RNA search engines empower the bacterial intranet

RNA acts not only as an information bearer in the biogenesis of proteins from genes, but also as a regulator that participates in the control of gene expression. In bacteria, small RNA molecules (sRNAs) play controlling roles in numerous processes and help to orchestrate complex regulatory networks. Such processes include cell growth and development, response to stress and metabolic change, transcription termination, cell-to-cell communication, and the launching of programmes for host invasion. All these processes require recognition of target messenger RNAs by the sRNAs. This review summarizes recent results that have provided insights into how bacterial sRNAs are recruited into effector ribonucleoprotein complexes that can seek out and act upon target transcripts. The results hint at how sRNAs and their protein partners act as pattern-matching search engines that efficaciously regulate gene expression, by performing with specificity and speed while avoiding off-target effects. The requirements for efficient searches of RNA patterns appear to be common to all domains of life

Plasma-enhanced atomic layer deposition of nanostructured gold near room temperature

A plasma-enhanced atomic layer deposition (PE-ALD) process to deposit metallic gold is reported, using the previously reported Me3Au(PMe3) precursor with H-2 plasma as the reactant. The process has a deposition window from 50 to 120 degrees C with a growth rate of 0.030 +/- 0.002 nm per cycle on gold seed layers, and it shows saturating behavior for both the precursor and reactant exposure. X-ray photoelectron spectroscopy measurements show that the gold films deposited at 120 degrees C are of higher purity than the previously reported ones (<1 at. % carbon and oxygen impurities and <0.1 at. % phosphorous). A low resistivity value was obtained (5.9 +/- 0.3 mu Omega/cm), and X-ray diffraction measurements confirm that films deposited at 50 and 120 degrees C are polycrystalline. The process forms gold nanoparticles on oxide surfaces, which coalesce into wormlike nanostructures during deposition. Nanostructures grown at 120 degrees C are evaluated as substrates for free-space surface-enhanced Raman spectroscopy (SERS) and exhibit an excellent enhancement factor that is without optimization, only one order of magnitude weaker than state-of-the-art gold nanodome substrates. The reported gold PE-ALD process therefore offers a deposition method to create SERS substrates that are template-free and does not require lithography. Using this process, it is possible to deposit nanostructured gold layers at low temperatures on complex three-dimensional (3D) substrates, opening up opportunities for the application of gold ALD in flexible electronics, heterogeneous catalysis, or the preparation of 3D SERS substrates

Reaction mechanism of the Me3AuPMe3-H-2 plasma-enhanced ALD process

The reaction mechanism of the recently reported Me3AuPMe3-H-2 plasma gold ALD process was investigated using in situ characterization techniques in a pump-type ALD system. In situ RAIRS and in vacuo XPS measurements confirm that the CH3 and PMe3 ligands remain on the gold surface after chemisorption of the precursor, causing self-limiting adsorption. Remaining surface groups are removed by the H-2 plasma in the form of CH4 and likely as PHxMey groups, allowing chemisorption of new precursor molecules during the next exposure. The decomposition behaviour of the Me3AuPMe3 precursor on a Au surface is also presented and linked to the stability of the precursor ligands that govern the self-limiting growth during ALD. Desorption of the CH3 ligands occurs at all substrate temperatures during evacuation to high vacuum, occurring faster at higher temperatures. The PMe3 ligand is found to be less stable on a gold surface at higher substrate temperatures and is accompanied by an increase in precusor decomposition on a gold surface, indicating that the temperature dependent stability of the precursor ligands is an important factor to ensure self-limiting precursor adsorption during ALD. Remarkably, precursor decomposition does not occur on a SiO2 surface, in situ transmission absorption infrared experiments indicate that nucleation on a SiO2 surface occurs on Si-OH groups. Finally, we comment on the use of different co-reactants during PE-ALD of Au and we report on different PE-ALD growth with the reported O-2 plasma and H2O process in pump-type versus flow-type ALD systems

Off-line studies of the laser ionization of yttrium at the IGISOL facility

A laser ion source is under development at the IGISOL facility, Jyvaskyla, in order to address deficiencies in the ion guide technique. The key elements of interest are those of a refractory nature, whose isotopes and isomers are widely studied using both laser spectroscopic and high precision mass measurement techniques. Yttrium has been the first element of choice for the new laser ion source. In this work we present a new coupled dye-Ti:Sapphire laser scheme and give a detailed discussion of the results obtained from laser ionization of yttrium atoms produced in an ion guide via joule heating of a filament. The importance of not only gas purity, but indeed the baseline vacuum pressure in the environment outside the ion guide is discussed in light of the fast gas phase chemistry seen in the yttrium system. A single laser shot model is introduced and is compared to the experimental data in order to extract the level of impurities within the gas cell.Comment: 18 pages submitted to NIM

An improved nearest neighbor method for the estimation of the gamma photon entry point in monolithic scintillator detectors for PET

Several improvements of the k-nearest neighbor (k-NN) method for the determination of the entry point (x, y) of a gamma photon in a monolithic scintillator PET detector have been investigated with the aim to obtain better spatial resolution and/or to enable faster detector calibration by reducing the amount of required reference data and by allowing for calibrating with a line source. These methods were tested on a dataset measured with a SiPM-array-based monolithic LYSO detector. It appears that 10% to 25% better spatial resolution can be obtained compared to the standard approach. Moreover, some of the improved methods using two orders of magnitude less reference data, yield essentially the same spatial resolution as the standard method, which reduces the time needed for calibration as well as entry point computation. Finally, line source calibration is shown to be possible with some of the methods, yielding better results than the standard method and allowing much faster and easier collection of the reference data.</p

It is not always chlorhexidine: Identification of benzoxonium chloride and lauramine oxide as culprit allergens in a popular antiseptic in Switzerland.

A popular antiseptic spray in Switzerland (Merfen spray), containing chlorhexidine digluconate, benzoxonium chloride and lauramine oxide, is frequently used to treat skin wounds. However, it is also increasingly reported as a major cause of adverse skin reactions, including allergic contact dermatitis (ACD). To investigate the contact allergens responsible for ACD from this antiseptic. Patch tests were performed on seven patients with a clinical history compatible with contact dermatitis from this antiseptic mixture. All patients presented with acute eczematous reactions following contact with either Merfen spray alone, or with multiple products including this spray. Patients showed positive reactions to this product in both patch tests and repeated open application tests (ROATs). Four patients showed dose-dependent reactions to both benzoxonium chloride and lauramine oxide. One patient showed a dose-dependent reaction to the former and a non-dose-dependent reaction to the latter. Finally, two subjects showed responses only to lauramine oxide. One patient reacted to chlorhexidine digluconate 0.5% aq. in addition to both other allergens. Two commercially unavailable allergens, that is, benzoxonium chloride and/or lauramine oxide were identified as major causes of ACD from Merfen antiseptic spray, whereas chlorhexidine digluconate was a contributing culprit in only one patient

Corrigendum: Short-lived positron emitters in beam-on PET imaging during proton therapy (2015 Phys. Med. Biol. 60 8923)

Because of strong indications of multiple counting by the multi-channel scaler (MCS) during most of the experiments described in Dendooven et al (2015 Phys. Med. Biol. 60 8923–47), the production of short-lived positron emitters in the stopping of 55 MeV protons in water, carbon, phosphorus and calcium was remeasured. The new results are reported here. With proper single counting of the MCS, the new production rates are 1.1 to 2.9 times smaller than reported in Dendooven et al (2015 Phys. Med. Biol. 60 8923–47). The omission of the conversion from MCS time bin to time unit in the previous data analysis was corrected, leading to an increase of the production rate by a factor of 2.5 or 10 for some nuclides. The most copiously produced short-lived nuclides and their production rates relative to the relevant long-lived nuclides are: 12N (T 1/2  =  11 ms) on carbon (5.3% of 11C), 29P (T 1/2  =  4.1 s) on phosphorus (23% of 30P) and 38mK (T 1/2  =  0.92 s) on calcium (173% of 38gK). The number of decays integrated from the start of an irradiation as a function of time during the irradiation of PMMA and 4 tissue materials has been determined. For (carbon-rich) adipose tissue, 12N dominates up to 70 s. On bone tissue, 38mK dominates the beam-on PET counts from 0.2–0.7 s until about 80–110 s. Considering nuclides created on phosphorus and calcium, the short-lived ones provide 8 times more decays than the long-lived ones during a 70 s irradiation. Bone tissue will thus be much better visible in beam-on PET compared to PET imaging after an irradiation. From the estimated number of 12N PET counts, we conclude that, for any tissue, except carbon-poor ones, 12N PET imaging potentially provides equal quality proton range information as prompt gamma imaging with an optimized knife-edge slit camera

Collinear laser spectroscopy of radioisotopes of zirconium

Isotope shifts and hyperfine structures have been measured for radioisotopes of ionic zirconium using on-line laser spectroscopy at the IGISOL facility in Jyväskylä, where the installation of an ion beam cooler/buncher has significantly improved the experimental sensitivity. Measurements have been made on all the neutron-deficient isotopes from 87Zr to 90Zr, including the isomers 87m,89mZr, and the neutron-rich isotopes from 96Zr to 102Zr. The change in mean square charge radii between the isotopes and the nuclear moments of the odd isotopes have been extracted. The data show a sudden increase in the mean square charge radius at mass A = 100, consistent with an onset of nuclear deformation which has been observed in the gamma ray spectroscopy of isotope chains in this region of the nuclear chart.</p

A sextupole ion beam guide to improve the efficiency and beam quality at IGISOL

The laser ion source project at the IGISOL facility, Jyvaskyla, has motivated the development and construction of an rf sextupole ion beam guide (SPIG) to replace the original skimmer electrode. The SPIG has been tested both off-line and on-line in proton-induced fission, light-ion and heavy-ion induced fusion-evaporation reactions and, in each case, has been directly compared to the skimmer system. For both fission and light-ion induced fusion, the SPIG has improved the mass-separated ion yields by a factor of typically 4 to 8. Correspondingly, the transmission efficiency of both systems has been studied in simulations with and without space charge effects. The transport capacity of the SPIG has been experimentally determined to be 10^12 ions/s before space charge effects start to take effect. A direct comparison with the simulation has been made using data obtained via light-ion fusion evaporation. Both experiment and simulation show an encouraging agreement as a function of current extracted from the ion guide.Comment: Latex formatted, submitted to NIM B, 17 pages with 22 .eps figure