Kevin M. Flaherty

Three-Dimensional Structure of Recoverin, a Calcium Sensor in Vision

Recoverin, a recently discovered member of the EF hand superfamily, serves as a calcium sensor in vision. We report here the crystal structure of recombinant unmyristoylated recoverin at 1.9 A resolution. The four EF hands of the protein are arranged in a compact array that contrasts with the dumbbell shape of calmodulin and troponin C. A calcium ion is bound to EF hand 3, while EF hand 2 can bind samarium but not calcium in this crystal form. The other two EF hands have novel structural features that prevent or impair calcium binding. A concave hydrophobic surface formed by EF hands 1 and 2 may participate in the read out of calcium signals by recoverin and its homologs.

Infrared Extinction toward Nearby Star-forming Regions

We present an independent estimate of the interstellar extinction law for the Spitzer IRAC bands, as well as a first attempt at extending the law to the 24 μm MIPS band. The source data for these measurements are observations of five nearby star-forming regions: the Orion A cloud, NGC 2068/2071, NGC 2024/2023, Serpens, and Ophiuchus. Color excess ratios E/E were measured for stars without infrared excess dust emission from circumstellar disks/envelopes. For four of these five regions, the extinction laws are similar at all wavelengths and differ systematically from a previous determination of the extinction law, which was dominated by the diffuse ISM, derived for the IRAC bands. This difference could be due to the difference in the dust properties of the dense molecular clouds observed here and those of the diffuse ISM. The extinction law at longer wavelengths toward the Ophiuchus region lies between that to the other four regions studied here and that for the ISM. In addition, we extended our extinction law determination to 24 μm for Serpens and NGC 2068/2071 using Spitzer MIPS data. We compare these results against several ISO extinction law determinations, although in each case there are assumptions which make absolute comparison uncertain. However, our work confirms a relatively flatter extinction curve from 4 to 8 μm than the previously assumed standard, as noted by all of these recent studies. The extinction law at 24 μm is consistent with previous measurements and models, although there are relatively large uncertainties.

THE SPITZER SPACE TELESCOPE SURVEY OF THE ORION A AND B MOLECULAR CLOUDS. I. A CENSUS OF DUSTY YOUNG STELLAR OBJECTS AND A STUDY OF THEIR MID-INFRARED VARIABILITY

We present a survey of the Orion A and B molecular clouds undertaken with the IRAC and MIPS instruments on board Spitzer. In total, five distinct fields were mapped, covering 9 deg^2 in five mid-IR bands spanning 3-24 μm. The survey includes the Orion Nebula Cluster, the Lynds 1641, 1630, and 1622 dark clouds, and the NGC 2023, 2024, 2068, and 2071 nebulae. These data are merged with the Two Micron All Sky Survey point source catalog to generate a catalog of eight-band photometry. We identify 3479 dusty young stellar objects (YSOs) in the Orion molecular clouds by searching for point sources with mid-IR colors indicative of reprocessed light from dusty disks or infalling envelopes. The YSOs are subsequently classified on the basis of their mid-IR colors and their spatial distributions are presented. We classify 2991 of the YSOs as pre-main-sequence stars with disks and 488 as likely protostars. Most of the sources were observed with IRAC in two to three epochs over six months; we search for variability between the epochs by looking for correlated variability in the 3.6 and 4.5 μm bands. We find that 50% of the dusty YSOs show variability. The variations are typically small (~0.2 mag) with the protostars showing a higher incidence of variability and larger variations. The observed correlations between the 3.6, 4.5, 5.8, and 8 μm variability suggests that we are observing variations in the heating of the inner disk due to changes in the accretion luminosity or rotating accretion hot spots.

Lysine 71 of the chaperone protein Hsc70 Is essential for ATP hydrolysis.

It has been proposed that lysine 71 of the bovine 70-kDa heat shock cognate protein might participate in catalysis of ATP hydrolysis by stabilizing an H2O molecule or an OH− ion for nucleophilic attack on the γ-phosphate of the nucleotide (Flaherty, K. M., Wilbanks, S. M., DeLuca-Flaherty, C., and McKay, D. B. (1994) J. Biol. Chem. 12899-12907; Wilbanks, S. M., DeLuca-Flaherty, C., and McKay, D. B. (1994) J. Biol. Chem. 269, 12893-12898). To test this hypothesis, lysine 71 of the ATPase fragment 70-kDa heat shock cognate protein has been mutated to glutamic acid, methionine, and alanine; and the kinetic and structural properties of the mutant proteins have been determined. All three mutant proteins are devoid of measurable ATP hydrolysis activity. Crystal structures of the mutant proteins have been determined to a resolution of 1.7 Å; all three have ATP in the nucleotide binding site. These data identify lysine 71 as a residue that is essential for chemical hydrolysis of ATP.

WEAK TURBULENCE IN THE HD 163296 PROTOPLANETARY DISK REVEALED BY ALMA CO OBSERVATIONS

Turbulence can transport angular momentum in protoplanetary disks and influence the growth and evolution of planets. With spatially and spectrally resolved molecular emission line measurements provided by (sub)millimeter interferometric observations, it is possible to directly measure non-thermal motions in the disk gas that can be attributed to this turbulence. We report a new constraint on the turbulence in the disk around HD 163296, a nearby young A star, determined from ALMA Science Verification observations of four CO emission lines (the CO(3-2), CO(2-1), 13CO(2-1), and C18O(2-1) transitions). The different optical depths for these lines permit probes of non-thermal line-widths at a range of physical conditions (temperature and density) and depths into the disk interior. We derive stringent limits on the non-thermal motions in the upper layers of the outer disk such that any contribution to the line-widths from turbulence is 30AU) disk than has been previously considered.

IN-SYNC. II. VIRIAL STARS FROM SUBVIRIAL CORES—THE VELOCITY DISPERSION OF EMBEDDED PRE-MAIN-SEQUENCE STARS IN NGC 1333

The initial velocity dispersion of newborn stars is a major unconstrained aspect of star formation theory. Using near-infrared spectra obtained with the APOGEE spectrograph, we show that the velocity dispersion of young (1-2 Myr) stars in NGC 1333 is 0.92 ± 0.12 km s^(–1) after correcting for measurement uncertainties and the effect of binaries. This velocity dispersion is consistent with the virial velocity of the region and the diffuse gas velocity dispersion, but significantly larger than the velocity dispersion of the dense, star-forming cores, which have a subvirial velocity dispersion of 0.5 km s^(–1). Since the NGC 1333 cluster is dynamically young and deeply embedded, this measurement provides a strong constraint on the initial velocity dispersion of newly formed stars. We propose that the difference in velocity dispersion between stars and dense cores may be due to the influence of a 70 μG magnetic field acting on the dense cores or be the signature of a cluster with initial substructure undergoing global collapse.

EVIDENCE FOR DYNAMICAL CHANGES IN A TRANSITIONAL PROTOPLANETARY DISK WITH MID-INFRARED VARIABILITY

We present multi-epoch Spitzer Space Telescope observations of the transitional disk LRLL 31 in the 2-3 Myr old star-forming region IC 348. Our measurements show remarkable mid-infrared variability on timescales as short as one week. The infrared continuum emission exhibits systematic wavelength-dependent changes that suggest corresponding dynamical changes in the inner disk structure and variable shadowing of outer disk material. We propose several possible sources for the structural changes, including a variable accretion rate or a stellar or planetary companion embedded in the disk. Our results indicate that variability studies in the infrared can provide important new constraints on protoplanetary disk behavior.

YOUNG STELLAR OBJECTS IN LYNDS 1641: DISKS, ACCRETION, AND STAR FORMATION HISTORY

We investigate the young stellar objects (YSOs) in the Lynds 1641 (L1641) cloud using multi-wavelength data including Spitzer, WISE, the Two Micron All Sky Survey, and XMM covering similar to 1390 YSOs across a range of evolutionary stages. In addition, we targeted a sub-sample of YSOs for optical spectroscopy with the MMT/Hectospec and the MMT/Hectochelle. We use these data, along with archival photometric data, to derive spectral types, extinction values, masses, ages, and accretion rates. We obtain a disk fraction of similar to 50% in L1641. The disk frequency is almost constant as a function of stellar mass with a slight peak at log(M-*/M-circle dot) approximate to -0.25. The analysis of multi-epoch spectroscopic data indicates that the accretion variability of YSOs cannot explain the two orders of magnitude of scatter for YSOs with similar masses. Forty-six new transition disk (TD) objects are confirmed in this work, and we find that the fraction of accreting TDs is lower than for optically thick disks (40%-45% versus 77%-79%, respectively). We confirm our previous result that the accreting TDs have a median accretion rate similar to normal optically thick disks. We confirm that two star formation modes (isolated versus clustered) exist in L1641. We find that the diskless YSOs are statistically older than the YSOs with optically thick disks and the TD objects have a median age that is intermediate between those of the other two populations. We tentatively study the star formation history in L1641 based on the age distribution and find that star formation started to be active 2-3 Myr ago.

Infrared Variability of Evolved Protoplanetary Disks: Evidence for Scale Height Variations in the Inner Disk

We present the results of a multi-wavelength multi-epoch survey of five evolved protoplanetary disks in the IC 348 cluster that show significant infrared variability. Using 3-8 {mu}m and 24 {mu}m photometry along with 5-40 {mu}m spectroscopy from the Spitzer Space Telescope, as well as ground-based 0.8-5 {mu}m spectroscopy, optical spectroscopy, and near-infrared photometry, covering timescales of days to years, we examine the variability in the disk, stellar, and accretion flux. We find substantial variations (10%-60%) at all infrared wavelengths on timescales of weeks to months for all of these young stellar objects. This behavior is not unique when compared to other cluster members and is consistent with changes in the structure of the inner disk, most likely scale height fluctuations on a dynamical timescale. Previous observations, along with our near-infrared photometry, indicate that the stellar fluxes are relatively constant; stellar variability does not appear to drive the large changes in the infrared fluxes. Based on our near-infrared spectroscopy of the Pa{beta} and Br{gamma} lines we find that the accretion rates are variable in most of the evolved disks but the overall rates are probably too small to cause the infrared variability. We discuss other possible physical causes for the variability,morexa0» including the influence of a companion, magnetic fields threading the disk, and X-ray flares.«xa0less

Young Stellar Object VARiability (YSOVAR): Long Timescale Variations in the Mid-infrared

The YSOVAR (Young Stellar Object VARiability) Spitzer Space Telescope observing program obtained the first extensive mid-infrared (3.6 and 4.5 μm) time series photometry of the Orion Nebula Cluster plus smaller footprints in 11 other star-forming cores (AFGL 490, NGC 1333, Mon R2, GGD 12-15, NGC 2264, L1688, Serpens Main, Serpens South, IRAS 20050+2720, IC 1396A, and Ceph C). There are ~29,000 unique objects with light curves in either or both IRAC channels in the YSOVAR data set. We present the data collection and reduction for the Spitzer and ancillary data, and define the standard sample on which we calculate statistics, consisting of fast cadence data, with epochs roughly twice per day for ~40 days. We also define a standard sample of members consisting of all the IR-selected members and X-ray-selected members. We characterize the standard sample in terms of other properties, such as spectral energy distribution shape. We use three mechanisms to identify variables in the fast cadence data—the Stetson index, a χ^2 fit to a flat light curve, and significant periodicity. We also identified variables on the longest timescales possible of six to seven years by comparing measurements taken early in the Spitzer mission with the mean from our YSOVAR campaign. The fraction of members in each cluster that are variable on these longest timescales is a function of the ratio of Class I/total members in each cluster, such that clusters with a higher fraction of Class I objects also have a higher fraction of long-term variables. For objects with a YSOVAR-determined period and a [3.6]-[8] color, we find that a star with a longer period is more likely than those with shorter periods to have an IR excess. We do not find any evidence for variability that causes [3.6]-[4.5] excesses to appear or vanish within our data set; out of members and field objects combined, at most 0.02% may have transient IR excesses.