Comparative transcriptomics indicates endogenous differences in detoxification capacity after formic acid treatment between honey bees and varroa mites

Formic acid (FA) has been used for decades to control Varroa destructor, one of the most important parasites of the western honey bee, Apis mellifera. The rather unselective molecular mode of action of FA and its possible effects on honeybees have long been a concern of beekeepers, as it has undesirable side effects that affect the health of bee colonies. This study focuses on short-term transcriptomic changes as analysed by RNAseq in both larval and adult honey bees and in mites after FA treatment under applied conditions. Our study aims to identify those genes in honey bees and varroa mites differentially expressed upon a typical FA hive exposure scenario. Five detoxification-related genes were identified with significantly enhanced and one gene with significantly decreased expression under FA exposure. Regulated genes in our test setting included members of various cytochrome P450 subfamilies, a flavin-dependent monooxygenase and a cytosolic 10-formyltetrahydrofolate dehydrogenase (FDH), known to be involved in formate metabolism in mammals. We were able to detect differences in the regulation of detoxification-associated genes between mites and honey bees as well as between the two different developmental stages of the honey bee. Additionally, we detected repressed regulation of Varroa genes involved in cellular respiration, suggesting mitochondrial dysfunction and supporting the current view on the mode of action of FA-inhibition of oxidative phosphorylation. This study shows distinct cellular effects induced by FA on the global transcriptome of both host and parasite in comparison. Our expression data might help to identify possible differences in the affected metabolic pathways and thus make a first contribution to elucidate the mode of detoxification of FA

Perfluoro‐ tert ‐butyl‐homoserine as a sensitive 19 F NMR reporter for peptide–membrane interactions in solution

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/97487/1/psc2501.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/97487/2/psc_2501_supplementary_material.pd

Do Flexible Administration Procedures Promote Individualized Clinical Assessments?:An Explorative Analysis of How Clinicians Utilize the Funnel Structure of the SCID-5-AMPD Module I: LPFS

The current study examined clinicians' utilization of the SCID-5-AMPD-I funnel structure. Across 237 interviews, conducted as part of the NorAMP study, we found that clinicians administered on average 2-3 adjacent levels under each subdomain, effectively administering only about 50% of available items. Comparing administration patterns of interviews, no two interviews contained the exact same set of administered items. On average, when comparing individual interviews, only about half of the administered items in each interview were administered in both interviews. Cross-classified mixed effects models were estimated to examine the factors affecting item administration. Results indicated that the interplay between patient preliminary scores and item level had a substantial impact on item administration, suggesting clinicians tend to administer items corresponding to expected patient severity. Overall, our findings suggest clinicians utilize the SCID-5-AMPD-I funnel structure to conduct efficient and individually tailored assessments informed by relevant patient characteristics. Adopting similar non-fixed administration procedures for other interviews could potentially provide similar benefits compared to traditional fixed-form administration procedures. The current study can serve as a template for verifying and evaluating future adoptions of non-fixed administration procedures in other interviews.</p

The cis-acting CTTC-P1BS module is indicative for gene function of LjVTI12, a Qb-SNARE protein gene that is required for arbuscule formation in Lotus japonicus

Lota F, Wegmueller S, Buer B, et al. The cis-acting CTTC-P1BS module is indicative for gene function of LjVTI12, a Qb-SNARE protein gene that is required for arbuscule formation in Lotus japonicus. The Plant Journal. 2013;74(2):280-293.The majority of land plants live in symbiosis with arbuscular mycorrhizal fungi from the phylum Glomeromycota. This symbiosis improves acquisition of phosphorus (P) by the host plant in exchange for carbohydrates, especially under low-P availability. The symbiosome, constituted by root cortex cells accommodating arbuscular mycorrhizal fungal hyphae, is the site at which bi-directional exchange of nutrients and metabolites takes place. Uptake of orthophosphate (Pi) in the symbiosome is facilitated by mycorrhiza-specific plant Pi transporters. Modifications of the potato Pi transporter 3 (StPT3) promoter were analysed in transgenic mycorrhizal roots, and it was found that the CTTC cis-regulatory element is necessary and sufficient for a transcriptional response to fungal colonization under low-Pi conditions. Phylogenetic foot-printing also revealed binary combination of the CTTC element with the Pi starvation response-associated PHR1-binding site (P1BS) in the promoters of several mycorrhiza-specific Pi transporter genes. Scanning of the Lotus japonicus genome for gene promoters containing both cis-regulatory elements revealed a strong over-representation of genes involved in transport processes. One of these, LjVTI12, encoding a member of the SNARE family of proteins involved in membrane transport, exhibited enhanced transcript levels in Lotus roots colonized with the arbuscular mycorrhizal fungus Glomus intraradices. Down-regulation of LjVTI12 by RNA interference resulted in a mycorrhiza-specific phenotype characterized by distorted arbuscule morphology. The results highlight cooperative cis-regulation which integrates mycorrhiza and Pi starvation signaling with vesicle trafficking in symbiosome development

A Psychometric Analysis of the Structured Clinical Interview for the DSM-5 Alternative Model for Personality Disorders Module I (SCID-5-AMPD-I):Level of Personality Functioning Scale

The current study aims to examine the psychometric properties of the Structured Clinical Interview for the DSM-5 Alternative Model for Personality Disorders Module I (SCID-5-AMPD-I) assessing the Level of Personality Functioning Scale (LPFS) in a heterogeneous sample of 282 nonpsychotic patients. Latent variable models were used to investigate the dimensionality of the LPFS. The results indicate that the LPFS, as assessed by the SCID-5-AMPD-I, can be considered as a unidimensional construct that can be measured reliably across a wide range of the latent trait. Threshold parameters for the 12 indicators of the LPFS increased gradually over the latent scale, indicating that the five LPFS levels were ordered as predicted by the model. In general, the increase of threshold parameters was relatively small for the shift from Level 2 to Level 3. A better distinction among the different severity levels might be obtained by fine-tuning the interview guidelines or the Level 2 indicators themselves

A scaffold-level genome assembly of a minute pirate bug, Orius laevigatus (Hemiptera: Anthocoridae), and a comparative analysis of insecticide resistance-related gene families with hemipteran crop pests

Background: Orius laevigatus, a minute pirate bug, is a highly effective beneficial predator of crop pests including aphids, spider mites and thrips in integrated pest management (IPM) programmes. No genomic information is currently available for O. laevigatus, as is the case for the majority of beneficial predators which feed on crop pests. In contrast, genomic information for crop pests is far more readily available. The lack of publicly available genomes for beneficial predators to date has limited our ability to perform comparative analyses of genes encoding potential insecticide resistance mechanisms between crop pests and their predators. These mechanisms include several gene/protein families including cytochrome P450s (P450s), ATP binding cassette transporters (ABCs), glutathione S-transferases (GSTs), UDP-glucosyltransferases (UGTs) and carboxyl/cholinesterases (CCEs). Methods and findings: In this study, a high-quality scaffold level de novo genome assembly for O. laevigatus has been generated using a hybrid approach with PacBio long-read and Illumina short-read data. The final assembly achieved a scaffold N50 of 125,649 bp and a total genome size of 150.98 Mb. The genome assembly achieved a level of completeness of 93.6% using a set of 1658 core insect genes present as full-length genes. Genome annotation identified 15,102 protein-coding genes - 87% of which were assigned a putative function. Comparative analyses revealed gene expansions of sigma class GSTs and CYP3 P450s. Conversely the UGT gene family showed limited expansion. Differences were seen in the distributions of resistance-associated gene families at the subfamily level between O. laevigatus and some of its targeted crop pests. A target site mutation in ryanodine receptors (I4790M, PxRyR) which has strong links to diamide resistance in crop pests and had previously only been identified in lepidopteran species was found to also be present in hemipteran species, including O. laevigatus. Conclusion and significance: This assembly is the first published genome for the Anthocoridae family and will serve as a useful resource for further research into target-site selectivity issues and potential resistance mechanisms in beneficial predators. Furthermore, the expansion of gene families often linked to insecticide resistance may be an indicator of the capacity of this predator to detoxify selective insecticides. These findings could be exploited by targeted pesticide screens and functional studies to increase effectiveness of IPM strategies, which aim to increase crop yields by sustainably, environmentally-friendly and effectively control pests without impacting beneficial predator populations.Biotechnology and Biological Sciences Research Council (BBSRC

A near-chromosome level genome assembly of the European hoverfly, Sphaerophoria rueppellii (Diptera: Syrphidae), provides comparative insights into insecticide resistance-related gene family evolution

Background Sphaerophoria rueppellii, a European species of hoverfly, is a highly effective beneficial predator of hemipteran crop pests including aphids, thrips and coleopteran/lepidopteran larvae in integrated pest management (IPM) programmes. It is also a key pollinator of a wide variety of important agricultural crops. No genomic information is currently available for S. rueppellii. Without genomic information for such beneficial predator species, we are unable to perform comparative analyses of insecticide target-sites and genes encoding metabolic enzymes potentially responsible for insecticide resistance, between crop pests and their predators. These metabolic mechanisms include several gene families - cytochrome P450 monooxygenases (P450s), ATP binding cassette transporters (ABCs), glutathione-S-transferases (GSTs), UDP-glycosyltransferases (UGTs) and carboxyl/choline esterases (CCEs). Methods and findings In this study, a high-quality near-chromosome level de novo genome assembly (as well as a mitochondrial genome assembly) for S. rueppellii has been generated using a hybrid approach with PacBio long-read and Illumina short-read data, followed by super scaffolding using Hi-C data. The final assembly achieved a scaffold N50 of 87Mb, a total genome size of 537.6Mb and a level of completeness of 96% using a set of 1,658 core insect genes present as full-length genes. The assembly was annotated with 14,249 protein-coding genes. Comparative analysis revealed gene expansions of CYP6Zx P450s, epsilon-class GSTs, dietary CCEs and multiple UGT families (UGT37/302/308/430/431). Conversely, ABCs, delta-class GSTs and non-CYP6Zx P450s showed limited expansion. Differences were seen in the distributions of resistance-associated gene families across subfamilies between S. rueppellii and some hemipteran crop pests. Additionally, S. rueppellii had larger numbers of detoxification genes than other pollinator species. Conclusion and significance This assembly is the first published genome for a predatory member of the Syrphidae family and will serve as a useful resource for further research into selectivity and potential tolerance of insecticides by beneficial predators. Furthermore, the expansion of some gene families often linked to insecticide resistance and selectivity may be an indicator of the capacity of this predator to detoxify IPM selective insecticides. These findings could be exploited by targeted insecticide screens and functional studies to increase effectiveness of IPM strategies, which aim to increase crop yields by sustainably and effectively controlling pests without impacting beneficial predator populations.Biotechnology and Biological Sciences Research Council (BBSRC): Bayer Crop Science and Syngenta AG

Vision, challenges and opportunities for a Plant Cell Atlas

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.</jats:p

Structural and Thermodynamic Investigation Into the Effects of Protein Fluorination

The introduction of non-canonical amino acids has been a useful tool to modify the properties of proteins. In particular, highly fluorinated amino acids have shown much promise in stabilizing a variety of protein folds towards degradation by proteases and unfolding by heat and chemical denaturants. The stability benefits of fluorine incorporation into proteins are known. However, structural requirements to accommodate these non-natural amino acids are not fully understood. It is also not known how the non-proteogenic nature of fluorine contributes to the thermodynamic parameters of enthalpy and entropy and whether they are similar to those of natural proteins. The research presented here aims to develop an understanding of how fluorination increases protein stability to inform future efforts of modulating proteins with non-canonical amino acids. The de novo designed 4-helix bundle, α4, was used to study the stabilizing properties of hexafluoroleucine (hFLeu) incorporation. The stabilizing of α4 proteins is dependent on the position of hFLeu incorporation, with proteins incorporating hFLeu into all a or all d positions displaying the highest per hFLeu residue stability. This enhanced stability through optimized core packing is contrary to predictions of fluorine-fluorine contacts increasing stability via the “fluorous effect”. X-ray crystal structure comparison of α4 proteins shows minimal protein structural perturbation from hFLeu due to the retention of hydrocarbon side chain shape. A lack of specific fluorous interactions indicates that stability-enhancing properties of hFLeu are better ascribed to hydrophobic volume. Comparing the stability of a highly fluorinated α4 protein, which contains nearly identical core volume to its non-fluorinated counterpart, confirms that fluorinated proteins enhance stability by a general increase in hydrophobicity. The protein compatibility of hFLeu is again confirmed through thermodynamic analysis of 12 α4 proteins. These proteins show a general trend of increased free energy of unfolding, entropy and heat capacity with increasing hydrophobic surface area, regardless of hydrocarbon or fluorocarbon nature. Lastly, the NMR properties of fluorine make fluorinated amino acids useful for studying transient biological interactions. Binding of trifluoroethylglycine (tFeG) containing antimicrobial peptide, MSI-78, to lipids is investigated. The trifluoromethyl fluorine reporter displays sequence-dependent chemical shift and conformational mobility upon binding.PHDChemical BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/94053/1/buerben_2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/94053/2/buerben_1.pd