Charge Inversion of Phospholipids by Dimetal Complexes for Positive Ion-Mode Electrospray Ionization Mass Spectrometry Analysis

Phospholipids are vital constituents of living cells, as they are involved in signaling and membrane formation. Mass spectrometry analysis of many phospholipids is preferentially performed in the negative ion-mode because of their acidic nature. Here we have studied the potential of a digallium and dizinc complex to charge-invert a range of different types of phospholipids and measured their ion yield and fragmentation behavior in positive ion-mode tandem mass spectrometry. The dimetal complexes bind specifically the phosphate groups of phospholipids and add an excess of up to three positive charges per phosphate group. Three different phosphoinositide phosphates (mono-, di-, and triphosphorylated inositides), a phosphatidic acid, a phosphatidylcholine, a phosphatidylethanolamine, and a phosphatidylglycerol were investigated. The intensities obtained in positive ion-mode of phosphoinositide phosphates and phosphatidic acid bound to {LGa₂}⁵⁺ were between 2.5- and 116-fold higher than that of the unmodified lipids in the negative ion-mode. Native phosphoinositide ions yielded upon CID in the negative ion-mode predominantly product ions due to losses of H₃PO₄, PO₃^– and H₂O. In comparison, CID spectra of {LGa₂}⁵⁺-bound phosphoinositides generally resulted in fragment ions corresponding to loss of the full diglyceride chain as well as the remaining headgroup bound to {LGa₂}⁵⁺ as the most abundant peaks. A number of signature fragment ions of moderate abundance were observed that allowed for distinction between the three regioisomers of 1,2-di­(9Z-octadecenoyl)-<i>sn</i>-glycero-3-[phosphoinositol-x,y-bisphosphate] (PI­(3,4)­P₂, PI­(3,5)­P₂, PI­(4,5)­P₂)

SuperQuant:a Data Processing Approach to Increase Quantitative Proteome Coverage

SuperQuant is a quantitative proteomics data processing approach that uses complementary fragment ions to identify multiple coisolated peptides in tandem mass spectra allowing for their quantification. This approach can be applied to any shotgun proteomics data set acquired with high mass accuracy for quantification at the MS¹ level. The SuperQuant approach was developed and implemented as a processing node within the Thermo Proteome Discoverer 2.x. The performance of the developed approach was tested using dimethyl-labeled HeLa lysate samples having a ratio between channels of 10­(heavy):4­(medium):1­(light). Peptides were fragmented with collision-induced dissociation using isolation windows of 1, 2, and 4 Th while recording data both with high-resolution and low-resolution. The results obtained using SuperQuant were compared to those using the conventional ion trap-based approach (low mass accuracy MS² spectra), which is known to achieve high identification performance. Compared to the common high-resolution approach, the SuperQuant approach identifies up to 70% more peptide–spectrum matches (PSMs), 40% more peptides, and 20% more proteins at the 0.01 FDR level. It identifies more PSMs and peptides than the ion trap-based approach. Improvements in identifications resulted in up to 10% more PSMs, 15% more peptides, and 10% more proteins quantified on the same raw data. The developed approach does not affect the accuracy of the quantification and observed coefficients of variation between replicates of the same proteins were close to the values typical for other precursor ion-based quantification methods. The raw data is deposited to ProteomeXchange (PXD001907). The developed node is available for testing at https://github.com/caetera/SuperQuantNode

Solar-like oscillations in the G2 subgiant beta Hydri from dual-site observations

We have observed oscillations in the nearby G2 subgiant star beta Hyi using high-precision velocity observations obtained over more than a week with the HARPS and UCLES spectrographs. The oscillation frequencies show a regular comb structure, as expected for solar-like oscillations, but with several l=1 modes being strongly affected by avoided crossings. The data, combined with those we obtained five years earlier, allow us to identify 28 oscillation modes. By scaling the large frequency separation from the Sun, we measure the mean density of beta Hyi to an accuracy of 0.6%. The amplitudes of the oscillations are about 2.5 times solar and the mode lifetime is 2.3 d. A detailed comparison of the mixed l=1 modes with theoretical models should allow a precise estimate of the age of the star.Comment: 13 pages, 14 figures, accepted by ApJ. Fixed minor typo (ref to Fig 14

Parity, mode of birth, and long-term gynecological health: A follow-up study of parous and nonporous women in the Australian Longitudinal Study on Women's Health cohort

Background:Although gynecological health issues are common and cause considerable distress, little is known about their causes. We examined how birth history is associated with urinary incontinence (UI), severe period pain, heavy periods, and endometriosis. Methods:We studied 7700 women in the Australian Longitudinal Study on Women's Health with an average follow-up of 10.9 years after their last birth. Surveys every third year provided information about birth history and gynecological health. Logistic regression was used to estimate how parity, mode of birth, and vaginal tears were associated with gynecological health issues. Presented results are adjusted odds ratios (OR) with 95% confidence intervals. Results:UI was reported by 16%, heavy periods by 31%, severe period pain by 28%, and endometriosis by 4%. Compared with women with two children, nonparous women had less UI (OR 0.35 [0.26–0.47]) but tended to have more endometriosis (OR 1.70 [0.97–2.96]). Also, women with only one child had less UI (OR 0.77 [0.61–0.98]), but more severe period pain (OR 1.24 [1.01–1.51]). Women with 4+ children had more heavy periods (OR 1.42 [1.07–1.88]). Compared with women with vaginal birth(s) only, women with only cesarean sections or vaginal birth after cesarean section had less UI (ORs 0.44 [0.34–0.58] and 0.55 [0.40–0.76]), but more endometriosis (ORs 1.91 [1.16–3.16] and 2.31 [1.25–4.28]) and heavy periods (ORs 1.21 [1.00–1.46] and 1.35 [1.06–1.72]). Vaginal tear(s) did not increase UI after accounting for parity and birth mode. Conclusion:While women with vaginal childbirth(s) reported more urinary incontinence, they had less menstrual complaints and endometriosis.</p

Purifying Selection and Molecular Adaptation in the Genome of Verminephrobacter, the Heritable Symbiotic Bacteria of Earthworms

While genomic erosion is common among intracellular symbionts, patterns of genome evolution in heritable extracellular endosymbionts remain elusive. We study vertically transmitted extracellular endosymbionts (Verminephrobacter, Betaproteobacteria) that form a beneficial, species-specific, and evolutionarily old (60–130 Myr) association with earthworms. We assembled a draft genome of Verminephrobacter aporrectodeae and compared it with the genomes of Verminephrobacter eiseniae and two nonsymbiotic close relatives (Acidovorax). Similar to V. eiseniae, the V. aporrectodeae genome was not markedly reduced in size and showed no A–T bias. We characterized the strength of purifying selection (ω = dN/dS) and codon usage bias in 876 orthologous genes. Symbiont genomes exhibited strong purifying selection (ω = 0.09 ± 0.07), although transition to symbiosis entailed relaxation of purifying selection as evidenced by 50% higher ω values and less codon usage bias in symbiont compared with reference genomes. Relaxation was not evenly distributed among functional gene categories but was overrepresented in genes involved in signal transduction and cell envelope biogenesis. The same gene categories also harbored instances of positive selection in the Verminephrobacter clade. In total, positive selection was detected in 89 genes, including also genes involved in DNA metabolism, tRNA modification, and TonB-dependent iron uptake, potentially highlighting functions important in symbiosis. Our results suggest that the transition to symbiosis was accompanied by molecular adaptation, while purifying selection was only moderately relaxed, despite the evolutionary age and stability of the host association. We hypothesize that biparental transmission of symbionts and rare genetic mixing during transmission can prevent genome erosion in heritable symbionts

An asteroseismic membership study of the red giants in three open clusters observed by Kepler: NGC6791, NGC6819, and NGC6811

Studying star clusters offers significant advances in stellar astrophysics due to the combined power of having many stars with essentially the same distance, age, and initial composition. This makes clusters excellent test benches for verification of stellar evolution theory. To fully exploit this potential, it is vital that the star sample is uncontaminated by stars that are not members of the cluster. Techniques for determining cluster membership therefore play a key role in the investigation of clusters. We present results on three clusters in the Kepler field of view based on a newly established technique that uses asteroseismology to identify fore- or background stars in the field, which demonstrates advantages over classical methods such as kinematic and photometry measurements. Four previously identified seismic non-members in NGC6819 are confirmed in this study, and three additional non-members are found -- two in NGC6819 and one in NGC6791. We further highlight which stars are, or might be, affected by blending, which needs to be taken into account when analysing these Kepler data.Comment: 12 pages, 9 figures, 5 tables, accepted by Ap