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Background: Global estimates for cholera annually approximate 4 million cases worldwide with 95,000 deaths. Recent outbreaks, including Haiti and Yemen, are reminders that cholera is still a global health concern. Cholera outbreaks can rapidly induce high death tolls by overwhelming the capacity of health facilities, especially in remote areas or areas of civil unrest. Recent studies demonstrated that stool specimens preserved on filter paper facilitate molecular analysis of Vibrio cholerae in resource limited settings. Specimens preserved in a rapid, low-cost, safe and sustainable manner for sequencing provides previously unavailable data about circulating cholera strains. This may ultimately provide new information to shape public policy response on cholera control and elimination. Methodology/Principal findings: Whole genome sequencing (WGS) recovered close to a complete sequence of the V. cholerae O1 genome with satisfactory genome coverage from stool specimens enriched in alkaline peptone water (APW) and V. cholerae culture isolates, both spotted on filter paper. The minimum concentration of V. cholerae DNA sufficient to produce quality genomic information was 0.02 ng/μL. The genomic data confirmed the presence or absence of genes of epidemiological interest, including cholera toxin and pilus loci. WGS identified a variety of diarrheal pathogens from APW-enriched specimen spotted filter paper, highlighting the potential for this technique to explore the gut microbiome, potentially identifying co-infections, which may impact the severity of disease. WGS demonstrated that these specimens fit within the current global cholera phylogenetic tree, identifying the strains as the 7th pandemic El Tor. Conclusions: WGS results allowed for mapping of short reads from APW-enriched specimen and culture isolate spotted filter papers this provided valuable molecular epidemiological sequence information on V. cholerae strains from remote, low-resource settings. These results identified the presence of co-infecting pathogens while providing rare insight into the specific V. cholerae strains causing outbreaks in cholera-endemic areas. [ABSTRACT FROM AUTHOR]

Early industrialization and the development of cheap production processes for paper have led to an exponential accumulation of paper-based documents during the last two centuries. Archives and libraries harbor vast amounts of ancient and modern documents and have to undertake extensive endeavors to protect them from abiotic and biotic deterioration. While services for mechanical preservation such as ex post de-acidification of historic documents are already commercially available, the possibilities for long-term protection of paper-based documents against fungal attack (apart from temperature and humidity control) are very limited. Novel processes for mechanical enhancement of damaged cellulosic documents use Ionic Liquids (IL) as essential process components. With some of these ILs having azole-functionalities similar to well-known fungicides such as Clotrimazole, the possibility of antifungal activities of these ILs was proposed but has not yet been experimentally confirmed. We evaluated the potency of four ILs with potential application in paper restoration for suppression of fungal growth on five relevant paper-infesting molds. The results revealed a general antifungal activity of all ILs, which increased with the size of the non-polar group. Physiological experiments and ultimate elemental analysis allowed to determine the minimal inhibitory concentration of each IL as well as the residual IL concentration in process-treated paper. These results provide valuable guidelines for IL-applications in paper restoration processes with antifungal activity as an added benefit. With azoles remaining in the paper after the process, simultaneous repair and biotic protection in treated documents could be facilitated. [ABSTRACT FROM AUTHOR]

Background: The use of filter paper as a simple, inexpensive tool for storage and transportation of blood, ‘Dried Blood Spots’ or Guthrie cards, for diagnostic assays is well-established. In contrast, there are a paucity of diagnostic evaluations of dried cerebrospinal fluid (CSF) spots. These have potential applications in low-resource settings, such as Laos, where laboratory facilities for central nervous system (CNS) diagnostics are only available in Vientiane. In Laos, a major cause of CNS infection is Japanese encephalitis virus (JEV). We aimed to develop a dried CSF spot protocol and to evaluate its diagnostic performance using the World Health Organisation recommended anti-JEV IgM antibody capture enzyme-linked immunosorbent assay (JEV MAC-ELISA). Methodology and Principal Findings: Sample volumes, spotting techniques and filter paper type were evaluated using a CSF-substitute of anti-JEV IgM positive serum diluted in Phosphate Buffer Solution (PBS) to end-limits of detection by JEV MAC-ELISA. A conventional protocol, involving eluting one paper punch in 200μl PBS, did not detect the end-dilution, nor did multiple punches utilising diverse spotting techniques. However, pre-cut filter paper enabled saturation with five times the volume of CSF-substitute, sufficiently improving sensitivity to detect the end-dilution. The diagnostic accuracy of this optimised protocol was compared with routine, neat CSF in a pilot, retrospective study of JEV MAC-ELISA on consecutive CSF samples, collected 2009–15, from three Lao hospitals. In comparison to neat CSF, 132 CSF samples stored as dried CSF spots for one month at 25–30°C showed 81.6% (65.7–92.3 95%CI) positive agreement, 96.8% (91.0–99.3 95%CI) negative agreement, with a kappa coefficient of 0.81 (0.70–0.92 95%CI). Conclusions/Significance: The novel design of pre-cut filter paper saturated with CSF could provide a useful tool for JEV diagnostics in settings with limited laboratory access. It has the potential to improve national JEV surveillance and inform vaccination policies. The saturation of filter paper has potential use in the wider context of pathogen detection, including dried spots for detecting other analytes in CSF, and other body fluids. [ABSTRACT FROM AUTHOR]

A pilot-scale aerated lagoon was used for the aerobic treatment of pulp and paper mill effluent from September 1 to December 1, 2014. The aerated lagoon was installed at the chemistry laboratory in the Chemical Engineering Department at the Durango Institute of Technology and was fed with real pulp and paper mill effluent. The experimental work was run under various operating conditions. The operating parameters (total and volatile suspended solids (VSS) and dissolved oxygen concentration (DO)) and environmental variables (temperature, pH, COD, and BOD5 of influent water) were monitored daily. In all the experiments conducted, the aerated lagoon generated an effluent of optimal quality complying with the requirements of SEMARNAT (2003) and CONAGUA (2003). A model that explains the behavior of the system under realistic operating conditions was obtained. The model indicated an optimal DO of approximately 4 mg/L for concentrations up to 1000 mg/L, showing variations in concentrations above this value. This data indicate that the flexibility of the bacterial formulation and its ability to adapt to environmental changes play an important role in the stability of an aerated lagoon. [ABSTRACT FROM AUTHOR]

Rupert Jethro Best (1903–91), working alone at the Waite Agricultural Research Institute in Adelaide between 1934 and 1937, was among the first to purify tobacco mosaic virus (TMV) and to propose that it was a complex macromolecule containing protein and another reactive group that was responsible for infectivity of the virus. However, his research was completely overshadowed by that of Wendell Stanley and the duo of Frederick Bawden and Norman (aka Bill) Pirie, working in the United States of America and Great Britain, respectively, to the point where Best is not even mentioned in modern histories of TMV. Many factors have contributed to this lack of recognition for Best. Professor James Prescott, a soil scientist and Best's supervisor at the Waite Institute, failed to appreciate the significance of his research, leading to critical delays in publication that prevented him from claiming precedence for purifying TMV. When Best's research was eventually published, it was in Australian journals that were not broadly distributed, resulting in minimal international exposure for his research. The plant virology community within which he worked in Australia was very small and entirely focused on plant disease control, and not concerned with fundamental questions about the composition of viruses. Communication with similarly interested scientists in the Northern Hemisphere was hindered by the great distances involved. In this paper, pioneering research done by Best on TMV is reviewed, and placed in context with that undertaken by Stanley and by Bawden and Pirie, who are best remembered for purifying TMV and characterising its physicochemical properties. Rupert Jethro Best, working alone in Adelaide at the Waite Agricultural Research Institute, was among the first to purify tobacco mosaic virus and to provide evidence that it was a heterogeneous macromolecule, composed mainly of protein but also small prosthetic groups with the properties of a weak acid, wherein lay the activity of the virus. This paper describes the contributions of Rupert Best to early theories on the material nature and mode of reproduction of viruses. Photographer unknown, State Library of South Australia. [ABSTRACT FROM AUTHOR]

Biosensors have emerged as a valuable tool with high specificity and sensitivity for fast and reliable detection of hazardous substances in drinking water. Numerous substances have been addressed using synthetic biology approaches. However, many proposed biosensors are based on living, genetically modified organisms and are therefore limited in shelf life, usability and biosafety. We addressed these issues by the construction of an extensible, cell-free biosensor. Storage is possible through freeze drying on paper. Following the addition of an aqueous sample, a highly efficient cell-free protein synthesis (CFPS) reaction is initiated. Specific allosteric transcription factors modulate the expression of ‘superfolder’ green fluorescent protein (sfGFP) depending on the presence of the substance of interest. The resulting fluorescence intensities are analyzed with a conventional smartphone accompanied by simple and cheap light filters. An ordinary differential equitation (ODE) model of the biosensors was developed, which enabled prediction and optimization of performance. With an optimized cell-free biosensor based on the Shigella flexneri MerR transcriptional activator, detection of 6 μg/L Hg(II) ions in water was achieved. Furthermore, a completely new biosensor for the detection of gamma-hydroxybutyrate (GHB), a substance used as date-rape drug, was established by employing the naturally occurring transcriptional repressor BlcR from Agrobacterium tumefaciens. [ABSTRACT FROM AUTHOR]

Background: The lack of information regarding the burden of acute bacterial meningitis in Latin America leads to a reduction in the estimated incidence rates of the disease, and impairs public health decisions on the use and follow-up of preventive interventions, particularly, the evaluation of existing vaccination policies. The use of the real-time PCR in diagnostic routine procedures has resulted in a substantial increase in confirmed bacterial meningitis cases. However, in resource-poor countries, these assays are only available in reference laboratories. Sample transportation to these laboratories is a critical constraint, as it requires specialized, high cost courier services. To overcome this barrier we evaluated the use of FTATM Elute filter paper cards for the conservation and processing of samples under normal environmental conditions, as they would be when transported from remote and under-equipped healthcare facilities to the reference centers. A total of 401 samples received in 2015 as part of Sao Paulo’s national surveillance for routine diagnosis were selected for this study. Methods: The sensitivity and specificity of real-time PCR were evaluated using fresh serum and cerebrospinal fluid (CSF) samples processed using our laboratory’s standard DNA extraction, and processing the same samples after being dried and stored on FTATM card, and DNA extracted following the manufacturer’s instructions. Results: The sensitivities for detection of Neisseria meningitidis, Streptococcus pneumoniae, and Haemophilus influenzae from CSF dried and stored on FTATM cards were 98%, 92%, and 100%, respectively, and with serum samples were 73%, 88%, and 100%, respectively. When compared to our laboratory’s standard methodology, results showed high concordance, with Kappa index ranges of 0.9877–1.00 for CSF, and 0.8004–1.00 for serum samples. Conclusion: The use of FTATM cards for CSF and serum conservation and transport represents a rapid, reliable, and cost-effective alternative that will allow obtaining valuable epidemiological information that would otherwise be lost. [ABSTRACT FROM AUTHOR]

Pyocyanin is a toxin produced by Pseudomonas aeruginosa. Here we describe a novel paper-based electrochemical sensor for pyocyanin detection, manufactured with a simple and inexpensive approach based on electrode printing on paper. The resulting sensors constitute an effective electrochemical method to quantify pyocyanin in bacterial cultures without the conventional time consuming pretreatment of the samples. The electrochemical properties of the paper-based sensors were evaluated by ferri/ferrocyanide as a redox mediator, and showed reliable sensing performance. The paper-based sensors readily allow for the determination of pyocyanin in bacterial cultures with high reproducibility, achieving a limit of detection of 95 nM and a sensitivity of 4.30 μA/μM in standard culture media. Compared to the similar commercial ceramic based sensors, it is a 2.3-fold enhanced performance. The simple in-house fabrication of sensors for pyocyanin quantification allows researchers to understand in vitro adaptation of P. aeruginosa infections via rapid screenings of bacterial cultures that otherwise are expensive and time-consuming. [ABSTRACT FROM AUTHOR]

The main goal of this work was to reinforce softwood pulp (SP) with bacterial cellulose (BC) to generate a sustainable biocomposite. BC is a nanocellulose, which was anticipated to increase interfacial adhesion between the cellulosic fibers and BC. The organism used was Gluconacetobacter xylinus , which was incubated in a static Hestrin-Schramm culture at 28 °C for 14 days. The specimens of BC, SP and the reinforced SP with BC were characterized using X-ray diffraction (XRD), FT-IR, FESEM, and physico-mechanical testing. The crystallinity index was found to be 83 and 54% for BC and SP, respectively. FT-IR spectra showed that the composition of BC was fully different from that of SP fibers. Based on FESEM images, one can conclude that BC and softwood fibers do form a good combination with a nonporous structure. BC fibers fill in among the softwood fibers in the sheet. The physical and mechanical properties showed that as the dosage of BC increased, the properties of tensile index, tear index, and burst index greatly improved, while the porosity and the elongation decreased. The reason for the improved mechanical properties can be attributed to the increase of interfibrillar bonding which reduced porosity. This would be due to the high aspect ratio of BC that is capable of connecting between the cellulosic fibers and BC nanofibers, enhancing a large contact surface and therefore producing excellent coherence. This study suggests that BC could be a promising material for reinforcing composites at low loading. [ABSTRACT FROM AUTHOR]

Virtual Reality (VR) laboratories are a new pedagogical approach to support psychomotor skills development in undergraduate programmes to achieve practical competency. VR laboratories are successfully used to carry out virtual experiments in science courses and for clinical skills training in professional courses. This paper describes the development and evaluation of a VR-based microbiology laboratory on Head-Mounted Display (HMD) for undergraduate students. Student and faculty perceptions and expectations were collected to incorporate into the laboratory design. An interactive 3-dimensional VR laboratory with a 360° view was developed simulating our physical laboratory setup. The laboratory environment was created using Unity with the (created) necessary assets and 3D models. The virtual laboratory was designed to replicate the physical laboratory environment as suggested by the students and faculty. In this VR laboratory, six microbiology experiments on Gram staining, bacterial streaking, bacterial motility, catalase test, oxidase test and biochemical tests were placed on the virtual platform. First-year biomedical science students were recruited to evaluate the VR laboratory. Students' perception of the virtual laboratory was positive and encouraging. About 70% of the students expressed they felt safe using the VR laboratory and that it was engaging. They felt that the VR laboratory provided an immersive learning experience. They appreciated that they could repeat each experiment multiple times without worrying about mistakes or mishaps. They could personalise their learning by concentrating on the specific experiments. Our in-house VR-based microbiology laboratory was later extended to other health professions programmes teaching microbiology. [ABSTRACT FROM AUTHOR]

This paper investigates the correlation of ResearchGate among the faculties of sciences in the central universities of North-East India using Altmetrics approaches. As more innovation is seen and the discipline is in its early stages, the Department of Biotechnology and Microbiology is the primary study area. The study focuses primarily on faculty activities on the ResearchGate platform, which include frequency of publications, citations, research interest, number of followers and followings, and various publication formats. It has also sparked interest in determining the relationships between different ResearchGate metrics. According to the study, most faculties have good citation scores and an average number of publications. The survey analysis reveals a lack of awareness, concentration, and dedication to the development of the disciplines. The result of the investigation shall serve as a pathway for various future goals for selfimprovement. [ABSTRACT FROM AUTHOR]

The human oral cavity is normally colonized by microorganisms including bacteria, fungi, archaea, viruses and protozoa. The aim of this study was to determine the frequency of Candida spp., in de oral cavity in a group of medical students from the north of Mexico. Oral sample were obtained from 240 healthy students. The specimens were analyzed by traditional microbiology cultures and DNA sequencing. Candida spp., grew in Sabouraud dextrose agar from 57 samples and subsequently were isolated and phenotyped. The definitive identification to the species level was done by sequence analysis. The yeasts were identified as follow: 28 Clavispora lusitaniae, 20 Candida albicans, 5 Pichia kudriavzevii and 4 Candida parapsilosis. Our findings revealed that 23.75% of the healthy population has a potential pathogen in their mouth. Surprisingly, C. albicans is not the predominant yeast; instead other non-Candida species are the colonizers of the oral cavity as normal microbiota. C. lusitaniae is considered an emerging opportunistic pathogen in immunosuppressive patients. This paper pretends to highlight the presence of this yeast in the oral cavity in immunocompetent young adults. [ABSTRACT FROM AUTHOR]

Culture conditions for the production of cellulase-free endo-β-1,4-xylanase by an alkalophilic strain of Bacillus subtilis SD8 (BsSD8-xylanase) isolated from paper mill effluent were optimized using 2 factorial design and response surface methodology. Statistical analysis of results showed that the linear and quadratic terms and interaction of 4 variables (temperature, pH, inoculum size and xylan concentration) had significant effects. The optimal conditions for production of the enzyme were: 37.5°C, initial pH of 8.5, inoculum size of 8.5% and xylan concentration of 2%. The predicted and verified BsSD8-xylanase activities under optimal conditions were 8.18 IU/mL. Analysis revealed that the enzyme gene consists of an ORF of 642 bp encoding a protein of 213 amino acids with a molecular mass of 23.5 kDa and pI of 9.67. Secondary and tertiary structure prediction using SOPMA and SWISS model showed a maximum homology of 95.14% with β1,4-xylanase (PDB Id.: 1BVV) of Bacillus circulans obtained from protein data bank. The results of the study indicate that this enzyme presents a potentially effective xylan-biodegrading tool that could be useful for pulp and paper biobleaching. [ABSTRACT FROM AUTHOR]

As more HIV-infected people gain access to antiretroviral therapy (ART), monitoring HIV drug resistance (HIVDR) becomes essential to combat both acquired and transmitted HIVDR. Studies have demonstrated dried blood spots (DBS) are a suitable alternative in HIVDR monitoring using DBS collected on Whatman 903 (W-903). In this study, we sought to evaluate two other commercially available filter papers, Ahlstrom 226 (A-226) and Munktell TFN (M-TFN), for HIVDR genotyping following ambient temperature storage. DBS were prepared from remnant blood specimens collected from 334 ART patients and stored at ambient temperature for a median time of 30 days. HIV-1 viral load was determined using NucliSENS EasyQ® HIV-1 v2.0 RUO test kits prior to genotyping of the protease and reverse transcriptase regions of the HIV-1 pol gene using an in-house assay. Among the DBS tested, 26 specimens had a viral load ≥1000 copies/mL in all three types of filter paper and were included in the genotyping analysis. Genotyping efficiencies were similar between DBS collected on W-903 (92.3%), A-226 (88.5%), and M-TFN (92.3%) filter papers (P = 1.00). We identified 50 DR-associated mutations in DBS collected on W-903, 33 in DBS collected on A-226, and 48 in DBS collected on M-TFN, resulting in mutation detection sensitivities of 66.0% for A-226 and 88.0% for M-TFN when compared to W-903. Our data indicate that differences among filter papers may exist at this storage condition and warrant further studies evaluating filter paper type for HIVDR monitoring. [ABSTRACT FROM AUTHOR]

This article is an editorial for a thematic issue on Polar and Alpine Microbiology in the journal FEMS Microbiology Ecology. The issue focuses on the microbial ecology of cold habitats and the importance of understanding the biodiversity and functional roles of microorganisms in these environments. The issue includes 30 peer-reviewed papers, most of which were presented at the 9th International Conference on Polar and Alpine Microbiology (PAM22). The papers cover a range of topics, including microbial communities, adaptation, carbon and nitrogen turnover, and plant-microbe interactions, with a particular emphasis on Arctic, mountain, and Antarctic regions. The issue is dedicated to the late researcher S. Craig Cary, who made significant contributions to the study of microbial life in extreme environments. [Extracted from the article]

Objective: Robust scientific and clinical evidence of how to appropriately manage denture plaque is lacking. This two-part study (i) developed an in vitro model of denture plaque removal, and (ii) assessed effectiveness of these approaches in a randomised clinical trial. Method: (i) a complex denture plaque model was developed using the dominant microbial genera from a recent microbiome analyses. Biofilms formed on polymethylmethacrylate were brushed daily with a wet toothbrush, then either treated daily for 5 days or only on Days 1 and 5 with Polident® denture cleanser tablets (3 min soaking). Quantitative and qualitative microbiological assessments were performed. (ii), an examiner-blind, randomised, crossover study of complete maxillary denture wearers was performed (n = 19). Either once-daily for 7 days or on Day 7 only, participants soaked dentures for 15 min using Corega® denture cleansing tables, then brushed. Denture plaque microbiological assessment used sterilized filter paper discs. Results: The in vitro model showed daily cleaning with denture cleanser plus brushing significantly reduced microbial numbers compared to intermittent denture cleaning with daily brushing (p < 0.001). The clinical component of the study showed a statistically significant reduction in denture plaque microbial numbers in favour of daily versus weekly treatment (aerobic bacteria p = 0.0144). Both in vitro and in vivo studies showed that denture plaque biofilm composition were affected by different treatment arms. Conclusions: This study demonstrated that daily denture cleansing regimens are superior to intermittent denture cleansing, and that cleansing regimens can induce denture plaque compositional changes. Clinicaltrials.gov registration: NCT02780661. [ABSTRACT FROM AUTHOR]

This document is a correction for an article titled "Vibrio fischeri Possesses Xds and Dns Nucleases That Differentially Influence Phosphate Scavenging, Aggregation, Competence, and Symbiotic Colonization of Squid." The correction addresses specific experiments that were repeated and confirms the previous findings regarding the nuclease activity of the xds mutant strain. The timing of measurable Dns activity was found to vary slightly, but these results do not change the conclusions of the original publication. The corrected and republished paper is available for further reference. [Extracted from the article]

The paper presents the results of a study aimed at evaluating whether prolonged consumption of a probiotic drink consisting of protective microorganisms (lactobacilli, enterococci, and bifidobacteria) and fermented from Saccaromyces would be beneficial to the human microbiological status and function of gastrointestinal tract (GIT). Ten volunteers (two males and eight females above 50 years of age) consumed the drink over the period of 3 months. We investigated microbiota of the intestine, upper airway (UA), and vagina (in females). Microbial samples from the intestine and UA were gathered four times: a week prior to the experiment and then every 30 days. Samples of the vaginal discharge were taken 7–10 days prior to the experiment and 7–10 after its completion. Evaluation of the gastric emptying function, hydrochloric acid production, fasting volume of the gastric juice, and GIT electrical activity was also performed at these time points. The experiment revealed positive trends of the intestinal microbiota. Changes in the species and quantitative composition of the UA microbiota were less pronounced as in the first half of the experiment changes in the UA microbiota were more like negative and displayed a marked positive trend in the second half. After the course of probiotic prophylaxis, colonization of the vagina and cervical channel by opportunistic microorganisms was reduced in six out of eight females. In addition, the probiotic drink stabilized the electrical activity of all GIT components and enhanced intestinal peristalsis. [ABSTRACT FROM AUTHOR]

• Coupling of demographic and environmental noise balances the effect of selection. • Fast switching effectively reduces the selection intensity. • New fixation scenarios: success depends on environmental variability. • EN makes the RPS competition more egalitarian, but does not prolong coexistence. Rock-paper-scissors games metaphorically model cyclic dominance in ecology and microbiology. In a static environment, these models are characterized by fixation probabilities obeying two different "laws" in large and small well-mixed populations. Here, we investigate the evolution of these three-species models subject to a randomly switching carrying capacity modeling the endless change between states of resources scarcity and abundance. Focusing mainly on the zero-sum rock-paper-scissors game, equivalent to the cyclic Lotka–Volterra model, we study how the coupling of demographic and environmental noise influences the fixation properties. More specifically, we investigate which species is the most likely to prevail in a population of fluctuating size and how the outcome depends on the environmental variability. We show that demographic noise coupled with environmental randomness "levels the field" of cyclic competition by balancing the effect of selection. In particular, we show that fast switching effectively reduces the selection intensity proportionally to the variance of the carrying capacity. We determine the conditions under which new fixation scenarios arise, where the most likely species to prevail changes with the rate of switching and the variance of the carrying capacity. Random switching has a limited effect on the mean fixation time that scales linearly with the average population size. Hence, environmental randomness makes the cyclic competition more egalitarian, but does not prolong the species coexistence. We also show how the fixation probabilities of close-to-zero-sum rock-paper-scissors games can be obtained from those of the zero-sum model by rescaling the selection intensity. [ABSTRACT FROM AUTHOR]

Recognising effects of care departs from previous conceptions of care within science education as an idealised, ethical, and normative dimension of being, thinking and relating. In this article, we hesitate with care's moralistic qualities to render visible disruptive and complicit moments of care in complex ethical and political situated practices. We follow care inside a college microbiology laboratory, documenting three practices: caring for bacteria, caring for logbooks, and caring for a nation. We show how these care practices potentialise/disrupt bacteria as technoscientific commodities and biotechnicians as a labour force for markets and nations organised along racial and gendered lines. Our paper attends to the complexities of care as an assembling force with its ambivalent ethical and political orientations. We conclude by reflecting on the possibilities of 'care-full' science educational analyses. How can we better care for care? What might care offer science education research and practice that other more popular explanatory units (such as concepts and effectiveness) do not? [ABSTRACT FROM AUTHOR]

Hackathons are collaborative events that bring together diverse groups to solve predefined challenges. The COVID-19 pandemic caused by SARS-CoV-2 has emphasized the need for portable and reproducible genomics analysis pipelines to study the genetic susceptibility of the human host and investigate human-SARS-CoV-2 protein interactions. To build and strengthen institutional capacities in OMICS data analysis applied to host-pathogen interaction (HPI), the PHINDaccess project organized two hackathons in 2020 and 2021. These hackathons are aimed at developing bioinformatics pipelines related to the SARS-CoV-2 viral genome, its phylodynamic transmission, and the identification of human genome host variants, with a focus on addressing global health challenges, particularly in low- and middle-income countries (LMIC). This paper outlines the preparation, proceedings, and lessons learned from these hackathons, including the challenges faced by participants and our recommendations based on our experience for organizing hackathons in LMIC and beyond. [ABSTRACT FROM AUTHOR]

Maintaining a healthy balance between commensal, and pathogenic bacteria within the gut microbiota is crucial for ensuring the overall health, and well-being of the host. In fact, by affecting innate, and adaptive immune responses, the gut microbiome plays a key role in maintaining intestinal homeostasis and barrier integrity. Dysbiosis is the loss of beneficial microorganisms and the growth of potentially hazardous microorganisms in a microbial community, which has been linked to numerous diseases. As the primary inducer of circadian rhythm, light can influence the human intestinal microbiome. Photobiomodulation therapy (PBMT), which is the use of red (630-700 nm), and near-infrared light (700 and 1200 nm), can stimulate healing, relieve pain, and reduce inflammation, and affect the circadian rhythm and gut microbiome beneficially. Our focus in this paper is on the effects of PBMT on gut microbiota, to provide an overview of how it can help control gut microbiota dysbiosis-related disorders. [ABSTRACT FROM AUTHOR]

Soil harbors a huge diversity of microorganisms and serves as the ecological and social foundation of human civilization. Hence, soil health management is of utmost and consistent importance, aligning with the United Nations Sustainable Development Goals. One of the most hazardous contaminants in soil matrix is potentially toxic elements (PTEs), which can cause stress in soil indigenous microorganisms and severely jeopardize soil health. Biochar technology has emerged as a promising means to alleviate PTE toxicity and benefit soil health management. Current literature has broadly integrated knowledge about the potential consequences of biochar-amended soil but has focused more on the physical and chemical responses of the soil system than microbiological attributes. In consideration of the indispensable roles of soil microbials, this paper first introduces PTE-induced stresses on soil microbials and then proposes the mechanisms of biochar's effects on soil microbials. Finally, microbial responses including variations in abundance, interspecific relationships, community composition and biological functions in biochar-amended soil are critically reviewed. This review thus aims to provide a comprehensive scientific view on the effect of biochar on soil microbiological health and its management. Highlights: Sketched a mechanistic overview of PTE-induced stress towards soil microorganisms. Demonstrated a synopsis of biochar impacts on soil microbiota from both direct and indirect pathways. Discussed the development prospects of biochar technology aiming for a healthier agro-ecosystem. [ABSTRACT FROM AUTHOR]

This review, for the occasion of the 40th anniversary of the Journal of Antimicrobial Chemotherapy (JAC), gives an overview of the manuscripts related to veterinary bacteriology published in the journal in the past 40 years with a focus on 'One Health' aspects. From 1975 to 2000 the number of manuscripts related to veterinary medicine was limited, but thereafter, the number steadily increased. Most manuscripts published were related to food-producing animals, but companion animals and minor species were also covered. Subjects included antimicrobial usage in animals and the consequences for human medicine, new resistance genes and mechanisms, the prevalence and epidemiology of antimicrobial resistance, and the emergence of resistant bacteria in animals with zoonotic potential such as livestock-associated MRSA (LA-MRSA), methicillin-resistant Staphylococcus pseudintermedius (MRSP) and ESBL-producing Enterobacteriaceae. These manuscripts have added to our knowledge on the risks of transmission of resistant bacteria from animals to humans and the importance of the prudent use of antimicrobial agents in veterinary medicine. [ABSTRACT FROM AUTHOR]

Microbiology is an area with a high research production, classified in different branches. Thus, it is difficult to identify research trends without many backgrounds. The present paper aims to apply bibliometric methods to identify the highly cited papers that contribute to the Microbiology development. Furthermore, a science mapping analysis allows discovering the main thematic areas covered by those detected papers. From the 572 153 papers (articles and reviews) indexed in the Web of Science Microbiology category (1900–2017), a total of 645 highly cited papers were detected. Concerning the main scientific producers in Microbiology, Applied and Environmental Microbiology as a journal, R. Knight from the University of Colorado (USA) as an author and the USA as a country are the most productive actors. Nevertheless, taking into account the gross domestic product per capita, China and Spain are remarkable countries. Furthermore, according to the relative priority index (RPI), Denmark, Belgium, Spain and The Netherlands are the countries that make a higher scientific effort in this field. About the co-word analysis, several important themes were detected, such as Next Generation Sequencing, Gene, Escherichia Coli or Gene Expression. Concerning these results, this work supposes a framework on which to base future research. [ABSTRACT FROM AUTHOR]

In order to better achieve the ideological and political teaching objectives of Microbiology, and on the basis of the established class hours, to achieve the goal of not reducing professional knowledge points, while also achieving moral education, patriotism, and professional dedication education, a reform of the teaching mode of microbiology has been carried out. This paper introduces the author’s team through the reform of microbiology teaching mode, the introduction of classic cases in each chapter, the development of relevant microbiology knowledge, the digging of ideological and political elements from examples, and the organic integration of ideological and political education into microbiology teaching content. Students’ thinking is developed, patriotism and scientific learning enthusiasm are stimulated, and correct life and values are established through modern teaching methods and enhancing the interaction between teachers and students. [ABSTRACT FROM AUTHOR]

From the very beginning of his adventures in the DC universe, the Joker has been associated with science, particularly (bio)chemistry and microbiology. Exploring some recently published narrative examples of Joker science together with the insight provided by virology and chemistry, this paper examines the scientific and cultural ideas of science conveyed by the violent clown and his scientific extravaganzas. Psychopathic, mannerist Joker science, this paper shows, is intrinsically linked to the realms of hypnotism, hysteria, ecstasy and the 'hysterical realities' of different historical, physical, medial and cultural settings. Joker science is not only about how chemistry and virology might affect the human body but it also explores notions of possession and control – contemporary notions of what was once investigated as 'criminal suggestion' or 'hypnotic crimes' on science stages and in early film. Joker science 'jokerises': it leads to loss of motor control, muscular contortions, cramps, fatal convulsions and frenetic, deadly laughter, reminiscent of the 'strange spectacle' of hysterics and the 'science performances' and 'hystericulture' developed by the showman and researcher Charcot and his many fictional revenants, all characterised by a peculiar position between science, entertainment and the occult. [ABSTRACT FROM AUTHOR]

Purpose: The increased demand for high-quality, nutritionally rich processed food has led to non-thermal food processing technologies like high pressure processing (HPP), a novel process for microbial inactivation with minimal loss of nutritional and sensory properties. The purpose of this paper is to highlight the impact of HPP on the microbiological, nutritional and sensory properties of food. Design/methodology/approach: Recent research on the role of HPP in maintaining food quality and safety and the impact of process conditions with respect to various food properties have been explored in this paper. Also, the hurdle approach and the effectiveness of HPP on food quality have been documented. Findings: HPP has been verified for industrial application, fulfilling the consumer demand for processed food with minimum nutrition loss at low temperatures. The positive impact of HPP with other treatments is known as the hurdle approach that enhances its impact against microorganism activity and minimizes the effects on nutrition and sensory attributes. Originality/value: This paper highlights the impact of HPP on various food properties and a good alternative as non-thermal technology for maintaining shelf life, sensory properties and retention of nutrients. [ABSTRACT FROM AUTHOR]

Nicola Low and colleagues announce a call for research papers on sexually transmitted infections, to accompany a Collection on the topic. [ABSTRACT FROM AUTHOR]

The teaching of microbiology at the university needs to overcome several difficulties and barriers to develop knowledge in the area, both by the professor and by the students. The main obstacle associated with teaching microbiology today is related to the object of study itself, since the universe of microorganisms is invisible to our eyes, requiring extra effort from educators and students. Practical microbiology classes are an important tool for this content. However, they had to be developed in alternative ways with remote classes in the pandemic. This paper describes a microbiology teaching model based on problem solving. The target audience was 89 students of the Degree in Biological Sciences. The proposal was divided into three stages: presentation of the disease, discussion of the problem and research work in the search for answers to the proposed problems. The activities were stimulating, inducing the active participation of most of the students, there was a commitment in carrying out the tasks and gaining knowledge, despite the initial difficulties pointed out. In higher education, there is a lack of interest or opportunity to use the most innovative teachinglearning tools, as it implies the search for knowledge. [ABSTRACT FROM AUTHOR]

Collectively, we have been reviewers for microbial ecology, genetics and genomics studies that include environmental DNA (eDNA), microbiome studies, and whole bacterial genome biology for Microbial Ecology and other journals for about three decades. Here, we wish to point out trends and point to areas of study that readers, especially those moving into the next generation of microbial ecology research, might learn and consider. In this communication, we are not saying the work currently being accomplished in microbial ecology and restoration biology is inadequate. What we are saying is that a significant milestone in microbial ecology has been reached, and approaches that may have been overlooked or were unable to be completed before should be reconsidered in moving forward into a new more ecological era where restoration of the ecological trajectory of systems has become critical. It is our hope that this introduction, along with the papers that make up this special issue, will address the sense of immediacy and focus needed to move into the next generation of microbial ecology study. [ABSTRACT FROM AUTHOR]

This scientific paper determined the microbiological quality of Macedonian white brined cheese. Four best variants of Macedonian white brined cheeses were analysed for their microbiological parameters. From pathogenic microflora the following parameters were examined: a total number of: Coliforms, E. coli, pathogenic staphylococci, Molds, Yeast, Listeria and Salmonella. From lactic acid bacteria the following parameters were examined: the total number of Lactococcus bacteria and the total number of Lactobacillus bacteria. In all examined cheese samples pathogenic bacteria were not detected. Lactococcus bacteria was dominant bacteria in all four cheese variants at the beginning of ripening period till day 20. After that and at the end of ripening period (60 day) the Lactobacillus bacteria were predominant. [ABSTRACT FROM AUTHOR]

Post-Mortem Microbiology (PMM) aims to detect infections that could be a cause of stillbirth. A newborn having no sign of life after delivery is defined as stillbirth. Different infections could cause a chain of events leading to stillbirth but the relationships between maternal infection and stillbirth are often not very clear; as a matter of fact, the positive serologic tests do not prove causality. Screening, prevention, and treatment of maternal infections are important to reduce the stillbirth risk. The identification of an infectious agent that causes stillbirth through PMM is a shared aim by microbiologists, pathologists and surgeons, and it is also the common goal in clinical and forensic autopsies. The aim of this paper is a review the major infections that lead to stillbirths. [ABSTRACT FROM AUTHOR]

Routine microbiology results are a valuable source of antimicrobial resistance (AMR) surveillance data in low- and middle-income countries (LMICs) as well as in high-income countries. Different approaches and strategies are used to generate AMR surveillance data. We aimed to review strategies for AMR surveillance using routine microbiology results in LMICs and to highlight areas that need support to generate high-quality AMR data. We searched PubMed for papers that used routine microbiology to describe the epidemiology of AMR and drug-resistant infections in LMICs. We also included papers that, from our perspective, were critical in highlighting the biases and challenges or employed specific strategies to overcome these in reporting AMR surveillance in LMICs. Topics covered included strategies of identifying AMR cases (including case-finding based on isolates from routine diagnostic specimens and case-based surveillance of clinical syndromes), of collecting data (including cohort, point-prevalence survey, and case–control), of sampling AMR cases (including lot quality assurance surveys), and of processing and analysing data for AMR surveillance in LMICs. The various AMR surveillance strategies warrant a thorough understanding of their limitations and potential biases to ensure maximum utilization and interpretation of local routine microbiology data across time and space. For instance, surveillance using case-finding based on results from clinical diagnostic specimens is relatively easy to implement and sustain in LMIC settings, but the estimates of incidence and proportion of AMR is at risk of biases due to underuse of microbiology. Case-based surveillance of clinical syndromes generates informative statistics that can be translated to clinical practices but needs financial and technical support as well as locally tailored trainings to sustain. Innovative AMR surveillance strategies that can easily be implemented and sustained with minimal costs will be useful for improving AMR data availability and quality in LMICs. [ABSTRACT FROM AUTHOR]

In the course of the past two decades, biodegradable polymers have established to serve in form of compostable or soil-biodegradable items as sustainable alternatives to standard plastics in applications where their property of biodegradability adds value. BASF has been a pioneer in this field of action with their commercially available products ecoflex® and ecovio®. Based on continuous research and development at the edge between polymer chemistry and microbiology, not only new developments were realized in the recent past but also a deep understanding about biodegradation under various conditions could be generated. This chapter provides an up-to-date picture about the chemistry and biodegradation, about processing, applications as well as the sustainability contribution of ecoflex® and ecovio®. [ABSTRACT FROM AUTHOR]

Introduction: An evidence synthesis approach compiling biological/laboratory data is effective in advancing health‐related knowledge. However, this approach is still underused in the oral health field. Methods: This commentary discusses the opportunities and challenges of systematic and scoping reviews of laboratory data in dentistry. Special focus is on the potential of these reviews to elucidate etiological and treatment concepts of oral diseases, such as periodontitis and peri‐implantitis. Results: The following difficulties associated with such studies are discussed: (i) selection of ideal study design, (ii) assessment of "risk of bias" and definition of "certainty of evidence", (iii) evidence assembly and summary, and (iv) the paper review process. Discussion: Despite those challenges, high‐quality reviews integrating laboratory data may generate relevant scientific information and help identify new avenues for future investigations. Experts in different oral health topics should build a process capable of helping researchers assemble and interpret these types of data. [ABSTRACT FROM AUTHOR]

The paper presents brief results of comprehensive studies of waters of the Tatar Strait and Sea of Japan, obtained on cruise 79 of the R/V Professor Gagarinsky in May–June 2022. The distribution of geophysical fields was obtained, the block's divisibility of the bottom of the water area was confirmed, and new data was obtained on the distribution of gases in the sedimentary sequence, bottom, and surface water. The electrokinetic parameters of microorganisms for evaluating their relationship with methane concentration was obtained, and micropalentological analysis of sedimentary deposits was performed. [ABSTRACT FROM AUTHOR]

I Microbiology Research i was able to uphold its high standards for published papers due to the outstanding efforts of our reviewers. Thanks to the efforts of our reviewers in 2022, the median time to first decision was 15 days and the median time to publication was 35 days. MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. [Extracted from the article]

Cellular microbiology, which is the interaction between harmful microbes and infected cells, is important in the determination of the bacterial infection processes and in the progression of data of different cellular mechanisms. The therapeutic role of bacteria has gained attention since the known methods such as radiation, chemotherapy, and immunotherapy have got drawbacks. Bacteria have demonstrated a favorable impact in treating cancer through eradication of tumors. Bacteria, in cancer treatment, have proven to be promising and have been shown in some of the previous work that it can successfully suppress the growth of tumors. In this paper, we analyzed the difficulties and settlement for using bacteria in cancer therapy as well the mechanisms in which bacteria works in order to achieve tumor eradication. Future works may focus on the use of bacteria along with other treatments in order to achieve effective tumor therapy. [ABSTRACT FROM AUTHOR]

Simple Summary: This paper presents an extended version of the Cox regression model to examine heterogeneous effects of risk factors on disease subtypes defined by a continuous biomarker. This approach can be easily applied to cancer studies and is accessible to researchers via user-friendly R scripts. Molecular pathologic diagnosis is important in clinical (oncology) practice. Integration of molecular pathology into epidemiological methods (i.e., molecular pathological epidemiology) allows for investigating the distinct etiology of disease subtypes based on biomarker analyses, thereby contributing to precision medicine and prevention. However, existing approaches for investigating etiological heterogeneity deal with categorical subtypes. We aimed to fully leverage continuous measures available in most biomarker readouts (gene/protein expression levels, signaling pathway activation, immune cell counts, microbiome/microbial abundance in tumor microenvironment, etc.). We present a cause-specific Cox proportional hazards regression model for evaluating how the exposure–disease subtype association changes across continuous subtyping biomarker levels. Utilizing two longitudinal observational prospective cohort studies, we investigated how the association of alcohol intake (a risk factor) with colorectal cancer incidence differed across the continuous values of tumor epigenetic DNA methylation at long interspersed nucleotide element-1 (LINE-1). The heterogeneous alcohol effect was modeled using different functions of the LINE-1 marker to demonstrate the method's flexibility. This real-world proof-of-principle computational application demonstrates how the new method enables visualizing the trend of the exposure effect over continuous marker levels. The utilization of continuous biomarker data without categorization for investigating etiological heterogeneity can advance our understanding of biological and pathogenic mechanisms. [ABSTRACT FROM AUTHOR]

On 17 September 1683, Antonie van Leeuwenhoek, a Dutch merchant who lacked formal education and fortune, wrote a letter to the Royal Society of London describing for the first time a single-celled organism. As a tribute to this revolutionary discovery, the Portuguese Society of Microbiology with the support of the Federation of European Microbiological Societies in 2017, designated this day as International Microorganism Day (IMD), a day aiming to raise awareness about the wonderful world of microbes. Six years after the establishment of IMD, the knowledge of microbiology outreach around this celebration has expanded greatly, with 5 years of in-person and 2 years of online events. The peak of these commemorations was in 2023, with 63 parallel outreach events and more than 5000 attendees, most of which were children, and young adults. While these in-person events were occurring in the month of September, the #InternationalMicroorganismDay hashtag reached nearly 2.3 million people online, reflecting the number of users who have seen a post containing this hashtag on social media. Using a decentralized model to facilitate 63 grass-roots teams to organize events locally, IMD achieved global representation both online and offline. This paper presents details behind the organization and data on the international impact of the IMD 2022 and 2023 events, outlines plans to expand reach to more countries and audiences, and encourages readers to participate with their own events in future IMD editions so that global impact can be expanded even further. [ABSTRACT FROM AUTHOR]

Though in the past, serious concerns have been raised about students' interest and learning gains in STEM courses, not much research has been done to examine the differences in learning science at community colleges and universities. The purpose of this paper is to close this gap. This paper analyzes the influence of students' demographics, preparedness, major, and attitudes on their learning gains in an introductory microbiology class at a community college vs. a university. Student demographics, information about their preparedness level, major, and attitudes were collected in a questionnaire and students' learning gains were assessed by comparing student performance on a pre- and post-test on four different topics in microbiology. Our results indicate that students' majors and attitudes such as their willingness to actively participate in the classroom discussions and spend time outside the classroom to learn are major factors that enhance their learning. Age and marital status positively impact learning gains while gender, employment status, and citizenship status show no impact on learning gains in students. Our results also indicate that students at the community college who had less exposure to science classes in high school or biology classes in college achieved statistically higher learning gains despite having overall lower scores on two of the four post-tests. [ABSTRACT FROM AUTHOR]

The article titled "Retraction for Ni et al., 'Autoregulation of Lantibiotic Bovicin HJ50 Biosynthesis by the BovK-BovR Two-Component Signal Transduction System in Streptococcus bovis HJ50'" has been retracted due to potential duplicated regions in gel images within the article. The authors apologize for the errors and any inconvenience caused. The original images are unavailable due to the age of the article, leading to the decision to retract the paper. [Extracted from the article]

It is widely acknowledged that gastric cancer seriously affects the quality of life and survival of patients. The correlation between the microbiota and gastric cancer has attracted extensive attention in recent years, nonetheless the specific mechanism of its impact on gastric cancer remain largely unclear. Recent studies have shown that in addition to its role in the host's inflammatory and immune response, the microbiota can also affect the occurrence and development of gastric cancer by affecting the expression of miRNAs. This paper brings together all currently available data on miRNAs, microbiota and gastric cancer, and preliminarily describes the relationship among them. [ABSTRACT FROM AUTHOR]

Eukaryotes and prokaryotes have distinct genome architectures, with marked differences in genome size, the ratio of coding/non-coding DNA, and the abundance of transposable elements (TEs). As TEs replicate independently of their hosts, the proliferation of TEs is thought to have driven genome expansion in eukaryotes. However, prokaryotes also have TEs in intergenic spaces, so why do prokaryotes have small, streamlined genomes? Using an in silico model describing the genomes of single-celled asexual organisms that coevolve with TEs, we show that TEs acquired from the environment by horizontal gene transfer can promote the evolution of genome streamlining. The process depends on local interactions and is underpinned by rock-paper-scissors dynamics in which populations of cells with streamlined genomes beat TEs, which beat non-streamlined genomes, which beat streamlined genomes, in continuous and repeating cycles. Streamlining is maladaptive to individual cells, but improves lineage viability by hindering the proliferation of TEs. Streamlining does not evolve in sexually reproducing populations because recombination partially frees TEs from the deleterious effects they cause. [ABSTRACT FROM AUTHOR]

The importance of defining and establishing professional standards for Clinical Microbiology (CM) in Europe has long been highlighted, starting with the development of a European curriculum. The first European Curriculum in Medical Microbiology (MM) was adopted by the European Union of Medical Specialists (UEMS) council in 2017. This paper assesses how training programmes in CM in Europe align with the European curriculum, just under 5 years after its introduction, and reviews what methods of assessment are in use to assess the CM trainees' progress during training programmes. Using an internet-based platform, a questionnaire was circulated to the full, associate and observer members of the UEMS MM section. Information collected related to the structure, content and delivery of CM training in the participating countries, as well as methods of assessment used to evaluate training progress. Twenty-one countries responded, from a total of 30 countries invited to participate. All had a structured CM training programme, with a curriculum, dedicated trainers and a record of training activities. Fifteen countries require trainees to pass an exit examination, and over 60% of countries participate in continuous workplace-based assessment. Of the participating countries, 57% meet the European Training Requirements recommendation that duration of specialist training is 60 months. Regarding core competencies, all trainees gain experience in laboratory skills and infection prevention and control, but the emphasis on clinical management and antimicrobial stewardship is more varied across countries. The UEMS MM curriculum has been largely adopted by 21 countries within less than 5 years of ratification, which speaks optimistically to a future of standardized quality training across Europe. The introduction of a pilot European Examination in Clinical Microbiology in 2021 is the start of a pan-European assessment of the success of the implementation of this curriculum and the first step in quality assurance for CM training in Europe. [ABSTRACT FROM AUTHOR]

Taste shapes evolution, microbes make tasty food, and humans and microbes have been shaping each other for a long while. Yet anthropological accounts of evolution and domestication have given little consideration to taste, microbes, or fermentation. In this paper we develop the concept of "taste-shaping-natures"—natures shaping and shaped by taste—to highlight these multispecies interactions, based on practices of translated fermentation in the New Nordic Cuisine. Here, chefs combine Japanese microbes and fermentation techniques with Scandinavian substrates to create new products and flavors. Focusing on novel misos made with the kōji fungus (Aspergillus oryzae), we illustrate how chefs sense their microbes through smell and taste, and identify the sources of kōji's exceptional microbial charisma. We situate the rise of kōji's allure in the context of New Nordic Cuisine, framed as a high-end response to anxieties about globalization and subsequent nationalisms, a reworking of the scientism of molecular gastronomy, and a postpastoral mobilization of different natures for the reconstruction of regional identity. The analysis traces the natural history of kōji's taste-shaping powers through the biogeographical, ecological, and evolutionary consequences of New Nordic fermentation experiments. The conclusion reflects on how this nascent microbiology of desire revises prevalent understandings of domestication. [ABSTRACT FROM AUTHOR]

I Ambio i . https://doi.org/10.1007/s13280-021-01627-6 In their review paper, Kanwischer et al. ([3]) discuss contaminants of emerging concern (CEC), and the use of state-of-the-art analytical chemistry and effect-based methods (EBM) that currently receive too little attention in Baltic Sea monitoring programs and suggest new approaches. The current review states that "current Baltic Sea monitoring programs do not address compounds of emerging concern.". [Extracted from the article]