Visualizing the entire DNA from a chromosome in a single frame.

The contiguity and phase of sequence information are intrinsic to obtain complete understanding of the genome and its relationship to phenotype. We report the fabrication and application of a novel nanochannel design that folds megabase lengths of genomic DNA into a systematic back-and-forth meandering path. Such meandering nanochannels enabled us to visualize the complete 5.7 Mbp (1 mm) stained DNA length of a Schizosaccharomyces pombe chromosome in a single frame of a CCD. We were able to hold the DNA in situ while implementing partial denaturation to obtain a barcode pattern that we could match to a reference map using the Poland-Scheraga model for DNA melting. The facility to compose such long linear lengths of genomic DNA in one field of view enabled us to directly visualize a repeat motif, count the repeat unit number, and chart its location in the genome by reference to unique barcode motifs found at measurable distances from the repeat. Meandering nanochannel dimensions can easily be tailored to human chromosome scales, which would enable the whole genome to be visualized in seconds.

Extension of nanoconfined DNA: Quantitative comparison between experiment and theory.

The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose, we performed experiments measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic strength of the buffer. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths, the agreement is less good. We discuss possible reasons. In principle, our approach allows us to measure the Kuhn length and the effective width of a single DNA molecule and more generally of semiflexible polymers in solution.

Orientational correlations in confined DNA.

We study how the orientational correlations of DNA confined to nanochannels depend on the channel diameter D by means of Monte Carlo simulations and a mean-field theory. This theory describes DNA conformations in the experimentally relevant regime where the Flory-de Gennes theory does not apply. We show how local correlations determine the dependence of the end-to-end distance of the DNA molecule upon D. Tapered nanochannels provide the necessary resolution in D to study experimentally how the extension of confined DNA molecules depends upon D. Our experimental and theoretical results are in qualitative agreement.

Nano-engineered living bacterial motors for active microfluidic mixing.

Active micromixers with rotating elements are attractive microfluidic actuators in many applications because of their mixing ability at a short distance. However, miniaturising the impeller design poses technical challenges including the fabrication and driving means. As a possible solution inspired by macro magnetic bar-stirrers, this study proposes the use of tethered, rotating bacteria as mixing elements. A tethered cell is a genetically engineered, harmless Escherichia coli (E. coli) attached to a surface by a single, shortened flagellum. The tethered flagellum acts as a pivot around which the entire cell body smoothly rotates. Videomicroscopy, image analysis and computational fluid dynamics (CFD) are utilised to demonstrate a proof-of-concept for the micro mixing process. Flow visualisation experiments show that a approximately 3 microm long tethered E. coli rotating at approximately 240 rpm can circulate a 1 microm polystyrene bead in the adjacent area at an average speed of nearly 4 microm/s. The Peclet (Peb) number for the stirred bead is evaluated to approximately 4. CFD simulations show that the rotary motion of a tethered E. coli rotating at 240 rpm can generate fluid velocities, up to 37 microm/s bordering the cell envelop. Based on these simulations, the Strouhal number (St) is calculated to about 2. This hybrid bio-inorganic micromxer could be used as a local, disposable mixer.

Near-field scanner for moving molecules.

We have fabricated using electron beam nanolithography a fixed slit near-field optical scanning device which uses near-field fluorimetry to achieve 200 nm spatial resolution of objects moving over the slits. We explore the basic physics of operating narrow slits in the waveguide cutoff mode and present data from the passage of extended double-stranded DNA molecules passing over the slits as a first example of how this device can be used to do ultrahigh spatial resolution mapping of long polymers.

Sorting biomolecules with microdevices.

Micro- and nanofabrication techniques have provided an unprecedented opportunity to create a designed world in which separation and fractionation technologies which normally occur on the macroscopic scale can be optimized by designing structures which utilize the basic physics of the process, or new processes can be realized by building structures which normally do not exist without external design. Since microfabrication is exceedingly sophisticated in its development, it is possible to design and construct highly creative microdevices which allow one to probe specific aspects of biological objects. We give examples of uses of micro- and nanofabrication which, as opposed to simply shrinking the size of the vessels or tubes used in macroscopic lab environments, utilize our understanding of the physics of the process to take advantage of fabrication technologies.

Presence of vitronectin and activated complement factor C9 on ventriculoperitoneal shunts and temporary ventricular drainage catheters.

OBJECT: The pathogenesis of cerebrospinal fluid (CSF) shunt infection is characterized by staphylococcal adhesion to the polymeric surface of the shunt catheter. Proteins from the CSF--fibronectin, vitronectin, and fibrinogen--are adsorbed to the surface of the catheter immediately after insertion. These proteins can interfere with the biological systems of the host and mediate staphylococcal adhesion to the surface of the catheter. In the present study, the presence of fibronectin, vitronectin, and fibrinogen on CSF shunts and temporary ventricular drainage catheters is shown. The presence of fragments of fibrinogen is also examined. METHODS: The authors used the following methods: binding radiolabeled antibodies to the catheter surface, immunoblotting of catheter eluates, and scanning force microscopy of immunogold bound to the catheter surface. The immunoblot showed that vitronectin was adsorbed in its native form and that fibronectin was degraded into small fragments. Furthermore, the study demonstrated that the level of vitronectin in CSF increased in patients with an impaired CSF-blood barrier. To study complement activation, an antibody that recognizes the neoepitope of activated complement factor C9 was used. The presence of activated complement factor C9 was shown on both temporary catheters and shunts. CONCLUSIONS: Activation of complement close to the surface of an inserted catheter could contribute to the pathogenesis of CSF shunt infection.

Quantitation of bacterial adhesion to polymer surfaces by bioluminescence.

Quantitation of microbes adhering to a surface is commonly used in studies of microbial adhesion to different surfaces. We have quantified different staphylococcal strains adhering to polymer surfaces by measuring bacterial ATP (adenosine triphosphate) by bioluminescence. The method is sensitive, having a detection limit of 10(4) bacterial cells. Viable counting of bacterial cells may yield falsely low results due to the presence of "dormant" and adherent bacteria. By using bioluminescence, this can be avoided. Cells of different bacterial species and cells of strains of the same species were shown to differ significantly in their basal ATP content (8.7 x 10(-13) - 5.2 x 10(-22) MATP). The size of adherent and planktonic bacteria decreased with time (0.7 micron-->0.3 micron, 20 days). During incubation in nutrient-poor buffer ("starvation"), the ATP content of adherent bacteria decreased after 24-96 h whereas that of planktonic bacteria was stable over 20 days. The presence of human serum or plasma did not interfere significantly with the test results. Since the ATP concentration of bacterial strains of different species varies and is also influenced by the growth conditions of bacteria (solid or liquid culture medium), a species-specific standard curve has to be established for bacteria grown under the same culture conditions. We conclude that the method is a sensitive tool to quantify adherent bacteria during experiments lasting for less than 6 h and constitutes a valuable method to be used in conjunction with different microscopical techniques.

Protein depositions on one hydrocephalus shunt and on fifteen temporary ventricular catheters.

Biomaterials are commonly used in modern medicine. Proteins are adsorbed to the surface of the biomaterial immediately after insertion. This report demonstrates the presence of adsorbed proteins in one infected cerebrospinal shunt from a child with hydrocephalus and on fifteen temporary ventricular catheters from adult patients with spontaneous or traumatic brain injuries. Depositions of vitronectin, fibrinogen and thrombospondin-fibronectin to some extent--on the shunt surface was imaged by field-emission scanning electron microscopy. Vitronectin, fibronectin, fibrinogen, and thrombospondin on the ventricular catheters were shown with radio-actively labelled antibodies. Furthermore, protein adsorption from human cerebrospinal fluid to heparinized and unheparinized polymers was studied under flowing conditions in vitro. On heparinized polymer, significantly reduced levels of vitronectin, fibronectin, and thrombospondin were exposed, as measured after 4 hours in vitro perfusion. After 24 hours perfusion, the differences in protein exposition between heparinized and unheparinized polymers were substantially reduced.