Body morphology differs in wild juvenile Chinook salmon Oncorhynchus tshawytscha that express different migratory phenotypes in the Willamette River, Oregon, U.S.A.

Body morphology of juvenile Chinook salmon Oncorhynchus tshawytscha in the upper Willamette River, Oregon, U.S.A., was analysed to determine if variation in body shape is correlated with migratory life-history tactics followed by juveniles. Body shape was compared between migrating juveniles that expressed different life-history tactics, i.e. autumn migrants and yearling smolts, and among parr sampled at three sites along a longitudinal river gradient. In the upper Willamette River, the expression of life-history tactics is associated with where juveniles rear in the basin with fish rearing in downstream locations generally completing ocean ward migrations earlier in life than fish rearing in upstream locations. The morphological differences that were apparent between autumn migrants and yearling smolts were similar to differences between parr rearing in downstream and upstream reaches, indicating that body morphology is correlated with life-history tactics. Autumn migrants and parr from downstream sampling sites had deeper bodies, shorter heads and deeper caudal peduncles compared with yearling smolts and parr from the upstream sampling site. This study did not distinguish between genetic and environmental effects on morphology; however, the results suggest that downstream movement of juveniles soon after emergence is associated with differentiation in morphology and with the expression of life-history variation.

Direct detection of genomic DNA with fluidic force discrimination assays.

Herein, we describe the direct detection of genomic DNA using fluidic force discrimination (FFD) assays. Starting with extracted bacterial DNA, samples are fragmented by restriction enzymes or sonication, then thermocycled in the presence of blocking and labeling sequences, and finally detected with microbead-based FFD assays. Both strain and species identification of extracted Bacillus DNA have been demonstrated in <30 min, without amplification (e.g., PCR). Femtomolar assays can be achieved with this rapid and simple procedure.

Attomolar protein detection in complex sample matrices with semi-homogeneous fluidic force discrimination assays.

We describe a semi-homogenous (SH) implementation of a fluidic force discrimination (FFD) assay using only two reagent mixtures and three assay steps that can be performed in as little as 10min. Previously microbead labels and FFD have been combined to achieve multiplexed, femtomolar nucleic acid hybridization and immunoassays in a microarray format [Mulvaney, S.P., Cole, C.L., Kniller, M.D., Malito, M., Tamanaha, C.R., Rife, J.C., Stanton, M.W., Whitman, L.J., 2007. Biosen. Bioelectron. 23, 191-200.]. In SH FFD assays, the microbeads and any required intermediate receptors (e.g., secondary antibodies) are first mixed directly with a sample, allowing target analytes to be efficiently captured onto the beads. The target-loaded beads are then specifically captured onto a microarray surface, with nonspecifically bound beads removed by controlled, laminar fluidic forces. The remaining beads on each microarray capture spot are counted to determine the targets' identities and concentrations. SH target collection provides a 1000-fold improvement in the assay sensitivity, down to attomolar concentrations, as demonstrated by our detection of staphylococcal enterotoxin B (SEB) at 35 aM (1 fg/ml). We also show that SH assays are adaptable for extraction, preconcentration, and identification of analytes in complex sample matrices, including assays for SEB and ricin toxoid in serum and whole blood. Finally, we present a detailed model of the reaction kinetics that reveals how capturing the targets onto the beads in solution provides a significant kinetic advantage at low target concentrations where mass transport to a microarray surface is most limited.

Magnetic labeling, detection, and system integration.

Among the plethora of affinity biosensor systems based on biomolecular recognition and labeling assays, magnetic labeling and detection is emerging as a promising new approach. Magnetic labels can be non-invasively detected by a wide range of methods, are physically and chemically stable, relatively inexpensive to produce, and can be easily made biocompatible. Here we provide an overview of the various approaches developed for magnetic labeling and detection as applied to biosensing. We illustrate the challenges to integrating one such approach into a complete sensing system with a more detailed discussion of the compact Bead Array Sensor System developed at the U.S. Naval Research Laboratory, the first system to use magnetic labels and microchip-based detection.

Rapid, femtomolar bioassays in complex matrices combining microfluidics and magnetoelectronics.

A significant challenge for all biosensor systems is to achieve high assay sensitivity and specificity while minimizing sample preparation requirements, operational complexity, and sample-to-answer time. We have achieved multiplexed, unamplified, femtomolar detection of both DNA and proteins in complex matrices (including whole blood, serum, plasma, and milk) in minutes using as few as two reagents by labeling conventional assay schemes with micrometer-scale magnetic beads, and applying fluidic force discrimination (FFD). In FFD assays, analytes captured onto a microarray surface are labeled with microbeads, and a controlled laminar flow is then used to apply microfluidic forces sufficient to preferentially remove only nonspecifically bound bead labels. The density of beads that remain bound is proportional to the analyte concentration and can be determined with either optical counting or magnetoelectronic detection of the magnetic labels. Combining FFD assays with chip-based magnetoelectronic detection enables a simple, potentially handheld, platform capable of both nucleic acid hybridization assays and immunoassays, including orthogonal detection and identification of bacterial and viral pathogens, and therefore suitable for a wide range of biosensing applications.

Quantifying the magnetic advantage in magnetotaxis.

Magnetotactic bacteria are characterized by the production of magnetosomes, nanoscale particles of lipid bilayer encapsulated magnetite, that act to orient the bacteria in magnetic fields. These magnetosomes allow magneto-aerotaxis, which is the motion of the bacteria along a magnetic field and toward preferred concentrations of oxygen. Magneto-aerotaxis has been shown to direct the motion of these bacteria downward toward sediments and microaerobic environments favorable for growth. Herein, we compare the magneto-aerotaxis of wild-type, magnetic Magnetospirillum magneticum AMB-1 with a nonmagnetic mutant we have engineered. Using an applied magnetic field and an advancing oxygen gradient, we have quantified the magnetic advantage in magneto-aerotaxis as a more rapid migration to preferred oxygen levels. Magnetic, wild-type cells swimming in an applied magnetic field more quickly migrate away from the advancing oxygen than either wild-type cells in a zero field or the nonmagnetic cells in any field. We find that the responses of the magnetic and mutant strains are well described by a relatively simple analytical model, an analysis of which indicates that the key benefit of magnetotaxis is an enhancement of a bacterium's ability to detect oxygen, not an increase in its average speed moving away from high oxygen concentrations.

Chemical structure and orientation of ethylene on Si(114)-(2 x 1)/c(2 x 2).

The basic chemical structure and orientation of ethylene chemisorbed on Si(114)-(2 x 1) at submonolayer coverage is characterized in ultrahigh vacuum using transmission Fourier transform infrared (FTIR) spectroscopy. The spectra are consistent with di-sigma bonding of ethylene to the surface with a preferential molecular orientation over macroscopic lengths. These results are supported by density functional theory (DFT) calculations of vibrational frequencies for optimized ethylene-Si(114) structures occupying the dimer and rebonded atom surface sites. A detailed analysis of the strong angular and polarization dependence of the C-H stretching mode intensities is also consistent with the adsorption structures identified by DFT, indicating that ethylene chemisorbs with the C-C bond axis parallel to the structural rows oriented along the [10] direction on the Si(114)-(2 x 1) surface. The results indicate that the unique structure of this surface makes it an excellent template for elucidating relationships between surface structure and organic reaction mechanisms on silicon.

Lowering the dose of hydroxyurea minimizes toxicity and maximizes anti-HIV potency.

The goal of this study was to optimize the hydroxyurea dosage in HIV-infected patients, and to minimize the toxicity and maximize the antiviral efficacy of the hydroxyurea-didanosine combination. In a randomized, open-label study (RIGHT 702, a multicenter trial performed in private and institutional practices), three daily doses (600 microg, 800-900 microg, and 1200 microg) of hydroxyurea were administered in combination with didanosine and stavudine to 115 chronically HIV-infected patients, one-third antiretroviral drug naive, with viremia between 5000 and 200,000 copies/ml regardless of CD4+ cell count. The primary efficacy end point was the proportion of patients with plasma HIV-1 RNA levels below 400 copies/ml after 24 weeks of therapy. In the RIGHT 702 intent-to-treat population the lowest (600 mg) dose of hydroxyurea was better tolerated, associated with fewer adverse events, and more potent by all efficacy parameters, including the primary end point (76 versus 60% patients with viremia<400 copies/ml at week 24 for the 600-mg and 800- to 900-mg dose groups, respectively; p=0.027), the mean area under the curve (60.3 versus 65.8; p=0.016), and the mean log10 decrease (-1.95 versus -0.77; p=0.001). Patients receiving 600 mg of hydroxyurea daily also had the highest CD4+ cell count, CD4+/CD8+ cell ratio, and lowest CD8+ cell count and percentage (p=0.035). The RIGHT 702 trial provides an explanation for the increased toxicity and decreased efficacy of hydroxyurea when it was used at high dosage (1200 mg daily). At the optimal dosage of 600 mg daily, hydroxyurea, in combination with didanosine, deserves reevaluation for the long-term management of HIV/AIDS worldwide, because of its excellent resistance profile, durability, and affordability.

A simple pen-spotting method for arraying biomolecules on solid substrates.

We describe a simple, relatively inexpensive method for depositing biomolecules on a solid substrate using Rapidograph drafting pens. The pens can be used without modification to accurately deposit spots between approximately 100 and 600 microm in diameter. When mounted on a suitable microtranslation stage, the pens can be used to easily deposit tens of spots aligned with underlying substrate features such as microfabricated sensors. The pens are particularly convenient because pre-mixed solutions can be stored in the pens for multiple uses. We demonstrate the use of this approach to deposit DNA probes on a microsensor array.

Thiol diffusion and the role of humidity in "Dip Pen Nanolithography".

The radii of octadecanethiol spots deposited by an atomic force microscope tip onto a gold surface were studied as a function of contact time and humidity. The deposition is well described by two-dimensional diffusion from an annular source of constant concentration, with a surface diffusion coefficient of 8400 nm(2) s(-1), independent of humidity. Facile transfer is observed even after near continuous deposition for more than 24 h in a dry N2 environment, indicating that a water meniscus is not required.

The BARC biosensor applied to the detection of biological warfare agents.

The Bead ARray Counter (BARC) is a multi-analyte biosensor that uses DNA hybridization, magnetic microbeads, and giant magnetoresistive (GMR) sensors to detect and identify biological warfare agents. The current prototype is a table-top instrument consisting of a microfabricated chip (solid substrate) with an array of GMR sensors, a chip carrier board with electronics for lock-in detection, a fluidics cell and cartridge, and an electromagnet. DNA probes are patterned onto the solid substrate chip directly above the GMR sensors, and sample analyte containing complementary DNA hybridizes with the probes on the surface. Labeled, micron-sized magnetic beads are then injected that specifically bind to the sample DNA. A magnetic field is applied, removing any beads that are not specifically bound to the surface. The beads remaining on the surface are detected by the GMR sensors, and the intensity and location of the signal indicate the concentration and identity of pathogens present in the sample. The current BARC chip contains a 64-element sensor array, however, with recent advances in magnetoresistive technology, chips with millions of these GMR sensors will soon be commercially available, allowing simultaneous detection of thousands of analytes. Because each GMR sensor is capable of detecting a single magnetic bead, in theory, the BARC biosensor should be able to detect the presence of a single analyte molecule.

Prevention of venous thromboembolism after knee arthroplasty. A randomized, double-blind trial comparing enoxaparin with warfarin.

OBJECTIVE: To compare the effectiveness and safety of fixed-dose enoxaparin and adjusted dose warfarin in preventing venous thromboembolism after knee arthroplasty. DESIGN: A randomized, double-blind controlled trial. SETTING: 8 university hospitals. PATIENTS: 670 consecutive patients who had knee arthroplasty. INTERVENTION: Patients were randomly assigned to receive enoxaparin (30 mg subcutaneously every 12 hours) or adjusted-dose warfarin (international normalized ratio, 2.0 to 3.0). Both regimens were started after surgery. MEASUREMENTS: The primary end point was the incidence of deep venous thrombosis in patients with adequate bilateral venograms; the secondary end point was hemorrhage. RESULTS: Among the 417 patients with adequate venograms, 109 of 211 warfarin recipients (51.7%) had deep venous thrombosis compared with 76 of 206 enoxaparin recipients (36.9%) (P = 0.003). The absolute risk difference was 14.8% in favor of enoxaparin (95% Cl, 5.3% to 24.1%) Twenty-two warfarin recipients (10.4%) and 24 enoxaparin recipients (11.7%) had proximal venous thrombosis (P>0.2). The absolute risk difference was 1.2% in favor of warfarin (Cl, -7.2% to 4.8%). The incidence of major bleeding was 1.8% (6 of 334 patients) in the warfarin group and 2.1% (7 of 336 patients) in the enoxaparin group (P>0.2). The absolute risk difference was 0.3% in favor of warfarin (Cl, -2.4% to 1.8%). CONCLUSIONS: A postoperative, fixed-dose enoxaparin regimen is more effective than adjusted-dose warfarin in preventing deep venous thrombosis after knee arthroplasty. No differences were seen in the incidence of proximal venous thrombosis or clinically overt hemorrhage.

A stable high-index surface of silicon: si(5 5 12).

A stable high-index surface of silicon, Si(5 5 12), is described. This surface forms a 2 x 1 reconstruction with one of the largest unit cells ever observed, 7.7 angstroms by 53.5 angstroms. Scanning tunneling microscopy (STM) reveals that the 68 surface atoms per 2 x 1 unit cell are reconstructed only on a local scale. A complete structural model for the surface is proposed, incorporating a variety of features known to exist on other stable silicon surfaces. Simulated STM images based on this model have been computed by first-principles electronic-structure methods and show excellent agreement with experiment.

The effects of amphotericin B, fluconazole and miconazole on neutrophil and lymphocyte function in a guinea pig model.

We studied the effects of amphotericin B, fluconazole and miconazole on guinea pig neutrophil and lymphocyte function. Neutrophil adherence, chemotaxis, and deoxyglucose uptake and mitogen-induced lymphocyte proliferation were examined. The drugs were administered intraperitoneally in varying dosages based on those used therapeutically, either as a single infusion or daily for 3 days. Miconazole at high dosage (60 mg/kg) suppressed mitogen-induced lymphocyte proliferation, otherwise a single dose of any of the drugs had no effect on neutrophil or lymphocyte function irrespective of concentration used. Variable stimulative or suppressive effects on neutrophil and lymphocyte function were observed after three daily doses of each drug, but there was no dose-response pattern and the effects were erratic. The data show that, contrary to previous findings in vitro, amphotericin B, fluconazole and miconazole were not consistently immunosuppressive in vivo in this animal model.

The use of an audiotaped analysis in a continuous case seminar.

The use of an audiotaped analysis in a continuous case seminar is evaluated. We compare this case seminar to the traditional one in which an analyst presents process notes, and find that the use of the tape lends itself readily to teaching microanalysis, principles of technique, and observation of affect. Listening to anonymous taped sessions allowed for the possibility of a freer climate for discussion, as none of the seminar participants had a personal relationship with the taped analyst. The disadvantages posed by the absence of the analyst during the seminar also are addressed.

Modulation of human neutrophil adherence by oral bacteria.

Polymorphonuclear neutrophils (PMNs) comprise over 90 per cent of leukocytes in the oral cavity. Although these phagocytic cells have primary defence roles in the gingiva, their stimulation by micro-organisms may also cause substantial tissue damage due to the release of lysosomal enzymes and oxygen radicals. Adherence of PMNs to the endothelium and their subsequent diapedesis and egress to areas of infection are considered early vital events in the inflammatory process. In this study, oral bacteria were screened to determine their direct effects on PMN activation using an in vitro method of measuring PMN adherence to Dacron fibres. Most of the bacteria investigated increased PMN adherence, indicating their potential to cause tissue damage through the release of PMN lysosomal enzymes and other products. In contrast, Bacteroides species suppressed PMNs, indicating their ability to circumvent the phagocytic cells, thus gaining a potential advantage in dental colonization. The modulatory effects of oral bacteria on PMN activation may have significant roles in the immunopathogenesis of oral disease.

Effect of human milk and infant milk formulae on adherence of Giardia intestinalis.

Human milk was shown to inhibit adherence of Giardia at concentrations as low as 0.5%. Unsaturated fatty acids were also found to cause significant inhibitory effects on adherence, with ED50 values less than 1 microM for arachidonic, linoleic and palmitic acids. A variety of infant feeding formulae derived from cow's milk and soy bean had suppressive effects on adherence. These observations may explain in part the low prevalence of giardiasis in young infants.