Genetics, genomics and mechanisms responsible for high levels of pyrethroid resistance in Musca domestica.

Insecticide resistance is both economically important and evolutionarily interesting phenomenon. Identification of the mutations responsible for resistance allows for highly sensitive resistance monitoring and allows tools to study the forces (population genetics, fitness costs, etc.) that shape the evolution of resistance. Genes coding for insecticide targets have many well-characterized mutations, but the mutations responsible for enhanced detoxification have proven difficult to identify. We employed multiple strategies to identify the mutations responsible for the extraordinarily high permethrin resistance in the KS17-R strain of house fly (Musca domestica): insecticide synergist assays, linkage analysis, bulk segregant analyses (BSA), transcriptomics and long read DNA (Nanopore) sequencing. The >85,100-fold resistance in KS17-R was partially suppressed by the insecticide synergists piperonyl butoxide and S,S,S-tributylphosphorothionate, but not by diethyl maleate nor by injection. This suggests the involvement of target site insensitivity, CYP-mediated resistance, possibly hydrolase mediated resistance and potentially other unknown factors. Linkage analysis identified chromosomes 1, 2, 3 and 5 as having a role in resistance. BSA mapped resistance loci on chromosomes 3 and 5. The locus on chromosome 3 was centered on the voltage sensitive sodium channel. The locus on chromosome 5 was associated with a duplication of multiple detoxification genes. Transcriptomic analyses and long read DNA sequencing revealed overexpressed CYPs and esterases and identified a complex set of structural variants at the chromosome 5 locus.

New insights into immune genes and other expanded gene families of the house fly, Musca domestica, from an improved whole genome sequence.

The house fly, Musca domestica, is a pest of livestock, transmits pathogens of human diseases, and is a model organism in multiple biological research areas. The first house fly genome assembly was published in 2014 and has been of tremendous use to the community of house fly biologists, but that genome is discontiguous and incomplete by contemporary standards. To improve the house fly reference genome, we sequenced, assembled, and annotated the house fly genome using improved techniques and technologies that were not available at the time of the original genome sequencing project. The new genome assembly is substantially more contiguous and complete than the previous genome. The new genome assembly has a scaffold N50 of 12.46 Mb, which is a 50-fold improvement over the previous assembly. In addition, the new genome assembly is within 1% of the estimated genome size based on flow cytometry, whereas the previous assembly was missing nearly one-third of the predicted genome sequence. The improved genome assembly has much more contiguous scaffolds containing large gene families. To provide an example of the benefit of the new genome, we used it to investigate tandemly arrayed immune gene families. The new contiguous assembly of these loci provides a clearer picture of the regulation of the expression of immune genes, and it leads to new insights into the selection pressures that shape their evolution.

Rational Design of Iron Spin-Crossover Complexes Using Heteroscorpionate Chelates.

The optical, structural, and magnetic properties of iron(II,III) sandwich complexes, Fe(Tp')2n+ (Tp' = bis(3,5-dimethylpyrazolyl)benzotriazolylborate), are described. The intensely colored FeII(Tp')2 (orange) and FeIII(Tp')2+ (purple) show strong MLCT bands. Geometric isomerism for M(Tp')2 is established crystallographically in the racemate of chiral cis-Fe(Tp')2. For the first time, paramagnetic 11B NMR describes solution-phase low-spin (LS, S = 0) to high-spin (HS, S = 2) crossover behavior in Fe(Tp')2. Thermochemical parameters for solution-phase SCO of Fe(Tp')2 demonstrate the endothermic LS to HS conversion and entropic preference of the HS state. Entropy changes for both Fe(Tp')2 isomers are significantly larger than for the majority of iron scorpionate SCO systems. Solid-state magnetic and thermochemical measurements show cis-Fe(Tp')2 to be thermally stable up to 520 K, allowing experimental investigation of a solid-state SCO magnetic hysteresis of over 45 K. A large solution vs solid-state SCO difference was observed: cis-Fe(Tp')2 shows Tc ≈ 270 K (solution) and Tc ≈ 385 K (solid), with the remarkably wide ΔTc ≈ 115 K; trans-Fe(Tp')2 shows Tc ≈ 278 K (solution) and Tc ≈ 372 K (solid). Solid-state Tc values are among the highest seen for iron(II) molecular systems. The large solution/solid ΔTc difference is explained by "anchoring" intermolecular interactions in the solid state that prevent thermal expansion of the LS iron(II) coordination sphere in its transition to the HS state. DFT calculations, validated against LS cis-Fe(Tp')2 crystallography and LS to HS SCO thermochemical parameters, demonstrate the role the benzotriazole rings play in its structural and optical properties. The Lewis basicity of M(Tp')2 is shown with the structural characterization of the air-stable tin(II) adduct [cis-Fe(Tp')2-SnCl2]; tin(II) coordination does not alter the iron(II) spin state. The Tp' chelate adds functionality (asymmetry, chirality, chemical reactivity) to the array of iron SCO materials for potential incorporation into nanoscale magnetic switches and spintronic devices.

Insecticide resistance monitoring of house fly populations from the United States.

Insecticide resistance in house fly populations is a major problem faced by livestock producers worldwide. A survey of insecticide resistance levels and pyrethroid resistance allele frequencies in the United States was conducted in 2008-09, but little is known about how resistance levels have changed over the last 10 years. In addition, new target-site pyrethroid resistance alleles that confer high levels of resistance have been recently identified in the voltage-sensitive sodium channel, and their frequencies in field populations are unknown. Our aim in this study was to reassess the resistance status of house flies from select locations in the United States by examining resistance levels against commonly used insecticides and frequencies of known resistance alleles. House flies were collected from animal production facilities in five different states between 2016 and 2018. Resistance levels to three insecticides (permethrin, tetrachlorvinphos, and methomyl), representing three classes of insecticides (pyrethroids, organophosphates and carbamates) varied geographically and were lowest in the population collected from New Mexico, intermediate in the population collected from Utah, and greatest in the population from Kansas. The recently identified 1B pyrethroid resistance allele increased dramatically in frequency compared to previous reports, most notably in populations from Kansas and Maryland, indicating that it may already be widespread around the United States. Based on comparison with historical data, the population collected from Kansas represents one of the most highly permethrin resistant populations ever sampled. If the alleles responsible for this level of resistance spread, pyrethroids may be of limited use for house fly control in the United States in the near future.

A functional connectome: regulation of Wnt/TCF-dependent transcription by pairs of pathway activators.

BACKGROUND: Wnt/ß-catenin signaling is often portrayed as a simple pathway that is initiated by Wnt ligand at the cell surface leading, via linear series of interactions between 'core pathway' members, to the induction of nuclear transcription from genes flanked by ß-catenin/TCF transcription factor binding sites. Wnt/ß-catenin signaling is also regulated by a much larger set of 'non-core regulators'. However the relationship between 'non-core regulators' is currently not well understood. Aberrant activation of the pathway has been shown to drive tumorgenesis in a number of different tissues. METHODS: Mammalian cells engineered to have a partially-active level of Wnt/ß-catenin signaling were screened by transfection for proteins that up or down-regulated a mid-level of TCF-dependent transcription induced by transient expression of an activated LRP6 Wnt co-receptor (∆NLRP). RESULTS: 141 novel regulators of TCF-dependent transcription were identified. Surprisingly, when tested without ∆NLRP activation, most up-regulators failed to alter TCF-dependent transcription. However, when expressed in pairs, 27 % (466/1170) functionally interacted to alter levels of TCF-dependent transcription. When proteins were displayed as nodes connected by their ability to co-operate in the regulation of TCF-dependent transcription, a network of functional interactions was revealed. In this network, 'core pathway' components (Eg. ß-catenin, GSK-3, Dsh) were found to be the most highly connected nodes. Activation of different nodes in this network impacted on the sensitivity to Wnt pathway small molecule antagonists. CONCLUSIONS: The 'functional connectome' identified here strongly supports an alternative model of the Wnt pathway as a complex context-dependent network. The network further suggests that mutational activation of highly connected Wnt signaling nodes predisposed cells to further context-dependent alterations in levels of TCF-dependent transcription that may be important during tumor progression and treatment.

Application of Gaussia luciferase in bicistronic and non-conventional secretion reporter constructs.

BACKGROUND: Secreted luciferases are highly useful bioluminescent reporters for cell-based assays and drug discovery. A variety of secreted luciferases from marine organisms have been described that harbor an N-terminal signal peptide for release along the classical secretory pathway. Here, we have characterized the secretion of Gaussia luciferase in more detail. RESULTS: We describe three basic mechanisms by which GLUC can be released from cells: first, classical secretion by virtue of the N-terminal signal peptide; second, internal signal peptide-mediated secretion and third, non-conventional secretion in the absence of an N-terminal signal peptide. Non-conventional release of dNGLUC is not stress-induced, does not require autophagy and can be enhanced by growth factor stimulation. Furthermore, we have identified the golgi-associated, gamma adaptin ear containing, ARF binding protein 1 (GGA1) as a suppressor of release of dNGLUC. CONCLUSIONS: Due to its secretion via multiple secretion pathways GLUC can find multiple applications as a research tool to study classical and non-conventional secretion. As GLUC can also be released from a reporter construct by internal signal peptide-mediated secretion it can be incorporated in a novel bicistronic secretion system.

All resistance alleles are not equal: the high fitness cost of super-kdr in the absence of insecticide.

BACKGROUND: Mutations in the voltage-sensitive sodium channel are an important mechanism of resistance to pyrethroid insecticides. In Musca domestica, common resistance alleles are kdr, super-kdr and kdr-his. The levels of resistance that these alleles confer is known, but the fitness of these alleles relative to each other and to susceptible alleles is unknown. We used crosses from congenic strains of M. domestica to establish populations with known allele frequencies and then examined the changes in allele and genotype frequencies over 25 generations under laboratory conditions. RESULTS: There was a significant fitness cost for the super-kdr allele, which decreased from the starting frequency of 0.25 to 0.05 after 25 generations. The fitness of the kdr, kdr-his and susceptible alleles were similar. The greatest change in genotype frequency was seen for the super-kdr/super-kdr genotype, which was no longer detected after 25 generations. CONCLUSION: The fitness cost associated with the super-kdr allele is consistent with previous reports and appears to be a factor in helping to restrain high levels of resistance in field populations (the super-kdr allele confers higher levels of resistance than kdr or kdr-his). It is known that the relative costs of different alleles are environmentally dependent, but our results also demonstrate that the relative fitness of given alleles depends on which alleles are present in a given population, as previous pairwise comparisons of allele fitness do not exactly match (except for super-kdr) the results obtained using this four allele study. © 2020 Society of Chemical Industry.

Fitness studies of insecticide resistant strains: lessons learned and future directions.

The evolution of insecticide resistance is generally thought to be associated with a fitness cost in the absence of insecticide exposure. However, it is not clear how these fitness costs manifest or how universal this phenomenon is. To investigate this, we conducted a literature review of publications that studied fitness costs of insecticide resistance, selected papers that met our criteria for scientific rigor, and analyzed each class of insecticides separately as well as in aggregate. The more than 170 publications on fitness costs of insecticide resistance show that in 60% of the experiments there is a cost to having resistance, particularly for measurements of reversion of resistance and reproduction. There were differences between classes of insecticides, with fitness costs seen less commonly for organochlorines. There was considerable variation in the experiments performed. We suggest that future papers will have maximum value to the community if they quantitatively determine resistance levels, identify the resistance mechanisms present (and the associated mutations), have replicated experiments, use related strains (optimally congenic with the resistance mutation introgressed into different genetic backgrounds) and measure fitness by multiple metrics. Studies on the fitness costs of insecticide resistance will continue to enlighten our understanding of the evolutionary process and provide valuable information for resistance management. © 2021 Society of Chemical Industry.

Correction: Signalling involving MET and FAK supports cell division independent of the activity of the cell cycle-regulating CDK4/6 kinases.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Signalling involving MET and FAK supports cell division independent of the activity of the cell cycle-regulating CDK4/6 kinases.

Deregulation of cyclin-dependent kinases 4 and 6 (CDK4/6) is highly prevalent in cancer; yet, inhibitors against these kinases are currently used only in restricted tumour contexts. The extent to which cancers depend on CDK4/6 and the mechanisms that may undermine such dependency are poorly understood. Here, we report that signalling engaging the MET proto-oncogene receptor tyrosine kinase/focal adhesion kinase (FAK) axis leads to CDK4/6-independent CDK2 activation, involving as critical mechanistic events loss of the CDKI p21CIP1 and gain of its regulator, the ubiquitin ligase subunit SKP2. Combined inhibition of MET/FAK and CDK4/6 eliminates the proliferation capacity of cancer cells in culture, and enhances tumour growth inhibition in vivo. Activation of the MET/FAK axis is known to arise through cancer extrinsic and intrinsic cues. Our work predicts that such cues support cell division independent of the activity of the cell cycle-regulating CDK4/6 kinases and identifies MET/FAK as a tractable route to broaden the utility of CDK4/6 inhibitor-based therapies in the clinic.

Identification of Kinases and Phosphatases That Regulate ATG4B Activity by siRNA and Small Molecule Screening in Cells.

Autophagy protease ATG4B is a key regulator of the LC3/GABARAP conjugation system required for autophagosome formation, maturation and closure. Members of the ATG4 and the LC3/GABARAP family have been implicated in various diseases including cancer, and targeting the ATG4B protease has been suggested as a potential therapeutic anti-cancer strategy. Recently, it has been demonstrated that ATG4B is regulated by multiple post-translational modifications, including phosphorylation and de-phosphorylation. In order to identify regulators of ATG4B activity, we optimized a cell-based luciferase assay based on ATG4B-dependent release of Gaussia luciferase. We applied this assay in a proof-of-concept small molecule compound screen and identified activating compounds that increase cellular ATG4B activity. Next, we performed a high-throughput screen to identify kinases and phosphatases that regulate cellular ATG4B activity using siRNA mediated knockdown and cDNA overexpression. Of these, we provide preliminary evidence that the kinase AKT2 enhances ATG4B activity in cells. We provide all raw and processed data from the screens as a resource for further analysis. Overall, our findings provide novel insights into the regulation of ATG4B and highlight the importance of post-translational modifications of ATG4B.

HDAC3 Regulates the Transition to the Homeostatic Myelinating Schwann Cell State.

The formation of myelinating Schwann cells (mSCs) involves the remarkable biogenic process, which rapidly generates the myelin sheath. Once formed, the mSC transitions to a stable homeostatic state, with loss of this stability associated with neuropathies. The histone deacetylases histone deacetylase 1 (HDAC1) and HDAC2 are required for the myelination transcriptional program. Here, we show a distinct role for HDAC3, in that, while dispensable for the formation of mSCs, it is essential for the stability of the myelin sheath once formed-with loss resulting in progressive severe neuropathy in adulthood. This is associated with the prior failure to downregulate the biogenic program upon entering the homeostatic state leading to hypertrophy and hypermyelination of the mSCs, progressing to the development of severe myelination defects. Our results highlight distinct roles of HDAC1/2 and HDAC3 in controlling the differentiation and homeostatic states of a cell with broad implications for the understanding of this important cell-state transition.

Image-based siRNA screen to identify kinases regulating Weibel-Palade body size control using electroporation.

High-content screening of kinase inhibitors is important in order to identify biogenesis and function mechanisms of subcellular organelles. Here, we present a human kinome siRNA high-content screen on primary human umbilical vein endothelial cells, that were transfected by electroporation. The data descriptor contains a confocal fluorescence, microscopic image dataset. We also describe an open source, automated image analysis workflow that can be reused to perform high-content analysis of other organelles. This dataset is suitable for analysis of morphological parameters that are linked to human umbilical vein endothelial cell (HUVEC) biology.

Corrigendum: Image-based siRNA screen to identify kinases regulating Weibel-Palade body size control using electroporation.

This corrects the article DOI: 10.1038/sdata.2017.22.

A two-tier Golgi-based control of organelle size underpins the functional plasticity of endothelial cells.

Weibel-Palade bodies (WPBs), endothelial-specific secretory granules that are central to primary hemostasis and inflammation, occur in dimensions ranging between 0.5 and 5 µm. How their size is determined and whether it has a functional relevance are at present unknown. Here, we provide evidence for a dual role of the Golgi apparatus in controlling the size of these secretory carriers. At the ministack level, cisternae constrain the size of nanostructures ("quanta") of von Willebrand factor (vWF), the main WPB cargo. The ribbon architecture of the Golgi then allows copackaging of a variable number of vWF quanta within the continuous lumen of the trans-Golgi network, thereby generating organelles of different sizes. Reducing the WPB size abates endothelial cell hemostatic function by drastically diminishing platelet recruitment, but, strikingly, the inflammatory response (the endothelial capacity to engage leukocytes) is unaltered. Size can thus confer functional plasticity to an organelle by differentially affecting its activities.

H-Prune through GSK-3ß interaction sustains canonical WNT/ß-catenin signaling enhancing cancer progression in NSCLC.

H-Prune hydrolyzes short-chain polyphosphates (PPase activity) together with an hitherto cAMP-phosphodiesterase (PDE), the latest influencing different human cancers by its overexpression. H-Prune promotes cell migration in cooperation with glycogen synthase kinase-3 (Gsk-3ß). Gsk-3ß is a negative regulator of canonical WNT/ß-catenin signaling. Here, we investigate the role of Gsk-3ß/h-Prune complex in the regulation of WNT/ß-catenin signaling, demonstrating the h-Prune capability to activate WNT signaling also in a paracrine manner, through Wnt3a secretion. In vivo study demonstrates that h-Prune silencing inhibits lung metastasis formation, increasing mouse survival. We assessed h-Prune levels in peripheral blood of lung cancer patients using ELISA assay, showing that h-Prune is an early diagnostic marker for lung cancer. Our study dissects out the mechanism of action of h-Prune in tumorigenic cells and also sheds light on the identification of a new therapeutic target in non-small-cell lung cancer.

A high-content imaging workflow to study Grb2 signaling complexes by expression cloning.

Signal transduction by growth factor receptors is essential for cells to maintain proliferation and differentiation and requires tight control. Signal transduction is initiated by binding of an external ligand to a transmembrane receptor and activation of downstream signaling cascades. A key regulator of mitogenic signaling is Grb2, a modular protein composed of an internal SH2 (Src Homology 2) domain flanked by two SH3 domains that lacks enzymatic activity. Grb2 is constitutively associated with the GTPase Son-Of-Sevenless (SOS) via its N-terminal SH3 domain. The SH2 domain of Grb2 binds to growth factor receptors at phosphorylated tyrosine residues thus coupling receptor activation to the SOS-Ras-MAP kinase signaling cascade. In addition, other roles for Grb2 as a positive or negative regulator of signaling and receptor endocytosis have been described. The modular composition of Grb2 suggests that it can dock to a variety of receptors and transduce signals along a multitude of different pathways(1-3). Described here is a simple microscopy assay that monitors recruitment of Grb2 to the plasma membrane. It is adapted from an assay that measures changes in sub-cellular localization of green-fluorescent protein (GFP)-tagged Grb2 in response to a stimulus(4-6). Plasma membrane receptors that bind Grb2 such as activated Epidermal Growth Factor Receptor (EGFR) recruit GFP-Grb2 to the plasma membrane upon cDNA expression and subsequently relocate to endosomal compartments in the cell. In order to identify in vivo protein complexes of Grb2, this technique can be used to perform a genome-wide high-content screen based on changes in Grb2 sub-cellular localization. The preparation of cDNA expression clones, transfection and image acquisition are described in detail below. Compared to other genomic methods used to identify protein interaction partners, such as yeast-two-hybrid, this technique allows the visualization of protein complexes in mammalian cells at the sub-cellular site of interaction by a simple microscopy-based assay. Hence both qualitative features, such as patterns of localization can be assessed, as well as the quantitative strength of the interaction.

High-throughput transfection of differentiated primary neurons from rat forebrain.

Primary neurons in culture are considered to be a highly relevant model in the study of neuronal development and activity. They can be cultivated and differentiated in vitro but are difficult to transfect using conventional methods. To address this problem, a capillary electroporation system called Cellaxess Elektra was developed for efficient and reproducible transfection of primary cortical and hippocampal neurons without significant impact on cell morphology and viability. The cells are transfected in any stage of differentiation and development, directly in cell culture plates. Genetic material is delivered in situ to as many as 384 samples at a time, which enables both high-throughput and high-quality screening for hard-to-transfect primary cells, meaning that gene function can be studied on a genome-wide scale in cells previously inaccessible to genetic manipulation.