A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida)

The proliferation of genomic sequencing approaches has significantly impacted the field of phylogenetics. Target capture approaches provide a cost-effective, fast and easily applied strategy for phylogenetic inference of non-model organisms. However, several existing target capture processing pipelines are incapable of incorporating whole genome sequencing (WGS). Here, we develop a new pipeline for capture and de novo assembly of the targeted regions using whole genome re-sequencing reads. This new pipeline captured targeted loci accurately, and given its unbiased nature, can be used with any target capture probe set. Moreover, due to its low computational demand, this new pipeline may be ideal for users with limited resources and when high-coverage sequencing outputs are required. We demonstrate the utility of our approach by incorporating WGS data into the first comprehensive phylogenomic reconstruction of the freshwater mussel family Margaritiferidae. We also provide a catalogue of well-curated functional annotations of these previously uncharacterized freshwater mussel-specific target regions, representing a complementary tool for scrutinizing phylogenetic inferences while expanding future applications of the probe set.     

The algal flora of a subtidal Zostera bed in ventry bay,Southwest Ireland

Ventry Bay in County Kerry, southwest Ireland, was surveyed in June 1977 to a depth of 17 m using SCUBA and a grid of stations which were 400 m apart. The principal substrate was sand. Zostera marina L. was dominant and widespread from 0.5 to 13 m below Chart Datum and is the deepest-growing Zostera in Northwest Europe. Sixty species of algae were found and their occurrence and that of Zostera marina was subjected to cluster analysis resulting in one distinct cluster of Zostera marina, Ulva lactuca L., Gracilaria verrucosa (Huds.) Papenf., Polysiphonia elongata (Huds.) Spreng., Ectocarpus sp., Ceramium rubrum (Huds.) C. Ag. and Brongniartella byssoides (Good. et Woodw.) Schmitz. These algae are so common and widespread in the subtidal zone that their co-occurrence with Zostera is not considered to be significant. Zostera occurs virtually as monospecific stands in sand and the co-occurrence of any macroalgae is largely fortuitous and dependent on the heterogeneity of the substrate.     

Using a logical model to predict the growth of yeast

Background  

A logical model of the known metabolic processes in S. cerevisiae was constructed from iFF708, an existing Flux Balance Analysis (FBA) model, and augmented with information from the KEGG online pathway database. The use of predicate logic as the knowledge representation for modelling enables an explicit representation of the structure of the metabolic network, and enables logical inference techniques to be used for model identification/improvement.     

The biogenesis of muscle glycogen: regulation of the activity of the autocatalytic primer protein

Glycogen synthesis in rabbit muscle is initiated by an autocatalytic, self-glucosylating protein (SGP). This creates a maltosaccharide primer on itself that in turn primes glycogen synthesis. Here we describe the powerful allosteric inhibition of autocatalysis by ATP and ADP, sufficient, at the physiological concentration of ATP in muscle, to inhibit autocatalysis. We also examined inhibition of self-glucosylation by analogues of the substrate UDPglucose. One of them, UDPxylose, acts as an alternative substrate and serves to block glucosylation. An improved purification procedure for the SGP is also described.