Plate Assay Research Articles

Phytochemicals Analysis, In vitro Anti-plasmodium Activity of Delonix regia Bark and Carica papaya Leaf Extracts in Combination with Chloroquine

Background: The effectiveness of treating malaria may be jeopardized by artemisinin-resistant parasites. Pharmaceutical companies have been using plants for a very long time to generate the prototype molecules needed to treat Plasmodium infections. Objective: To evaluate anti-plasmodial potency of extracts of Delonix regia and Carica papaya when used in combinations with chloroquine. Methods: The plants were collected from Homa-Bay County in Kenya, dried under shade to a consistent weight, and then milled into a fine powder. Organic solvents were then used for extraction. After phytochemical screening of the extracts was conducted, In vitro tests were done on the extracts against Plasmodium falciparum, with a starting concentration of 100µg/mL. To prepare the test concentration ranges, the extracts were serially diluted 2-fold in growth medium. In a sealed gas chamber, the assay plates were incubated at 370C for 72 hours with 3% O2 and 4% CO2 with N2 as the balance. By comparing each well's absorbance to that of a well that contained the drug-free control, the number of parasites still present at each concentration of the test substance were ascertained. Plotting survival against concentration enabled the determination of the IC50 values by a non-linear dose response curve fitting. Results: In this investigation, the extracts from Delonix regia showed significant synergism (based on IC50 shifts) with CQ for both the ethyl acetate and methanol extracts with the exception of the highest combination dosage. Carica papaya extracts were much improved by the presence of CQ; however, this was not consistently reflected in the corresponding CQ IC50. Conclusion: The results of this study which revealed synergism between the study plants extracts and chloroquine, support the reasons why some traditional healers have started combining medicinal herbs with chloroquine to boost its potency.

A Comparison of Antibiotics' Resistance Patterns of E. coli and B. Subtilis in their Biofilms and Planktonic Forms.

A biofilm refers to a community of microbial cells that adhere to surfaces that are surrounded by an extracellular polymeric substance. Bacteria employ various defence mechanisms, including biofilm formation, to enhance their survival and resistance against antibiotics. The current study aims to investigate the resistance patterns of Escherichia coli (E. coli) and Bacillus subtilis (B. subtilis) in both biofilms and their planktonic forms. E. coli and B. subtilis were used to compare resistance patterns in biofilms versus planktonic forms of bacteria. An antibiotic disc diffusion test was performed to check the resistance pattern of biofilm and planktonic bacteria against different antibiotics such as penicillin G, streptomycin, and ampicillin. Biofilm formation and its validation were done by using quantitative (microtiter plate assay) and qualitative analysis (Congo red agar media). A study of surface-association curves of E. coli and B. subtilis revealed that surface adhesion in biofilms was continuously constant as compared to their planktonic forms, thereby confirming the increased survival of bacteria in biofilms. Also, biofilms have shown high resistance towards the penicillin G, ampicillin and streptomycin as compared to their planktonic form. It is safely inferred that E. coli and B. subtilis, in their biofilms, become increasingly resistant to penicillin G, ampicillin and streptomycin.

Isolation and Identification of Xylanase Producing Bacteria from Soil Samples of Kerala

Microorganisms play a very vital role in the biological recycling of plant bio-matter. Xylan is the second most plentiful polysaccharide and is found as an interface between lignin and other polysaccharide in the secondary cell wall. When these polysaccharides are hydrolyzed by a suitable strain of bacteria it will become an end to many environmental issues and had many useful applications such as in paper and pulp industry, food and feed industry, bread quality improvement, agro waste treatment, seed germination, generation of bio-fuels etc. To isolate a suitable strain of bacteria which possess good xylanase activity several samples of soils were collected from various regions of Kerala and were undergone a three step enrichment process. In the primary screening 85 bacterial strains were obtained. 22 isolates produces clear zone during plate assay using beech wood xylan. The isolates which possess more than 0.5cm clear zone were undergone final screening process and the strain PSS 1 showed the maximum enzyme activity of 112.38 U/ml.

Molecular characterization, antibiotic resistant pattern and biofilm forming potentiality of bacterial community associated with Ompok pabda fish farming in southwestern Bangladesh

Ompok pabda is gaining popularity in the aquaculture industry due to its increasing demand; however research on microbial diversity and antibiotic susceptibility remains limited. The present study was designed to identify the bacterial pathogens commonly found in the pabda farming system with their biofilm forming potential and antibiotic susceptibility. Different bacterial strains were isolated from water, sediments and gut, gill of pabda fish and the isolates were identified based on their morphological traits, biochemical and molecular analysis. Antibiotic susceptibilities, antibiotic resistance gene determination and biofilm formation capabilities were evaluated by disc diffusion method, PCR amplification and Microtiter plate (MTP) assay, respectively. The respective isolates of gill and gut of pabda aquaculture and their environments were: Exiguobacterium spp. (25 %), Enterococcus spp. (20 %), Bacillus spp. (10 %), Acinetobacter spp. (10 %), Enterobacter spp. (10 %), Aeromonas spp. (10 %), Lactococcus spp. (5 %), Klebsiella spp. (5 %) and Kurthia spp. (5 %). Antibiotic resistance frequencies were found to be relatively high, especially for trimethoprim (95 %), sulfafurazole (75 %), ampicillin (60 %), amoxicillin-clavulanic acid (55 %), and cephradine (50 %). 30 % isolates were categorized as DR bacteria followed by 30 % isolates were MDR bacteria and 40 % were classified as XDR bacteria. Moreover, 4 antibiotic resistant genes were detected with sul1 (30 %), dfrA1 (10 %), tetC (40 %), and qnrA (5 %) of isolates. Based on the microtiter plate method, 20 %, 25 %, and 30 % of isolates were found to produce strong, moderate, and weak biofilms, respectively. The findings suggest that biofilm forming bacterial strains found in O. pabda fish farm may be a potential source of numerous antibiotic-resistant bacteria. The study sheds new light on antibiotic resistance genes, which are typically inherited by bacteria and play an important role in developing effective treatments or control strategies.

Characterization of raw starch hydrolysing and detergent-compatible amylase from newly isolated Bacillus subtilis from bakery chimney

Amylases are highly needful product in food, beverage, and detergent industry. With the objective of isolating α-amylases producing strains, samples were collected from local bakery chimneys and kitchens, Chennai, Tamil Nadu, India. The potential α-amylase producers were isolated and screened by Starch-Iodine plate assay method. The optimized parameters such as 1.5% of starch concentration in the media with 7.2-pH at 35 °C for 36 h enhanced the production of α-amylase. The strain showing high potential, identified by 16s rRNA sequencing was found to be Bacillus subtilis. The Bacillus subtilis strain produced extracellular α-amylase with activity of 1330.14 U/mL. Further partial purification by ammonium sulphate precipitation followed by dialysis and column chromatography enhanced the specific activity to 1695.306 U/mg. The molecular weight of enzymes was found to be around 36 kDa. The enzyme stability and activity characterization revealed that the enzyme was thermotolerant which was able to retain more than 70% activity at 70 °C, 80 °C and 90 °C. The purified enzyme was also found to be Ca2+ independent. The hydrolysis of raw starch from rice, wheat and corn flour using the purified α-amylase from Bacillus subtilis showed significant activity of 72.8%, 76.1% and 65.2% with 4 h incubation respectively. The potentiality of the enzyme as an additive with commercial detergent was also determined to be effective. This study favourably attracts the attention towards industrial applications.

Towards sustainable biocontrol: inhibition of soil borne fungi by microalgae from harsh environments.

Using microorganisms as biocontrol agents against soilborne plant pathogens is a promising alternative to chemical pesticides. However, only some biocontrol agents have proven effective under field conditions. This study explores the potential of highly resilient microalgae isolated from harsh environments, such as Biological Soil Crusts and agricultural fields in semi-arid regions, as a novel and sustainable approach to biocontrol. Fifty-nine microalgal strains, including thirteen cyanobacteria and forty-six green algae, were isolated and identified. Dual-culture plate assays and toxicity tests of microalgal growth media were conducted to evaluate the antifungal activity of the isolates against eight representative soilborne pathogens. The results showed that many microalgae strains exhibited significant inhibitory effects on the growth of specific fungal pathogens, although the activity varied among different microalgal strains and pathogen species. Some strains even promoted the growth of certain fungi. The lack of a clear pattern in the antifungal activity highlights the complexity and specificity of the interactions between microalgae and soilborne pathogens. An "Inhibition Effectiveness" metric was developed to quantify biocontrol potential based on fungal growth inhibition. The green algal genus Desmodesmus, particularly Desmodesmus subspicatus isolates, showed higher antifungal efficacy than other genera. While the inhibitory mechanisms remain unclear, the results demonstrate the promising biocontrol capabilities of microalgae from extreme environments like BSCs. Further research could unlock novel opportunities for sustainable disease management by harnessing specific microalgal strains or synergistic strain combinations targeting soilborne pathogens.

Three Ecological Models to Evaluate the Effectiveness of Trichoderma spp. for Suppressing Aflatoxigenic Aspergillus flavus and Aspergillus parasiticus.

Chemical pesticides help reduce crop loss during production and storage. However, the carbon footprints and ecological costs associated with this strategy are unsustainable. Here, we used three in vitro models to characterize how different Trichoderma species interact with two aflatoxin producers, Aspergillus flavus and Aspergillus parasiticus, to help develop a climate-resilient biological control strategy against aflatoxigenic Aspergillus species. The growth rate of Trichoderma species is a critical factor in suppressing aflatoxigenic strains via physical interactions. The dual plate assay suggests that Trichoderma mainly suppresses A. flavus via antibiosis, whereas the suppression of A. parasiticus occurs through mycoparasitism. Volatile organic compounds (VOCs) produced by Trichoderma inhibited the growth of A. parasiticus (34.6 ± 3.3%) and A. flavus (20.9 ± 1.6%). The VOCs released by T. asperellum BTU and T. harzianum OSK-34 were most effective in suppressing A. flavus growth. Metabolites secreted by T. asperellum OSK-38, T. asperellum BTU, T. virens OSK-13, and T. virens OSK-36 reduced the growth of both aflatoxigenic species. Overall, T. asperellum BTU was the most effective at suppressing the growth and aflatoxin B1 production of both species across all models. This work will guide efforts to screen for effective biological control agents to mitigate aflatoxin accumulation.

Mentha longifolia assisted nanostructures: An approach to obliterate microbial biofilms.

Microbes maneuver strategies to become incessant and biofilms perfectly play a role in scaling up virulence to cause long-lasting infections. The present study was designed to assess the use of an eco-friendly formulation of functionalized silver nanoparticles generated from Mentha longifolia leaf extract (MℓE) for the treatment of biofilm-producing microbes. Nanoparticles synthesized using MℓE as a reducing agent were optimized at different strengths of AgNO3 (1 mM, 2 mM, 3 mM, and 4 mM). Synthesis of M. longifolia silver nanoparticles (MℓAgNPs) was observed spectrophotometrically (450 nm) showing that MℓAgNPs (4 mM) had the highest absorbance. Various techniques e.g., Fourier transforms Infrared spectroscopy (FTIR), Dynamic light scattering (DLS), zeta potential (ZP), X-ray Diffraction (XRD), scanning electron microscope (SEM), and transmission electron microscope (TEM) were used to characterize MℓAgNPs. In the present study, the Kirby-Bauer method revealed 4mM was the most detrimental conc. of MℓAgNPs with MIC and MBC values of 0.62 μg/mL and 1.25 μg/mL, 0.03 μg/mL and 0.078 μg/mL, and 0.07 μg/mL and 0.15 μg/mL against previously isolated and identified clinical strains of Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Staphylococcus aureus, respectively. Moreover, the MℓAgNP antibiofilm activity was examined via tissue culture plate (TCP) assay that revealed biofilm inhibition of up to 87.09%, 85.6%, 83.11%, and 75.09% against E. coli, P. aeruginosa, K. pneumonia, and S. aureus, respectively. Herbal synthesized silver nanoparticles (MℓAgNPs) tend to have excellent antibacterial and antibiofilm properties and are promising for other biomedical applications involving the extrication of irksome biofilms. For our best knowledge, it is the first study on the use of the green-synthesized silver nanoparticle MℓAgNP as an antibiofilm agent, suggesting that this material has antibiotic, therapeutic, and industrial applications.

Genomic Insights into the Landfill Microbial Community: Denitrifying Activity Supporting One-Carbon Utilization.

In spite of the developments in understanding of denitrifying methylotrophy in the recent years, challenges still exist in unravelling the overall biochemistry of nitrate-dependent methane oxidation in novel or poorly characterized/not-yet-cultured bacteria. In the present study, landfill site was mined for novel C1-carbon-metabolizing bacteria which can use nitrate/nitrite as an electron acceptor. A high-throughput rapid plate assay identified three bacterial isolates with eminent ability for nitrate-dependent methane metabolism under anaerobic conditions. Taxonomic identification by whole-genome sequence-based overall genome relatedness indices accurately assigned the isolates AAK_M13, AAK_M29, and AAK_M39 at the species level to Enterobacter cloacae, Bacillus subtilis, and Bacillus halotolerans, respectively. Several genes encoding sub-components involved in alcohol utilization and denitrification pathways, such as adh, fdh, fdo, nar, nir, and nor, were identified in all the genomes. Though no gene clusters encoding MMO/AMO were annotated, sequencing of PCR amplicons revealed similarity with pMMO/AMO gene using translated nucleotide sequence of strains AAK_M29 and AAK_M39, while strain AAK_M13 showed similarity with XRE family transcriptional regulator. This suggests the horizontal gene transfer and/or presence of a truncated version of a housekeeping enzyme encoded by genes exhibiting partial sequence similarity with pMMO genes that mimicked its function at greenhouse gas emission sites. Owing to lack of conclusive evidence for presence of methane metabolism genes in the selected isolates, further experiment was performed to validate their nitrate-dependent methane oxidation capacities. Bacillus subtilis AAK_M29, Bacillus halotolerans AAK_M39, and Enterobacter cloacae AAK_M13 could oxidize 60%, 75%, and 85% of the added methane respectively accompanied by high nitrate reduction (56-62%) thus supporting the correlation between these two activities. The remarkable ability of these isolates for nitrate-dependent methane metabolism has highlighted their role in ecological contribution and biotechnological potential to serve as methane and nitrate sinks in the landfill sites.

Unveiling the microevolution of antimicrobial resistance in selected Pseudomonas aeruginosa isolates from Egyptian healthcare settings: A genomic approach

The incidence of Pseudomonas aeruginosa infections in healthcare environments, particularly in low-and middle-income countries, is on the rise. The purpose of this study was to provide comprehensive genomic insights into thirteen P. aeruginosa isolates obtained from Egyptian healthcare settings. Phenotypic analysis of the antimicrobial resistance profile and biofilm formation were performed using minimum inhibitory concentration and microtiter plate assay, respectively. Whole genome sequencing was employed to identify sequence typing, resistome, virulome, and mobile genetic elements. Our findings indicate that 92.3% of the isolates were classified as extensively drug-resistant, with 53.85% of these demonstrating strong biofilm production capabilities. The predominant clone observed in the study was ST773, followed by ST235, both of which were associated with the O11 serotype. Core genome multi-locus sequence typing comparison of these clones with global isolates suggested their potential global expansion and adaptation. A significant portion of the isolates harbored Col plasmids and various MGEs, all of which were linked to antimicrobial resistance genes. Single nucleotide polymorphisms in different genes were associated with the development of antimicrobial resistance in these isolates. In conclusion, this pilot study underscores the prevalence of extensively drug-resistant P. aeruginosa isolates and emphasizes the role of horizontal gene transfer facilitated by a diverse array of mobile genetic elements within various clones. Furthermore, specific insertion sequences and mutations were found to be associated with antibiotic resistance.

Investigation on biofilm composition and virulence traits of S. pseudintermedius isolated from infected and colonized dogs.

Staphylococcus pseudintermedius, which is part of the skin microbiome of dogs, causes a variety of opportunistic infections. These infections may become more difficult to treat due to the formation of biofilm. The capacity of S. pseudintermedius to form biofilm, as well as the associated genes, has not been elucidated. This study evaluated the production and composition of S. pseudintermedius biofilm. Samples were collected from both infected dogs and asymptomatic dogs. Isolates were identified using mass spectrometry and Multiplex-PCR. Biofilm production and composition were assessed using a quantitative microtiter plate assay. The presence of ica operon genes and sps genes was investigated using conventional PCR. The investigation of Agr type and virulence genes was conducted in silico on 24 sequenced samples. All strains could produce strong biofilms, with most of the isolates presenting a polysaccharide biofilm. 63.6% of the isolates carried the complete ica operon (ADBC). All samples showed the presence of the genes spsK, spsA, and spsL, while the distribution of other genes varied. Agr type III was the most prevalent (52.2%). All sequenced samples carried the cytotoxins hlb, luk-S, luk-F, as well as the exfoliative toxins siet and se_int. No isolate displayed other exfoliative toxins. Only LB1733 presented a set of different enterotoxins (sea, seb, sec_canine, seh, sek, sel, and seq). Our findings suggest that S. pseudintermedius is a strong producer of biofilm and carries virulence genes.

Trichoderma produces methyl jasmonate-rich metabolites in the presence of Fusarium, showing biostimulant activity and wilt resistance in tomatoes

Bioactive secondary metabolites from fungi, including Trichoderma, are an excellent source of plant biostimulants. Although production of novel biostimulants from known microbes is critical, challenging them may produce novel bioactive compounds. With this hypothesis, the study used live Fusarium chlamydosporum (FOL7) culture as the inducer during T. harzianum (IF63) growth in broth. Plate assays and gas chromatography-mass spectrometry (GC-MS) analysis were used to characterise the metabolites. Microscopy, pot experiments and, biochemical estimations of the defence-related enzymes in tomato plants established the biostimulant activity of the induced Trichoderma metabolites. Fungal crude metabolites (FCM) obtained from IF63+FOL7 extracts (TF.ex) showed increased antimicrobial activity. TF.ex at 50 μg mL−1, inhibited the FOL7 growth by 68.33% compared to the Trichoderma alone extract. Scanning electron microscopy (SEM) revealed morphological disruption of FOL7 mycelia by TF.ex. GC-MS analysis of the extracts revealed the presence of approximately 64 compounds, of which at least 13 were detected explicitly in TF.ex. Methyl (3-oxo-2-pentylcyclopentyl) acetate (Methyl dihydrojasmonate), a lipid functionally related to jasmonic acid, was the major metabolite (∼21%) present in TF.ex. Tomato seed dressing with TF.ex promoted plant growth and induced systemic resistance against FOL7 compared to alone Trichoderma and Fusarium extracts. The TF.ex treatment increased the superoxide dismutase (33%) and catalase activity by 2.5-fold in tomato plants. The study concludes that fungal secondary metabolites may be modulated by providing appropriate challenges to produce effective metabolite-based biostimulants for agricultural applications.

Use of the Saccharomycopsis schoenii MET17 promoter for regulated heterologous gene expression

The ability to regulate the expression of genes is a central tool for the characterization of fungal genes. This is of particular interest to study genes required for specific processes or the effect of genes expressed only under specific conditions. Saccharomycopsis species show a unique property of necrotrophic mycoparasitism that is activated upon starvation. Here we describe the use of the MET17 promoter of S. schoenii as a tool to regulate gene expression based on the availability of methionine. Conditional expression was tested using lacZ and GFP reporter genes. Gene expression could be strongly down-regulated by the addition of methionine or cysteine to the growth medium and upregulated by starvation for methionine. We used X-gal (5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside) to detect lacZ-expression in plate assays and ONPG (ortho-nitrophenyl-β-galactopyranoside) as a substrate for β-galactosidase in liquid-phase assays. For in vivo expression analyses we used fluorescence microscopy for the detection and localization of a MET17-driven histone H4-GFP reporter gene. With these assays we demonstrated the usefulness of the MET17 promoter to regulate expression of genes based on methionine availability. In silico analyses revealed similar promoter motifs as found in MET3 genes of Saccharomyces cerevisiae and Ashbya gossypii. This suggests a regulation of the MET17 promoter by CBF1 and MET31/MET32 in conjunction with the transcriptional activator MET4, which were also identified in the S. schoenii genome.

Collaborative robotics to enable ultra-high-throughput IR-MALDESI

Over the last 5 years, IR-MALDESI-MS (Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometry) has been demonstrated for use in a range of high-throughput biochemical and cellular assays with remarkable sample acquisition rates up to 22 Hz for a single 384-well assay plate. With such high single plate acquisition rates, the rate limiting step becomes how fast subsequent plates can be presented to the MS for analysis. To make this transfer as fast as possible while maintaining safe operation in a laboratory environment, we developed a collaborative robotic plate transfer system (CRPTS) that combines a 6-axis robot with dual plate grippers, a 7th axis conveyor stage, and a 420-plate capacity sample loading window. As a demonstration of the throughput and flexibility of CRPTS, we performed a biochemical assay that monitored the oxidation of tris(2-carboxyethyl)phosphine (TCEP) to screen for nuisance compounds. Using continuous and step motion scan profiles, we analyzed 158,799 compounds contained in 448 assay plates over the course of 12.5 h (Z-Factor=0.87) and 17.5 h (Z-factor=0.99), respectively. Extrapolating these results enables the screening of a million compounds within 6–7 working days.

A novel highly sensitive inner filter effect-based fluorescence immunoassay with quantum dots for bioanalysis of zolbetuximab, a monoclonal antibody used for immunotherapy of gastric and gastroesophageal junction adenocarcinoma

Zolbetuximab (ZOL) is a groundbreaking monoclonal antibody targeting CLDN 18.2, a cancer cell surface protein. It is a first-in-class therapy for gastric and gastroesophageal junction adenocarcinoma. However, there is currently any immunoassay available for bioanalysis of ZOL, hindering its pharmacokinetic studies, therapeutic monitoring, and safety profile refinement. To address this gap, this study presents the development and validation of a novel highly sensitive inner filter effect-based fluorescence immunoassay (IFE-FIA) with quantum dots (QDs) as a probe. This assay enables the quantitative determination of ZOL in plasma samples. The assay involved non-competitive capturing of ZOL from the samples using a specific antigen (CLDN 18.2 protein) immobilized on assay plate microwells. A horseradish peroxidase (HRP)-labelled anti-human IgG was used to measure the immune complex. The assay's detection system relies on the formation of a light-absorbing colored product through an HRP-catalyzed oxidative reaction with the substrate 3,3′,5,5′-tetramethylbenzidine. This light absorption efficiently quenched the fluorescence of QDs via the IFE. The measured fluorescence signals corresponded to the concentrations of ZOL in the samples. The conditions of the IFE-FIA and its detection system were refined, and the optimum procedures were established. Following the guidelines of immunoassay validation for bioanalysis, the assay was validated, and all the validation criteria were acceptable. The assay demonstrates high sensitivity, accurately quantifying ZOL at concentrations as low as 10 ng/mL in plasma samples, with acceptable precision. Importantly, it avoids interferences from endogenous substances and plasma matrix. The recoveries in spiked human plasma ranged from 96.8 % to 104.5 %, with relative standard deviations of 4.1 %–6.5 %. The proposed IFE-FIA represents a valuable tool for quantifying ZOL in clinical settings, enabling assessment of its pharmacokinetics, therapeutic drug monitoring, and safety profile refinement.

SYNERGISTIC ANTIBIOFILM ACTIVITY OF PROBIOTIC LACTOBACILLUS ACIDOPHILUS AND PUNICA GRANATUM L., AGAINST PSEUDOMONAS AERUGINOSA BIOFILM.

Antibiotic resistance is one of the most urgent public health concerns. Biofilm formation is well linked with chronic wounds, chronic obstructive pulmonary disease, urinary tract infections, and cystic fibrosis. Our goal was to assess the biofilm activity of P. aeruginosa and the individual and combined anti-biofilm forming activity of probiotic Lactobacillus acidophilus and Pomegranate peel extract Punica granatum L., against P. aeruginosa. A total of 150 swabs of urine, blood, pus, and CSF were collected from PNS Shifa Hospital Karachi, and P. aeruginosa was isolated and identified according to standard bacteriological methods. The ability of P. aeruginosa to form biofilms was assessed using a microtiter plate assay. The anti-biofilm forming activity of pomegranate peels extract against P. aeruginosa was 29.26±19.09 whereas the anti-biofilm forming activity of Lactobacillus acidophilus against P. aeruginosa was 0.5×106. When used in combination, there was significant synergistic activity between Punica granatum L. (pomegranate peel extract) and Lactobacillus acidophilus. The unique synergistic mixture of natural product extracts and probiotics has demonstrated more efficiency against rapidly evolving pathogens, serving as promising candidates for developing biofilm inhibitors and perhaps proving as possible environmentally friendly agents against bacteria that produce antibiotic-resistant biofilms.

Arabidopsis transcriptome responses to low water potential using high-throughput plate assays.

Soil-free assays that induce water stress are routinely used to investigate drought responses in the plant Arabidopsis thaliana. Due to their ease of use, the research community often relies on polyethylene glycol (PEG), mannitol, and salt (NaCl) treatments to reduce the water potential of agar media, and thus induce drought conditions in the laboratory. However, while these types of stress can create phenotypes that resemble those of water deficit experienced by soil-grown plants, it remains unclear how these treatments compare at the transcriptional level. Here, we demonstrate that these different methods of lowering water potential elicit both shared and distinct transcriptional responses in Arabidopsis shoot and root tissue. When we compared these transcriptional responses to those found in Arabidopsis roots subject to vermiculite drying, we discovered many genes induced by vermiculite drying were repressed by low water potential treatments on agar plates (and vice versa). Additionally, we also tested another method for lowering water potential of agar media. By increasing the nutrient content and tensile strength of agar, we show the 'hard agar' (HA) treatment can be leveraged as a high-throughput assay to investigate natural variation in Arabidopsis growth responses to low water potential.

Arabidopsis transcriptome responses to low water potential using high-throughput plate assays

Arabidopsis transcriptome responses to low water potential using high-throughput plate assays

RosetteArray® Platform for Quantitative High-Throughput Screening of Human Neurodevelopmental Risk.

Neural organoids have revolutionized how human neurodevelopmental disorders (NDDs) are studied. Yet, their utility for screening complex NDD etiologies and in drug discovery is limited by a lack of scalable and quantifiable derivation formats. Here, we describe the RosetteArray® platform's ability to be used as an off-the-shelf, 96-well plate assay that standardizes incipient forebrain and spinal cord organoid morphogenesis as micropatterned, 3-D, singularly polarized neural rosette tissues (>9000 per plate). RosetteArrays are seeded from cryopreserved human pluripotent stem cells, cultured over 6-8 days, and immunostained images can be quantified using artificial intelligence-based software. We demonstrate the platform's suitability for screening developmental neurotoxicity and genetic and environmental factors known to cause neural tube defect risk. Given the presence of rosette morphogenesis perturbation in neural organoid models of NDDs and neurodegenerative disorders, the RosetteArray platform could enable quantitative high-throughput screening (qHTS) of human neurodevelopmental risk across regulatory and precision medicine applications.

The dynamics of biofilm development and dispersal should be taken into account when quantifying biofilm via the crystal violet microtiter plate assay

The crystal violet microtiter plate biofilm assay is often used to compare the amount of biofilm formed by a mutant versus wild-type or a compound-treated biofilm versus the non-treatment control. In many of these studies the amount of biofilm is assessed only at one single time point. However, if the dynamics of biofilm development of the mutant (or compound-treated biofilm) is different than that of the wild-type (or non-treatment control), then biofilm quantification at a single time point may give misleading results. To overcome this shortcoming of the common biofilm quantification technique, we recommend to use a serial dilution-based crystal violet microtiter plate biofilm assay for easy assessment of the dynamics of biofilm development and dispersal. We demonstrate that the dilution-resolved crystal violet assay displays the dynamics of Pseudomonas aeruginosa biofilm development and dispersal as efficient as a time-resolved crystal violet assay. In addition, focusing on mutants of different parts of the c-di-GMP signaling system in P. aeruginosa, we provide an example illustrating the need to assess biofilm dynamics instead of quantifying biofilm biomass at a single time point.