Digital Microfluidics and Magnetic Bead-Based Intact Proteoform Elution for Quantitative Top-down Nanoproteomics of Single C. elegans Nematodes

While most nanoproteomics approaches for the analysis of low-input samples are based on bottom-up proteomics workflows, top-down approaches enabling proteoform characterization are still underrepresented. Using mammalian cell proteomes, we established a facile one-pot sample preparation protocol based on protein aggregation on magnetic beads and intact proteoform elution using 40 % formic acid. Performed on a digital microfluidics device, the workflow enabled sensitive analyses of single Caenorhabditis elegans nematodes, thereby increasing the number of proteoform identifications compared to in-tube sample preparation by 46 %. Label-free quantification of single nematodes grown under different conditions allowed to identify changes in the abundance of proteoforms not distinguishable by bottom-up proteomics. The presented workflow will facilitate proteoform-directed analysis on samples of limited availability.     

Protection of flows under targeted attacks

We present a new robust optimization model for the problem of maximizing the amount of flow surviving the attack of an interdictor. Given some path flow, our model allows the interdictor to specify the amount of flow removed from each path individually. In contrast to previous models, for which no efficient algorithms are known, the most important basic variants of our model can be solved in poly-time. We also consider extensions where there is a budget to set the interdiction costs.     

Voice characteristics, effects of voice therapy, and long-term follow-up of contact granuloma patients

This study evaluates the laryngoscopic findings and voice characteristics of male contact granuloma patients before and after voice therapy and at a follow-up about 9 years later. Pre- and posttherapy recordings as well as follow-up recordings were made for 19 granuloma patients. Pretherapy revealed the most salient perceptual voice characteristics were low pitch, monotony, and a high degree of vocal fry and hyperfunction. Interjudge reliability for these traits was high. Immediately following therapy the healed patients (n = 10) had a decrease in hyperfunction, vocal fry, and monotony, while the unhealed patients (n = 9) had an increase in hyperfunction and vocal fry decreased only marginally. Monotony decreased significantly in this group. As regards the acoustic analyses, no significant differences were found in mean fundamental frequency (F₀) or perturbation. At the follow-up assessment 4 patients had granuloma while 15 had normal laryngeal status. Perceptually their voice characteristics resembled those pretherapy independently of the laryngeal findings. The results suggest that reduced hyperfunction and decreased vocal fry may create better circumstances for the healing process at the posterior glottis.     

Picosecond thermometer in the amide I band of myoglobin

The amide I and II bands in myoglobin show a heterogeneous temperature dependence, with bands at 6.17 and 6.43 microm which are more intense at low temperatures. The amide I band temperature dependence is on the long wavelength edge of the band, while the short wavelength side has almost no temperature dependence. We compare concepts of anharmonic solid-state crystal physics and chemical physics for the origins of these bands. We suggest that the long wavelength side is composed of those amino acids which hydrogen bond to the hydration shell of the protein, and that temperature dependent bands can be used to determine the time it takes vibrational energy to flow into the hydration shell. We determine that vibrational energy flow to the hydration shell from the amide I takes approximately 20 ps to occur.     

An electrochemical study into the interaction between complement-derived peptides and DOPC mono- and bilayers

Electrochemical methods employing the hanging mercury drop electrode were used to study the interaction between variants of the complement-derived antimicrobial peptide CNY21 (CNYITELRRQH ARASHLGLAR) and dioleoyl phosphatidylcholine (DOPC) monolayers. Capacitance potential and impedance measurements showed that the CNY21 analogues investigated interact with DOPC monolayers coating the mercury drop. Increasing the peptide hydrophobicity by substituting the two histidine residues with leucine resulted in a deeper peptide penetration into the hydrophobic region of the DOPC monolayer, indicated by an increase in the dielectric constant of the lipid monolayer (Deltaepsilon = 2.0 after 15 min interaction). Increasing the peptide net charge from +3 to +5 by replacing the histidines by lysines, on the other hand, arrests the peptide in the lipid head group region. Reduction of electroactive ions (Tl+, Pb2+, Cd2+, and Eu3+) at the monolayer-coated electrode was employed to further characterize the types of defects induced by the peptides. All peptides studied permeabilize the monolayer to Tl+ to an appreciable extent, but this effect is more pronounced for the more hydrophobic peptide (CNY21L), which also allows penetration of larger ions and ions of higher valency. The results for the various ions indicate that charge repulsion rather than ion size is the determining factor for cation penetration through peptide-induced defects in the DOPC monolayer. The effects obtained for monolayers were compared to results obtained with bilayers from liposome leakage and circular dichroism studies for unilamellar DOPC vesicles, and in situ ellipsometry for supported DOPC bilayers. Trends in peptide-induced liposome leakage were similar to peptide effects on electrochemical impedance and permeability of electroactive ions for the monolayer system, demonstrating that formation of transmembrane pores alone does not constitute the mechanism of action for the peptides investigated. Instead, our results point to the importance of local packing defects in the lipid membrane in close proximity to the adsorbed peptide molecules.     

Nonclassical Recrystallization

Applications in the fields of materials science and nanotechnology increasingly demand monodisperse nanoparticles in size and shape. Up to now, no general purification procedure exists to thoroughly narrow the size and shape distributions of nanoparticles. Here, we show by analytical ultracentrifugation (AUC) as an absolute and quantitative high-resolution method that multiple recrystallizations of nanocrystals to mesocrystals is a very efficient tool to generate nanocrystals with an excellent and so-far unsurpassed size-distribution (PDI_c=1.0001) and shape. Similar to the crystallization of molecular building blocks, nonclassical recrystallization removes “colloidal” impurities (i.e., nanoparticles, which are different in shape and size from the majority) by assembling them into a mesocrystal. In the case of nanocrystals, this assembly can be size- and shape-selective, since mesocrystals show both long-range packing ordering and preferable crystallographic orientation of nanocrystals. Besides the generation of highly monodisperse nanoparticles, these findings provide highly relevant insights into the crystallization of mesocrystals.     

Improved synthesis of oligonucleotides with an allylic backbone. Oligonucleotides containing acyclic, achiral nucleoside analogues: N-1 or N-9-[3-hydroxy-2-(hydroxymethyl)prop-1-enyl]nucleobases

An improved phosphoramidite method is described to prepare oligonucleotides modified with the acyclic, achiral monomers 1. Examination of dimers, prepared on solid support or in solution, showed that phosphortriester dimers containing the allylic unit 1 were unstable towards bases, whereas phosphordiester dimers were stable. Phosphordiester dimers were obtained by replacing cyanoethyl phosphoramidites 2 with phosphoramidites 3, which gave phosphordiesters directly upon oxidation. The phosphordiester dimers were found to be stable towards capping and oxidation, but were somewhat labile towards acids. By reducing the contact time to acids during detritylation it was possible to prepare oligonucleotides containing 4 or 8 modified A, G or T units. The modified oligonucleotides hybridized to complementary DNA and RNA, although with reduced affinity (DeltaT(m) per modification -1 to -5 degrees C).     

Development of a robust technique for sampling volatile metal(loid)s in wetlands

The formation of volatile organic and inorganic metals and metalloids in aquatic environments is a known, but not very intensively investigated, process. Several techniques have been developed over the past 10 years to determine these trace components. These techniques are of limited use in wetland environments, where samples have to be taken from the soil-water interface, and require an immediate sample analysis due to thermodynamic instabilities of the volatile metal(loid)s. This paper presents an innovative sampling technique for total concentrations of volatile metal(loid)s in wetlands, based on an in situ gas-water separation via a porous PTFE membrane and stabilising the volatile metal(loid)s in a liquid sorbent (NaOCl solution). Samples may thus be collected even at remote sites, where longer storage times have to be accounted for. The sampling system was tested by means of a laboratory facility simulating the generation of arsine and dimethyl arsine under abiotic conditions as well as under field conditions. Results for sampling efficiency, reproducibility, and long-term storage are presented. Application of the sampling system in the field is shown.     

Prediction of the vibrational spectra of interacting water molecules

A system of computer programs has been developed to predict and interpret the infrared spectra of molecules, ions, radicals and of chemically interacting species. The frequency parameters (or force constants) and the intensity parameters (or atomic polar tensors (APTs)) are calculated using the Gaussian-76 program for $\text{ab}$$\text{initio}$ quantum mechanical calculations with a 4–31G basis set. The resultant wavenumbers and intensities have been used to predict the fundamental infrared spectra of water molecules interacting with different molecular species. The corresponding wavenumber shifts and intensity changes from the spectrum of the non-interacting water molecule are dependent upon both the geometrical orientation and the electron-donating properties of the interacting species. The intensity parameters can be further analyzed by using the charge-charge flux-overlap (CCFO) interpretation of the APTs. This interpretation is helpful in pinpointing the exact source of the perturbation that produces the intensity change. The significance is discussed of each of these CCFO terms in predicting the infrared intensities of molecules undergoing intermolecular interaction.     

Aldehyde

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