Newt-omics: a comprehensive repository for omics data from the newt Notophthalmus viridescens

Notophthalmus viridescens, a member of the salamander family is an excellent model organism to study regenerative processes due to its unique ability to replace lost appendages and to repair internal organs. Molecular insights into regenerative events have been severely hampered by the lack of genomic, transcriptomic and proteomic data, as well as an appropriate database to store such novel information. Here, we describe ‘Newt-omics’ (http://newt-omics.mpi-bn.mpg.de), a database, which enables researchers to locate, retrieve and store data sets dedicated to the molecular characterization of newts. Newt-omics is a transcript-centred database, based on an Expressed Sequence Tag (EST) data set from the newt, covering ∼50 000 Sanger sequenced transcripts and a set of high-density microarray data, generated from regenerating hearts. Newt-omics also contains a large set of peptides identified by mass spectrometry, which was used to validate 13 810 ESTs as true protein coding. Newt-omics is open to implement additional high-throughput data sets without changing the database structure. Via a user-friendly interface Newt-omics allows access to a huge set of molecular data without the need for prior bioinformatical expertise

Airborne methane remote measurements reveal heavy-tail flux distribution in Four Corners region

Methane (CH_4) impacts climate as the second strongest anthropogenic greenhouse gas and air quality by influencing tropospheric ozone levels. Space-based observations have identified the Four Corners region in the Southwest United States as an area of large CH_4 enhancements. We conducted an airborne campaign in Four Corners during April 2015 with the next-generation Airborne Visible/Infrared Imaging Spectrometer (near-infrared) and Hyperspectral Thermal Emission Spectrometer (thermal infrared) imaging spectrometers to better understand the source of methane by measuring methane plumes at 1- to 3-m spatial resolution. Our analysis detected more than 250 individual methane plumes from fossil fuel harvesting, processing, and distributing infrastructures, spanning an emission range from the detection limit ∼2 kg/h to 5 kg/h through ∼5,000 kg/h. Observed sources include gas processing facilities, storage tanks, pipeline leaks, and well pads, as well as a coal mine venting shaft. Overall, plume enhancements and inferred fluxes follow a lognormal distribution, with the top 10% emitters contributing 49 to 66% to the inferred total point source flux of 0.23 Tg/y to 0.39 Tg/y. With the observed confirmation of a lognormal emission distribution, this airborne observing strategy and its ability to locate previously unknown point sources in real time provides an efficient and effective method to identify and mitigate major emissions contributors over a wide geographic area. With improved instrumentation, this capability scales to spaceborne applications [Thompson DR, et al. (2016) Geophys Res Lett 43(12):6571–6578]. Further illustration of this potential is demonstrated with two detected, confirmed, and repaired pipeline leaks during the campaign

A high-throughput screen for the identification of compounds that inhibit nematode gene expression by targeting spliced leader trans-splicing

The work was supported by the Biotechnology and Biological Sciences Research Council [Project grant BB/J007137/1] and a Medical Research Council (MRC) Confidence in Concept (2014) - University of Aberdeen Award (MC_PC_14114v.2). AA was supported by a PhD stipend from the Saudi Arabia. Research data will be made available on requestPeer reviewedPublisher PD

Quantification of CH4 coal mining emissions in Upper Silesia by passive airborne remote sensing observations with the Methane Airborne MAP (MAMAP) instrument during the CO2 and Methane (CoMet) campaign

Methane (CH4) is the second most important anthropogenic greenhouse gas, whose atmospheric concentration is modulated by human-induced activities, and it has a larger global warming potential than carbon dioxide (CO2). Because of its short atmospheric lifetime relative to that of CO2, the reduction of the atmospheric abundance of CH4 is an attractive target for short-term climate mitigation strategies. However, reducing the atmospheric CH4 concentration requires a reduction of its emissions and, therefore, knowledge of its sources. For this reason, the CO2 and Methane (CoMet) campaign in May and June 2018 assessed emissions of one of the largest CH4 emission hot spots in Europe, the Upper Silesian Coal Basin (USCB) in southern Poland, using top-down approaches and inventory data. In this study, we will focus on CH4 column anomalies retrieved from spectral radiance observations, which were acquired by the 1D nadir-looking passive remote sensing Methane Airborne MAPper (MAMAP) instrument, using the weighting-function-modified differential optical absorption spectroscopy (WFM-DOAS) method. The column anomalies, combined with wind lidar measurements, are inverted to cross-sectional fluxes using a mass balance approach. With the help of these fluxes, reported emissions of small clusters of coal mine ventilation shafts are then assessed. The MAMAP CH4 column observations enable an accurate assignment of observed fluxes to small clusters of ventilation shafts. CH4 fluxes are estimated for four clusters with a total of 23 ventilation shafts, which are responsible for about 40 % of the total CH4 mining emissions in the target area. The observations were made during several overflights on different days. The final average CH4 fluxes for the single clusters (or sub-clusters) range from about 1 to 9 t CH4 h−1 at the time of the campaign. The fluxes observed at one cluster during different overflights vary by as much as 50 % of the average value. Associated errors (1σ) are usually between 15 % and 59 % of the average flux, depending mainly on the prevailing wind conditions, the number of flight tracks, and the magnitude of the flux itself. Comparison to known hourly emissions, where available, shows good agreement within the uncertainties. If only emissions reported annually are available for comparison with the observations, caution is advised due to possible fluctuations in emissions during a year or even within hours. To measure emissions even more precisely and to break them down further for allocation to individual shafts in a complex source region such as the USCB, imaging remote sensing instruments are recommended

Current trends in the cardiovascular clinical trial arena (I)

The existence of effective therapies for most cardiovascular disease states, coupled with increased requirements that potential benefits of new drugs be evaluated on clinical rather than surrogate endpoints, makes it increasingly difficult to substantiate any incremental improvements in efficacy that these new drugs might offer. Compounding the problem is the highly controversial issue of comparing new agents with placebos rather than active pharmaceuticals in drug efficacy trials. Despite the recent consensus that placebos may be used ethically in well-defined, justifiable circumstances, the problem persists, in part because of increased scrutiny by ethics committees but also because of considerable lingering disagreement regarding the propriety and scientific value of placebo-controlled trials (and trials of antihypertensive drugs in particular). The disagreement also substantially affects the most viable alternative to placebo-controlled trials: actively controlled equivalence/noninferiority trials. To a great extent, this situation was prompted by numerous previous trials of this type that were marked by fundamental methodological flaws and consequent false claims, inconsistencies, and potential harm to patients. As the development and use of generic drugs continue to escalate, along with concurrent pressure to control medical costs by substituting less-expensive therapies for established ones, any claim that a new drug, intervention, or therapy is "equivalent" to another should not be accepted without close scrutiny. Adherence to proper methods in conducting studies of equivalence will help investigators to avoid false claims and inconsistencies. These matters will be addressed in the third article of this three-part series