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.

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.

Magnetic convection heat transfer in an open ended enclosure filled with paramagnetic fluids

Numerical simulations of thermomagnetic convection of paramagnetic fluids placed in a micro-gravity condition (g nearly 0) and under a uniform vertical gradient magnetic field in an open ended square enclosure with ramp heating temperature condition applied on a vertical wall is investigated in this study. In presence of the strong magnetic gradient field thermal convection of the paramagnetic fluid might take place even in a zero-gravity environment as a direct consequence of temperature differences occurring within the fluid. The thermal boundary layer develops adjacent to the hot wall as soon as the ramp temperature condition is applied on it. There are two scenario that can be observed based on the ramp heating time. The steady state of the thermal boundary layer can be reached before the ramp time is finished or vice versa. If the ramp time is larger than the quasi-steady time then the thermal boundary layer is in a quasi-steady mode with convection balancing conduction after the quasi-steady time. Further increase of the heat input simply accelerates the flow to maintain the proper thermal balance. Finally, the boundary layer becomes completely steady state when the ramp time is finished. Effects of magnetic Rayleigh number, Prandtl number and paramagnetic fluid parameter on the flow pattern and heat transfer are presented.

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.

MT1-MMP-dependent and -independent regulation of gelatinase A activation in long-term, ascorbate-treated fibroblast cultures: Regulation by fibrillar collagen

Human skin fibroblasts were cultured long-term in the presence of ascorbic acid to allow formation of a three-dimensional collagen matrix, and the effects of this on activation of secreted matrix metalloproteinase-2 (MMP-2) were examined. Accumulation of collagen over time correlated with increased levels of both mature MMP-2 and cell-associated membrane type 1-MMP (MT1-MMP), and subsequently increased mRNA levels for MT1-MMP, providing temporal resolution of the "nontranscriptional" and "transcriptional" effects of collagen on MT-1MMP functionality. MMP-2 activation by these cultures was blocked by inhibitors of prolyl-4-hydroxylase, or when fibroblasts derived from the collagen α1(I) gene-deficient Mov-13 mouse were used. MMP-2 activation by the Mov-13 fibroblasts was rescued by transfection of a full-length α1(I) collagen cDNA, and to our surprise, also by transfection with an α1(I) collagen cDNA carrying a mutation at the C-proteinase cleavage, which almost abrogated fibrillogenesis. Although studies with ascorbate-cultured MT1-MMP-/- fibroblasts showed that MT1-MMP played a significant role in the collagen-induced MMP-2 activation, a residual MT1-MMP-independent activation of MMP-2 was seen which resembled the level of MMP-2 activation persisting when wild-type fibroblasts were cultured in the presence of both ascorbic acid and MMP inhibitors. We were also unable to block this residual activation with inhibitors specific for serinyl, aspartyl, or cysteinyl enzymes.

A qualitative investigation of adolescents’ perceived mechanisms of change from a universal school-based depression prevention program

A recent meta-analysis provides evidence supporting the universal application of school-based prevention programs for adolescent depression. The mechanisms underlying such successful interventions, however, are largely unknown. We report on a qualitative analysis of 109 Grade 9 students’ beliefs about what they gained from an evidence-based depression prevention intervention, the Resourceful Adolescent Program (RAP-A). Fifty-four percent of interviewees articulated at least one specific example of program benefit. A thematic analysis of responses revealed two major themes, improved interpersonal relationships and improved self-regulation, both stronger than originally assumed. A more minor theme also emerged—more helpful cognitions. It is postulated that both improved interpersonal relationships and improved self-regulation are likely to enhance one another, and more helpful cognitions may express its contribution through enhanced self-regulation. These findings broaden our understanding of the impact of depression prevention programs, beginning to illuminate how such programs benefit participants.

Experimental and finite element analysis to identify the source of vibration of a coach

This paper presents an investigation on the cause of severe vibration problem of a coach with four-cylinder engine running at an idle state using vibration and impact hammer modal experiments to obtain the main vibration frequency components and the natural characteristics of the coach. The vibration results indicate that the main vibration component comes from the vibration transmitted from the engine to the chassis frame, which is closely related with the engine idle speed. Based on structural simulation analysis of the coach’s chassis frame and comparison with modal testing, the coach severe vibration problem was due to coupling resonance between the engine idle frequency and the fourth natural frequency of the chassis frame. The solution to eliminate the vibration problem is provided by changing the local structure stiffness of the chassis frame. The contribution of this paper lies in providing a solution to solve similar problems.

Peripheral vision benefits spatial learning by guiding eye movements

The loss of peripheral vision impairs spatial learning and navigation. However, the mechanisms underlying these impairments remain poorly understood. One advantage of having peripheral vision is that objects in an environment are easily detected and readily foveated via eye movements. The present study examined this potential benefit of peripheral vision by investigating whether competent performance in spatial learning requires effective eye movements. In Experiment 1, participants learned room-sized spatial layouts with or without restriction on direct eye movements to objects. Eye movements were restricted by having participants view the objects through small apertures in front of their eyes. Results showed that impeding effective eye movements made subsequent retrieval of spatial memory slower and less accurate. The small apertures also occluded much of the environmental surroundings, but the importance of this kind of occlusion was ruled out in Experiment 2 by showing that participants exhibited intact learning of the same spatial layouts when luminescent objects were viewed in an otherwise dark room. Together, these findings suggest that one of the roles of peripheral vision in spatial learning is to guide eye movements, highlighting the importance of spatial information derived from eye movements for learning environmental layouts.

Cryptanalysis of FORK-256

In this paper we present a cryptanalysis of a new 256-bit hash function, FORK-256, proposed by Hong et al. at FSE 2006. This cryptanalysis is based on some unexpected differentials existing for the step transformation. We show their possible uses in different attack scenarios by giving a 1-bit (resp. 2-bit) near collision attack against the full compression function of FORK-256 running with complexity of 2^125 (resp. 2^120) and with negligible memory, and by exhibiting a 22-bit near pseudo-collision. We also show that we can find collisions for the full compression function with a small amount of memory with complexity not exceeding 2^126.6 hash evaluations. We further show how to reduce this complexity to 2^109.6 hash computations by using 273 memory words. Finally, we show that this attack can be extended with no additional cost to find collisions for the full hash function, i.e. with the predefined IV.

Treatment with the vascular disruptive agent OXi4503 induces an immediate and widespread epithelial to mesenchymal transition in the surviving tumor

Epithelial to mesenchymal transition (EMT) is considered an important mechanism in tumor resistance to drug treatments; however, in vivo observation of this process has been limited. In this study we demonstrated an immediate and widespread EMT involving all surviving tumor cells following treatment of a mouse model of colorectal liver metastases with the vascular disruptive agent OXi4503. EMT was characterized by significant downregulation of E-cadherin, relocation and nuclear accumulation of b-catenin as well as significant upregulation of ZEB1 and vimentin. Concomitantly, significant temporal upregulation in hypoxia and the pro-angiogenic growth factors hypoxia-inducible factor 1-alpha, hepatocyte growth factor, vascular endothelial growth factor and transforming growth factor-beta were seen within the surviving tumor. The process of EMT was transient and by 5 days after treatment tumor cell reversion to epithelial morphology was evident. This reversal, termed mesenchymal to epithelial transition (MET) is a process implicated in the development of new metastases but has not been observed in vivo histologically. Similar EMT changes were observed in response to other antitumor treatments including chemotherapy, thermal ablation, and antiangiogenic treatments in our mouse colorectal metastasis model and in a murine orthotopic breast cancer model after OXi4503 treatment. These results suggest that EMT may be an early mechanism adopted by tumors in response to injury and hypoxic stress, such that inhibition of EMT in combination with other therapies could play a significant role in future cancer therapy.

Real-time monitoring of nucleation-growth cycle of carbon nanoparticles in acetylene plasmas

Quantum cascade laserabsorption spectroscopy was used to measure the absolute concentration of acetylene in situ during the nanoparticle growth in Ar + C2H2 RF plasmas. It is demonstrated that the nanoparticle growth exhibits a periodical behavior, with the growth cycle period strongly dependent on the initial acetylene concentration in the chamber. Being 300 s at 7.5% of acetylene in the gas mixture, the growth cycle period decreases with the acetylene concentration increasing; the growth eventually disappears when the acetylene concentration exceeds 32%. During the nanoparticle growth, the acetylene concentration is small and does not exceed 4.2% at radio frequency (RF) power of 4 W, and 0.5% at RF power of 20 W. An injection of a single acetylene pulse into the discharge also results in the nanoparticlenucleation and growth. The absorption spectroscopy technique was found to be very effective for the time-resolved measurement of the hydrocarbon content in nanoparticle-generatingplasmas.

Magnetic control of breakdown : toward energy-efficient hollow-cathode magnetron discharges

Characteristics of electrical breakdown of a planar magnetron enhanced with an electromagnet and a hollow-cathode structure, are studied experimentally and numerically. At lower pressures the breakdown voltage shows a dependence on the applied magnetic field, and the voltage necessary to achieve the self-sustained discharge regime can be significantly reduced. At higher pressures, the dependence is less sensitive to the magnetic field magnitude and shows a tendency of increased breakdown voltage at the stronger magnetic fields. A model of the magnetron discharge breakdown is developed with the background gas pressure and the magnetic field used as parameters. The model describes the motion of electrons, which gain energy by passing the electric field across the magnetic field and undergo collisions with neutrals, thus generating new bulk electrons. The electrons are in turn accelerated in the electric field and effectively ionize a sufficient amount of neutrals to enable the discharge self-sustainment regime. The model is based on the assumption about the combined classical and near-wall mechanisms of electron conductivity across the magnetic field, and is consistent with the experimental results. The obtained results represent a significant advance toward energy-efficient multipurpose magnetron discharges.

Plasma-controlled adatom delivery and (re)distribution: Enabling uninterrupted, low-temperature growth of ultralong vertically aligned single walled carbon nanotubes

Large-scale (∼109 atoms) numerical simulations reveal that plasma-controlled dynamic delivery and redistribution of carbon atoms between the substrate and nanotube surfaces enable the growth of ultralong single walled carbon nanotubes (SWCNTs) and explain the common experimental observation of slower growth at advanced stages. It is shown that the plasma-based processes feature up to two orders of magnitude higher growth rates than equivalent neutral-gas systems and are better suited for the SWCNT synthesis at low nanodevice friendly temperatures. © 2008 American Institute of Physics.

Catalyst size effects on the growth of single-walled nanotubes in neutral and plasma systems

The results of large-scale (∼109 atoms) numerical simulations of the growth of different-diameter vertically-aligned single-walled carbon nanotubes in plasma systems with different sheath widths and in neutral gases with the same operating parameters are reported. It is shown that the nanotube lengths and growth rates can be effectively controlled by varying the process conditions. The SWCNT growth rates in the plasma can be up to two orders of magnitude higher than in the equivalent neutral gas systems. Under specific process conditions, thin SWCNTs can grow much faster than their thicker counterparts despite the higher energies required for catalyst activation and nanotube nucleation. This selective growth of thin SWCNTs opens new avenues for the solution of the currently intractable problem of simultaneous control of the nanotube chirality and length during the growth stage.