Specific and non specific hybridization of oligonucleotide probes on microarrays

Gene expression analysis by means of microarrays is based on the sequence specific binding of mRNA to DNA oligonucleotide probes and its measurement using fluorescent labels. The binding of RNA fragments involving other sequences than the intended target is problematic because it adds a "chemical background" to the signal, which is not related to the expression degree of the target gene. The paper presents a molecular signature of specific and non specific hybridization with potential consequences for gene expression analysis. We analyzed the signal intensities of perfect match (PM) and mismatch (MM) probes of GeneChip microarrays to specify the effect of specific and non specific hybridization. We found that these events give rise to different relations between the PM and MM intensities as function of the middle base of the PMs, namely a triplet- (C>G=T>A>0) and a duplet-like (C=T>0>G=A) pattern of the PM-MM log-intensity difference upon binding of specific and non specific RNA fragments, respectively. The systematic behaviour of the intensity difference can be rationalized on the level of base pairings of DNA/RNA oligonucleotide duplexes in the middle of the probe sequence. Non-specific binding is characterized by the reversal of the central Watson Crick (WC) pairing for each PM/MM probe pair, whereas specific binding refers to the combination of a WC and a self complementary (SC) pairing in PM and MM probes, respectively. The intensity of complementary MM introduces a systematic source of variation which decreases the precision of expression measures based on the MM intensities

Sequentially Triggered Star Formation in OB Associations

We discuss observational evidence for sequential and triggered star formation in OB associations. We first review the star formation process in the Scorpius-Centaurus OB association, the nearest OB association to the Sun, where several recent extensive studies have allowed us to reconstruct the star formation history in a rather detailed way. We then compare the observational results with those obtained for other OB associations and with recent models of rapid cloud and star formation in the turbulent interstellar medium. We conclude that the formation of whole OB subgroups (each consisting of several thousand stars) requires large-scale triggering mechanisms such as shocks from expanding wind and supernova driven superbubbles surrounding older subgroups. Other triggering mechanisms, like radiatively driven implosion of globules, also operate, but seem to be secondary processes, forming only small stellar groups rather than whole OB subgroups with thousands of stars.Comment: Invited talk at the IAU Symposium 237: "Triggered Star Formation in a Turbulent ISM", Prague, Czech Republic, August 200

X-ray view of IC348 in the light of an updated cluster census

We study the properties of the coronae of the low-mass stars in the young (~2-3Myr), nearby (~310pc) open cluster IC348 combining X-ray and optical/infrared data. The four existing Chandra observations of IC348 are merged, thus providing a deeper and spatially more complete X-ray view than previous X-ray studies of the cluster. We have compiled a comprehensive catalog of IC348 members taking into account recent updates to the cluster census. Our data collection comprises fundamental stellar parameters, infrared excess indicating the presence of disks, Halpha emission as a tracer of chromospheric emission or accretion and mass accretion rates. We have detected 290 X-ray sources in four merged Chandra exposures, of which 187 are associated with known cluster members. Only four of the X-ray sources are brown dwarfs (spectral type M6 and later). The detection rate is highest for diskless Class III stars and increases with stellar mass. This may be explained with higher X-ray luminosities for higher mass and later evolutionary stage that is evident in the X-ray luminosity functions. In particular, we find that for the lowest examined masses (0.1-0.25 Msun) there is a difference between the X-ray luminosity functions of accreting and non-accreting stars (classified on the basis of their Halpha emission strength) as well as those of disk-bearing and diskless stars (classified on the basis of the slope of the spectral energy distribution). These differences disappear for higher masses. This is related to our finding that the L_x/L_bol ratio is non-constant across the mass/luminosity sequence of IC348 with a decrease towards lower luminosity stars. Our analysis of an analogous stellar sample in the Orion Nebula Cluster suggests that the decline of L_x/L_ bol for young stars at the low-mass end of the stellar sequence is likely universal.Comment: Accepted for publication in Astronomy & Astrophysic

Age spreads in clusters and associations: the lithium test

We report the evidence that several low-mass stars (<~0.4 Msun) of the Orion and Upper Scorpius clusters have lithium abundances well below the interstellar value. Due to time-dependent depletion, our result implies stellar ages greater than ~5 Myr, suggesting that star formation has been proceeding for a long time in these systems.Comment: to appear in IMF@50: The Initial Mass Function 50 years later, eds. E. Corbelli et al. (Kluwer Acad. Press), 2004, in pres

The Clump Mass Function of the Dense Clouds in the Carina Nebula Complex

We want to characterize the properties of the cold dust clumps in the Carina Nebula Complex (CNC), which shows a very high level of massive star feedback. We derive the Clump Mass Function (ClMF), explore the reliability of different clump extraction algorithms, and investigate the influence of the temperatures within the clouds on the resulting shape of the ClMF. We analyze a 1.25x1.25 deg^2 wide-field sub-mm map obtained with LABOCA (APEX), which provides the first spatially complete survey of the clouds in the CNC. We use the three clump-finding algorithms CLUMPFIND (CF), GAUSSCLUMPS (GC) and SExtractor (SE) to identify individual clumps and determine their total fluxes. In addition to assuming a common `typical' temperature for all clouds, we also employ an empirical relation between cloud column densities and temperature to determine an estimate of the individual clump temperatures, and use this to determine individual clump masses. While the ClMF based on the CF extraction is very well described by a power-law, the ClMFs based on GC and SE are better represented by a log-normal distribution. We also find that the use of individual clump temperatures leads to a shallower ClMF slope than the assumption of a common temperature (e.g. 20 K) of all clumps. The power-law of dN/dM \propto M^-1.95 we find for the CF sample is in good agreement with ClMF slopes found in previous studies of other regions. The dependence of the ClMF shape (power-law vs. log-normal distribution) on the employed extraction method suggests that observational determinations of the ClMF shape yields only very limited information about the true structure of the cloud. Interpretations of log-normal ClMF shape as a signature of turbulent pre-stellar clouds vs. power-law ClMFs as a signature of star-forming clouds may be taken with caution for a single extraction algorithm without additional information.Comment: 8 pages, 7 figures, accepted by A&

Direct Imaging and Spectroscopy of a Planetary Mass Candidate Companion to a Young Solar Analog

We present Gemini near-infrared adaptive optics imaging and spectroscopy of a planetary mass candidate companion to 1RXS J160929.1-210524, a roughly solar-mass member of the 5 Myr-old Upper Scorpius association. The object, separated by 2.22" or 330 AU at ~150 pc, has infrared colors and spectra suggesting a temperature of 1800(-100/+200) K, and spectral type of L4(-2/+1). The H- and K-band spectra provide clear evidence of low surface gravity, and thus youth. Based on the widely used DUSTY models, we infer a mass of 8(-2/+4)Mjupiter. If gravitationally bound, this would be the lowest mass companion imaged around a normal star thus far, and its existence at such a large separation would pose a serious challenge to theories of star and planet formation.Comment: Revised accepted version, ApJL, in pres

The onset of X-ray emission in young stellar objects: a Chandra observation of the Serpens star-forming region

AIMS: To study the properties of X-ray emissions from young stellar objects (YSOs), through their evolution from Class I to Class III and determine whether Class 0 protostars emit in X-rays. METHODS: A deep Chandra X-ray observation of the Serpens star-forming region was obtained. The Serpens Cloud Core is ideally suited for this type of investigation, being populated by a dense and extremely young cluster whose members are found in all different evolutionary stages, including six well studied Class 0 sources. RESULTS: None of the six Class 0 protostars is detected in our observations, excluding the presence of sources with X-ray luminosities > 0.4 10^30 erg/s (for column densities of the order of 4 10^{23} cm^-2, or A_V ~ 200). A total of 85 X-ray sources are detected and the light curves and spectra of 35 YSOs are derived. There is a clear trend of decreasing absorbing column densities as one moves from Class I to Class III sources, and, possibly, evidence of decreasing plasma temperatures, too. We observe a strong, long-duration, flare from a Class II low-mass star, for which we derive a flaring loop length of the order of 20 stellar radii. We interpret the flaring event as originating from a magnetic flux tube connecting the star to its circumstellar disk. The presence of such a disk is supported by the detection, in the spectrum of this star, of 6.4 keV Fe fluorescent emission.Comment: Accepted for publication in A&