A High-Resolution Atlas of Uranium-Neon in the H Band

We present a high-resolution (R ~ 50 000) atlas of a uranium-neon (U/Ne) hollow-cathode spectrum in the H-band (1454 nm to 1638 nm) for the calibration of near-infrared spectrographs. We obtained this U/Ne spectrum simultaneously with a laser-frequency comb spectrum, which we used to provide a first-order calibration to the U/Ne spectrum. We then calibrated the U/Ne spectrum using the recently-published uranium line list of Redman et al. (2011), which is derived from high-resolution Fourier transform spectrometer measurements. These two independent calibrations allowed us to easily identify emission lines in the hollow cathode lamp that do not correspond to known (classified) lines of either uranium or neon, and to compare the achievable precision of each source. Our frequency comb precision was limited by modal noise and detector effects, while the U/Ne precision was limited primarily by the signal-to-noise ratio (S/N) of the observed emission lines and our ability to model blended lines. The standard deviation in the dispersion solution residuals from the S/N-limited U/Ne hollow cathode lamp were 50% larger than the standard deviation of the dispersion solution residuals from the modal-noise-limited laser frequency comb. We advocate the use of U/Ne lamps for precision calibration of near-infrared spectrographs, and this H-band atlas makes these lamps significantly easier to use for wavelength calibration.Comment: 23 pages, 7 figures, submitted and accepted in ApJSS. Online-only material to be published online by ApJS

A near infrared frequency comb for Y+J band astronomical spectroscopy

Radial velocity (RV) surveys supported by high precision wavelength references (notably ThAr lamps and I2 cells) have successfully identified hundreds of exoplanets; however, as the search for exoplanets moves to cooler, lower mass stars, the optimum wave band for observation for these objects moves into the near infrared (NIR) and new wavelength standards are required. To address this need we are following up our successful deployment of an H band(1.45-1.7{\mu}m) laser frequency comb based wavelength reference with a comb working in the Y and J bands (0.98-1.3{\mu}m). This comb will be optimized for use with a 50,000 resolution NIR spectrograph such as the Penn State Habitable Zone Planet Finder. We present design and performance details of the current Y+J band comb.Comment: Submitted to SPIE, conference proceedings 845

The Infrared Spectrum of Uranium Hollow Cathode Lamps from 850 nm to 4000 nm: Wavenumbers and Line Identifications from Fourier Transform Spectra

We provide new measurements of wavenumbers and line identifications of 10 100 UI and UII near-infrared (NIR) emission lines between 2500 cm-1 and 12 000 cm-1 (4000 nm to 850 nm) using archival FTS spectra from the National Solar Observatory (NSO). This line list includes isolated uranium lines in the Y, J, H, K, and L bands (0.9 {\mu}m to 1.1 {\mu}m, 1.2 {\mu}m to 1.35 {\mu}m, 1.5 {\mu}m to 1.65 {\mu}m, 2.0 {\mu}m to 2.4 {\mu}m, and 3.0 {\mu}m to 4.0 {\mu}m, respectively), and provides six times as many calibration lines as thorium in the NIR spectral range. The line lists we provide enable inexpensive, commercially-available uranium hollow-cathode lamps to be used for high-precision wavelength calibration of existing and future high-resolution NIR spectrographs.Comment: 23 pages, 6 Figure

Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm

International audienceHaemonchus contortus is a globally distributed and economically important gastrointestinal pathogen of small ruminants and has become a key nematode model for studying anthelmintic resistance and other parasite-specific traits among a wider group of parasites including major human pathogens. Here, we report using PacBio long-read and OpGen and 10X Genomics long-molecule methods to generate a highly contiguous 283.4 Mbp chromosome-scale genome assembly including a resolved sex chromosome for the MHco3(ISE).N1 isolate. We show a remarkable pattern of conservation of chromosome content with Caenorhabditis elegans, but almost no conservation of gene order. Short and long-read transcriptome sequencing allowed us to define coordinated transcriptional regulation throughout the parasite’s life cycle and refine our understanding of cis- and trans-splicing. Finally, we provide a comprehensive picture of chromosome-wide genetic diversity both within a single isolate and globally. These data provide a high-quality comparison for understanding the evolution and genomics of Caenorhabditis and other nematodes and extend the experimental tractability of this model parasitic nematode in understanding helminth biology, drug discovery and vaccine development, as well as important adaptive traits such as drug resistance

GDF15 Provides an Endocrine Signal of Nutritional Stress in Mice and Humans.

GDF15 is an established biomarker of cellular stress. The fact that it signals via a specific hindbrain receptor, GFRAL, and that mice lacking GDF15 manifest diet-induced obesity suggest that GDF15 may play a physiological role in energy balance. We performed experiments in humans, mice, and cells to determine if and how nutritional perturbations modify GDF15 expression. Circulating GDF15 levels manifest very modest changes in response to moderate caloric surpluses or deficits in mice or humans, differentiating it from classical intestinally derived satiety hormones and leptin. However, GDF15 levels do increase following sustained high-fat feeding or dietary amino acid imbalance in mice. We demonstrate that GDF15 expression is regulated by the integrated stress response and is induced in selected tissues in mice in these settings. Finally, we show that pharmacological GDF15 administration to mice can trigger conditioned taste aversion, suggesting that GDF15 may induce an aversive response to nutritional stress.This work and authors were funded by the NIHR Cambridge Biomedical Research Centre; NIHR Rare Disease Translational Research Collaboration; Medical Research Council [MC_UU_12012/2 and MRC_MC_UU_12012/3]; MRC Metabolic Diseases Unit [MRC_MC_UU_12012/5 and MRC_MC_UU_12012.1]; Wellcome Trust Strategic Award [100574/Z/12/Z and 100140]; Wellcome Trust [107064 , 095515/Z/11/Z , 098497/Z/12/Z, 106262/Z/14/Z and 106263/Z/14/Z]; British Heart Foundation [RG/12/13/29853]; Addenbrooke’s Charitable Trust / Evelyn Trust Cambridge Clinical Research Fellowship [16-69] US Department of Agriculture: 2010-34323-21052; EFSD project grant and a Royal College of Surgeons Research Fellowship, Diabetes UK Harry Keen intermediate clinical fellowship (17/0005712). European Research Council, Bernard Wolfe Health Neuroscience Endowment, Experimental Medicine Training Initiative/AstraZeneca and Medimmune

SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species

A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources

Oxamniquine resistance alleles are widespread in Old World Schistosoma mansoni and predate drug deployment

Do mutations required for adaptation occur de novo, or are they segregating within populations as standing genetic variation? This question is key to understanding adaptive change in nature, and has important practical consequences for the evolution of drug resistance. We provide evidence that alleles conferring resistance to oxamniquine (OXA), an antischistosomal drug, are widespread in natural parasite populations under minimal drug pressure and predate OXA deployment. OXA has been used since the 1970s to treat Schistosoma mansoni infections in the New World where S. mansoni established during the slave trade. Recessive loss-of-function mutations within a parasite sulfotransferase (SmSULT-OR) underlie resistance, and several verified resistance mutations, including a deletion (p.E142del), have been identified in the New World. Here we investigate sequence variation in SmSULT-OR in S. mansoni from the Old World, where OXA has seen minimal usage. We sequenced exomes of 204 S. mansoni parasites from West Africa, East Africa and the Middle East, and scored variants in SmSULT-OR and flanking regions. We identified 39 non-synonymous SNPs, 4 deletions, 1 duplication and 1 premature stop codon in the SmSULT-OR coding sequence, including one confirmed resistance deletion (p.E142del). We expressed recombinant proteins and used an in vitro OXA activation assay to functionally validate the OXA-resistance phenotype for four predicted OXA-resistance mutations. Three aspects of the data are of particular interest: (i) segregating OXA-resistance alleles are widespread in Old World populations (4.29–14.91% frequency), despite minimal OXA usage, (ii) two OXA-resistance mutations (p.W120R, p.N171IfsX28) are particularly common (>5%) in East African and Middle-Eastern populations, (iii) the p.E142del allele has identical flanking SNPs in both West Africa and Puerto Rico, suggesting that parasites bearing this allele colonized the New World during the slave trade and therefore predate OXA deployment. We conclude that standing variation for OXA resistance is widespread in S. mansoni