CYP450 phenotyping and metabolite identification of quinine by accurate mass UPLC-MS analysis: a possible metabolic link to blackwater fever

BACKGROUND: The naturally occurring alkaloid drug, quinine is commonly used for the treatment of severe malaria. Despite centuries of use, its metabolism is still not fully understood, and may play a role in the haemolytic disorders associated with the drug. METHODS: Incubations of quinine with CYPs 1A2, 2C9, 2C19, 2D6, and 3A4 were conducted, and the metabolites were characterized by accurate mass UPLC-MS(E) analysis. Reactive oxygen species generation was also measured in human erythrocytes incubated in the presence of quinine with and without microsomes. RESULTS: The metabolites 3-hydroxyquinine, 2’-oxoquininone, and O-desmethylquinine were observed after incubation with CYPs 3A4 (3-hydroxyquinine and 2’-oxoquininone) and 2D6 (O-desmethylquinine). In addition, multiple hydroxylations were observed both on the quinoline core and the quinuclidine ring system. Of the five primary abundance CYPs tested, 3A4, 2D6, 2C9, and 2C19 all demonstrated activity toward quinine, while 1A2 did not. Further, quinine produced robust dose-dependent oxidative stress in human erythrocytes in the presence of microsomes. CONCLUSIONS: Taken in context, these data suggest a CYP-mediated link between quinine metabolism and the poorly understood haemolytic condition known as blackwater fever, often associated with quinine ingestion

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

Hot, rocky and warm, puffy super-Earths orbiting TOI-402 (HD 15337)

Context: The Transiting Exoplanet Survey Satellite (TESS) is revolutionising the search for planets orbiting bright and nearby stars. In sectors 3 and 4, TESS observed TOI-402 (TIC-120896927), a bright V = 9.1 K1 dwarf also known as HD 15337, and found two transiting signals with periods of 4.76 and 17.18 days and radii of 1.90 and 2.21 R⊕, respectively. This star was observed prior to the TESS detection as part of the radial-velocity (RV) search for planets using the HARPS spectrometer, and 85 precise RV measurements were obtained before the launch of TESS over a period of 14 yr. Aims: In this paper, we analyse the HARPS RV measurements in hand to confirm the planetary nature of these two signals. Methods: HD 15337 happens to present a stellar activity level similar to the Sun, with a magnetic cycle of similar amplitude and RV measurements that are affected by stellar activity. By modelling this stellar activity in the HARPS radial velocities using a linear dependence with the calcium activity index log(RHK′), we are able, with a periodogram approach, to confirm the periods and the planetary nature of TOI-402.01 and TOI-402.02. We then derive robust estimates from the HARPS RVs for the orbital parameters of these two planets by modelling stellar activity with a Gaussian process and using the marginalised posterior probability density functions obtained from our analysis of TESS photometry for the orbital period and time of transit. Results: By modelling TESS photometry and the stellar host characteristics, we find that TOI-402.01 and TOI-402.02 have periods of 4.75642 ± 0.00021 and 17.1784 ± 0.0016 days and radii of 1.70 ± 0.06 and 2.52 ± 0.11 R⊕ (precision 3.6 and 4.2%), respectively. By analysing the HARPS RV measurements, we find that those planets are both super-Earths with masses of 7.20 ± 0.81 and 8.79 ± 1.68 M⊕ (precision 11.3 and 19.1%), and small eccentricities compatible with zero at 2σ. Conclusions: Although having rather similar masses, the radii of these two planets are very different, putting them on different sides of the radius gap. By studying the temporal evolution under X-ray and UV (XUV) driven atmospheric escape of the TOI-402 planetary system, we confirm, under the given assumptions, that photo-evaporation is a plausible explanation for this radius difference. Those two planets, being in the same system and therefore being in the same irradiation environment are therefore extremely useful for comparative exoplanetology across the evaporation valley and thus bring constraints on the mechanisms responsible for the radius gap

Room temperature coherent control of coupled single spins in solid

Coherent coupling between single quantum objects is at the heart of modern quantum physics. When coupling is strong enough to prevail over decoherence, it can be used for the engineering of correlated quantum states. Especially for solid-state systems, control of quantum correlations has attracted widespread attention because of applications in quantum computing. Such coherent coupling has been demonstrated in a variety of systems at low temperature1, 2. Of all quantum systems, spins are potentially the most important, because they offer very long phase memories, sometimes even at room temperature. Although precise control of spins is well established in conventional magnetic resonance3, 4, existing techniques usually do not allow the readout of single spins because of limited sensitivity. In this paper, we explore dipolar magnetic coupling between two single defects in diamond (nitrogen-vacancy and nitrogen) using optical readout of the single nitrogen-vacancy spin states. Long phase memory combined with a defect separation of a few lattice spacings allow us to explore the strong magnetic coupling regime. As the two-defect system was well-isolated from other defects, the long phase memory times of the single spins was not diminished, despite the fact that dipolar interactions are usually seen as undesirable sources of decoherence. A coherent superposition of spin pair quantum states was achieved. The dipolar coupling was used to transfer spin polarisation from a nitrogen-vacancy centre spin to a nitrogen spin, with optical pumping of a nitrogen-vacancy centre leading to efficient initialisation. At the level anticrossing efficient nuclear spin polarisation was achieved. Our results demonstrate an important step towards controlled spin coupling and multi-particle entanglement in the solid state

The Magellan-TESS Survey I: Survey Description and Mid-Survey Results

One of the most significant revelations from Kepler is that roughly one-third of Sun-like stars host planets which orbit their stars within 100 days and are between the size of Earth and Neptune. How do these super-Earth and sub-Neptune planets form, what are they made of, and do they represent a continuous population or naturally divide into separate groups? Measuring their masses and thus bulk densities can help address these questions of their origin and composition. To that end, we began the Magellan-TESS Survey (MTS), which uses Magellan II/PFS to obtain radial velocity (RV) masses of 30 transiting exoplanets discovered by TESS and develops an analysis framework that connects observed planet distributions to underlying populations. In the past, RV measurements of small planets have been challenging to obtain due to the faintness and low RV semi-amplitudes of most Kepler systems, and challenging to interpret due to the potential biases in the existing ensemble of small planet masses from non-algorithmic decisions for target selection and observation plans. The MTS attempts to minimize these biases by focusing on bright TESS targets and employing a quantitative selection function and multi-year observing strategy. In this paper, we (1) describe the motivation and survey strategy behind the MTS, (2) present our first catalog of planet mass and density constraints for 25 TESS Objects of Interest (TOIs; 20 in our population analysis sample, five that are members of the same systems), and (3) employ a hierarchical Bayesian model to produce preliminary constraints on the mass-radius (M-R) relation. We find qualitative agreement with prior mass-radius relations but some quantitative differences (abridged). The the results of this work can inform more detailed studies of individual systems and offer a framework that can be applied to future RV surveys with the goal of population inferences.Comment: 101 pages (39 of main text and references, the rest an appendix of figures and tables). Submitted to AAS Journal

Critical Loss of the Balance between Th17 and T Regulatory Cell Populations in Pathogenic SIV Infection

Chronic immune activation and progression to AIDS are observed after SIV infection in macaques but not in natural host primate species. To better understand this dichotomy, we compared acute pathogenic SIV infection in pigtailed macaques (PTs) to non-pathogenic infection in African green monkeys (AGMs). SIVagm-infected PTs, but not SIVagm-infected AGMs, rapidly developed systemic immune activation, marked and selective depletion of IL-17-secreting (Th17) cells, and loss of the balance between Th17 and T regulatory (Treg) cells in blood, lymphoid organs, and mucosal tissue. The loss of Th17 cells was found to be predictive of systemic and sustained T cell activation. Collectively, these data indicate that loss of the Th17 to Treg balance is related to SIV disease progression

Long-term thermal sensitivity of Earth’s tropical forests

The sensitivity of tropical forest carbon to climate is a key uncertainty in predicting global climate change. Although short-term drying and warming are known to affect forests, it is unknown if such effects translate into long-term responses. Here, we analyze 590 permanent plots measured across the tropics to derive the equilibrium climate controls on forest carbon. Maximum temperature is the most important predictor of aboveground biomass (−9.1 megagrams of carbon per hectare per degree Celsius), primarily by reducing woody productivity, and has a greater impact per °C in the hottest forests (>32.2°C). Our results nevertheless reveal greater thermal resilience than observations of short-term variation imply. To realize the long-term climate adaptation potential of tropical forests requires both protecting them and stabilizing Earth’s climate

Consistent patterns of common species across tropical tree communities

Trees structure the Earth’s most biodiverse ecosystem, tropical forests. The vast number of tree species presents a formidable challenge to understanding these forests, including their response to environmental change, as very little is known about most tropical tree species. A focus on the common species may circumvent this challenge. Here we investigate abundance patterns of common tree species using inventory data on 1,003,805 trees with trunk diameters of at least 10 cm across 1,568 locations1,2,3,4,5,6 in closed-canopy, structurally intact old-growth tropical forests in Africa, Amazonia and Southeast Asia. We estimate that 2.2%, 2.2% and 2.3% of species comprise 50% of the tropical trees in these regions, respectively. Extrapolating across all closed-canopy tropical forests, we estimate that just 1,053 species comprise half of Earth’s 800 billion tropical trees with trunk diameters of at least 10 cm. Despite differing biogeographic, climatic and anthropogenic histories7, we find notably consistent patterns of common species and species abundance distributions across the continents. This suggests that fundamental mechanisms of tree community assembly may apply to all tropical forests. Resampling analyses show that the most common species are likely to belong to a manageable list of known species, enabling targeted efforts to understand their ecology. Although they do not detract from the importance of rare species, our results open new opportunities to understand the world’s most diverse forests, including modelling their response to environmental change, by focusing on the common species that constitute the majority of their trees.Publisher PDFPeer reviewe

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.

The early detection of relapse following primary surgery for non-small-cell lung cancer and the characterization of emerging subclones, which seed metastatic sites, might offer new therapeutic approaches for limiting tumour recurrence. The ability to track the evolutionary dynamics of early-stage lung cancer non-invasively in circulating tumour DNA (ctDNA) has not yet been demonstrated. Here we use a tumour-specific phylogenetic approach to profile the ctDNA of the first 100 TRACERx (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy (Rx)) study participants, including one patient who was also recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release and analyse the tumour-volume detection limit. Through blinded profiling of postoperative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients who are very likely to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastasis, providing a new approach for ctDNA-driven therapeutic studies