Identification and sequence determination of a novel double-stranded RNA mycovirus from the entopathogenic fungus Beauveria bassina

The final publication is available at Springer via https://doi.org/10.1007/s00705-014-2332-8.An isolate of the entomopathogenic fungus Beauveria bassiana was found to contain five double-stranded (ds) RNA elements ranging from 1.5 to more than 3 kbp. The complete sequence of the largest dsRNA element is described here. Analysis of the RdRp nucleotide sequence reveals its similarity to unclassified dsRNA elements, such as Alternaria longipes dsRNA virus 1, and its distant relationship to the RNA-dependent RNA polymerases of members of the family PartitiviridaePeer reviewedFinal Accepted Versio

Trophic interactions between native and alien palaemonid prawns and an alien gammarid in a brackish water ecosystem

Macroalgae are an important habitat for small mobile invertebrates such as gammarid amphipods and palaemonid prawns. Gammarid amphipods are important grazers of micro- and macroalgae whereas palaemonid prawns are feeding on macroalgae and small aquatic invertebrates including gammarids. Recently the invasive palaemonid prawn Palaemon elegans established in the Baltic Sea. As P. elegans occurs within the same habitats as the native Palaemon adspersus, it is expected that this invasion modifies the existing trophic interactions. To address this question, we experimentally investigated the feeding of the native P. adspersus and the invasive P. elegans on the benthic macroalga Cladophora glomerata and on the invasive gammarid amphipod Gammarus tigrinus. In the course of the experiment neither G. tigrinus nor Palaemon spp. had effects on filamentous macroalgae. The presence of prawns drastically increased the mortality of amphipods with no difference in the feeding efficiency between the two prawn species. To conclude, the alien prawn does not add an extra function to the trophic system of the coastal ecosystem of the Baltic Sea. Nevertheless, due to its progressively increasing densities and wide habitat range, P. elegans is expected to exert stronger predation pressure on gammarid amphipods as compared to P. adspersus alone

Single-step method for β-galactosidase assays in Escherichia coli using a 96-well microplate reader

AbstractHistorically, the lacZ gene is one of the most universally used reporters of gene expression in molecular biology. Its activity can be quantified using an artificial substrate, o-nitrophenyl-ß-d-galactopyranoside (ONPG). However, the traditional method for measuring LacZ activity (first described by J. H. Miller in 1972) can be challenging for a large number of samples, is prone to variability, and involves hazardous compounds for lysis (e.g., chloroform, toluene).Here we describe a single-step assay using a 96-well microplate reader with a proven alternative cell permeabilization method. This modified protocol reduces handling time by 90%

Cellular and molecular phenotypes depending upon the RNA repair system RtcAB of Escherichia coli

Biotechnology and Biological Sciences Research Council (BBSRC) [BB/J00717X/1]; Medical Research Council (MRC) [MR/M017672/1]; Queen's Fellowship (Queen's University Belfast, UK) (to C.E.); Antimicrobial Resistance Cross Council Initiative. Funding for open access charge: BBSRC [BB/J00717X/1]; MRC [MR/M017672/1]

A data comparison between a traditional and the single-step β-galactosidase assay

This article describes reproducibility of a single-step automated β-galactosidase, and the equivalence of its data to the traditional assay ("Experiments in Molecular Genetics" [1]). This was done via a pairwise comparison of both methods using strains with Miller Unit [MU] values ranging from 0 to over 2000. The data presented in this article is associated with the research article entitled "A single-step method for mid to high throughput β-galactosidase assays in Escherichia coli using a microplate reader" [2]

The polymycovirus-mediated growth enhancement of the entomopathogenic fungus Beauveria bassiana is dependent on carbon and nitrogen metabolism

Polymycoviridae is a growing family of mycoviruses whose members typically have non-conventional capsids and multi-segmented, double-stranded (ds) RNA genomes. Beauveria bassiana polymycovirus (BbPmV) 1 is known to enhance the growth and virulence of its fungal host, the entomopathogenic ascomycete and popular biological control agent B. bassiana. Here we report the complete sequence of BbPmV-3, which has six genomic dsRNA segments. Phylogenetic analysis of RNA-dependent RNA polymerase (RdRp) protein sequences revealed that BbPmV-3 is closely related to the partially sequenced BbPmV-2 but not BbPmV-1. Nevertheless, both BbPmV-3 and BbPmV-1 have similar effects on their respective host isolates ATHUM 4946 and EABb 92/11-Dm, affecting pigmentation, sporulation, and radial growth. Production of conidia and radial growth are significantly enhanced in virus-infected isolates as compared to virus-free isogenic lines on Czapek-Dox complete and minimal media that contain sucrose and sodium nitrate. However, this polymycovirus-mediated effect on growth is dependent on the carbon and nitrogen sources available to the host fungus. Both BbPmV-3 and BbPmV-1 increase growth of ATHUM 4946 and EABb 92/11-Dm when sucrose is replaced by lactose, trehalose, glucose, or glycerol, while the effect is reversed on maltose and fructose. Similarly, both BbPmV-3 and BbPmV-1 decrease growth of ATHUM 4946 and EABb 92/11-Dm when sodium nitrate is replaced by sodium nitrite, potassium nitrate, or ammonium nitrate. In conclusion, the effects of polymycoviruses on B. bassiana are at least partially mediated via its metabolic pathways

Molecular origins of transcriptional heterogeneity in diazotrophic Klebsiella oxytoca.

Phenotypic heterogeneity in clonal bacterial batch cultures has been shown for a range of bacterial systems; however, the molecular origins of such heterogeneity and its magnitude are not well understood. Under conditions of extreme low-nitrogen stress in the model diazotroph Klebsiella oxytoca, we found remarkably high heterogeneity of nifHDK gene expression, which codes for the structural genes of nitrogenase, one key enzyme of the global nitrogen cycle. This heterogeneity limited the bulk observed nitrogen-fixing capacity of the population. Using dual-probe, single-cell RNA fluorescent in situ hybridization, we correlated nifHDK expression with that of nifLA and glnK-amtB, which code for the main upstream regulatory components. Through stochastic transcription models and mutual information analysis, we revealed likely molecular origins for heterogeneity in nitrogenase expression. In the wild type and regulatory variants, we found that nifHDK transcription was inherently bursty, but we established that noise propagation through signaling was also significant. The regulatory gene glnK had the highest discernible effect on nifHDK variance, while noise from factors outside the regulatory pathway were negligible. Understanding the basis of inherent heterogeneity of nitrogenase expression and its origins can inform biotechnology strategies seeking to enhance biological nitrogen fixation. Finally, we speculate on potential benefits of diazotrophic heterogeneity in natural soil environments

A New Curriculum to Train Chemical Engineers to Solve 21st Century Grand Challenges

The Department of Chemical and Biological Engineering at the University of Sheffield is embarked on a curriculum change project with roll out starting with level 1 in September 2017. The drivers behind the change included the need to modernise the curriculum both in terms of content, structure and delivery. The main objective was to develop a modern Sheffield Chemical Engineer. The study is primarily about investigating the efficacy of the change efforts that have been introduced, to track progress and to determine whether we are meeting our stated objectives. The objectives are in relation to student success, student experience, curriculum coherence and student and staff well-being. Specifically, the new curriculum will be coherent, embedded in design and practice with an emphasis on critical thinking, problem solving, professionalism, ethics and sustainability. It will offer flexible learning environments and pathways to facilitate deep engagement. It will promote and facilitate industry involvement by focusing on both process and product engineering to develop industry ready practical graduates with hands on experience. It will produce graduates who are integrators, change agents and self-directed learners to lead multidisciplinary teams, and be at the forefront of innovation. It will provide exposure to niche research areas built on a strong core in engineering fundamentals. Lastly, it will produce graduates capable of Engineering from molecules by applying systems level thinking at many length scales. We have identified a third year module process design as a significant check point to determine whether some of our curriculum objectives are being met (Patwardhan et al, 2017)

A somatic genetic clock for clonal species.

Age and longevity are key parameters for demography and life-history evolution of organisms. In clonal species, a widespread life history among animals, plants, macroalgae and fungi, the sexually produced offspring (genet) grows indeterminately by producing iterative modules, or ramets, and so obscure their age. Here we present a novel molecular clock based on the accumulation of fixed somatic genetic variation that segregates among ramets. Using a stochastic model, we demonstrate that the accumulation of fixed somatic genetic variation will approach linearity after a lag phase, and is determined by the mitotic mutation rate, without direct dependence on asexual generation time. The lag phase decreased with lower stem cell population size, number of founder cells for the formation of new modules, and the ratio of symmetric versus asymmetric cell divisions. We calibrated the somatic genetic clock on cultivated eelgrass Zostera marina genets (4 and 17 years respectively). In a global data set of 20 eelgrass populations, genet ages were up to 1,403 years. The somatic genetic clock is applicable to any multicellular clonal species where the number of founder cells is small, opening novel research avenues to study longevity and, hence, demography and population dynamics of clonal species