General calibration of microbial growth in microplate readers

Simulating the activity of the natural antimicrobial system of milk on the growth of selected cultures involved in cheesemaking and ripening

The impact of three antimicrobial proteins (lactoferrin, lactoperoxidase, lysozyme) on the growth of cultures involved in cheesemaking and ripening was studied. Strains were grown in the optimal media growth of each strain or in cheese simulated environment. The media were supplemented with the antimicrobial proteins together (MIX; 1:1:1) or individually at concentrations found in milk (1x) and cheese (2.5x). Growth properties were evaluated using a novel approach by combining flow cytometry and spectrophotometric assay. Flow cytometry measures cell viability (live/injured/dead cells; total cells). Lactococcus cremoris CUC-C (starter culture) was stimulated by lactoperoxidase and lysozyme reaching higher optical density and total cells than control (without antimicrobial proteins). In cheese simulated environment, the live cells of L. cremoris CUC-C increased of more than 30% in the MIX condition without an increase in total cells. Flow cytometry allowed to show this protective effect. For cultures involved in ripening, the total cells of Lactiplantibacillus plantarum ATCC 14917 and Lacticaseibacillus paracasei subsp. tolerans LMA-1802 decreased of 1 log in the MIX condition. Although the same log reduction, different inhibition behavior was observed. Live cells for Lpb. plantarum ATCC 14917 remained unchanged while for Lcb. paracasei LMA-1802, injured cells increased. These observations were only possible by flow cytometry. The higher concentration (2.5x) tended to decrease the growth properties (lower maximal rate, longer lag phase) of strains as compared to the lower one (1x). The strain-dependent sensitivity to the three antimicrobial proteins underlines the importance of evaluating their effect on cultures prior cheesemaking to ensure proper functionality.

Contribution of efflux activity in resistance to antibiotics in Escherichia coli clinical isolates

BACKGROUND

In an attempt to find new therapeutic strategies for multidrug-resistant infections, understanding the contribution of efflux pumps is of particular importance. This study aimed to determine the contribution of efflux pumps in development of resistance to different classes of antibiotics in clinical isolates of E. coli in order to adopt more effective strategies in the treatment of related infections.

METHODS

Two methods, i.e. measurement the expression level of some efflux related genes and assessment of efflux activity by H33342 accumulation assay using CCCP as an efflux inhibitor, were applied. The relationship of efflux activity with antibiotic resistance, was evaluated using three criteria including HA (dye accumulation in the absence of CCCP), HAC (dye accumulation in the presence of CCCP) and HAR (HAC/HA).

RESULTS

Expression of tolC in ceftazidime, cefotaxime and azithromycin resistant groups and expression of acrA and mdfA in tetracycline resistant isolates were significantly higher than susceptible ones (p < 0.05). By investigating the simultaneous meeting of three proposed criteria for any studied antibiotics, no significant association was found between efflux activity and antibiotic resistance.

CONCLUSION

Finding a relation between the overexpression of some efflux genes and resistance to tetracycline, azithromycin and beta-lactams, confirmed the role of these pumps in resistance to mentioned antibiotics and highlighted the neglected role of efflux pumps in resistance to beta-lactams. Meeting two criteria in >70% of investigated antibiotics, confirmed the contribution of efflux as a partial resistance mechanism in these isolates.

Probiotic Antimicrobial Evaluation Via Real-Time Profiling of Bacterial Cell Proliferation Using Stochastic Kinetics

Probiotic metabolites are gaining attention as potential antibiotic candidates against antibiotic-resistant bacteria. The disk diffusion test, by measuring bacterial aggregate responses, faces challenges in accurately evaluating antimicrobial efficacy when these responses to different probiotic strains are indistinguishable at a macroscopic level. Here, this study presents an analytical method for accurately evaluating antimicrobial activity by analyzing bacterial cell proliferation suppression at a microscopic level. This assay can be used in a coculture system, designed to continuously expose pathogenic bacteria growing on the bottom surface of the culture plate to probiotic metabolites, selectively released from porous capsules positioned above. Bacterial proliferation is optically monitored in real-time and tracked via a computer vision algorithm. Specifically, bacterial proliferation is quantified as their doubling time, calculated using a proposed stochastic kinetic model. This method identifies the most potent antimicrobial strains by determining which probiotic candidates most effectively extend the bacterial doubling time. In comparative experiments using the same strains, this proposed method demonstrated clear distinctions in the antimicrobial efficacy of each strain, unlike the disk diffusion test. Therefore, this approach provides a reliable solution for identifying superior probiotic strains, with potential for widespread use in discovering new antimicrobial agents.

Protocol for the development, assembly, and testing of a synthetic skin microbial community

A reproducible study system is essential for understanding the role of microbes in human skin health and disease. We present a protocol for constructing a synthetic microbial community (SkinCom) of nine strains dominant to native human skin microbiome. We describe steps for computing growth metrics, constructing communities, and extracting DNA and library preparation for shotgun sequencing. We detail steps for data preprocessing and analysis of community samples. We illustrate SkinCom's application with an epicutaneous murine model and downstream multiomic analysis. For complete details on the use and execution of this protocol, please refer to Lekbua et al.1.

Real-time microbial growth curve (RMGC) system: an improved microplate reader with a graphical interface for automatic and high-throughput monitoring of microbial growth curves

The study of microbial growth curves is essential for comprehending microbial behavior and enhancing related processes. Current monitoring methods face limitations, including low automation, inefficient detection, and insufficient throughput. To address these challenges, we developed the Real-Time Microbial Growth Curve (RMGC) system, which offers fully automated and high-throughput monitoring of microbial growth through an Improved Microplate Reader (IMR) with a user-friendly graphical interface. By optimizing and calibrating the optical pathways, we achieve high-precision and consistent absorbance detection using LED light sources, surpassing traditional xenon lamp microplate readers, which lack continuous operation capabilities. We validated the RMGC system by cultivating 96 samples of Escherichia coli (E. coli) at a concentration of 105 CFU mL-1. After approximately 12 hours of continuous monitoring, the system exhibited a relative standard deviation (RSD) of less than 3.25% for optical density (OD) measurements and an RSD of 2.52% for the point of inflection (POI). These results indicate a similar level of precision but a longer monitoring time compared to conventional microplate readers, reflecting the effectiveness of the RMGC system in accurately monitoring microbial growth. The RMGC system showcases its versatility through various applications, such as microorganism gradient cultures, anaerobic microbial cultures, and antimicrobial susceptibility testing (AST). Its capabilities have important implications for multiple industries, including pharmaceuticals for antibiotic development, food safety for microbial contamination testing, and microbiological research.

Population Ecology-Quantitative Microbial Risk Assessment (QMRA) Model for Antibiotic-Resistant and Susceptible E. coli in Recreational Water

Understanding and predicting the role of waterborne environments in transmitting antimicrobial-resistant (AMR) infections are critical for public health. A population ecology-quantitative microbial risk assessment (QMRA) model is proposed to evaluate urinary tract infection (UTI) development due to recreational waterborne exposures to Escherichia coli (E. coli) and antibiotic-resistant extended-spectrum β-lactamase-producing (ESBL) E. coli. The horizontal gene transfer (HGT) mechanism of conjugation and other evolutionary factors were modeled separately in the environment and the gut. Persistence/dilution dominated HGT in the environment; however, HGT highly impacted predicted ESBL populations in the body. Predicted disability life year (DALY) risks from exposure to ESBL E. coli at concentrations consistent with US recreational water criteria were less than the 10-6 pppy benchmark value but greater than the susceptible E. coli DALY risks associated with a UTI health outcome. However, the prevailing susceptible dose-response relationship may underestimate ESBL risk if HGT rates in vivo approach those reported in vitro. A sensitivity analysis demonstrated that DALY values, E. coli/ESBL concentrations, and exposure parameters were influential on predicted risks. The model is a preliminary tool to begin the expansion of the QMRA paradigm to explore the impacts of evolutionary changes in AMR risk assessment.

The type of carbon source not the growth rate it supports can determine diauxie in Saccharomyces cerevisiae

How cells choose between carbon sources is a classic example of cellular decision-making. Microbes often prioritise glucose, but there has been little investigation of whether other sugars are also preferred. Here we study budding yeast growing on mixtures of sugars with palatinose, a sucrose isomer that cells catabolise with the MAL regulon. We find that the decision-making involves more than carbon flux-sensing: yeast prioritise galactose over palatinose, but sucrose and fructose weakly if at all despite each allowing faster growth than palatinose. With genetic perturbations and transcriptomics, we show that the regulation is active with repression of the MAL genes via Gal4, the GAL regulon's master regulator. We argue, using mathematical modelling, that cells enforce their preference for galactose through weakening the MAL regulon's positive feedback. They do so through decreasing intracellular palatinose by repressing MAL11, the palatinose transporter, and expressing the isomaltases IMA1 and IMA5. Supporting these predictions, we show that deleting IMA1 abolishes diauxie. Our results demonstrate that budding yeast actively prioritises carbon sources other than glucose and that such priorities need not reflect differences in growth rates. They imply that carbon-sensing strategies even in model organisms are more complex than previously thought.

Endolysins as Effective Agents for Decontaminating S. typhimurium, E. coli, and L. monocytogenes on Mung Bean Seeds

Seeds are a major source of contamination by foodborne pathogens such as Salmonella typhimurium, Escherichia coli, and Listeria monocytogenes, significantly increasing the risk of foodborne diseases associated with fresh produce like sprouts. In this study, we described novel endolysins and the engineered variants that exhibited potent bactericidal activity against these pathogens. These endolysins demonstrated strong bactericidal effects independently of outer membrane permeabilizers, effectively killing S. typhimurium, E. coli, and L. monocytogenes to undetectable levels (>4-log kill) at concentrations as low as 12.5 μg/mL. The enzymes retained their activity in complex environments, such as a wide range of temperatures (4-100 °C), pH values (4-10), serum concentrations (0-50%), and sodium chloride concentrations (0-500 mM). Furthermore, their rapid bactericidal kinetics, excellent storage stability (>18 months), and broad-spectrum antimicrobial activity enhanced their potential for application. These endolysins remained effective against stationary-phase bacteria and biofilm-forming bacteria, achieving more than 99% biofilm eradication at 200 μg/mL. Notably, at concentrations as low as 50 μg/mL, these enzymes completely decontaminated foodborne pathogens in a mung bean seed model contaminated with 4-5 log CFU of bacteria. This study is the first to report the successful use of lysins to control both Gram-negative and Gram-positive pathogens on mung bean seeds.

Age-Dependent Pleomorphism in Mycobacterium monacense Cultures

Changes in cell shape have been shown to be an integral part of the mycobacterial life cycle; however, systematic investigations into its patterns of pleomorphic behaviour in connection with stages or conditions of growth are scarce. We have studied the complete growth cycle of Mycobacterium monacense cultures, a Non-Tuberculous Mycobacterium (NTM), in solid as well as in liquid media. We provide data showing changes in cell shape from rod to coccoid and occurrence of refractive cells ranging from Phase Grey to phase Bright (PGB) in appearance upon ageing. Changes in cell shape could be correlated to the bi-phasic nature of the growth curves for M. monacense (and the NTM Mycobacterium boenickei) as measured by the absorbance of liquid cultures while growth measured by colony-forming units (CFU) on solid media showed a uniform exponential growth. Based on the complete M. monacense genome we identified genes involved in cell morphology, and analyses of their mRNA levels revealed changes at different stages of growth. One gene, dnaK_3 (encoding a chaperone), showed significantly increased transcript levels in stationary phase cells relative to exponentially growing cells. Based on protein domain architecture, we identified that the DnaK_3 N-terminus domain is an MreB-like homolog. Endogenous overexpression of M. monacense dnaK_3 in M. monacense was unsuccessful (appears to be lethal) while exogenous overexpression in Mycobacterium marinum resulted in morphological changes with an impact on the frequency of appearance of PGB cells. However, the introduction of an anti-sense "gene" targeting the M. marinum dnaK_3 did not show significant effects. Using dnaK_3-lacZ reporter constructs we also provide data suggesting that the morphological differences could be due to differences in the regulation of dnaK_3 in the two species. Together these data suggest that, although its regulation may vary between mycobacterial species, the dnaK_3 might have a direct or indirect role in the processes influencing mycobacterial cell shape.

Development of a Quinoa-Based Fermentation Medium for Propagation of Lactobacillus Plantarum and Weissella Confusa in Opaque Beer Production

Product inconsistency of opaque beer has for long been a tenacious problem in the brewing industry since the current process relies on spontaneous lactic acid fermentation. In order to impede this challenge, there is a need to add lactic acid bacteria (LAB) starter cultures in opaque beer brewing to improve its organoleptic qualities. This study sought to develop a quinoa-based fermentation medium for propagation of Lactobacillus plantarum and Weissella confusa as potential starter cultures in opaque beer production. An evaluation of the stability and tolerance of the LAB under various stress conditions was also done. Fermentation wort from opaque beer brewing and different quinoa-based synthetic media with varying nutritional components was prepared for propagation of LAB. Physiochemical analyses which included pH, Brix value and total titratable acidity (TTA) of monocultured and cocultured synthetic media were measured. The measurements were done at 24 h time intervals ranging from 0 to 96 h. Tolerance studies which included the effect of heat shock, cold shock, oxidative stress and osmotic pressure on the survival rate of LAB were conducted to determine the stability of LAB. MRS with L. plantarum monoculture (MRSp) had a notable change in pH from 4.5 to 3.6 after 24 h. The cocultured (M5p + w) synthetic media and cocultured MRS (MRSp + w) also exhibited change in pH from 4.3 to 3.2 and 4.3 to 3.3, respectively, after 72 h. Brix value in all media samples decreased after 24 h except for the uninoculated MRS sample (MRS C). The synthetic and coculture medium (M5p + w) exhibited an increase in TTA (0.79% (m/v) lactic acid) within the first 24 h. Exposure to heat shock had a significance effect (p < 0.05) on the survival rate of L. plantarum and W. confusa. The W. confusa in synthetic media recorded a higher survival rate (27 ± 0.03%) upon exposure to heat shock than L. plantarum (7 ± 0.01%). In contrast, L. plantarum in MRS recorded a higher survival rate (67 ± 0.02%) upon exposure to cold shock and oxidative stress (34 ± 0.01%). The starter cultures tested survived upon exposure to the stress conditions, indicating their potential use in opaque beer production.

Bioluminescent Pseudomonas aeruginosa and Escherichia coli for whole-cell screening of antibacterial and adjuvant compounds

Continued efforts to discover new antibacterial molecules are critical to achieve a robust pre-clinical pipeline for new antibiotics. Screening of compound or natural product extract libraries remains a widespread approach and can benefit from the development of whole cell assays that are robust, simple and versatile, and allow for high throughput testing of antibacterial activity. In this study, we created and validated two bioluminescent reporter strains for high-throughput screening, one in Pseudomonas aeruginosa, and another in a hyperporinated and efflux-deficient Escherichia coli. We show that the bioluminescent strains have a large dynamic range that closely correlates with cell viability and is superior to conventional optical density (OD600) measurements, can detect dose-dependent antibacterial activity and be used for different drug discovery applications. We evaluated the assays' performance characteristics (signal to background ratio, signal window, Z' robust) and demonstrated their potential utility for antibiotic drug discovery in two examples. The P. aeruginosa bioluminescent reporter was used in a pilot screen of 960 repurposed compound libraries to identify adjuvants that potentiate the fluoroquinolone antibiotic ofloxacin. The E. coli bioluminescent reporter was used to test the antibacterial activity of bioactive bacterial supernatants and assist with bioassay-guided fractionation of the crude extracts.

Shining a Light on Spectrophotometry in Bacteriology

Spectrophotometry is widely used in biological sciences. In bacteriology, spectrophotometric monitoring of cell numbers during cultivation provides a rapid assessment of growth. Unfortunately, familiarity with this technique has led scientists to become complacent in its usage. Here, we review some guiding principles of spectrophotometry and practical considerations that may influence the outcome of experiments. This perspective is intended to assist both new and seasoned scientists in presenting robust and reproducible growth data based on spectrophotometric readings.

Recombinant T7 RNA polymerase production using ClearColi BL21(DE3) and animal-free media for in vitro transcription

In vitro transcription (IVT) using T7 RNA polymerase (RNAP) is integral to RNA research, yet producing this enzyme in E. coli presents challenges regarding endotoxins and animal-sourced toxins. This study demonstrates the viable production and characterization of T7 RNAP using ClearColi BL21(DE3) (an endotoxin-free E. coli strain) and animal-free media. Compared to BL21(DE3) with animal-free medium, soluble T7 RNAP expression is ~50% lower in ClearColi BL21(DE3). Optimal soluble T7 RNAP expression in flask fermentation is achieved through the design of experiments (DoE). Specification and functional testing showed that the endotoxin-free T7 RNAP has comparable activity to conventional T7 RNAP. After Ni-NTA purification, endotoxin levels were approximately 109-fold lower than T7 RNAP from BL21(DE3) with animal-free medium. Furthermore, a full factorial DoE created an optimal IVT system that maximized mRNA yield from the endotoxin-free and animal-free T7 RNAP. This work addresses critical challenges in recombinant T7 RNAP production through innovative host and medium combinations, avoided endotoxin risks and animal-derived toxins. Together with an optimized IVT reaction system, this study represents a significant advance for safe and reliable reagent manufacturing and RNA therapeutics. KEY POINTS: • Optimized IVT system maximizes mRNA yields, enabling the synthesis of long RNAs. • Novel production method yields endotoxin-free and animal-free T7 RNAP. • The T7 RNAP has equivalent specifications and function to conventional T7 RNAP.

Biosynthesis of pH-Responsive Mesoporous Silica Nanoparticles from Cucumber Peels for Targeting 3D Lung Tumor Spheroids

Lung adenocarcinoma is considered to be one of the primary causes of cancer-related deaths globally. Conventional treatments, such as chemotherapy and radiation therapy taken together, have not significantly lowered mortality rates. Repositioning of authorized anticancer medications supported by nanotechnology has therefore emerged as an effective strategy to close such gaps. In this context, mesoporous silica nanoparticles (MSNs) were biosynthesized from cucumber peels and were loaded with doxorubicin, a common anticancer drug to form doxorubicin-bound mesoporous silica nanoparticles (DMSNs). The study addresses a sustainable method for turning waste materials into MSNs, which can be used to create multifunctional nanosystems. The therapeutic module (DMSNs) was designed specifically to target 2D monolayer cells and 3D tumor spheroids of lung adenocarcinoma cancer. The DMSNs demonstrated notable antiproliferative activity and effective intracellular localization in addition to being biocompatible and innately fluorescent. Subsequent investigations revealed significant antibacterial activity against Staphylococcal infection, which is primarily prevalent in lung cancer patients. Thus, the developed MSNs held promising potential for anticancer drug delivery systems and have antibacterial potential to treat bacterial infections in patients with lung cancer. Furthermore, the cucumber peel-mediated synthesis of MSNs could also aid in the management of food waste and promote the adoption of the waste-to-health paradigm for sustainable solutions.

The Salmonella enterica EnvE is an Outer Membrane Lipoprotein and Its Gene Expression Leads to Transcriptional Repression of the Virulence Gene msgA

The envE gene of Salmonella enterica serovar Typhimurium is encoded within Salmonella Pathogenicity Island-11 (SPI-11) and is located immediately upstream of the virulence gene msgA (macrophage survival gene A) in the same transcriptional orientation. To date, the characteristics and roles of envE remain largely unexplored. In this study, we show that EnvE, a predicted lipoprotein, is localized on the outer membrane using sucrose gradient ultracentrifugation. Under oxidative stress conditions, envE transcription is suppressed, while msgA transcription is induced, indicating an inverse correlation between the mRNA levels of the two neighboring genes. Importantly, inactivation of envE leads to constitutive transcription of msgA regardless of the presence of oxidative stress. Moreover, trans-complementation of the envE mutant with a plasmid-borne envE fails to prevent the induction of msgA transcription, suggesting that envE functions as a cis-regulatory element rather than a trans-acting factor. We further show that both inactivation and complementation of envE confer wild-type levels of resistance to oxidative stress by ensuring the expression of msgA. Our data suggest that the S. enterica envE gene encodes an outer membrane lipoprotein, and its transcription represses msgA expression in a cis-acting manner, probably by transcriptional interference, although the exact molecular details are yet unclear.

High throughput parameter estimation and uncertainty analysis applied to the production of mycoprotein from synthetic lignocellulosic hydrolysates

The current global food system produces substantial waste and carbon emissions while exacerbating the effects of global hunger and protein deficiency. This study aims to address these challenges by exploring the use of lignocellulosic agricultural residues as feedstocks for microbial protein fermentation, focusing on Fusarium venenatum A3/5, a mycelial strain known for its high protein yield and nutritional quality. We propose a high throughput microlitre batch fermentation system paired with analytical chemistry to generate time series data of microbial growth and substrate utilisation. An unstructured biokinetic model was developed using a bootstrap sampling approach to quantify uncertainty in the parameter estimates. The model was validated against an independent data set of a different glucose-xylose composition to assess the predictive performance. Our results indicate a robust model fit with high coefficients of determination and low root mean squared errors for biomass, glucose, and xylose concentrations. Estimated parameter values provided insights into the resource utilisation strategies of Fusarium venenatum A3/5 in mixed substrate cultures, aligning well with previous research findings. Significant correlations between estimated parameters were observed, highlighting challenges in parameter identifiability. The high throughput workflow presents a novel, rapid methodology for biokinetic model development, enabling efficient exploration of microbial growth dynamics and substrate utilisation. This innovative method directly supports the development of a foundational model for optimising microbial protein production from lignocellulosic hydrolysates, contributing to a more sustainable global food system.

Rapid growth rate of Enterobacter sp. SM3 determined using several methods

BACKGROUND

Bacterial growth rate, commonly reported in terms of doubling time, is frequently determined by one of two techniques: either by measuring optical absorption of a growing culture or by taking samples at different times during their growth phase, diluting them, spreading them on agar plates, incubating them, and counting the colonies that form. Both techniques require measurements of multiple repeats, as well careful assessment of reproducibility and consistency. Existing literature using either technique gives a wide range of growth rate values for even the most extensively studied species of bacteria, such as Escherichia coli, Pseudomonas aeruginosa, and  Staphylococcus aureus. This work aims to apply several methods to reliably determine the growth rate of a recently identified species of Enterobacteriaceae, called Enterobacter sp. SM3, and to compare that rate with that of a well-known wildtype E. coli strain KP437.

RESULTS

We extend conventional optical density (OD) measurements to determine the growth rate of Enterobacter sp. SM3. To assess the reliability of this technique, we compare growth rates obtained by fitting the OD data to exponential growth, applying a relative density method, and measuring shifts in OD curves following set factors of dilution. The main source of error in applying the OD technique is due to the reliance on an exponential growth phase with a short span. With proper choice of parameter range, however, we show that these three methods yield consistent results. We also measured the SM3 division rate by counting colony-forming units (CFU) versus time, yielding results consistent with the OD measurements. In lysogeny broth at 37oC, SM3 divides every 21 ± 3 min, notably faster than the RP437 strain of E. coli, which divides every 29 ± 2 min.

CONCLUSION

The main conclusion of this report is that conventional optical density (OD) measurements and the colony-forming units (CFU) method can yield consistent values of bacterial growth rate. However, to ensure the reproducibility and reliability of the measured growth rate of each bacterial strain, different methods ought to be applied in close comparison. The effort of checking for consistency among multiple techniques, as we have done in this study, is necessary to avoid reporting variable values of doubling time for particular species or strains of bacteria, as seen in the literature.

A liquid culture method assisted by ATP analysis for accelerating laboratory experiments on ultraviolet disinfection of airborne bacteria

The solid culture method for measuring the efficiency of ultraviolet (UV) disinfection of airborne bacteria is time-consuming, typically taking 12-48 h. To expedite such experiments, this study proposed a liquid culture method assisted by adenosine triphosphate (ATP) analysis, as a liquid culture is faster than a solid culture, and measurement of ATP does not require waiting for visible colonies to form. Escherichia coli (E. coli) was used as the experimental bacterium. This study first compared the log reduction of bacteria in liquid as measured by the proposed method and by the traditional solid culture method. The minimum liquid culture time was determined for different bacterial concentration ranges. Finally, the feasibility of the proposed method was validated by UV disinfection experiments on airborne bacteria. The results indicated that the proposed method measured a similar log reduction to that of the solid culture method in liquid experiments. The minimum liquid culture time for E. coli in 105-106 colony forming units (CFU)/mL was 2 h. The validation experiments demonstrated that the proposed method is capable of measuring the UV disinfection efficiency of airborne bacteria. The proposed method can accelerate laboratory experiments on UV disinfection of airborne bacteria, which in turn can support the effective design and utilization of UV disinfection in real life.

The [(bathophenanthroline)3:Fe2+] complex as an aromatic non-polymeric medium for purification of human lactoferrin

We describe a non-chromatographic, ligand-free platform for the efficient purification of recombinant human lactoferrin (LF). The platform consists of a [metal:chelator] complex precipitate in the presence of osmotically active polyethylene glycol 6000 (PEG-6000). Purification is achieved in three stages. Following formation of the complex, LF is captured under neutral conditions by the aggregated complexes (Step I), a washing step follows (Step II) and then, (Step III) LF is extracted in pure form with 100 mM tribasic Na citrate buffer (pH 7). Of the four complexes investigated, [bathophenanthroline (batho)3:Fe2+] was determined to be the most efficient. LF is recovered with high yield (∼90%, by densitometry) and purity (≥97%, by SDS polyacrylamide gel electrophoresis (SDS-PAGE)) from an artificial contamination background comprising E. coli lysate proteins. Purified LF is demonstrated to be monomeric by dynamic light scattering (DLS); to preserve its native secondary structure by circular dichroism (CD) spectroscopy; and, as apo-LF, to efficiently inhibit bacterial growth. Process yield is not affected by a 45-fold increase in LF concentration from 0.2 to 9 mg/mL. We provide evidence that protein capture relies on [cation:π] interactions between the lysine and arginine residues of LF with the fully aromatic [(batho)3:Fe2+] complexes. The use of [metal:chelator] complex aggregates is demonstrated to provide an economical and efficient avenue for LF purification.

Using bacterial population dynamics to count phages and their lysogens

Traditional assays for counting bacteriophages and their lysogens are labor-intensive and perturbative to the host cells. Here, we present a high-throughput infection method in a microplate reader, where the growth dynamics of the infected culture is measured using the optical density (OD). We find that the OD at which the culture lyses scales linearly with the logarithm of the initial phage concentration, providing a way of measuring phage numbers over nine orders of magnitude and down to single-phage sensitivity. Interpreting the measured dynamics using a mathematical model allows us to infer the phage growth rate, which is a function of the phage-cell encounter rate, latent period, and burst size. Adding antibiotic selection provides the ability to measure the rate of host lysogenization. Using this method, we found that when E. coli growth slows down, the lytic growth rate of lambda phages decreases, and the propensity for lysogeny increases, demonstrating how host physiology influences the viral developmental program.

Escherichia coli grown in inexpensive conical flat-bottom polypropylene tubes produce a high level of pUC vector

The pUC-derived plasmid yield from E. coli using polypropylene tubes (PP) was compared among round and conical tubes. The yield from cells grown in a cheaper conical-PP with flat-bottom was 1.5-fold higher (p < 0.001) than other PP. The use of the conical-PP can save research budgets in the current inflationary environment.

Synthesis and Antimicrobial Activity of Newly Synthesized Nicotinamides

Antioxidants are promising compounds with antimicrobial activity against drug-resistant pathogens, especially when combined with conventional antimicrobials. Our study aimed to characterize the structure of nicotinamides synthesized from nicotinic acid and thiocarbohydrazones and to evaluate their antibacterial and antifungal activity. Seven nicotinic acid hydrazides (NC 1-7) were synthesized using mono-thiocarbohydrazones with hydroxyl group substituents, along with quinolone, phenolic, and pyridine rings known for their antimicrobial activity. The in vitro antimicrobial activity of NC 1-7, at concentrations ranging from 0.001 to 1 mM, was tested against Staphylococcus aureus (ATCC 6538), Enterococcus faecalis (ATCC 29212), Pseudomonas aeruginosa (ATCC 27853), Klebsiella pneumoniae (NCIMB 9111), and Candida albicans (ATCC 24433) using the broth microdilution method per EUCAST 2024 guidelines. Microorganism survival percentages were calculated based on optical density, and target fishing using the PharmMapper database identified potential molecular targets. The results showed that P. aeruginosa was most susceptible to the compounds, while C. albicans was the least susceptible. NC 3 significantly inhibited P. aeruginosa and K. pneumoniae growth at 0.016 mM, while higher concentrations were required for S. aureus, E. faecalis, and C. albicans. NC 5 was most effective against gram-positive bacteria at 0.03 mM. Only NC 4 completely inhibited C. albicans below 1 mM. NC 3, with the lowest concentration for 50% growth inhibition (0.016-0.064 mM), showed promising antibacterial potential against specific AMR-related proteins (bleomycin resistance protein, HTH-type transcriptional regulator QacR, and streptogramin A acetyltransferase), suggesting that this class of compounds could enhance or restore the activity of established antibiotics.

What is holding back cyanobacterial research and applications? A survey of the cyanobacterial research community

Cyanobacteria are a diverse group of prokaryotic organisms that have been the subject of intense basic research, resulting in a wealth of knowledge about fundamental cellular processes such as photosynthesis. However, the translation of that research towards industry-relevant applications is still limited. To understand the reasons for this contradictory situation, we conducted a quantitative survey among researchers in the cyanobacterial community, a set of individual interviews with established researchers, and a literature analysis. Our results show that the community seems to be committed to embracing cyanobacterial diversity and promoting collaboration. Additionally, participants expressed a strong desire to develop standardized protocols for research and establish larger consortia to accelerate progress. The results of the survey highlight the need for a more integrated approach to cyanobacterial research that encompasses both basic and applied aspects. Based on the survey and interview results as well as our literature analysis, we highlight areas for potential improvement, strategies to enhance cyanobacterial research, and open questions that demand further exploration. Addressing these challenges should accelerate the development of industrial applications based on cyanobacterial research.

Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data

MOTIVATION

Quantitative dynamical models facilitate the understanding of biological processes and the prediction of their dynamics. The parameters of these models are commonly estimated from experimental data. Yet, experimental data generated from different techniques do not provide direct information about the state of the system but a nonlinear (monotonic) transformation of it. For such semi-quantitative data, when this transformation is unknown, it is not apparent how the model simulations and the experimental data can be compared.

RESULTS

We propose a versatile spline-based approach for the integration of a broad spectrum of semi-quantitative data into parameter estimation. We derive analytical formulas for the gradients of the hierarchical objective function and show that this substantially increases the estimation efficiency. Subsequently, we demonstrate that the method allows for the reliable discovery of unknown measurement transformations. Furthermore, we show that this approach can significantly improve the parameter inference based on semi-quantitative data in comparison to available methods.

AVAILABILITY AND IMPLEMENTATION

Modelers can easily apply our method by using our implementation in the open-source Python Parameter EStimation TOolbox (pyPESTO) available at https://github.com/ICB-DCM/pyPESTO.

XTT assay for detection of bacterial metabolic activity in water-based polyester polyurethane

Cellular metabolic activity can be detected by tetrazolium-based colorimetric assays, which rely on dehydrogenase enzymes from living cells to reduce tetrazolium compounds into colored formazan products. Although these methods have been used in different fields of microbiology, their application to the detection of bacteria with plastic-degrading activity has not been well documented. Here, we report a microplate-adapted method for the detection of bacteria metabolically active on the commercial polyester polyurethane (PU) Impranil®DLN using the tetrazolium salt 2,3-bis [2-methyloxy-4-nitro-5-sulfophenyl]-2H-tetrazolium-5-carboxanilide (XTT). Bacterial cells that are active on PU reduce XTT to a water-soluble orange dye, which can be quantitatively measured using a microplate reader. We used the Pseudomonas putida KT2440 strain as a study model. Its metabolic activity on Impranil detected by our novel method was further verified by Fourier-transform infrared spectroscopy (FTIR) analyses. Measurements of the absorbance of reduced XTT at 470 nm in microplate wells were not affected by the colloidal properties of Impranil or cell density. In summary, we provide here an easy and high-throughput method for screening bacteria active on PU that can be adapted to other plastic substrates.

The relationship between cell density and cell count differs among Saccharomyces yeast species

There is a recent push to develop wild and non-domesticated Saccharomyces yeast strains into useful model systems for research in ecology and evolution. Yet, the variation between species and strains in important population parameters remains largely undescribed. Here, we investigated the relationship between two commonly used measures in microbiology to estimate growth rate - cell density and cell count - in 23 strains across all eight Saccharomyces species . We found that the slope of this relationship significantly differs among species and a given optical density (OD) does not translate into the same number of cells across species. We provide a cell number calculator based on our OD measurements for each strain used in this study. Surprisingly, we found a slightly positive relationship between cell size and the slope of the cell density-cell count relationship. Our results show that the strain- and species-specificity of the cell density and cell count relationship should be taken into account, for instance when running competition experiments requiring equal starting population sizes or when estimating the fitness of strains with different genetic backgrounds in experimental evolution studies.

An improved mouse model of sepsis based on intraperitoneal injections of the enriched culture of cecum slurry

AIM

Sepsis is a life-threatening clinical syndrome comprising multiorgan dysfunctions caused by a disproportionate body immune response. There are several animal sepsis models which are based on cecum ligation, cecal puncture, and cecum slurry injection. The major limitation of all current sepsis models is the high variability owing to the variable degree of ligation, puncture and inconsistent microbial composition used for sepsis initiation. The primary objective of this work is to demonstrate the feasibility of a standardized method for sepsis development.

MATERIALS AND METHODS

The cecal slurry bacterial culture was developed and preserved in glycerol stocks. Antibiotics aztreonam and vancomycin were used for generating several defined, enriched cecal slurry bacterial cultures. Mice survival was assessed until 48 hrs post injection, and the tissue samples were collected after 10 hrs from sepsis initiation.

KEY FINDINGS

The results indicate that increasing polymicrobial load resulted in lower survival rates and was associated with the higher number of infiltrating immune cells and necrosis. H&E (haematoxylin & eosin) staining & serum markers revealed that septic mice exhibited increased inflammation and significant damage to the liver and kidneys. The defined Gram-negative and Gram-positive specific cecal slurry bacterial cultures were developed and their efficiency in inducing sepsis was characterized.

SIGNIFICANCE

Enriched cecal slurry bacterial cultures can be stored in glycerol stocks at -80 °C. This has an ethical advantage of avoiding unnecessary animal euthanasia for each experiment and provides a standardization capability of sepsis development.

Blue light-mediated gene expression as a promising strategy to reduce antibiotic resistance in Escherichia coli

The discovery of antibiotics has noticeably promoted the development of human civilization; however, antibiotic resistance in bacteria caused by abusing and overusing greatly challenges human health and food safety. Considering the worsening situation, it is an urgent demand to develop emerging nontraditional technologies or methods to address this issue. With the expanding of synthetic biology, optogenetics exhibits a tempting prospect for precisely regulating gene expression in many fields. Consequently, it is attractive to employ optogenetics to reduce the risk of antibiotic resistance. Here, a blue light-controllable gene expression system was established in Escherichia coli based on a photosensitive DNA-binding protein (EL222). Further, this strategy was successfully applied to repress the expression of β-lactamase gene (bla) using blue light illumination, resulting a dramatic reduction of ampicillin resistance in engineered E. coli. Moreover, blue light was utilized to induce the expression of the mechanosensitive channel of large conductance (MscL), triumphantly leading to the increase of streptomycin susceptibility in engineered E. coli. Finally, the increased susceptibility of ampicillin and streptomycin was simultaneously induced by blue light in the same E. coli cell, revealing the excellent potential of this strategy in controlling multidrug-resistant (MDR) bacteria. As a proof of concept, our work demonstrates that light can be used as an alternative tool to prolong the use period of common antibiotics without developing new antibiotics. And this novel strategy based on optogenetics shows a promising foreground to combat antibiotic resistance in the future.

Inferring fungal growth rates from optical density data

Quantifying fungal growth underpins our ability to effectively treat severe fungal infections. Current methods quantify fungal growth rates from time-course morphology-specific data, such as hyphal length data. However, automated large-scale collection of such data lies beyond the scope of most clinical microbiology laboratories. In this paper, we propose a mathematical model of fungal growth to estimate morphology-specific growth rates from easy-to-collect, but indirect, optical density (OD600) data of Aspergillus fumigatus growth (filamentous fungus). Our method accounts for OD600 being an indirect measure by explicitly including the relationship between the indirect OD600 measurements and the calibrating true fungal growth in the model. Therefore, the method does not require de novo generation of calibration data. Our model outperformed reference models at fitting to and predicting OD600 growth curves and overcame observed discrepancies between morphology-specific rates inferred from OD600 versus directly measured data in reference models that did not include calibration.

Harnessing Nature's Defence: The Antimicrobial Efficacy of Pasteurised Cattle Milk-Derived Extracellular Vesicles on Staphylococcus aureus ATCC 25923

Increasing antimicrobial resistance (AMR) challenges conventional antibiotics, prompting the search for alternatives. Extracellular vesicles (EVs) from pasteurised cattle milk offer promise, due to their unique properties. This study investigates their efficacy against five pathogenic bacteria, including Staphylococcus aureus ATCC 25923, aiming to combat AMR and to develop new therapies. EVs were characterised and tested using various methods. Co-culture experiments with S. aureus showed significant growth inhibition, with colony-forming units decreasing from 2.4 × 105 CFU/mL (single dose) to 7.4 × 104 CFU/mL (triple doses) after 12 h. Milk EVs extended lag time (6 to 9 h) and increased generation time (2.8 to 4.8 h) dose-dependently, compared to controls. In conclusion, milk EVs exhibit dose-dependent inhibition against S. aureus, prolonging lag and generation times. Despite limitations, this suggests their potential in addressing AMR.

TbsP and TrmB jointly regulate gapII to influence cell development phenotypes in the archaeon Haloferax volcanii

Microbial cells must continually adapt their physiology in the face of changing environmental conditions. Archaea living in extreme conditions, such as saturated salinity, represent important examples of such resilience. The model salt-loving organism Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. However, the mechanisms regulating these lifestyle transitions remain unclear. In prior research, we showed that the transcriptional regulator, TrmB, maintains the rod shape in the related species Halobacterium salinarum by activating the expression of enzyme-coding genes in the gluconeogenesis metabolic pathway. In Hbt. salinarum, TrmB-dependent production of glucose moieties is required for cell surface glycoprotein biogenesis. Here, we use a combination of genetics and quantitative phenotyping assays to demonstrate that TrmB is essential for growth under gluconeogenic conditions in Hfx. volcanii. The ∆trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name trmB suppressor, or TbsP (a.k.a. "tablespoon"). TbsP is required for adhesion to abiotic surfaces (i.e., biofilm formation) and maintains wild-type cell morphology and motility. We use functional genomics and promoter fusion assays to characterize the regulons controlled by each of TrmB and TbsP, including joint regulation of the glucose-dependent transcription of gapII, which encodes an important gluconeogenic enzyme. We conclude that TrmB and TbsP coregulate gluconeogenesis, with downstream impacts on lifestyle transitions in response to nutrients in Hfx. volcanii.

Streptomyces-based whole-cell biosensors for detecting diverse cell envelope-targeting antibiotics

Cell envelope-targeting antibiotics are potent therapeutic agents against various bacterial infections. The emergence of multiple antibiotic-resistant strains underscores the significance of identifying potent antimicrobials specifically targeting the cell envelope. However, current drug screening approaches are tedious and lack sufficient specificity and sensitivity, warranting the development of more efficient methods. Genetic circuit-based whole-cell biosensors hold great promise for targeted drug discovery from natural products. Here, we performed comparative transcriptomic analysis of Streptomyces coelicolor M1146 exposed to diverse cell envelope-targeting antibiotics, aiming to identify regulatory elements involved in perceiving and responding to these compounds. Differential gene expression analysis revealed significant activation of VanS/R two-component system in response to the glycopeptide class of cell envelope-acting antibiotics. Therefore, we engineered a pair of VanS/R-based biosensors that exhibit functional complementarity and possess exceptional sensitivity and specificity for glycopeptides detection. Additionally, through promoter screening and characterization, we expanded the biosensor's detection range to include various cell envelope-acting antibiotics beyond glycopeptides. Our genetically engineered biosensor exhibits superior performance, including a dynamic range of up to 887-fold for detecting subtle antibiotic concentration changes in a rapid 2-h response time, enabling high-throughput screening of natural product libraries for antimicrobial agents targeting the bacterial cell envelope.

Co-exposure to pentachlorophenol (PCP) and cadmium (Cd) triggers apoptosis-like cell death in Eschericia coli

Pentachlorophenol (PCP) - cadmium (Cd) complex pollution has been identified as a form of persistent soil pollution in south China, exerting detrimental impacts on the indigenous soil bacterial communities. Hence, it is worthwhile to investigate whether and how bacterial populations alter in response to these pollutants. In this study, Escherichia coli was used as a model bacterium. Results showed that PCP exposure caused bacterial cell membrane permeability changes, intracellular ROS elevation, and DNA fragmentation, and triggered apoptosis-like cell death at low exposure concentration and necrosis at high exposure concentration. Cd exposure caused severe oxidative damage and cell necrosis in the tested bacterial strain. The co-exposure to PCP and Cd elevated the ROS level, stimulated the bacterial caspase activity, and induced DNA fragmentation, thereby leading to an apoptosis-like cell death. In conclusion, PCP-Cd complex pollution can cause bacterial population to decrease through apoptosis-like cell death pathway. However, it is worth noting that the subpopulation survives under the complex pollution stress.

Evaluation of the effects of canning variables on the mineral composition of canned cowpeas (Vigna unguiculata l. Walp) using multi-response analysis

This study aims to investigate the effects of canning variables (cooking time, storage time, volume of vinegar, salt and sugar) on the mineral composition of canned cowpea (Vigna unguiculata (L.) Walp) and which conditions provide optimised preservation of the mineral content of the grains. Different formulations of canned cowpeas were produced following two levels factorial experimental design using five variables. A set of 11 different formulations were evaluated using the desirability function with essential minerals (Ca, Cu, Fe, Mn, Mg, P and Zn) as the response. The optimal multi-response conditions for higher mineral retention were: 360 days of storage at 30 ± 5 °C (ST2), 30 ml of vinegar, 9.0 g of NaCl, 18 min of cooking time, and 9.0 g, 19.5 g or 30 g of sugar (the effect of the sugar content at the evaluated range was not significant at 95% confidence level).

cAMP in budding yeast: Also a messenger for sucrose metabolism?

S. cerevisiae (or budding yeast) is an important micro-organism for sucrose-based fermentation in biotechnology. Yet, it is largely unknown how budding yeast adapts to sucrose transitions. Sucrose can only be metabolized when the invertase or the maltose machinery are expressed and we propose that the Gpr1p receptor signals extracellular sucrose availability via the cAMP peak to adapt cells accordingly. A transition to sucrose or glucose gave a transient cAMP peak which was maximally induced for sucrose. When transitioned to sucrose, cAMP signalling mutants showed an impaired cAMP peak together with a lower growth rate, a longer lag phase and a higher final OD600 compared to a glucose transition. These effects were not caused by altered activity or expression of enzymes involved in sucrose metabolism and imply a more general metabolic adaptation defect. Basal cAMP levels were comparable among the mutant strains, suggesting that the transient cAMP peak is required to adapt cells correctly to sucrose. We propose that the short-term dynamics of the cAMP signalling cascade detects long-term extracellular sucrose availability and speculate that its function is to maintain a fermentative phenotype at continuously low glucose and fructose concentrations.

Sea bass (Lateolabrax maculatus) exerts anti‐ulcerative colitis effects through gut microbiota modulation

Traditional Chinese medicinal books have noted that sea bass (Lateolabrax maculatus) may effectively manage inflammation‐linked conditions. The folk use of sea bass during pregnancy as nutritional care is also popular in China. However, scientific verification of health benefits of sea bass remains a lack of report. Our previous studies have proven that sea bass has therapeutic benefits for ulcerative colitis (UC). However, a further investigation on the interacted mechanism among sea bass, UC, and gut microbiota has still not been fully explored and clarified. Hence, gut microbiota as the crucial mechanism of UC was evaluated. Gut ecosystem was analyzed by 16sRNA sequencing. The potential microbial biomarker was found through LEfSe analysis. Flow cytometry was then further applied to verify the identified biomarker. Results revealed that sea bass could effectively recover the abundance of UC‐mediated microbiota. LEfSe analysis found that Christensenellaceae could be identified as the potential biomarker for sea bass‐mediated gut microbiota in UC. Further in vitro study conjointly confirmed that the identified bioactive constituent of sea bass could significantly promote the growth of Christensenella minuta. Sufficient results derived that sea bass could ameliorate UC through gut microbiota modulation. C. minuta was identified as the promising microbial biomarker for the mechanism of sea bass in treating intestinal inflammation. It provided further elucidation on the pharmacological mechanism of sea bass in alleviating UC through gut microbiota modulation. It is a crucial driving force for the progress of scientific research on the dietary therapy of sea bass.

OPTIMIZATION OF EXPERIMENTAL MODEL SYSTEMS FOR EVALUATING RECIPROCAL INFLUENCE OF BIFIDOBACTERIUM ANIMALIS AND HUMAN BREAST CANCER CELLS IN VITRO

BACKGROUND

The development of human breast cancer (BC) is known to be closely related to disturbances in the mammary gland microbiota. Bacteria of the genus Bifidobacterium are an important component of normal breast microbiota and exert antitumor activity. The molecular-biological mechanisms of interaction between BC cells and microbiota members remain poorly studied yet. The aim of this study was to develop and optimize an experimental model system for the co-cultivation of BC cells with Bifidobacterium animalis in vitro.

MATERIALS AND METHODS

Human ВС cells of the MCF-7, T47D, and MDA-MB-231 lines, as well as live and heat-inactivated bacteria of Bifidobacterium animalis subsp. lactis (B. animalis) were used as research objects. The growth kinetics and viability of B. animalis in the presence of different ВС cell lines and without them were determined by both the turbidimetry method and seeding on an elective nutrient medium. Glucose consumption and lactate production by bifidobacteria were assessed by biochemical methods. The viability of BC cells was determined by a standard colorimetric method.

RESULTS

The growth kinetics of B. animalis in the complete DMEM nutrient medium showed standard patterns. The indicators of glucose consumption and lactate production of B. animalis confirm its physiological metabolic activity under the growth conditions. The presence of BC cells in the model system did not affect the duration of the growth phases of the B. animalis cells' population but contributed to the increase in their counts. A significant decrease in the number of live BC cells of all studied lines was observed only after 48 h of co-cultivation with live B. animalis. To achieve similar suppression of the BC cell viability, 10-30-fold higher counts of heatinactivated bacteria were required compared to live ones.

CONCLUSIONS

The optimal conditions for co-cultivation of human BC cells and living B. animalis cells in vitro have been identified.

Counter-on-chip for bacterial cell quantification, growth, and live-dead estimations

Quantifying bacterial cell numbers is crucial for experimental assessment and reproducibility, but the current technologies have limitations. The commonly used colony forming units (CFU) method causes a time delay in determining the actual numbers. Manual microscope counts are often error-prone for submicron bacteria. Automated systems are costly, require specialized knowledge, and are erroneous when counting smaller bacteria. In this study, we took a different approach by constructing three sequential generations (G1, G2, and G3) of counter-on-chip that accurately and timely count small particles and/or bacterial cells. We employed 2-photon polymerization (2PP) fabrication technology; and optimized the printing and molding process to produce high-quality, reproducible, accurate, and efficient counters. Our straightforward and refined methodology has shown itself to be highly effective in fabricating structures, allowing for the rapid construction of polydimethylsiloxane (PDMS)-based microfluidic devices. The G1 comprises three counting chambers with a depth of 20 µm, which showed accurate counting of 1 µm and 5 µm microbeads. G2 and G3 have eight counting chambers with depths of 20 µm and 5 µm, respectively, and can quickly and precisely count Escherichia coli cells. These systems are reusable, accurate, and easy to use (compared to CFU/ml). The G3 device can give (1) accurate bacterial counts, (2) serve as a growth chamber for bacteria, and (3) allow for live/dead bacterial cell estimates using staining kits or growth assay activities (live imaging, cell tracking, and counting). We made these devices out of necessity; we know no device on the market that encompasses all these features.

Mammalian cell growth characterisation by a non-invasive plate reader assay

Automated and non-invasive mammalian cell analysis is currently lagging behind due to a lack of methods suitable for a variety of cell lines and applications. Here, we report the development of a high throughput non-invasive method for tracking mammalian cell growth and performance based on plate reader measurements. We show the method to be suitable for both suspension and adhesion cell lines, and we demonstrate it can be adopted when cells are grown under different environmental conditions. We establish that the method is suitable to inform on effective drug treatments to be used depending on the cell line considered, and that it can support characterisation of engineered mammalian cells over time. This work provides the scientific community with an innovative approach to mammalian cell screening, also contributing to the current efforts towards high throughput and automated mammalian cell engineering.

Wireless monitoring of cell cultures based on light scattering: A novel optical scheme and portable prototype

Cell cultures are widely used in scientific research, biomedicine, and industry. When culturing, it is important to maintain certain conditions, including the concentration of cells. Monitoring of the culture growth and cell counting is an urgent task for the optimization of technological processes. Most existing methods require sampling from a culture flask. This procedure is time-consuming and associated with the risks of contamination. We present a device able to monitor the growth of cells number in a suspension noninvasively. The device uses a laser beam that pass through the culture flask and measures the intensity of scattered light as a function of coordinate along the beam. This optical scheme allows one to obtain accurate results for both high- and low-scattering samples. We constructed the wireless portable prototype for monitoring of cell culture growth directly in the incubator and demonstrated the applicability of the device for Jurkat cells and Escherichia coli bacteria.

Standardization of Fluorescent Reporter Assays in Synthetic Biology across the Visible Light Spectrum

In synthetic biology, Fluorescent reporters are frequently used to characterize the expression levels obtained from both genetic parts such as promoters and ribosome binding sites as well as from complex genetic circuits. To this end, plate readers offer an easy and high-throughput way of characterizing both the growth and fluorescence expression levels of cell cultures. However, despite the similar mode of action used in different devices, their output is not comparable due to intrinsic differences in their setup. Additionally, the generated output is expressed using arbitrary units, limiting reliable comparison of results to measurements taken within one single experiment using one specific plate reader, hampering the transferability of data across different plate readers and laboratories. This article presents an easy and accessible calibration method for transforming the device-specific output into a standardized output expressing the amount of fluorescence per well as a known equivalent fluorophore concentration per cell for fluorescent reporters spanning the visible light spectrum. This calibration method follows a 2-fold approach determining both the estimated number of cells and the equivalent chemical fluorophore concentration per well. It will contribute to the comparison of plate reader experiments between different laboratories across the world and will therefore greatly improve the reliability and exchange of both results and genetic parts between research groups.

C-di-AMP levels modulate Staphylococcus aureus cell wall thickness, response to oxidative stress, and antibiotic resistance and tolerance

IMPORTANCE

Antibiotic resistance and tolerance are substantial healthcare-related problems, hampering effective treatment of bacterial infections. Mutations in the phosphodiesterase GdpP, which degrades cyclic di-3', 5'-adenosine monophosphate (c-di-AMP), have recently been associated with resistance to beta-lactam antibiotics in clinical Staphylococcus aureus isolates. In this study, we show that high c-di-AMP levels decreased the cell size and increased the cell wall thickness in S. aureus mutant strains. As a consequence, an increase in resistance to cell wall targeting antibiotics, such as oxacillin and fosfomycin as well as in tolerance to ceftaroline, a cephalosporine used to treat methicillin-resistant S. aureus infections, was observed. These findings underline the importance of investigating the role of c-di-AMP in the development of tolerance and resistance to antibiotics in order to optimize treatment in the clinical setting.

First-passage-time statistics of growing microbial populations carry an imprint of initial conditions

In exponential population growth, variability in the timing of individual division events and environmental factors (including stochastic inoculation) compound to produce variable growth trajectories. In several stochastic models of exponential growth we show power-law relationships that relate variability in the time required to reach a threshold population size to growth rate and inoculum size. Population-growth experiments in E. coli and S. aureus with inoculum sizes ranging between 1 and 100 are consistent with these relationships. We quantify how noise accumulates over time, finding that it encodes-and can be used to deduce-information about the early growth rate of a population.

Functional Prokaryotic-Like Deoxycytidine Triphosphate Deaminases and Thymidylate Synthase in Eukaryotic Social Amoebae: Vertical, Endosymbiotic, or Horizontal Gene Transfer?

The de novo synthesis of deoxythymidine triphosphate uses several pathways: gram-negative bacteria use deoxycytidine triphosphate deaminase to convert deoxycytidine triphosphate into deoxyuridine triphosphate, whereas eukaryotes and gram-positive bacteria instead use deoxycytidine monophosphate deaminase to transform deoxycytidine monophosphate to deoxyuridine monophosphate. It is then unusual that in addition to deoxycytidine monophosphate deaminases, the eukaryote Dictyostelium discoideum has 2 deoxycytidine triphosphate deaminases (Dcd1Dicty and Dcd2Dicty). Expression of either DcdDicty can fully rescue the slow growth of an Escherichia coli dcd knockout. Both DcdDicty mitigate the hydroxyurea sensitivity of a Schizosaccharomyces pombe deoxycytidine monophosphate deaminase knockout. Phylogenies show that Dcd1Dicty homologs may have entered the common ancestor of the eukaryotic groups of Amoebozoa, Obazoa, Metamonada, and Discoba through an ancient horizontal gene transfer from a prokaryote or an ancient endosymbiotic gene transfer from a mitochondrion, followed by horizontal gene transfer from Amoebozoa to several other unrelated groups of eukaryotes. In contrast, the Dcd2Dicty homologs were a separate horizontal gene transfer from a prokaryote or a virus into either Amoebozoa or Rhizaria, followed by a horizontal gene transfer between them. ThyXDicty, the D. discoideum thymidylate synthase, another enzyme of the deoxythymidine triphosphate biosynthesis pathway, was suggested previously to be acquired from the ancestral mitochondria or by horizontal gene transfer from alpha-proteobacteria. ThyXDicty can fully rescue the E. coli thymidylate synthase knockout, and we establish that it was obtained by the common ancestor of social amoebae not from mitochondria but from a bacterium. We propose horizontal gene transfer and endosymbiotic gene transfer contributed to the enzyme diversity of the deoxythymidine triphosphate synthesis pathway in most social amoebae, many Amoebozoa, and other eukaryotes.

Preshaped 4D Photocurable Ultratough Organogel Microcoils for Personalized Endovascular Embolization

Endovascular embolization using microcoils can be an effective technique to treat artery aneurysms. However, microcoils with fixed designs are difficult to adapt to all aneurysm types. In this paper, a photocurable ultratough shape memory organogel with a curing time of only 2 s and megapascal-level mechanical properties is proposed. Then, it is used to manufacture the personalized 4D microcoil with a wire diameter of only 0.3 mm. The improved mechanical modulus (511.63 MPa) can reduce the possibility of microcoils' fracture during embolization. Besides, the fast body-temperature-triggering shape memory ability makes the 4D microcoil applicable in vivo. These 4D microcoils are finally delivered into the rabbit, and successfully blocked the blood flow inside different aneurysms, with neoendothelial cells and collagen fibers growing on the microcoil surface snugly, indicating full aneurysm recovery. This 4D organogel microcoil can potentially be used in personalized clinical translation on human beings.

The evolution of resistance to synergistic multi-drug combinations is more complex than evolving resistance to each individual drug component

Multidrug antibiotic resistance is an urgent public health concern. Multiple strategies have been suggested to alleviate this problem, including the use of antibiotic combinations and cyclic therapies. We examine how adaptation to (1) combinations of drugs affects resistance to individual drugs, and to (2) individual drugs alters responses to drug combinations. To evaluate this, we evolved multiple strains of drug resistant Staphylococcus epidermidis in the lab. We show that evolving resistance to four highly synergistic combinations does not result in cross-resistance to all of their components. Likewise, prior resistance to one antibiotic in a combination does not guarantee survival when exposed to the combination. We also identify four 3-step and four 2-step treatments that inhibit bacterial growth and confer collateral sensitivity with each step, impeding the development of multidrug resistance. This study highlights the importance of considering higher-order drug combinations in sequential therapies and how antibiotic interactions can influence the evolutionary trajectory of bacterial populations.

Nunchaku: optimally partitioning data into piece-wise contiguous segments

MOTIVATION

When analyzing 1D time series, scientists are often interested in identifying regions where one variable depends linearly on the other. Typically, they use an ad hoc and therefore often subjective method to do so.

RESULTS

Here, we develop a statistically rigorous, Bayesian approach to infer the optimal partitioning of a dataset not only into contiguous piece-wise linear segments, but also into contiguous segments described by linear combinations of arbitrary basis functions. We therefore present a general solution to the problem of identifying discontinuous change points. Focusing on microbial growth, we use the algorithm to find the range of optical density where this density is linearly proportional to the number of cells and to automatically find the regions of exponential growth for both Escherichia coli and Saccharomyces cerevisiae. For budding yeast, we consequently are able to infer the Monod constant for growth on fructose. Our algorithm lends itself to automation and high throughput studies, increases reproducibility, and should facilitate data analyses for a broad range of scientists.

AVAILABILITY AND IMPLEMENTATION

The corresponding Python package, entitled Nunchaku, is available at PyPI: https://pypi.org/project/nunchaku.

High-throughput feedback-enabled optogenetic stimulation and spectroscopy in microwell plates

The ability to perform sophisticated, high-throughput optogenetic experiments has been greatly enhanced by recent open-source illumination devices that allow independent programming of light patterns in single wells of microwell plates. However, there is currently a lack of instrumentation to monitor such experiments in real time, necessitating repeated transfers of the samples to stand-alone analytical instruments, thus limiting the types of experiments that could be performed. Here we address this gap with the development of the optoPlateReader (oPR), an open-source, solid-state, compact device that allows automated optogenetic stimulation and spectroscopy in each well of a 96-well plate. The oPR integrates an optoPlate illumination module with a module called the optoReader, an array of 96 photodiodes and LEDs that allows 96 parallel light measurements. The oPR was optimized for stimulation with blue light and for measurements of optical density and fluorescence. After calibration of all device components, we used the oPR to measure growth and to induce and measure fluorescent protein expression in E. coli. We further demonstrated how the optical read/write capabilities of the oPR permit computer-in-the-loop feedback control, where the current state of the sample can be used to adjust the optical stimulation parameters of the sample according to pre-defined feedback algorithms. The oPR will thus help realize an untapped potential for optogenetic experiments by enabling automated reading, writing, and feedback in microwell plates through open-source hardware that is accessible, customizable, and inexpensive.

Rapid Synthesis of Robust Antibacterial and Biodegradable Hydrogels via Frontal Polymerization

Chitosan (CS) is widely used in biomedical hydrogels due to their similarity to extracellular matrix. However, the preparation method of CS-based hydrogel suffers the drawbacks of tedious operation, time-consuming and energy consumption. Thus, there is an urgent need to develop a rapid synthesis pathway towards hydrogels. In this work, we used a modified CS as a cross-linking agent and acrylic acid (AA) as monomer to prepare a hydrogel through frontal polymerization (FP), which facilitates a facile and rapid method achieved in several minutes. The occurrence of pure FP was confirmed via the frontal velocity and temperature profile measurement. In addition, the as-prepared hydrogel shows excellent mechanical strength up to 1.76 MPa, and the Young's modulus (ranging from 0.16 to 0.56 MPa) is comparable to human skin. The degradation mechanism is revealed by the micro-IR images through the distribution of the functional groups, which is attributed to the breakage of the ether bond. Moreover, the hydrogel exhibits excellent degradability, biocompatibility and antibacterial properties, offering great potentials in tissue engineering. We believe this work not only offers a facile and rapid FP method to fabricate a robust degradable hydrogel, but also provides an effective pathway for the investigation of the degradation mechanism at the chemical bond analysis level.

Microwell-enhanced optical rapid antibiotic susceptibility testing of single bacteria

Bacteria that are resistant to antibiotics present an increasing burden on healthcare. To address this emerging crisis, novel rapid antibiotic susceptibility testing (AST) methods are eagerly needed. Here, we present an optical AST technique that can determine the bacterial viability within 1 h down to a resolution of single bacteria. The method is based on measuring intensity fluctuations of a reflected laser focused on a bacterium in reflective microwells. Using numerical simulations, we show that both refraction and absorption of light by the bacterium contribute to the observed signal. By administering antibiotics that kill the bacteria, we show that the variance of the detected fluctuations vanishes within 1 h, indicating the potential of this technique for rapid sensing of bacterial antibiotic susceptibility. We envisage the use of this method for massively parallelizable AST tests and fast detection of drug-resistant pathogens.