Context. Deuterium fractionation has been used to study the thermal history of prestellar environments. Their formation pathways trace different regions of the disk and may shed light into the ...physical structure of the disk, including locations of important features for planetary formation. Aims. We aim to constrain the radial extent of the main deuterated species; we are particularly interested in spatially characterizing the high and low temperature pathways for enhancing deuteration of these species. Methods. We observed the disk surrounding the Herbig Ae star HD 163296 using ALMA in Band 6 and obtained resolved spectral imaging data of DCO+ (J = 3 − 2), DCN (J = 3 − 2) and N2D+ (J = 3 − 2) with synthesized beam sizes of 0.̋53 × 0.̋42, 0.̋53 × 0.̋42, and 0.̋50 × 0.̋39, respectively. We adopted a physical model of the disk from the literature and use the 3D radiative transfer code LIME to estimate an excitation temperature profile for our detected lines. We modeled the radial emission profiles of DCO+, DCN, and N2D+, assuming their emission is optically thin, using a parametric model of their abundances and our excitation temperature estimates. Results. DCO+ can be described by a three-region model with constant-abundance rings centered at 70 AU, 150 AU, and 260 AU. The DCN radial profile peaks at about 60 AU and N2D+ is seen in a ring at 160 AU. Simple models of both molecules using constant abundances reproduce the data. Assuming reasonable average excitation temperatures for the whole disk, their disk-averaged column densities (and deuterium fractionation ratios) are 1.6–2.6×1012 cm-2 (0.04–0.07), 2.9–5.2×1012 cm-2 (~0.02), and 1.6–2.5×1011 cm-2 (0.34–0.45) for DCO+, DCN, and N2D+, respectively. Conclusions. Our simple best-fit models show a correlation between the radial location of the first two rings in DCO+ and the DCN and N2D+ abundance distributions that can be interpreted as the high and low temperature deuteration pathways regimes. The origin of the third DCO+ ring at 260 AU is unknown but may be due to a local decrease of ultraviolet opacity allowing the photodesorption of CO or due to thermal desorption of CO as a consequence of radial drift and settlement of dust grains. The derived Df values agree with previous estimates of 0.05 for DCO+/HCO+ and 0.02 for DCN/HCN in HD 163296, and 0.3−0.5 for N2D+/N2H+ in AS 209, a T Tauri disk. The high N2D+/N2H+ confirms N2D+ as a good candidate for tracing ionization in the cold outer disk.
Context. The gas and dust in circumstellar disks provide the raw materials to form planets. The study of organic molecules and their building blocks in such disks offers insight into the origin of ...the prebiotic environment of terrestrial planets. Aims. We aim to determine the distribution of formaldehyde, H2CO, in the disk around HD 163296 to assess the contribution of gas- and solid-phase formation routes of this simple organic. Methods. Three formaldehyde lines were observed (H2CO 303–202, H2CO 322–221, and H2CO 321–220) in the protoplanetary disk around the Herbig Ae star HD 163296 with ALMA at ~0.5″ (60 AU) spatial resolution. Different parameterizations of the H2CO abundance were compared to the observed visibilities, using either a characteristic temperature, a characteristic radius or a radial power law index to describe the H2CO chemistry. Similar models were applied to ALMA Science Verification data of C18O. In each scenario, χ2 minimization on the visibilities was used to determine the best-fit model in each scenario. Results. H2CO 303–202 was readily detected via imaging, while the weaker H2CO 322–221 and H2CO 321–220 lines required matched filter analysis to detect. H2CO is present throughout most of the gaseous disk, extending out to ~550 AU. An apparent 50 AU inner radius of the H2CO emission is likely caused by an optically thick dust continuum. The H2CO radial intensity profile shows a peak at ~100 AU and a secondary bump at ~300 AU, suggesting increased production in the outer disk. In all modeling scenarios, fits to the H2CO data show an increased abundance in the outer disk. The overall best-fit H2CO model shows a factor of two enhancement beyond a radius of 270 ± 20 AU, with an inner abundance (relative to H2) of 2 − 5 × 10-12. The H2CO emitting region has a lower limit on the kinetic temperature of T> 20 K. The C18O modeling suggests an order of magnitude depletion of C18O in the outer disk and an abundance of 4 − 12 × 10-8 in the inner disk. Conclusions. There is a desorption front seen in the H2CO emission that roughly coincides with the outer edge of the 1.3 millimeter continuum. The increase in H2CO outer disk emission could be a result of hydrogenation of CO ices on dust grains that are then sublimated via thermal desorption or UV photodesorption. Alternatively, there could be more efficient gas-phase production of H2CO beyond ~300 AU if CO is photodisocciated in this region.
Context. In planet-forming disks, deuterated species like DCO+ often show up in rings. Two chemical formation routes contribute: cold deuteration at temperatures below 30 K and warm deuteration at ...temperatures up to 80 K. Aims. We aim to reproduce the DCO+ emission in the disk around HD 163296 using a simple 2D chemical model for the formation of DCO+ through the cold deuteration channel and a parametric treatment of the warm deuteration channel. Methods. We use data from ALMA in band 6 to obtain a resolved spectral imaging data cube of the DCO+ J = 3–2 line in HD 163296 with a synthesized beam of 0.′′53 × 0.′′42. We adopt a physical structure of the disk from the literature that reproduces the spectral energy distribution. We then apply a simplified chemical network for the formation of DCO+ that uses the physical structure of the disk as parameters along with a CO abundance profile, a constant HD abundance, and a constant ionization rate. We model the contribution of the warm deuteration channel with two parameters: an effective activation temperature and a constant abundance. Finally, from the resulting DCO+ abundances, we calculate the non-LTE emission using the 3D radiative transfer code LIME. Results. The observed DCO+ emission is reproduced by a model with cold deuteration producing abundances up to 1.6 × 10−11. Warm deuteration, at a constant abundance of 3.2 × 10−12, becomes fully effective below 32 K and tapers off at higher temperatures, reproducing the lack of DCO+ inside 90 AU. Throughout the DCO+ emitting zone a CO abundance of 2 × 10−7 is found, with ~99% of it frozen out below 19 K. At radii where both cold and warm deuteration are active, warm deuteration contributes up to 20% of DCO+, consistent with detailed chemical models. The decrease in DCO+ at large radii is attributed to a temperature inversion at 250 AU, which raises temperatures above values where cold deuteration operates. Increased photodesorption may also limit the radial extent of DCO+. The corresponding return of the DCO+ layer to the midplane, together with a radially increasing ionization fraction, reproduces the local DCO+ emission maximum at ~260 AU. Conclusions. We can successfully reproduce the observed morphology of DCO+ at large radii by only considering the dependence on temperature in the chemical reactions that produce it. Predictions on the location of DCO+ within the disk from simple models depend strongly on the gas temperature. Outer disk temperature inversions, expected when grains decouple from the gas and drift inward, can lead to secondary maxima in DCO+ emission and a reduction of its radial extent. This can appear as an outer emission ring, and can be used to identify a second CO desorption front.
Selenoprotein Gene Nomenclature Gladyshev, Vadim N.; Arnér, Elias S.; Berry, Marla J. ...
The Journal of biological chemistry,
11/2016, Volume:
291, Issue:
46
Journal Article
Peer reviewed
Open access
The human genome contains 25 genes coding for selenocysteine-containing proteins (selenoproteins). These proteins are involved in a variety of functions, most notably redox homeostasis. Selenoprotein ...enzymes with known functions are designated according to these functions: TXNRD1, TXNRD2, and TXNRD3 (thioredoxin reductases), GPX1, GPX2, GPX3, GPX4, and GPX6 (glutathione peroxidases), DIO1, DIO2, and DIO3 (iodothyronine deiodinases), MSRB1 (methionine sulfoxide reductase B1), and SEPHS2 (selenophosphate synthetase 2). Selenoproteins without known functions have traditionally been denoted by SEL or SEP symbols. However, these symbols are sometimes ambiguous and conflict with the approved nomenclature for several other genes. Therefore, there is a need to implement a rational and coherent nomenclature system for selenoprotein-encoding genes. Our solution is to use the root symbol SELENO followed by a letter. This nomenclature applies to SELENOF (selenoprotein F, the 15-kDa selenoprotein, SEP15), SELENOH (selenoprotein H, SELH, C11orf31), SELENOI (selenoprotein I, SELI, EPT1), SELENOK (selenoprotein K, SELK), SELENOM (selenoprotein M, SELM), SELENON (selenoprotein N, SEPN1, SELN), SELENOO (selenoprotein O, SELO), SELENOP (selenoprotein P, SeP, SEPP1, SELP), SELENOS (selenoprotein S, SELS, SEPS1, VIMP), SELENOT (selenoprotein T, SELT), SELENOV (selenoprotein V, SELV), and SELENOW (selenoprotein W, SELW, SEPW1). This system, approved by the HUGO Gene Nomenclature Committee, also resolves conflicting, missing, and ambiguous designations for selenoprotein genes and is applicable to selenoproteins across vertebrates.
Synaptic vesicle protein 2A (SV2A) is an integral membrane protein necessary for the proper function of the central nervous system and is associated to the physiopathology of epilepsy. SV2A is the ...molecular target of the anti-epileptic drug levetiracetam and its racetam analogs. The racetam binding site in SV2A and the non-covalent interactions between racetams and SV2A are currently unknown; therefore, an in silico study was performed to explore these issues. Since SV2A has not been structurally characterized with X-ray crystallography or nuclear magnetic resonance, a three-dimensional (3D) model was built. The model was refined by performing a molecular dynamics simulation (MDS) and the interactions of SV2A with the racetams were determined by docking studies. A reliable 3D model of SV2A was obtained; it reached structural equilibrium during the last 15 ns of the MDS (50 ns) with remaining structural motions in the N-terminus and long cytoplasmic loop. The docking studies revealed that hydrophobic interactions and hydrogen bonds participate importantly in ligand recognition within the binding site. Residues T456, S665, W666, D670 and L689 were important for racetam binding within the trans-membrane hydrophilic core of SV2A. Identifying the racetam binding site within SV2A should facilitate the synthesis of suitable radio-ligands to study treatment response and possibly epilepsy progression.
We present the first measurements of the electroluminescence response to the emission of single electrons in a two-phase noble gas detector. Single ionization electrons generated in liquid xenon are ...detected in a thin gas layer during the 31-day background run of the ZEPLIN-II experiment, a two-phase xenon detector for WIMP dark matter searches. Both the pressure dependence and magnitude of the single electron response are in agreement with previous measurements of electroluminescence yield in xenon. We discuss different photoionization processes as possible cause for the sample of single electrons studied in this work. This observation may have implications for the design and operation of future large-scale two-phase systems.
Respiration hydrogen analyzer H
2
Rate has been used in pilot examinations of a group of students. This method for noninvasive diagnosis of small intestinal diseases promotes proper interpretation of ...the results. Free hydrogen level in the exhaled air increases as a result of lactulose (diagnostic agent) cleavage by enteric microflora within about 3 h. Based on the experimental data, the main groups with characteristic curves reflecting the time course of hydrogen concentrations have been distinguished. Excessive bacterial colonization of the intestine can correspond to emergence of characteristic peaks of hydrogen concentrations in the curve. Hydrogen concentrations in exhaled air can also be analyzed to evaluate the rate of the substrate propulsion in the middle compartment of the intestine.
This paper describes the development of an immunosensor coupled to glassy carbon electrode (GCE) modified with multiwall carbon nanotubes (MWCNT) (CNT-GCE) integrated with microfluidic systems for ...rapid and sensitive quantification of prostate specific antigen (PSA) in human serum samples. Mouse monoclonal (5G6) to PSA antibodies were immobilized on a rotating disk. PSA in the serum sample are allowed to react immunologically with the immobilized anti-tPSA and horseradish peroxidase (HRP) enzyme-labeled second antibodies specific to PSA. HRP, in the presence of hydrogen peroxide (H
2O
2) catalyzes the oxidation of 4-
tert-butylcatechol (4-TBC), whose back electrochemical reduction was detected on CNT-GCE at −0.15
V. The electrochemical detection can be done within 1
min and total assay time was 30
min. The calculated detection limits for electrochemical detection and the ELISA procedure are 0.08 and 0.5
μg
L
−1, respectively and the intra- and inter-assay coefficients of variation were below 4.5%. The electrochemical immunosensor showed higher sensitivity and lower time consumed than the standard spectrophotometric detection ELISA method, which shows potential for detecting PSA in clinical diagnosis.
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