Quantitative stem-loop RT-PCR for detection of microRNAs

Plant microRNAs (miRNAs) are a class of endogenous small RNAs that are essential for plant development and survival. They arise from larger precursor RNAs with a characteristic hairpin structure and regulate gene activity by targeting mRNA transcripts for cleavage or translational repression. Efficient and reliable detection and quantification of miRNA expression has become an essential step in understanding their specific roles. The expression levels of miRNAs can vary dramatically between samples and they often escape detection by conventional technologies such as cloning, northern hybridization and microarray analysis. The stem-loop RT-PCR method described here is designed to detect and quantify mature miRNAs in a fast, specific, accurate and reliable manner. First, a miRNA-specific stem-loop RT primer is hybridized to the miRNA and then reverse transcribed. Next, the RT product is amplified and monitored in real time using a miRNA-specific forward primer and the universal reverse primer. This method enables miRNA expression profiling from as little as 10 pg of total RNA and is suitable for high-throughput miRNA expression analysis.

qRT-PCR of Small RNAs

Plant small RNAs are a class of 19- to 25-nucleotide (nt) RNA molecules that are essential for genome stability, development and differentiation, disease, cellular communication, signaling, and adaptive responses to biotic and abiotic stress. Small RNAs comprise two major RNA classes, short interfering RNAs (siRNAs) and microRNAs (miRNAs). Efficient and reliable detection and quantification of small RNA expression has become an essential step in understanding their roles in specific cells and tissues. Here we provide protocols for the detection of miRNAs by stem-loop RT-PCR. This method enables fast and reliable miRNA expression profiling from as little as 20 pg of total RNA extracted from plant tissue and is suitable for high-throughput miRNA expression analysis. In addition, this method can be used to detect other classes of small RNAs, provided the sequence is known and their GC contents are similar to those specific for miRNAs.

The loss of CO from the ortho, meta and para forms of deprotonated methyl benzoate in the gas phase

The ortho, meta and para anions of methyl benzoate may be made in the source of a mass spectrometer by the S(N)2(Si) reactions between HO- and methyl (o-, m-, and p-trimethylsilyl)benzoate respectively. All three anions lose CO upon collisional activation to form the ortho anion of anisole in the ratio ortho>>meta > para. The rearrangement process is charge directed through the ortho anion. Theoretical calculations at the B3LYP/6-311++G(d,p)//HF/6-31+G(d) level of theory indicate that the conversion of the meta and para anions to the ortho anion prior to loss of CO involve 1,2-H transfer(s), rather than carbon scrambling of the methoxycarbonylphenyl anion. There are two mechanisms which can account for this rearrangement, viz. (A) cyclisation of the ortho anion centre to the carbonyl group of the ester to give a cyclic carbonyl system in which the incipient methoxide anion substitutes at one of the two equivalent ring carbons of the three membered ring to yield an intermediate which loses CO to give the ortho anion of anisole, and (B) an elimination reaction to give an intermediate benzyne-methoxycarbonyl anion complex in which the MeOCO- species acts as a MeO- donor, which then adds to benzyne to yield the ortho anion of anisole. Calculations at the B3LYP/6-311++G(d,p)//HF/6-31+G(d) level of theory indicate that (i) the barrier in the first step (the rate determining step) of process A is 87 kJ mol(-1) less than that for the synchronous benzyne process B, and (ii) there are more low frequency vibrations in the transition state for benzyne process B than for the corresponding transition state for process A. Stepwise process A has the lower barrier for the rate determining step, and the lower Arrhenius factor: we cannot differentiate between these two mechanisms on available evidence.

Photoelectron spectroscopic study of the oxyallyl diradical

The photoelectron spectrum of the oxyallyl (OXA) radical anion has been measured. The radical anion has been generated in the reaction of the atomic oxygen radical anion (O center dot-) with acetone. Three low-lying electronic states of OXA have been observed in the spectrum. Electronic structure calculations have been performed for the triplet states (B-3(2) and B-3(1)) of OXA and the ground doublet state ((2)A(2)) of the radical anion using density, functional theory (DFT). Spectral simulations have been carried out for the triplet statics based on the results of the DFT calculations. The simulation identifies a vibrational progression of the CCC bending mode of the B-3(2) state of OXA in the lower electron binding energy (eBE) portion of the spectrum. On top of the B-3(2) feature, however, the experimental spectrum exhibits additional photoelectron peaks whose angular distribution is distinct from that for the vibronic peaks of the B-3(2) state. Complete active space self-consistent field (CASSCF) method and second-order perturbation theory based on the CASSCF wave function (CASPT2) have been employed to study the lowest singlet state ((1)A(1)) of OXA. The simulation based on the results of these electronic structure calculations establishes that the overlapping peaks represent the vibrational ground level of the (1)A(1) state and its vibrational progression of the CO stretching mode. The A, state is the lowest electronic state of,OXA, and the electron affinity (EA) of OXA is 1.940 +/- 0.010 eV. The B-3(2) state is the first excited state with an electronic term energy of 55 +/- 2 meV. The widths of the vibronic peaks of the (X) over tilde (1)A(1) state are much broader than those of the (a) over tilde B-3(2) state, implying that the (1)A(1) state is indeed a transition state. The CASSCF and CASPT2 calculations suggest that the (1)A(1) state is at a potential maximum along the nuclear coordinate representing disrotatory motion of the two methylene groups, which leads to three-membered-ring formation, i.e., cydopropanone. The simulation of (b) over tilde B-3(1) OXA reproduces the higher eBE portion of the spectrum very well. The term energy of the B-3(1) state is 0.883 +/- 0.012 eV. Photoelectron spectroscopic measurements have also been conducted for the other ion products of the O center dot- reaction with acetone. The photoelectron imaging spectrum of the acetylcarbene (AC) radical anion exhibits a broad, structureless feature, which is assigned to the (X) over tilde (3)A '' state of AC. The ground ((2)A '') and first excited ((2)A') states of the 1-methylvinoxy (1-MVO) radical have been observed in the photoelectron spectrum of the 1-MVO ion, and their vibronic structure has been analyzed.

Oxidation of 4-substituted TEMPO derivatives reveals modifications at the 1-and 4-positions

Potenital pathways for the deactivation of hindered amine light stabilisers (HALS) have been investigated by observing reactions of model compounds-based on 4-substituted derivatives of 2,2,6,6-tetramethylpiperidine-N-oxyl (TEMPO)-with hydroxyl radicals. In these reactions, dilute aqueous suspensions of photocatalytic nanoparticulate titanium dioxide were irradiated with UV light in the presence of water-soluble TEMPO derivatives. Electron spin resonance (ESR) and electrospray ionisation mass-spectrometry (ESI-MS) data were acquired to provide complementary structural elucidation of the odd-and even-electron products of these reactions and both techniques show evidence for the formation of 4-oxo-TEMPO (TEMPONE). TEMPONE formation from the 4-substituted TEMPO compounds is proposed to be initiated by hydrogen abstraction at the 4-position by hydroxyl radical. High-level ab initio calculations reveal a thermodynamic preference for abstraction of this hydrogen but computed activation barriers indicate that, although viable, it is less favoured than hydrogen abstraction from elsewhere on the TEMPO scaffold. If a radical is formed at the 4-position however, calculations elucidate two reaction pathways leading to TEMPONE following combination with either a second hydroxyl radical or dioxygen. An alternate mechanism for conversion of TEMPOL to TEMPONE via an alkoxyl radical intermediate is also considered and found to be competitive with the other pathways. ESI-MS analysis also shows an increased abundance of analogous 4-substituted piperidines during the course of irradiation, suggesting competitive modification at the 1-position to produce a secondary amine. This modification is confirmed by characteristic fragmentation patterns of the ionised piperidines obtained by tandem mass spectrometry. The conclusions describe how reaction at the 4-position could be responsible for the gradual depletion of HALS in pigmented surface coatings and secondly, that modification at nitrogen to form the corresponding secondary amine species may play a greater role in the stabilisation mechanisms of HALS than previously considered.

Reactions of the hydroperoxide anion with dimethyl methylphosphonate in an ion trap mass spectrometer : evidence for a gas phase alpha-effect

The gas phase degradation reactions of the chemical warfare agent (CWA) simulant, dimethyl methylphosphonate (DMMP), with the hydroperoxide anion (HOO(-)) were investigated using a modified quadrupole ion trap mass spectrometer. The HOO(-) anion reacts readily with neutral DMMP forming two significant product ions at m/z 109 and m/z 123. The major reaction pathways correspond to (i) the nucleophilic substitution at carbon to form \[CH(3)P(O)(OCH(3))O](-) (m/z 109) in a highly exothermic process and (ii) exothermic proton transfer. The branching ratios of the two reaction pathways, 89% and 11% respectively, indicate that the former reaction is significantly faster than the latter. This is in contrast to the trend for the methoxide anion with DMMP, where proton transfer dominates. The difference in the observed reactivities of the HOO(-) and CH(3)O(-) anions can be considered as evidence for an a-effect in the gas phase and is supported by electronic structure calculations at the B3LYP/aug-cc-pVTZ//B3LYP/6-31+G(d) level of theory that indicate the S(N)2(carbon) process has an activation energy 7.8 kJ mol(-1) lower for HOO(-) as compared to CH(3)O(-). A similar alpha-effect was calculated for nucleophilic addition-elimination at phosphorus, but this process an important step in the perhydrolysis degradation of CWAs in solution - was not observed to occur with DMMP in the gas phase. A theoretical investigation revealed that all processes are energetically accessible with negative activation energies. However, comparison of the relative Arrhenius pre-exponential factors indicate that substitution at phosphorus is not kinetically competitive with respect to the S(N)2(carbon) and deprotonation processes.

Skill development in first year law students : an evaluation of peer assisted learning across two law units

Universities no longer equip graduates solely with the content knowledge of their discipline, but also with prospective employment skills. Professions also seek graduates who can ‘collaborate, share skills and knowledge, and communicate their ideas effectively’ (Kruck and Reif, 2001, p 37). However, as admission to university does not always guarantee that one is well equipped for the task, first year students also need guidance in the development of academic skills. This session describes two models of peer assisted learning embedded within the Torts and Legal Foundations B units at the Faculty of Law, Queensland University of Technology, and how they are used to supplement student understanding of substantive law with the development of academic and work-related skills. Student perceptions of the programs developed are considered, together with the challenges faced. Session participants will be asked to contribute to a discussion of these challenges and to offer ideas on their redress.

The loss of carbon dioxide from activated perbenzoate anions in the gas phase : Unimolecular rearrangement via epoxidation of the benzene ring

The unimolecular reactivities of a range of perbenzoate anions (X-C6H5CO3-), including the perbenzoate anion itself (X=H), nitroperbenzoates (X=para-, meta-, ortho-NO2), and methoxyperbenzoates (X=para-, meta-OCH3) were investigated in the gas phase by electrospray ionization tandem mass spectrometry. The collision-induced dissociation mass spectra of these compounds reveal product ions consistent with a major loss of carbon dioxide requiring unimolecular rearrangement of the perbenzoate anion prior to fragmentation. Isotopic labeling of the perbenzoate anion supports rearrangement via an initial nucleophilic aromatic substitution at the ortho carbon of the benzene ring, while data from substituted perbenzoates indicate that nucleophilic attack at the ipso carbon can be induced in the presence of electron-withdrawing moieties at the ortho and para positions. Electronic structure calculations carried out at the B3LYP/6311++G(d,p) level of theory reveal two competing reaction pathways for decarboxylation of perbenzoate anions via initial nucleophilic substitution at the ortho and ipso positions, respectively. Somewhat surprisingly, however, the computational data indicate that the reaction proceeds in both instances via epoxidation of the benzene ring with decarboxylation resulting-at least initially-in the formation of oxepin or benzene oxide anions rather than the energetically favored phenoxide anion. As such, this novel rearrangement of perbenzoate anions provides an intriguing new pathway for epoxidation of the usually inert benzene ring.

Ion-molecule reactions of O,S-Dimethyl methylphosphonothioate : Evidence for intramolecular sulfur oxidation during VX perhydrolysis

The alkaline perhydrolysis of the nerve agent O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothioate (VX) was investigated by studying the ion-molecule reactions of HOO(-) with O,S-dimethyl methylphosphonothioate in a modified linear ion-trap mass spectrometer. In addition to simple proton transfer, two other abundant product ions are observed at m/z 125 and 109 corresponding to the S-methyl methylphosphonothioate and methyl methylphosphonate anions, respectively. The structure of these product ions is demonstrated by a combination of collision-induced dissociation and isotope-labeling experiments that also provide evidence for their formation by nucleophilic reaction pathways, namely, (i) S(N)2 at carbon to yield the S-methyl methylphosphonothioate anion and (ii) nucleophilic addition at phosphorus affording a reactive pentavalent intermediate that readily undergoes internal sulfur oxidation and concomitant elimination of CH(3)SOH to yield the methyl methylphosphonate anion. Consistent with previous Solution phase observations of VX perhydrolysis, the toxic P-O cleavage product is not observed in this VX model system and theoretical calculations identify P-O cleavage to be energetically uncompetitive. Conversely, intramolecular sulfur oxidation is calculated to be extremely exothermic and kinetically accessible explaining its competitiveness with the facile gas phase proton transfer process. Elimination of a sulfur moiety deactivates the nerve agent VX and thus the intramolecular sulfur oxidation process reported here is also able to explain the selective perhydrolysis of the nerve agent to relatively nontoxic products.

Effect of handling and fixation processes on fluorescence spectroscopy of mouse skeletal muscles under two-photon excitation

We investigated the effects of handling and fixation processes on the two-photon fluorescence spectroscopy of endogenous fluorophors in mouse skeletal muscle. The skeletal muscle was handled in one of two ways: either sectioned without storage or sectioned following storage in a freezer. The two-photon fluorescence spectra measured for different storage or fixation periods show a differential among those samples that were stored in water or were fixed either in formalin or methanol. The spectroscopic results indicate that formalin was the least disruptive fixative, having only a weak effect on the two-photon fluorescence spectroscopy of muscle tissue, whereas methanol had a significant influence on one of the autofluorescence peaks. The two handling processes yielded similar spectral information, indicating no different effects between them.

Modeling and sensorless direct torque and flux control of a dual-airgap axial flux permanent-magnet machine with field-weakening operation

This paper presents the modeling and motion-sensorless direct torque and flux control of a novel dual-airgap axial-flux permanent-magnet machine optimized for use in flywheel energy storage system (FESS) applications. Independent closed-loop torque and stator flux regulation are performed in the stator flux ( x-y) reference frame via two PI controllers. This facilitates fast torque dynamics, which is critical as far as energy charging/discharging in the FESS is concerned. As FESS applications demand high-speed operation, a new field-weakening algorithm is proposed in this paper. Flux weakening is achieved autonomously once the y-axis voltage exceeds the available inverter voltage. An inherently speed sensorless stator flux observer immune to stator resistance variations and dc-offset effects is also proposed for accurate flux and speed estimation. The proposed observer eliminates the rotary encoder, which in turn reduces the overall weight and cost of the system while improving its reliability. The effectiveness of the proposed control scheme has been verified by simulations and experiments on a machine prototype.

Bluetooth vehicle trajectory by fusing Bluetooth and loops : motorway travel time statistics

Loop detectors are widely used on the motorway networks where they provide point speed and traffic volumes. Models have been proposed for temporal and spatial generalization of speed for average travel time estimation. Advancement in technology provides complementary data sources such as Bluetooth MAC Scanner (BMS), detecting the MAC ID of the Bluetooth devices transported by the traveller. Matching the data from two BMS stations provides individual vehicle travel time. Generally, on the motorways loops are closely spaced, whereas BMS are placed few kilometres apart. In this research, we fuse BMSs and loops data to define the trajectories of the Bluetooth vehicles. The trajectories are utilised to estimate the travel time statistics between any two points along the motorway. The proposed model is tested using simulation and validated with real data from Pacific motorway, Brisbane. Comparing the model with the linear interpolation based trajectory provides significant improvements.

When two is better than one : a study of ranking paradigms and their integrations for subtopic retrieval

In this paper, we consider the problem of document ranking in a non-traditional retrieval task, called subtopic retrieval. This task involves promoting relevant documents that cover many subtopics of a query at early ranks, providing thus diversity within the ranking. In the past years, several approaches have been proposed to diversify retrieval results. These approaches can be classified into two main paradigms, depending upon how the ranks of documents are revised for promoting diversity. In the first approach subtopic diversification is achieved implicitly, by choosing documents that are different from each other, while in the second approach this is done explicitly, by estimating the subtopics covered by documents. Within this context, we compare methods belonging to the two paradigms. Furthermore, we investigate possible strategies for integrating the two paradigms with the aim of formulating a new ranking method for subtopic retrieval. We conduct a number of experiments to empirically validate and contrast the state-of-the-art approaches as well as instantiations of our integration approach. The results show that the integration approach outperforms state-of-the-art strategies with respect to a number of measures.

An arteriovenous loop in a protected space generates a permanent, highly vascular, tissue-engineered construct

A major obstacle to 3-dimensional tissue engineering is incorporation of a functional vascular supply to support the expanding new tissue. This is overcome in an in vivo intrinsic vascularization model where an arteriovenous loop (AVL) is placed in a noncollapsible space protected by a polycarbonate chamber. Vascular development and hypoxia were examined from 3 days to 112 days by vascular casting, morphometric, and morphological techniques to understand the model's vascular growth and remodeling parameters for tissue engineering purposes. At 3 days a fibrin exudate surrounded the AVL, providing a scaffold to migrating inflammatory, endothelial, and mesenchymal cells. Capillaries formed between 3 and 7 days. Hypoxia and cell proliferation were maximal at 7 days, followed by a peak in percent vascular volume at 10 days (23.20±3.14% compared with 3.59±2.68% at 3 days, P<0.001). Maximal apoptosis was observed at 112 days. The protected space and spontaneous microcirculatory development in this model suggest it would be applicable for in vivo tissue engineering. A temporal window in a period of intense angiogenesis at 7 to 10 days is optimal for exogenous cell seeding and survival in the chamber, potentially enabling specific tissue outcomes to be achieved.

Beyond tasks and gateways: discovering BPMN models with subprocesses, boundary events and activity markers

Existing techniques for automated discovery of process models from event logs largely focus on extracting flat process models. In other words, they fail to exploit the notion of subprocess, as well as structured error handling and repetition constructs provided by contemporary process modeling notations, such as the Business Process Model and Notation (BPMN). This paper presents a technique for automated discovery of BPMN models containing subprocesses, interrupting and non-interrupting boundary events, and loop and multi-instance markers. The technique analyzes dependencies between data attributes associated with events, in order to identify subprocesses and to extract their associated logs. Parent process and subprocess models are then discovered separately using existing techniques for flat process model discovery. Finally, the resulting models and logs are heuristically analyzed in order to identify boundary events and markers. A validation with one synthetic and two real-life logs shows that process models derived using the proposed technique are more accurate and less complex than those derived with flat process model discovery techniques.