Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the Drosophila melanogaster group

Here, we provide revised gene models for D. ananassae, D. yakuba, and D. simulans, which include UTRs and empirically verified intron-exon boundaries, as well as ortholog groups identified using a fuzzy reciprocal-best-hit blast comparison. Using these revised annotations, we perform differential expression testing using the cufflinks suite to provide a broad overview of differential expression between reproductive tissues and the carcass. We identify thousands of genes that are differentially expressed across tissues in D. yakuba and D. simulans, with roughly 60% agreement in expression patterns of orthologs in D. yakuba and D. simulans. We identify several cases of putative polycistronic transcripts, pointing to a combination of transcriptional read-through in the genome as well as putative gene fusion and fission events across taxa. We furthermore identify hundreds of lineage specific genes in each species with no blast hits among transcripts of any other Drosophila species, which are candidates for neofunctionalized proteins and a potential source of genetic novelty.Comment: Revised manuscript, also available online preprint at G3: Genes, Genomes, Genetics. Gene models, ortholog calls, and tissue specific expression results are available at http://github.com/ThorntonLab/GFF or the UCSC browser on the Thornton Lab public track hub at http://genome.ucsc.ed

Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans

We have used whole genome paired-end Illumina sequence data to identify tandem duplications in 20 isofemale lines of D. yakuba, and 20 isofemale lines of D. simulans and performed genome wide validation with PacBio long molecule sequencing. We identify 1,415 tandem duplications that are segregating in D. yakuba as well as 975 duplications in D. simulans, indicating greater variation in D. yakuba. Additionally, we observe high rates of secondary deletions at duplicated sites, with 8% of duplicated sites in D. simulans and 17% of sites in D. yakuba modified with deletions. These secondary deletions are consistent with the action of the large loop mismatch repair system acting to remove polymorphic tandem duplication, resulting in rapid dynamics of gain and loss in duplicated alleles and a richer substrate of genetic novelty than has been previously reported. Most duplications are present in only single strains, suggesting deleterious impacts are common. D. simulans shows larger numbers of whole gene duplications in comparison to larger proportions of gene fragments in D. yakuba. D. simulans displays an excess of high frequency variants on the X chromosome, consistent with adaptive evolution through duplications on the D. simulans X or demographic forces driving duplicates to high frequency. We identify 78 chimeric genes in D. yakuba and 38 chimeric genes in D. simulans, as well as 143 cases of recruited non-coding sequence in D. yakuba and 96 in D. simulans, in agreement with rates of chimeric gene origination in D. melanogaster. Together, these results suggest that tandem duplications often result in complex variation beyond whole gene duplications that offers a rich substrate of standing variation that is likely to contribute both to detrimental phenotypes and disease, as well as to adaptive evolutionary change.Comment: Revised Version- Accepted at Molecular Biology and Evolutio

Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content

BACKGROUND: Introns comprise a large fraction of eukaryotic genomes, yet little is known about their functional significance. Regulatory elements have been mapped to some introns, though these are believed to account for only a small fraction of genome wide intronic DNA. No consistent patterns have emerged from studies that have investigated general levels of evolutionary constraint in introns. RESULTS: We examine the relationship between intron length and levels of evolutionary constraint by analyzing inter-specific divergence at 225 intron fragments in Drosophila melanogaster and Drosophila simulans, sampled from a broad distribution of intron lengths. We document a strongly negative correlation between intron length and divergence. Interestingly, we also find that divergence in introns is negatively correlated with GC content. This relationship does not account for the correlation between intron length and divergence, however, and may simply reflect local variation in mutational rates or biases. CONCLUSION: Short introns make up only a small fraction of total intronic DNA in the genome. Our finding that long introns evolve more slowly than average implies that, while the majority of introns in the Drosophila genome may experience little or no selective constraint, most intronic DNA in the genome is likely to be evolving under considerable constraint. Our results suggest that functional elements may be ubiquitous within longer introns and that these introns may have a more general role in regulating gene expression than previously appreciated. Our finding that GC content and divergence are negatively correlated in introns has important implications for the interpretation of the correlation between divergence and levels of codon bias observed in Drosophila

Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship

International audienceIn Drosophila, male flies perform innate, stereotyped courtship behavior. This innate behavior evolves rapidly between fly species, and is likely to have contributed to reproductive isolation and species divergence. We currently understand little about the neurobiological and genetic mechanisms that contributed to the evolution of courtship behavior. Here we describe a novel behavioral difference between the two closely related species D. yakuba and D. santomea: the frequency of wing rowing during courtship. During courtship, D. santomea males repeatedly rotate their wing blades to face forward and then back (rowing), while D. yakuba males rarely row their wings. We found little intraspecific variation in the frequency of wing rowing for both species. We exploited multiplexed shotgun genotyping (MSG) to genotype two backcross populations with a single lane of Illumina sequencing. We performed quantitative trait locus (QTL) mapping using the ancestry information estimated by MSG and found that the species difference in wing rowing mapped to four or five genetically separable regions. We found no evidence that these loci display epistasis. The identified loci all act in the same direction and can account for most of the species difference

Hill chart modelling using the Hermite polynomial chaos expansion for the performance prediction of pumps running as turbines

Pumps running as turbines are suitable hydraulic machines for micro hydropower applications. The selection of the proper pumps to install in a given site still remains a major challenge, as pump manufacturers do not provide the characteristic curves data in the turbine mode. Also, the accurate prediction and modelling of the pumps running as turbines characteristic curves still remain a major difficulty as existing methodologies still lack ac-curacy, especially in the part load and full load operating regions. This paper proposes a new two-step methodology based on the Hermite polynomial chaos expansion for predicting the characteristic curves of pumps running as turbines and modelling their variable speed operation, aiming at improving the prediction accuracy. Firstly, bivariate continuous surrogate functions are established for predicting the turbine mode and the ex-tended operation mode characteristic curves inside a closed interval of unit specific speed values. These surrogate functions are developed by calibrating empirical coefficients based on collected experimental data. Secondly, a hill chart model is determined for describing the variable speed operation of a given pump running as a turbine. This hill chart model allows identifying the discharge and the rotational speed set points for maximising efficiency for a given operating condition. The proposed prediction surrogate functions and the variable speed hill chart model are useful engineering tools for improving the design of pump as turbine hydropower plants and for optimising the pump running as turbine control settings to maximise the produced energy

Simulation of energy recovery on water utility networks by a micro-turbine with counter-rotating runners

Wherever relief valves and other energy dissipation devices are installed to limit the pressure, water utility networks provide unexploited hydropower potentials. This is mainly due to a lack of economically viable technologies for energy recovery in the pico and micro hydropower range below 100 kW. Micro-turbine with counter-rotating runners proved suitable to harvest these potentials with limited investments and almost no environmental impact. An appropriate command strategy must therefore be applied to maximize the recovered energy. This paper deals with the construction of a Virtual Energy Recovery Station (VERS) model to simulate the energy recovery on a given installation site. It includes models of the turbine, of the water consumption and it allows to implement various command strategies. The VERS can serve various purposes. The fine-tuning of the command algorithm for a specific installation site is demonstrated in the paper

AVALIAÇÃO DA ATIVIDADE ANTIMICROBIANA DE METABÓLITOS SECUNDÁRIOS PRODUZIDOS POR ACTINOBACTÉRIAS FRENTE À ISOLADOS CLÍNICOS DE ESCHERICHIA COLI ORIUNDAS DE INFECÇÕES DO TRATO URINÁRIO

As infecções do trato urinário (ITU) estão entre as principais doenças infecciosas evidenciadas na prática clínica, sendo o principal agente causador a bactéria Escherichia coli. A exposição frequente desta bactéria aos antimicrobianos vem acarretando o desenvolvimento de mecanismos de resistência, tornando-se necessário a obtenção de novos medicamentos com ação bactericida ou bacteriostática. Neste sentido, as actinobactérias se destacam pelo notável potencial na produção de novos compostos antibacterianos. O objetivo deste trabalho foi avaliar a atividade antimicrobiana de metabólitos secundários produzidos por actinobactérias frente à isolados clínicos de E. coli oriundos de infecções do trato urinário. Para tanto, foram empregados 88 isolados de actinobactérias provenientes da rizosfera de plantas. Como microrganismos teste utilizou-se um isolado de E. coli sensível e um resistente a antimicrobianos, bem como uma cepa ATCC 25922 desta espécie, como controle. Dos 88 isolados de actinobactérias testados, 9,10% (8) apresentaram atividade antimicrobiana frente aos isolados de E. coli. Destacaram-se os isolados R18(6), CT-149, M1-2, M1-23 de actinobactérias, pois apresentaram os melhores índices de antibiose (IA) respectivamente, sendo que o isolado de actinobactéria que apresentou o maior índice de antibiose aos isolados de E. coli foi o isolado R18(6) com IA= 4,28. Os resultados demostram que os metabólitos secundários das actinobactérias contra espécies patogênicas de E. coli, são uma fonte viável de compostos bioativos para a produção de novos antimicrobianos

Evidence for Pervasive Adaptive Protein Evolution in Wild Mice

The relative contributions of neutral and adaptive substitutions to molecular evolution has been one of the most controversial issues in evolutionary biology for more than 40 years. The analysis of within-species nucleotide polymorphism and between-species divergence data supports a widespread role for adaptive protein evolution in certain taxa. For example, estimates of the proportion of adaptive amino acid substitutions (alpha) are 50% or more in enteric bacteria and Drosophila. In contrast, recent estimates of alpha for hominids have been at most 13%. Here, we estimate alpha for protein sequences of murid rodents based on nucleotide polymorphism data from multiple genes in a population of the house mouse subspecies Mus musculus castaneus, which inhabits the ancestral range of the Mus species complex and nucleotide divergence between M. m. castaneus and M. famulus or the rat. We estimate that 57% of amino acid substitutions in murids have been driven by positive selection. Hominids, therefore, are exceptional in having low apparent levels of adaptive protein evolution. The high frequency of adaptive amino acid substitutions in wild mice is consistent with their large effective population size, leading to effective natural selection at the molecular level. Effective natural selection also manifests itself as a paucity of effectively neutral nonsynonymous mutations in M. m. castaneus compared to humans

Engineering & Performance of DuoTurbo: Microturbine with Counter-Rotating Runners

Considering the nuclear phase-out strategy of several European countries and the future tendency to promote renewable energies, the exploitation of small hydropower sites (<10 MW) becomes increasingly important. In this framework DuoTurbo Turbine, a new DuoTurbo-microturbine prototype for drinking water networks has been jointly developed by the HES-SO Valais//Wallis , the EPFL-Laboratory for Hydraulic Machines and industrial partners. The modular in- line “plug & play” technology requires low investment, reaching economic feasibility with an available power between 5 kW and 25 kW. One stage of the microturbine consists of two axial counter-rotating runners that form a compact independent unit. Each runner of the turbine holds its own rim generator, the DuoTurbo-configuration involving that each hydraulic runner is integral with each electrical rotor. The possibility of stacking several stages in series enables covering quite a wide range of hydraulic power and, thus, recovering a maximum of energy dissipated in release valves of water supply systems. The present work introduces the global concept of the implemented prototype of the DuoTurbo-microturbine, to target a maxim al injected power of 5 kW for a discharge of 9 l/ s and a head of 24.5 m per stage. The main features of the hydraulic, the mechanical, the electrical and the electronic design are presented. The hydraulic performance is, then, assessed using CFD simulations for the expected operating range. Finally, the performance measurements of the single-stage prototype installed in the hydraulic test rig of the HES-SO Valais//Wallis are presented