Benchmarking MicrobIEM – a user-friendly tool for decontamination of microbiome sequencing data

Background Microbiome analysis is becoming a standard component in many scientific studies, but also requires extensive quality control of the 16S rRNA gene sequencing data prior to analysis. In particular, when investigating low-biomass microbial environments such as human skin, contaminants distort the true microbiome sample composition and need to be removed bioinformatically. We introduce MicrobIEM, a novel tool to bioinformatically remove contaminants using negative controls. Results We benchmarked MicrobIEM against five established decontamination approaches in four 16S rRNA amplicon sequencing datasets: three serially diluted mock communities (108–103 cells, 0.4–80% contamination) with even or staggered taxon compositions and a skin microbiome dataset. Results depended strongly on user-selected algorithm parameters. Overall, sample-based algorithms separated mock and contaminant sequences best in the even mock, whereas control-based algorithms performed better in the two staggered mocks, particularly in low-biomass samples (≤ 106 cells). We show that a correct decontamination benchmarking requires realistic staggered mock communities and unbiased evaluation measures such as Youden’s index. In the skin dataset, the Decontam prevalence filter and MicrobIEM’s ratio filter effectively reduced common contaminants while keeping skin-associated genera. Conclusions MicrobIEM’s ratio filter for decontamination performs better or as good as established bioinformatic decontamination tools. In contrast to established tools, MicrobIEM additionally provides interactive plots and supports selecting appropriate filtering parameters via a user-friendly graphical user interface. Therefore, MicrobIEM is the first quality control tool for microbiome experts without coding experience

Sub-stellar companions of intermediate-mass stars with CoRoT: CoRoT–34b, CoRoT–35b, and CoRoT–36b

Theories of planet formation give contradicting results of how frequent close-in giant planets of intermediate mass stars (IMSs; 1.3≤M⋆≤3.2M⊙⁠) are. Some theories predict a high rate of IMSs with close-in gas giants, while others predict a very low rate. Thus, determining the frequency of close-in giant planets of IMSs is an important test for theories of planet formation. We use the CoRoT survey to determine the absolute frequency of IMSs that harbour at least one close-in giant planet and compare it to that of solar-like stars. The CoRoT transit survey is ideal for this purpose, because of its completeness for gas-giant planets with orbital periods of less than 10 d and its large sample of main-sequence IMSs. We present a high precision radial velocity follow-up programme and conclude on 17 promising transit candidates of IMSs, observed with CoRoT. We report the detection of CoRoT–34b, a brown dwarf close to the hydrogen burning limit, orbiting a 1.1 Gyr A-type main-sequence star. We also confirm two inflated giant planets, CoRoT–35b, part of a possible planetary system around a metal-poor star, and CoRoT–36b on a misaligned orbit. We find that 0.12±0.10 per cent of IMSs between 1.3≤M⋆≤1.6M⊙ observed by CoRoT do harbour at least one close-in giant planet. This is significantly lower than the frequency (⁠0.70±0.16 per cent⁠) for solar-mass stars, as well as the frequency of IMSs harbouring long-period planets (⁠∼8 per cent⁠)

Dust observations of Comet 9P/Tempel 1 at the time of the Deep Impact

On 4 July 2005 at 05:52 UT, the impactor of NASA's Deep Impact (DI) mission crashed into comet 9P/Tempel 1 with a velocity of about 10 km/s. The material ejected by the impact expanded into the normal coma, produced by ordinary cometary activity. The characteristics of the non-impact coma and cloud produced by the impact were studied by observations in the visible wavelengths and in the near-IR. The scattering characteristics of the "normal" coma of solid particles were studied by comparing images in various spectral regions, from the UV to the near-IR. For the non-impact coma, a proxy of the dust production has been measured in various spectral regions. The presence of sublimating grains has been detected. Their lifetime was found to be about 11 hours. Regarding the cloud produced by the impact, the total geometric cross section multiplied by the albedo was measured as a function of the color and time. The projected velocity appeared to obey a Gaussian distribution with the average velocity of the order of 115 m/s. By comparing the observations taken about 3 hours after the impact, we have found a strong decrease in the cross section in J filter, while that in Ks remained almost constant. This is interpreted as the result of sublimation of grains dominated by particles of sizes of the order of some microns.Comment: Accepted by A&

The Dusty View of DI from ESO Chile

Around the time of the impact of NASA's Deep Impact (DI) mission at comet 9P/Tempel 1, in total 6 telescopes with altogether 7 different instruments, located at the La Silla (LSO) and Paranal (VLT) Observatories of the European Southern Observatory (ESO) in Chile, were used to characterize the dust properties before and after the event. The ejecta cloud expanded at an average speed of about 200 ms[SUP]-1[/SUP]during the first hours after the event. It reached stagnation distance of 25000 km about 3 days after impact. The pre-impact dust jet and fan activity (`porcupine' pattern) remained undisturbed after impact. In our measurements the jet activity can be traced to a few 100 km nucleus distance. In total 9 comastructures are identified which may originate from at least 4 regions of enhanced dust emission on the nucleus - one of this region may in fact be multiple. No obvious signatures of a new active region created by DI are found. The overall dust production during the impact compares to about 5-10 h of normal activity. The global expansion geometry of the DI cloud is compatible with a majority of dust grains in the micron size range. Indications exist for asymmetric brightness and colour distributions of the dust in the ejecta cloud. The dust temperature rose from about 280-290 K before to 330 K one day after the event and fell to pre-impact level the day thereafter. The dust reflected sunlight was found to be linearly polarized at about 7.5% in the visible and near-IR, at constant level within about 4000 km from the nucleus. No circular polarization of the dust is detected.Peer reviewe

Solar-like oscillations in distant stars as seen by CoRoT : the special case of HD 42618, a solar sister

We report the observations of a main-sequence star, HD 42618 (T[SUB]eff[/SUB] = 5765 K, G3V) by the space telescope CoRoT. This is the closest star to the Sun ever observed by CoRoT in term of its fundamental parameters. Using a preliminary version of CoRoT light curves of HD 42618, p modes are detected around 3.2 mHz associated to l = 0, 1 and 2 modes with a large spacing of 142 μHz. Various methods are then used to derive the mass and radius of this star (scaling relations from solar values as well as comparison between theoretical and observationnal frequencies) giving values in the range of (0.80 - 1.02)M[SUB]solar[/SUB] and (0.91 - 1.01)R[SUB]solar[/SUB]. A preliminary analysis of l = 0 and 1 modes allows us also to study the amount of penetrative convection at the base of the convective envelope

The Main Belt Comets and ice in the Solar System

We review the evidence for buried ice in the asteroid belt; specifically the questions around the so-called Main Belt Comets (MBCs). We summarise the evidence for water throughout the Solar System, and describe the various methods for detecting it, including remote sensing from ultraviolet to radio wavelengths. We review progress in the first decade of study of MBCs, including observations, modelling of ice survival, and discussion on their origins. We then look at which methods will likely be most effective for further progress, including the key challenge of direct detection of (escaping) water in these bodies

Circumstellar discs: What will be next?

This prospective chapter gives our view on the evolution of the study of circumstellar discs within the next 20 years from both observational and theoretical sides. We first present the expected improvements in our knowledge of protoplanetary discs as for their masses, sizes, chemistry, the presence of planets as well as the evolutionary processes shaping these discs. We then explore the older debris disc stage and explain what will be learnt concerning their birth, the intrinsic links between these discs and planets, the hot dust and the gas detected around main sequence stars as well as discs around white dwarfs.Comment: invited review; comments welcome (32 pages

Cerebrospinal fluid findings in adults with acute Lyme neuroborreliosis

Presence of BB-specific antibodies in the cerebrospinal fluid (CSF) with evidence of their intrathecal production in conjunction with the white cell count in the CSF and typical clinical symptoms is the traditional diagnostic gold standard of Lyme neuroborreliosis (LNB). Few data are available on the CSF lactate concentration in European adults with the diagnosis of acute LNB. The objective of the study was to investigate the CSF changes during acute LNB. Routine CSF parameters [leukocyte count, protein, lactate and albumin concentrations, CSF/serum quotients of albumin (QAlb), IgG, IgA and IgM, and oligoclonal IgG bands] and the Borrelia burgdorferi (BB)-specific antibody index were retrospectively studied in relation to the clinical presentation in patients diagnosed with acute LNB. A total of 118 patients with LNB were categorized into the following groups according to their symptoms at presentation; group 1: polyradiculoneuritis (Bannwarth’s syndrome), group 2: isolated facial palsy and group 3: predominantly meningitic course of the disease. In addition to the CSF of patients with acute LNB, CSF of 19 patients with viral meningitis (VM) and 3 with neurolues (NL) were analyzed. There were 97 patients classified with definite LNB, and 21 as probable LNB. Neck stiffness and fever were reported by 15.3% of patients. Most of these patients were younger than 50 years. Polyradiculoneuritis was frequently found in patients older than 50 years. Lymphopleocytosis was found in all patients. Only 5 patients had a CSF lactate ≥3.5 mmol/l, and the mean CSF lactate level was not elevated (2.1 ± 0.6 mmol/l). The patients with definite LNB had significantly higher lactate levels than patients with probable LNB. Elevated lactate levels were accompanied by fever and headache. In the Reiber nomograms, intrathecal immunoglobulin synthesis was found for IgM in 70.2% followed by IgG in 19.5%. Isoelectric focussing detected an intrathecal IgG synthesis in 83 patients (70.3%). Elevated BB AIs in the CSF were found in 97 patients (82.2%). Patients with VM showed lower CSF protein concentration and CSF/serum quotients of albumin than LNB patients. In acute LNB, all patients had elevated cerebrospinal fluid (CSF) leukocyte counts. In contrast to infections by other bacteria, CSF lactate was lower than 3.5 mmol/l in all but 5 patients. The CSF findings did not differ between polyradiculoneuritis, facial palsy, and meningitis. The CSF in LNB patients strongly differed from CSF in VM patients with respect to protein concentration and the CSF/serum albumin quotient

Martian atmosphere as observed by VIRTIS‐M on Rosetta spacecraft

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95134/1/jgre2651.pd

Detecting life outside our solar system with a large high-contrast-imaging mission

In this White Paper, which was submitted in response to the European Space Agency (ESA) Voyage 2050 Call, we recommend the ESA plays a proactive role in developing a global collaborative effort to construct a large high-contrast imaging space telescope, e.g. as currently under study by NASA. Such a mission will be needed to characterize a sizable sample of temperate Earth-like planets in the habitable zones of nearby Sun-like stars and to search for extraterrestrial biological activity. We provide an overview of relevant European expertise, and advocate ESA to start a technology development program towards detecting life outside the Solar System.Publisher PDFPeer reviewe