Sensitivity of Ru(bpy)_2dppz^(2+) Luminescence to DNA Defects

The luminescent characteristics of Ru(bpy)_2dppz^(2+) (dppz = dipyrido[3,2-a:2′,3′-c]phenazine), a DNA light switch, were investigated in the presence of oligonucleotides containing single base mismatches or an abasic site. In water, the ruthenium luminescence is quenched, but, bound to well matched duplex DNA, the Ru complex luminesces. Here we show that with DNAs containing a defect, rac-, Δ-, and Λ-Ru(bpy)_2dppz^(2+) exhibit significant luminescent enhancements above that with well matched DNA. In the presence of a single base mismatch, large luminescent enhancements are evident for the Δ-Ru isomer; the Λ-isomer shows particularly high luminescence bound to an oligonucleotide containing an abasic site. Similar increases are not evident with two common DNA-binding organic fluorophores, ethidium bromide and TO-PRO-3. Titrations with hairpin oligonucleotides containing a variable mismatch site show correlation between the level of luminescent enhancement and the thermodynamic destabilization associated with the mismatch. This correlation is reminiscent of that found earlier for a bulky rhodium complex that binds mismatched DNA sites through metalloinsertion, where the complex binds the DNA from the minor groove side, ejecting the mismatched bases into the major groove. Differential quenching studies with minor and major groove quenchers and time-resolved emission studies support this metalloinsertion mode for the dppz complex at the defect site. Certainly these data underscore the utility of Ru(bpy)_2dppz^(2+) as a sensitive luminescent reporter of DNA and its defects

Tidally Triggered Star Formation in Close Pairs of Galaxies: Major and Minor Interactions

We study star formation in a sample of 345 galaxies in 167 pairs and compact groups drawn from the original CfA2 Redshift Survey and from a follow-up search for companions. We construct our sample with attention to including pairs with luminosity contrast |\Delta m_R| >= 2. These 57 galaxies with |\Delta m_R| >= 2 provide a set of nearby representative cases of minor interactions, a central feature of the hierarchical galaxy formation model. Here we report the redshifts and positions of the 345 galaxies in our sample, and of 136 galaxies in apparent pairs that are superpositions. In the pairs sample as a whole, there are strong correlations between the equivalent width of the H\alpha emission line and the projected spatial and the line-of-sight velocity separation of the pair. For pairs of small luminosity contrast, |\Delta m_R| < 2, the member galaxies show a correlation between the equivalent width of H\alpha and the projected spatial separation of the pair. However, for pairs with large luminosity contrast, |\Delta m_R| >= 2, we detect no correlation between the equivalent width of H\alpha and the projected spatial separation. The relative luminosity of the companion galaxy is more important in a gravitational tidal interaction than the intrinsic luminosity of the galaxy. Central star formation across the entire pairs sample depends strongly on the luminosity ratio, |\Delta m_R|, a reasonable proxy for the mass ratio of the pair; pairs composed of similarly luminous galaxies produce the strongest bursts of star formation. Pairs with |\Delta m_R| >= 2 rarely have EW(H\alpha) >~ 70 Ang.Comment: Minor revisions following journal proof

The infrared imaging spectrograph (IRIS) for TMT: sensitivities and simulations

We present sensitivity estimates for point and resolved astronomical sources for the current design of the InfraRed Imaging Spectrograph (IRIS) on the future Thirty Meter Telescope (TMT). IRIS, with TMT's adaptive optics system, will achieve unprecedented point source sensitivities in the near-infrared (0.84 - 2.45 {\mu}m) when compared to systems on current 8-10m ground based telescopes. The IRIS imager, in 5 hours of total integration, will be able to perform a few percent photometry on 26 - 29 magnitude (AB) point sources in the near-infrared broadband filters (Z, Y, J, H, K). The integral field spectrograph, with a range of scales and filters, will achieve good signal-to-noise on 22 - 26 magnitude (AB) point sources with a spectral resolution of R=4,000 in 5 hours of total integration time. We also present simulated 3D IRIS data of resolved high-redshift star forming galaxies (1 < z < 5), illustrating the extraordinary potential of this instrument to probe the dynamics, assembly, and chemical abundances of galaxies in the early universe. With its finest spatial scales, IRIS will be able to study luminous, massive, high-redshift star forming galaxies (star formation rates ~ 10 - 100 M yr-1) at ~100 pc resolution. Utilizing the coarsest spatial scales, IRIS will be able to observe fainter, less massive high-redshift galaxies, with integrated star formation rates less than 1 M yr-1, yielding a factor of 3 to 10 gain in sensitivity compared to current integral field spectrographs. The combination of both fine and coarse spatial scales with the diffraction-limit of the TMT will significantly advance our understanding of early galaxy formation processes and their subsequent evolution into presentday galaxies.Comment: SPIE Astronomical Instrumentation 201

Substrate Binding Regulates Redox Signaling in Human DNA Primase

Generation of daughter strands during DNA replication requires the action of DNA primase to synthesize an initial short RNA primer on the single-stranded DNA template. Primase is a heterodimeric enzyme containing two domains whose activity must be coordinated during primer synthesis: an RNA polymerase domain in the small subunit (p48) and a [4Fe4S] cluster-containing C-terminal domain of the large subunit (p58C). Here we examine the redox switching properties of the [4Fe4S] cluster in the full p48/p58 heterodimer using DNA electrochemistry. Unlike with isolated p58C, robust redox signaling in the primase heterodimer requires binding of both DNA and NTPs; NTP binding shifts the p48/p58 cluster redox potential into the physiological range, generating a signal near 160 mV vs NHE. Preloading of primase with NTPs enhances catalytic activity on primed DNA, suggesting that primase configurations promoting activity are more highly populated in the NTP-bound protein. We propose that p48/p58 binding of anionic DNA and NTPs affects the redox properties of the [4Fe4S] cluster; this electrostatic change is likely influenced by the alignment of primase subunits during activity because the configuration affects the [4Fe4S] cluster environment and coupling to DNA bases for redox signaling. Thus, both binding of polyanionic substrates and configurational dynamics appear to influence [4Fe4S] redox signaling properties. These results suggest that these factors should be considered generally in characterizing signaling networks of large, multisubunit DNA-processing [4Fe4S] enzymes

The infrared imaging spectrograph (IRIS) for TMT: spectrograph design

The Infra-Red Imaging Spectrograph (IRIS) is one of the three first light instruments for the Thirty Meter Telescope (TMT) and is the only one to directly sample the diffraction limit. The instrument consists of a parallel imager and off-axis Integral Field Spectrograph (IFS) for optimum use of the near infrared (0.84um-2.4um) Adaptive Optics corrected focal surface. We present an overview of the IRIS spectrograph that is designed to probe a range of scientific targets from the dynamics and morphology of high-z galaxies to studying the atmospheres and surfaces of solar system objects, the latter requiring a narrow field and high Strehl performance. The IRIS spectrograph is a hybrid system consisting of two state of the art IFS technologies providing four plate scales (4mas, 9mas, 25mas, 50mas spaxel sizes). We present the design of the unique hybrid system that combines the power of a lenslet spectrograph and image slicer spectrograph in a configuration where major hardware is shared. The result is a powerful yet economical solution to what would otherwise require two separate 30m-class instruments.Comment: 15 pages, 11 figure

Prospects for measuring supermassive black hole masses with future extremely large telescopes

The next generation of giant-segmented mirror telescopes ($>$ 20 m) will enable us to observe galactic nuclei at much higher angular resolution and sensitivity than ever before. These capabilities will introduce a revolutionary shift in our understanding of the origin and evolution of supermassive black holes by enabling more precise black hole mass measurements in a mass range that is unreachable today. We present simulations and predictions of the observations of nuclei that will be made with the Thirty Meter Telescope (TMT) and the adaptive optics assisted integral-field spectrograph IRIS, which is capable of diffraction-limited spectroscopy from $Z$ band (0.9 $\mu$m) to $K$ band (2.2 $\mu$m). These simulations, for the first time, use realistic values for the sky, telescope, adaptive optics system, and instrument, to determine the expected signal-to-noise ratio of a range of possible targets spanning intermediate mass black holes of $\sim10^4$ \msun to the most massive black holes known today of $>10^{10}$ $M_\odot$. We find that IRIS will be able to observe Milky Way-mass black holes out the distance of the Virgo cluster, and will allow us to observe many more brightest cluster galaxies where the most massive black holes are thought to reside. We also evaluate how well the kinematic moments of the velocity distributions can be constrained at the different spectral resolutions and plate scales designed for IRIS. We find that a spectral resolution of $\sim8000$ will be necessary to measure the masses of intermediate mass black holes. By simulating the observations of galaxies found in SDSS DR7, we find that over $10^5$ massive black holes will be observable at distances between $0.005 < z < 0.18$ with the estimated sensitivity and angular resolution provided by access to $Z$-band (0.9 $\mu$m) spectroscopy from IRIS and the TMT adaptive optics system. (Abridged)Comment: 19 pages, 20 figures, accepted to A

Tidally-Triggered Star Formation in Close Pairs of Galaxies

We analyze new optical spectra of a sample of 502 galaxies in close pairs and n-tuples, separated by <= 50/h kpc. We extracted the sample objectively from the CfA2 redshift survey, without regard to the surroundings of the tight systems. We probe the relationship between star formation and the dynamics of the systems of galaxies. The equivalent widths of H\alpha (EW(H\alpha) and other emission lines anti-correlate strongly with pair spatial separation (\Delta D) and velocity separation. We use the measured EW(H\alpha) and the starburst models of Leitherer et al. to estimate the time since the most recent burst of star for- mation began for each galaxy. In the absence of a large contribution from an old stellar population to the continuum around H\alpha, the observed \Delta D -- EW(H\alpha) correlation signifies that starbursts with larger separations on the sky are, on average, older. By matching the dynamical timescale to the burst timescale, we show that the data support a simple picture in which a close pass initiates a starburst; EW(H\alpha) decreases with time as the pair separation increases, accounting for the anti-correlation. This picture leads to a method for measuring the duration and the initial mass function of interaction-induced starbursts: our data are compatible with the starburst and orbit models in many respects, as long as the starburst lasts longer than \sim10^8 years and the delay between the close pass and the initiation of the starburst is less than a few \times 10^7 years. If there is no large contribution from an old stellar population to the continuum around H\alpha the Miller-Scalo and cutoff (M <= 30 M_\sun) Salpeter initial mass functions fit the data much better than a standard Salpeter IMF. (Abridged.)Comment: 43 pages, 22 figures, to appear in the ApJ; we correct an error which had minor effects on numerical values in the pape

C-terminal methylation of truncated neuropeptides: An enzyme- assistedextraction artifact involving methanol

Neuropeptides are the largest class of signaling molecules used by nervous systems. Today, neuropeptidediscovery commonly involves chemical extraction from a tissue source followed by mass spectrometriccharacterization. Ideally, the extraction procedure accurately preserves the sequence and any inher-ent modifications of the native peptides. Here, we present data showing that this is not always true.Specifically, we present evidence showing that, in the lobster Homarus americanus, the orcokinin fam-ily members, NFDEIDRSGFG-OMe and SSEDMDRLGFG-OMe, are non-native peptides generated fromfull-length orcokinin precursors as the result of a highly selective peptide modification (peptide trun-cation with C-terminal methylation) that occurs during extraction. These peptides were observed byMALDI-FTMS and LC-Q-TOFMS analyses when eyestalk ganglia were extracted in a methanolic solvent,but not when tissues were dissected, co-crystallized with matrix, and analyzed directly with methanolexcluded from the sample preparation. The identity of NFDEIDRSGFG-OMe was established using MALDI-FTMS/SORI-CID, LC-Q-TOFMS/MS, and comparison with a peptide standard. Extraction substitutingdeuterated methanol for methanol confirmed that the latter is the source of the C-terminal methyl group,and MS/MS confirmed the C-terminal localization of the added CD3. Surprisingly, NFDEIDRSGFG-OMe isnot produced via a chemical acid-catalyzed esterification. Instead, the methylated peptide appears toresult from proteolytic truncation in the presence of methanol, as evidenced by a reduction in conver-sion with the addition of a protease-inhibitor cocktail; heat effectively eliminated the conversion. Thisunusual and highly specific extraction-derived peptide conversion exemplifies the need to consider bothchemical and biochemical processes that may modify the structure of endogenous neuropeptides. © 2013 The Authors. Published by Elsevier Inc. All rights reserved