Highlights in Analytical Chemistry in Switzerland: OMA & OPA - A Software Tool for Mass Spectrometric Sequencing of Nucleic Acids

Oligonucleotides comprising unnatural building blocks, which interfere with the translation machinery, have gained increased attention for the treatment of gene-related diseases (e.g. antisense, RNAi). Due to structural modifications, synthetic oligonucleotides exhibit increased biostability and bioavailability upon administration. Consequently, classical enzyme-based sequencing methods are not applicable to their sequence elucidation and verification. Tandem mass spectrometry is the method of choice for performing such tasks, since gas-phase dissociation is not restricted to natural nucleic acids. However, tandem mass spectrometric analysis can generate product ion spectra of tremendous complexity, as the number of possible fragments grows rapidly with increasing sequence length. The fact that structural modifications affect the dissociation pathways greatly increases the variety of analytically valuable fragment ions. The gas-phase dissociation of oligonucleotides is characterized by the cleavage of one of the four bonds along the phosphodiester chain, by the accompanying loss of nucleases, and by the generation of internal fragments due to secondary backbone cleavage. For example, an 18-mer oligonucleotide yields a total number of 272’920 theoretical fragment ions. In contrast to the processing of peptide product ion spectra, which nowadays is highly automated, there is a lack of tools assisting the interpretation of oligonucleotide data. The existing web-based and stand-alone software applications are primarily designed for the sequence analysis of natural nucleic acids, but do not account for chemical modifications and adducts. Consequently, we developed a software to support the interpretation of mass spectrometric data of natural and modified nucleic acids and their adducts with chemotherapeutic agents.

Gas composition of the main volatile elements in protoplanetary discs and its implication for planet formation

Context. Direct observations of gaseous exoplanets reveal that their gas envelope has a higher C/O ratio than that of the host star (e.g., Wasp 12-b). This has been explained by considering that the gas phase of the disc could be inhomogeneous, exceeding the stellar C/O ratio in regions where these planets formed; but few studies have considered the drift of the gas and planet migration. Aims. We aim to derive the gas composition in planets through planet formation to evaluate if the formation of giant planets with an enriched C/O ratio is possible. The study focusses on the effects of different processes on the C/O ratio, such as the disc evolution, the drift of gas, and planet migration. Methods. We used our previous models for computing the chemical composition, together with a planet formation model, to which we added the composition and drift of the gas phase of the disc, which is composed of the main volatile species H2O, CO, CO2, NH3, N2, CH3OH, CH4, and H2S, H2 and He. The study focusses on the region where ice lines are present and influence the C/O ratio of the planets. Results. Modelling shows that the condensation of volatile species as a function of radial distance allows for C/O enrichment in specific parts of the protoplanetary disc of up to four times the solar value. This leads to the formation of planets that can be enriched in C/O in their envelope up to three times the solar value. Planet migration, gas phase evolution and disc irradiation enables the evolution of the initial C/O ratio that decreases in the outer part of the disc and increases in the inner part of the disc. The total C/O ratio of the planets is governed by the contribution of ices accreted, suggesting that high C/O ratios measured in planetary atmospheres are indicative of a lack of exchange of material between the core of a planet and its envelope or an observational bias. It also suggests that the observed C/O ratio is not representative of the total C/O ratio of the planet.

Oral Lutein Supplementation Enhances Macular Pigment Density and Contrast Sensitivity but Not in Combination With Polyunsaturated Fatty Acids.

Purpose It has been shown that lutein and zeaxanthin accumulate in the macula where they enhance contrast sensitivity and may reduce the risk of progression to advanced age-related macular degeneration (AMD). Furthermore, omega-3 long-chain polyunsaturated fatty acids (PUFA) might further reduce this risk. However, controversy exists regarding whether PUFA may reduce the bioavailability of lutein. Methods This was a prospective 12-month, randomized, open label study evaluating the effect of supplementation with lutein, other antioxidants, and minerals on contrast sensitivity (CS) and macular pigment optical density (MPOD) in patients with age-related maculopathy. A total of 79 patients were randomized to either lutein (10 mg) and antioxidant supplement or lutein and antioxidant supplement in combination with PUFA. Patients received supplementation for a period of 6 months and were followed for a total of 12 months. Results Serum lutein and zeaxanthin increased significantly by the first follow-up visit at 1 month, and remained elevated throughout the intervention period of 6 months in the lutein-only group but not in the lutein+PUFA group. Macular pigment optical density and CS increased significantly in the lutein-only group (P < 0.005) but not in the lutein+PUFA group (P = 0.059) compared to baseline. Best-corrected visual acuity remained unchanged during the entire study period in both groups. Conclusions Addition of PUFA may reduce the bioavailability of lutein and therefore lessen the beneficial effect on macular pigment and CS. This needs to be considered when prescribing lutein supplements to patients with low lutein levels. (ClinicalTrials.gov number, NCT00563979.).