Laboratory Determination of the Infrared Band Strengths of Pyrene Frozen in Water Ice: Implications for the Composition of Interstellar Ices

Broad infrared emission features (e.g., at 3.3, 6.2, 7.7, 8.6, and 11.3 microns) from the gas phase interstellar medium have long been attributed to polycyclic aromatic hydrocarbons (PAHs). A significant portion (10%-20%) of the Milky Way's carbon reservoir is locked in PAH molecules, which makes their characterization integral to our understanding of astrochemistry. In molecular clouds and the dense envelopes and disks of young stellar objects (YSOs), PAHs are expected to be frozen in the icy mantles of dust grains where they should reveal themselves through infrared absorption. To facilitate the search for frozen interstellar PAHs, laboratory experiments were conducted to determine the positions and strengths of the bands of pyrene mixed with H2O and D2O ices. The D2O mixtures are used to measure pyrene bands that are masked by the strong bands of H2O, leading to the first laboratory determination of the band strength for the CH stretching mode of pyrene in water ice near 3.25 microns. Our infrared band strengths were normalized to experimentally determined ultraviolet band strengths, and we find that they are generally ~50% larger than those reported by Bouwman et al. based on theoretical strengths. These improved band strengths were used to reexamine YSO spectra published by Boogert et al. to estimate the contribution of frozen PAHs to absorption in the 5-8 micron spectral region, taking into account the strength of the 3.25 micron CH stretching mode. It is found that frozen neutral PAHs contain 5%-9% of the cosmic carbon budget, and account for 2%-9% of the unidentified absorption in the 5-8 micron region.Comment: Accepted for publication in ApJ on 14 Feb 201

Reduced production of bacterial membrane vesicles predicts mortality in ST45/USA600 methicillin-resistant Staphylococcus aureus bacteremia

Immune biomarkers can stratify mortality risk in staphylococcal bacteremia. Microbial biomarkers may provide more consistent signals during early infection. We demonstrate that in ST45/USA600 bacteremia, bacterial membrane vesicle production in vitro predicts clinical mortality (773 vs. 116 RFU, survivors vs. decedents, p \u3c 0.0001). Using a threshold of 301 relative fluorescence units (RFU), the sensitivity and specificity of the membrane vesicles to predict mortality are 78% and 90%, respectively. This platform is facile, scalable and can be integrated into clinical microbiology lab workflows

The impact of recent advances in laboratory astrophysics on our understanding of the cosmos

An emerging theme in modern astrophysics is the connection between astronomical observations and the underlying physical phenomena that drive our cosmos. Both the mechanisms responsible for the observed astrophysical phenomena and the tools used to probe such phenomena—the radiation and particle spectra we observe—have their roots in atomic, molecular, condensed matter, plasma, nuclear and particle physics. Chemistry is implicitly included in both molecular and condensed matter physics. This connection is the theme of the present report, which provides a broad, though non-exhaustive, overview of progress in our understanding of the cosmos resulting from recent theoretical and experimental advances in what is commonly called laboratory astrophysics. This work, carried out by a diverse community of laboratory astrophysicists, is increasingly important as astrophysics transitions into an era of precise measurement and high fidelity modeling

Cooperative Interaction of Transcription Termination Factors with the RNA Polymerase II C-terminal Domain

Phosphorylation of the C-terminal domain of RNA polymerase II controls the co-transcriptional assembly of RNA processing and transcription factors. Recruitment relies on conserved CTDinteracting domains that recognize different CTD phosphoisoforms during the transcription cycle, but the molecular basis for their specificity remains unclear. We show that the CTD-interacting domains of two transcription termination factors, Rtt103 and Pcf11, achieve high affinity and specificity both by specifically recognizing the phosphorylated CTD and by cooperatively binding to neighboring CTD repeats. Single amino acid mutations at the protein-protein interface abolish cooperativity and affect recruitment at the 3′-end processing site in vivo. We suggest that this cooperativity provides a signal-response mechanism to ensure that its action is confined only to proper polyadenylation sites where Serine 2 phosphorylation density is highest

Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress

RNA-binding proteins play a key role in shaping gene expression profiles during stress, however, little is known about the dynamic nature of these interactions and how this influences the kinetics of gene expression. To address this, we developed kinetic cross-linking and analysis of cDNAs (\u3c7CRAC), an ultraviolet cross-linking method that enabled us to quantitatively measure the dynamics of protein\u2013RNA interactions in vivo on a minute time-scale. Here, using \u3c7CRAC we measure the global RNA-binding dynamics of the yeast transcription termination factor Nab3 in response to glucose starvation. These measurements reveal rapid changes in protein\u2013RNA interactions within 1\u2009min following stress imposition. Changes in Nab3 binding are largely independent of alterations in transcription rate during the early stages of stress response, indicating orthogonal transcriptional control mechanisms. We also uncover a function for Nab3 in dampening expression of stress-responsive genes. \u3c7CRAC has the potential to greatly enhance our understanding of in vivo dynamics of protein\u2013RNA interactions

Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1

RNA polymerase II synthesizes a diverse set of transcripts including both protein-coding and non-coding RNAs. One major difference between these two classes of transcripts is the mechanism of termination. Messenger RNA transcripts terminate downstream of the coding region in a process that is coupled to cleavage and polyadenylation reactions. Non-coding transcripts like Saccharomyces cerevisiae snoRNAs terminate in a process that requires the RNA–binding proteins Nrd1, Nab3, and Sen1. We report here the transcriptome-wide distribution of these termination factors. These data sets derived from in vivo protein–RNA cross-linking provide high-resolution definition of non-poly(A) terminators, identify novel genes regulated by attenuation of nascent transcripts close to the promoter, and demonstrate the widespread occurrence of Nrd1-bound 3′ antisense transcripts on genes that are poorly expressed. In addition, we show that Sen1 does not cross-link efficiently to many expected non-coding RNAs but does cross-link to the 3′ end of most pre–mRNA transcripts, suggesting an extensive role in mRNA 3′ end formation and/or termination

Planned geological investigations of the Europa Clipper mission

Geological investigations planned for the Europa Clipper mission will examine the formation, evolution, and expression of geomorphic structures found on the surface. Understanding geologic features, their formation, and any recent activity are key inputs in constraining Europa’s potential for habitability. In addition to providing information about the moon’s habitability, the geologic study of Europa is compelling in and of itself. Here we provide a high-level, cross-instrument, and cross-discipline overview of the geologic investigations planned within the Europa Clipper mission. Europa’s fascinating collection of ice-focused geology provides an unparalleled opportunity to investigate the dynamics of icy shells, ice-ocean exchange processes, and global-scale tectonic and tidal stresses. We present an overview of what is currently known about the geology of Europa, from global to local scales, highlighting outstanding issues and open questions, and detailing how the Europa Clipper mission will address them. We describe the mission’s strategy for searching for and characterizing current activity in the form of possible active plumes, thermal anomalies, evidence for surface changes, and extremely fresh surface exposures. The complementary and synergistic nature of the data sets from the various instruments and their integration will be key to significantly advancing our understanding of Europa’s geology