Plasmonic Metasurfaces for Specific SERS Detection of Shiga Toxins.

The interest in the development of nanoscale plasmonic technologies has dramatically increased in recent years. The photonic properties of plasmonic nanopatterns can be controlled and tuned via their size, shape, or the arrangement of their constituents. In this work, we propose a 2D hybrid metallic polymeric nanostructure based on the octupolar framework with enhanced sensing property. We analyze its plasmonic features both numerically and experimentally, demonstrating the higher values of their relevant figures of merit: we estimated a surface-enhanced Raman spectroscopy (SERS) enhancement factor of 9 × 107 and a SPR bulk sensitivity of 430 nm/RIU. In addition, our nanostructure exhibits a dual resonance in the visible and near-infrared region, enabling our system toward multispectral plasmonic analysis. Finally, we illustrate our design engineering strategy as enabled by electron beam lithography by the outstanding performance of a SERS-based biosensor that targets the Shiga toxin 2a, a clinically relevant bacterial toxin. To the best of our knowledge, this is the first time that a SERS fingerprint of this toxin has been evidenced.

Dodecagonal plasmonic quasicrystals for phage-based biosensing.

In this work, we fabricate and characterize a novel sensitive two-dimensional surface enhanced Raman spectroscopy (SERS) substrate made of plasmonic nanocavities in a photonic quasicrystal arrangement characterized by a 12-fold rotational symmetry. Our SERS device is capable of detecting chemisorbed bacteriophages at a femtomolar range. Most importantly, the paper presents for the first time a study on the procedure to functionalize the plasmonic quasicrystal with bacteriophages of the Podoviridae family. The immobilization of the phages on the plasmonic substrate has been studied and verified through SERS measurements. A new stable peak, visible in the SERS spectra at 1326 cm-1 at a greater than 60 times amplification, confirms the immobilization of the phages on the substrate. This functionalization approach can be used also for other types of phages or plasmonic sensors and hence, our achievements could allow the development of novel systems for the specific detection of different species of bacteria.

Engineered nanopatterned substrates for high-sensitive localized surface plasmon resonance: an assay on biomacromolecules.

In this paper, we report on novel iso-Y-shaped-nanopillar based photonic crystals (PCs) engineered for plasmonic lab-on-a-chip advanced diagnostics. The iso-Y shaped units are selected on the basis of their plasmonic properties, analyzed numerically and experimentally. We show that by accurately choosing the nanopillar shape, dimensions and their geometrical disposal it is possible to obtain efficient optical 2D structures for biomolecule detection by high-sensitive localized surface plasmonic resonance (LSPR). In particular, an assay is realized by using bovine serum albumin (BSA), a widely recognized model for biosystem studies. BSA was simply deposited on a self-assembled monolayer (SAM) of 4-mercaptobenzoic acid (4-MBA) previously grown-up on the plasmonic substrate. We demonstrate that the geometries considered allow the design of LSPR nano-assays working in the visible-NIR region based on both intensity interrogation and the resonance peak shift permitting the sensing of BSA with a limit of detection in the order of picomoles (LOD = 233 pM).

A novel hybrid organic/inorganic photonic crystal slab showing a resonance action at the band edge.

Here we propose and experimentally demonstrate a hybrid photonic crystal (PC) slab consisting of air rods in a nanocomposite prepared by incorporating CdSe/CdS core/shell NRs (NR) in a polymer. Since the styrene methyl acrylate based polymer (ZEP) is transparent in the visible spectral range and is an electron-sensitive material, it was chosen as the embedding matrix for the NRs. Scanning electron microscopy and luminance measurements were used to characterize the experimental structure. The vertical extraction of the light, by the coupling of the modes guided by the PC slab to the free radiation via Bragg scattering, consists of a narrow orange emission band at 592 nm with a full width at half-maximum (FWHM) of 17 nm. The original characteristics of hybrid materials based on polymers and colloidal NRs, able to combine the unique optical properties of the inorganic moiety with the processability of the host matrix, are extremely appealing in view of their technological impact on the development of new high performing optical devices such as organic light-emitting diodes, ultra-low threshold lasers and non-linear devices.

An integrated superconductive magnetic nanosensor for high-sensitivity nanoscale applications.

An integrated magnetic nanosensor based on a niobium dc SQUID (superconducting quantum interference device) for nanoscale applications is presented. The sensor, having a washer shape with a hole of 200 nm and two Josephson-Dayem nanobridges of 80 nm × 100 nm, consists of a Nb(30 nm)/Al(30 nm) bilayer patterned by electron beam lithography (EBL) and shaped by lift-off and reactive ion etch (RIE) processes. The presence of the niobium coils, integrated on-chip and tightly coupled to the SQUID, allows us to easily excite the sensor in order to get the voltage-flux characteristics and to flux bias the SQUID at its optimal point. The measurements were performed at liquid helium temperature. A voltage swing of 75 µV and a maximum voltage-flux transfer coefficient (responsivity) as high as 1 mV/Φ(0) were directly measured from the voltage-flux characteristic. The noise measurements were performed in open loop mode, biasing the SQUID with a dc magnetic flux at its maximum responsivity point and using direct-coupled low-noise readout electronics. A white magnetic flux noise spectral density as low as 2.5 µΦ(0) Hz(-1/2) was achieved, corresponding to a magnetization or spin sensitivity in units of the Bohr magneton of 100 spin Hz(-1/2). Possible applications of this nanosensor can be envisaged in magnetic detection of nanoparticles and small clusters of atoms and molecules, in the measurement of nanoobject magnetization, and in quantum computing.

Transformation of mortal human fibroblasts and activation of a growth inhibitory pathway by the bovine papillomavirus E5 oncoprotein.

The 44-amino acid bovine papillomavirus E5 protein induces tumorigenic transformation of immortal rodent fibroblasts by binding to and activating the platelet-derived growth factor beta receptor (PDGFbetaR). Here E5 was expressed in mortal human diploid fibroblasts (HDFs), which lack the accumulated genetic changes that are present in immortal rodent cells. E5 induced focus formation and morphological transformation of HDFs without inducing anchorage independence or immortalization. Similar effects were observed with the v-sis and neu* oncogenes. E5-PDGFbetaR complexes were observed in the E5-expressing HDFs, as was constitutive PDGFbetaR activation, which was required for the transforming activity of E5. The E5 HDFs attained a higher saturation density than the control cells, expressing increased levels of hyperphosphorylated retinoblastoma protein at subconfluent densities. However, when these cells reached confluence, growth inhibition accompanied by dramatic down-regulation of the PDGFbetaR, and retinoblastoma protein was induced apparently by a factor secreted into the medium. This may represent a novel negative feedback mechanism controlling PDGFbetaR-induced proliferation and thereby protecting against complete transformation.

Oncogenic activation of the PDGF beta receptor by the transmembrane domain of p185neu*.

We replaced the transmembrane domain of the wild type murine PDGF beta receptor with that of p185neu*, the oncogenic form of p185neu, thereby generating a constitutively activated chimeric receptor PR/neu*. Unlike the wild type PDGF beta receptor or a chimeric receptor containing the transmembrane domain of wild type p185neu (PR/neu), PR/neu* induced morphologic transformation, focus formation, and tumorigenicity in mouse C127 fibroblasts. Expression of PR/neu* in mouse Ba/F3 hematopoietic cells, which normally depend on IL-3 for survival and sustained proliferation, induced proliferation in the absence of IL-3. The PR/neu chimera conferred limited IL-3-independent growth of Ba/F3 cells. Only PR/neu* and not PR/neu displayed significantly increased levels of phosphotyrosine compared to the wild type PDGF receptor in C127 and Ba/F3 cells. In addition, PR/neu* immune complexes displayed increased levels of kinase activity in vitro compared to immune complexes of the wild type receptor. Furthermore, novel tyrosine phosphorylated proteins of approximately 60 kDa appeared to specifically complex with PR/neu*, suggesting that PR/neu* may activate distinct signaling pathways. We speculate that the p185neu* transmembrane domain in the context of the PDGF beta receptor facilitates receptor homodimerization, thereby inducing tyrosine autophosphorylation followed by association with important signaling substrates and transforming activity. Thus, PR/neu* should be a useful reagent for further characterizing activation and signaling mechanisms of the PDGF beta receptor.

Identification of amino acids in the transmembrane and juxtamembrane domains of the platelet-derived growth factor receptor required for productive interaction with the bovine papillomavirus E5 protein.

The bovine papillomavirus E5 protein forms a stable complex with the cellular platelet-derived growth factor (PDGF) beta receptor, resulting in receptor activation and cell transformation. Amino acids in both the putative transmembrane domain and extracytoplasmic carboxyl-terminal domain of the E5 protein appear important for PDGF receptor binding and activation. Previous analysis indicated that the transmembrane domain of the receptor was also required for complex formation and receptor activation. Here we analyzed receptor chimeras and point mutants to identify specific amino acids in the PDGF beta receptor required for productive interaction with the E5 protein. These receptor mutants were analyzed in murine Ba/F3 cells, which do not express endogenous receptor. Our results confirmed the importance of the transmembrane domain of the receptor for complex formation, receptor tyrosine phosphorylation, and mitogenic signaling in response to the E5 protein and established that the threonine residue in this domain is required for these activities. In addition, a positive charge in the extracellular juxtamembrane domain of the receptor was required for E5 interaction and signaling, whereas replacement of the wild-type lysine with either a neutral or acidic amino acid inhibited E5-induced receptor activation and transformation. All of the receptor mutants defective for activation by the E5 protein responded to acute treatment with PDGF and to stable expression of v-Sis, a form of PDGF. The required juxtamembrane lysine and transmembrane threonine are predicted to align precisely on the same face of an alpha helix packed in a left-handed coiled-coil geometry. These results establish that the E5 protein and v-Sis recognize distinct binding sites on the PDGF beta receptor and further clarify the nature of the interaction between the viral transforming protein and its cellular target.

Polycyclic aromatic hydrocarbons in bovine lens.

A study was performed to detect the presence of polycyclic aromatic hydrocarbons (PAHs) in bovine eyes. Twenty fresh bovine eyes were used to detect the presence of PAHs in lens, vitreous and aqueous by HPLC and spectrofluorometer. In lenticular tissue the mean amount of PAHs was 0.0271 microgram/g and the mean level of PAH in each lens was 0.059 microgram. Five types of PAHs (pyrene, fluoranthene, triphenylene, 1.2-benzanthracene and chrysene) were found in the lenses but none in vitreous and aqueous. These data indicate that PAHs are present only in the lens of the bovine eye. The source of these substances in mammalian clear lens is unclear.

Specific interaction between the bovine papillomavirus E5 transforming protein and the beta receptor for platelet-derived growth factor in stably transformed and acutely transfected cells.

The E5 protein of bovine papillomavirus is a 44-amino-acid membrane protein which induces morphologic and tumorigenic transformation of fibroblasts. We previously showed that the E5 protein activates and forms a complex with the endogenous beta receptor for platelet-derived growth factor (PDGF) in transformed rodent fibroblasts and that the PDGF beta receptor can mediate tumorigenic transformation by the E5 protein in a heterologous cell system. Other workers have identified the receptor for epidermal growth factor (EGF) as a potential target of the E5 protein in NIH 3T3 cells. Here, we investigate the specificity of the interaction of the E5 protein with various growth factor receptors, with particular emphasis on the PDGF beta receptor and the EGF receptor. Under conditions where both the PDGF beta receptor and the EGF receptor are stably expressed in E5-transformed mouse and bovine fibroblasts and in E5-transformed epithelial cells, the E5 protein specifically forms a complex with and activates the PDGF receptor and not the EGF receptor. Under conditions of transient overexpression in COS cells, the E5 protein has the potential to associate with several growth factor receptors, including the EGF receptor. However, upon coexpression of PDGF beta receptors and EGF receptors in COS cells, the E5 protein preferentially forms a complex with the PDGF receptor. Therefore, we conclude that the PDGF beta receptor is the primary target for the E5 protein in a variety of cell types, including bovine fibroblasts.

Precipitation of the Epstein-Barr virus protein EBNA 2 by an EBNA 3c-specific monoclonal antibody.

Two monoclonal antibodies, E3cD8 and E3cA10, were generated to the EBNA 3c nuclear protein from the B95.8 isolate of Epstein-Barr virus (EBV). Both antibodies efficiently precipitate EBNA 3c from B95.8-transformed lymphoblastoid cell lines, and E3cA10 also detects EBNA 3c on Western blots. Whereas E3cD8 reacts with all 11 Type-1 isolates of EBV tested, and E3cA10 reacts with 14 of 17 Type-1 isolates, neither antibody detects the EBNA 3c protein encoded by Type-2 isolates. E3cD8 recognizes a peptide sequence (PA/PPQAPYQGY) in a repeat region of the B95.8 EBNA 3c coding sequence which is not present in the prototype Type-2 AG876 sequence. The E3cA10 antibody epitope has been mapped to the minimal five amino acid B95.8 peptide, WAPSV, which has an alanine to valine substitution in the AG876 virus isolate. This substitution was also found in three Type-1 EBV isolates that expressed EBNA 3c proteins not detected by E3cA10. In immunoprecipitation studies E3cA10 additionally coprecipitated the EBNA 2 protein from Type-1 isolates of EBV. The possibility of a direct interaction between EBNA 2 and EBNA 3c was ruled out by the demonstration that the antibody precipitated EBNA 2 from the Raji cell line which carries a virus with a deleted EBNA 3c gene. Since the WAPSV epitope identified in EBNA 3c is not present in EBNA 2, and no EBNA 2 linear peptide reactivity was detected in ELISA, it seems likely that E3cA10 recognizes a conformational epitope on EBNA 2. However, from the present data we cannot exclude the possibility that the antibody reacts with a cellular protein that physically associates with EBNA 2.

Design and outcomes of computer-based cognitive prosthetics for brain injury: a field study of three subjects.

Three traumatic brain injury (TBI) patients achieved a significant increase in level of function in a short period of time using a Computer-Based Cognitive Prosthesis (CBCP). A CBCP is a compensatory strategy which applies computer science concepts to brain injury rehabilitation. One-of-a-kind software is designed to assist the brain injury survivor in performing functional activities. New techniques of rehabilitation are also applied. Research subjects were between one and five years post injury. Patients were able to make substantial contributions to the design of their prosthetic software. Increases in level of functioning were seen both in everyday activities targeted for the intervention, as well as generalized increase on neurobehavioral and psychological dimensions.

Stable association between the bovine papillomavirus E5 transforming protein and activated platelet-derived growth factor receptor in transformed mouse cells.

The 44-amino acid E5 transforming protein of bovine papillomavirus is the shortest protein known to induce tumorigenic transformation of fibroblasts. We showed previously that expression of the E5 protein activates the cellular beta receptor for platelet-derived growth factor (PDGF) and proposed that the activated receptor transmits the transforming signal to the cell. Here we use coimmunoprecipitation analysis to show that the E5 protein and the activated PDGF receptor exist in a stable complex in transformed mouse C127 cells. These results suggest a distinct mechanism of growth factor receptor activation and provide further evidence that the PDGF receptor is an important target of the E5 protein.

Activation of the platelet-derived growth factor receptor by the bovine papillomavirus E5 transforming protein.

The bovine papillomavirus E5 gene encodes a 44 amino acid membrane-associated protein that can induce tumorigenic transformation of rodent fibroblast cell lines. Genetic studies suggest that the E5 protein may transform cells by influencing the activity of cellular proteins involved in growth regulation. We report here that the endogenous cellular beta type receptor for the platelet-derived growth factor (PDGF) is constitutively activated in C127 and FR3T3 cells stably transformed by the E5 protein, but not in these cell types transformed by a variety of other oncogenes. In C127 cells, a metabolic precursor as well as the mature form of the receptor is activated by E5 transformation. Activation of the receptor also occurs upon acute E5-mediated transformation of these cells and precedes mitogenic stimulation in this system. Moreover, activation of the receptor by addition of PDGF or the v-sis gene to untransformed cells is sufficient to induce DNA synthesis and stable growth transformation. We propose that the PDGF receptor is an important cellular intermediate in the transforming activity of the bovine papillomavirus E5 protein. There is a short region of sequence similarity between the fibropapillomavirus E5 proteins and PDGF, suggesting that the E5 proteins may activate the PDGF receptor by binding directly to it.

Subnuclear localization and phosphorylation of Epstein-Barr virus latent infection nuclear proteins.

Functions of the six Epstein-Barr virus latent infection nuclear proteins (EBNA-1, -2, -3A, -3B, -3C, or -LP) in maintaining latent infection or cell growth transformation are only partially understood. Using antibodies specific for each EBNA in immunofluorescence microscopy, EBNA-2, -3A, and -3C localized to subnuclear granules which fill much of the nucleus, excluding nucleoli. EBNA-LP localized to a small number of discrete subnuclear particles, also excluding nucleoli. Only EBNA-1 associated with metaphase chromosomes. Concordantly, in biochemical nuclear fractionation studies, EBNA-1 was the major chromatin-associated EBNA. EBNA-1 also differed from the other EBNAs in the extent of its association with the nucleoplasm and in its lack of nuclear matrix association. EBNA-LP, -2, -3A, and -3C were associated with the nuclear matrix, although they were also found in the nucleoplasm and to a lesser extent in the chromatin fractions. Metabolic 32Pi-labeling of cells followed by two-dimensional gel electrophoresis showed that EBNA-LP could be resolved into multiple phosphorylated isoforms. EBNA-2 was also phosphorylated and many isoforms were detected by isoelectric focusing.

Distinction between Epstein-Barr virus type A (EBNA 2A) and type B (EBNA 2B) isolates extends to the EBNA 3 family of nuclear proteins.

The Epstein-Barr virus (EBV) nuclear antigens EBNA 3a, 3b, and 3c have recently been mapped to adjacent reading frames in the BamHI L and E fragments of the B95.8 EBV genome. We studied by immunoblotting the expression of the family of EBNA 3 proteins in a panel of 20 EBV-transformed lymphoblastoid cell lines (LCLs) carrying either type A (EBNA 2A-encoding) or type B (EBNA 2B-encoding) virus isolates. Certain human sera from donors naturally infected with type A isolates detected the EBNA 3a, 3b, and 3c proteins in all type A virus-transformed LCLs (with a single exception in which EBNA 3b was not detected) but detected only EBNA 3a in LCLs carrying type B isolates. These results were confirmed with human and murine antibodies with specific reactivity against sequences of the type A EBNA 3a, 3b, or 3c expressed in bacterial fusion proteins. Conversely, selected human sera from donors naturally infected with type B strains of EBV identified the EBNA 3a encoded by both types of isolates plus two novel EBNAs present only in type B, and not in type A, virus-transformed LCLs; these novel proteins appear to be the type B homologs of EBNA 3b and 3c. The distinction between type A and type B EBV isolates therefore extends beyond the EBNA 2 gene to the EBNA 3 family of proteins. This has important implications with respect to the evolutionary origin of these two EBV types and also places in a new light recent studies which identified differences between type A and type B transformants in terms of growth phenotype (A. B. Rickinson, L. S. Young, and M. Rowe, J. Virol. 61:1310-1317, 1987) and of detection by EBV-specific cytotoxic T cells (D. J. Moss, I. S. Misko, S. R. Burrows, K. Burman, R. McCarthy, and T. B. Sculley, Nature [London] 331:719-721, 1988).

A sixth Epstein-Barr virus nuclear protein (EBNA3B) is expressed in latently infected growth-transformed lymphocytes.

In the Epstein-Barr virus BamHI E genomic fragment, there are three distantly homologous long open reading frames, BERF1, BERF2b, and BERF4, each of which is preceded by a short open reading frame. The most leftward and most rightward short and long open reading frame pairs encode 145- and 155-kilodalton proteins in latently infected cells (EBNA3A and EBNA3C, respectively). In this report, we demonstrate that the middle long open reading frame, BERF2b, encodes part of a 165-kilodalton nuclear protein in every latently infected cell. Therefore, this protein is designated EBNA3B.

A fifth Epstein-Barr virus nuclear protein (EBNA3C) is expressed in latently infected growth-transformed lymphocytes.

Three distantly homologous neighboring long open reading frames in the Epstein-Barr virus (EBV) genome are preceded by short open reading frames. The leftmost short and long open reading frames encode EBNA3, a nuclear protein which is slightly smaller (145 kilodaltons [kDa]) than two other nuclear proteins (150 to 155 kDa) detected in Western blots (immunoblots) of latently infected cell protein (K. Hennessy, F. Wang, E. Woodland-Bushman, and E. Kieff, Proc. Natl. Acad. Sci. USA 83:5693-5697, 1986; I. Joab, D. T. Rowe, M. Bodescot, J.-C. Nicolas, P. J. Farrell, and M. Perricaudet, J. Virol. 61:3340-3344, 1987). We have demonstrated that the most rightward short (BERF3) and long (BERF4) open reading frames are spliced in frame at the 3' end of a 5-kilobase latently infected cell RNA and that this RNA begins within or upstream of the EBV long internal repeat. EBV-immune human antibodies specific for the long open reading frame translation product identified a 155-kDa protein on Western blots of latently infected cell protein and specifically reacted with large nonnucleolar nuclear granules in every latently infected cell. Expression of the cDNA in BALB/c 3T3 cells resulted in translation of full-size EBNA3C but had no effect on cell morphology, contact inhibition, or serum independence.

Biochemical and biophysical characteristics of Rio Bravo virus (Flaviviridae).

Rio Bravo (RB) virus has been assigned to the family Flaviviridae on the basis of its antigenic relatedness to other members of this family. RB virus, unlike most members of the Flaviviridae, is believed not to have an arthropod vector. We examined biochemical and biophysical characteristics of RB virus to determine whether it should be assigned to the Flaviviridae and to compare it with arthropod-borne flaviviruses. Purified RB virus banded at a density of 1.18 g/ml in sucrose and had a sedimentation coefficient of about 200 S. Virions, negatively stained with ammonium molybdate, were spherical, had diameters of 42 nm, and appeared to be surrounded by envelopes bearing surface projections. The loss of infectivity after infectious virus was incubated with diethyl ether or sodium deoxycholate confirmed the presence of envelopes. Partially purified RB virions contained single-stranded RNA, lacking 3' poly(A) tracts, that sedimented in a 15% to 30% sucrose gradient as one discrete band with a sedimentation coefficient of about 40 S. Most of the viral proteins in preparations of purified virus and in immunoprecipitates had similar electrophoretic mobilities and glycosylation patterns to known flavivirus proteins. Therefore, they were assigned the following tentative designations using the nomenclature for flavivirus proteins: gp52 and gp47, envelope proteins; gp46, non-structural protein 1; p25, gp20(prM), precursor to membrane protein; gp less than 18K. Putative core and membrane proteins were not identified. These physical and biochemical characteristics of RB virus are remarkably similar to those of the arthropod-borne members of the Flaviviridae and they confirm the classification of RB virus in this family. This is the first report of biochemical and physical properties of a non-arthropod-borne member of the Flaviviridae.

Identification of an Epstein-Barr virus early gene encoding a second component of the restricted early antigen complex.

When the latent Epstein-Barr virus (EBV) genome in B95-8 cells is induced into a replicative phase, two abundant early RNAs are transcribed rightward from the EBV BamHI H DNA fragment into BamHI F. Analysis of cDNA clones prepared from the RNA of cells replicating EBV revealed that both RNAs contain the BHRF1 open reading frame. Part of BHRF1, cloned into a prokaryotic fusion protein expression vector, expressed a fusion protein in Escherichia coli and the purified fusion protein was used to generate a monoclonal antibody against BHRF1. This antibody was then employed to characterize the protein encoded by BHRF1 in cells replicating EBV. The monoclonal antibody reacted with a 17-kDa protein component of the restricted early antigen (EA) complex. The distribution of the protein in cells was similar to that noted when sera from patients with African Burkitt's lymphoma were used to stain these cells. The protein was synthesized before the major 47-56 kDa protein associated with the diffuse component of EA in superinfected Raji cells. All human sera containing antibodies to EA as determined by immunofluorescence (IF) reacted with the protein as did some sera determined to be anti-VCA positive and anti-EA negative by IF. The predicted amino acid sequence of the protein has characteristics which suggest that it is a membrane protein. It also has significant homology with both the anchor region of polyoma middle T antigen and with the predicted protein product of the bcl-2 mRNA activated by the 14/18 chromosome translocation characteristic of follicular lymphomas. This latter homology is extensive and colinear, suggesting common evolution and function. However, neither a mRNA which could efficiently translate the BHRF1 protein nor the BHRF1 protein could be detected in latently infected cells. Thus, the bcl-2 predicted protein is similar to an EBV protein synthesized in the early phase of virus infection.