Identification of a novel gene encoding a flavin-dependent tRNA:m(5)U methyltransferase in bacteria—evolutionary implications

Formation of 5-methyluridine (ribothymidine) at position 54 of the T-psi loop of tRNA is catalyzed by site-specific tRNA methyltransferases (tRNA:m(5)U-54 MTase). In all Eukarya and many Gram-negative Bacteria, the methyl donor for this reaction is S-adenosyl-l-methionine (S-AdoMet), while in several Gram-positive Bacteria, the source of carbon is N(5), N(10)-methylenetetrahydrofolate (CH(2)H(4)folate). We have identified the gene for Bacillus subtilis tRNA:m(5)U-54 MTase. The encoded recombinant protein contains tightly bound flavin and is active in Escherichia coli mutant lacking m(5)U-54 in tRNAs and in vitro using T7 tRNA transcript as substrate. This gene is currently annotated gid in Genome Data Banks and it is here renamed trmFO. TrmFO (Gid) orthologs have also been identified in many other bacterial genomes and comparison of their amino acid sequences reveals that they are phylogenetically distinct from either ThyA or ThyX class of thymidylate synthases, which catalyze folate-dependent formation of deoxyribothymine monophosphate, the universal DNA precursor

Lack of dietary polyunsaturated fatty acids causes synapse dysfunction in the drosophila visual system

Polyunsaturated fatty acids (PUFAs) are essential nutrients for animals and necessary for the normal functioning of the nervous system. A lack of PUFAs can result from the consumption of a deficient diet or genetic factors, which impact PUFA uptake and metabolism. Both can cause synaptic dysfunction, which is associated with numerous disorders. However, there is a knowledge gap linking these neuronal dysfunctions and their underlying molecular mechanisms. Because of its genetic manipulability and its easy, fast, and cheap breeding, Drosophila melanogaster has emerged as an excellent model organism for genetic screens, helping to identify the genetic bases of such events. As a first step towards the understanding of PUFA implications in Drosophila synaptic physiology we designed a breeding medium containing only very low amounts of PUFAs. We then used the fly’s visual system, a well-established model for studying signal transmission and neurological disorders, to measure the effects of a PUFA deficiency on synaptic function. Using both visual performance and eye electrophysiology, we found that PUFA deficiency strongly affected synaptic transmission in the fly’s visual system. These defects were rescued by diets containing omega-3 or omega-6 PUFAs alone or in combination. In summary, manipulating PUFA contents in the fly’s diet was powerful to investigate the role of these nutrients on the fly´s visual synaptic function. This study aims at showing how the first visual synapse of Drosophila can serve as a simple model to study the effects of PUFAs on synapse function. A similar approach could be further used to screen for genetic factors underlying the molecular mechanisms of synaptic dysfunctions associated with altered PUFA levels

Copper toxicity on coral holobiont photosynthetic processes

Copper (Cu), an essential micronutrient to organisms, may become toxic when present at too high environmental concentrations. This metal remains an aquatic contaminant of concern, notably because of its recent re-use as biocide in metal-based antifouling paints. The aim of this study was to monitor the physiological alterations in a zooxanthellate coral species and its endosymbionts (i.e. the coral holobiont) exposed to increasing Cu concentrations. Nubbins of Seriatopora hystrix were exposed for 8 days in 1 L intermittent respirometers to 5 nominal Cu concentrations: 0-2-5-15-50 ppb. Respirometers were maintained at 25.0±0.2°C with successive open/close cycles of 30 min. A 12/12 hours day-night light regime was applied with constant daylight intensity of 200 μmol photons m-2 s-1. Water renewal rate during the 30 min open cycles was 15 mL.min-1. The photosynthetic performances of coral endosymbionts were assessed daily with a fluorescence imaging system (imaging-PAM). At the end of the 8-days experiment, the maximal photochemical quantum yield (FV/FM) of coral nubbins had decreased by 12% and 38%, respectively, in the 15 ppb and 50 ppb treatments. This decrease was even greater for the effective photochemical quantum yield (ɸPSII) with values dropping by 41% and 54%, respectively. Cu exposure also affected the symbiosis between the coral host and its endosymbionts. Nubbins of the 15 ppb treatment slightly lightened from day 6, whilst nubbins exposed to the 50 ppb treatment lightened from day 3, and started to bleach from day 6. The analysis of nubbins' primary productivity did not coincide with the above observations, the oxygen production within each respirometer remaining relatively constant during the overall experiment for all treatments. This unexpected observation may be the sign of a compensation mechanism. In conclusion, Cu affected the photosynthetic processes of S. histrix within 8 days from relevant environmental concentrations of 15 ppb. The exposure of corals to toxic chemicals thus has to be considered as an additional stressor to, e.g., ocean acidification or elevated temperature, which may disturb their ecophysiology and lead to bleaching

Aircraft Numerical "Twin": A Time Series Regression Competition

International audienceThis paper presents the design and analysis of a data science competition on a problem of time series regression from aeronautics data. For the purpose of performing predictive maintenance, aviation companies seek to create aircraft "numerical twins", which are programs capable of accurately predicting strains at strategic positions in various body parts of the aircraft. Given a number of input parameters (sensor data) recorded in sequence during the flight, the competition participants had to predict output values (gauges), also recorded sequentially during test flights, but not recorded during regular flights. The competition data included hundreds of complete flights. It was a code submission competition with complete blind testing of algorithms. The results indicate that such a problem can be effectively solved with gradient boosted trees, after preprocessing and feature engineering. Deep learning methods did not prove as efficient

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

FIGURE 3 in Description of two Staurois tadpoles from Borneo, Staurois parvus and Staurois tuberilinguis (Anura: Ranidae)

FIGURE 3. Dorsal (A) and lateral (B) views of the tadpole of Staurois parvus (MNHN-RA 2012.342, Stage 35, TL 37.3 mm), scale bar 10 mm.Published as part of Grosjean, Stéphane, 2020, Description of two Staurois tadpoles from Borneo, Staurois parvus and Staurois tuberilinguis (Anura: Ranidae), pp. 523-534 in Zootaxa 4896 (4) on page 528, DOI: 10.11646/zootaxa.4896.4.4, http://zenodo.org/record/438782

FIGURE 2 in Description of two Staurois tadpoles from Borneo, Staurois parvus and Staurois tuberilinguis (Anura: Ranidae)

FIGURE 2. Oral disc of Staurois tuberilinguis (MNHN-RA 2012.330, Stage 34, TL 46.6 mm), scale bar 1 mm (A); keratodonts of the row A1 of the tadpole of S. tuberilinguis (MNHN-RA unnumbered, Stage 31), scale bar 50 µm (B).Published as part of Grosjean, Stéphane, 2020, Description of two Staurois tadpoles from Borneo, Staurois parvus and Staurois tuberilinguis (Anura: Ranidae), pp. 523-534 in Zootaxa 4896 (4) on page 526, DOI: 10.11646/zootaxa.4896.4.4, http://zenodo.org/record/438782

The tadpole of Leptobrachium (Vibrissaphora) echinatum (Amphibia, Anura, Megophryidae)

Grosjean, Stéphane (2001): The tadpole of Leptobrachium (Vibrissaphora) echinatum (Amphibia, Anura, Megophryidae). Zoosystema 23 (1): 143-156, DOI: http://doi.org/10.5281/zenodo.539421

FIGURE 1 in Description of two Staurois tadpoles from Borneo, Staurois parvus and Staurois tuberilinguis (Anura: Ranidae)

FIGURE 1. Dorsal (A) and lateral (B) views of the tadpole of Staurois tuberilinguis (MNHN-RA 2012.330, Stage 34, TL 46.6 mm), scale bar 10 mm.Published as part of Grosjean, Stéphane, 2020, Description of two Staurois tadpoles from Borneo, Staurois parvus and Staurois tuberilinguis (Anura: Ranidae), pp. 523-534 in Zootaxa 4896 (4) on page 526, DOI: 10.11646/zootaxa.4896.4.4, http://zenodo.org/record/438782