Reproducible science: What, why, how

Most scientific papers are not reproducible: it is really hard, if not impossible, to understand how results are derived from data, and being able to regenerate them in the future (even by the same researchers). However, traceability and reproducibility of results are indispensable elements of highquality science, and an increasing requirement of many journals and funding sources. Reproducible studies include code able to regenerate results from the original data. This practice not only provides a perfect record of the whole analysis but also reduces the probability of errors and facilitates code reuse, thus accelerating scientific progress. But doing reproducible science also brings many benefits to the individual researcher, including saving time and effort, improved collaborations, and higher quality and impact of final publications. In this article we introduce reproducible science, why it is important, and how we can improve the reproducibility of our work. We introduce principles and tools for data management, analysis, version control, and software management that help us achieve reproducible workflows in the context of ecology.Peer Reviewe

Ecoinformática: Nuevo grupo de trabajo de la asociación Española de ecología terrestre

Peer Reviewe

Identification of an hepatitis delta virus-like ribozyme at the mRNA 5′-end of the L1Tc retrotransposon from Trypanosoma cruzi

L1Tc is a non-LTR LINE element from Trypanosoma cruzi that encodes its transposition machinery and bears an internal promoter. Herewith, we report the identification of an in vitro active hepatitis delta virus-like ribozyme located in the first 77 nt at the 5′-end of the L1Tc mRNA (L1TcRz). The data presented show that L1TcRz has a co-transcriptional function. Using gel-purified uncleaved RNA transcripts, the data presented indicate that the kinetics of the self-cleaving, in a magnesium-dependent reaction, fits to a two-phase decay curve. The cleavage point identified by primer extension takes place at +1 position of the element. The hydroxyl nature of the 5′-end of the 3′-fragment generated by the cleavage activity of L1TcRz was confirmed. Since we have previously described that the 77-nt long fragment located at the 5′-end of L1Tc has promoter activity, the existence of a ribozyme in L1Tc makes this element to be the first described non-LTR retroelement that has an internal promoter–ribozyme dual function. The L1Tc nucleotides located downstream of the ribozyme catalytic motif appear to inhibit its activity. This inhibition may be influenced by the existence of a specific L1Tc RNA conformation that is recognized by RNase P

Efficient HIV-1 inhibition by a 16 nt-long RNA aptamer designed by combining in vitro selection and in silico optimisation strategies

The human immunodeficiency virus type-1 (HIV-1) genome contains multiple, highly conserved structural RNA domains that play key roles in essential viral processes. Interference with the function of these RNA domains either by disrupting their structures or by blocking their interaction with viral or cellular factors may seriously compromise HIV-1 viability. RNA aptamers are amongst the most promising synthetic molecules able to interact with structural domains of viral genomes. However, aptamer shortening up to their minimal active domain is usually necessary for scaling up production, what requires very time-consuming, trial-and-error approaches. Here we report on the in vitro selection of 64 nt-long specific aptamers against the complete 5' -untranslated region of HIV-1 genome, which inhibit more than 75% of HIV-1 production in a human cell line. The analysis of the selected sequences and structures allowed for the identification of a highly conserved 16 nt-long stem-loop motif containing a common 8 nt-long apical loop. Based on this result, an in silico designed 16 nt-long RNA aptamer, termed RNApt16, was synthesized, with sequence 5'-CCCCGGCAAGGAGGGG-3-'. The HIV-1 inhibition efficiency of such an aptamer was close to 85%, thus constituting the shortest RNA molecule so far described that efficiently interferes with HIV-1 replication

GRASSP: a spectrograph for the study of transient luminous events

We present the main parameters, design features, and optical characterization of the Granada Sprite Spectrograph and Polarimeter (GRASSP), a ground- based spectrographic system intended for the analysis of the spectroscopic signature of transient luminous events (TLEs) occurring in the mesosphere of the Earth. It has been designed to measure the spectra of the light emitted from TLEs with a mean spectral resolution of 0.235 nm and 0.07 nm/px dispersion in the wavelength range between 700 and 800 nm. (C) 2016 Optical Society of AmericaSpanish Ministry of Science and Innovation, Ministerio de Economia y Competitividad (MINECO) (ESP2013-48032-C5-5-R, ESP2015-69909-C5-2-R, FIS2014-61774-EXP); European Union FEDER Program; Ramon y Cajal Contract (RYC-2011-07801).Peer reviewe

Use of Polar Heliostats to Improve Levels of Natural Lighting inside Buildings with Little Access to Sunlight

The growing need to increase environmental and energy sustainability in buildings (housing, offices, warehouses, etc.) requires the use of solar radiation as a renewable source of energy that can help to lower carbon footprint, making buildings more efficient and thereby contributing to a more sustainable planet, while enhancing the health and wellbeing of its occupants. One of the technologies deployed in the use of solar energy in buildings is heliostats. In this context, this paper presents an analysis of the performance of a heliostat illuminator to improve illumination in a classroom at the Campus of Rabanales of the University of Cordoba (Spain). A design of a system in charge of monitoring and measuring daylighting variables using Arduino hardware technology and free software is shown. This equipment develops the communications, programming and collection of lighting data. In parallel, installation of an artificial lighting system complementary to the natural lighting system is implemented. Finally, an analysis of the impact of the proposed solution on the improvement of energy efficiency is presented. Specifically, it is estimated that up to 64% of savings in artificial lighting can be achieved in spaces with heliostatic illuminators compared to those without them

Submicrosecond Spectroscopy of Lightning-Like Discharges: Exploring New Time Regimes

Abstract Submicrosecond (0.476 μs per frame with an exposure time of 160 ns) high-resolution (0.38 nm) time-resolved spectra of laboratory-produced lightning-like electrical discharges have been recorded for the first time within the visible spectral range (645–665 nm). The spectra were recorded with the GrAnada LIghtning Ultrafast Spectrograph (GALIUS), a high-speed imaging spectrograph recently developed for lightning research in the IAA-CSIC. Unprecedented spectral time dynamics are explored for meter long laboratory electrical discharges produced with a 2.0 MV Marx generator. The maximum electron density and gas temperature measured in a timescale of ≤0.50 μs (160 ns) were, respectively, ≃1018 cm−3 and ≃32,000 K. Overpressure in the lightning-like plasma channel, black-body dynamics, and self-absorption in spectral lines were investigated

Nitro-fatty acids in plant signaling: Nitro-linolenic acid induces the molecular chaperone network in Arabidopsis

Nitro-fatty acids (NO-FAs) are the product of the reaction between reactive nitrogen species derived of nitric oxide (NO) and unsaturated fatty acids. In animal systems, NO-FAs are considered novel signaling mediators of cell function based on a proven antiinflammatory response. Nevertheless, the interaction of NO with fatty acids in plant systems has scarcely been studied. Here, we examine the endogenous occurrence of nitro-linolenic acid (NO-Ln) in Arabidopsis and the modulation of NO-Ln levels throughout this plant’s development by mass spectrometry. The observed levels of this NO-FA at picomolar concentrations suggested its role as a signaling effector of cell function. In fact, a transcriptomic analysis by RNA-seq technology established a clear signaling role for this molecule, demonstrating that NO-Ln was involved in plant defense response against different abiotic-stress conditions, mainly by inducing heat shock proteins and supporting a conserved mechanism of action in both animal and plant defense processes. Bioinformatics analysis revealed that NO-Ln was also involved in the response to oxidative stress conditions, mainly depicted by HO, reactive oxygen species, and oxygen-containing compound responses, with a high induction of ascorbate peroxidase expression. Closely related to these results, NO-Ln levels significantly rose under several abiotic-stress conditions such as wounding or exposure to salinity, cadmium, and low temperature, thus validating the outcomes found by RNA-seq technology. Jointly, to our knowledge, these are the first results showing the endogenous presence of NO-Ln in Arabidopsis (Arabidopsis thaliana) and supporting the strong signaling role of these molecules in the defense mechanism against different abiotic-stress situations.C.M.-P. thanks the University of Jaén for funding the Ph.D. fellowship. LC-MS/MS analyses were carried out at the Technical Services Department of the University of Granada, Spain. ACSCs were kindly provided by Dr. Juan Bautista Arellano from the Institute of Natural Resources and Agrobiology (IRNASA-CSIC, Salamanca, Spain).Peer Reviewe

High-resolution spectra of sprites and halos with GRASSP

The first and simultaneous spectroscopic campaigns of TLEs were carried out in the mid 1990s [1, 2], soon after the discovery of TLEs in 1989 [3]. These initial campaigns provided preliminary results on the optical emissions of TLEs corresponding to the first positive system (FPS) of N2(B3¿g) ¿ N2(A3S+u ) in the visible and near infrared (NIR) spectral range (540–840 nm) recorded at standard video rate (30 fps) and at low (between 9 and 6 nm) spectral resolution. More recently, in 2007, spectroscopic observations of sprite optical emissions between 640 nm and 820 nm pro- vided information on the relative vibrational concentrations of the emitting electronic state N2(B3¿g, v’) at differ- ent altitudes using higher video rate (300 fps) and higher spectral resolution (3 nm) spectrographs [4] originally designed for aurora spectroscopy [5]. The above mentioned sporadic TLE spectroscopic campaigns identified some of the key optical emissions from sprites (a type of TLE) and were even able to quantify some of the vibrational concentrations of the emitting levels in reasonable agreement with model predictions [6–8]. However, the best spectral resolution achieved to date is 3 nm and it is not enough to spectrally resolve the different low-lying vibro-rotational transitions of the FPS of N2. This contribution focuses on (1) the latest upgrades of the GRanada Sprite Spectrograph and Polarimeter (GRASSP), a ground-based medium-high spectral resolution spectrograph aimed at characterizing from ground the spectroscopic fingerprints of all sort of TLEs occurring in the mesosphere of the Earth and (2) the GRASSP 2015, 2016 summer-autumn TLE spectroscopic campaign in Europe when we recorded high-resolution spectra of sprite halos and columniform and carrot-like sprites. GRASSP works at 0.235 nm spectral resolution covering the spectral range between 700 nm and 800 nm. The last version of GRASSP is currently installed in Castellgalí, Barcelona (Spain), it is aimed and operated manually by the operator from the UPC group on-site or operated remotely from IAA-CSIC in Granada.Peer ReviewedPreprin

Differential molecular response of monodehydroascorbate reductase and glutathione reductase by nitration and S-nitrosylation

The ascorbate–glutathione cycle is a metabolic pathway that detoxifies hydrogen peroxide and involves enzymatic and non-enzymatic antioxidants. Proteomic studies have shown that some enzymes in this cycle such as ascorbate peroxidase (APX), monodehydroascorbate reductase (MDAR), and glutathione reductase (GR) are potential targets for post-translational modifications (PMTs) mediated by nitric oxide-derived molecules. Using purified recombinant pea peroxisomal MDAR and cytosolic and chloroplastic GR enzymes produced in Escherichia coli, the effects of peroxynitrite (ONOO–) and S-nitrosoglutathione (GSNO) which are known to mediate protein nitration and S-nitrosylation processes, respectively, were analysed. Although ONOO– and GSNO inhibit peroxisomal MDAR activity, chloroplastic and cytosolic GR were not affected by these molecules. Mass spectrometric analysis of the nitrated MDAR revealed that Tyr213, Try292, and Tyr345 were exclusively nitrated to 3-nitrotyrosine by ONOO–. The location of these residues in the structure of pea peroxisomal MDAR reveals that Tyr345 is found at 3.3 Å of His313 which is involved in the NADPbinding site. Site-directed mutagenesis confirmed Tyr345 as the primary site of nitration responsible for the inhibition of MDAR activity by ONOO–. These results provide new insights into the molecular regulation of MDAR which is deactivated by nitration and S-nitrosylation. However, GR was not affected by ONOO– or GSNO, suggesting the existence of a mechanism to conserve redox status by maintaining the level of reduced GSH. Under a nitro-oxidative stress induced by salinity (150 mM NaCl), MDAR expression (mRNA, protein, and enzyme activity levels) was increased, probably to compensate the inhibitory effects of S-nitrosylation and nitration on the enzyme. The present data show the modulation of the antioxidative response of key enzymes in the ascorbate–glutathione cycle by nitric oxide (NO)- PTMs, thus indicating the close involvement of NO and reactive oxygen species metabolism in antioxidant defence against nitro-oxidative stress situations in plants.Spanish GovernmentERDF - Ministry of Economy and Competitiveness BIO2012-33904Junta de Andalucía BIO286 BIO19