Low-cost, high-throughput, automated counting of bacterial colonies

A new method for non-invasive biomass determination based on stereo photogrammetry

A novel, non-destructive method for the biomass estimation of biological samples on culture dishes was developed. To achieve this, a photogrammetric system, which consists of a digital single-lens reflex camera (DSLR), an illuminated platform where the culture dishes are positioned and an Arduino board which controls the capturing process, was constructed. The camera was mounted on a holder which set the camera at different title angles and the platform rotated, to capture images from different directions. A software, based on stereo photogrammetry, was developed for the three-dimensional (3D) reconstruction of the samples. The proof-of-concept was demonstrated in a series of experiments with plant tissue cultures and specifically with calli cultures of Salvia fruticosa and Ocimum basilicum. For a period of 14 days images of these cultures were acquired and 3D-reconstructions and volumetric data were obtained. The volumetric data correlated well with the experimental measurements and made the calculation of the specific growth rate, µ _max, possible. The µ _max value for S. fruticosa samples was 0.14 day^-1 and for O. basilicum 0.16 day^-1. The developed method demonstrated the high potential of this photogrammetric approach in the biological sciences.

Area-based cell colony surviving fraction evaluation: A novel fully automatic approach using general-purpose acquisition hardware

BACKGROUND

The current methodology for the Surviving Fraction (SF) measurement in clonogenic assay, which is a technique to study the anti-proliferative effect of treatments on cell cultures, involves manual counting of cell colony forming units. This procedure is operator-dependent and error-prone. Moreover, the identification of the exact colony number is often not feasible due to the high growth rate leading to the adjacent colony merging. As a matter of fact, conventional assessment does not deal with the colony size, which is generally correlated with the delivered radiation dose or the administered cytotoxic agent.

METHOD

Considering that the Area Covered by Colony (ACC) is proportional to the colony number and size as well as to the growth rate, we propose a novel fully automatic approach exploiting Circle Hough Transform, to automatically detect the wells in the plate, and local adaptive thresholding, which calculates the percentage of ACC for the SF quantification. This measurement relies just on this covering percentage and does not consider the colony number, preventing inconsistencies due to intra- and inter-operator variability.

RESULTS

To evaluate the accuracy of the proposed approach, we compared the SFs obtained by our automatic ACC-based method against the conventional counting procedure. The achieved results (r = 0.9791 and r = 0.9682 on MCF7 and MCF10A cells, respectively) showed values highly correlated with the measurements using the traditional approach based on colony number alone.

CONCLUSIONS

The proposed computer-assisted methodology could be integrated in laboratory practice as an expert system for the SF evaluation in clonogenic assays.

The Pneumococcal Serotype 15C Capsule Is Partially O-Acetylated and Allows for Limited Evasion of 23-Valent Pneumococcal Polysaccharide Vaccine-Elicited Anti-Serotype 15B Antibodies

As a species, Streptococcus pneumoniae (the pneumococcus) utilizes a diverse array of capsular polysaccharides to evade the host. In contrast to large variations in sugar composition and linkage formation, O-acetylation is a subtle capsular modification that nonetheless has a large impact on capsular shielding and recognition of the capsule by vaccine-elicited antibodies. Serotype 15B, which is included in the 23-valent pneumococcal polysaccharide vaccine (PPV23), carries the putative O-acetyltransferase gene wciZ The coding sequence of wciZ contains eight consecutive TA repeats [(TA)₈]. Replication slippage is thought to result in the addition or loss of TA repeats, subsequently causing frameshift and truncation of WciZ to yield a nonacetylated serotype, 15C. Using sensitive serological tools, we show that serotype 15C isolates whose wciZ contains seven or nine TA repeats retain partial O-acetylation, while serotype 15C isolates whose wciZ contains six TA repeats have barely detectable O-acetylation. We confirmed by inhibition enzyme-linked immunosorbent assay that (TA)₇ serotype 15C is ∼0.1% as acetylated as serotype 15B, while serotype 15X is nonacetylated. To eliminate the impact of genetic background, we created isogenic serotype 15B, (TA)₇ serotype 15C, and 15BΔwciZ (15X) strains and found that reduction or absence of WciZ-mediated O-acetylation did not affect capsular shielding from phagocytes, biofilm formation, adhesion to nasopharyngeal cells, desiccation tolerance, or murine colonization. Sera from PPV23-immunized persons opsonized serotype 15B significantly but only slightly better than serotypes 15C and 15X; thus, PPV23 may not result in expansion of serotype 15C.

Opsonophagocytic Antibodies to Serotype Ia, Ib, and III Group B Streptococcus among Korean Infants and in Intravenous Immunoglobulin Products

Group B streptococcus (GBS) infection is a leading cause of sepsis and meningitis among infants, and is associated with high rates of morbidity and mortality in many countries. Protection against GBS typically involves antibody-mediated opsonization by phagocytes and complement components. The present study evaluated serotype-specific functional antibodies to GBS among Korean infants and in intravenous immunoglobulin (IVIG) products. An opsonophagocytic killing assay (OPA) was used to calculate the opsonization indices (OIs) of functional antibodies to serotypes Ia, Ib, and III in 19 IVIG products from 5 international manufacturers and among 98 Korean infants (age: 0-11 months). The GBS Ia, Ib, and III serotypes were selected because they are included in a trivalent GBS vaccine formulation that is being developed. The OI values for the IVIG products were 635-5,706 (serotype Ia), 488-1,421 (serotype Ib), and 962-3,315 (serotype III), and none of the IVIG lots exhibited undetectable OI values (< 4). The geometric mean OI values were similar for all 3 serotypes when we compared the Korean manufacturers. The seropositive rate among infants was significantly lower for serotype Ia (18.4%), compared to serotype Ib and serotype III (both, 38.8%). Infant age of ≥ 3 months was positively correlated with the seropositive rates for each serotype. Therefore, only a limited proportion of infants exhibited protective immunity against serotype Ia, Ib, and III GBS infections. IVIG products that exhibit high antibody titers may be a useful therapeutic or preventive measure for infants. Further studies are needed to evaluate additional serotypes and age groups.

Screening of breast cancer stem cell inhibitors using a protein kinase inhibitor library

BACKGROUND

Cancer stem cells (CSCs), a subpopulation in tumors, are known to cause drug resistance, tumor recurrence and metastasis. Based on the characteristic formation of mammospheres in in vitro conditions, the mammosphere formation assay has become an essential tool for quantifying CSC activity in breast cancer research. However, manual counting of mammospheres is a time-consuming process that is not amenable to high-throughput screening, and there are occasional inaccuracies in the process of determining the mammosphere diameter. In this study, we proposed a novel automated counting method of mammosphere using the National Institute of Standards and Technology (NIST)'s Integrated Colony Enumerator (NICE) with a screening of protein kinase library.

METHODS

Human breast cancer cell line MCF-7 was used for evaluation of tumor sphere efficiency, migration, and phenotype transition. Cell viability was assessed using MTT assay, and CSCs were identified by an analysis of CD44 expression and ALDEFLUOR assay using flow cytometry. Automated counting of mammosphere using NICE program was performed with a comparison to the result of manual counting. After identification of inhibitors to ameliorate CSC formation by screening a library of 79 protein kinase inhibitors using automated counting in primary, secondary and tertiary mammosphere assay, the effect of selected kinase inhibitors on migration, colony formation and epithelial-to-mesenchymal transition (EMT) of MCF-7 cells was investigated.

RESULTS

Automated counting of mammosphere using NICE program was an easy and less time-consuming process (<1 min for reading 6-well plate) which provided a comparable result with manual counting. Inhibition of calcium/calmodulin-dependent protein kinase II (CaMKII), Janus kinase-3 (JAK-3), and IκB kinase (IKK) were identified to decrease the formation of MCF-7-derived CSCs in primary, secondary and tertiary mammosphere assay. These protein kinase inhibitors alleviated TGF-β1-induced migration, colony formation and EMT of MCF-7 cells.

CONCLUSIONS

We have developed a novel automated cell-based screening method which provided an easy, accurate and reproducible way for mammosphere quantification. This study is the first to show the efficacy of an automated medium-throughput mammosphere-counting method in CSC-related research with an identification of protein kinase inhibitors to ameliorate CSC formation.

Growth-Based Bacterial Viability Assay for Interference-Free and High-Throughput Toxicity Screening of Nanomaterials

Current high-throughput approaches evaluating toxicity of chemical agents toward bacteria typically rely on optical assays, such as luminescence and absorbance, to probe the viability of the bacteria. However, when applied to toxicity induced by nanomaterials, scattering and absorbance from the nanomaterials act as interferences that complicate quantitative analysis. Herein, we describe a bacterial viability assay that is free of optical interference from nanomaterials and can be performed in a high-throughput format on 96-well plates. In this assay, bacteria were exposed to various materials and then diluted by a large factor into fresh growth medium. The large dilution ensured minimal optical interference from the nanomaterial when reading optical density, and the residue left from the exposure mixture after dilution was confirmed not to impact the bacterial growth profile. The fractions of viable cells after exposure were allowed to grow in fresh medium to generate measurable growth curves. Bacterial viability was then quantitatively correlated to the delay of bacterial growth compared to a reference regarded as 100% viable cells; data analysis was inspired by that in quantitative polymerase chain reactions, where the delay in the amplification curve is correlated to the starting amount of the template nucleic acid. Fast and robust data analysis was achieved by developing computer algorithms carried out using R. This method was tested on four bacterial strains, including both Gram-negative and Gram-positive bacteria, showing great potential for application to all culturable bacterial strains. With the increasing diversity of engineered nanomaterials being considered for large-scale use, this high-throughput screening method will facilitate rapid screening of nanomaterial toxicity and thus inform the risk assessment of nanoparticles in a timely fashion.

Safety and Immunogenicity of a Candidate Bioconjugate Vaccine against Shigella flexneri 2a Administered to Healthy Adults: a Single-Blind, Randomized Phase I Study

Several candidate vaccines against Shigella spp. are in development, but the lack of a clear correlate of protection from challenge with the induction of adequate immune responses among the youngest age groups in the developing world has hampered Shigella vaccine development over the past several decades. Bioconjugation technology, exploited here for an Shigella flexneri 2a candidate vaccine, offers a novel and potentially cost-effective way to develop and produce vaccines against a major pathogen of global health importance. Flexyn2a, a novel S. flexneri 2a bioconjugate vaccine made of the polysaccharide component of the S. flexneri 2a O-antigen, conjugated to the exotoxin protein A of Pseudomonas aeruginosa (EPA), was evaluated for safety and immunogenicity among healthy adults in a single-blind, phase I study with a staggered randomization approach. Thirty subjects (12 receiving 10 μg Flexyn2a, 12 receiving Flexyn2a with aluminum adjuvant, and 6 receiving placebo) were administered two injections 4 weeks apart and were followed for 168 days. Flexyn2a was well-tolerated, independently of the adjuvant and number of injections. The Flexyn2a vaccine elicited statistically significant S. flexneri 2a lipopolysaccharide (LPS)-specific humoral responses at all time points postimmunization in all groups that received the vaccine. Elicited serum antibodies were functional, as evidenced by bactericidal activity against S. flexneri 2a. The bioconjugate candidate vaccine Flexyn2a has a satisfactory safety profile and elicited a robust humoral response to S. flexneri 2a LPS with or without inclusion of an adjuvant. Moreover, the bioconjugate also induced functional antibodies, showing the technology's features in producing a promising candidate vaccine. (This study has been registered at ClinicalTrials.gov under registration no. NCT02388009.).

A high throughput serum bactericidal assay for antibodies to Haemophilus influenzae type b

BACKGROUND

The protective capacities of antibodies induced with Haemophilus influenzae type b (Hib) vaccines can be directly assessed in vitro with a Hib-specific serum bactericidal assay (SBA). However, the conventional SBA requires several tedious steps including manual counting of bacterial colonies, and therefore, it is seldom used.

METHODS

To overcome these limitations, we have improved the conventional SBA by using frozen target bacteria and by developing an automated colony counting method based on agar plates with the chromogenic dye 2, 3, 5-triphenyl tetrazolium chloride (TTC).

RESULTS

These changes enabled us to analyze about 100 serum samples per day per person by SBA. When the intra- and inter-assay precisions were studied, this assay showed a coefficient of variation (CV) ranging from 1 to 38 %. To monitor the long term assay stability for assays involving different bacteria lots, complement lots, and operators, we analyzed bactericidal indices of quality control samples obtained over a 6 year period and found the CV to be about 35-50 %. Lastly, our SBA results were compared with the ELISA results obtained using 90 serum samples from children. We showed that the bactericidal index correlated with IgG anti-Hib antibody levels (r = 0.84), with a bactericidal index of 10 corresponding approximately to 0.15 μg/mL IgG, the widely accepted protective level of antibody.

CONCLUSION

We describe a simple high throughput SBA for anti-Hib antibodies that would be useful for evaluating various Hib vaccines. While additional work will be needed to standardize the assay, this SBA should greatly facilitate studies of Hib vaccines.

Monoclonal Antibodies to Shigella Lipopolysaccharide Are Useful for Vaccine Production

There is a significant need for an effective multivalent Shigella vaccine that targets the most prevalent serotypes. Most Shigella vaccines under development utilize serotype-specific lipopolysaccharides (LPSs) as a major component based on protection and epidemiological data. As vaccine formulations advance from monovalent to multivalent, assays and reagents need to be developed to accurately and reproducibly quantitate the amount of LPSs from multiple serotypes in the final product. To facilitate this effort, we produced 36 hybridomas that secrete monoclonal antibodies (MAbs) against the O antigen on the LPS from Shigella flexneri 2a, Shigella flexneri 3a, and Shigella sonnei We used six of these monoclonal antibodies for an inhibition enzyme-linked immunosorbent assay (iELISA), measuring LPSs with high sensitivity and specificity. It was also demonstrated that the Shigella serotype-specific MAbs were useful for bacterial surface staining detected by flow cytometry. These MAbs are also useful for standardizing the serum bactericidal assay (SBA) for Shigella Functional assays, such as the in vitro bactericidal assay, are necessary for vaccine evaluation and may serve as immunological correlates of immunity. An S. flexneri 2a-specific monoclonal antibody killed S. flexneri 2b isolates, suggesting that S. flexneri 2a LPS may induce cross-protection against S. flexneri 2b. Overall, the Shigella LPS-specific MAbs described have potential utility to the vaccine development community for assessing multivalent vaccine composition and as a reliable control for multiple immunoassays used to assess vaccine potency.

High-Throughput Method for Automated Colony and Cell Counting by Digital Image Analysis Based on Edge Detection

Counting cells and colonies is an integral part of high-throughput screens and quantitative cellular assays. Due to its subjective and time-intensive nature, manual counting has hindered the adoption of cellular assays such as tumor spheroid formation in high-throughput screens. The objective of this study was to develop an automated method for quick and reliable counting of cells and colonies from digital images. For this purpose, I developed an ImageJ macro Cell Colony Edge and a CellProfiler Pipeline Cell Colony Counting, and compared them to other open-source digital methods and manual counts. The ImageJ macro Cell Colony Edge is valuable in counting cells and colonies, and measuring their area, volume, morphology, and intensity. In this study, I demonstrate that Cell Colony Edge is superior to other open-source methods, in speed, accuracy and applicability to diverse cellular assays. It can fulfill the need to automate colony/cell counting in high-throughput screens, colony forming assays, and cellular assays.

Automatic image classification for the urinoculture screening

Urinary tract infections (UTIs) are considered to be the most common bacterial infection and, actually, it is estimated that about 150 million UTIs occur world wide yearly, giving rise to roughly $6 billion in healthcare expenditures and resulting in 100,000 hospitalizations. Nevertheless, it is difficult to carefully assess the incidence of UTIs, since an accurate diagnosis depends both on the presence of symptoms and on a positive urinoculture, whereas in most outpatient settings this diagnosis is made without an ad hoc analysis protocol. On the other hand, in the traditional urinoculture test, a sample of midstream urine is put onto a Petri dish, where a growth medium favors the proliferation of germ colonies. Then, the infection severity is evaluated by a visual inspection of a human expert, an error prone and lengthy process. In this paper, we propose a fully automated system for the urinoculture screening that can provide quick and easily traceable results for UTIs. Based on advanced image processing and machine learning tools, the infection type recognition, together with the estimation of the bacterial load, can be automatically carried out, yielding accurate diagnoses. The proposed AID (Automatic Infection Detector) system provides support during the whole analysis process: first, digital color images of Petri dishes are automatically captured, then specific preprocessing and spatial clustering algorithms are applied to isolate the colonies from the culture ground and, finally, an accurate classification of the infections and their severity evaluation are performed. The AID system speeds up the analysis, contributes to the standardization of the process, allows result repeatability, and reduces the costs. Moreover, the continuous transition between sterile and external environments (typical of the standard analysis procedure) is completely avoided.

Evaluation of heterotrophic plate and chromogenic agar colony counting in water quality laboratories

The enumeration of bacteria using plate-based counts is a core technique used by food and water microbiology testing laboratories. However, manual counting of bacterial colonies is both time and labour intensive, can vary between operators and also requires manual entry of results into laboratory information management systems, which can be a source of data entry error. An alternative is to use automated digital colony counters, but there is a lack of peer-reviewed validation data to allow incorporation into standards. We compared the performance of digital counting technology (ProtoCOL3) against manual counting using criteria defined in internationally recognized standard methods. Digital colony counting provided a robust, standardized system suitable for adoption in a commercial testing environment. The digital technology has several advantages:•Improved measurement of uncertainty by using a standard and consistent counting methodology with less operator error.•Efficiency for labour and time (reduced cost).•Elimination of manual entry of data onto LIMS.•Faster result reporting to customers.

Current status and future prospects of using advanced computer-based methods to study bacterial colonial morphology

Despite the advancement of recent molecular technologies, culturing is still considered the gold standard for microbial sample analysis. Here we review three different bacterial colony-based screening modalities that provide significant information beyond the simple shape and color of the colony. The plate imaging technique provides numeration and quantitative spectral reflectance information for each colony, while Raman spectroscopic analysis of bacteria colonies relates the Raman-shifted peaks to specific chemical bonding. Finally, the elastic-light-scatter technique provides a volumetric interaction of the whole colony through laser-bacteria interactions, instantly capturing the morphological traits of the colony and allowing quantitative classifications.

Rapid and retrievable recording of big data of time-lapse 3D shadow images of microbial colonies

We formerly developed an automatic colony count system based on the time-lapse shadow image analysis (TSIA). Here this system has been upgraded and applied to practical rapid decision. A microbial sample was spread on/in an agar plate with 90 mm in diameter as homogeneously as possible. We could obtain the results with several strains that most of colonies appeared within a limited time span. Consequently the number of colonies reached a steady level (Nstdy) and then unchanged until the end of long culture time to give the confirmed value (Nconf). The equivalence of Nstdy and Nconf as well as the difference of times for Nstdy and Nconf determinations were statistically significant at p < 0.001. Nstdy meets the requirement of practical routines treating a large number of plates. The difference of Nstdy and Nconf, if any, may be elucidated by means of retrievable big data. Therefore Nconf is valid for official documentation.

Automated counting of bacterial colonies by image analysis

Research on microorganisms often involves culturing as a means to determine the survival and proliferation of bacteria. The number of colonies in a culture is counted to calculate the concentration of bacteria in the original broth; however, manual counting can be time-consuming and imprecise. To save time and prevent inconsistencies, this study proposes a fully automated counting system using image processing methods. To accurately estimate the number of viable bacteria in a known volume of suspension, colonies distributing over the whole surface area of a plate, including the central and rim areas of a Petri dish are taken into account. The performance of the proposed system is compared with verified manual counts, as well as with two freely available counting software programs. Comparisons show that the proposed system is an effective method with excellent accuracy with mean value of absolute percentage error of 3.37%. A user-friendly graphical user interface is also developed and freely available for download, providing researchers in biomedicine with a more convenient instrument for the enumeration of bacterial colonies.

Biomedical imaging and sensing using flatbed scanners

In this Review, we provide an overview of flatbed scanner based biomedical imaging and sensing techniques. The extremely large imaging field-of-view (e.g., ~600-700 cm(2)) of these devices coupled with their cost-effectiveness provide unique opportunities for digital imaging of samples that are too large for regular optical microscopes, and for collection of large amounts of statistical data in various automated imaging or sensing tasks. Here we give a short introduction to the basic features of flatbed scanners also highlighting the key parameters for designing scientific experiments using these devices, followed by a discussion of some of the significant examples, where scanner-based systems were constructed to conduct various biomedical imaging and/or sensing experiments. Along with mobile phones and other emerging consumer electronics devices, flatbed scanners and their use in advanced imaging and sensing experiments might help us transform current practices of medicine, engineering and sciences through democratization of measurement science and empowerment of citizen scientists, science educators and researchers in resource limited settings.

RNase L restricts the mobility of engineered retrotransposons in cultured human cells

Retrotransposons are mobile genetic elements, and their mobility can lead to genomic instability. Retrotransposon insertions are associated with a diverse range of sporadic diseases, including cancer. Thus, it is not a surprise that multiple host defense mechanisms suppress retrotransposition. The 2′,5′-oligoadenylate (2-5A) synthetase (OAS)-RNase L system is a mechanism for restricting viral infections during the interferon antiviral response. Here, we investigated a potential role for the OAS-RNase L system in the restriction of retrotransposons. Expression of wild type (WT) and a constitutively active form of RNase L (NΔ385), but not a catalytically inactive RNase L mutant (R667A), impaired the mobility of engineered human LINE-1 (L1) and mouse intracisternal A-type particle retrotransposons in cultured human cells. Furthermore, WT RNase L, but not an inactive RNase L mutant (R667A), reduced L1 RNA levels and subsequent expression of the L1-encoded proteins (ORF1p and ORF2p). Consistently, confocal immunofluorescent microscopy demonstrated that WT RNase L, but not RNase L R667A, prevented formation of L1 cytoplasmic foci. Finally, siRNA-mediated depletion of endogenous RNase L in a human ovarian cancer cell line (Hey1b) increased the levels of L1 retrotransposition by ∼2-fold. Together, these data suggest that RNase L might function as a suppressor of structurally distinct retrotransposons.

OpenCFU, a new free and open-source software to count cell colonies and other circular objects

Counting circular objects such as cell colonies is an important source of information for biologists. Although this task is often time-consuming and subjective, it is still predominantly performed manually. The aim of the present work is to provide a new tool to enumerate circular objects from digital pictures and video streams. Here, I demonstrate that the created program, OpenCFU, is very robust, accurate and fast. In addition, it provides control over the processing parameters and is implemented in an intuitive and modern interface. OpenCFU is a cross-platform and open-source software freely available at http://opencfu.sourceforge.net.

Noise-free accurate count of microbial colonies by time-lapse shadow image analysis

Microbial colonies in food matrices could be counted accurately by a novel noise-free method based on time-lapse shadow image analysis. An agar plate containing many clusters of microbial colonies and/or meat fragments was trans-illuminated to project their 2-dimensional (2D) shadow images on a color CCD camera. The 2D shadow images of every cluster distributed within a 3-mm thick agar layer were captured in focus simultaneously by means of a multiple focusing system, and were then converted to 3-dimensional (3D) shadow images. By time-lapse analysis of the 3D shadow images, it was determined whether each cluster comprised single or multiple colonies or a meat fragment. The analytical precision was high enough to be able to distinguish a microbial colony from a meat fragment, to recognize an oval image as two colonies contacting each other, and to detect microbial colonies hidden under a food fragment. The detection of hidden colonies is its outstanding performance in comparison with other systems. The present system attained accuracy for counting fewer than 5 colonies and is therefore of practical importance.

Portable bacterial identification system based on elastic light scatter patterns

Background

Conventional diagnosis and identification of bacteria requires shipment of samples to a laboratory for genetic and biochemical analysis. This process can take days and imposes significant delay to action in situations where timely intervention can save lives and reduce associated costs. To enable faster response to an outbreak, a low-cost, small-footprint, portable microbial-identification instrument using forward scatterometry has been developed.

Results

This device, weighing 9 lb and measuring 12 × 6 × 10.5 in., utilizes elastic light scatter (ELS) patterns to accurately capture bacterial colony characteristics and delivers the classification results via wireless access. The overall system consists of two CCD cameras, one rotational and one translational stage, and a 635-nm laser diode. Various software algorithms such as Hough transform, 2-D geometric moments, and the traveling salesman problem (TSP) have been implemented to provide colony count and circularity, centering process, and minimized travel time among colonies.

Conclusions

Experiments were conducted with four bacteria genera using pure and mixed plate and as proof of principle a field test was conducted in four different locations where the average classification rate ranged between 95 and 100%.

Development of a microbial high-throughput screening instrument based on elastic light scatter patterns

A microbial high-throughput screening (HTS) system was developed that enabled high-speed combinatorial studies directly on bacterial colonies. The system consists of a forward scatterometer for elastic light scatter (ELS) detection, a plate transporter for sample handling, and a robotic incubator for automatic incubation. To minimize the ELS pattern-capturing time, a new calibration plate and correction algorithms were both designed, which dramatically reduced correction steps during acquisition of the circularly symmetric ELS patterns. Integration of three different control software programs was implemented, and the performance of the system was demonstrated with single-species detection for library generation and with time-resolved measurement for understanding ELS colony growth correlation, using Escherichia coli and Listeria. An in-house colony-tracking module enabled researchers to easily understand the time-dependent variation of the ELS from identical colony, which enabled further analysis in other biochemical experiments. The microbial HTS system provided an average scan time of 4.9 s per colony and the capability of automatically collecting more than 4000 ELS patterns within a 7-h time span.

WormScan: a technique for high-throughput phenotypic analysis of Caenorhabditis elegans

Background

There are four main phenotypes that are assessed in whole organism studies of Caenorhabditis elegans; mortality, movement, fecundity and size. Procedures have been developed that focus on the digital analysis of some, but not all of these phenotypes and may be limited by expense and limited throughput. We have developed WormScan, an automated image acquisition system that allows quantitative analysis of each of these four phenotypes on standard NGM plates seeded with E. coli. This system is very easy to implement and has the capacity to be used in high-throughput analysis.

Methodology/Principal Findings

Our system employs a readily available consumer grade flatbed scanner. The method uses light stimulus from the scanner rather than physical stimulus to induce movement. With two sequential scans it is possible to quantify the induced phototactic response. To demonstrate the utility of the method, we measured the phenotypic response of C. elegans to phosphine gas exposure. We found that stimulation of movement by the light of the scanner was equivalent to physical stimulation for the determination of mortality. WormScan also provided a quantitative assessment of health for the survivors. Habituation from light stimulation of continuous scans was similar to habituation caused by physical stimulus.

Conclusions/Significance

There are existing systems for the automated phenotypic data collection of C. elegans. The specific advantages of our method over existing systems are high-throughput assessment of a greater range of phenotypic endpoints including determination of mortality and quantification of the mobility of survivors. Our system is also inexpensive and very easy to implement. Even though we have focused on demonstrating the usefulness of WormScan in toxicology, it can be used in a wide range of additional C. elegans studies including lifespan determination, development, pathology and behavior. Moreover, we have even adapted the method to study other species of similar dimensions.

Mathematics make microbes beautiful, beneficial, and bountiful

Microbiology is a rich area for visualizing the importance of mathematics in terms of designing experiments, data mining, testing hypotheses, and visualizing relationships. Historically, Nobel Prizes have acknowledged the close interplay between mathematics and microbiology in such examples as the fluctuation test and mutation rates using Poisson statistics by Luria and Delbrück and the use of graph theory of polyhedra by Caspar and Klug. More and more contemporary microbiology journals feature mathematical models, computational algorithms and heuristics, and multidimensional visualizations. While revolutions in research have driven these initiatives, a commensurate effort needs to be made to incorporate much more mathematics into the professional preparation of microbiologists. In order not to be daunting to many educators, a Bloom-like "Taxonomy of Quantitative Reasoning" is shared with explicit examples of microbiological activities for engaging students in (a) counting, measuring, calculating using image analysis of bacterial colonies and viral infections on variegated leaves, measurement of fractal dimensions of beautiful colony morphologies, and counting vertices, edges, and faces on viral capsids and using graph theory to understand self assembly; (b) graphing, mapping, ordering by applying linear, exponential, and logistic growth models of public health and sanitation problems, revisiting Snow's epidemiological map of cholera with computational geometry, and using interval graphs to do complementation mapping, deletion mapping, food webs, and microarray heatmaps; (c) problem solving by doing gene mapping and experimental design, and applying Boolean algebra to gene regulation of operons; (d) analysis of the "Bacterial Bonanza" of microbial sequence and genomic data using bioinformatics and phylogenetics; (e) hypothesis testing-again with phylogenetic trees and use of Poisson statistics and the Luria-Delbrück fluctuation test; and (f) modeling of biodiversity by using game theory, of epidemics with algebraic models, bacterial motion by using motion picture analysis and fluid mechanics of motility in multiple dimensions through the physics of "Life at Low Reynolds Numbers," and pattern formation of quorum sensing bacterial populations. Through a developmental model for preprofessional education that emphasizes the beauty, utility, and diversity of microbiological systems, we hope to foster creativity as well as mathematically rigorous reasoning.

A simple 96 well microfluidic chip combined with visual and densitometry detection for resource-poor point of care testing

There is a well-recognized need for low cost biodetection technologies for resource-poor settings with minimal medical infrastructure. Lab-on-a-chip (LOC) technology has the ability to perform biological assays in such settings. The aim of this work is to develop a low cost, high-throughput detection system for the analysis of 96 samples simultaneously outside the laboratory setting. To achieve this aim, several biosensing elements were combined: a syringe operated ELISA lab-on-a-chip (ELISA-LOC) which integrates fluid delivery system into a miniature 96-well plate; a simplified non-enzymatic reporter and detection approach using a gold nanoparticle-antibody conjugate as a secondary antibody and silver enhancement of the visual signal; and Carbon nanotubes (CNT) to increase primary antibody immobilization and improve assay sensitivity. Combined, these elements obviate the need for an ELISA washer, electrical power for operation and a sophisticated detector. We demonstrate the use of the device for detection of Staphylococcal enterotoxin B, a major foodborne toxin using three modes of detection, visual detection, CCD camera and document scanner. With visual detection or using a document scanner to measure the signal, the limit of detection (LOD) was 0.5ng/ml. In addition to visual detection, for precise quantitation of signal using densitometry and a CCD camera, the LOD was 0.1ng/ml for the CCD analysis and 0.5 ng/ml for the document scanner. The observed sensitivity is in the same range as laboratory-based ELISA testing. The point of care device can analyze 96 samples simultaneously, permitting high throughput diagnostics in the field and in resource poor areas without ready access to laboratory facilities or electricity.