ABSTRACT Chemical models used to study the chemical composition of the gas and the ices in the interstellar medium are based on a network of chemical reactions and associated rate coefficients. These ...reactions and rate coefficients are partially compiled from data in the literature, when available. We present in this paper kida.uva.2014, a new updated version of the kida.uva public gas-phase network first released in 2012. In addition to a description of the many specific updates, we illustrate changes in the predicted abundances of molecules for cold dense cloud conditions as compared with the results of the previous version of our network, kida.uva.2011.
The localization of transcriptional activity in specialized transcription bodies is a hallmark of gene expression in eukaryotic cells.1–3 How proteins of the transcriptional machinery come together ...to form such bodies, however, is unclear. Here, we take advantage of two large, isolated, and long-lived transcription bodies that reproducibly form during early zebrafish embryogenesis to characterize the dynamics of transcription body formation. Once formed, these transcription bodies are enriched for initiating and elongating RNA polymerase II, as well as the transcription factors Nanog and Sox19b. Analyzing the events leading up to transcription, we find that Nanog and Sox19b cluster prior to transcription. The clustering of transcription factors is sequential; Nanog clusters first, and this is required for the clustering of Sox19b and the initiation of transcription. Mutant analysis revealed that both the DNA-binding domain as well as one of the two intrinsically disordered regions of Nanog are required to organize the two bodies of transcriptional activity. Taken together, our data suggest that the clustering of transcription factors dictates the formation of transcription bodies.
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•Transcription factors cluster prior to transcription•Transcriptional activity results in the disassembly of transcription factor clusters•Nanog can recruit Sox19b as well as RNA polymerase II into transcription bodies•This organizing activity of Nanog requires its DBD as well as one of its IDRs
The localization of transcriptional activity in specialized transcription bodies is a hallmark of gene expression in eukaryotic cells. Here, Kuznetsova et al. show that the transcription factor Nanog can recruit other components of the transcriptional machinery to form such transcription bodies.
Plasma chemistry is widely used in diagnostic and research settings in sea turtles. However, plasma discolorations such as hemolysis are often not considered in data interpretation. The objectives of ...this study were to (1) evaluate the effects of moderate hemolysis on plasma electrolytes, minerals, and proteins using dry chemistry analysis (DCA) and protein electrophoresis from nesting leatherback sea turtles (Dermochelys coriacea) from Florida and to (2) establish blood analyte reference intervals. Twenty-six plasma samples with absence of hemolysis were selected and sub-divided into one non-hemolytic aliquot and an aliquot that was experimentally manipulated to mimic moderate hemolysis. Plasma samples were analyzed for hemoglobin using a handheld photometer; sodium, potassium, chloride, magnesium, calcium, phosphorus, and total protein using DCA; and protein electrophoresis. Packed cell volume and hemoglobin were measured in corresponding whole blood samples. Reference intervals were established. All analytes except calcium and pre-albumin were significantly higher and the calcium:phosphorus and albumin:globulin ratios were significantly lower in hemolytic plasma compared to non-hemolytic plasma. Alpha2-globulins and potassium were the analytes most impacted by hemolysis, averaging 3.3- and 2.0-fold higher in hemolyzed samples, respectively, indicating that (1) hemoglobin migrates into the alpha2-globulin region in this species and (2) notable intracellular potassium is released into plasma with hemolysis. Attempted conversion factors for compensation of hemolysis were considered inaccurate for 4 of 16 analytes due to non-significant regression lines. We also report that PCV provides an estimate of hemoglobin (g/L) using the formula: (2.59 × PCV) + 24.59. Given the spurious effects of hemolysis, the degree of this artifact should be reported with biochemistry data, and samples with moderate to severe hemolysis should be excluded from datasets when interpreting electrolyte, mineral, and protein results. This will ensure accurate data interpretation for individual turtles in rehabilitation or research settings and population-level data relevant to conservation-focused projects.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
A KINETIC DATABASE FOR ASTROCHEMISTRY (KIDA) Wakelam, V; Herbst, E; Loison, J-C ...
The Astrophysical journal. Supplement series,
03/2012, Letnik:
199, Številka:
1
Journal Article
Recenzirano
Odprti dostop
We present a novel chemical database for gas-phase astrochemistry. Named the KInetic Database for Astrochemistry (KIDA), this database consists of gas-phase reactions with rate coefficients and ...uncertainties that will be vetted to the greatest extent possible. Submissions of measured and calculated rate coefficients are welcome, and will be studied by experts before inclusion into the database. Besides providing kinetic information for the interstellar medium, KIDA is planned to contain such data for planetary atmospheres and for circumstellar envelopes. each year, a subset of the reactions in the database (kida.uva) will be provided as a network for the simulation of the chemistry of dense interstellar clouds with temperatures between 10 K and 300 K. We also provide a code, named Nahoon, to study the time-dependent gas-phase chemistry of zero-dimensional and one-dimensional interstellar sources.
Cosmic rays (CRs) process the matter of the interstellar medium (ISM), not only modifying the interstellar matter but also injecting chemical species in the gas phase. In this work, we study the ...effect of CRs on astrophysical polycyclic aromatic hydrocarbons (PAHs). For events in which many electrons are stripped out from the PAHs, coulomb explosion takes place and carbon chains are produced. We computed PAH multi-ionization cross sections with a collisional model. We used another model to predict the fragmentation pattern following coulomb explosion. Experimental measurements were used to assess the validity of the calculations. The production rates of carbon chains were calculated using different CR fluxes and elemental compositions, to account for the variations expected in different astrophysical environments. PAHs with a range of sizes and levels of compactness were explored. As an average over the explored PAHs, the PAH lifetime with respect to a standard interstellar CR flux is found to be on the order of a few billion years. The production rates of chains (5-15 carbons) are slightly below the H2 ionization rate ζ. In the diffuse ISM, with 10% of the available cosmic carbon locked in PAHs, this process leads to carbon chain fractional abundances at steady state, in the range of 10−15-10−14, with a confidence interval of 1 order of magnitude. It reaches 10−13 in quiescent dense clouds. This is not sufficient to explain the observed abundances of carbon chains and complex organic molecules in dense clouds.
Context. Under cosmic irradiation, the interstellar water ice mantles evolve towards a compact amorphous state. Crystalline ice amorphisation was previously monitored mainly in the keV to hundreds of ...keV ion energies. Aims. We experimentally investigate heavy ion irradiation amorphisation of crystalline ice, at high energies closer to true cosmic rays, and explore the water-ice sputtering yield. Methods. We irradiated thin crystalline ice films with MeV to GeV swift ion beams, produced at the GANIL accelerator. The ice infrared spectral evolution as a function of fluence is monitored with in-situ infrared spectroscopy (induced amorphisation of the initial crystalline state into a compact amorphous phase). Results. The crystalline ice amorphisation cross-section is measured in the high electronic stopping-power range for different temperatures. At large fluence, the ice sputtering is measured on the infrared spectra, and the fitted sputtering-yield dependence, combined with previous measurements, is quadratic over three decades of electronic stopping power. Conclusions. The final state of cosmic ray irradiation for porous amorphous and crystalline ice, as monitored by infrared spectroscopy, is the same, but with a large difference in cross-section, hence in time scale in an astrophysical context. The cosmic ray water-ice sputtering rates compete with the UV photodesorption yields reported in the literature. The prevalence of direct cosmic ray sputtering over cosmic-ray induced photons photodesorption may be particularly true for ices strongly bonded to the ice mantles surfaces, such as hydrogen-bonded ice structures or more generally the so-called polar ices.
For species reaching maturity at a range of ages or sizes, factors that influence juvenile growth and size at maturity may have lasting impacts on overall fitness. Assessing when animals reach ...maturity is especially challenging for species which are difficult to follow through time as a result of highly migratory behavior, long life spans, or both. We examined nesting female size in a reproductive assemblage of green turtles (Chelonia mydas) and loggerheads (Caretta caretta) on the east coast of Florida, USA. We used a long‐term dataset from 1982 to 2019 to estimate a minimum size at maturity interval on the basis of two standard deviations below mean female size for each species. The minimum size intervals for green turtles (81.4–89.3 cm) and loggerheads (68.1–79.1 cm) were lower than most previous estimates in the literature, many of which were simply the smallest individual ever observed. There was a significant decrease in the upper bound of the minimum size interval over the study period for both green turtles (1.6 cm) and loggerheads (4.1 cm). These shifts in size at maturity may be the result of changes in population demographics, habitat quality, and behavioral reactions to these changes. The development and periodic reassessment of robust estimators of maturity are an important part of programs centered around the monitoring and conservation of vulnerable wildlife populations.
Abstract
Physics teachers often use active learning techniques such as “clicker questions” in their lectures. We created a set of asynchronous online lectures that include clicker questions. Five ...instructors created and shared their Interactive Online Lectures for the first semester of an introductory calculus-based course. Each lecture consists of short video lecture segments interspersed with required multiple-choice clicker questions designed to help students understand the content. After submitting an answer, the student sees an explanation of why that answer is right or wrong. Instructors at five institutions used the lectures during the Fall Semester of 2020.
Context.
Ice is ubiquitous in the interstellar medium. As soon as it becomes slightly opaque in the visible, it can be seen for visual extinctions (
A
V
) above ~1.5. The
James Webb
Space Telescope ...(JWST) will observe the ice composition toward hundreds of lines of sight, covering a broad range of physical conditions in these extinct regions.
Aims.
We model the formation of the main constituents of interstellar ices, including H
2
O, CO
2
, CO, and CH
3
OH. We strive to understand what physical or chemical parameters influence the final composition of the ice and how they benchmark to what has already been observed, with the aim of applying these models to the preparation and analysis of JWST observations.
Methods.
We used the Nautilus gas-grain model, which computes the gas and ice composition as a function of time for a set of physical conditions, starting from an initial gas phase composition. All important processes (gas-phase reactions, gas-grain interactions, and grain surface processes) are included and solved with the rate equation approximation.
Results.
We first ran an astrochemical code for fixed conditions of temperature and density mapped in the cold core L429-C to benchmark the chemistry. One key parameter was revealed to be the dust temperature. When the dust temperature is higher than 12 K, CO
2
will form efficiently at the expense of H
2
O, while at temperatures below 12 K, it will not form. Whatever hypothesis we assumed for the chemistry (within realistic conditions), the static simulations failed to reproduce the observed trends of interstellar ices in our target core. In a second step, we simulated the chemical evolution of parcels of gas undergoing different physical and chemical situations throughout the molecular cloud evolution and starting a few 10
7
yr prior to the core formation (dynamical simulations). We obtained a large sample of possible ice compositions. The ratio of the different ice components seems to be approximately constant for
A
V
> 5, and in good agreement with the observations. Interestingly, we find that grain temperature and low
A
V
conditions significantly affect the production of ice, especially for CO
2
, which shows the highest variability.
Conclusions.
Our dynamical simulations satisfactorily reproduce the main trends already observed for interstellar ices. Moreover, we predict that the apparent constant ratio of CO
2
/H
2
O observed to date is probably not true for regions of low
A
V
, and that the history of the evolution of clouds plays an essential role, even prior to their formation.
Hydrogenated amorphous carbons (a-C :H) are a major component of the carbonaceous solids present in the interstellar medium. The production and existence of these grains is connected in particular ...with the balance between their photolysis, radiolysis, and hydrogenation. We perform photolytic experiments on laboratory produced interstellar a-C :H analogues to monitor and quantify the release of species and compare to relevant observations in the interstellar medium. Hydrogenated amorphous carbon analogues at low temperature are exposed to ultraviolet (UV) photons, under ultrahigh vacuum conditions. We implement the laboratory measured yields for the released species in a time dependent model to investigate the effect of the UV photon irradiation of hydrogenated amorphous carbons in a photon dominated region, and estimate the associated time scale. The UV photolysis of hydrogenated amorphous carbons leads to the production of H2 molecules and small hydrocarbons. This time scale is consistent with the estimated advection front of a photon dominated region, which replenishes it with freshly exposed material.
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