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Scrobicularia plana is a coastal and estuarine bivalve widely used in ecotoxicological studies. However, the underlying molecular mechanisms for S. plana pollutant responses are hardly known due to the lack of molecular databases. Thus, in this study we present a holistic approach to assess a robust reference transcriptome and proteome of this clam. A mixture of control and metal-exposed individuals was used for mRNA isolation. Four sets of high quality filtered preprocessed reads were generated (two quality scores and two sequenced lengths) and assembled with Mira, Ray and Trinity algorithms. The sixty-four generated assemblies were refined, filtered and evaluated for their proteomic quality. Eight assemblies presented top Detonate scores but one was selected due to its compactness and biological representation, which was generated: (i) from the highest quality dataset (Q20L100), (ii) using Trinity algorithm with all k-mers (AtKa), (iii) removing redundancy by CD-HIT (RR80), and (iv) filtering out poor contigs (F), that was subsequently named Q20L100AtKaRR80F. S. plana proteomic analysis revealed 10,017 peptide groups that corresponded to 2066 proteins with a wide coverage of molecular functions and biological processes, confirming the strength of the database generated., This study was supported by the Ministry of Economy and Competitiveness, Spain (CTM2016-75908-R). We would like to thank Dr. Mercedes Cousinou and Ms. Laura Redondo (Genomic Unit, SCAI, UCO) for their technical help in transcriptome sequencing. A.M. Herruzo-Ruiz received a predoctoral contract of the University of Cordoba (“Plan Propio”).

Complicated conservation problems may arise if predator numbers increase beyond their natural boundaries due to anthropogenic influence. For example, dramatic declines in ground-nesting birds are linked to increased nest predation by alien or human-subsidized mammals. While predator control can be temporarily effective, it is often laborious and carries ethical issues. Thus, we need alternative, non-lethal methods for reducing predator impact on their prey. We performed a landscape-scale experiment to study whether two non-lethal methods could protect ground-nesting waterfowl from nests predation. We spread either non-rewarding waterfowl odour (chemical camouflage) or eggs containing an aversive agent (conditioned food aversion) in the surroundings of study wetlands located in southern Finland. Predation of artificial waterfowl nests by red foxes decreased in sites with chemical camouflage, while there was no effect on predation by invasive raccoon dogs. Food aversion created less obvious effects than the chemical camouflage, but both methods indicated potential for reducing nest predation. Based on wildlife-camera data mesopredator observations did not, however, decrease near treatment wetlands. This suggests that treatments did not reduce predator activity, but affected foraging behaviour of predators and reduced their ability to find the nests. We conclude that managers considering non-lethal methods should carefully consider the effectiveness of different methods and potential species-specific responses. Nevertheless, our study support calls for wider use of non-lethal methods in reducing predator impacts on prey. These methods offer ethical and potentially effective approaches which keep native predator fauna intact, but create protection for vulnerable prey., Finnish Ministry of Agriculture and Forestry has funded the study via SOTKA-program (for TL and VS). PBB was supported by an ARC Discovery Grant (DP200103148) from the Australian Government. JT benefitted from a postdoctoral contract from the University of Cordoba funded by the Consejería de Transformación Económica, Industria, Conocimiento y Universidades of Junta de Andalucía through the grants program “Plan Andaluz de Investigación, Desarrollo e Innovación (PAIDI 2020)”.

REIPI/GEIH Study Group., Sigma factor B (SigB) controls the expression of Staphylococcus aureus genes including virulence factors and plays a role in the bacterial secretion system through membrane vesicle production. Inhibition of SigB could attenuate SigB dependent virulence and secretion system. The objective of this study was to determine the effects of rhodomyrtone on SigB and virulence factors related to SigB. Minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) values of rhodomyrtone against 67 clinical methicillin-resistant S. aureus isolates were 0.25–8 μg/ml, which were similar to those of vancomycin. Using luciferase gene fused to SigB dependent promoters of asp23, five time reduction in SigB activity was observed when the bacteria were treated with rhodomyrtone for 3 h. Rhodomyrtone significantly reduced SigB activity in a concentration dependent manner in exponentially growing cells (P, This work was financially supported by The Royal Golden Jubilee Ph.D. Program (Grant No. PHD/0033/2553) and TRF Senior Research Scholar (Grant No. RTA 6180006), the Thailand Research Fund. M.J.R.O. was funded by the 'XXII Programa Propio de Fomento de la Investigación', University of Córdoba.

In this work efficient semi-implicit methods for sediment bedload transport models with gravitational effects under subcritical regimes is proposed. Several families of models with gravitational effects are presented and rewritten under a general formulation that allows us to apply the semi-implicit method. In the numerical tests we focus on the application of a generalization of the Ashida-Michiue model, which includes the gradient of both the bedload and the fluid surface. Analytical steady states solutions (both lake at rest and non vanishing velocity) are deduced an approximated with the proposed scheme. In all the pre sented tests, the computational efforts are notably reduced thanks to the proposed method without losing the accuracy in the results Ministerio de Ciencia, Innovación y Universidades RTI2018- 096064-B-C22

PMCID: PMC4104696, In this paper we analyzed changes in hepatocyte mitochondrial mass and ultrastructure as well as in mitochondrial markers of fission/fusion and biogenesis in mice subjected to 40% calorie restriction (CR) for 18. months versus ad libitum-fed controls. Animals subjected to CR were separated into three groups with different dietary fats: soybean oil (also in controls), fish oil and lard. Therefore, the effect of the dietary fat under CR was studied as well. Our results show that CR induced changes in hepatocyte and mitochondrial size, in the volume fraction occupied by mitochondria, and in the number of mitochondria per hepatocyte. Also, mean number of mitochondrial cristae and lengths were significantly higher in all CR groups compared with controls. Finally, CR had no remarkable effects on the expression levels of fission and fusion protein markers. However, considerable differences in many of these parameters were found when comparing the CR groups, supporting the idea that dietary fat plays a relevant role in the modulation of CR effects in aged mice., Supported by NIH grant 1R01AG028125-01A1 (to JJR, PN and JMV), Ministerio de Economía y Competitividad and European FEDERBFU2011-23578 (to JMV), Junta de Andalucía Proyectos de Excelencia grant P09-CVI-4887 (to JMV), Junta de Andalucía Proyectos Internacionales (to JMV), and BIO-276 (Junta de Andalucía and the University of Córdoba, to JMV and EGC). JALD and LFdR were funded by predoctoral fellowships of the Spanish Ministerio de Educación and by BIO-276. HK was funded by a predoctoral fellowship of the Agencia Española de Cooperación Internacional al Desarrollo and by BIO-276.

9 páginas, 5 figuras, 1 tabla., We studied ubiquinone (Q), Q homologue ratio, and steady-state levels of mCOQ transcripts in tissues from mice fed ad libitum or under calorie restriction. Maximum ubiquinone levels on a protein basis were found in kidney and heart, followed by liver, brain, and skeletal muscle. Liver and skeletal muscle showed the highest Q9/Q10 ratios with significant interindividual variability. Heart, kidney, and particularly brain exhibited lower Q9/Q10 ratios and interindividual variability. In skeletal muscle and heart, the most abundant mCOQ transcript was mCOQ7, followed by mCOQ8, mCOQ2, mPDSS2, mPDSS1, and mCOQ3. In nonmuscular tissues (liver, kidney, and brain) the most abundant mCOQ transcript was mCOQ2, followed by mCOQ7, mCOQ8, mPDSS1, mPDSS2, and mCOQ3. Calorie restriction increased both ubiquinone homologues and mPDSS2 mRNA in skeletal muscle, but mCOQ7 was decreased. In contrast, Q9 and most mCOQ transcripts were decreased in heart. Calorie restriction also modified the Q9/Q10 ratio, which was increased in kidney and decreased in heart without alterations in mPDSS1 or mPDSS2 transcripts. We demonstrate for the first time that unique patterns of mCOQ transcripts exist in muscular and nonmuscular tissues and that Q and COQ genes are targets of calorie restriction in a tissue-specific way., This work was supported by NIH Grant 1R01AG028125-01A1 (to J.J.R., P.N., and J.M.V.), Junta de Andalucía Proyectos de Excelencia Grant CVI-00648 (to P.N.), Junta de Andalucía Proyectos de Excelencia Grant P09-CVI-4887 (to J.M.V.), a Junta de Andalucía Proyectos Internacionales grant (to J.M.V.), and BIO-276 (Junta de Andalucía and the University of Córdoba, to J.M.V.). C.P. was funded by Grant CVI-00648.

Current computer engineering evolves at an accelerated pace, with hardware advancing towards new chip multiprocessors (CMP) architectures and with supporting software gearing towards new programming and abstraction paradigms, to obtain the maximum efficiency of the hardware at a low cost. In this context, Tilera Corporation has developed a brand new CMP architecture with 64 cores (tiles) called Tile64, and has launched several Peripheral Component Interconnect Express (PCIe) cards to be used and monitored from a host Personal Computer (PC). These cards may execute parallel applications built in C/C++ and compiled with the Tile-GCC compiler. We have previously demonstrated the usefulness of the Tile64 architecture for bioinformatics [S. Gálvez, D. Díaz, P. Hernández, F.J. Esteban, J.A. Caballero, G. Dorado, Next-generation bioinformatics: using many-core processor architecture to develop a web service for sequence alignment, Bioinformatics, 26 (2010) 683-686]. We have chosen a bioinformatics algorithm to test this many-core Tile64 architecture because of actual bioinformatics challenging needs: data-intensive workloads, space and time-consuming requirements and massive calculation. This algorithm, known as Needleman-Wunsch/Smith-Waterman (NW/SW), obtains an optimal sequence alignment in quadratic time and space cost, yet requires to be optimized to take full advantage of computing parallelization. In this paper we redesign, implement and fine-tune this algorithm, introducing key optimizations and changes that take advantage of specific Tile64 characteristics: RISC architecture, local tile's cache, length of memory word, shared memory usage, RAM file system, tile's intercommunication and job selection from a pool. The resulting algorithm - named MC64-NW/SW for Multicore64 Needleman-Wunsch/Smith-Waterman - achieves a gain of ∼1000% when compared with the same algorithm on a ×86 multi-core architecture. As far as we know, our NW/SW implementation is the fastest ever published for a standalone PC when aligning a pair of sequences larger than 20 kb. © 2011 Elsevier Inc. All rights reserved., This work was supported by “Ministerio de Ciencia e Innovación” (AGL2010-17316 and BIO2009-07443-E grants); “Consejería de Agricultura y Pesca” of “Junta de Andalucía” (041/C/2007, 75/C/2009 and 56/C/2010); “Grupo PAI” (AGR-248); and “Universidad de Córdoba” (“Ayuda a Grupos”), Spain.