Application of NMR SHAPES screening to an RNA target

Several NMR screening techniques have been developed in recent years to aid in the identification of lead drug compounds. These NMR methods have traditionally been used for protein targets, and here we examine their applicability for an RNA target. We used the SHAPES compound library to test three different NMR screening methodologies: the saturation transfer difference (STD), the 2D trNOESY, and the WaterLOGSY experiments. We found that the WaterLOGSY experiment was the most sensitive method for our RNA target, the P4P6 domain of the Tetrahymena thermophila Group I intron. Using the WaterLOGSY experiment, we found that 23 of the 112 SHAPES compounds interact with P4P6. To identify which of these 23 hits bind through nonspecific interactions, we counterscreened with a linear duplex RNA control and identified one of the SHAPES compounds as interacting with P4P6 specifically. We thus demonstrated that the WaterLOGSY experiment in combination with the SHAPES compound library can be used to efficiently find RNA binding lead compounds.     

Ex vivo study of carotid endarterectomy specimens: quantitative relaxation times within atherosclerotic plaque tissues

Purpose

Previous studies reporting relaxation times within atherosclerotic plaque have typically used dedicated small-bore high-field systems and small sample sizes. This study reports quantitative T₁, T₂ and T₂^? relaxation times within plaque tissue at 1.5 T using spatially co-matched histology to determine tissue constituents.

Methods

Ten carotid endarterectomy specimens were removed from patients with advanced atherosclerosis. Imaging was performed on a 1.5-T whole-body scanner using a custom built 10-mm diameter receive-only solenoid coil. A protocol was defined to allow subsequent computation of T₁, T₂ and T₂^? relaxation times using multi-flip angle spoiled gradient echo, multi-echo fast spin echo and multi-echo gradient echo sequences, respectively. The specimens were subsequently processed for histology and individually sectioned into 2-mm blocks to allow subsequent co-registration. Each imaging sequence was imported into in-house software and displayed alongside the digitized histology sections. Regions of interest were defined to demarcate fibrous cap, connective tissue and lipid/necrotic core at matched slice-locations. Relaxation times were calculated using Levenberg-Marquardt's least squares curve fitting algorithm. A linear-mixed effect model was applied to account for multiple measurements from the same patient and establish if there was a statistically significant difference between the plaque tissue constituents.

Results

T₂ and T₂^? relaxation times were statistically different between all plaque tissues (P=.026 and P=.002 respectively) [T₂: lipid/necrotic core was lower 47±13.7 ms than connective tissue (67±22.5 ms) and fibrous cap (60±13.2 ms); T₂^?: fibrous cap was higher (48±15.5ms) than connective tissue (19±10.6 ms) and lipid/necrotic core (24±8.2 ms)]. T₁ relaxation times were not significantly different (P=.287) [T₁: Fibrous cap: 933±271.9 ms; connective tissue (1002±272.9 ms) and lipid/necrotic core (1044±304.0 ms)]. We were unable to demarcate hemorrhage and calcium following histology processing.

Conclusions

This study demonstrates that there is a significant difference between qT₂ and qT₂^? in plaque tissues types. Derivation of quantitative relaxation times shows promise for determining plaque tissue constituents.     

Label-free optical biosensing with slot-waveguides

We demonstrate label-free molecule detection by using an integrated biosensor based on a Si(3)N(4)/SiO(2) slot-waveguide microring resonator. Bovine serum albumin (BSA) and anti-BSA molecular binding events on the sensor surface are monitored through the measurement of resonant wavelength shifts with varying biomolecule concentrations. The biosensor exhibited sensitivities of 1.8 and 3.2 nm/(ng/mm(2)) for the detection of anti-BSA and BSA, respectively. The estimated detection limits are 28 and 16 pg/mm(2) for anti-BSA and BSA, respectively, limited by wavelength resolution.     

Interaction of the mu-opioid receptor with GPR177 (Wntless) inhibits Wnt secretion: potential implications for opioid dependence

Background  

Opioid agonist drugs produce analgesia. However, long-term exposure to opioid agonists may lead to opioid dependence. The analgesic and addictive properties of opioid agonist drugs are mediated primarily via the mu-opioid receptor (MOR). Opioid agonists appear to alter neuronal morphology in key brain regions implicated in the development of opioid dependence. However, the precise role of the MOR in the development of these neuronal alterations remains elusive. We hypothesize that identifying and characterizing novel MOR interacting proteins (MORIPs) may help to elucidate the underlying mechanisms involved in the development of opioid dependence.     

Left inferior frontal gyrus is critical for response inhibition

Background  

Lesion studies in human and non-human primates have linked several different regions of prefrontal cortex (PFC) with the ability to inhibit inappropriate motor responses. However, recent functional neuroimaging studies have specifically implicated right inferior PFC in response inhibition. Right frontal dominance for inhibitory motor control has become a commonly accepted view, although support for this position has not been consistent. Particularly conspicuous is the lack of data on the importance of the homologous region in the left hemisphere. To investigate whether the left inferior frontal gyrus (IFG) is critical for response inhibition, we used neuropsychological methodology with carefully characterized brain lesions in neurological patients.     

Iron homeostasis in neuronal cells: a role for IREG1

Background  

Iron is necessary for neuronal function but in excess generates neurodegeneration. Although most of the components of the iron homeostasis machinery have been described in neurons, little is known about the particulars of their iron homeostasis. In this work we characterized the response of SH-SY5Y neuroblastoma cells and hippocampal neurons to a model of progressive iron accumulation.     

Idempotent bounded C-semigroups

A semigroup with zero isidempotent bounded (IB) if it is the 0-direct union of idempotent generated principal left ideals and the 0-direct union of idempotent generated principal right ideals. Notable examples are completely 0-simple semigroups and the wider class of primitive abundant semigroups. Significant to the structure of these semigroups is that they are all categorical at zero. In this paper we describe IB semigroups that are categorical at zero in terms ofdouble blocked Rees matrix semigroups. This generalises Fountain's characterisation of primitive abundant semigroups via blocked Rees matrix semigroups [1], which in turn yields the Rees theorem for completely 0-simple semigroups.     

Tunable light source for coherent anti-Stokes Raman scattering microspectroscopy based on the soliton self-frequency shift

We present a photonic crystal fiber (PCF)-based light source for generating tunable excitation pulses (pump and Stokes) that are applicable to coherent anti-Stokes Raman scattering (CARS) microspectroscopy. The laser employed is an unamplified Ti:sapphire femtosecond laser oscillator. The CARS pump pulse is generated by spectral compression of a laser pulse in a PCF. The Stokes pulse is generated by redshifting a laser pulse in a PCF through the soliton self-frequency shift. This setup allows for probing up to 4000 cm(-1) with a spectral resolution of approximately 25 cm(-1). We characterize the stability and robustness of CARS microspectroscopy employing this light source.     

Synthesis and magnetic characterization of cobalt-substituted ferrite (CoxFe3−xO4) nanoparticles

Cobalt-substituted ferrite nanoparticles were synthesized with a narrow size distribution using reverse micelles formed in the system water/AOT/isooctane. Fe:Co ratios of 3:1, 4:1, and 5:1 were used in the synthesis, obtaining cobalt-substituted ferrites (Co_xFe_3−xO₄) and some indication of γ-Fe₃O₄ when 4:1 and 5:1 Fe:Co ratios were used. Inductively coupled plasma mass spectroscopy (ICP-MS) verified the presence of cobalt in all samples. Fourier transform infrared (FTIR) showed bands at ∼560 and ∼400 cm⁻¹, characteristic of the metal–oxygen bond in ferrites. Transmission electron microscopy showed that the number median diameter of the particles was ∼3 nm with a geometric deviation of ∼0.2. X-ray diffraction (XRD) confirmed the inverse spinel structure typical of ferrites with a lattice parameter of a=8.388 Å for Co_0.61Fe_0.39O₄, which is near that of CoFe₂O₄ (a=8.394 Å). Magnetic properties were determined using a superconducting quantum interference device (SQUID). Coercivities higher than 8 kOe were observed at 5 K, whereas at 300 K the particles showed superparamagnetic behavior. The anisotropy constant was determined based on the Debye model for a magnetic dipole in an oscillating field and an expression relating χ′ and the temperature of the in-phase susceptibility peak. Anisotropy constant values in the order of ∼10⁶ erg/cm³ were determined using the Debye model, whereas anisotropy constants in the order of ∼10⁷ erg/cm³ were calculated assuming Ωτ=1 at the temperature peak of the in-phase component of the susceptibility curve as commonly done in the literature. Our analysis demonstrates that the assumption Ωτ=1 at the temperature peak of χ′ is rigorously incorrect.