SBILib: a handle for protein modeling and engineering.

SUMMARY: The SBILib Python library provides an integrated platform for the analysis of macromolecular structures and interactions. It combines simple 3D file parsing and workup methods with more advanced analytical tools. SBILib includes modules for macromolecular interactions, loops, super-secondary structures, and biological sequences, as well as wrappers for external tools with which to integrate their results and facilitate the comparative analysis of protein structures and their complexes. The library can handle macromolecular complexes formed by proteins and/or nucleic acid molecules (i.e. DNA and RNA). It is uniquely capable of parsing and calculating protein super-secondary structure and loop geometry. We have compiled a list of example scenarios which SBILib may be applied to and provided access to these within the library. AVAILABILITY AND IMPLEMENTATION: SBILib is made available on Github at https://github.com/structuralbioinformatics/SBILib.

Diet and ontogeny drastically alter the larval microbiome of the invertebrate model Galleria mellonella.

Larvae of the greater wax moth (Galleria mellonella) are an emerging animal model to study the innate immune response and biodegradation of plastic polymers. Both of these complex biological processes are likely impacted by the plasticity of host-microbe interactions, which remains understudied in lepidopterans. Consequently, we carried out 16S rRNA sequencing to explore the effect diet (natural, artificial) has on the bacterial assemblages of G. mellonella in different tissues (gut, fat bodies, silk glands) throughout development (eggs, six instar stages, adults). The microbiome was rich in diversity, with Proteobacteria and Firmicutes being the most represented phyla. Contrary to other lepidopterans, G. mellonella appears to possess a resident microbiome dominated by Ralstonia. As larvae progress through development, the bacterial assemblages become increasingly shaped by the caterpillar's diet. In particular, a number of bacteria genera widely associated with the G. mellonella microbiome (e.g., Enterococcus and Enterbacter) were significantly enriched on an artificial diet. Overall, these results indicate that the G. mellonella microbiome is not as simplistic and homogenous as previously described. Rather, its bacterial communities are drastically affected by both diet and ontogeny, which should be taken into consideration in future studies planning to use G. mellonella as model species.

Three years of surveillance associates agro-environmental factors with wireworm infestations in Manitoba, Canada.

BACKGROUND: Wireworms, the soil-dwelling larvae of click beetles, are a major threat to global agricultural production. This is largely due to their generalist polyphagous feeding capabilities, extended and cryptic life cycles, and limited management options available. Although wireworms are well-documented as economically important pests in the Canadian Prairies, including Manitoba, there are gaps in knowledge on species distributions, subterranean behaviour and life cycles, feeding ecology and damage capacity, and economic thresholds for crop yield loss. RESULTS: We carried out 3 years (2018-2020) of intensive surveillance of larval populations across Manitoba. A total of 31 fields (24 in ≥ 2 consecutive years) were surveyed in early spring using standardized bait trapping approaches. Wireworms were present in 94% of surveyed sites, but the catch within fields varied year to year. While Hypnoidus bicolor predominated (94% of larvae), several other pest species were identified. We then explored the relationships between wireworm trap numbers and agro-environmental factors. The larval catch tended to decrease under conditions of low soil temperatures and increased clay content, coupled with high soil moisture and precipitation during the trapping period. Treatment and cultural methods appeared less influential; however, wheat production in either of the previous two growing seasons was associated with increased wireworm catch. Our models failed to predict a relationship between wireworm catch and crop yields, although infestations were rare in our region. CONCLUSION: Our findings better infer the risks posed by wireworms to crop production in the Canadian Prairies, and the agro-environmental factors that represent the greatest contributors to these risks. This information should be incorporated into future integrated pest management (IPM) strategies for wireworms. © 2021 Her Majesty the Queen in Right of Canada Pest Management Science © 2021 Society of Chemical Industry Reproduced with the permission of the Minister of Agriculture and Agri-Food Canada.