High throughput screening of library compounds against an oligonucleotide substructure of an RNA target

Approximately 300,000 compounds from selected libraries were screened against a subdomain of a hepatitis C viral (HCV) RNA using a high throughput flow injection mass spectrometry (FIA-MS) method with automated data storage and analysis. Samples contained 2 microM RNA target and 10 microM of each of up to ten ligands. Preliminary studies to optimize operational parameters used the binding of aminoglycosides to the A44 subdomain of bacterial RNA. Binding (confirmed by titration) and sensitivity were maximized within the constraints of the library and throughput. The mobile phase of 5 mM ammonium acetate in 50% isopropanol maintained the noncovalent complexes and provided good detection by electrospray mass spectrometry. Additionally, this composition maximized general solubility of the various classes of compounds including the oligonucleotide and organic library molecules. Cation adduction was insignificant in this screen although some solute and target dependent acetate adduction was observed. The ion trap mass spectrometer provided sufficient mass resolution to identify complexes of RNA with known components of the library. Converted mass spectral data (netCDF) were subjected to two types of statistical evaluation based on binding. The first algorithm identified noncovalent complexes that correlated with the molecular weights of the injected compounds. The second yielded the largest peak in the noncovalent complex region of the spectrum; this spectrum may or may not correlate with expected well components. Sixty-three compounds were confirmed to bind by more stringent secondary testing. Titrations, which were carried out with selected binding compounds, yielded a range of dissociation constants. Biological activity was observed for eleven confirmed binders.     

Elucidation of matrix effects and performance of solid-phase extraction for LC-MS/MS analysis of β-N-methylamino-L-alanine (BMAA) and 2,4-diaminobutyric acid (DAB) neurotoxins in cyanobacteria

A liquid chromatography-mass spectrometry (LC-MS/MS) method using hydrophilic interaction liquid chromatography (HILIC) was developed for the analysis of neurotoxins β-N-methylamino-L-alanine (BMAA) and 2,4-diaminobutyric acid (DAB), using multiple reaction monitoring (MRM) scan mode. Oasis-MCX and Strata-X-C polymeric cation-exchange cartridges were used to clean extracts of cyanobacterial cultures, including two strains of Microcystis aeruginosa and one strain of Nostoc sp. The performance of the solid-phase extraction (SPE) cartridges for BMAA and DAB were evaluated using mixed standards and spiked cyanobacterial extracts, which demonstrated recoveries of BMAA and DAB ranging from 66% to 91%. Matrix effects in LC-MS/MS were evaluated, and while there was no effect on BMAA quantitation, suppression of DAB was found. Full scan (Q1) and enhanced product ion (EPI) monitoring showed that the DAB suppression may be due to closely eluting compounds, including lysine, histidine, arginine and three other compounds with [M + H](+) m/z of 88, 164 and 191. The procedures developed allow the sensitive and effective analysis of trace BMAA and DAB levels in cyanobacteria. While DAB was confirmed to be present, no BMAA was found in the cyanobacterial samples tested in the present study.     

Detection and confirmation of saxitoxin analogues in freshwater benthic Lyngbya wollei algae collected in the St. Lawrence River (Canada) by liquid chromatography–tandem mass spectrometry

The presence of cyanotoxins in benthic Lyngbya wollei algae samples collected in a fluvial lake along the St. Lawrence River, Canada, was investigated using a multi-toxins method. Hydrophilic interaction liquid chromatography (HILIC) and reverse phased liquid chromatography (RPLC) were coupled to triple quadrupole mass spectrometry (LC-QqQMS) for quantification and to quadrupole-time of flight mass spectrometry (LC-QqTOFMS) for screening and confirmation. The presence of two saxitoxin analogues, LWTX-1 and LWTX-6, was confirmed in benthic Lyngbya wollei algae samples. Concentration of LWTX-1 was between 209 ± 5 and 279 ± 9 μg g^?1. No other targeted cyanotoxin (such as anatoxin-a, nodularin, microcystin-LR, microcystins-RR and saxitoxin) was found in the samples. The presence of LWTX-6 was observed by using a screening approach based on an in-house database of cyanotoxins, an algorithm of identification and high resolution mass spectrometry measurements on the precursor and product ions. This work demonstrates the need for more research on the fate of benthic cyanotoxins in aquatic ecosystems such the St. Lawrence River.     

Positional targets for lingual consonants defined using electromagnetic articulography

The study examined the positional targets for lingual consonants defined using a point-parameterized approach with Wave (NDI, Waterloo, ON, Canada). The overall goal was to determine which consonants had unique tongue positions with respect to other consonants. Nineteen talkers repeated vowel-consonant-vowel (VCV) syllables that included consonants /t, d, s, z, , k, g/ in symmetrical vowel contexts /i, u, a/, embedded in a carrier phrase. Target regions for each consonant, characterized in terms of x,y,z tongue positions at the point of maximum tongue elevation, were extracted. Distances and overlaps were computed between all consonant pairs and compared to the distances and overlaps of their contextual targets. Cognates and postalveolar homorganics were found to share the location of their target regions. On average, alveolar stops showed distinctively different target regions than alveolar fricatives, which in turn showed different target region locations than the postalveolar consonants. Across talker variability in target locations was partially explained by differences in habitual speaking rate and hard palate characteristics.     

Dynamic Activation of Ga Sites by Pt Dopant in Low-Temperature Liquid-Metal Catalysts

Liquid GaPt catalysts with Pt concentrations as low as 1×10⁻⁴ atomic % have recently been identified as highly active for the oxidation of methanol and pyrogallol under mild reaction conditions. However, almost nothing is known about how liquid state catalysts support these significant improvements in activity. Here, ab initio molecular dynamics simulations are employed to examine GaPt catalysts in isolation and interacting with adsorbates. We find that persistent geometric features can exist in the liquid state, given the correct environment. We postulate that the Pt dopant may not be limited to direct involvement in catalysis of reactions, but rather that its presence can also enable Ga atoms to become catalytically active.     

Nano-formulations for transdermal drug delivery: A review

The different applications of nano-formulations (vesicles or nanoparticles and nanoemulsions) have been widely studied. Here, the classification, characteristics, transdermal mechanism, and application of the most popular nano-formulations in transdermal drug delivery system are reviewed.     

Proline editing: a divergent strategy for the synthesis of conformationally diverse peptides

[reaction: see text] Strong conformational biases in peptides and proteins can be achieved with 4-substituted proline residues (cis-, trans-, or disubstituted fluoroproline or hydroxyproline). The practical, divergent synthesis of peptides containing these residues, via postsynthetic modification of a peptide containing an internal trans-hydroxyproline residue, is described. Significant differences in the conformations of the peptides Ac-TYXN-NH2 were observed, including K(trans/cis) values, which varied from 1.5 (X = cis-fluoroproline) to 7.0 (X = trans-fluoroproline).     

Self-assembly combining two bioactive peptide-amphiphile molecules into nanofibers by electrostatic attraction

We describe a new approach to peptide-amphiphile (PA) nanofiber preparation that allows PAs with different bioactive amino acid sequences to be combined into a single fiber. Oppositely charged PAs are synthesized separately and then mixed to produce gels of nanofiber networks at physiological pH. Transmission electron microscopy reveals the formation of fibers approximately 7 nm in diameter and several micrometers long in these dimeric systems. On the basis of NMR and microscopy, we suggest that these nanofibers are cylindrical micelles of mixed composition, formed due to electrostatic attraction between the oppositely charged PAs. This strategy for self-assembly may be useful in cell therapies that can be implemented without invasive surgery or in in vitro tissue engineering.     

SCON—a Short Conditional intrON for conditional knockout with one-step zygote injection

The generation of conditional alleles using CRISPR technology is still challenging. Here, we introduce a Short Conditional intrON (SCON, 189 bp) that enables the rapid generation of conditional alleles via one-step zygote injection. In this study, a total of 13 SCON mouse lines were successfully generated by 2 different laboratories. SCON has conditional intronic functions in various vertebrate species, and its target insertion is as simple as CRISPR/Cas9-mediated gene tagging.Subject terms: Genetic engineering, Gene targeting, Genetic models