Quantification Of Colonies Research Articles

Symbiosis culture of probiotic Escherichia coli Nissle 1917 and Lactobacillus rhamnosus GG using lactate utilization protein YkgG

The abundance and biodiversity of intestinal bacteria play a critical role in immune system. Escherichia coli Nissle 1917 (EcN), a tractable probiotic cell has emerged as a ‘smart microbe’ that can provide therapeutic modalities at the sites of disease. Additionally, Lactobacillus rhamnosus GG (LGG) represents one of the key probiotics in clinical studies with the ability to enhance intestinal immunity in symbiosis with other cells. To fully exploit the advantages of EcN and LGG, we optimized the commensal culture medium for LGG and EcN, succeeded by the establishment of a novel fluorescence-based colony quantification. From the metabolite analysis, more lactate was consumed when LGG is co-cultured with EcN; thus, YkgG was further explored as it was foreseen to be the enzyme responsible for lactate conversion to pyruvate. The YkgG enzyme from EcN has Vmax of 64.5 mM min-1 and catalytic ability kcat/Km of 2055 mM-1 min-1, that is 6-fold compared to E. coli MG1655. Co-culture strategy of EcN with LGG in the mimic gastrointestinal tract increased the CFU by 50 % and 40 % within 5 mins and 10 mins, respectively. This practical, feasible, and promising symbiosis system aims to accelerate the application of probiotic in healthy food industries.

Colony forming units quantification in mycoplasma cultures by artificial vision system

This research proposes the application of an automatic system for the recognition and counting of colony forming units (CFU) for mycoplasmas, applying a digital image treatment technique. This initiative will facilitate the quantification of colonies, in order to accelerate the diagnostic processes in research where these microorganisms of relevance in public health are involved.

Modeling the Development of SRSF2 Mutated Myeloid Malignancies By CRISPR/Cas9 Mediated Genome Engineering of Primary Human Hematopoietic Stem and Progenitor Cells

Introduction: Acute Myeloid Leukemia (AML) is a malignant disease of the bone marrow that can arise from a premalignant condition called clonal hematopoiesis of indeterminate potential (CHIP). Mutations in Serine and Arginine-rich Splicing Factor 2 (SRSF2) are detected in CHIP and mediate a high risk for AML development. Here we used CRISPR/Cas9-mediated genome engineering to introduce a heterozygous SRSF2P95H mutation into primary human hematopoietic stem and progenitor cells (HSPCs) and investigated its functional consequences using both in vitro and in vivo assays.Methods: We used CRISPR/Cas9 technology to introduce a heterozygous mutant (mut) SRSF2P95H into the endogenous SRSF2 gene locus of healthy cord blood HSPCs. Our approach is based on homologous recombination using DNA repair templates delivered by adeno-associated virus serotype 6 (AAV6) (Figure A). This allows for targeted in-frame integration of mut and/or wildtype (WT) SRSF2 cDNA under the control of the endogenous SRSF2 promoter. Notably, an integrated fluorescent reporter enables the isolation and tracking of heterozygously mutated HSPCs (Figure B). Methylcellulose colony and long-term competition assays of SRSF2 mut and WT HSPCs were performed in vitro. Cells were analyzed by flow cytometry and characterized cytomorphologically. In addition, bulk RNA-seq analyses were performed to characterize differential gene expression and abnormal splicing events. Xenotransplantation into NSG-SGM3 mice was performed in order to assess stem cell characteristics and the in vivo leukemogenic potential of SRSF2 mut HSPCs. Finally, we investigated the mutation-specific effect of the splicing inhibitor Indisulam to determine if SRSF2 mut cells are particularly vulnerable to splicing inhibition.Results: Colony assays (n=9) revealed impaired erythroid and increased monocytic differentiation of SRSF2 mut HSPCs. Quantification of colonies showed a lower frequency of erythroid BFU-E in SRSF2 mut compared to SRSF2 WT HSPCs (mean ± SD; 33.3 ± 12.5% vs. 17.4 ± 10.8%, p=0.00002). In contrast, the frequency of myeloid CFU-M colonies was higher in SRSF2 mut HSPCs compared to SRSF2 WT HSPCs (38.3 ± 7.3% vs. 22.6 ± 6.8%, p = 0.0003) (Figure C). Long-term in vitro competition assays revealed an outgrowth of SRSF2 mut over WT cells in 2 out of 7 donors. Strikingly, after three months of in vitro culture, in one donor, the SRSF2 mut cells developed a blast-like morphology with strong CD34 expression (Figure D). To assess stem cell characteristics and the leukemogenic potential in vivo, we transplanted SRSF2 mut HSPCs from 4 different donors into immunodeficient NSG-SGM3 mice (n=11). SRSF2 mut cells showed a myeloid-skewed engraftment. Cytomorphologic analysis of long-term engrafted SRSF2 mut myeloid cells revealed dysplastic changes such as nuclear abnormalities and extensive cytoplasmic vacuolization. In 4 out of 11 xenografts, human engraftment substantially increased over time with a parallel outgrowth of the SRSF2 mut clone and the appearance of blast-like cells resembling transformation into myeloid leukemia (Figure E). Comparative RNA-seq analysis identified 138 differentially spliced genes, with exon skipping being the dominant altered splicing type. Gene ontology (GO) analysis on differentially expressed genes revealed “Acute Myeloid Leukemia” among the most enriched terms (p-val = 8.2E-07, min FDR = 1.486E-04). When testing the SRSF2-mutation specific effect of the splicing inhibitor Indisulam, SRSF2 mut HSPCs show a significantly lower IC-50 than WT cells (977nM vs. 3574 nM). Strikingly, in competition- and CFU-assays, Indisulam preferentially eradicates SRSF2 mut hematopoietic cells, while sparing WT cells.Conclusion: Using our CRISPR/Cas9 approach, we can successfully introduce heterozygous SRSF2P95H mutants in primary human HSPCs. Mutant SRSF2P95H leads to increased monocytic differentiation, impaired erythroid differentiation, and phenocopy SRSF2P95H driven diseases in patients. Importantly, we show for the first time that the SRSF2 mutation alone is sufficient to induce dysplastic features and even transform healthy human HSPCs into AML-like blasts. Our model allows the identification and therapeutic investigation of specific cellular vulnerabilities caused by SRSF2 mutations and highlights Indisulam as a potential compound to specifically treat individuals carrying a SRSF2 mutation. [Display omitted] DisclosuresEdiriwickrema: Nanosive SAS: Patents & Royalties. Greinix: Novartis: Consultancy; Celgene: Consultancy; Takeda: Consultancy; Sanofi: Consultancy; Therakos: Consultancy. Sill: Astellas: Consultancy, Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees; AbbVie: Consultancy, Membership on an entity's Board of Directors or advisory committees. Zebisch: Celgene: Consultancy, Honoraria; AbbVie: Consultancy; Novartis: Consultancy. Majeti: BeyondSpring Inc.: Membership on an entity's Board of Directors or advisory committees; CircBio Inc.: Membership on an entity's Board of Directors or advisory committees; Kodikaz Therapeutic Solutions Inc.: Membership on an entity's Board of Directors or advisory committees; Coherus Biosciences: Membership on an entity's Board of Directors or advisory committees; Acuta Capital Partners: Consultancy; Gilead: Patents & Royalties: inventor on a number of patents related to CD47 cancer immunotherapy licensed to Gilead Sciences, Inc.. Reinisch: Pfizer: Consultancy; Celgene: Research Funding.

A fully automated deep learning pipeline for high-throughput colony segmentation and classification.

ABSTRACTAdenine auxotrophy is a commonly used non-selective genetic marker in yeast research. It allows investigators to easily visualize and quantify various genetic and epigenetic events by simply reading out colony color. However, manual counting of large numbers of colonies is extremely time-consuming, difficult to reproduce and possibly inaccurate. Using cutting-edge neural networks, we have developed a fully automated pipeline for colony segmentation and classification, which speeds up white/red colony quantification 100-fold over manual counting by an experienced researcher. Our approach uses readily available training data and can be smoothly integrated into existing protocols, vastly speeding up screening assays and increasing the statistical power of experiments that employ adenine auxotrophy.

Silver Nanoparticles Derived from Albizia lebbeck Bark Extract Demonstrate Killing of Multidrug‐Resistant Bacteria by Damaging Cellular Architecture with Antioxidant Activity

AbstractSilver nanoparticles (Ag‐NP‐AE) are synthesized and stabilized by the extract of an ethnomedicine, Albizia lebbeck bark aqueous extract (AE). Ag‐NP‐AE is active against several multidrug‐resistant (MDR) clinical isolates. The nanoparticles are characterized by UV‐vis spectroscopy, Fourier‐transform infrared spectroscopy (FTIR), Dynamic light scattering (DLS), Scanning electron microscope (SEM), Transmission electron microscope (TEM) and X‐ray diffraction (XRD) studies. The antibacterial potency of Ag‐NP‐AE is determined by Disc diffusion, Agar and Broth dilution assays against 14 MDR isolates along with their minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC). The growth kinetics was determined by quantification of colonies; while toxicity by quantification of viable cells. The Ag‐NP‐AE shows free‐radical scavenging activity at 15–20 μM and is non‐toxic up to 50 μM but demonstrated significant antibacterial activity against all the test isolates with zone diameter of 10.4–19.5 mm and MIC of 0.5–0.84 μM (0.085‐0.143 μg); while the zone diameter with AE was 10.2–15 mm and MIC of 128–1024 μg/mL, respectively; while 100 % killing was observed at 0.50 μM within 2–4 h of exposure due to damage of cellular architectures.

High-Throughput Zika Viral Titer Assay for Rapid Screening of Antiviral Drugs.

Zika virus has recently emerged as a worldwide pathogen and public health burden due to its rapid spread and identification as a causative agent for multiple neurological defects, including congenital microcephaly. While there has been a flurry of recent research to address this emerging pathogen, there are currently no approved drug treatments for ZIKV infection. The gold standard for testing antiviral activity is to quantify infectious virion production. However, current infectious viral production assays, such as the plaque-forming or focus-forming unit assay, are tedious and labor intensive with a low-screening throughput. To facilitate drug development, we developed a Zika viral titration assay using an automated imaging system and an image analysis algorithm for viral colony quantification. This assay retained the principle of the classical virus titer assay, while improving workflow and offering higher screening throughput. In addition, this assay can be broadly adapted to quantification of other viruses.

Effect of Chloroaluminium phthalocyanine in cationic nanoemulsion on photoinactivation of multispecies biofilm.

Photosensitizers in nanocarriers have been investigated for antimicrobial Photodynamic Therapy (aPDT). However, most studies are focused against microorganisms in planktonic or monospecies biofilm. Thus, this in vitro study evaluated the effect of aPDT using Chloroaluminium phthalocyanine (ClAlPc) in cationic nanoemulsion (NE) against Candida albicans, Candida glabrata and Streptococcus mutans grown as multispecies biofilm. Standard suspensions of each microorganism were added into wells of a microtiter plate for biofilm growth for 48 h in a candle jar. The biofilms were incubated with ClAlPc in cationic NE at 31.8 μM for 30 min and illuminated with red light fluence of 39.3 J/cm2 (P+L+ group). Additional samples were treated only with photosensitizer (P+L-) or red light (P-L+) or neither (P-L-, control group). aPDT efficacy was assessed by colony quantification, biofilm's metabolic activity, total biomass, and confocal microscopy. Data were analyzed by ANOVA/Welch and post-hoc Tukey/Games-Howell tests (α = 0.05). aPDT (P+L+) reduced the colony count in 1.30 to 2.24 lg10 and the metabolic activity in 53.7% compared with the control group (P-L-). The total biomass showed no statistical difference among the groups. The confocal microscopy analyzes showed uptake of the PS in the biofilm, and dead cells were observed in the biofilm treated with aPDT. aPDT mediated by ClAlPc in cationic NE promoted photoinactivation of the multispecies biofilm, which was confirmed by colony quantification, metabolic activity, and confocal microscopy. However, the total biomass of the biofilm was not affected by the treatment.

Fluorescence-Based Reporters for Detection of Mutagenesis in E. coli.

Mutagenesis in model organisms following exposure to chemicals is used as an indicator of genotoxicity. Mutagenesis assays are also used to study mechanisms of DNA homeostasis. This chapter focuses on detection of mutagenesis in prokaryotes, which boils down to two approaches: reporter inactivation (forward mutation assay) and reversion of an inactivating mutation (reversion mutation assay). Both methods are labor intensive, involving visual screening, quantification of colonies on solid media, or determining a Poisson distribution in liquid culture. Here, we present two reversion reporters for in vivo mutagenesis that produce a quantitative output, and thus have the potential to greatly reduce the amount of test chemical and labor involved in these assays. This output is obtained by coupling a TEM β lactamase-based reversion assay with GFP fluorescence, either by placing the two genes on the same plasmid or by fusing them translationally and interrupting the N-terminus of the chimeric ORF with a stop codon. We also describe a reporter aimed at facilitating the monitoring of continuous mutagenesis in mutator strains. This reporter couples two reversion markers, allowing the temporal separation of mutation events in time, thus providing information about the dynamics of mutagenesis in mutator strains. Here, we describe these reporter systems, provide protocols for use, and demonstrate their key functional features using error-prone Pol I mutagenesis as a source of mutations.

Effect of topical anti-Streptococcus mutans IgY gel on quantity of S. mutans on rats' tooth surface.

This study aims to evaluate the effect of anti-Streptococcus mutans IgY gel on quantity of S. mutans on rats' tooth surface. Sprague Dawley rats were exposed intra-orally with S. mutans Xc and were fed a caries-inducing diet 2000. The 24 rats were divided into four groups: group A had their teeth coated with IgY gel; group B received sterilized water as a control; group C had their teeth coated with IgY gel starting on the 29(th) day; and group D had their teeth coated with a gel without IgY. Plaque samples were swabbed from the anterior teeth for S. mutans colony quantification, and saliva was collected to measure immunoreactivity by enzyme-linked immunosorbent assay. The results indicated that the quantity of S. mutans in rats treated with IgY gel showed significant difference compared with the controls. After coating with IgY anti-S. mutans gel, the mean immunoreactivity in rat saliva was higher than that of the no treatment group. In conclusion, topical application with anti-S. mutans IgY gel reduced the quantity of S. mutans on the tooth surface.

WE‐E‐BRE‐07: High‐Throughput Mapping of Proton Biologic Effect

Purpose:To systematically relate the relative biological effectives (RBE) of proton therapy to beam linear energy transfer (LET) and dose.Methods:Using a custom irradiation apparatus previously characterized by our group, H460 NSCLCs were irradiated using a clinical 80MeV spot scanning proton beam. Utilizing this system allowed for high‐throughput clonogenic assays performed in 96‐well tissue culture plates as opposed to the traditional 6‐well technique. Each column in the 96‐well plate received a set LET‐dose combination. By altering the total number of dose repaintings, numerous dose‐LET configurations were examined to effectively generate surviving fraction (SF) data over the entire Bragg peak. The clonogenic assay was performed post‐irradiation using an INCell Analyzer for colony quantification. SF data were fit to the linear‐quadratic model for analysis.Results:Irradiation with increasing LETs resulted in decreased cell survival largely independent of dose. A significant correlation between LET and SF was identified by two‐way ANOVA and the extra sum‐of‐squares F test. This trend was obscured at the lower LET values in the plateau region of the Bragg peak; however, it was clear for LET values at and beyond the Bragg peak. Data fits revealed the SF at a dose of 2Gy (SF2) to be 0.48 for the lowest tested LET (1.55keV/um), 0.47 at the end of the plateau region (4.74keV/um) and 0.33 for protons at the Bragg peak (10.35keV/um). Beyond the Bragg peak we measured SF2s of 0.16 for 15.01keV/um, 0.02 for 16.79keV/um, and 0.004 for 18.06keV/um.Conclusion:We have shown that our methodology enables high‐content automated screening for proton irradiations over a range of LETs. The observed decrease in cellular SF in high LET regions confirms an increased RBE of the radiation and suggests further evaluation of proton RBE values is necessary to optimize clinical outcomes.Rosalie B. Hite Graduate Fellowship in Cancer Research, NIH Program Project Grant P01CA021239

Susceptibility of multispecies biofilm to photodynamic therapy using Photodithazine®

This in vitro study evaluated the effect of photodynamic therapy (PDT) on the multispecies biofilm of Candida albicans, Candida glabrata, and Streptococcus mutans. Standardized fungal and bacterial suspensions were cultivated appropriately for each species and inoculated in 96-well microtiter plates for mix-biofilm formation. After 48h of incubation, the biofilms were submitted to PDT (P + L+) using Photodithazine® (PDZ) at 100, 150, 175, 200, or 250mg/mL for 20min and 37.5J/cm(2) of light-emitting diode (LED) (660nm). Additional samples were treated only with PDZ (P + L-) or LED (P-L+), or neither (control, P-L-). Afterwards, the biofilms were evaluated by quantification of colonies (CFU/mL), metabolic activity (XTT reduction assay), total biomass (crystal violet staining), and confocal scanning laser microscopy (CSLM). Data were analyzed by one-way ANOVA and Tukey tests (p < 0.05). Compared with the control, PDT promoted a significant reduction in colonies viability of the three species evaluated with 175 and 200mg/mL of PDZ. PDT also significantly reduced the metabolic activity of the biofilms compared with the control, despite the PDZ concentration. However, no significant difference was found in the total biomass of samples submitted or not to PDT. For all analysis, no significant difference was verified among P-L-, P + L-, and P-L+. CSLM showed a visual increase of dead cells after PDT. PDT-mediated PDZ was effective in reducing the cell viability of multispecies biofilm.

Micropatterned Surfaces for Reducing the Risk of Catheter-Associated Urinary Tract Infection: AnIn VitroStudy on the Effect of Sharklet Micropatterned Surfaces to Inhibit Bacterial Colonization and Migration of UropathogenicEscherichia coli

Catheter-associated urinary tract infection (CAUTI) is the most common device-associated infection and can result in serious medical consequences. We studied the efficacy of a novel microscopic physical surface modification (Sharklet) for preventing bacterial colonization and migration of uropathogenic Escherichia coli on silicone elastomer. In vitro growth assays evaluated E coli colonization using three variations of micropatterned silicone surfaces vs a smooth silicone control. Enumeration techniques included quantification of colonies on surfaces and analysis of bacterial area coverage and colony size. In vitro migration assays involved placement of micropatterned and smooth silicone rod segments between two agar islands to measure incidence of migration. All three variations of the Sharklet micropattern outperformed the control surfaces in inhibiting E coli colonization. On average, 47% reduction in colony-forming units (CFUs) and bacterial area coverage plus 77% reduction in colony size were achieved with the Sharklet surfaces in tryptic soy broth and artificial urine compared with the control nonpatterned surfaces. The incidence of E coli migration over the rod segments was reduced by more than 80% for the Sharklet transverse patterned rods compared with the unpatterned control rods. The Sharklet micropattern is effective at inhibiting colonization and migration of a common uropathogen. This performance is achieved through a physical surface modification without the use of any antimicrobial agents. Because deterrence of bacterial colonization and migration is a critical step to prevent CAUTI, the Sharklet micropattern offers a novel concept in addressing this important problem.

Characterization of Functional Domains Necessary for Mutant p53 Gain of Function

Tumor cells, including SW480 carcinoma cells that carry a mutant p53, are addicted to the mutant for their survival and resistance to growth suppression by chemotherapeutic agents. Here, we investigated whether various classes of p53 mutants share a common property and functional domains necessary for mutant p53 gain of function. To test this, we generated SW480 cell lines in which endogenous mutant R273H/P309S can be inducibly or stably knocked down, whereas a small interfering RNA-resistant mutant p53 along with a mutated functional domain can be inducibly or stably expressed. We found that both contact-site (R248W and R273H) and conformation (G245S and R249S) mutants are able to maintain the transformed phenotypes of SW480 cells conferred by endogenous mutant p53. We also found that activation domains 1-2 and the proline-rich domain are required for mutant p53 gain of function. Interestingly, we showed that the C-terminal basic domain, which is required for wild-type p53 activity, is an inhibitory domain for mutant p53. Furthermore, we showed that deletion of the basic domain enhances, whereas a mutation in activation domains 1-2 and deletion of the proline-rich domain abolish mutant p53 to regulate Gro1 and Id2, both of which are regulated by and mediate endogenous mutant p53 gain of function. These results indicate that both conformation and contact-site mutants share a property for cell transformation, and the domains critical for wild-type p53 tumor suppression are also required for mutant p53 tumor promotion. Thus, the inhibitory basic domain and the common property for p53 mutants can be explored for targeting tumors with mutant p53.

Counting clonogenic assays from normoxic and anoxic irradiation experiments manually or by using densitometric software

The clonogenic assay is the method of choice to determine cell reproductive death after in vitro irradiation treatment. Traditionally, colony quantification has been performed by manual counting, a very laborious, time-consuming and rather subjective task. In this study, we compared manual counting by two skilled investigators with automated counting using the freely available ClonoCounter program. Five human tumour cell lines were irradiated under normoxia (21% O2) or anoxia (<0.1% O2), after 24 h or 6 h anoxic preincubation. Colonies were quantified manually or using the ClonoCounter software. A positive correlation between the absolute number of colonies counted manually and automatically was shown. Though there was a general trend of underpredicting the absolute number of cell colonies when counting automatically, survival curves were very similar, and in none of the cell lines were significant differences in radiobiological parameters such as mean inactivation dose, surviving fraction at 2 Gy and oxygen enhancement ratio detected. Our results suggest that the ClonoCounter provides sufficient reliability to be implemented for counting human tumour colonies in in vitro irradiation experiments. In contrast to several previously reported computer-aided colony-counting methods, it is a freely available program, requiring only minimal instrument costs.

Changes in epidermal radiosensitivity with time associated with increased colony numbers.

Epidermal clonogenic cell survival and colony formation following irradiation were investigated and related to radiosensitivity. A rapid in vivo/in vitro assay was developed for the quantification of colonies arising from surviving clonogenic cells in pig epidermis after irradiation. Bromodeoxyuridine (BrdU)-labelled cells in full thickness epidermal sheets were visualized using standard immunohistochemistry. In unirradiated skin, approximately 900 BrdU-positive cells mm(-2) were counted. In a time sequence experiment, BrdU-positive cell numbers increased from an average of 900 cells mm(-2) to approximately 1400 cells mm(-2) after BrdU-labelling for 2-24 h. In irradiated skin, colonies containing >/=16 BrdU-positive cells were seen for the first time at days 14/15 after irradiation. The number of these colonies per cm(2) as a function of skin surface dose yielded a cell survival curve with a D(0)-value (+/-SE) of 3.9+/-0.6 Gy. This relatively high D(0)-value is possibly due to a rapid fall off in depth dose distribution for the iridium-192 source and consequently a substantial contribution of hair follicular epithelium to colony formation. At 14/15 days after irradiation, the ED(50) level of 33.6 Gy for the in vivo response of moist desquamation corresponded with 2.7 colonies cm(-2). Surprisingly, the number of colonies increased with time after irradiation with an estimated doubling time of approximately 4 days, while the D(0)-value remained virtually unchanged. This increase in colony numbers could be due to migration of clonogenic cells, to the recruitment of dormant clonogenic cell survivors by elevated levels of cytokines, or to both. Although frequent biopsying caused increased cytokine levels, which had a systemic effect on unirradiated skin, it had no influence on colony formation in irradiated skin. Smaller colonies, containing 4-8 cells or 9-15 cells, were abundant, particularly after higher doses, which resulted in higher D(0)-values. The majority of these small colonies were abortive and did not progress to larger colonies. There was no statistical evidence for significant variations in the interanimal responses.