Different Real Time PCR Approaches for the Fine Quantification of SNP's Alleles in DNA Pools: Assays Development, Characterization and Pre-validation

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Comparative genomic hybridization on microarray (a-CGH) in constitutional and acquired mosaicism may detect as low as 8% abnormal cells

<p>Abstract</p> <p>Background</p> <p>The results of cytogenetic investigations on unbalanced chromosome anomalies, both constitutional and acquired, were largely improved by comparative genomic hybridization on microarray (a-CGH), but in mosaicism the ability of a-CGH to reliably detect imbalances is not yet well established. This problem of sensitivity is even more relevant in acquired mosaicism in neoplastic diseases, where cells carrying acquired imbalances coexist with normal cells, in particular when the proportion of abnormal cells may be low.</p> <p>We constructed a synthetic mosaicism by mixing the DNA of three patients carrying altogether seven chromosome imbalances with normal sex-matched DNA. Dilutions were prepared mimicking 5%, 6%, 7%, 8%, 10% and 15% levels of mosaicism. Oligomer-based a-CGH (244 K whole-genome system) was applied on the patients' DNA and customized slides designed around the regions of imbalance were used for the synthetic mosaics.</p> <p>Results and conclusions</p> <p>The a-CGH on the synthetic mosaics proved to be able to detect as low as 8% abnormal cells in the tissue examined. Although in our experiment some regions of imbalances escaped to be revealed at this level, and were detected only at 10-15% level, it should be remarked that these ones were the smallest analyzed, and that the imbalances recurrent as clonal anomalies in cancer and leukaemia are similar in size to those revealed at 8% level.</p

The HARPS search for southern extra-solar planets. IX. Exoplanets orbiting HD 100777, HD 190647, and HD 221287

The HARPS high-resolution high-accuracy spectrograph is offered to the astronomical community since the second half of 2003. Since then, we have been using this instrument for monitoring radial velocities of a large sample of Solar-type stars (~1400 stars) in order to search for their possible low-mass companions. Amongst the goals of our survey, one is to significantly increase the number of detected extra-solar planets in a volume-limited sample to improve our knowledge of their orbital elements distributions and thus obtain better constraints for planet-formation models. In this paper, we present the HARPS radial-velocity data and orbital solutions for 3 Solar-type stars: HD 100777, HD 190647, and HD 221287. The radial-velocity data of HD 100777 is best explained by the presence of a 1.1 M_Jup planetary companion on a 384--day eccentric orbit (e=0.36). The orbital fit obtained for the slightly evolved star HD 190647 reveals the presence of a long-period (P=1038 d) 1.9 M_Jup planetary companion on a moderately eccentric orbit (e=0.18). HD 221287 is hosting a 3.1 M_Jup planet on a 456--day orbit. The shape of this orbit is not very well constrained because of our non-optimal temporal coverage and because of the presence of abnormally large residuals. We find clues for these large residuals to result from spectral line profile variations probably induced by stellar activity related processes.Comment: 7 pages, 4 figures, RV data added in paper. A&A in pres

Clonal chromosome anomalies and propensity to myeloid malignancies in congenital amegakaryocytic thrombocytopenia (OMIM 604498).

Congenital amegakaryocytic thrombocytopenia (CAMT, OMIM 604498) is an autosomal recessive disorder characterized by absent or reduced number of megakaryocytes in the bone marrow (BM) since birth, elevated serum levels of thrombopoietin (TPO), and very low platelet count. Prognosis of CAMT patient

Chromosome anomalies in bone marrow as primarycause of aplastic or hypoplastic conditions andperipheral cytopenia: disorders due to secondaryimpairment of RUNX1 and MPL genes

Background Chromosome changes in the bone marrow (BM) of patients with persistent cytopenia are often considered diagnostic for a myelodysplastic syndrome (MDS). Comprehensive cytogenetic evaluations may give evidence of the real pathogenetic role of these changes in cases with cytopenia without morphological signs of MDS. Results Chromosome anomalies were found in the BM of three patients, without any morphological evidence of MDS: 1) an acquired complex rearrangement of chromosome 21 in a boy with severe aplastic anaemia (SAA); the rearrangement caused the loss of exons 2-8 of the RUNX1 gene with subsequent hypoexpression. 2) a constitutional complex rearrangement of chromosome 21 in a girl with congenital thrombocytopenia; the rearrangement led to RUNX1 disruption and hypoexpression. 3) an acquired paracentric inversion of chromosome 1, in which two regions at the breakpoints were shown to be lost, in a boy with aplastic anaemia; the MPL gene, localized in chromosome 1 short arms was not mutated neither disrupted, but its expression was severely reduced: we postulate that the aplastic anaemia was due to position effects acting both in cis and in trans, and causing Congenital Amegakaryocytic Thrombocytopenia (CAMT). Conclusions A clonal anomaly in BM does not imply per se a diagnosis of MDS: a subgroup of BM hypoplastic disorders is directly due to chromosome structural anomalies with effects on specific genes, as was the case of RUNX1 and MPL in the patients here reported with diagnosis of SAA, thrombocytopenia, and CAMT. The anomaly may be either acquired or constitutional, and it may act by deletion/disruption of the gene, or by position effects. Full cytogenetic investigations, including a-CGH, should always be part of the diagnostic evaluation of patients with BM aplasia/hypoplasia and peripheral cytopenias

The HARPS search for southern extra-solar planets: XXVIII. Two giant planets around M0 dwarfs

Fewer giants planets are found around M dwarfs than around more massive stars, and this dependence of planetary characteristics on the mass of the central star is an important observational diagnostic of planetary formation theories. In part to improve on those statistics, we are monitoring the radial velocities of nearby M dwarfs with the HARPS spectrograph on the ESO 3.6 m telescope. We present here the detection of giant planets around two nearby M0 dwarfs: planets, with minimum masses of respectively 5 Jupiter masses and 1 Saturn mass, orbit around Gl 676A and HIP 12961. The latter is, by over a factor of two, the most massive planet found by radial velocity monitoring of an M dwarf, but its being found around an early M-dwarf is in approximate line with the upper envelope of the planetary vs stellar mass diagram. HIP 12961 ([Fe/H]=-0.07) is slightly more metal-rich than the average solar neighborhood ([Fe/H]=-0.17), and Gl 676A ([Fe/H=0.18) significantly so. The two stars together therefore reinforce the growing trend for giant planets being more frequent around more metal-rich M dwarfs, and the 5~Jupiter mass Gl 676Ab being found around a metal-rich star is consistent with the expectation that the most massive planets preferentially form in disks with large condensate masses.Comment: Corrected an error in the labelling of one line in Table

Rotational and Rotational-Vibrational Raman Spectroscopy of Air to Characterize Astronomical Spectrographs

Raman scattering enables unforeseen uses for the laser guide-star system of the Very Large Telescope. Here, we present the observation of one up-link sodium laser beam acquired with the ESPRESSO spectrograph at a resolution λ /Δ λ ˜140 000 . In 900 s on source, we detect the pure rotational Raman lines of 16O2, 14N2, and 14N 15N (tentatively) up to rotational quantum numbers J of 27, 24, and 9, respectively. We detect the 16O2 fine-structure lines induced by the interaction of the electronic spin S and end-over-end rotational angular momentum N in the electronic ground state of this molecule up to N =9 . The same spectrum also reveals the ν1 ←0 rotational-vibrational Q-branch for 16O2 and 14N2 14. These observations demonstrate the potential of using laser guide-star systems as accurate calibration sources for characterizing new astronomical spectrographs

Nightside condensation of iron in an ultra-hot giant exoplanet

Ultra-hot giant exoplanets receive thousands of times Earth's insolation. Their high-temperature atmospheres (>2,000 K) are ideal laboratories for studying extreme planetary climates and chemistry. Daysides are predicted to be cloud-free, dominated by atomic species and substantially hotter than nightsides. Atoms are expected to recombine into molecules over the nightside, resulting in different day-night chemistry. While metallic elements and a large temperature contrast have been observed, no chemical gradient has been measured across the surface of such an exoplanet. Different atmospheric chemistry between the day-to-night ("evening") and night-to-day ("morning") terminators could, however, be revealed as an asymmetric absorption signature during transit. Here, we report the detection of an asymmetric atmospheric signature in the ultra-hot exoplanet WASP-76b. We spectrally and temporally resolve this signature thanks to the combination of high-dispersion spectroscopy with a large photon-collecting area. The absorption signal, attributed to neutral iron, is blueshifted by -11+/-0.7 km s-1 on the trailing limb, which can be explained by a combination of planetary rotation and wind blowing from the hot dayside. In contrast, no signal arises from the nightside close to the morning terminator, showing that atomic iron is not absorbing starlight there. Iron must thus condense during its journey across the nightside.Comment: Published in Nature (Accepted on 24 January 2020.) 33 pages, 11 figures, 3 table

ESPRESSO at VLT. On-sky performance and first results

Context. ESPRESSO is the new high-resolution spectrograph of ESO's Very Large Telescope (VLT). It was designed for ultra-high radial-velocity (RV) precision and extreme spectral fidelity with the aim of performing exoplanet research and fundamental astrophysical experiments with unprecedented precision and accuracy. It is able to observe with any of the four Unit Telescopes (UTs) of the VLT at a spectral resolving power of 140 000 or 190 000 over the 378.2 to 788.7 nm wavelength range; it can also observe with all four UTs together, turning the VLT into a 16 m diameter equivalent telescope in terms of collecting area while still providing a resolving power of 70 000. Aims: We provide a general description of the ESPRESSO instrument, report on its on-sky performance, and present our Guaranteed Time Observation (GTO) program along with its first results. Methods: ESPRESSO was installed on the Paranal Observatory in fall 2017. Commissioning (on-sky testing) was conducted between December 2017 and September 2018. The instrument saw its official start of operations on October 1, 2018, but improvements to the instrument and recommissioning runs were conducted until July 2019. Results: The measured overall optical throughput of ESPRESSO at 550 nm and a seeing of 0.65″ exceeds the 10% mark under nominal astroclimatic conditions. We demonstrate an RV precision of better than 25 cm s-1 during a single night and 50 cm s-1 over several months. These values being limited by photon noise and stellar jitter shows that the performance is compatible with an instrumental precision of 10 cm s-1. No difference has been measured across the UTs, neither in throughput nor RV precision. Conclusions: The combination of the large collecting telescope area with the efficiency and the exquisite spectral fidelity of ESPRESSO opens a new parameter space in RV measurements, the study of planetary atmospheres, fundamental constants, stellar characterization, and many other fields. Based on GTOs collected at the European Southern Observatory under ESO program(s) 1102.C-0744, 1102.C-0958 and 1104.C-0350 by the ESPRESSO Consortium