Environmental modification via a quorum sensing molecule influences the social landscape of siderophore production

Bacteria produce a wide variety of exoproducts that favourably modify their environment and increase their fitness. These are often termed ‘public goods’ because they are costly for individuals to produce and can be exploited by non-producers (‘cheats’). The outcome of conflict over public goods is dependent upon the prevailing environment and the phenotype of the individuals in competition. Many bacterial species use quorum sensing (QS) signalling molecules to regulate the production of public goods. QS therefore determines the cooperative phenotype of individuals, and influences conflict over public goods. In addition to their regulatory functions, many QS molecules have additional properties that directly modify the prevailing environment. This leads to the possibility that QS molecules could influence conflict over public goods indirectly through non-signalling effects, and the impact of this on social competition has not previously been explored. The Pseudomonas aeruginosa QS signal molecule PQS is a powerful chelator of iron which can cause an iron starvation response. Here we show that PQS stimulates a concentration-dependent increase in the cooperative production of iron scavenging siderophores, resulting in an increase in the relative fitness of non-producing siderophore cheats. This is likely due to an increased cost of siderophore output by producing cells and a concurrent increase in the shared benefits, which accrue to both producers and cheats. Although PQS can be a beneficial signalling molecule for P. aeruginosa, our data suggests that it can also render a siderophore-producing population vulnerable to competition from cheating strains. More generally our results indicate that the production of one social trait can indirectly affect the costs and benefits of another social trait

Data from Maturation of the 90S pre-ribosome requires Mrd1 dependent U3 snoRNA and 35S pre-rRNA structural rearrangements

Two different ribosomal RNA species were probed with 1M7 This series contains 4 samples re-analyzed from GSE83821. The raw data associated with these samples in this series (GSM2856218-GSM286221) include the barcodes not present in the raw data from the original samples from GSE83821 (GSM2219115-GSM2219118).In eukaryotes, biogenesis of ribosomes requires folding and assembly of the precursor rRNA (pre-rRNA) with a large number of proteins and snoRNPs into huge RNA-protein complexes. In spite of intense genetic, biochemical and high resolution cryo-EM studies in Saccharomyces cerevisiae, information about the conformation of the earliest 35S pre-rRNA is limited. To overcome this, we performed high-throughput SHAPE chemical probing on the 35S pre-rRNA associated with 90S pre-ribosomes. We focused our analyses on external (5´ETS) and internal (ITS1) transcribed spacers as well as the 18S region. We show that in the 35S pre-rRNA, the central region of the 18S is in a more open configuration compared to 20S pre-rRNA and that the central pseudoknot is not formed. The essential ribosome biogenesis protein Mrd1 influences the structure of the 18S part locally and is involved in organizing the central pseudoknot and surrounding structures. Our results demonstrate that the U3 snoRNA dynamically interacts with the 35S pre-rRNA and that Mrd1 is required for disrupting U3 snoRNA base-pairing interactions in the 5'ETS. We propose that the dynamic U3 snoRNA interactions and Mrd1 are essential for establishing the structure of the central region of 18S that is required for processing and 40S subunit function.The ChemModSeq next generation sequencing data and processed data (counts for RT stops and read coverage over 35S) is available from the NCBI Gene Expression Omnibus (GEO) under accession number GSE106868. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10686

Spatiotemporal clock patterns in the leaf blade

We used luciferase reporter gene imaging to monitor circadian rhythms in leaves of Arabidopsis thaliana plants, achieving resolution close to the cellular level. Leaves grown without environmental cycles for up to 3 wk reproducibly showed spatiotemporal waves of gene expression consistent with intercellular coupling, using several reporter genes. This dataset contains: 1) Experiments performed by Benedicte Wenden: - 35S_LL_120310 - CCA1_LDgrownLLimaged_180310 - CCA1_LL_040210 - CCA1_LL_251109 - CCR2_LL_300610 - TOC1_LL_140710 2) Experiments performed by Sarah Hodge after the publication of Wenden et al., 2012: - 2012-CCA1-Sarah_Hodge-good_quality - 2012-CCA1-Sarah_Hodge-med_qualityMillar, Andrew; Wenden, Benedicte; Hodge, Sarah. (2021). Spatiotemporal clock patterns in the leaf blade, [dataset]. University of Edinburgh. School of Biological Sciences. SynthSys.. https://doi.org/10.7488/ds/3030

ChromarFM

FM-lite and FM-life model files in the Haskell implementation of modelling language Chroma

Parallel speciation in Antirrhinum

The dataset comprises four files. 1) Alpujarra_Antirrhinum_species_AFLP_genotypes.txt contains amplified fragment length polymorphism (AFLP) genotypes of wild populations of five Antirrhinum species (A. barrelieri, A. rupestre, A. hispanicum, A. molle and A. tortuosum) from the Alpujarra region of southeast Spain. 2) Alpujarra_Antirrhinum_species_phenotypes.txt contains phenotype data for the same populations. 3) A.barrelieri_x_A.rupestre_F2_traits_and_genotypes.txt contains restriction-site associated DNA (RAD) genotypes and phenotype data for an F2 population of A. barrelieri x A. rupestre, the F1 parents and species grandparents. 4) Key_to_RAD_indices.txt contains the index sequences needed to assign RADseq reads to individuals. Further details are given in the ReadMe.txt file.Hudson, Andrew. (2022). Parallel speciation in Antirrhinum, [dataset]. School of Biological Sciences. https://doi.org/10.7488/ds/3456

Stancheva lab data set: Epigenetics and regulatory methylation of DNA

Dataset from Dr. Irina Stancheva's lab

Data from: The relative efficiency of modular and non-modular networks of different size

Most biological networks are modular but previous work with small model networks has indicated that modularity does not necessarily lead to increased functional efficiency. Most biological networks are large, however, and here we examine the relative functional efficiency of modular and non-modular neural networks at a range of sizes. We conduct a detailed analysis of efficiency in networks of two size classes: ‘small’ and ‘large’, and a less detailed analysis across a range of network sizes. The former analysis reveals that while the modular network is less efficient than one of the two non-modular networks considered when networks are small, it is usually equally or more efficient than both non-modular networks when networks are large. The latter analysis shows that in networks of small to intermediate size, modular networks are much more efficient that non-modular networks of the same (low) connective density. If connective density must be kept low to reduce energy needs for example, this could promote modularity. We have shown how relative functionality/performance scales with network size, but the precise nature of evolutionary relationship between network size and prevalence of modularity will depend on the costs of connectivity.Tosh, Colin R.; McNally, Luke (2015), Data from: The relative efficiency of modular and non-modular networks of different size, Dryad, Dataset, https://doi.org/10.5061/dryad.g206

Data sets for Millar et al. bioRxiv 2015

Provides URLs to the Data for Millar et al. bioRxiv 2015 article entitled, "Changing planetary rotation rescues the biological clock mutant lhy cca1 of Arabidopsis thaliana"Background: Pervasive, 24-hour rhythms from the biological clock affect diverse biological processes in metabolism and behaviour, including the human cell division cycle and sleep-wake cycle, nightly transpiration and energy balance in plants, and seasonal breeding in both plants and animals. The clock mechanism in the laboratory model plant species Arabidopsis thaliana is complex, in part due to the multiple interlocking, negative feedback loops that link the clock genes. Clock gene mutants are powerful tools to manipulate and understand the clock mechanism and its effects on physiology. The LATE ELONGATED HYPOCOTYL and CIRCADIAN CLOCK ASSOCIATED 1 genes encode dawn-expressed, Myb-related repressor proteins that delay the expression of other clock genes until late in the day. Double mutant plants (lhy cca1) have low-amplitude, short-period rhythms that have been used in multiple studies of the plant circadian clock. Results: We used in vivo imaging of several luciferase (LUC) reporter genes to test how the rhythmic gene expression of wild-type and lhy cca1 mutant plants responded to light:dark cycles. Red, blue and red+blue light were similarly able to entrain these gene expression rhythms. The timing of expression rhythms in double mutant plants showed little or no response to the duration of light under 24h light:dark cycles (dusk sensitivity), in contrast to the wild type. As the period of the mutant clock is about 18h, we tested light:dark cycles of different duration (T cycles), simulating altered rotation of planet Earth. lhy cca1 double mutants regained as much dusk sensitivity in 20h T cycles as the wild type in 24h cycles, though the phase of the rhythm in the mutants was much earlier than wild type. The severe, triple lhy cca1 gi mutants also regained dusk sensitivity in 20h cycles. The double mutant showed some dusk sensitivity under 28h cycles. lhy cca1 double mutants under 28h cycles with short photoperiods, however, had the same apparent phase as wild-type plants. Conclusion: Simulating altered planetary rotation with light:dark cycles can reveal normal circadian performance in clock mutants that have been described as arrhythmic under standard conditions. The features rescued here comprise a dynamic behaviour (apparent phase under 28h cycles) and a dynamic property (dusk sensitivity under 20h cycles). These conditional clock phenotypes indicate that parts of the clock mechanism continue to function independently of LHY and CCA1, despite the major role of these genes in wild-type plants under standard conditions. Accessibility: Most results here will be published only in this format, citable by the DOI. Data and analysis are publicly accessible on the BioDare resource (www.biodare.ed.ac.uk), as detailed in the links below. Transgenic lines are linked to Stock Centre IDs below (Table 7).Citations are detailed for each URL listed below

Micellar catalysis of the Suzuki Miyaura reaction using biogenic Pd nanoparticles from Desulfovibrio alaskensis

NMR data supporting the paper "Micellar catalysis of the Suzuki Miyaura reaction using biogenic Pd nanoparticles from Desulfovibrio alaskensis".Era, Yuta; Dennis, Jonathan Andrew; Wallace, Stephen; Horsfall, Louise Elizabeth. (2021). Micellar catalysis of the Suzuki Miyaura reaction using biogenic Pd nanoparticles from Desulfovibrio alaskensis, [dataset]. University of Edinburgh. School of Biological Sciences. https://doi.org/10.7488/ds/3108

Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers

Responding to change is a fundamental property of life, making time-series data invaluable in biology. For microbes, plate readers are a popular, convenient means to measure growth and also gene expression using fluorescent reporters. Nevertheless, the difficulties of analysing the resulting data can be a bottleneck, particularly when combining measurements from different wells and plates. Here we present omniplate, a Python module that corrects and normalises plate-reader data, estimates growth rates and fluorescence per cell as function of time, calculates errors, exports in different formats, and enables meta-analysis of multiple plates. The software corrects for autofluorescence, the optical density's non-linear dependence on the number of cells, and the effects of the media. We use omniplate to measure the Monod relationship for growth of budding yeast in raffinose, showing that raffinose is a convenient carbon source for controlling growth rates. Using fluorescent tagging, we study yeast's glucose transport. Our results are consistent with the regulation of the hexose transporter (HXT) genes being approximately bipartite: the medium and high affinity transporters are regulated by both the high affinity glucose sensor Snf3 and the kinase complex SNF1 via the repressors Mth1, Mig1, and Mig2; the low affinity transporters are predominately regulated by the low affinity sensor Rgt2 via the co-repressor Std1. We thus demonstrate that omniplate is a powerful tool for exploiting the advantages offered by time-series data in revealing biological regulation.Montano-Gutierrez, Luis Fernando; Manzanaro Moreno, Nahuel; Swain, Peter. (2021). Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers, [dataset]. University of Edinburgh. School of Biological Sciences. https://doi.org/10.7488/ds/3263