic engineering approaches to improve beneficial metabolite biosynthesis and better probiotic-based cures.

Innate immunity mediated by Toll-like receptors (TLRs), which can recognize pathogen molecular patterns, plays a critical role in type 1 diabetes development. TLR7 is a pattern recognition receptor that senses single-stranded RNAs from viruses and host tissue cells; however, its role in type 1 diabetes development remains unclear. In our study, we discovered that Tlr7-deficient (Tlr7 -/- ) nonobese diabetic (NOD) mice, a model of human type 1 diabetes, exhibited a significantly delayed onset and reduced incidence of type 1 diabetes compared with Tlr7-sufficient (Tlr7 +/+ ) NOD mice. Mechanistic investigations showed that Tlr7 deficiency significantly altered B-cell differentiation and immunoglobulin production. Moreover, Tlr7 -/- NOD B cells were found to suppress diabetogenic CD4 + T-cell responses and protect immunodeficient NOD mice from developing diabetes induced by diabetogenic T cells. In addition, we found that Tlr7 deficiency suppressed the antigen-presenting functions of B cells and inhibited cytotoxic CD8 + T-cell activation by downregulating the expression of both nonclassical and classical MHC class I (MHC-I) molecules on B cells. Our data suggest that TLR7 contributes to type 1 diabetes development by regulating B-cell functions and subsequent interactions with T cells. Therefore, therapeutically targeting TLR7 may prove beneficial for disease protection.

Heather honey was tested for its effect on the formation of biofilms by Staphylococcus aureus , Pseudomonas aeruginosa , Escherichia coli , Klebsiella pneumoniae , Enterococcus faecalis , Salmonella Enteriditis and Acinetobacter baumanii in comparison with Manuka honey. At 0.25 mg/mL, Heather honey inhibited biofilm formation in S. aureus , A. baumanii , E. coli , S. Enteriditis and P. aeruginosa , but promoted the growth of E. faecalis and K. pneumoniae biofilms. Manuka honey inhibited biofilm formation in K. pneumoniae , E. faecalis , and S. Enteriditis , A. baumanii , E. coli and P. aeruginosa , but promoted S. aureus biofilm formation. Molecular docking with Autodock Vina was performed to calculate the predictive binding affinities and ligand efficiencies of Manuka and Heather honey constituents for PaDsbA1, the main enzyme controlling the correct folding of virulence proteins in Pseudomonas aeruginosa . A number of constituents, including benzoic acid and methylglyoxal, present in Heather and/or Manuka honey, revealed high ligand efficiencies for the target enzyme. This helps support, to some extent, the decrease in P. aeruginosa biofilm formation observed for such honeys.

Introducing creative workshops in higher education curricula, in addition to formal lectures, is an excellent way of reinforcing knowledge and encouraging creative thinking. In particular, the use of card games as a tool for inducing student engagement and enthusiasm has been reported to be a very effective approach. Here, we report an innovative card game-based workshop for use at the intermediate undergraduate level. The name of the game is Microbes Against Humanity and has been adapted from the widely known party game Cards Against Humanity, which is freely available under a creative commons licence. Overall, 64 students and two academics participated in this 2 h workshop. Our students found the workshop to be very enjoyable, considered it to be helpful for their learning and suggested interesting ideas for further improvement. In conclusion, it was shown that such exciting workshops can trigger students' enthusiasm for microbiology and enhance their learning potential., Competing Interests: The authors declare that there are no conflicts of interest., (© 2021 The Authors.)

Methicillin-resistant Staphylococcus aureus (MRSA) strains are important human pathogens and a significant health hazard for hospitals and the food industry. They are resistant to β-lactam antibiotics including methicillin and extremely difficult to treat. In this study, we show that the Staphylococcus aureus COL (MRSA) strain, with a known complete genome, can easily survive and grow under acidic and alkaline conditions (pH5 and pH9, respectively), both planktonically and as a biofilm. A microarray-based analysis of both planktonic and biofilm cells was performed under acidic and alkaline conditions showing that several genes are up- or down-regulated under different environmental conditions and growth modes. These genes were coding for transcription regulators, ion transporters, cell wall biosynthetic enzymes, autolytic enzymes, adhesion proteins and antibiotic resistance factors, most of which are associated with biofilm formation. These results will facilitate a better understanding of the physiological adjustments occurring in biofilm-associated S. aureus COL cells growing in acidic or alkaline environments, which will enable the development of new efficient treatment or disinfection strategies., (Copyright © 2019 Efthimiou, Tsiamis, Typas and Pappas.)

Radiation from the deposited radionuclides is indispensable information for environmental impact assessment of nuclear power plants and emergency management during nuclear accidents. Ground shine estimation is related to multiple physical processes, including atmospheric dispersion, deposition, soil and air radiation shielding. It still remains unclear that whether the normally adopted "infinite plane" source assumption for the ground shine calculation is accurate enough, especially for the area with highly heterogeneous deposition distribution near the release point. In this study, a new ground shine calculation scheme, which accounts for both the spatial deposition distribution and the properties of air and soil layers, is developed based on point kernel method. Two sets of "detector-centered" grids are proposed and optimized for both the deposition and radiation calculations to better simulate the results measured by the detectors, which will be beneficial for the applications such as source term estimation. The evaluation against the available data of Monte Carlo methods in the literature indicates that the errors of the new scheme are within 5% for the key radionuclides in nuclear accidents. The comparisons between the new scheme and "infinite plane" assumption indicate that the assumption is tenable (relative errors within 20%) for the area located 1 km away from the release source. Within 1 km range, the assumption mainly causes errors for wet deposition and the errors are independent of rain intensities. The results suggest that the new scheme should be adopted if the detectors are within 1 km from the source under the stable atmosphere (classes E and F), or the detectors are within 500 m under slightly unstable (class C) or neutral (class D) atmosphere. Otherwise, the infinite plane assumption is reasonable since the relative errors induced by this assumption are within 20%. The results here are only based on theoretical investigations. They should be further thoroughly evaluated with real measurements in the future., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

The emergence of methicillin-resistant Staphylococcus aureus (MRSA) in food has provoked a great concern about the presence of MRSA in associated foodstuff. Although MRSA is often detected in various retailed meat products, it seems that food handlers are more strongly associated with this type of food contamination. Thus, it can be easily postulated that any food could be contaminated with this pathogen in an industrial environment or in household and cause food poisoning. To this direction, the effect of rocket (Eruca sativa ) extract on MRSA growth and proteome was examined in the present study. This goal was achieved with the comparative study of the MRSA strain COL proteome, cultivated in rocket extract versus the standard Luria-Bertani growth medium. The obtained results showed that MRSA was able to grow in rocket extract. In addition, proteome analysis using 2-DE method showed that MRSA strain COL is taking advantage of the sugar-, lipid-, and vitamin-rich substrate in the liquid rocket extract, although its growth was delayed in rocket extract compared to Luria-Bertani medium. This work could initiate further research about bacterial metabolism in plant-based media and defense mechanisms against plant-derived antibacterials.