A Simple Bioluminescent Method for Measuring D-Amino Acid Oxidase Activity

D-Amino acid oxidase (DAO) plays important roles in regulating D-amino acid neurotransmitters and was recently identified as a key enzyme integral to hydrogen sulfide production from D-Cys. We report here the development of a simple biocompatible, bioluminescent method for measuring DAO activity based on the highly selective condensation of D-Cys with 6-hydroxy-2-cyanobenzothiazole (CBT-OH) to form D-luciferin

Eye lens β-crystallins are predicted by native ion mobility-mass spectrometry and computations to form compact higher-ordered heterooligomers

Eye lens crystallin proteins maintain the refractive properties of the lens but are not replaced after denucleation. Rolland et al. use native ion mobility-mass spectrometry, kinetics experiments, and computations to reveal that b-crystallins form heterodimers. These likely assemble into compact heterooligomers that enable the very high protein concentrations found in lens tissue

Protein Shape Sampled by Ion Mobility Mass Spectrometry Consistently Improves Protein Structure Prediction

Ion mobility (IM) mass spectrometry provides structural information about protein shape and size in the form of an orientationally-averaged collision cross-section (CCSIM). While IM data have been used with various computational methods, they have not yet been utilized to predict monomeric protein structure from sequence. Here, we show that IM data can significantly improve protein structure determination using the modelling suite Rosetta. We develop the Rosetta Projection Approximation using Rough Circular Shapes (PARCS) algorithm that allows for fast and accurate prediction of CCSIM from structure. Following successful testing of the PARCS algorithm, we use an integrative modelling approach to utilize IM data for protein structure prediction. Additionally, we propose a confidence metric that identifies near native models in the absence of a known structure. The results of this study demonstrate the ability of IM data to consistently improve protein structure prediction

Protonation Isomers of Highly Charged Protein Ions Can Be Separated in FAIMS-MS

High-field asymmetric waveform ion mobility spectrometry-mass spectrometry (FAIMS-MS) can resolve over an order of magnitude more conformers for a given protein ion than alternative methods. Such an expansion in separation space results, in part, from protein ions with masses of \u3e29 kDa undergoing dipole alignment in the high electric field of FAIMS, and the resolution of ions that adopt pendular vs free rotor states. In this study, FAIMS-MS, collision-induced dissociation (CID), and travelling wave (TW) IMS-MS were used to investigate the pendular and free rotor states of protonated carbonic anhydrase II (CAII, 29 kDa). The electrospray ionization additive 1,2-butylene carbonate was used to increase protein charge states and ensure extended ion conformations were formed. For relatively high charge states in which dipole alignment occurs (30e38þ), FAIMS-MS can baseline resolve the isobaric pendular and free rotor ion populations. For TWIMS-MS, these same charge states resulted in monomodal arrival time distributions with collision cross sections corresponding to highly extended ion conformations. Interestingly, CID of FAIMS-selected pendular and free rotor ion populations resulted in significantly different frag-mentation patterns. For example, CID of the dipole aligned CAII 37þ resulted in cleavages C-terminal to residue 183, 192 and 196, whereas cleavage sites for the free rotor population occurred near residues 12 and 238. Given that the cleavage sites are ’directed’ by protonation sites in the CID of protein ions, and highly charged protein ions adopt extended conformations with the same or very similar collision cross sections, these results indicate that the pendular and free rotor populations separated in FAIMS can be attributed to protonation isomers. Moreover, the extent of protein ion charging in FAIMS-MS decreased substantially as the carrier gas flow rate decreased, indicating that ion charging in FAIMS-MS can be limited by proton-transfer reactions. Given that the total mass of proton charge carriers corresponds to less than 0.2% the mass of CAII, we anticipate that FAIMS-MS can be used to separate intact isobaric proteoforms with masses of at least ~29 kDa that result from alternative sites of post-translational modifications

Dynamic Time-Warping Correction for Shifts in Ultrahigh Resolving Power Ion Mobility Spectrometry and Structures for Lossless Ion Manipulations

Detection of arrival time shifts between ion mobility spectrometry (IMS) separations can limit achievable resolving power (Rp), particularly when multiple separations are summed or averaged, as commonly practiced in IMS. Such variations can be apparent in higher Rp measurements and are particularly evident in long path length traveling wave structures for lossless ion manipulations (SLIM) IMS due to their typically much longer separation times. Here, we explore data processing approaches employing single value alignment (SVA) and nonlinear dynamic time warping (DTW) to correct for variations between IMS separations, such as due to pressure fluctuations, to enable more effective spectrum summation for improving Rp and detection of low-intensity species. For multipass SLIM IMS separations, where narrow mobility range measurements have arrival times that can extend to several seconds, the SVA approach effectively corrected for such variations and significantly improved Rp for summed separations. However, SVA was much less effective for broad mobility range separations, such as obtained with multilevel SLIM IMS. Changes in ions’ arrival times were observed to be correlated with small pressure changes, with approximately 0.6% relative arrival time shifts being common, sufficient to result in a loss of Rp for summed separations. Comparison of the approaches showed that DTW alignment performed similarly to SVA when used over a narrow mobility range but was significantly better (providing narrower peaks and higher signal intensities) for wide mobility range data. We found that the DTW approach increased Rp by as much as 115% for measurements in which 50 IMS separations over 2 s were summed. We conclude that DTW is superior to SVA for ultra-high-resolution broad mobility range SLIM IMS separations and leads to a large improvement in effective Rp, correcting for ion arrival time shifts regardless of the cause, as well as improving the detectability of low-abundance species. Our tool is publicly available for use with universal ion mobility format (.UIMF) and text (.txt) files

Measurement and Theory of Gas-Phase Ion Mobility Shifts Resulting from Isotopomer Mass Distribution Changes

The unanticipated discovery of recent ultra-high-resolution ion mobility spectrometry (IMS) measurements revealing that isotopomers—compounds that differ only in the isotopic substitution sites—can be separated has raised questions as to the physical basis for their separation. A study comparing IMS separations for two isotopomer sets in conjunction with theory and simulations accounting for ion rotational effects provides the first-ever prediction of rotation-mediated shifts. The simulations produce observable mobility shifts due to differences in gas−ion collision frequency and translational-to-rotational energy transfer. These differences can be attributed to distinct changes in the moment of inertia and center of mass between isotopomers. The simulations are in broad agreement with the observed experiments and consistent with relative mobility differences between isotopomers. These results provide a basis for refining IMS theory and a new foundation to obtain additional structural insights through IMS

Strong chemical tagging with APOGEE: 21 candidate star clusters that have dissolved across the Milky Way disc

Chemically tagging groups of stars born in the same birth cluster is a major goal of spectroscopic surveys. To investigate the feasibility of such strong chemical tagging, we perform a blind chemical tagging experiment on abundances measured from APOGEE survey spectra. We apply a density-based clustering algorithm to the eight dimensional chemical space defined by [Mg/Fe], [Al/Fe], [Si/Fe], [K/Fe], [Ti/Fe], [Mn/Fe], [Fe/H], and [Ni/Fe], abundances ratios which together span multiple nucleosynthetic channels. In a high quality sample of 182,538 giant stars, we detect twenty-one candidate clusters with more than fifteen members. Our candidate clusters are more chemically homogeneous than a population of non-member stars with similar [Mg/Fe] and [Fe/H], even in abundances not used for tagging. Group members are consistent with having the same age and fall along a single stellar-population track in logg vs. Teff space. Each group's members are distributed over multiple kpc, and the spread in their radial and azimuthal actions increases with age. We qualitatively reproduce this increase using N-body simulations of cluster dissolution in Galactic potentials that include transient winding spiral arms. Observing our candidate birth clusters with high-resolution spectroscopy in other wavebands to investigate their chemical homogeneity in other nucleosynthetic groups will be essential to confirming the efficacy of strong chemical tagging. Our initially spatially-compact but now widely dispersed candidate clusters will provide novel limits on chemical evolution and orbital diffusion in the Galactic disc, and constraints on star formation in loosely-bound groups.Comment: 15 pages, 9 figures, accepted by MNRA

Health system performance at the district level in Indonesia after decentralization

<p>Abstract</p> <p>Background</p> <p>Assessments over the last two decades have showed an overall low level of performance of the health system in Indonesia with wide variation between districts. The reasons advanced for these low levels of performance include the low level of public funding for health and the lack of discretion for health system managers at the district level. When, in 2001, Indonesia implemented a radical decentralization and significantly increased the central transfer of funds to district governments it was widely expected that the performance of the health system would improve. This paper assesses the extent to which the performance of the health system has improved since decentralization.</p> <p>Methods</p> <p>We measured a set of indicators relevant to assessing changes in performance of the health system between two surveys in three areas: utilization of maternal antenatal and delivery care; immunization coverage; and contraceptive source and use. We also measured respondents' demographic characteristics and their living circumstances. These measurements were made in population-based surveys in 10 districts in 2002-03 and repeated in 2007 in the same 10 districts using the same instruments and sampling methods.</p> <p>Results</p> <p>The dominant providers of maternal and child health in these 10 districts are in the private sector. There was a significant decrease in birth deliveries at home, and a corresponding increase in deliveries in health facilities in 5 of the 10 districts, largely due to increased use of private facilities with little change in the already low use of public facilities. Overall, there was no improvement in vaccination of mothers and their children. Of those using modern contraceptive methods, the majority obtained them from the private sector in all districts.</p> <p>Conclusions</p> <p>There has been little improvement in the performance of the health system since decentralization occurred in 2001 even though there have also been significant increases in public funding for health. In fact, the decentralization has been limited in extent and structural problems make management of the system as a whole difficult. At the national level there has been no real attempt to envision the health system that Indonesia will need for the next 20 to 30 years or how the substantial public subsidy to this lightly regulated private system could be used in creative ways to stimulate innovation, mitigate market failures, improve equity and quality, and to enhance the performance of the system as a whole.</p

APOGEE Data and Spectral Analysis from SDSS Data Release 16: Seven Years of Observations Including First Results from APOGEE-South

The spectral analysis and data products in Data Release 16 (DR16; December 2019) from the high-resolution near-infrared APOGEE-2/SDSS-IV survey are described. Compared to the previous APOGEE data release (DR14; July 2017), APOGEE DR16 includes about 200000 new stellar spectra, of which 100000 are from a new southern APOGEE instrument mounted on the 2.5 m du Pont telescope at Las Campanas Observatory in Chile. DR16 includes all data taken up to August 2018, including data released in previous data releases. All of the data have been re-reduced and re-analyzed using the latest pipelines, resulting in a total of 473307 spectra of 437445 stars. Changes to the analysis methods for this release include, but are not limited to, the use of MARCS model atmospheres for calculation of the entire main grid of synthetic spectra used in the analysis, a new method for filling "holes" in the grids due to unconverged model atmospheres, and a new scheme for continuum normalization. Abundances of the neutron capture element Ce are included for the first time. A new scheme for estimating uncertainties of the derived quantities using stars with multiple observations has been applied, and calibrated values of surface gravities for dwarf stars are now supplied. Compared to DR14, the radial velocities derived for this release more closely match those in the Gaia DR2 data base, and a clear improvement in the spectral analysis of the coolest giants can be seen. The reduced spectra as well as the result of the analysis can be downloaded using links provided in the SDSS DR16 web page