A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data

Background: A better understanding of the mechanisms involved in gas-phase fragmentation of peptides is essential for the development of more reliable algorithms for high-throughput protein identification using mass spectrometry (MS). Current methodologies depend predominantly on the use of derived m/z values of fragment ions, and, the knowledge provided by the intensity information present in MS/MS spectra has not been fully exploited. Indeed spectrum intensity information is very rarely utilized in the algorithms currently in use for high-throughput protein identification. Results: In this work, a Bayesian neural network approach is employed to analyze ion intensity information present in 13878 different MS/MS spectra. The influence of a library of 35 features on peptide fragmentation is examined under different proton mobility conditions. Useful rules involved in peptide fragmentation are found and subsets of features which have significant influence on fragmentation pathway of peptides are characterised. An intensity model is built based on the selected features and the model can make an accurate prediction of the intensity patterns for given MS/MS spectra. The predictions include not only the mean values of spectra intensity but also the variances that can be used to tolerate noises and system biases within experimental MS/MS spectra. Conclusion: The intensity patterns of fragmentation spectra are informative and can be used to analyze the influence of various characteristics of fragmented peptides on their fragmentation pathway. The features with significant influence can be used in turn to predict spectra intensities. Such information can help develop more reliable algorithms for peptide and protein identification

Editorial: Evolution of Animal Microbial Communities in Response to Environmental Stress

info:eu-repo/semantics/publishedVersio

Evolution of Animal Microbial Communities in Response to Environmental Stress

info:eu-repo/semantics/publishedVersio

The Young Substellar Companion ROXs 12 B: Near-Infrared Spectrum, System Architecture, and Spin-Orbit Misalignment

ROXs 12 (2MASS J16262803-2526477) is a young star hosting a directly imaged companion near the deuterium-burning limit. We present a suite of spectroscopic, imaging, and time-series observations to characterize the physical and environmental properties of this system. Moderate-resolution near-infrared spectroscopy of ROXs 12 B from Gemini-North/NIFS and Keck/OSIRIS reveals signatures of low surface gravity including weak alkali absorption lines and a triangular $H$-band pseudo-continuum shape. No signs of Pa$\beta$ emission are evident. As a population, however, we find that about half (46 $\pm$ 14\%) of young ($\lesssim$15 Myr) companions with masses $\lesssim$20 $M_\mathrm{Jup}$ possess actively accreting subdisks detected via Pa$\beta$ line emission, which represents a lower limit on the prevalence of circumplanetary disks in general as some are expected to be in a quiescent phase of accretion. The bolometric luminosity of the companion and age of the host star (6$^{+4}_{-2}$ Myr) imply a mass of 17.5 $\pm$ 1.5 $M_\mathrm{Jup}$ for ROXs 12 B based on hot-start evolutionary models. We identify a wide (5100 AU) tertiary companion to this system, 2MASS J16262774-2527247, which is heavily accreting and exhibits stochastic variability in its $K2$ light curve. By combining $v$sin$i_*$ measurements with rotation periods from $K2$, we constrain the line-of-sight inclinations of ROXs 12 A and 2MASS J16262774-2527247 and find that they are misaligned by 60$^{+7}_{-11}$$^{\circ}$. In addition, the orbital axis of ROXs 12 B is likely misaligned from the spin axis of its host star ROXs 12 A, suggesting that ROXs 12 B formed akin to fragmenting binary stars or in an equatorial disk that was torqued by the wide stellar tertiary.Comment: AJ, accepte

The S. pombe translation initiation factor eIF4G is sumoylated and associates with the SUMO protease Ulp2

SUMO is a small post-translational modifier, that is attached to lysine residues in target proteins. It acts by altering proteinprotein interactions, protein localisation and protein activity. SUMO chains can also act as substrates for ubiquitination, resulting in proteasome-mediated degradation of the target protein. SUMO is removed from target proteins by one of a number of specific proteases. The processes of sumoylation and desumoylation have well documented roles in DNA metabolism and in the maintenance of chromatin structure. To further analyse the role of this modification, we have purified protein complexes containing the S. pombe SUMO protease, Ulp2. These complexes contain proteins required for ribosome biogenesis, RNA stability and protein synthesis. Here we have focussed on two translation initiation factors that we identified as co-purifying with Ulp2, eIF4G and eIF3h. We demonstrate that eIF4G, but not eIF3h, is sumoylated. This modification is increased under conditions that produce cytoplasmic stress granules. Consistent with this we observe partial co-localisation of eIF4G and SUMO in stressed cells. Using HeLa cells, we demonstrate that human eIF4GI is also sumoylated; in vitro studies indicate that human eIF4GI is modified on K1368 and K1588, that are located in the C-terminal eIF4A- and Mnk-binding sites respectively

Three Wide Planetary-mass Companions to FW Tau, ROXs 12, and ROXs 42B

We report the discovery of three planetary-mass companions (M = 6-20 M_(Jup)) in wide orbits (ρ ~ 150-300 AU) around the young stars FW Tau (Taurus-Auriga), ROXs 12 (Ophiuchus), and ROXs 42B (Ophiuchus). All three wide planetary-mass companions (PMCs) were reported as candidate companions in previous binary survey programs, but then were neglected for >10 yr. We therefore obtained followup observations that demonstrate that each candidate is comoving with its host star. Based on the absolute M_K' magnitudes, we infer masses (from hot-start evolutionary models) and projected separations of 10 ± 4 M_(Jup) and 330 ± 30 AU for FW Tau b, 16 ± 4 M_(Jup) and 210 ± 20 AU for ROXs 12, and 10 ± 4 M_(Jup) and 140 ± 10 AU for ROXs 42B b. We also present similar observations for 10 other candidates that show that they are unassociated field stars, as well as multicolor JHK'L' near-infrared photometry for our new PMCs and for five previously identified substellar or planetary-mass companions. The near-infrared photometry for our sample of eight known and new companions generally parallels the properties of free-floating, low-mass brown dwarfs in these star-forming regions. However, five of the seven objects with M < 30 M_(Jup) are redder in K' – L' than the distribution of young free-floating counterparts of similar J – K' color. We speculate that this distinction could indicate a structural difference in circumplanetary disks, perhaps tied to higher disk mass since at least two of the objects in our sample are known to be accreting more vigorously than typical free-floating counterparts

The Multiplicity of M-Dwarfs in Young Moving Groups

We image 104 newly identified low-mass (mostly M-dwarf) pre-main sequence members of nearby young moving groups with Magellan Adaptive Optics (MagAO) and identify 27 binaries with instantaneous projected separation as small as 40 mas. 15 were previously unknown. The total number of multiple systems in this sample including spectroscopic and visual binaries from the literature is 36, giving a raw multiplicity rate of at least $35^{+5}_{-4}\%$ for this population. In the separation range of roughly 1 - 300 AU in which infrared AO imaging is most sensitive, the raw multiplicity rate is at least $24^{+5}_{-4}\%$ for binaries resolved by the MagAO infrared camera (Clio). The M-star sub-sample of 87 stars yields a raw multiplicity of at least $30^{+5}_{-4}\%$ over all separations, $21^{+5}_{-4}\%$ for secondary companions resolved by Clio from 1 to 300 AU ($23^{+5}_{-4}\%$ for all known binaries in this separation range). A combined analysis with binaries discovered by the Search for Associations Containing Young stars shows that multiplicity fraction as a function of mass and age over the range of 0.2 to 1.2 $M_\odot$ and 10 - 200 Myr appears to be linearly flat in both parameters and across YMGs. This suggests that multiplicity rates are largely set by 100 Myr without appreciable evolution thereafter. After bias corrections are applied, the multiplicity fraction of low-mass YMG members ($< 0.6 M_\odot$) is in excess of the field.Comment: 25 page

Role of interspecies transfer of chromosomal genes in the evolution of penicillin resistance in pathogenic and commensal Neisseria species

The two pathogenic species of Neisseria, N. meningitidis and N. gonorrhoeae , have evolved resistance to penicillin by alterations in chromosomal genes encoding the high molecular weight penicillin-binding proteins, or PBPs. The PBP 2 gene ( penA ) has been sequenced from over 20 Neisseria isolates, including susceptible and resistant strains of the two pathogenic species, and five human commensal species. The genes from penicillin-susceptible strains of N. meningitidis and N. gonorrhoeae are very uniform, whereas those from penicillin-resistant strains consist of a mosaic of regions resembling those in susceptible strains of the same species, interspersed with regions resembling those in one, or in some cases, two of the commensal species. The mosaic structure is interpreted as having arisen from the horizontal transfer, by genetic transformation, of blocks of DNA, usually of a few hundred base pairs. The commensal species identified as donors in these interspecies recombinational events ( N. flavescens and N. cinerea ) are intrinsically more resistant to penicillin than typical isolates of the pathogenic species. Transformation has apparently provided N. meningitidis and N. gonorrhoeae with a mechanism by which they can obtain increased resistance to penicillin by replacing their penA genes (or the relevant parts of them) with the penA genes of related species that fortuitously produce forms of PBP 2 that are less susceptible to inhibition by the antibiotic. The ends of the diverged blocks of DNA in the penA genes of different penicillin-resistant strains are located at the same position more often than would be the case if they represent independent crossovers at random points along the gene. Some of these common crossover points may represent common ancestry, but reasons are given for thinking that some may represent independent events occurring at recombinational hotspots.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/48045/1/239_2004_Article_BF00182388.pd

Planets Around Low-Mass Stars (PALMS). I. A Substellar Companion to the Young M Dwarf 1RXS J235133.3+312720

We report the discovery of a brown dwarf companion to the young M dwarf 1RXS J235133.3+312720 as part of a high contrast imaging search for planets around nearby young low-mass stars with Keck-II/NIRC2 and Subaru/HiCIAO. The 2.4" (~120 AU) pair is confirmed to be comoving from two epochs of high resolution imaging. Follow-up low- and moderate-resolution near-infrared spectroscopy of 1RXS J2351+3127 B with IRTF/SpeX and Keck-II/OSIRIS reveals a spectral type of L0$^{+2}_{-1}$. The M2 primary star 1RXS J2351+3127 A exhibits X-ray and UV activity levels comparable to young moving group members with ages of ~10-100 Myr. UVW kinematics based the measured radial velocity of the primary and the system's photometric distance (50 +/- 10 pc) indicate it is likely a member of the ~50-150 Myr AB Dor moving group. The near-infrared spectrum of 1RXS J2351+3127 B does not exhibit obvious signs of youth, but its H-band morphology shows subtle hints of intermediate surface gravity. The spectrum is also an excellent match to the ~200 Myr M9 brown dwarf LP 944-20. Assuming an age of 50-150 Myr, evolutionary models imply a mass of 32 +/- 6 Mjup for the companion, making 1RXS J2351+3127 B the second lowest-mass member of the AB Dor moving group after the L4 companion CD-35 2722 B and one of the few benchmark brown dwarfs known at young ages.Comment: Accepted for publication in ApJ. 24 pages, 12 figures, 4 table