CiteULike: perpetuale's library [156 articles]

Optofluidic microscopy--a method for implementing a high resolution optical microscope on a chip.

X Heng — 2008-06-01T13:44:00-00:00

Lab on a chip, Vol. 6, No. 10. (October 2006), pp. 1274-1276.

We report a novel microfluidics-based lensless imaging technique, termed optofluidic microscopy (OFM), and demonstrate Caenorhabditis elegans imaging with an OFM prototype that gives comparable resolution to a conventional microscope and a measured resolution limit of 490 +/- 40 nm.

Developing optofluidic technology through the fusion of microfluidics and optics

Demetri Psaltis — 2006-07-28T05:50:51-00:00

Nature, Vol. 442, No. 7101. (26 July 2006), pp. 381-386.

Massively parallel manipulation of single cells and microparticles using optical images

Pei Chiou — 2005-07-21T05:11:07-00:00

Nature, Vol. 436, No. 7049., pp. 370-372.

Rapid discrimination of bacterial species with different ampicillin susceptibility levels by means of flow cytometry.

M Walberg — 2008-05-05T22:30:39-00:00

Cytometry, Vol. 29, No. 3. (1 November 1997), pp. 267-272.

An in vitro model for flow cytometric detection of heterogeneous drug response in exponentially growing Escherichia coli and Klebsiella pneumoniae was studied to evaluate the potential of this technology for rapid antibiotic susceptibility testing in polymicrobial samples. The cells, which exhibited 80-fold difference in in ampicillin susceptibility, were cultivated in the presence of ampicillin at a concentration equaling 1 MIC of the low-susceptibility strain (E. coli). Prior to flow cytometric analysis, the cells were fixed in 70% ethanol and stained with a DNA-specific dye. After 1 h of ampicillin incubation, the light scattering and fluorescence intensities of the susceptible cells increased 4.3-fold and 5-fold, respectively, but remained about constant for the resistant cells. The corresponding cell number increase for the resistant and the susceptible cells was 9.4 and 1.7, respectively. The two strains could be distinguished in the histograms on the basis of their light scattering and fluorescence intensities and by cell number. With an incubation of up to 3 h, the light scattering and fluorescence intensities of the susceptible cells grew stronger, at the expense of cell number. By combination of histograms, the discrimination of different cell populations could be improved. The results demonstrate the ability of flow cytometry to discriminate between species in heterogeneous cultures and suggest the potential of the technique for rapid assessment of bacterial susceptibility. However, the present results are preliminary, and the application to biological liquids and clinical samples has to be demonstrated further.

A journey into space.

J Hayles — 2007-06-04T10:32:04-00:00

Nat Rev Mol Cell Biol, Vol. 2, No. 9. (September 2001), pp. 647-656.

The fission yeast, Schizosaccharomyces pombe, has been used as a model eukaryote to study processes such as the cell cycle and cell morphology. In this single-celled organism, growing in a straight line and maintaining the nucleus in the centre of the cell depend on intracellular positional information. Microtubules and microtubular transport are important for generating positional information within the fission yeast cell, and these molecular mechanisms are also probably relevant for generating positional information in other eukaryotic cells.

Microbial analysis at the single-cell level: tasks and techniques

Howard Shapiro — 2006-05-19T16:43:04-00:00

Journal of Microbiological Methods, Vol. 42, No. 1. (September 2000), pp. 3-16.

The heterogeneity of microorganisms themselves is orders of magnitude greater than the heterogeneity of perspectives from which they are contemplated by human observers. Even closely related species may exhibit marked differences in biochemistry and behavior, and, under many conditions, similar, striking heterogeneity may exist within a clonal population of organisms which, in the aggregate, occupy too small a region of space to be visible to the unaided human eye. Using methods of microscopy, microspectrophotometry, and cytometry developed and refined since the 1960s, it is now possible to characterize the physiology and pharmacology of individual microorganisms, and, in many cases, to isolate organisms with selected characteristics for culture and/or further analysis. These methods include fluorescent and confocal microscopy, scanning and image cytometry, and flow cytometry. Fluorescence measurements are particularly important in single-cell analysis; they allow demonstration and quantification of cells’ nucleic acid content and sequence, of the presence of specific antigens, and of physiologic characteristics such as enzyme activity and membrane potential. Multiparameter cytometry, combined with cell sorting, provides insight into population heterogeneity and allows selected cells to be separated for further analysis and culture. The technology is applicable to a wide range of problems in contemporary microbiology, including strain selection and the development of antimicrobial agents.

Single-cell microbiology: tools, technologies, and applications.

BF Brehm-Stecher — 2005-03-16T17:14:49-00:00

Microbiol Mol Biol Rev, Vol. 68, No. 3. (September 2004)

The field of microbiology has traditionally been concerned with and focused on studies at the population level. Information on how cells respond to their environment, interact with each other, or undergo complex processes such as cellular differentiation or gene expression has been obtained mostly by inference from population-level data. Individual microorganisms, even those in supposedly "clonal" populations, may differ widely from each other in terms of their genetic composition, physiology, biochemistry, or behavior. This genetic and phenotypic heterogeneity has important practical consequences for a number of human interests, including antibiotic or biocide resistance, the productivity and stability of industrial fermentations, the efficacy of food preservatives, and the potential of pathogens to cause disease. New appreciation of the importance of cellular heterogeneity, coupled with recent advances in technology, has driven the development of new tools and techniques for the study of individual microbial cells. Because observations made at the single-cell level are not subject to the "averaging" effects characteristic of bulk-phase, population-level methods, they offer the unique capacity to observe discrete microbiological phenomena unavailable using traditional approaches. As a result, scientists have been able to characterize microorganisms, their activities, and their interactions at unprecedented levels of detail.

CELL SIGNALLING DYNAMICS IN TIME AND SPACE

Boris Kholodenko — 2008-04-04T12:47:16-00:00

Nat Rev Mol Cell Biol., Vol. 7 (2006), pp. 165-176.

Janus Particles

Andreas Walther — 2008-04-04T12:45:08-00:00

Soft Matter, Vol. 4 (2008), pp. 663-668.

Robustness of cellular functions.

J Stelling — 2004-11-22T00:52:45-00:00

Cell, Vol. 118, No. 6. (17 September 2004), pp. 675-685.

Robustness, the ability to maintain performance in the face of perturbations and uncertainty, is a long-recognized key property of living systems. Owing to intimate links to cellular complexity, however, its molecular and cellular basis has only recently begun to be understood. Theoretical approaches to complex engineered systems can provide guidelines for investigating cellular robustness because biology and engineering employ a common set of basic mechanisms in different combinations. Robustness may be a key to understanding cellular complexity, elucidating design principles, and fostering closer interactions between experimentation and theory.

`Growth of bacterial cultures' 50 years on: towards an uncertainty principle instead of constants in bacterial growth kinetics

Thomas Ferenci — 2008-01-17T16:16:30-00:00

Research in Microbiology, Vol. 150, No. 7. (September 1999), pp. 431-438.

Ever since Monod's efforts to study bacterial cultures in quantitative terms, the growth of Escherichia coli on sugars like glucose has appeared an attractive subject for the mathematical description of nutrient conversion into biomass. But instead of simplicity, it is becoming evident that bacterial adaptations affect `constants' such as Ks (growth affinity constant) and are, in turn, a complex function of nutrient concentration. Instead of a single affinity, bacteria exhibit a continuum of nutrient scavenging abilities peaking at micromolar sugar levels; there is lower affinity with millimolar or submicromolar glucose in the medium. Similar problems arise in defining parameters such as Y (growth yield constant), because nutrient-limited growth at low exponential growth rates induces a continuum of hunger and starvation responses. Autocatalytic changes to the environment caused by growth (as well as external factors) ensure that bacteria present an ever-adapting interface to the outside world. The regulatory interaction between the organism and environment means that no universal kinetic constants describe bacterial growth.

Microbiological safety of natural mineral water

Henri Leclerc — 2008-04-04T12:14:51-00:00

FEMS Microbiology Reviews, Vol. 26, No. 2. (2002), pp. 207-222.

Abstract Natural mineral water originates from groundwater, an oligotrophic ecosystem where the level of organic matter is low and of a very limited bioavailability. The bacterial populations that evolve in these ecosystems are heterotrophic and in starvation-survival state resulting from an insufficient amount of nutrients; for this reason they enter a viable but non-culturable state. After bottling, the number of viable counts increases rapidly, attaining 104-105 colony-forming units ml-1 within 3-7 days. These bacterial communities, identified by culture or with specific probes, are primarily aerobic, saprophytic, Gram-negative rods. Groundwater sources for natural mineral waters are selected such that they are not vulnerable to fecal contamination. Ecological data, especially the diversity and physiological properties of bacterial communities, are essential together with epidemiological studies in order to perform a risk analysis for natural mineral waters. On a continuing basis, the management of microbial risks has to rely on assessment of the heterotrophic plate count and, more specially, on detection of marker organisms, i.e. the classic fecal contamination indicators that have to be absent, and vulnerability indicators for which the occurrence should be as low as possible. It is also recommended to search regularly, but not routinely, for viral and protozoan pathogens.

Hungry bacteria - definition and properties of a nutritional state

Thomas Ferenci — 2008-04-04T12:11:31-00:00

Environmental Microbiology, Vol. 3, No. 10. (2001), pp. 605-611.

Summary Bacteria are sometimes neither starving nor under nutrient-excess conditions. When growing with suboptimal levels of nutrients, hungry bacteria express appropriate cellular responses. This review discusses approaches to defining the hunger response in both molecular and growth kinetic terms. The gene expression changes unique to hunger conditions are described, using Escherichia coli as the primary example. Metabolite changes with hunger and starvation and the differing role of the stationary phase regulator RpoS also lead to the hypothesis proposed in this review that bacteria undertake distinct approaches to hunger and starvation. Indeed, an understanding of the difference between hunger and starvation and the incompatibility between hunger and starvation responses explains some of the paradoxical mutational adaptations, such as rpoS inactivation, found in natural populations.

Growth Kinetics of Suspended Microbial Cells: From Single-Substrate-Controlled Growth to Mixed-Substrate Kinetics

Karin Kovarova-Kovar — 2006-01-15T04:53:09-00:00

Microbiol. Mol. Biol. Rev., Vol. 62, No. 3. (1 September 1998), pp. 646-666.

Growth kinetics, i.e., the relationship between specific growth rate and the concentration of a substrate, is one of the basic tools in microbiology. However, despite more than half a century of research, many fundamental questions about the validity and application of growth kinetics as observed in the laboratory to environmental growth conditions are still unanswered. For pure cultures growing with single substrates, enormous inconsistencies exist in the growth kinetic data reported. The low quality of experimental data has so far hampered the comparison and validation of the different growth models proposed, and only recently have data collected from nutrient-controlled chemostat cultures allowed us to compare different kinetic models on a statistical basis. The problems are mainly due to (i) the analytical difficulty in measuring substrates at growth-controlling concentrations and (ii) the fact that during a kinetic experiment, particularly in batch systems, microorganisms alter their kinetic properties because of adaptation to the changing environment. For example, for Escherichia coli growing with glucose, a physiological long-term adaptation results in a change in KS for glucose from some 5 mg liter[-]1 to ca. 30 microg liter[-]1. The data suggest that a dilemma exists, namely, that either "intrinsic" KS (under substrate-controlled conditions in chemostat culture) or micromax (under substrate-excess conditions in batch culture) can be measured but both cannot be determined at the same time. The above-described conventional growth kinetics derived from single-substrate-controlled laboratory experiments have invariably been used for describing both growth and substrate utilization in ecosystems. However, in nature, microbial cells are exposed to a wide spectrum of potential substrates, many of which they utilize simultaneously (in particular carbon sources). The kinetic data available to date for growth of pure cultures in carbon-controlled continuous culture with defined mixtures of two or more carbon sources (including pollutants) clearly demonstrate that simultaneous utilization results in lowered residual steady-state concentrations of all substrates. This should result in a competitive advantage of a cell capable of mixed-substrate growth because it can grow much faster at low substrate concentrations than one would expect from single-substrate kinetics. Additionally, the relevance of the kinetic principles obtained from defined culture systems with single, mixed, or multicomponent substrates to the kinetics of pollutant degradation as it occurs in the presence of alternative carbon sources in complex environmental systems is discussed. The presented overview indicates that many of the environmentally relevant apects in growth kinetics are still waiting to be discovered, established, and exploited.

Bacterial population genetics, evolution and epidemiology

BG Spratt — 2007-08-02T12:23:13-00:00

Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 354, No. 1384. (29 April 1999), pp. 701-710.

Asexual bacterial populations inevitably consist of an assemblage of distinct clonal lineages. However, bacterial populations are not entirely asexual since recombinational exchanges occur, mobilizing small genome segments among lineages and species. The relative contribution of recombination, as opposed to de novo mutation, in the generation of new bacterial genotypes varies among bacterial populations and, as this contribution increases, the clonality of a given population decreases. In consequence, a spectrum of possible population structures exists, with few bacterial species occupying the extremes of highly clonal and completely non-clonal, most containing both clonal and non-clonal elements. The analysis of collections of bacterial isolates, which accurately represent the natural population, by nucleotide sequence determination of multiple housekeeping loci provides data that can be used both to investigate the population structure of bacterial pathogens and for the molecular characterization of bacterial isolates. Understanding the population structure of a given pathogen is important since it impacts on the questions that can be addressed by, and the methods and samples required for, effective molecular epidemiological studies.

The Nature and Dynamics of Bacterial Genomes

Howard Ochman — 2006-03-24T03:20:00-00:00

Science, Vol. 311, No. 5768. (24 March 2006), pp. 1730-1733.

Though generally small and gene rich, bacterial genomes are constantly subjected to both mutational and population-level processes that operate to increase amounts of functionless DNA. As a result, the coding potential of bacterial genomes can be substantially lower than originally predicted. Whereas only a single pseudogene was included in the original annotation of the bacterium Escherichia coli, we estimate that this genome harbors hundreds of inactivated and otherwise functionless genes. Such regions will never yield a detectable phenotype, but their identification is vital to efforts to elucidate the biological role of all the proteins within the cell. 10.1126/science.1119966

What are bacterial species?

FM Cohan — 2006-02-08T16:03:51-00:00

Annu Rev Microbiol, Vol. 56 (2002), pp. 457-487.

Bacterial systematics has not yet reached a consensus for defining the fundamental unit of biological diversity, the species. The past half-century of bacterial systematics has been characterized by improvements in methods for demarcating species as phenotypic and genetic clusters, but species demarcation has not been guided by a theory-based concept of species. Eukaryote systematists have developed a universal concept of species: A species is a group of organisms whose divergence is capped by a force of cohesion; divergence between different species is irreversible; and different species are ecologically distinct. In the case of bacteria, these universal properties are held not by the named species of systematics but by ecotypes. These are populations of organisms occupying the same ecological niche, whose divergence is purged recurrently by natural selection. These ecotypes can be discovered by several universal sequence-based approaches. These molecular methods suggest that a typical named species contains many ecotypes, each with the universal attributes of species. A named bacterial species is thus more like a genus than a species.

Hydrodynamics of bacterial colonies: phase diagrams.

J Lega — 2006-01-13T12:16:18-00:00

Chaos, Vol. 14, No. 3. (September 2004), pp. 562-570.

We present numerical simulations of a recent hydrodynamic model describing the growth of bacterial colonies on agar plates. We show that this model is able to qualitatively reproduce experimentally observed phase diagrams, which relate a colony shape to the initial quantity of nutrients on the plate and the initial wetness of the agar. We also discuss the principal features resulting from the interplay between hydrodynamic motions and colony growth, as described by our model.

Modeling of the Bacterial Growth Curve.

M H Zwietering — 2007-11-19T15:54:46-00:00

Appl Environ Microbiol, Vol. 56, No. 6. (June 1990), pp. 1875-1881.

Several sigmoidal functions (logistic, Gompertz, Richards, Schnute, and Stannard) were compared to describe a bacterial growth curve. They were compared statistically by using the model of Schnute, which is a comprehensive model, encompassing all other models. The t test and the F test were used. With the t test, confidence intervals for parameters can be calculated and can be used to distinguish between models. In the F test, the lack of fit of the models is compared with the measuring error. Moreover, the models were compared with respect to their ease of use. All sigmoidal functions were modified so that they contained biologically relevant parameters. The models of Richards, Schnute, and Stannard appeared to be basically the same equation. In the cases tested, the modified Gompertz equation was statistically sufficient to describe the growth data of Lactobacillus plantarum and was easy to use.

From the Cover: The micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms

Colin Ingham — 2007-11-13T23:29:56-00:00

Proceedings of the National Academy of Sciences, Vol. 104, No. 46. (13 November 2007), pp. 18217-18222.

A miniaturized, disposable microbial culture chip has been fabricated by microengineering a highly porous ceramic sheet with up to one million growth compartments. This versatile culture format, with discrete compartments as small as 7 x 7 microm, allowed the growth of segregated microbial samples at an unprecedented density. The chip has been used for four complementary applications in microbiology. (i) As a fast viable counting system that showed a dynamic range of over 10,000, a low degree of bias, and a high culturing efficiency. (ii) In high-throughput screening, with the recovery of 1 fluorescent microcolony in 10,000. (iii) In screening for an enzyme-based, nondominant phenotype by the targeted recovery of Escherichia coli transformed with the plasmid pUC18, based on expression of the lacZ reporter gene without antibiotic-resistance selection. The ease of rapid, successive changes in the environment of the organisms on the chip, needed for detection of [beta]-galactosidase activity, highlights an advantageous feature that was also used to screen a metagenomic library for the same activity. (iv) In high-throughput screening of >200,000 isolates from Rhine water based on metabolism of a fluorogenic organophosphate compound, resulting in the recovery of 22 microcolonies with the desired phenotype. These isolates were predicted, on the basis of rRNA sequence, to include six new species. These four applications suggest that the potential for such simple, readily manufactured chips to impact microbial culture is extensive and may facilitate the full automation and multiplexing of microbial culturing, screening, counting, and selection. 10.1073/pnas.0701693104

BacSim, a simulator for individual-based modelling of bacterial colony growth.

JU Kreft — 2006-01-13T12:13:28-00:00

Microbiology, Vol. 144 ( Pt 12) (December 1998), pp. 3275-3287.

The generic, quantitative, spatially explicit, individual-based model BacSim was developed to simulate growth and behaviour of bacteria. The potential of this approach is in relating the properties of microscopic entities - cells - to the properties of macroscopic, complex systems such as biofilms. Here, the growth of a single Escherichia coli cell into a colony was studied. The object-oriented program BacSim is an extension of Gecko, an ecosystem dynamics model which uses the Swarm toolkit for multi-agent simulations. The model describes bacterial properties including substrate uptake, metabolism, maintenance, cell division and death at the individual cell level. With the aim of making the model easily applicable to various bacteria under different conditions, the model uses as few as eight readily obtainable parameters which can be randomly varied. For substrate diffusion, a two-dimensional diffusion lattice is used. For growth-rate-dependent cell size variation, a conceptual model of cell division proposed by Donachie was examined. A mechanistic version of the Donachie model led to unbalanced growth at higher growth rates, whereas including a minimum period between subsequent replication initiations ensured balanced growth only if this period was unphysiologically long. Only a descriptive version of the Donachie model predicted cell sizes correctly. For maintenance, the Herbert model (constant specific rate of biomass consumption) and for substrate uptake, the Michaelis-Menten or the Best equations were implemented. The simulator output faithfully reproduced all input parameters. Growth characteristics when maintenance and uptake rates were proportional to either cell mass or surface area are compared. The authors propose a new generic measure of growth synchrony to quantify the loss of synchrony due to random variation of cell parameters or spatial heterogeneity. Variation of the maximal uptake rate completely desynchronizes the simulated culture but variation of the volume-at-division does not. A new measure for spatial heterogeneity is introduced: the standard deviation of substrate concentrations as experienced by the cells. Spatial heterogeneity desynchronizes population growth by subdividing the population into parts synchronously growing at different rates. At a high enough spatial heterogeneity, the population appears to grow completely asynchronously.

Cells on chips

Jamil El-Ali — 2006-07-28T05:50:51-00:00

Nature, Vol. 442, No. 7101. (26 July 2006), pp. 403-411.

Use of polystyrene spin-coated compact discs for microimmunoassaying

Jesus Tamarit-Lopez — 2008-02-19T01:50:42-00:00

Analytica Chimica Acta, Vol. 609, No. 1. (18 February 2008), pp. 120-130.

The analytical potential of polystyrene (PS) spin-coated modified compact discs (CDs) surface as platforms for the development of microarray immunoassays is presented. The surface maintained the optical characteristics of compact discs, obtaining a transparent and smooth film polymer of 70 nm thickness, the track being read ([lambda] 780 nm) without errors in a commercial CD reader/writer. The analytical capability of the methodology was demonstrated through an analysis of a neurotoxic compound (2560 spots per disc), reaching 0.08 [mu]g L-1 as limit of detection. These figures demonstrate the enormous potential of using PS spin-coated compact discs in combination with CD players as an easy-to-operate and portable device to develop lab-on-a-disc analytical applications.

DNA microarray scanner with a DVD pick-up head

Kyung-Ho Kim — 2008-02-19T01:40:43-00:00

Current Applied Physics, Vol. In Press, Corrected Proof

A low-cost highly sensitive DNA microarray scanner for fluorescent detection is developed based on the pick-up head of a commercially available optical storage device, DVD. A laser beam of 650 nm, generated by a DVD laser diode, is used for dynamic auto-focusing as well as the excitation of Cy5 fluorescent dye. The fluorescence intensity emitted from Cy5 dye is measured by a photomultiplier tube (PMT). In contrast to other microarray scanners, the DVD-based scanner offers the auto-focusing function using the focus error signal (FES) and a voice coil motor (VCM), and this enables fast response, high accuracy and compact size. The fluorescence-detecting performance of the scanner is inspected by using a commercial BAC (bacterial artificial chromosome) oligonucleotide chip and a scanner evaluation microarray (DS01). Experiments have shown that the DVD-based scanner meets the limit of detection, ensuring the feasibility of a low-cost, highly sensitive DNA microarray scanner.

Disc-based immunoassay microarrays

Horacio Kido — 2008-02-19T01:34:28-00:00

Analytica Chimica Acta, Vol. 411, No. 1-2. (1 May 2000), pp. 1-11.

Microarray technology as applied to areas that include genomics, diagnostics, environmental, and drug discovery, is an interesting research topic for which different chip-based devices have been developed. As an alternative, we have explored the principle of compact disc-based microarrays. This new methodology successfully combined high-density microarrays applied via a piezoelectric inkjet applicator with circular indexing on a polycarbonate disc. As a demonstration of the principle, we ran competitive inhibition immunoassays for hydroxyatrazine, carbaryl, and molinate. The resulting microspots were approximately 75 micrometers in diameter and were visualized by using an antibody labeled with a fluorescent tag and a commercially available fluorescence scanner. The results of this work suggest that compact disc-based microarray technology can give qualitative and quantitative results and has potential for simultaneous multianalyte analyses.

Antimicrobial resistance and susceptibility testing: an evergreen topic

Pietro Varaldo — 2008-02-10T18:43:53-00:00

J. Antimicrob. Chemother., Vol. 50, No. 1. (1 July 2002), pp. 1-4.

10.1093/jac/dkf093

Immunomagnetic separation of Escherichia coli O26, O111 and O157 from vegetables

M Safarikova — 2008-02-09T23:58:34-00:00

Letters in Applied Microbiology, Vol. 33, No. 1. (2001), pp. 36-39.

Aims: Raw fruits and vegetables have been increasingly associated with human infections caused by Shiga toxin-producing Escherichia coli. This study evaluates the isolation and detection of E. coli O26, O111 and O157 from vegetable samples using immunomagnetic particles. Methods and Results: Standard cultivation and immunomagnetic separation (IMS) procedures were compared. It was found that immunomagnetic particles could efficiently concentrate E. coli cells, detecting significantly more bacteria than with standard cultivation procedures. Conclusions: Bacteria were detected in 93-100% of the inoculated samples using the IMS procedure, but only 36-93% samples tested by standard cultivation procedures were found to be positive. Significance and Impact of the Study: The results indicate that E. coli O26, O111 and O157 immunomagnetic particles can be a very useful and efficient tool for the detection of E. coli strains in raw vegetables, and could probably be used with samples of animal origin.

Use of magnetic techniques for the isolation of cells

Ivo Safari'k — 2008-02-09T23:37:13-00:00

Journal of Chromatography B: Biomedical Sciences and Applications, Vol. 722, No. 1-2. (5 February 1999), pp. 33-53.

Magnetic separation is an emerging technology using magnetism, sometimes in combination with conventional separation or identification methods, to purify cells, cell organelles and biologically active compounds (nucleic acids, proteins, xenobiotics) directly from crude samples. Several magnetic separation procedures have been developed to isolate target cells specifically. The purpose of this short review is to summarize various methodologies, strategies and materials which can be employed for the selection and separation of target cells with the help of magnetic field and thus to help the novices in this field to be able to orient themselves in vast amount of literature available. Immunomagnetic separations employing specific antibodies to label the target cells represent the most often used approach and are discussed in detail.

Rapid detection of Escherichia coli O157:H7 spiked into food matrices

Lisa Shriver-Lake — 2008-02-09T23:21:47-00:00

Analytica Chimica Acta, Vol. 584, No. 1. (12 February 2007), pp. 66-71.

Food poisoning causes untold discomfort to many people each year. One of the primary culprits in food poisoning is Escherichia coli O157:H7. While most cases cause intestinal discomfort, up to 7% of the incidences lead to a severe complication called hemolytic uremic syndrome which may be fatal. The traditional method for detection of E. coli O157:H7 in cases of food poisoning is to culture the food matrices and/or human stool. Additional performance-based antibody methods are also being used. The NRL array biosensor was developed to detect multiple antigens in multiple samples with little sample pretreatment in under 30 min. An assay for the specific detection of E. coli O157:H7 was developed, optimized and tested with a variety of spiked food matrices in this study. With no sample pre-enrichment, 5 x 103 cells mL-1 were detected in buffer in less than 30 min. Slight losses of sensitivity (1-5 x 10-4 cell mL-1) but not specificity occur in the presence of high levels of extraneous bacteria and in various food matrices (ground beef, turkey sausage, carcass wash, and apple juice). No significant difference was observed in the detection of E. coli O157:H7 in typical culture media (Luria Broth and Tryptic Soy Broth).

DETECTION OF ESCHERICHIA COLI O157:H7 THROUGH THE FORMATION OF SANDWICHED COMPLEXES WITH IMMUNOMAGNETIC AND FLUORESCENT BEADS†

Shu Tu — 2008-02-09T23:19:22-00:00

Journal of Rapid Methods and Automation in Microbiology, Vol. 13, No. 4. (2005), pp. 269-282.

ABSTRACT A new fluorescent sandwich method for the detection of Escherichia coli O157:H7 in ground beef was developed. Immunomagnetic beads (IMBs) precoated with anti-E. coli O157:H7 antibody were used to capture and concentrate E. coli O157:H7 present in ground beef. Streptavidin-coated fluorescent beads with anti-E. coli O157:H7 to form immunofluorescent beads (IFBs) were used to detect the E. coli O157:H7 captured by the IMBs by forming IMBM-E. coli O157:H7N-IFBO sandwich complexes, where the subscripts M, N and O were variable but integral numbers. This sandwich technique was able to detect 500 cfu of the bacteria in a 0.5-mL sample taken from a quantified and diluted broth culture. The method was then applied to detect E. coli O157:H7 in artificially contaminated ground beef. Known quantities of freshly cultured E. coli O157:H7 cells were added to 25-g ground beef patties held in sterile bags with filters. The inoculated patties were stored at 7C overnight; 75 mL of E. coli broth was added to each sample, and the bags were incubated at 40C with shaking at 160 rpm for 4.5 h. After the enrichment, E. coli O157:H7 in the filtrate was captured and concentrated with IMBs and further conjugated with IFBs for detection. The results demonstrate that, after a 4.5-h enrichment period, the developed procedure can detect the presence of E. coli O157:H7 in ground beef previously spiked with 1 cfu/g.

General Concepts About Cell Sorting Techniques

Alberto Orfao — 2008-02-09T23:06:07-00:00

Clinical Biochemistry, Vol. 29, No. 1. (February 1996), pp. 5-9.

Research involving cell analysis frequently requires isolation of certain cell types or subcellular components either as a final objective or as a preparative tool for further assays. At present, there are a high number of cell sorting methods that are suitable for being used in the clinical laboratory. These methods can be divided into two major groups: (1) bulk sorters and (2) single-cell-based sorters. This latter group mainly refers to fluorescence-activated cell sorting (FACS) by flow cytometry (FCM). In both cases, separation of cell subsets is based on their classification according to one or more cell characteristics. In bulk sorters, cell classification and sorting are usually achieved in a single step; by contrast, in FACS techniques, these two steps are independent sequential processes. In addition, bulk sorters generally use a single-cell characteristic to isolate cell subsets and have a higher throughput rate, as compared with FACS by FCM, where several parameters can be used simultaneously to classify cells for their further isolation. As a consequence of the mechanisms underlying these two cell sorting methods, the balance between cell purity and cell recovery on the sorted fraction are generally different, the single-cell-based methods usually providing both a higher purity and recovery. Thus, in practice, bulk separation methods are frequently used either as a preparative step for FCM-based cell sorting or for the enrichment of the sample in specific cell subsets, when a high throughput rate is required; in contrast, FACS by FCM is selected for the isolation of cell subsets when a high purity and, especially, recovery of a specific subpopulation of cells present in a sample are needed.

Magnetic separation techniques in diagnostic microbiology

Olsvik — 2008-02-09T23:05:03-00:00

Clinical Microbiology Reviews, Vol. 7, No. 1., pp. 43-54.

High gradient magnetic cell separation with MACS

Stefan Miltenyi — 2008-02-09T22:53:57-00:00

Cytometry, Vol. 11, No. 2. (1990), pp. 231-238.

A flexible, fast and simple magnetic cell sorting system for separation of large numbers of cells according to specific cell surface markers was developed and tested. Cells stained sequentially with biotinylated antibodies, fluorochrome-conjugated avidin, and superparamagnetic biotinylated-microparticles (about 100 nm diameter) are separated on high gradient magnetic (HGM) columns. Unlabelled cells pass through the column, while labelled cells are retained. The retained cells can be easily eluted. More than 109 cells can be processed in about 15 min. Enrichment rates of more than 100-fold and depletion rates of several 1,000-fold can be achieved. The simultaneous tagging of cells with fluorochromes and very small, invisible magnetic beads makes this system an ideal complement to flow cytometry. Light scatter and fluorescent parameters of the cells are not changed by the bound particles. Magnetically separated cells can be analysed by fluorescence microscopy or flow cytometry or sorted by fluorescence-activated cell sorting without further treatment. Magnetic tagging and separation does not affect cell viability and proliferation.

Magnetic separation techniques: their application to medicine

JT Kemsheadl — 2008-02-09T22:47:42-00:00

Molecular and Cellular Biochemistry, Vol. 67, No. 1. (1 May 1985), pp. 11-18.

Whilst separation techniques relying on gravitational forces have become relatively sophisticated in their application to biology the same is not true for magnetic separation procedures. The use of the latter has been limited to the few cells which contain paramagnetic iron. However with the development of several different types of magnetic particles and selective delivery system (e.g. monoclonal antibodies) the use of magnetic separation techniques is growing rapidly. This review describes the different types of particles currently available, the magnetic separation technique applied to the different magnetic compounds and illustrates major uses to which magnetic separation procedures are currently applied in the area of biology and medicine.

Sliding rocks at the Racetrack, Death Valley: What makes them move?

John Reid — 2007-12-21T16:50:00-00:00

Geology, Vol. 23, No. 9. (1 September 1995), pp. 819-822.

Sharply angular boulders as large as 320 kg sit on the Racetrack Playa, Death Valley, California; trails leading to them indicate that the rocks have moved large distances. The process has never been witnessed. Although high winds and a wetted surface seem necessary, controversy persists about the need for other conditions, especially ice sheets. On the basis of experiments with a wetted Racetrack surface (soft mud [~]3 cm deep), we find the effective coefficient of friction to be surprisingly high, [~]0.8. Movement by wind alone of moderate-sized (20 kg) rocks with cubic shape requires sustained winds close to the ground of [~]80 m/s ([~]180 mph). Larger flat-lying rocks require much higher winds. To assess the ice-sheet hypothesis, we mapped a large number of tracks into a precise coordinate system with an electronic theodolite. Certain tracks, separated by 830 m, have nearly identical curving patterns near their starts. The distance between a distinctive bend on one such track and its mate on another matches the distance for another mated pair of bends on these same tracks within several centimetres, even for tracks 830 m apart. As proposed by Stanley (1955), it seems that the rocks, resting on mud, were locked into a single floating ice sheet, in this case at least 850 X 500 m. Final resting places of these rocks are much more widely scattered than their starting points, suggesting that the sheet broke into smaller plates. Large ice sheets can move rocks even with light winds and may explain the gentle curvature of tracks hundreds of metres long, a pattern very unlikely with gusty high winds and no ice. 10.1130/0091-7613(1995)023<0819:SRATRD>2.3.CO;2

Magnetic field driven nanowire rotation in suspension

K Keshoju — 2007-10-27T23:16:46-00:00

Applied Physics Letters, Vol. 91, No. 12. (2007)

Magnetic field driven nanowire rotation in liquids has been investigated. This approach provides a noncontact, sensitive, cost effective, and easy to scale up scenario to manipulate the motion of magnetized one-dimensional nanostructures for “nanomachine” and anisotropic nanomaterial development. Due to the small dimensions, viscous behavior dominates the nanowire motion. Qualitative analyses considering the competing magnetic field induced torque and resisting fluid drag torque have been conducted for nanowire rotation under different circumstances. The analyses and experimental observations can provide key information for the understanding of hydrodynamics at the nanoscale. ©2007 American Institute of Physics

Nonlabeled Quartz Crystal Microbalance Biosensor for Bacterial Detection Using Carbohydrate and Lectin Recognitions

Z Shen — 2007-10-20T02:56:46-00:00

Anal. Chem., Vol. 79, No. 6. (15 March 2007), pp. 2312-2319.

Abstract: High percentages of harmful microbes or their secreting toxins bind to specific carbohydrate sequences on human cells at the recognition and attachment sites. A number of studies also show that lectins react with specific structures of bacteria and fungi. In this report, we take advantage of the fact that a high percentage of microorganisms have both carbohydrate and lectin binding pockets at their surface. We demonstrate here for the first time that a carbohydrate nonlabeled mass sensor in combination with lectin-bacterial O-antigen recognition can be used for detection of high molecular weight bacterial targets with remarkably high sensitivity and enhanced specificity. A functional mannose self-assembled monolayer in combination with lectin concanavalin A (Con A) was used as molecular recognition elements for the detection of Escherichia coli W1485 using a quartz crytsal microbalance (QCM) as a transducer. The multivalent binding of Con A to the E. coli surface O-antigen favors the strong adhesion of E. coli to the mannose-modified QCM surface by forming bridges between these two. As a result, the contact area between cell and QCM surface that increases leads to rigid and strong attachment. Therefore, it enhances the binding between E. coli and the mannose. Our results show a significant improvement of the sensitivity and specificity of the carbohydrate QCM biosensor with a experimental detection limit of a few hundred bacterial cells. The linear range is from 7.5 × 102 to 7.5 × 107 cells/mL, which is four decades wider than the mannose-alone QCM sensor. The change of damping resistances for E. coli adhesion experiments was no more than 1.4%, suggesting that the bacterial attachment was rigid, rather than a viscoelastic behavior. Little nonspecific binding was observed for Staphylococcus aureus and other proteins (fetal bovine serum, Erythrina cristagalli lectin). Our approach not only overcomes the challenges of applying QCM technology for bacterial detection but also increases the binding of bacteria to their carbohydrate receptor through bacterial surface binding lectins that significantly enhanced specificity and sensitivity of QCM biosensors. Combining carbohydrate and lectin recognition events with an appropriate QCM transducer can yield sensor devices highly suitable for the fast, reversible, and straightforward on-line screening and detection of bacteria in food, water, and clinical and biodefense areas.

Magnetic Fluid and Nanoparticle Applications to Nanotechnology

Markus Zahn — 2007-10-14T02:19:24-00:00

Journal of Nanoparticle Research, Vol. 3, No. 1. (21 February 2001), pp. 73-78.

Magnetic field based micro/nanoelectromechanical systems (MEMS/NEMS) devices are proposed that use 10 nm diameter magnetic particles, with and without a carrier fluid, for a new class of nanoduct flows, nanomotors, nanogenerators, nanopumps, nanoactuators, and other similar nanoscale devices. A few examples of macroscopic ferrohydrodynamic instabilities that result in patterns, lines, and structures are shown that can be scaled down to sub-micron dimensions.

Behavior of a magnetic fluid microdrop in a rotating magnetic field

JC Bacri — 2007-10-14T02:02:26-00:00

Physical Review Letters, Vol. 72, No. 17. (25 April 1994), 2705.

The response of a magnetic fluid microdrop to a rotating magnetic field is studied for the first time. An unexpected shape instability is observed; leading to the formation of a spiny starfish shape that slowly corotates with the field. A simple model accounts for (i) the stability range of an oblate ellipsoidal shape that is a precursor to the starfish; (ii) the rotational frequency which is substantially lower than that of the applied magnetic field; and (iii) a lateral peak instability that is responsible for growth of the spiny arms of the starfish.

Knowledge of magnetism in pre-Columbian Mesoamerica

Vincent Malmstrom — 2007-09-17T17:30:25-00:00

Nature, Vol. 259, No. 5542. (5 February 1976), pp. 390-391.

Lodestone Compass: Chinese or Olmec Primacy?: Multidisciplinary analysis of an Olmec hematite artifact from San Lorenzo, Veracruz, Mexico

John Carlson — 2007-09-17T17:26:40-00:00

Science, Vol. 189, No. 4205. (5 September 1975), pp. 753-760.

Considering the unique morphology (purposefully shaped polished bar with a groove) and composition (magnetic mineral with magnetic moment vector in the floating plane) of M-160, and acknowledging that the Olmec were a sophisticated people who possessed advanced knowledge and skill in working iron ore minerals, I would suggest for consideration that the Early Formative artifact M-160 was probably manufactured and used as what I have called a zeroth-order compass, if not a first-order compass. The data I have presented in this article support this hypothesis, although they are not sufficient to prove it. That M-160 could be used today as a geomagnetically directed pointer is undeniable. The original whole bar may indeed have pointed close to magnetic north-south. The groove functions well as a sighting mark, and the slight angle it makes with the axis of the bar appears to be the result of calibration rather than accident. A negative supporting argument is that M-160 looks utilitarian rather than decorative, and no function for the object other than that of a compass pointer has been suggested by anyone who has examined it critically. Whether such a pointer would have been used to point to something astronomical (zeroth-order compass) or to geomagnetic north-south (first-order compass) is entirely open to speculation.The observation of the family of Olmec site alignments 8degrees west of north is a curiosity in its own right, and the possibility that these alignments have an astronomical or geomagnetic origin should be explored.I also believe that it is constructive to compare the first millennium Chinese, who used the lodestone compass for geomancy, with the Gulf Coast Olmec since both were agrarian-terrestrial societies. The Olmec's apparent concern with orientation and skillful use of magnetic minerals also stimulates one to draw cross-cultural parallels.The evidence and analysis offered in this article provide a basis for hypotheses of parallel cultural developments in China and the Olmec New World. If the Olmec did discover the geomagnetic orienting properties of lodestone, as did the Han Chinese, it is most reasonable to speculate that they would have used their compass for comparable geomantic purposes. It should, however, be recognized that the Olmec claim, if documented, predates the Chinese discovery of the geomagnetic lodestone compass by more than a millennium.At present, M-160 is a unique artifact and San Lorenzo a unique site: "The first civilized center of Mesoamerica and probably of the New World" (19, p. 89). Further documentation of the Olmec claim must await the discovery of similar artifacts in museums, private collections, or as yet undiscovered Olmec sites.I would welcome communications from anyone possessing information relating to such artifacts. Regardless of shape, purposefully grooved and highly polished specimens of magnetic minerals are of particular interest. It would also be useful for the archeologist excavating Olmec burials and offerings to carefully note their alignments and consider them in a geomantic context.In addition to the discovery of supporting artifacts, establishment of Olmec primacy of the lodestone compass depends on the acquisition of the archeomagnetic data for the Early Formative period. I appeal to archeologists who find good archeomagnetic samples (burned hearths and post-holes) from the Formative periods to convey this information to R. DuBois of the University of Oklahoma. In a few years, the archeomagnetic data should be available for the last three millennia and the possibilities are very exciting. 10.1126/science.189.4205.753

Dynamic self-assembly of magnetic particles on the fluid interface: surface wave assisted effective magnetic exchange

A Snezhko — 2007-09-09T18:30:03-00:00

APS Meeting Abstracts (March 2006), 33002.

Novel dynamic self-assembled multi-segment magnetic structures (“snakes”) induced by a vertical alternating magnetic field in an ensemble of magnetic particles suspended on a liquid/air interface are reported. We demonstrate that these structures are directly related to surface waves in the liquid generated by the collective response of magnetic microparticles to the alternating magnetic field. The segments of magnetic “snake” exhibit long-range antiferromagnetic ordering mediated by the surface waves, while each segment is composed of ferromagnetically aligned chains of microparticles. To describe observed magnetic behavior of the generated structures we propose a simple phenomenological model where the effect of surface waves is replaced by an effective exchange interaction. In the framework of the proposed model the effective exchange constants corresponding to different regimes of magnetic driving were extracted from the experimental data.

Characterization of magnetic colloids by means of magnetooptics

L Baraban — 2007-09-09T18:27:05-00:00

The European Physical Journal E - Soft Matter, Vol. 23, No. 1. (7 May 2007), pp. 129-133.

Abstract. A new, efficient method for the characterization of magnetic colloids based on the Faraday effect is proposed. According to the main principles of this technique, it is possible to detect the stray magnetic field of the colloidal particles induced inside the magnetooptical layer. The magnetic properties of individual particles can be determined providing measurements in a wide range of magnetic fields. The magnetization curves of capped colloids and paramagnetic colloids were measured by means of the proposed approach. The registration of the magnetooptical signals from each colloidal particle in an ensemble permits the use of this technique for testing the magnetic monodispersity of colloidal suspensions.

Planar magnetic colloidal crystals.

W Wen — 2007-09-09T18:17:05-00:00

Phys Rev Lett, Vol. 85, No. 25. (18 December 2000), pp. 5464-5467.

We report a novel form of planar magnetic colloidal crystals formed by coated magnetic microspheres floating on a liquid meniscus. Under an external magnetic field, the balance between the repulsive magnetic interaction and the "attractive" interaction, due to the weight of the particles projected along the surface tangent, yields not only the triangular lattice with a variable lattice constant, but also all the other planar crystal symmetries such as the oblique, centered-rectangular, rectangular, and square lattices. By using two different sized magnetic particles, local formations of 2D quasi-crystallites with fivefold symmetry are also observed.

Frequency-controlled interaction between magnetic microspheres

X Zhang — 2007-09-09T18:14:55-00:00

Applied Physics Letters, Vol. 88 (March 2006), 4107.

We show that the interaction between magnetic microspheres, fabricated by coating glass microspheres with a layer of nickel, can be controlled by varying the frequency of the applied magnetic field. By floating two such microspheres on the meniscus of glycerin and applying an ac magnetic field, it is shown that the spheres achieve an equilibrium separation owing to the balance between the repulsive dipole-dipole interaction and the “attractive” force due to the weight of the particles. A monotonic decrease of the magnetorheological effect with frequency increasing is observed. Good agreement between theory and experiment is observed.

Self-assembly of floating magnetic particles into ordered structures: A promising route for the fabrication of tunable photonic band gap materials

M Golosovsky — 2007-09-09T18:08:28-00:00

Applied Physics Letters, Vol. 75 (December 1999), 4168.

We report stable ordered arrays of millimeter-size magnetic particles floating on a liquid surface. Self-assembly into a regular two-dimensional lattice results from lateral magnetic interactions between the particles. The lattice constant may be easily tuned by the application of external magnetic field. The array symmetry is designed by using different particle shapes, magnets, and magnet position inside the particle, so that complex symmetries may be achieved. Three-dimensional ordered arrays are obtained in a stack of troughs containing floating magnets. Computer simulations of electromagnetic wave propagation in such three-dimensional structures suggest an opening of a tunable photonic band gap in the microwave range.

Brownian motion of an asymmetrical particle in a potential field.

R Grima — 2007-09-06T20:33:18-00:00

J Chem Phys, Vol. 127, No. 8. (28 August 2007)

It is well known that a free ellipsoidal Brownian particle exhibits anisotropic diffusion for short times which changes to isotropic at long times, and, that the long-time diffusion coefficient is an average of the translational diffusion coefficients along the different semiaxes of the particle. We show analytically that in the presence of external forces, the long-time diffusion coefficient is different from that of a free particle. The magnitude of the difference in the two diffusion coefficients is found to increase proportionately with the particle's asymmetry, being zero only for a perfectly spherical Brownian particle. It is also found that, for asymmetrical particles, the application of external forces can amplify the non-Gaussian character of the spatial probability distributions which consequently delays the transition to the classical behavior. We illustrate these phenomena by considering the quasi-two-dimensional Brownian motion of an ellipsoidal rigid particle in linear and harmonic potential fields. These two examples provide insight into the role played by particle asymmetry in electrophoresis and microconfinement due to a laser trap or due to intracellular macromolecular crowding.

A compact CMOS biochip immunosensor towards the detection of a single bacteria

Joon Song — 2007-09-06T20:14:56-00:00

Biosensors and Bioelectronics, Vol. 20, No. 11. (15 May 2005), pp. 2203-2209.

Recent use of biological warfare (BW) agents has led to a growing interest in the rapid and sensitive detection of pathogens. Therefore, the development of field-usable detection devices for sensitive and selective detection of BW agents is an important issue. In this work, we report a portable biochip system based on complementary metal oxide semiconductor (CMOS) technology that has great potential as a device for single-bacteria detection. The possibility of single-bacteria detection is reported using an immunoassay coupled to laser-induced fluorescence (LIF) detection. Bacillus globigii spores, which are a surrogate species for B. anthracis spores, were used as the test sample. Enzymatic amplification following immunocomplex formation allowed remarkably sensitive detection of B. globigii spores, and could preclude a complicated optical and instrumental system usually required for high-sensitive detection. Atomic force microscopy (AFM) was employed to investigate whether B. globigii spores detected in the portable biochip system exist in single-cell or multicellular form. It was found that B. globigii spores mostly exist in multicellular form with a small minority of single-cell form. The results showed that the portable biochip system has great potential as a device for single-particle or possibly even single-organism detection.

A novel magnetic bead bioassay platform using a microchip-based sensor for infectious disease diagnosis

Turgut Aytur — 2007-09-06T20:03:53-00:00

Journal of Immunological Methods, Vol. 314, No. 1-2. (31 July 2006), pp. 21-29.

New technologies are greatly needed to improve laboratory tests that can be used in point-of-care clinical settings. Here, a biosensor was used to detect micron-scale paramagnetic beads in order to replace the conventional enzymatic label used in ELISAs. This novel biosensor was fabricated through standard complementary metal oxide semiconductor (CMOS) manufacturing and was used to quantify magnetic beads bound to the sensor surface by immunological recognition, analogous to ELISA. CMOS technology can integrate multiple laboratory functions into the sensor chip, potentially enabling inexpensive, compact and sophisticated diagnostic systems for a number of diseases. We present results for two immunological assays: antigen capture of purified mouse IgG and detection of human anti-dengue virus IgG in clinical serum samples. The sensitivity of detecting purified protein with magnetic beads was comparable to ELISA. We found a high correlation between the ELISA optical density and the biosensor output in the clinical assay. We also demonstrate the use of a controlled magnetic field to remove non-specifically bound magnetic beads from the sensor surface, effectively washing the sensor surface. This novel sensor can be mass-produced at low cost and can detect magnetic beads bound to the surface through specific antibody-antigen interactions, making it a potential platform for new simplified and rapid point-of-care diagnostic tests.

Improved hydrodynamic interaction in macromolecular bead models

B Carrasco — 2007-08-29T20:49:24-00:00

The Journal of Chemical Physics, Vol. 111, No. 10. (1999), pp. 4817-4826.

The calculation of hydrodynamic properties of macromolecules in terms of bead models requires an adequate description of the hydrodynamic interaction between the spherical elements. For this purpose, the original or modified Oseen tensor are customarily used, although it has been shown that this simple description may lead to erroneous results, particularly for rotational coefficients. In this paper we study several more elaborate theories for multisphere systems. We apply those treatments to our problem of rigid bead models, implementing them in computer programs, and making calculations for various test structures. The comparison of the results from the various theories, and from other, presumably very accurate procedures, allow us to give some guidelines to improve the treatment of hydrodynamic interactions in macromolecular bead models. These advances are introduced in new versions of our public-domain computer software. ©1999 American Institute of Physics.