Defining and using microbial spectral databases

AbstractThis work shows how fingerprints of mass spectral patterns from microbial isolates are affected by variations in instrumental condition, by sample environment, and by sample handling factors. It describes a novel method by which pattern distortions can be mathematically corrected for variations in factors not amenable to experimental control. One uncontrollable variable is “between-batch” differences in culture media. Another, relevant for determination of noncultured extracts, is differences between the cells’ environmental experience (e.g., starved environmental extracts versus cultured standards). The method suggests that, after a single growth cycle on a solid medium (perhaps, a selective one), pyrolysis MS spectra of microbial isolates can be algorithmically compensated and an unknown isolate identified using a spectral database defined by culture on a different (perhaps, nonselective) medium. This reduces identification time to as few as 24 h from sample collection. The concept also proposes a possible way to compensate certain noncultured, nonisolated samples (e.g., cells concentrated from urine or impacted from aerosol or semi-selectively extracted by immunoaffinity methods from heavily contaminated matrices) for identification within half an hour. Using the method, microbial mass spectra from different labs can be assembled into coherent databases similar to those routinely used to identify pure compounds. This type of data treatment is applicable for rapid detection in biowarfare and bioterror events as well as in forensic, research, and clinical laboratory contexts

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics

BACKGROUND: Quantitative proteomics holds great promise for identifying proteins that are differentially abundant between populations representing different physiological or disease states. A range of computational tools is now available for both isotopically labeled and label-free liquid chromatography mass spectrometry (LC-MS) based quantitative proteomics. However, they are generally not comparable to each other in terms of functionality, user interfaces, information input/output, and do not readily facilitate appropriate statistical data analysis. These limitations, along with the array of choices, present a daunting prospect for biologists, and other researchers not trained in bioinformatics, who wish to use LC-MS-based quantitative proteomics. RESULTS: We have developed Corra, a computational framework and tools for discovery-based LC-MS proteomics. Corra extends and adapts existing algorithms used for LC-MS-based proteomics, and statistical algorithms, originally developed for microarray data analyses, appropriate for LC-MS data analysis. Corra also adapts software engineering technologies (e.g. Google Web Toolkit, distributed processing) so that computationally intense data processing and statistical analyses can run on a remote server, while the user controls and manages the process from their own computer via a simple web interface. Corra also allows the user to output significantly differentially abundant LC-MS-detected peptide features in a form compatible with subsequent sequence identification via tandem mass spectrometry (MS/MS). We present two case studies to illustrate the application of Corra to commonly performed LC-MS-based biological workflows: a pilot biomarker discovery study of glycoproteins isolated from human plasma samples relevant to type 2 diabetes, and a study in yeast to identify in vivo targets of the protein kinase Ark1 via phosphopeptide profiling. CONCLUSION: The Corra computational framework leverages computational innovation to enable biologists or other researchers to process, analyze and visualize LC-MS data with what would otherwise be a complex and not user-friendly suite of tools. Corra enables appropriate statistical analyses, with controlled false-discovery rates, ultimately to inform subsequent targeted identification of differentially abundant peptides by MS/MS. For the user not trained in bioinformatics, Corra represents a complete, customizable, free and open source computational platform enabling LC-MS-based proteomic workflows, and as such, addresses an unmet need in the LC-MS proteomics field

Abundance analysis of the outer halo globular cluster Palomar 14

We determine the elemental abundances of nine red giant stars belonging to Palomar 14 (Pal 14). Pal 14 is an outer halo globular cluster (GC) at a distance of \sim 70 kpc. Our abundance analysis is based on high-resolution spectra and one-dimensional stellar model atmospheres.We derived the abundances for the iron peak elements Sc, V, Cr, Mn, Co, Ni, the {\alpha}-elements O, Mg, Si, Ca, Ti, the light odd element Na, and the neutron-capture elements Y, Zr, Ba, La, Ce, Nd, Eu, Dy, and Cu. Our data do not permit us to investigate light element (i.e., O to Mg) abundance variations. The neutron-capture elements show an r-process signature. We compare our measurements with the abundance ratios of inner and other outer halo GCs, halo field stars, GCs of recognized extragalactic origin, and stars in dwarf spheroidal galaxies (dSphs). The abundance pattern of Pal 14 is almost identical to those of Pal 3 and Pal 4, the next distant members of the outer halo GC population after Pal 14. The abundance pattern of Pal 14 is also similar to those of the inner halo GCs, halo field stars, and GCs of recognized extragalactic origin, but differs from what is customarily found in dSphs field stars. The abundance properties of Pal 14 as well as those of the other outer halo GCs are thus compatible with an accretion origin from dSphs. Whether or not GC accretion played a role, it seems that the formation conditions of outer halo GCs and GCs in dSphs were similar.Comment: 19 pages, 15 figures. Accepted by A&

The Chemical Evolution of the Ursa Minor Dwarf Spheroidal Galaxy

We present an abundance analysis based on high resolution spectra of 10 stars selected to span the full range in metallicity in the Ursa Minor dwarf spheroidal galaxy. We find [Fe/H] for the sample stars ranges from -1.35 to -3.10 dex and establish the trends of the abundance ratios [X/Fe]. In key cases, particularly for the alpha-elements, these resemble those for stars in the outer part of the Galactic halo, especially at the lowest metallicities probed. The n-capture elements show a r-process distribution over the full range of Fe-metallicity. This suggests that the duration of star formation in the UMi dSph was shorter than in other dSph galaxies. The derived ages for a larger sample of UMi stars with more uncertain metallicities also suggest a population dominated by uniformly old (~13 Gyr) stars, with a hint of an age-metallicity relationship. In comparing our results for UMi, our earlier work in Draco, and published studies of more metal-rich dSph Galactic satellites, there appears to be a pattern of moving from a chemical inventory for dSph giants with [Fe/H] < -2 dex which is very similar to that of stars in the outer part of the Galactic halo (enhanced alpha/Fe relative to the Sun, coupled with subsolar [X/Fe] for the heavy neutron capture elements and r-process domination), switching to subsolar alpha-elements and super-solar s-process dominated neutron capture elements for the highest [Fe/H] dSph stars. The combination of low star formation rates over a varying and sometimes extended duration that produced the stellar populations in the local dSph galaxies with [Fe/H] > -1.5 dex leads to a chemical inventory wildly discrepant from that of any component of the Milky Way.Comment: Accepted to the Astrophysical Journal. 22 pages of text, total length 68 pages includes 11 page table 3 to be published in full in electronic form onl

The kinematic footprints of five stellar streams in Andromeda's halo

(abridged) We present a spectroscopic analysis of five stellar streams (`A', `B', `Cr', `Cp' and `D') as well as the extended star cluster, EC4, which lies within streamC, all discovered in the halo of M31 from our CFHT/MegaCam survey. These spectroscopic results were initially serendipitous, making use of our existing observations from the DEep Imaging Multi-Object Spectrograph mounted on the Keck II telescope, and thereby emphasizing the ubiquity of tidal streams that account for ~70% of the M31 halo stars in the targeted fields. Subsequent spectroscopy was then procured in streamCr/p and streamD to trace the velocity gradient along the streams. For the cluster EC4, candidate member stars with average [Fe/H]~-1.4 (Fe/H_spec=-1.6), are found at v_{hel}=-285 km/s suggesting it could be related to streamCp. No similarly obvious cold kinematic candidate is found for streamD, although candidates are proposed in both of two spectroscopic pointings along the stream (both at -400 km/s). Spectroscopy near the edge of streamB suggests a likely kinematic detection, while a candidate kinematic detection of streamA is found (plausibly associated to M33 rather than M31). The low dispersion of the streams in kinematics, physical thickness, and metallicity makes it hard to reconcile with a scenario whereby these stream structures as an ensemble are related to the giant southern stream. We conclude that the M31 stellar halo is largely made up of multiple kinematically cold streams.Comment: 19 pages, 12 figures, accepted in MNRAS. High resolution version, with fig10 here: http://www.ast.cam.ac.uk/~schapman/streams.pd

The Masses of the Milky Way and Andromeda galaxies

We present a family of robust tracer mass estimators to compute the enclosed mass of galaxy haloes from samples of discrete positional and kinematical data of tracers, such as halo stars, globular clusters and dwarf satellites. The data may be projected positions, distances, line of sight velocities or proper motions. Forms of the estimator tailored for the Milky Way galaxy and for M31 are given. Monte Carlo simulations are used to quantify the uncertainty as a function of sample size. For the Milky Way, the satellite sample consists of 26 galaxies with line-of-sight velocities. We find that the mass of the Milky Way within 300 kpc is ~ 0.9 x 10^12 solar masses assuming velocity isotropy. However, the mass estimate is sensitive to the anisotropy and could plausibly lie between 0.7 - 3.4 x 10^12 solar masses. Incorporating the proper motions of 6 Milky Way satellites into the dataset, we find ~ 1.4 x 10^12 solar masses. The range here if plausible anisotropies are used is still broader, from 1.2 - 2.7 x 10^12 solar masses. For M31, there are 23 satellite galaxies with measured line-of-sight velocities, but only M33 and IC 10 have proper motions. We use the line of sight velocities and distances of the satellite galaxies to estimate the mass of M31 within 300 kpc as ~ 1.4 x 10^12 solar masses assuming isotropy. There is only a modest dependence on anisotropy, with the mass varying between 1.3 -1.6 x 10^12 solar masses. Given the uncertainties, we conclude that the satellite data by themselves yield no reliable insights into which of the two galaxies is actually the more massive.Comment: 15 pages, submitted to MNRA

Extremely metal-poor stars in classical dwarf spheroidal galaxies: Fornax, Sculptor and Sextans

We present the results of a dedicated search for extremely metal-poor stars in the Fornax, Sculptor and Sextans dSphs. Five stars were selected from two earlier VLT/Giraffe and HET/HRS surveys and subsequently followed up at high spectroscopic resolution with VLT/UVES. All of them turned out to have [Fe/H] <= -3 and three stars are below [Fe/H] -3.5. This constitutes the first evidence that the classical dSphs Fornax and Sextans join Sculptor in containing extremely metal-poor stars and suggests that all of the classical dSphs contain extremely metal-poor stars. One giant in Sculptor at [Fe/H]=-3.96 +- 0.10 is the most metal-poor star ever observed in an external galaxy. We carried out a detailed analysis of the chemical abundances of the alpha, iron peak, and the heavy elements, and we performed a comparison with the Milky Way halo and the ultra faint dwarf stellar populations. Carbon, barium and strontium show distinct features characterized by the early stages of galaxy formation and can constrain the origin of their nucleosynthesis.Comment: In A&A. This version corrects a few typographical errors in the coordinates of some of our stars (Table 1

Satellite Survival in Highly Resolved Milky Way Class Halos

Surprisingly little is known about the origin and evolution of the Milky Way's satellite galaxy companions. UV photoionisation, supernova feedback and interactions with the larger host halo are all thought to play a role in shaping the population of satellites that we observe today, but there is still no consensus as to which of these effects, if any, dominates. In this paper, we revisit the issue by re-simulating a Milky Way class dark matter (DM) halo with unprecedented resolution. Our set of cosmological hydrodynamic Adaptive Mesh Refinement (AMR) simulations, called the Nut suite, allows us to investigate the effect of supernova feedback and UV photoionisation at high redshift with sub-parsec resolution. We subsequently follow the effect of interactions with the Milky Way-like halo using a lower spatial resolution (50pc) version of the simulation down to z=0. This latter produces a population of simulated satellites that we compare to the observed satellites of the Milky Way and M31. We find that supernova feedback reduces star formation in the least massive satellites but enhances it in the more massive ones. Photoionisation appears to play a very minor role in suppressing star and galaxy formation in all progenitors of satellite halos. By far the largest effect on the satellite population is found to be the mass of the host and whether gas cooling is included in the simulation or not. Indeed, inclusion of gas cooling dramatically reduces the number of satellites captured at high redshift which survive down to z=0.Comment: 22 pages, 16 figures, accepted for publication in MNRA

A Keck/DEIMOS spectroscopic survey of the faint M31 satellites And IX, And XI, And XII, and And XIII

We present the first spectroscopic analysis of the faint M31 satellite galaxies, AndXI and AndXIII, and a reanalysis of existing spectroscopic data for two further faint companions, And IX and AndXII. By combining data obtained using the DEIMOS spectrograph mounted on the Keck II telescope with deep photometry from the Suprime-Cam instrument on Subaru, we have calculated global properties for the dwarfs, such as systemic velocities, metallicites and half-light radii.We find each dwarf to be very metal poor ([Fe/H] -2 both photometrically and spectroscopically, from their stacked spectrum), and as such, they continue to follow the luminosity-metallicity relationship established with brighter dwarfs. We are unable to resolve a dispersion for And XI due to small sample size and low S/N, but we set a one sigma upper limit of sigma-v <5 km/s. For And IX, And XII and And XIII we resolve velocity dispersions of v=4.5 (+3.4,-3.2), 2.6(+5.1,-2.6) and 9.7(+8.9,-4.5) km/s, and derive masses within the half light radii of 6.2(+5.3,-5.1)x10^6 Msun, 2.4 (+6.5,-2.4)x10^6 Msun and 1.1(+1.4,-0.7)x10^7 Msun respectively. We discuss each satellite in the context of the Mateo relations for dwarf spheroidal galaxies, and the Universal halo profiles established for Milky Way dwarfs (Walker et al. 2009). For both galaxies, this sees them fall below the Universal halo profiles of Walker et al. (2009). When combined with the findings of McConnachie & Irwin (2006a), which reveal that the M31 satellites are twice as extended (in terms of both half-light and tidal radii) as their Milky Way counterparts, these results suggest that the satellite population of the Andromeda system could inhabit halos that are significantly different from those of the Milky Way in terms of their central densities (abridged).Comment: 26 pages, 18 figures, MNRAS submitte

Infall Times for Milky Way Satellites From Their Present-Day Kinematics

We analyze subhalos in the Via Lactea II (VL2) cosmological simulation to look for correlations among their infall times and z = 0 dynamical properties. We find that the present day orbital energy is tightly correlated with the time at which subhalos last crossed into the virial radius. This energy-infall correlation provides a means to infer infall times for Milky Way satellite galaxies. Assuming that the Milky Way's assembly can be modeled by VL2, we show that the infall times of some satellites are well constrained given only their Galactocentric positions and line-of-sight velocities. The constraints sharpen for satellites with proper motion measurements. We find that Carina, Ursa Minor, and Sculptor were all accreted early, more than 8 Gyr ago. Five other dwarfs, including Sextans and Segue 1, are also probable early accreters, though with larger uncertainties. On the other extreme, Leo T is just falling into the Milky Way for the first time while Leo I fell in \sim 2 Gyr ago and is now climbing out of the Milky Way's potential after its first perigalacticon. The energies of several other dwarfs, including Fornax and Hercules, point to intermediate infall times, 2 - 8 Gyr ago. We compare our infall time estimates to published star formation histories and find hints of a dichotomy between ultrafaint and classical dwarfs. The classical dwarfs appear to have quenched star formation after infall but the ultrafaint dwarfs tend to be quenched long before infall, at least for the cases in which our uncertainties allow us to discern differences. Our analysis suggests that the Large Magellanic Cloud crossed inside the Milky Way virial radius recently, within the last \sim 4 billion years.Comment: 15 pages, 7 figures, all figures include colors, submitted for publication in MNRA