Enzymes of respiratory iron oxidation

This report focuses on the progress made in three areas of research concerned with enzymes involved in respiratory iron oxidation. The three areas are as follows: development of an improved procedure for the routine large scale culture of iron oxidizing chemolithotrophs based on the in-situ electrolysis of the soluble iron in the growth medium; to perform iron oxidation kinetic studies on whole cells using the oxygen electrode; and to identify, separate, purify, and characterize the individual cellular components

Molecular characterization of bacterial respiration on minerals. Final technical report, August 4, 1994--August 3, 1996

The scope of work outlined in the original proposal contained two specific aims. Highlights of the results obtained and published on each specific aim during the grant period in question are summarized. The first aim continued the identification, separation, and characterization of the cellular components necessary for aerobic respiration on iron. An electrochemical apparatus for the large scale cultivation of chemolithotrophic bacteria that respire aerobically on ferrous ions was perfected. The kinetic properties of an acid-stable iron:rusticyanin oxidoreductase from T. ferrooxidans were determined. The overall tertiary structure of rusticyanin in solution was elucidated from a combination of homonuclear proton and heteronuclear {sup 15}N-edited NMR spectra. An artificial gene for rusticyanin was designed, synthesized, and successfully expressed in E. coli. The X-ray crystallographic structure of rusticyanin was solved to a resolution of 1.9 {angstrom} by multiwavelength anomalous dispersion (MAD) phasing. The second aim initiated an investigation of the molecular principles whereby these bacteria recognize and adhere to their insoluble inorganic substrates. The electrophoretic mobility of T. ferrooxidans with and without its insoluble substrates was determined by laser Doppler velocimetry under physiological conditions. The adherence of T. ferrooxidans to the surface of pyrite was observed directly in a video-enhanced light microscope

Hot Organic Molecules Toward a Young Low-Mass Star: A Look at Inner Disk Chemistry

Spitzer Space Telescope spectra of the low mass young stellar object (YSO) IRS 46 (L_bol ~ 0.6 L_sun) in Ophiuchus reveal strong vibration-rotation absorption bands of gaseous C2H2, HCN, and CO2. This is the only source out of a sample of ~100 YSO's that shows these features and the first time they are seen in the spectrum of a solar-mass YSO. Analysis of the Spitzer data combined with Keck L- and M-band spectra gives excitation temperatures of > 350 K and abundances of 10(-6)-10(-5) with respect to H2, orders of magnitude higher than those found in cold clouds. In spite of this high abundance, the HCN J=4-3 line is barely detected with the James Clerk Maxwell Telescope, indicating a source diameter less than 13 AU. The (sub)millimeter continuum emission and the absence of scattered light in near-infrared images limits the mass and temperature of any remnant collapse envelope to less than 0.01 M_sun and 100 K, respectively. This excludes a hot-core type region as found in high-mass YSO's. The most plausible origin of this hot gas rich in organic molecules is in the inner (<6 AU radius) region of the disk around IRS 46, either the disk itself or a disk wind. A nearly edge-on 2-D disk model fits the spectral energy distribution (SED) and gives a column of dense warm gas along the line of sight that is consistent with the absorption data. These data illustrate the unique potential of high-resolution infrared spectroscopy to probe organic chemistry, gas temperatures and kinematics in the planet-forming zones close to a young star.Comment: 4 pages, 4 figures; To appear in Astrophysical Journal Letter

The Spitzer c2d Survey of Large, Nearby, Interstellar Clouds. VIII. Serpens Observed with MIPS

We present maps of 1.5 deg^2 of the Serpens dark cloud at 24, 70, and 160 μm observed with the Spitzer Space Telescope MIPS camera. We describe the observations and briefly discuss the data processing carried out by the c2d team on these data. More than 2400 compact sources have been extracted at 24 μm, nearly 100 at 70 μm, and four at 160 μm. We estimate completeness limits for our 24 μm survey from Monte Carlo tests with artificial sources inserted into the Spitzer maps. We compare source counts, colors, and magnitudes in the Serpens cloud to two reference data sets: a 0.50 deg^2 set on a low-extinction region near the dark cloud, and a 5.3 deg^2 subset of the SWIRE ELAIS N1 data that was processed through our pipeline. These results show that there is an easily identifiable population of young stellar object candidates in the Serpens cloud that is not present in either of the reference data sets. We also show a comparison of visual extinction and cool dust emission illustrating a close correlation between the two and find that the most embedded YSO candidates are located in the areas of highest visual extinction

From Molecular Cores to Planet-forming Disks: An SIRTF Legacy Program

Crucial steps in the formation of stars and planets can be studied only at mid‐ to far‐infrared wavelengths, where the Space Infrared Telescope (SIRTF) provides an unprecedented improvement in sensitivity. We will use all three SIRTF instruments (Infrared Array Camera [IRAC], Multiband Imaging Photometer for SIRTF [MIPS], and Infrared Spectrograph [IRS]) to observe sources that span the evolutionary sequence from molecular cores to protoplanetary disks, encompassing a wide range of cloud masses, stellar masses, and star‐forming environments. In addition to targeting about 150 known compact cores, we will survey with IRAC and MIPS (3.6–70 μm) the entire areas of five of the nearest large molecular clouds for new candidate protostars and substellar objects as faint as 0.001 solar luminosities. We will also observe with IRAC and MIPS about 190 systems likely to be in the early stages of planetary system formation (ages up to about 10 Myr), probing the evolution of the circumstellar dust, the raw material for planetary cores. Candidate planet‐forming disks as small as 0.1 lunar masses will be detectable. Spectroscopy with IRS of new objects found in the surveys and of a select group of known objects will add vital information on the changing chemical and physical conditions in the disks and envelopes. The resulting data products will include catalogs of thousands of previously unknown sources, multiwavelength maps of about 20 deg^2 of molecular clouds, photometry of about 190 known young stars, spectra of at least 170 sources, ancillary data from ground‐based telescopes, and new tools for analysis and modeling. These products will constitute the foundations for many follow‐up studies with ground‐based telescopes, as well as with SIRTF itself and other space missions such as SIM, JWST, Herschel, and TPF/Darwin

The Spitzer c2d Survey of Large, Nearby, Interstellar Clouds. I. Chamaeleon II Observed with MIPS

We present maps of over 1.5 square degrees in Chamaeleon (Cha) II at 24, 70, and 160 micron observed with the Spitzer Space Telescope Multiband Imaging Photometer for Spitzer (MIPS) and a 1.2 square degree millimeter map from SIMBA on the Swedish-ESO Submillimetre Telescope (SEST). The c2d Spitzer Legacy Team's data reduction pipeline is described in detail. Over 1500 24 micron sources and 41 70 micron sources were detected by MIPS with fluxes greater than 10-sigma. More than 40 potential YSOs are identified with a MIPS and 2MASS color-color diagram and by their spectral indices, including two previously unknown sources with 24 micron excesses. Our new SIMBA millimeter map of Cha II shows that only a small fraction of the gas is in compact structures with high column densities. The extended emission seen by MIPS is compared with previous CO observations. Some selected interesting sources, including two detected at 1 mm, associated with Cha II are discussed in detail and their SEDs presented. The classification of these sources using MIPS data is found to be consistent with previous studies.Comment: 44 pages, 12 figures (1 color), to be published in Ap

The Spitzer c2d survey of Large, Nearby, Interstellar Clouds. V. Chamaeleon II Observed with IRAC

We present IRAC (3.6, 4.5, 5.8, and 8.0 micron) observations of the Chamaeleon II molecular cloud. The observed area covers about 1 square degree defined by $A_V >2$. Analysis of the data in the 2005 c2d catalogs reveals a small number of sources (40) with properties similar to those of young stellaror substellar objects (YSOs). The surface density of these YSO candidates is low, and contamination by background galaxies appears to be substantial, especially for sources classified as Class I or flat SED. We discuss this problem in some detail and conclude that very few of the candidate YSOs in early evolutionary stages are actually in the Cha II cloud. Using a refined set of criteria, we define a smaller, but more reliable, set of 24 YSO candidates.Comment: 19 pages, 10 figures, in press Ap

The Spitzer c2d Survey of Weak-line T Tauri Stars II: New Constraints on the Timescale for Planet Building

One of the central goals of the Spitzer Legacy Project ``From Molecular Cores to Planet-forming Disks'' (c2d) is to determine the frequency of remnant circumstellar disks around weak-line T Tauri stars (wTTs) and to study the properties and evolutionary status of these disks. Here we present a census of disks for a sample of over 230 spectroscopically identified wTTs located in the c2d IRAC (3.6, 4.5, 4.8, and 8.0 um) and MIPS (24 um) maps of the Ophiuchus, Lupus, and Perseus Molecular Clouds. We find that ~20% of the wTTs in a magnitude limited subsample have noticeable IR-excesses at IRAC wavelengths indicating the presence of a circumstellar disk. The disk frequencies we find in these 3 regions are ~3-6 times larger than that recently found for a sample of 83 relatively isolated wTTs located, for the most part, outside the highest extinction regions covered by the c2d IRAC and MIPS maps. The disk fractions we find are more consistent with those obtained in recent Spitzer studies of wTTs in young clusters such as IC 348 and Tr 37. From their location in the H-R diagram, we find that, in our sample, the wTTs with excesses are among the younger part of the age distribution. Still, up to ~50% of the apparently youngest stars in the sample show no evidence of IR excess, suggesting that the circumstellar disks of a sizable fraction of pre-main-sequence stars dissipate in a timescale of ~1 Myr. We also find that none of the stars in our sample apparently older than ~10 Myrs have detectable circumstellar disks at wavelengths < 24 um. Also, we find that the wTTs disks in our sample exhibit a wide range of properties (SED morphology, inner radius, L_DISK/L*, etc) which bridge the gaps observed between the cTTs and the debris disk regimes.Comment: 54 pages, 13 figures, Accepted by Ap

The Spitzer c2d Survey of Large, Nearby, Interstellar Clouds. VII. Ophiuchus Observed with MIPS

We present maps of 14.4 deg^2 of the Ophiuchus dark clouds observed by the Spitzer Space Telescope Multiband Imaging Photometer for Spitzer (MIPS). These high-quality maps depict both numerous point sources and extended dust emission within the star-forming and non–star-forming portions of these clouds. Using PSF-fitting photometry, we detect 5779 sources at 24 μm and 81 sources at 70 μm at the 10 σ level of significance. Three hundred twenty-three candidate young stellar objects (YSOs) were identified according to their positions on the MIPS/2MASS K versus color-magnitude diagrams, as compared to 24 μm detections in the SWIRE extragalactic survey. We find that more than half of the YSO candidates, and almost all those with protostellar Class I spectral energy distributions, are confined to the known cluster and aggregates

The Spitzer c2d Survey of Large, Nearby, Interstellar Clouds. IV. Lupus Observed with MIPS

We present maps of 7.78 square degrees of the Lupus molecular cloud complex at 24, 70, and $160\:\mu$m. They were made with the Spitzer Space Telescope's Multiband Imaging Photometer for Spitzer (MIPS) instrument as part of the Spitzer Legacy Program, ``From Molecular Cores to Planet-Forming Disks'' (c2d). The maps cover three separate regions in Lupus, denoted I, III, and IV. We discuss the c2d pipeline and how our data processing differs from it. We compare source counts in the three regions with two other data sets and predicted star counts from the Wainscoat model. This comparison shows the contribution from background galaxies in Lupus I. We also create two color magnitude diagrams using the 2MASS and MIPS data. From these results, we can identify background galaxies and distinguish them from probable young stellar objects. The sources in our catalogs are classified based on their spectral energy distribution (SED) from 2MASS and Spitzer wavelengths to create a sample of young stellar object candidates. From 2MASS data, we create extinction maps for each region and note a strong corresponence between the extinction and the $160\:\mu$m emission. The masses we derived in each Lupus cloud from our extinction maps are compared to masses estimated from $^{13}$CO and C$^{18}$O and found to be similar to our extinction masses in some regions, but significantly different in others. Finally, based on our color-magnitude diagrams, we selected 12 of our reddest candidate young stellar objects for individual discussion. Five of the 12 appear to be newly-discovered YSOs.Comment: 15 pages, 17 figures, uses emulateapj.cls. Accepted for publication in ApJ. A version with high-quality figures can be found at http://peggysue.as.utexas.edu/SIRTF