Long-period gratings in photonic crystal fiber as an optofluidic label-free biosensor

Using long-period gratings (LPG) inscribed in photonic crystal fiber (PCF) and coupling this structure with an optically aligned flow cell, we have developed an optofluidic refractive index transduction platform for label-free biosensing. The LPG-PCF scheme possesses extremely high sensitivity to the change in refractive index induced by localized binding event in different solution media. A model immunoassay experiment was carried out inside the air channels of PCF by a series of surface modification steps in sequence that include adsorption of poly(allylamine hydrochloride) monolayer, immobilization of anti-rat bone sialoprotein monoclonal primary antibody, and binding interactions with non-specific goat anti-rabbit IgG (H+L) and specific secondary goat anti-mouse IgG (H+L) antibodies. These adsorption and binding events were monitored in situ using the LPG-PCF by measuring the shift of the core-to-cladding mode coupling resonance wavelength. Steady and significant resonance changes, about 0.75 nm per nanometer-thick adsorbed/bound bio-molecules, have been observed following the sequence of the surface events with monolayer sensitivity, suggesting the promising potential of LPG-PCF for biological sensing and evaluation.     

Multidepth screening of living cells using optical waveguides

The use of planar optical waveguides as substrata for label-free, non-invasive monitoring of cells growing on them is demonstrated. Different submicrometre depths (measured from and perpendicular to the substratum surface) can be selected for monitoring. The so-called symmetry waveguide configuration with a low refractive index waveguide support (nanoporous silica with refractive index approximately 1.2) and a polystyrene waveguiding film with a heat-embossed grating coupler is exploited to obtain practically useful differences between the penetration depths of different waveguide modes. Robust data processing techniques are developed to obtain quantitative information about the cell refractive index profile perpendicular to the substratum from the measured effective refractive indices of the modes. In particular, a method is introduced with which cell refractive index variations above and below a predefined and tunable depth can be separated using two modes. The technique can be extended to more modes to gain even more comprehensive information from predefined submicrometre slices of the cell layer. The introduced methods are also suitable for monitoring the kinetics of changes in cell refractive index profiles.     

The adsorption of prothrombin to phosphatidylserine multilayers quantitated by ellipsometry

We investigated by means of an automated ellipsometer the adsorption of prothrombin from a buffer solution by multilayers of 14:0/14:0- and 18:1/18:1-phosphatidylserine (PS) stacked on chromium slides. In this instrument thickness and refractive index of the adsorbed phospholipid and proteins are monitored continuously. Two equations are derived to relate the mass of stacked phospholipids and the mass of protein adsorbed to the thickness and refractive index. These equations are based upon the Lorentz-Lorenz relation among the molar refractivities, refractive indices, and the densities of binary mixtures. Experimental validation of these equations is performed by measuring stacked multilayers of known mass of phosphatidylserine and the adsorption of [125I] albumin and [3H]prothrombin on these multilayers. Using these equations we measured the dissociation constants Kd and the number of binding sites nb of prothrombin. Values of Kd = 0.15 x 10(-8) M and nb = 122 molecules of PS/molecule of prothrombin were observed for di C14:0 PS and values of Kd = 0.45 x 10(-8) M and nb = 54 molecules of PS/molecule of prothrombin for di C18:1 PS. These data compare well to data obtained by other methods available in the literature.     

Computational determination of refractive index distribution in the crystalline cones of the compound eye of Antarctic krill (Euphausia superba)

In order to understand how a compound eye channels light to the retina and forms an image, one needs to know the refractive index distribution in the crystalline cones. Direct measurements of the refractive indices require sections of fresh, unfixed tissue and the use of an interference microscope, but frequently neither is available. Using the eye of the Antarctic krill Euphausia superba (the main food of baleen whales) we developed a computational method to predict a likely refractive index distribution non-invasively from sections of fixed material without the need of an interference microscope. We used a computer model of the eye and calculated the most realistic spatial distribution of the refractive index gradient in the crystalline cone that would enable the eye to produce a sharp image on the retina. The animals are known to see well and on the basis of our computations we predict that for the eyes of the adult a maximum refractive index of 1.45-1.50 in the centre of the cone yields a better angular sensitivity and light absorption in a target receptor of the retina than if N(max) were 1.55. In juveniles with a narrower spatial separation between dioptric structures and retina, however, an N(max) of 1.50-1.55 gives a superior result. Our method to determine the most likely refractive index distribution in the cone without the need of fresh material and an interference microscope could be useful in the study of other invertebrate eyes that are known to possess good resolving power, but for a variety of reasons are not suitable for or will not permit direct refractive index measurements of their dioptric tissues to be taken.     

Towards a biosensor based on anti resonant reflecting optical waveguide fabricated from porous silicon

Recently, we demonstrated that Anti Resonant Reflecting Optical Waveguide (ARROW) based on porous silicon (PS) material can be used as a transducer for the development of a new optical biosensor. Compared to a conventional biosensor waveguide based on evanescent waves, the ARROW structure is designed to allow a better overlap between the propagated optical field and the molecules infiltrated in the porous core layer and so to provide better molecular interactions sensitivity. The aim of this work is to investigate the operating mode of an optical biosensor using the ARROW structure. We reported here an extensive study where the antiresonance conditions were adjusted just before the grafting of the studied molecules for a given refractive index range. The interesting feature of the studied ARROW structure is that it is elaborated from the same material which is the porous silicon obtained via a single electrochemical anodization process. After oxidation and preparation of the inner surface of porous silicon by a chemical functionalization process, bovine serum albumin (BSA) molecules, were attached essentially in the upper layer. Simulation study indicates that the proposed sensor works at the refractive index values ranging from 1.3560 to 1.3655. The experimental optical detection of the biomolecules was obtained through the modification of the propagated optical field and losses. The results indicated that the optical attenuation decreases after biomolecules attachment, corresponding to a refractive index change Δn(c) of the core. This reduction was of about 2 dB/cm and 3 dB/cm for Transverse Electric (TE) and Transverse Magnetic (TM) polarizations respectively. Moreover, at the detection step, the optical field was almost located inside the core layer. This result was in good agreement with the simulated near field profiles.     

Bragg-Scattered Surface Plasmon Microscopy: Theoretical Study

We present a new approach to surface plasmon microscopy with high refractive index sensitivity and spatial resolution that is not limited by the propagation length of surface plasmons. It is based on a nanostructured metallic sensor surface supporting Bragg-scattered surface plasmons. We show that these non-propagating surface plasmon modes are excellently suited for spatially resolved observations of refractive index variations on the sensor surface owing to their highly confined field profile perpendicular to as well as parallel to the metal interface. The presented theoretical study reveals that this approach enables reaching similar refractive index sensitivity as regular surface plasmon resonance (SPR) microscopy and offers the advantage of improved spatial resolution when observing dielectric features with lateral size <10???m for the wavelength around 800?nm and gold as the SPR-active metal. This paper demonstrates the potential of Bragg-scattered surface plasmon microscopy for high-throughput SPR biosensing with high-density microarrays.     

Lipophosphoglycan is not required for infection of macrophages or mice by Leishmania mexicana

Cell surface lipophosphoglycan (LPG) is commonly regarded as a multifunctional Leishmania virulence factor required for survival and development of these parasites in mammals. In this study, the LPG biosynthesis gene lpg1 was deleted in Leishmania mexicana by targeted gene replacement. The resulting mutants are deficient in LPG synthesis but still display on their surface and secrete phosphoglycan-modified molecules, most likely in the form of proteophosphoglycans, whose expression appears to be up-regulated. LPG-deficient L.mexicana promastigotes show no significant differences to LPG-expressing parasites with respect to attachment to, uptake into and multiplication inside macrophages. Moreover, in Balb/c and C57/BL6 mice, LPG-deficient L.mexicana clones are at least as virulent as the parental wild-type strain and lead to lethal disseminated disease. The results demonstrate that at least L. mexicana does not require LPG for experimental infections of macrophages or mice. Leishmania mexicana LPG is therefore not a virulence factor in the mammalian host.     

Localized Surface Plasmon Resonance-Based Fiber Optic U-Shaped Biosensor for the Detection of Blood Glucose

In the present study, we report the first fiber optic glucose sensor utilizing localized surface plasmon resonance of metal nanoparticles. The fiber was bent in the form of a U-shaped probe for point detection and sensitivity enhancement. The probe was prepared by first attaching gold nanoparticles on the optical fiber core and then immobilizing glucose oxidase over it. The sensor operates in the intensity modulation scheme in which the absorbance is measured with respect to the changes in the glucose concentration. The presence of glucose in the vicinity of the sensing region changes the refractive index of the film due to the chemical reactions with glucose oxidase. The absorbance of the metal nanoparticle changes significantly due to local refractive index change. The fiber optic U-shaped probes of different bending radii were fabricated and it has been found that the probe with bending radius around 0.982?mm possesses the maximum sensitivity. The response of the sensor is fast and requires very small volume of sensing sample (??150???l) which makes it more suitable for commercialization and better than present commercial sensors, which require about 1.5?ml of blood for the detection of glucose.     

Hydrogels for an accommodating intraocular lens. An explorative study

In this study it was investigated whether hydrogels could be used for an accommodating lens. The requirements of such a hydrogels are a low modulus, high refractive index, transparency, and strength. Since conventional hydrogels do not possess this combination of properties, a novel preparation method and new polymers are introduced. As starting materials poly(1-hydroxy-1,3-propanediyl), poly(ethylene-co-vinyl alcohol), poly(vinyl alcohol), and poly(allyl alcohol) were used. The first three were cross-linked with a number of diisocyanate compounds. Network formation was performed at low concentrations in a good solvent. Mixing of the polymer solution and cross-linker appeared to be crucial for transparency. Poly(1-hydroxy-1,3-propanediyl), cross-linked with a slow reacting diisocyanate block, shows the most promising properties with respect to refractive index, transparency, tensile strength, and modulus. Poly(allyl alcohol) hydrogel was made by compression molding. The hydrogel was transparent and had a high refractive index and low modulus. It was concluded that hydrogels could be used as accommodating lens material.     

A polycarbonate based surface plasmon resonance sensing cartridge for high sensitivity HBV loop-mediated isothermal amplification

In this study, we report a simple, low-cost surface plasmon resonance (SPR)-sensing cartridge based on a loop-mediated isothermal amplification (LAMP) method for the on-site detection of the hepatitis B virus (HBV). For LAMP detection, a SPR based LAMP sensing system (SPRLAMP) was constructed, including a novel SPRLAMP sensing cartridge integrating a polymethyl methacrylate (PMMA) micro-reactor with a polycarbonate (PC)-based prism coated with a 50 nm Au film. First, we found that the change of refractive index of the bulk solution was approximately 0.0011 refractive index (RI) units after LAMP reaction. The PC-based prism's linearity and thermal responses were compared to those of a traditional glass prism to show that a PC-based prism can be used for SPR measurement. Finally, the HBV template mixed in the 10 μl LAMP solution could be detected by SPRLAMP system in 17 min even at the detection-limited concentration of 2 fg/ml. We also analyzed the correlation coefficients between the initial concentrations of HBV DNA templates and the system response (ΔRU) at varying amplification times to establish an optimal amplification time endpoint of 25 min (R(2)=0.98). In conclusion, the LAMP reaction could be detected with the SPRLAMP sensing cartridge based on direct sensing of the bulk refractive index.     

Localization of lipophosphonoglycan in membranes of Acanthamoeba by using specific antibodies.

Antibodies against two electrophoretically distinct forms of lipophosphonoglycan (LPG) were produced in rabbits. Antibody specificity was demonstrated by the coupled antibody 125I-protein A assay (Adair et al., J. Cell Biol. 79:281-285, 1978). Indirect immunofluorescent labeling of intact Acanthamoeba showed that antibodies to both LPG components had the same uniform distribution on the cell surface. Both antibodies also bound to the cytoplasmic surface of isolated phagosomes. The location of LPG in other membranes of the amoeba was demonstrated on sections by the unlabeled antibody method. Although LPG was absent from the nuclear membrane, virtually all of the internal vacuole membranes were labeled, including the contractile vacuole. Antibodies directed against LPG were utilized to label lipophosphonoglycan in the plasma membrane of living amoebae. Labeled membrane was internalized and then localized by immunofluorescence in cytoplasmic vacuoles within 10 min of incubation. Although these results are evidence for exchange between plasma and cytoplasmic vacuolar membranes, the contractile vacuole remained unlabeled and can be considered, therefore, a separate membrane compartment. Concanavalin A also was bound and internalized by the amoeba, but electron microscopy showed that this label caused pronounced membrane perturbation, limiting its usefulness as a membrane marker in this system.     

Design of Infrared Plasma Absorber with High Refractive Index Sensitivity

Three layers of periodic artificial metamaterial sensing structure (including the upper metal particles, intermediate dielectric layer, and the lower reflective layer) with ultra-narrow band absorption were designed. The resonance characteristics and sensing properties were analyzed by the finite difference time domain (FDTD) method. The effect of localized surface plasmon resonance (LSPR) was obviously observed at the resonance wavelength of 911 nm, and it achieves nearly perfect absorption of exceeding 98% with a full width at half maximum (FWHM) of 3.5 nm. In addition, a wavelength sensitivity of 542 nm/RIU with a figure of merit (FOM) of 155 was obtained in the refractive index (RI) range from 1.00 to 1.35, which has a wide range of applications. The results show that the proposed structure has high absorption and RI sensitivity, which is suitable for bioengineering and medical detection.

     

Quantitation of Leishmania lipophosphoglycan repeat units by capillary electrophoresis

The glycosylphosphatidylinositol (GPI)-anchored lipophosphoglycan (LPG) of Leishmania is the dominant cell surface glycoconjugate of these pathogenic parasites. LPG is structurally characterized by a series of phosphoglycan repeat units. Determining the number of repeat units per LPG molecule has proven difficult using current technologies, such as mass spectrometry. As an alternative method to quantitate the number of repeat units in LPG, a procedure based on capillary electrophoretic analysis of the proportion of mannose to 2,5-anhydromannose (derived from the nonacetylated glucosamine of the GPI anchor of LPG) was developed. The CE-based technique is sensitive and relatively rapid compared to GC-MS-based protocols. Its application was demonstrated in quantitating the number of LPG repeat units from several species of Leishmania as well as from two life-cycle stages of these organisms.     

Femtomol SPR detection of DNA-PNA hybridization with the assistance of DNA-guided polyaniline deposition

The inability of surface plasmon resonance (SPR) spectroscopy to detect extremely small refractive index changes has hindered its applications in ultrasensitive DNA analysis. In this study we report a signal amplification strategy that uses DNA-templated polyaniline deposition, suitable for DNA hybridization analysis with charge neutral peptide nucleic acid (PNA) being probes. Under acidic conditions, protonated aniline monomers are adsorbed on DNA backbones through electrostatic interaction. The microenvironment provided by the DNA facilitates oxidative aniline polymerization initialized by H₂O₂ in the presence of horseradish peroxide. Under optimal conditions, the detection limit is lowered from 5 nM for conventional SPR detection to 0.1 pM. The significant sensitivity improvement is attributed to the in-situ polymer chain growth along DNA strands, which introduces drastic refractive index increases. This signal amplification approach does not involve secondary hybridization processes. The detection sensitivity obtained is much better than that of gold nanoparticle-based amplification involving a secondary hybridization process and labeled DNA detection probes.     

A comparative study of protein immobilization techniques for optical immunosensors.

This paper presents the results of a study of a number of antibody immobilization techniques for application to optical immunosensors. In particular, well-known methods such as covalent binding and physical adsorption have been extended to the Langmiur-Blodgett method in an attempt to improve the density and possibly the uniformity of orientation of monoclonal antibodies on an optical surface. The surface density of active immobilized antibodies was determined from enzyme immunoassay and their thickness and refractive index were deduced from ellipsometry. It is shown that, although high surface densities (500 ng/cm2) of antibody can be obtained, the major obstacle to the detection of low concentrations of antigens or haptens is the non-specific binding of foreign molecules to the sensing surface.     

Infrared absorbance spectroscopy of aqueous proteins: Comparison of transmission and ATR data collection and analysis for secondary structure fitting

Attenuated total reflectance (ATR) infrared absorbance spectroscopy of proteins in aqueous solution is much easier to perform than transmission spectroscopy, where short path‐length cells need to be assembled reproducibly. However, the shape of the resulting ATR infrared spectrum varies with the refractive index of the sample and the instrument configuration. Refractive index in turn depends on the absorbance of the sample. In this work, it is shown that a room temperature triglycine sulfate detector and a ZnSe ATR unit can be used to collect reproducible spectra of proteins. A simple method for transforming the protein ATR spectrum into the shape of the transmission spectrum is also given, which proceeds by approximating a Kramers‐Krönig–determined refractive index of water as a sum of four linear components across the amide I and II regions. The light intensity at the crystal surface (with 45° incidence) and its rate of decay away from the surface is determined as a function of the wave number–dependent refractive index as well as the decay of the evanescent wave from the surface. The result is a single correction factor at each wave number. The spectra were normalized to a maximum of 1 between 1600 cm^?1 and 1700 cm^?1 and a self‐organizing map secondary structure fitting algorithm, SOMSpec, applied using the BioTools reference set. The resulting secondary structure estimates are encouraging for the future of ATR spectroscopy for biopharmaceutical characterization and quality control applications.     

Leishmania promastigotes require lipophosphoglycan to actively modulate the fusion properties of phagosomes at an early step of phagocytosis

The lipophosphoglycan (LPG) of Leishmania promastigotes plays key roles in parasite survival in both insect and mammalian hosts. Evidence suggests that LPG decreases phagosome fusion properties at the onset of infection in macrophages. The mechanisms of action of this molecule are, however, poorly understood. In the present study, we used a panoply of Leishmania mutants displaying modified LPG structures to determine more precisely how LPG modulates phagosome-endosome fusion. Using an in vivo fusion assay measuring, at the electron microscope, the transfer of solute materials from endosomes to phagosomes, we provided further evidence that the repeating Gal(beta1,4)Man(alpha1-PO4) units of LPG are responsible for the alteration in phagosome fusion. The inhibitory effect of LPG on phagosome fusion was shown to be more potent towards late endocytic organelles and lysosomes than early endosomes, explaining how Leishmania promastigotes can avoid degradation in hydrolase-enriched compartments. The involvement of other repeating unit-containing molecules, including the secreted acid phosphatase, in the inhibition process was ruled out, as an LPG-defective mutant (Ipg1-) which secretes repeating unit-containing glycoconjugates was present in highly fusogenic phagosomes. In L. major, oligosaccharide side-chains of LPG did not contribute to the inhibition process, as Spock, an L. major mutant lacking LPG side-chains, blocked fusion to the same extent as wild-type parasites. Finally, dead parasites internalized from the culture medium were not as efficient as live parasites in altering phagosome-endosome fusion, despite the presence of LPG. However, the killing of parasites with vital dyes after their sequestration in phagosomes had no effect on the fusion properties of this organelle. Collectively, these results suggest that living promastigotes displaying full-length cell surface LPG can actively influence macrophages at an early stage of phagocytosis to generate phagosomes with poor fusogenic properties.     

Resonance of Different Waveguide Structures with Various Vertical Indirect Coupled Cavities

In the paper, resonances of different waveguide structures with various vertical indirect coupled cavities were investigated by FDTD (finite difference-time domain). In the silicon cavity, Fano resonance could be observed at about 1430 nm. The coupling distance for the gold cavity/air cavity had less effect on the transmittance of the main waveguide but had a great influence on the transmission for water cavity in the visible region, which showed that water cavity could adjust resonance of waveguide structures. In addition, with the increment of refractive index n, the resonance peak at about 850 nm moved to the long wavelength (redshift). Dispersion rate about 2 × 10^–3/nm indicated that the transparent dielectric selectively absorbed the surface plasmon polariton wave and the sensitivity of the waveguide structure designed in this paper has high stability for the refractive index of the main waveguide cavity. Obvious Fano resonance could be observed with the increase of refractive index for silicon cavity. Among the four dielectrics, silicon and water are suitable for studying Fano resonance and filter dielectrics.

     

Sensitivity enhancement of spectral surface plasmon resonance biosensors for the analysis of protein arrays

A novel method for sensitivity enhancement of spectral surface plasmon resonance (SPR) biosensors was presented by reducing the refractive index of the sensing prism in the analysis of protein arrays. Sensitivity of spectral SPR biosensors with two different prisms (BK-7, fused silica) was analyzed by net shifts of resonance wavelength for specific interactions of GST–GTPase binding domain of p21-activated kinase-1 and anti-GST on a mixed thiol surface. Sensitivity was modulated by the refractive index of the sensing prism of the spectral SPR biosensors with the same incidence angle. The sensitivity of a spectral SPR biosensor with a fused silica prism was 1.6 times higher than that with a BK-7 prism at the same incidence angle of 46.2°. This result was interpreted by increment of the penetration depth correlated with evanescent field intensity at the metal/dielectric interface. Therefore, it is suggested that sensitivity enhancement is readily achieved by reducing the refractive index of the sensing prism of spectral SPR biosensors to be operated at long wavelength ranges for the analysis of protein arrays.     

Surface Phonon Resonance Assisted Refractive Index Sensing in Mid-Infrared Wavelength Range

We propose a highly sensitive refractive index sensor based on the surface phonon resonance (SPhR) in the mid-IR spectral range. Surface phonon polaritons (SPhPs) are formed on polar dielectrics such as SiC in mid-IR wavelength range and can be excited with the help of a metallic grating at specific wavelength termed as resonance wavelength. The resonance wavelength of SPhP is significantly affected by the refractive index of the analyte medium placed over the grating. This forms the basis of a refractive index sensor. We have numerically evaluated the performance of such an SPhP-based refractive index sensor by using rigorous coupled wave analysis (RCWA) in terms of sensitivity, detection accuracy, and quality factor. The quality factor and detection accuracy of the sensor formed on SiC substrate are found to be 225.1 RIU^–1 (inverse of refractive index unit) and 6.75, respectively. We have also extended the study for other polar dielectric substrates cBN and GaN and observed considerable enhancement in the performance of the sensor for GaN. The values of quality factor and detection accuracy could be increased to 361.2 RIU^–1 and 10.84, respectively, by using GaN substrate. The proposed sensor finds applications in refractive index sensing of liquids and biomolecules having refractive index in the range 1.33–1.36.