Immunoassays with rolling circle DNA amplification: A versatile platform for ultrasensitive antigen detection

We describe an adaptation of the rolling circle amplification (RCA) reporter system for the detection of protein Ags, termed “immunoRCA.” In immunoRCA, an oligonucleotide primer is covalently attached to an Ab; thus, in the presence of circular DNA, DNA polymerase, and nucleotides, amplification results in a long DNA molecule containing hundreds of copies of the circular DNA sequence that remain attached to the Ab and that can be detected in a variety of ways. Using immunoRCA, analytes were detected at sensitivities exceeding those of conventional enzyme immunoassays in ELISA and microparticle formats. The signal amplification afforded by immunoRCA also enabled immunoassays to be carried out in microspot and microarray formats with exquisite sensitivity. When Ags are present at concentrations down to fM levels, specifically bound Abs can be scored by counting discrete fluorescent signals arising from individual Ag–Ab complexes. Multiplex immunoRCA also was demonstrated by accurately quantifying Ags mixed in different ratios in a two-color, single-molecule-counting assay on a glass slide. ImmunoRCA thus combines high sensitivity and a very wide dynamic range with an unprecedented capability for single molecule detection. This Ag-detection method is of general applicability and is extendable to multiplexed immunoassays that employ a battery of different Abs, each labeled with a unique oligonucleotide primer, that can be discriminated by a color-coded visualization system. ImmunoRCA-profiling based on the simultaneous quantitation of multiple Ags should expand the power of immunoassays by exploiting the increased information content of ratio-based expression analysis.

X-ray absorption fine structure as a monitor of zinc coordination sites during oogenesis of Xenopus laevis.

The x-ray absorption fine structure (XAFS) zinc K-edge steps for intact stages I,II and V,VI Xenopus laevis oocytes demonstrate that the zinc concentration is about 3 and 1 mM, respectively. However, the chi(k) function for the early stage oocytes differs markedly from that for the late one. Analysis of the XAFS data for stage I,II oocytes indicates that zinc is bound to 2.0 +/- 0.5 sulfur atoms at an average coordination distance of 2.29 +/- 0.02 angstroms and 2.0 +/- 0.5 nitrogen or oxygen (N/O) atoms at 2.02 +/- 0.02 angstroms. In marked contrast, in stage V,VI oocytes, zinc is bound to 4.1 +/- 0.4 N/O atoms at an average distance of 1.98 +/- 0.01 angstroms. Our previous studies demonstrated that 90% of the zinc in stage VI oocytes is sequestered within yolk platelets, associated with a single molecule, lipovitellin, the proteolytically processed product of vitellogenin. XAFS analysis of yolk platelets, lipovitellin, and vitellogenin demonstrates that zinc is bound to 4.0 +/- 0.5 N/O ligands at an average distance of 1.98 +/- 0.01 angstroms in each case, identical to that of stage V,VI oocytes. The higher shell contributions in the Fourier transforms indicate that two of the N/O zinc ligands are His in both stage V,VI and I,II oocytes. The results show that in stage I,II oocytes, there is a high concentration of a zinc protein whose zinc coordination site likely is composed of (His)2(Cys)2, such as, e.g., TFIIIA. As the oocytes develop, the predominant zinc species becomes one that exhibits the (His)2(N/0)2 zinc site found in lipovitellin. Hence, the ligands to the zinc atoms in intact oocytes and the changes that take place as a function of oogenesis and after their fertilization, during embryogenesis, now can be examined and explored.

Chicken double-stranded RNA adenosine deaminase has apparent specificity for Z-DNA.

A M(r) 140,000 protein has been purified from chicken lungs to apparent homogeneity. The protein binds with high affinity to a non-BNA conformation, which is most likely to the Z-DNA. The protein also has a binding site for double-stranded RNA (dsRNA). Peptide sequences from this protein show similarity to dsRNA adenosine deaminase, an enzyme that deaminates adenosine in dsRNA to form inosine. Assays for this enzyme confirm that dsRNA adenosine deaminase activity and Z-DNA binding are properties of the same molecule. The coupling of these two activities in a single molecule may indicate a distinctive mechanism of gene regulation that is, in part, dependent on DNA topology. As such, DNA topology, through its effects on the efficiency and extent of RNA editing may be important in the generation of new phenotypes during evolution.

The old problems of glass and the glass transition, and the many new twists.

In this paper I review the ways in which the glassy state is obtained both in nature and in materials science and highlight a "new twist"--the recent recognition of polymorphism within the glassy state. The formation of glass by continuous cooling (viscous slowdown) is then examined, the strong/fragile liquids classification is reviewed, and a new twist-the possibility that the slowdown is a result of an avoided critical point-is noted. The three canonical characteristics of relaxing liquids are correlated through the fragility. As a further new twist, the conversion of strong liquids to fragile liquids by pressure-induced coordination number increases is demonstrated. It is then shown that, for comparable systems, it is possible to have the same conversion accomplished via a first-order transition within the liquid state during quenching. This occurs in the systems in which "polyamorphism" (polymorphism in the glassy state) is observed, and the whole phenomenology is accounted for by Poole's bond-modified van der Waals model. The sudden loss of some liquid degrees of freedom through such weak first-order transitions is then related to the polyamorphic transition between native and denatured hydrated proteins, since the latter are also glass-forming systems--water-plasticized, hydrogen bond-cross-linked chain polymers (and single molecule glass formers). The circle is closed with a final new twist by noting that a short time scale phenomenon much studied by protein physicists-namely, the onset of a sharp change in d/dT ( is the Debye-Waller factor)--is general for glass-forming liquids, including computer-simulated strong and fragile ionic liquids, and is closely correlated with the experimental glass transition temperature. The latter thus originates in strong anharmonicity in certain components of the vibrational density of states, which permits the system to access the multiple minima of its configuration space. The connection between the anharmonicity in these modes, vibrational localization, the Kauzmann temperature, and the fragility of the liquid is proposed as the key problem in glass science.

Recent developments in the synthesis of novel xanthone-1,2,3-triazole dyads

The development of multi-target drugs for treating complex multifactorial diseases constitutes an active research ield. This kind of drugs has gained much importance as alternative strategy to combination therapy (“cocktail drugs”).1 A common way to design them brings together two different pharmacophores in one single molecule (so-called dyads). Following this idea and being aware that xanthones2 and 1,2,3-triazoles3 possess important pharmacological properties, we combined these two heterocycles in one molecule to create new dyads with improved therapeutic potential. In this work, new xanthone-1,2,3-triazole dyads were prepared from novel (E)-2-(4-arylbut-1-en-3-yn-1-yl)chromones by two different approaches to evaluate their eficiency and sustainability. Both methodologies involved Diels-Alder reactions to build the xanthone core, which were optimized using microwave irradiation as alternative heating method, and 1,3-dipolar cycloadditions to insert the 1,2,3-triazole moiety (Figure 1).4 All final and intermediate compounds were fully characterized by 1D and 2D NMR techniques.

Investigating the Effect of Histone H4 Sumoylation on Chromatin Structure and Function

Thesis (Ph.D.)--University of Washington, 2016-06

High-fidelity measurement and quantum feedback control in circuit QED

Circuit QED is a promising solid-state quantum computing architecture. It also has excellent potential as a platform for quantum control-especially quantum feedback control-experiments. However, the current scheme for measurement in circuit QED is low efficiency and has low signal-to-noise ratio for single-shot measurements. The low quality of this measurement makes the implementation of feedback difficult, and here we propose two schemes for measurement in circuit QED architectures that can significantly improve signal-to-noise ratio and potentially achieve quantum-limited measurement. Such measurements would enable the implementation of quantum feedback protocols and we illustrate this with a simple entanglement-stabilization scheme.

Lipid rafts: contentious only from simplistic standpoints

The hypothesis that lipid rafts exist in plasma membranes and have crucial biological functions remains controversial. The lateral heterogeneity of proteins in the plasma membrane is undisputed, but the contribution of cholesterol-dependent lipid assemblies to this complex, non-random organization promotes vigorous debate. In the light of recent studies with model membranes, computational modelling and innovative cell biology, I propose an updated model of lipid rafts that readily accommodates diverse views on plasma-membrane micro-organization.

Preparation of high purity ZnO nanobelts by thermal evaporation of ZnS

High purity one-dimensional ZnO nanobelts were synthesized by thermally evaporating commercial ZnS powders in a hydrogen-oxygen mixture gas at 1050 degrees C. It was found that these ZnO nanobelts had a single crystal hexagonal wurtzite structure growing along the [0001] direction. They had a rectangle-shaped cross-section with typical widths of 20 to 100 nanometers and lengths of up to hundreds of micrometers with lattice constants of a = 0.325 nm and c = 0.520 nm. The self-catalytic hydrogen-oxygen assisted growth of ZnO nanobelt is discussed. The photoluminescence (PL) characterization of the ZnO nanobelts shows strong near-band UV emission (about 383 nm) and one broad peak at 501 nm, which indicates that the ZnO nanobelts have good potential application in optoelectronic devices.

Spin-detection in a quantum electromechanical shuttle system

We study the electrical transport of a harmonically bound, single-molecule C-60 shuttle operating in the Coulomb blockade regime, i.e. single electron shuttling. In particular, we examine the dependance of the tunnel current on an ultra-small stationary force exerted on the shuttle. As an example, we consider the force exerted on an endohedral N@C-60 by the magnetic field gradient generated by a nearby nanomagnet. We derive a Hamiltonian for the full shuttle system which includes the metallic contacts, the spatially dependent tunnel couplings to the shuttle, the electronic and motional degrees of freedom of the shuttle itself and a coupling of the shuttle's motion to a phonon bath. We analyse the resulting quantum master equation and find that, due to the exponential dependence of the tunnel probability on the shuttle-contact separation, the current is highly sensitive to very small forces. In particular, we predict that the spin state of the endohedral electrons of N@C-60 in a large magnetic gradient field can be distinguished from the resulting current signals within a few tens of nanoseconds. This effect could prove useful for the detection of the endohedral spin-state of individual paramagnetic molecules such as N@C-60 and P@C-60, or the detection of very small static forces acting on a C-60 shuttle.

Increased diversity of libraries from libraries: chemoinformatic analysis of bis-diazacyclic libraries

Combinatorial libraries continue to play a key role in drug discovery. To increase structural diversity, several experimental methods have been developed. However, limited efforts have been performed so far to quantify the diversity of the broadly used diversity-oriented synthetic (DOS) libraries. Herein we report a comprehensive characterization of 15 bis-diazacyclic combinatorial libraries obtained through libraries from libraries, which is a DOS approach. Using MACCS keys, radial and different pharmacophoric fingerprints as well as six molecular properties, it was demonstrated the increased structural and property diversity of the libraries from libraries over the individual libraries. Comparison of the libraries to existing drugs, NCI Diversity and the Molecular Libraries Small Molecule Repository revealed the structural uniqueness of the combinatorial libraries (mean similarity < 0.5 for any fingerprint representation). In particular, bis-cyclic thiourea libraries were the most structurally dissimilar to drugs retaining drug-like character in property space. This study represents the first comprehensive quantification of the diversity of libraries from libraries providing a solid quantitative approach to compare and contrast the diversity of DOS libraries with existing drugs or any other compound collection.

Noise in gallium nitride-based quantum well structures used for nanometer devices in the frequency range 1 Hz--3 Mhz and temperature range 77K--324K

Electronic noise has been investigated in AlxGa1−x N/GaN Modulation-Doped Field Effect Transistors (MODFETs) of submicron dimensions, grown for us by MBE (Molecular Beam Epitaxy) techniques at Virginia Commonwealth University by Dr. H. Morkoç and coworkers. Some 20 devices were grown on a GaN substrate, four of which have leads bonded to source (S), drain (D), and gate (G) pads, respectively. Conduction takes place in the quasi-2D layer of the junction (xy plane) which is perpendicular to the quantum well (z-direction) of average triangular width ∼3 nm. A non-doped intrinsic buffer layer of ∼5 nm separates the Si-doped donors in the AlxGa1−xN layer from the 2D-transistor plane, which affords a very high electron mobility, thus enabling high-speed devices. Since all contacts (S, D, and G) must reach through the AlxGa1−xN layer to connect internally to the 2D plane, parallel conduction through this layer is a feature of all modulation-doped devices. While the shunting effect may account for no more than a few percent of the current IDS, it is responsible for most excess noise, over and above thermal noise of the device. ^ The excess noise has been analyzed as a sum of Lorentzian spectra and 1/f noise. The Lorentzian noise has been ascribed to trapping of the carriers in the AlxGa1−xN layer. A detailed, multitrapping generation-recombination noise theory is presented, which shows that an exponential relationship exists for the time constants obtained from the spectral components as a function of 1/kT. The trap depths have been obtained from Arrhenius plots of log (τT2) vs. 1000/T. Comparison with previous noise results for GaAs devices shows that: (a) many more trapping levels are present in these nitride-based devices; (b) the traps are deeper (farther below the conduction band) than for GaAs. Furthermore, the magnitude of the noise is strongly dependent on the level of depletion of the AlxGa1−xN donor layer, which can be altered by a negative or positive gate bias VGS. ^ Altogether, these frontier nitride-based devices are promising for bluish light optoelectronic devices and lasers; however, the noise, though well understood, indicates that the purity of the constituent layers should be greatly improved for future technological applications. ^

Obtenção de organovermiculitas utilizando tensoativos e microemulsões e suas aplicações na separação de isômeros do Xileno

Surfactants are versatile organic compounds that have, in a single molecule, double chemical affinity. The surfactant molecule is composed by a hy drophobic tail group, a hydrocarbon chain (linear, branched, or mixed), and by a hydrophilic head group, which contains polar groups that makes it able to be applied in the organophilization process of natural clays. Microemulsions are microheterogeneous b lends composed by: a surfactant, an oily phase (non - polar solvent), an aqueous phase, and, sometimes, a co - surfactant (short - chain alcohol). They are systems with thermodynamic stability, transparent, and have high solubility power. Vermiculite is a clay m ineral with an expandable crystalline structure that has high cation exchange capacity. In this work vermiculite was used to obtain organoclays. The ionic surfactants dodecyl ammonium chlori de (DDAC) and cetyltrimethylammonium bromide (C 16 TAB) were used in the organophilization process. They were used as surfactant aqueous solutions and, for DDAC, as a microemulsion system. The organoclays were used to promote the separation of binary mixtures of xylene isomers (ortho - and meta - xylene). Dif ferent analytical techniques were used to characterize microemulsion systems and also the nanoclays. It was produced a water - rich microemulsion system with 0.92 nm droplet average diameter. The vermiculite used in this work has a cationic exchange capacity of 172 meq/100g and magnesium as main cation (24.25%). The basal spacing of natural vermiculite and organo - vermiculites were obtained by X - ray Diffraction technique. The basal spacing was 1.48nm for natural vermiculite, 4.01nm for CTAB - vermiculite (CTAB 4 ) , and 3.03nm for DDAC - vermiculite (DDAC M1A), that proves the intercalation process. Separation tests were carried out in glass columns using three binary mixtures of xylene (ortho - xylene and meta - xylene). The results showed that the organovermiculite pre sented an enhanced chemical affinity by the mixture of hydrocarbons, when compared with the natural vermiculite, and also its preference by ortho - xylene. A factorial experimental design 2 2 with triplicate at the central point was used to optimize the xylen e separation process. The experimental design revealed that the initial concentration of isomers in the mixture and the mass of organovermiculite were the significant factors for an improved separation of isomers. In the experiments carried out using a bin ary mixture of ortho - xylene and meta - xylene (2:1), after its percolating through the organovermiculite bed (DDAC M1), it was observed the preference of the organoclay by the ortho - xylene isomer, which was retained in greater quantity than the meta - xylene o ne. At the end of the treatment, it was obtained a final concentration in meta - xylene of 47.52%.

Design, fabrication and characterization of resonant waveguide grating based optical biosensors

The absence of rapid, low cost and highly sensitive biodetection platform has hindered the implementation of next generation cheap and early stage clinical or home based point-of-care diagnostics. Label-free optical biosensing with high sensitivity, throughput, compactness, and low cost, plays an important role to resolve these diagnostic challenges and pushes the detection limit down to single molecule. Optical nanostructures, specifically the resonant waveguide grating (RWG) and nano-ribbon cavity based biodetection are promising in this context. The main element of this dissertation is design, fabrication and characterization of RWG sensors for different spectral regions (e.g. visible, near infrared) for use in label-free optical biosensing and also to explore different RWG parameters to maximize sensitivity and increase detection accuracy. Design and fabrication of the waveguide embedded resonant nano-cavity are also studied. Multi-parametric analyses were done using customized optical simulator to understand the operational principle of these sensors and more important the relationship between the physical design parameters and sensor sensitivities. Silicon nitride (SixNy) is a useful waveguide material because of its wide transparency across the whole infrared, visible and part of UV spectrum, and comparatively higher refractive index than glass substrate. SixNy based RWGs on glass substrate are designed and fabricated applying both electron beam lithography and low cost nano-imprint lithography techniques. A Chromium hard mask aided nano-fabrication technique is developed for making very high aspect ratio optical nano-structure on glass substrate. An aspect ratio of 10 for very narrow (~60 nm wide) grating lines is achieved which is the highest presented so far. The fabricated RWG sensors are characterized for both bulk (183.3 nm/RIU) and surface sensitivity (0.21nm/nm-layer), and then used for successful detection of Immunoglobulin-G (IgG) antibodies and antigen (~1μg/ml) both in buffer and serum. Widely used optical biosensors like surface plasmon resonance and optical microcavities are limited in the separation of bulk response from the surface binding events which is crucial for ultralow biosensing application with thermal or other perturbations. A RWG based dual resonance approach is proposed and verified by controlled experiments for separating the response of bulk and surface sensitivity. The dual resonance approach gives sensitivity ratio of 9.4 whereas the competitive polarization based approach can offer only 2.5. The improved performance of the dual resonance approach would help reducing probability of false reading in precise bio-assay experiments where thermal variations are probable like portable diagnostics.

Electric Field Effects on Graphene Materials

Understanding the effect of electric fields on the physical and chemical properties of two-dimensional (2D) nanostructures is instrumental in the design of novel electronic and optoelectronic devices. Several of those properties are characterized in terms of the dielectric constant which play an important role on capacitance, conductivity, screening, dielectric losses and refractive index. Here we review our recent theoretical studies using density functional calculations including van der Waals interactions on two types of layered materials of similar two-dimensional molecular geometry but remarkably different electronic structures, that is, graphene and molybdenum disulphide (MoS2). We focus on such two-dimensional crystals because of they complementary physical and chemical properties, and the appealing interest to incorporate them in the next generation of electronic and optoelectronic devices. We predict that the effective dielectric constant (ε) of few-layer graphene and MoS2 is tunable by external electric fields (E ext). We show that at low fields (E ext < 0.01 V/Å) ε assumes a nearly constant value ∼4 for both materials, but increases at higher fields to values that depend on the layer thickness. The thicker the structure the stronger is the modulation of ε with the electric field. Increasing of the external field perpendicular to the layer surface above a critical value can drive the systems to an unstable state where the layers are weakly coupled and can be easily separated. The observed dependence of ε on the external field is due to charge polarization driven by the bias, which show several similar characteristics despite of the layer considered. All these results provide key information about control and understanding of the screening properties in two-dimensional crystals beyond graphene and MoS2