Testimonial Disclosure:Testimonials appearing on www.strategyquant.com may not be representative of the experience of other clients or customers and is not a guarantee of future performance or success.
Strategy Quant EA Wizard.133
Whole genome data sequences of strains SB and GN were obtained by using an Illumina pair end strategy. Briefly, genomic DNA was extracted from a saturated culture of 100 ml under anaerobic condition (YPD) using the genomic tip-100 kit (Qiagen, Courtaboeuf, FRANCE). Paired-end Illumina sequencing libraries were prepared from sonicated genomic DNA according to manufacturer protocols (Genomic DNA Sample Preparation) and were carried out by the Genomic and Transcriptomic facility of Bordeaux, FRANCE. Sequencing was performed on Illumina Genome Analyzer IIx (Illumina, CA) with a read length of 54 pb. The genome of both strains was first mapped on the reference genome using stampy program. The detection of SNP and short INDEL was carried out according to different criterions such alignment quality, read coverage, and genotype quality using the SAMtools mpileup [45] and vcftools programs [46]. The SNP and their relative effect of protein sequence were determined by snpEff. De novo assembly was then carried out using mira3 [47] with 8 iterations. In this work we specially analyzed the contigs c343 and c23 of GN as well as c9 and c7 of SB containing the genes present in the dissected QTL. The annotated contig c343 and c23 of the strain GN containing the newly described XV-t-XVI translocation was deposited on EMBL database with the following study accession number: PRJEB4706.
In a previous work [44] we identified by QTL mapping a major locus controlling the time necessary to initiate the alcoholic fermentation in winemaking conditions (lag phase). This QTL named QTL-XV was narrowed between the gene HAL9 (YOL089c) and ATG19 (YOL082w) in a region of nearly 20 kb containing 8 genes. The aim of this work is to dissect this QTL and find the genetic polymorphisms explaining the phenotypic difference between the parental strains SB and GN. By sequencing the whole genome of parental strains using an Illumina pair end strategy, between the parental strains, 33 Single Nucleotide Polymorphisms were detected in this region generation fifteen non synonymous mutations affecting five genes (Table S3). Putative deleterious mutations were found for two of them (HAL9 and ATG34) and we tested their impact on lag phase by reciprocal hemizygosity assay (RHA) according to Steinmetz et al. [6] (Figure S1 and S2). This first tentative failed to identify the cause of lag phase difference suggesting the role of other genetic modifications such as gross chromosomal rearrangements. To identify such modifications, the genomes of parental strains SB and GN were de novo assembled generating between 360 to 400 contigs per strains (Table S4). We used as query sequence, the 20 kb region of QTL-XV of the strain S288c and we carried out a blastn analysis against the parental set of de novo contigs. For the strain SB the entire sequence match with one contig showing the same syntheny than S288c strain. In contrast for the parental strain GN, we found evidence for a reciprocal translocation between the chromosome XV and the chromosome XVI covered by the contigs c343 and c23. The translocation event was localized between the coding sequences of ADH1 and PHM7 (chromosome XV) and between the coding sequence of SSU1 and NOG1 (chromosome XVI). The exact chromosomal break point occurs at the position 161342 and 373561 for the chromosome XV and XVI, respectively, as confirmed by PCR sequencing. This break point occurs in a low complexity AT rich region without evident homology between chromosomes. As shown in Figure 1, this chromosomal rearrangement generates one XV-t-XVI chromosome, remodeling the promoter environment of the SSU1 gene. This gene encodes for a plasma membrane protein playing a major role in sulfite detoxification. The expression regulation of SSU1 has been widely investigated in the past and depends on the transcription factor Fzf1p, a protein subjected to positive selection within Saccharomyces species [54] and among wine S. cerevisiae strains [42]. In the translocation XV-t-XVI described in this work, the start codon of SSU1 is then located at 501 bp of an Fzf1p binding site (CTATCA) and at 607 bp of an Adr1p binding site (GGGGG) known to activate the transcription of alcohol dehydrogenase during fermentation conditions [55]. The presence of these promoter regions suggest that the expression of this gene might be enhanced. The role of the SSU1 gene in lag phase was further investigated by analyzing the time course of cell growth and CO2 production during the first hours of alcoholic fermentation by RHA. As shown in Figure 2, the SSU1GN allele allowed initiating the fermentation 28.3 h sooner than its SSU1SB counterpart (Wilcoxon test, p
You simply create a new strategy in your supported platform, copy a source code from StrategyQuant and you can backtest or trade it.You can use data from us or from any other source. You can also write down the strategy rules and trade it manually if you want.
Feeding on plant material is common among animals, but how different animals overcome the dietary deficiencies imposed by this feeding strategy is not well understood. Microorganisms are generally considered to play a vital role in the nutritional ecology of plant feeding animals. Commonly microbes living inside animal bodies are considered more important, but recent studies suggest external microbes significantly shape plant-feeding strategies in invertebrates. Here we investigate how external microbes that typically form biofilm on primary plant material affect growth rates in a terrestrial isopod species Porcellio scaber. We experimentally manipulated the amount of biofilm on three different primary diet sources and quantified growth and survival of individuals that fed on food with either a small or large amount of biofilm. In addition, we tested how dietary manipulation shapes the composition of bacterial communities in the gut. The presence of visible biofilm significantly affected the growth of isopods: individuals that fed on the primary diet source with a large amount of biofilm gained more mass than individuals feeding on a diet with marginal biofilm. Diet also significantly affected the bacterial gut community. The primary diet source mainly determined the taxonomic composition of the bacterial community in the isopod gut, whereas the amount of biofilm affected the relative abundance of bacterial taxa. Our study suggests that terrestrial isopods may cope with low-quality plant matter by feeding on biofilm, with decomposition of plant material by organisms outside of the feeding organism (here a terrestrial isopod) probably playing a major role. Future investigations may be directed towards the primary diet source, plant matter, and the secondary diet source, biofilm, and should assess if both components are indeed uptaken in detritivorous species.
Plant material is the common food source for herbivorous and detritivorous animals, although it has low nutritional quality and is difficult to digest. While herbivores may not obtain enough nitrogen by feeding on living plants (Pierce and Berry 2011), the nutrient content of dead plant material is even lower for detritivorous species (Zimmer 2002a). Nevertheless, many herbivores and detritivores successfully consume plant material, but how they actually meet their nutritional requirements is still an unresolved question (but see Filipiak and Weiner 2014). Animals have employed different strategies to compensate for low-quality diet by simply processing more food per unit time (Woods 1999) or aggregate in social groups to have better access to food (Lihoreau et al. 2015). Herbivores benefit from mutualistic associations with symbionts that provide them with essential nutrients (e.g. aphids and amino acid requirements, Gunduz and Douglas 2009), and detritivorous species may profit from microbial colonization of dead plant material (Kautz et al. 2002; Zimmer 2002a; Zimmer et al. 2003). Another strategy used by wood boring beetles promotes a significant nutritional contribution of fungi that are ingested along with decomposed wood (Filipiak and Weiner 2014; Tanahashi et al. 2009). Beetles thus may cover their nutritional needs by feeding on an organism that itself lives on plant material.
To test for the general role of biofilm as an important food source for detritivorous isopods, we experimentally manipulated the amount of biofilm. We offered a primary diet source ad libitum, but we replaced the diet either after two days or after eight days, which allowed biofilm to develop on the primary diet source for different periods of time (see Figure 1B). Even after 8 days the primary food pellet was not substantially consumed indicating true ad libitum conditions with respect to primary food source for both, 2-day and 8-day groups. However, our feeding regime also resulted in a much larger amount of biofilm in the 8-day group from day two onwards, the day when the food pellet was replaced with a new one only in the 2-day treatment. We quantified the nutritional contribution of biofilm by determining the growth and survival rates of individuals of the terrestrial isopod species Porcellio scaber Latreille, 1804 that fed on three different primary diet sources, each overgrown by either low or high amount of biofilm. We also estimated microbial community composition in the gut for a subset of individuals by 16S metagenomics. We used the species P. scaber which is considered to feed on plant material and is generally described as a detritivore, though it preferentially feeds on a diet inoculated with microbes (Ihnen and Zimmer 2008). We tested the following predictions: i) a primary diet source with a large amount of biofilm improves the growth and survival of individuals compared to a primary diet source with a small amount of biofilm, and ii) a similar amount of biofilm, regardless of the primary diet source, promotes similar patterns of isopod growth and survival. Bacterial communities of biofilm are mainly shaped by the type of substrate (Li et al. 2014) and the formation of biofilm is also characterized by the proliferation of attached microbial cells and by changes in species composition (effect of time, Sauer et al. 2002). Therefore, we further predicted that iii) the primary diet source or iv) the amount of biofilm on the primary diet source, affect bacterial gut communities in terms of taxonomic composition and the relative abundance of particular taxa. 2ff7e9595c
Comments