bluuebunny/crossref_metadata_2025 huggingface dataset:
CWHM-974 is a fluphenazine derivative with improved antifungal activity againstCandida albicansdue to reduced susceptibility to multidrug transporter-mediated resistance mechanisms
Authors: Miron-Ocampo Aracely , Beattie Sarah R. , Guin Soumitra , Conway Thomas , Meyers Marvin J. , Moye-Rowley W. Scott , Krysan Damian J.
Published: May 2023

Multidrug resistance (MDR) transporters such as ATP Binding Cassette (ABC) and Major Facilitator Superfamily (MFS) proteins are important mediators of antifungal drug resistance, particularly with respect to azole class drugs. Consequently, identifying molecules that are not susceptible to this mechanism of resistance is an important goal for new antifungal drug discovery. As part of a project to optimize the antifungal activity of clinically used phenothiazines, we synthesized a fluphenazine derivative (CWHM-974) with 8-fold higher activity againstCandidaspp. compared to the fluphenazine and with activity againstCandidaspp. with reduced fluconazole susceptibility due to increased multidrug resistance transporters. Here, we show that the improvedC. albicansactivity is because fluphenazine induces its own resistance by triggering expression of CDR transporters while CWHM-974 induces expression but does not appear to be a substrate for the transporters or is insensitive to their effects through other mechanisms. We also found that fluphenazine and CWHM-974 are antagonistic with fluconazole inC. albicansbut not inC. glabrata, despite inducingCDR1expression to high levels. Overall, CWHM-974 represents a unique example of a medicinal chemistry-based conversion of chemical scaffold from MDR-sensitive to MDR-resistant and, hence, active against fungi that have developed resistance to clinically used antifungals such as the azoles.
The landscape of tolerated genetic variation in humans and primates
Authors: Gao Hong , Hamp Tobias , Ede Jeffrey , Schraiber Joshua G. , McRae Jeremy , Singer-Berk Moriel , Yang Yanshen , Dietrich Anastasia , Fiziev Petko , Kuderna Lukas , Sundaram Laksshman , Wu Yibing , Adhikari Aashish , Field Yair , Chen Chen , Batzoglou Serafim , Aguet Francois , Lemire Gabrielle , Reimers Rebecca , Balick Daniel , Janiak Mareike C. , Kuhlwilm Martin , Orkin Joseph D. , Manu Shivakumara , Valenzuela Alejandro , Bergman Juraj , Rouselle Marjolaine , Silva Felipe Ennes , Agueda Lidia , Blanc Julie , Gut Marta , Vries Dorien de , Goodhead Ian , Harris R. Alan , Raveendran Muthuswamy , Jensen Axel , Chuma Idriss S. , Horvath Julie , Hvilsom Christina , Juan David , Frandsen Peter , Melo Fabiano R. de , Bertuol Fabricio , Byrne Hazel , Sampaio Iracilda , Farias Izeni , Valsecchi do Amaral João , Messias Mariluce , Silva Maria N. F. da , Trivedi Mihir , Rossi Rogerio , Hrbek Tomas , Andriaholinirina Nicole , Rabarivola Clément J. , Zaramody Alphonse , Jolly Clifford J. , Phillips-Conroy Jane , Wilkerson Gregory , Abee Christian , Simmons Joe H. , Fernandez-Duque Eduardo , Kanthaswamy ee , Shiferaw Fekadu , Wu Dongdong , Zhou Long , Shao Yong , Zhang Guojie , Keyyu Julius D. , Knauf Sascha , Le Minh D. , Lizano Esther , Merker Stefan , Navarro Arcadi , Batallion Thomas , Nadler Tilo , Khor Chiea Chuen , Lee Jessica , Tan Patrick , Lim Weng Khong , Kitchener Andrew C. , Zinner Dietmar , Gut Ivo , Melin Amanda , Guschanski Katerina , Schierup Mikkel Heide , Beck Robin M. D. , Umapathy Govindhaswamy , Roos Christian , Boubli Jean P. , Lek Monkol , Sunyaev Shamil , O’Donnell Anne , Rehm Heidi , Xu Jinbo , Rogers Jeffrey , Marques-Bonet Tomas , Farh Kyle Kai-How
Published: May 2023

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.

One Sentence Summary

Deep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.
Molecular dissection of PI3Kβ synergistic activation by receptor tyrosine kinases, GβGγ, and Rho-family GTPases
Authors: Duewell Benjamin R. , Wilson Naomi E. , Bailey Gabriela M. , Peabody Sarah E. , Hansen Scott D.
Published: May 2023

The class 1A phosphoinositide 3-kinase (PI3K) beta (PI3Kβ) is functionally unique in the ability to integrate signals derived from receptor tyrosine kinases (RTKs), heterotrimeric guanine nucleotide-binding protein (G-protein)-coupled receptors (GPCRs), and Rho-family GTPases. The mechanism by which PI3Kβ prioritizes interactions with various membrane tethered signaling inputs, however, remains unclear. Previous experiments have not been able to elucidate whether interactions with membrane-tethered proteins primarily control PI3Kβ localization versus directly modulate lipid kinase activity. To address this gap in our understanding of PI3Kβ regulation, we established an assay to directly visualize and decipher how three distinct protein interactions regulate PI3Kβ when presented to the kinase in a biologically relevant configuration on supported lipid bilayers. Using single molecule Total Internal Reflection Fluorescence (TIRF) Microscopy, we determined the mechanism controlling membrane localization of PI3Kβ, prioritization of signaling inputs, and lipid kinase activation. We find that auto-inhibited PI3Kβ prioritizes interactions with RTK-derived tyrosine phosphorylated (pY) peptides before engaging either GβGγ or Rac1(GTP). Although pY peptides strongly localize PI3Kβ to membranes, stimulation of lipid kinase activity is modest. In the presence of either pY/GβGγ or pY/Rac1(GTP), PI3Kβ activity is dramatically enhanced beyond what can be explained by simply increasing the strength of membrane localization. Instead, PI3Kβ is synergistically activated by pY/GβGγ and pY/Rac1(GTP) through a mechanism consistent with allosteric regulation.
Quantifying marine larval dispersal to assess MPA network connectivity and inform future national and transboundary planning efforts
Authors: Cristiani John , Rubidge Emily M. , Thompson Patrick L. , Robb Carrie , Lewis Margot Hessing- , O’Connor Mary I.
Published: May 2023

A Marine Protected Area (MPA) network, in which multiple reserves are designated in a region, can promote the protection of biodiversity across space. To be effective as a network, the design must consider whether MPAs are likely to be connected through the movement of individuals of species of interest. Additionally, network design may explicitly incorporate design features that promote biodiversity in unprotected habitats through the dispersal or spillover of multiple species. Patterns of dispersal and the ability of MPAs to function as an interacting network, however, are difficult to estimate at broad and transboundary spatial scales, and therefore connectivity is often not fully integrated in the design and assessment of MPA networks. Here, we model the dispersal of multiple nearshore species to estimate the potential connectivity of the existing MPAs in British Columbia, Canada, including connections to MPAs in the United States by simulating dispersal using a biophysical model with regional oceanographic currents. We found that MPAs in BC potentially meet connectivity design criteria for nearshore invertebrate species: the majority of MPAs (65-90%) are likely to exchange individuals (i.e. functional connectivity) and support persistent metapopulations, and more than half the unprotected coast (55-85%) receives a large proportion of the larvae produced in MPAs. Furthermore, we found that species’ dispersal abilities and the level of exposure of an MPA to open ocean can predict dispersal distance when we account for the random effects of dispersal location and season. Therefore, future predictions of connectivity are possible based on these core biological and physical attributes, without running new simulations. Together, these analyses provide a robust and novel assessment of multi-species connectivity that can support the design of new MPAs with transboundary connectivity on the northwest coast of North America.
Susceptibility-induced internal gradients reveal axon morphology and cause anisotropic effects in the dMRI signal
Authors: Winther S. , Lundell H. , Rafael-Patiño J. , Andersson M. , Thiran J-P. , Dyrby T. B.
Published: May 2023

Diffusion-weighted MRI is our most promising method for estimating microscopic tissue morphology in vivo. The signal acquisition is based on scanner-generatedexternal magnetic gradients. However, it will also be affected by susceptibility-inducedinternal magnetic gradients caused by interaction between the tissue and the static magnetic field of the scanner. With 3D in silico experiments, we show how internal gradients cause morphology-, compartment-, and orientation-dependence of spin-echo and pulsed-gradient spin-echo experiments in myelinated axons. These effects are unseen in previous 2D modelling. For an ex vivo monkey brain, we observe the orientation-dependency generated only when including non-circular cross-sections in the in silico morphological configurations, and find orientation-dependent deviation of up to 17% for diffusion tensor metrics. Our findings underline the importance of accounting for realistic 3D axon morphology in modelling. Interestingly, the morphology-specific orientation-dependency trends show potential for a novel sensitivity to morphology, which is not attainable by the theoretical diffusion-weighted MRI signal itself.
A 2D convolutional neural network for taxonomic classification applied to viruses in the phylumCressdnaviricota
Authors: Gomes Ruither A. L. , Zerbini F. Murilo
Published: May 2023

Taxonomy, defined as the classification of different objects/organisms into defined stable hierarchical categories (taxa), is fundamental for proper scientific communication. In virology, taxonomic assignments based on sequence alone are now possible and their use may contribute to a more precise and comprehensive framework. The current major challenge is to develop tools for the automated classification of the millions of putative new viruses discovered in metagenomic studies. Among the many tools that have been proposed, those applying machine learning (ML), mainly in the deep learning branch, stand out with highly accurate results. One ML tool recently released that uses k-mers, VirusTaxo, was the first one to be applied with success, 93% average accuracy, to all types of viruses. Nevertheless, there is a demand for new tools that are less computationally intensive. Viruses classified in the phylumCressdnaviricota, with their small and compact genomes, are good subjects for testing these new tools. Here we tested the usage of 2D convolutional neural networks for the taxonomic classification of cressdnaviricots, also testing the effect of data imbalance and two augmentation techniques by benchmarking against VirusTaxo. We were able to get perfect classification during k-fold test evaluations for balanced taxas, and more than 98% accuracy in the final pipeline tested for imbalanced datasets. The mixture of augmentation on more imbalanced groups and no augmentation for more balanced ones achieved the best score in the final test. These results indicate that these architectures can classify DNA sequences with high precision.
Towards Preclinical Validation of Arbaclofen (R-baclofen) Treatment for 16p11.2 Deletion Syndrome
Authors: Gundersen Brigitta B. , O’Brien William T. , Schaffler Melanie D. , Schultz Maria N. , Tsukahara Tatsuya , Lorenzo Sandra Martin , Nalesso Valerie , Luo Clayton Alice H. , Abel Ted , Crawley Jacqueline N. , Datta Sandeep Robert , Herault Yann
Published: May 2023

A microdeletion on human chromosome 16p11.2 is one of the most common copy number variants associated with autism spectrum disorder and other neurodevelopmental disabilities. Arbaclofen, a GABA(B) receptor agonist, is a component of racemic baclofen, which is FDA-approved for treating spasticity, and has been shown to alleviate behavioral phenotypes, including recognition memory deficits, in animal models of 16p11.2 deletion. Given the lack of reproducibility sometimes observed in mouse behavioral studies, we brought together a consortium of four laboratories to study the effects of arbaclofen on behavior in three different mouse lines with deletions in the mouse region syntenic to human 16p11.2 to test the robustness of these findings. Arbaclofen rescued cognitive deficits seen in two 16p11.2 deletion mouse lines in traditional recognition memory paradigms. Using an unsupervised machine-learning approach to analyze behavior, one lab found that arbaclofen also rescued differences in exploratory behavior in the open field in 16p11.2 deletion mice. Arbaclofen was not sedating and had modest off-target behavioral effects at the doses tested. Our studies show that arbaclofen consistently rescues behavioral phenotypes in 16p11.2 deletion mice, providing support for clinical trials of arbaclofen in humans with this deletion.

One sentence summary

Experiments across four laboratories found that arbaclofen rescued cognitive deficits in mouse models of 16p11.2 deletion, without sedation or significant off-target behavioral effects.
Synergistic effects of predation and parasitism on competition between edible and inedible phytoplankton
Authors: Kasada Minoru , Thongthaisong Patch , Wollrab Sabine , Van den Wyngaert Silke , Kiel Christine , Berger Stella A. , Grossart Hans-Peter
Published: May 2023

Fungi can affect aquatic ecosystems through syntrophic and parasitic interactions with other organisms and organic matter. In pelagic systems, fungal parasites on phytoplankton can control trophic interactions and food-web dynamics, e.g., zooplankton grazing on fungal parasite zoospores creates an alternative energy pathway (termed “mycoloop”) from otherwise inedible phytoplankton species. We aim to investigate how the mycoloop influences community dynamics in aquatic food-webs combining experimental and modelling approaches. We assembled an experimental system consisting of an inedible (host) phytoplankton species and its parasitic chytrid, an edible (non-host) phytoplankton species, and a zooplankton grazer. Chytrids parasitizing increased edible phytoplankton abundance, while zooplankton grazing decreased edible phytoplankton abundance. In the presence of zooplankton and chytrids, competition effects between edible and inedible phytoplankton species depended on nutrient levels. At high nutrient levels, competition was balanced by an indirect positive chytrid effect and negative zooplankton grazing effects on edible phytoplankton. In contrast, at low nutrient levels, we found chytrid had a negative impact on edible phytoplankton synergistically with zooplankton. Mathematical investigations suggest that the synergistic effect can be caused by the mycoloop. This indicates that the mycoloop substantially affects predator-prey interactions and phytoplankton competition with yet unknown ecological consequences.
Loss ofIRF5increases ribosome biogenesis leading to alterations in mammary gland architecture and metastasis
Authors: Brune Zarina , Li Dan , Song Su , Li Dan Iris , Castro Isabel , Rasquinha Rhea , Rice Matthew R. , Guo Qin , Kampta Kyle , Moss Matthew , Lallo Morgan , Pimenta Erica , Somerville Carter , Lapan Margaret , Nelson Victoria , dos Santos Camila O. , Blanc Lionel , Pruitt Kevin , Barnes Betsy J.
Published: May 2023

Despite the progress made in identifying cellular factors and mechanisms that predict progression and metastasis, breast cancer remains the second leading cause of death for women in the US. Using The Cancer Genome Atlas and mouse models of spontaneous and invasive mammary tumorigenesis, we identified that loss of function of interferon regulatory factor 5 (IRF5) is a predictor of metastasis and survival. Histologic analysis ofIrf5-/-mammary glands revealed expansion of luminal and myoepithelial cells, loss of organized glandular structure, and altered terminal end budding and migration. RNA-seq and ChIP-seq analyses of primary mammary epithelial cells fromIrf5+/+andIrf5-/-littermate mice revealed IRF5-mediated transcriptional regulation of proteins involved in ribosomal biogenesis. Using an invasive model of breast cancer lackingIrf5, we demonstrate that IRF5 re-expression inhibits tumor growth and metastasis via increased trafficking of tumor infiltrating lymphocytes and altered tumor cell protein synthesis. These findings uncover a new function for IRF5 in the regulation of mammary tumorigenesis and metastasis.

Highlights

Loss of IRF5 is a predictor of metastasis and survival in breast cancer.

IRF5 contributes to the regulation of ribosome biogenesis in mammary epithelial cells.

Loss of IRF5 function in mammary epithelial cells leads to increased protein translation.
Molecule-Morphology Contrastive Pretraining for Transferable Molecular Representation
Authors: Nguyen Cuong Q. , Pertusi Dante , Branson Kim M.
Published: May 2023

Image-based profiling techniques have become increasingly popular over the past decade for their applications in target identification, mechanism-of-action inference, and assay development. These techniques have generated large datasets of cellular morphologies, which are typically used to investigate the effects of small molecule perturbagens. In this work, we extend the impact of such dataset to improving quantitative structure-activity relationship (QSAR) models by introducing Molecule-Morphology Contrastive Pretraining (MoCoP), a framework for learning multi-modal representation of molecular graphs and cellular morphologies. We scale MoCoP to approximately 100K molecules and 600K morphological profiles using data from the JUMP-CP Consortium and show that MoCoP consistently improves performances of graph neural networks (GNNs) on molecular property prediction tasks in ChEMBL20 across all dataset sizes. The pretrained GNNs are also evaluated on internal GSK pharmacokinetic data and show an average improvement of 2.6% and 6.3% in AUPRC for full and low data regimes, respectively. Our findings suggest that integrating cellular morphologies with molecular graphs using MoCoP can significantly improve the performance of QSAR models, ultimately expanding the deep learning toolbox available for QSAR applications.
Targeting metabolic fluxes reverts metastatic transitions in ovarian cancer
Authors: Arora Garhima , Langthasa Jimpi , Banerjee Mallar , Bhat Ramray , Chatterjee Samrat
Published: May 2023

Spheroids formation during epithelial ovarian cancer progression correlates with peritoneal organ colonization, disease recurrence, and poor prognosis. Although cancer progression has been demonstrated to be associated with and driven by metabolic changes within transformed cells, possible associations between metabolic dynamics and metastatic morphological transitions remain unexplored. To address this problem, we performed quantitative proteomics to identify protein signatures associated with three distinct morphologies (2D monolayers and two geometrically individual three-dimensional spheroidal states) of the high-grade serous ovarian cancer line OVCAR-3. Integrating the protein states onto genome-scale metabolic models allowed us to construct context-specific metabolic models for each morphological stage of the OVCAR-3 cell line and systematically evaluate their metabolic functionalities. We obtained disease-driving metabolic reaction modules using these models and elucidated gene knockout strategies to reduce metabolic alterations associated with disease progression. We explored the DrugBank database to mine pharmacological agents and evaluated the effect of drugs in impairing cancer progression. Finally, we experimentally validated our predictions by confirming the ability of one of our predicted drugs: the neuraminidase inhibitor oseltamivir, to disrupt the metastatic spheroidal morphologies without any cytotoxic effect on untransformed stromal mesothelial monolayers.
Rapid memory encoding in a recurrent network model with behavioral time scale synaptic plasticity
Authors: Li Pan Ye , Roxin Alex
Published: May 2023

Episodic memories are formed after a single exposure to novel stimuli. The plasticity mechanisms underlying such fast learning still remain largely unknown. Recently, it was shown that cells in area CA1 of the hippocampus of mice could form or shift their place fields after a single traversal of a virtual linear track. In-vivo intracellular recordings in CA1 cells revealed that previously silent inputs from CA3 could be switched on when they occurred within a few seconds of a dendritic plateau potential (PP) in the post-synaptic cell, a phenomenon dubbed Behavioral Time-scale Plasticity (BTSP). A recently developed computational framework for BTSP in which the dynamics of synaptic traces related to the pre-synaptic activity and post-synaptic PP are explicitly modelled, can account for experimental findings. Here we show that this model of plasticity can be further simplified to simple map which describes changes to the synaptic weights after a single trial. The map can be solved analytically and provides a quantitative fit to experimental data from CA1. We use a temporally symmetric version of this map to study the storage of a large number of spatial memories in a recurrent network, such as CA3. Specifically, the simplicity of the map allows us to calculate the correlation of the synaptic weight matrix with any given past environment analytically. We show that the calculated memory trace can be used to predict the emergence and stability of bump attractors in a high dimensional neural network model endowed with BTSP.

Author summary

A recently discovered form of in-vivo plasticity, called Behavioral Time-scale Plasticity (BTSP), leads to the generation of a place cell in CA1 from a previously silent cell after a single intracellular plateau potential (PP). We show that this one-shot learning process is well-described by a 1D map, which updates the synaptic weight matrix after the PP. We use the map to study the storage of spatial memories in a recurrent network, such as CA3. The map allows us to calculate the correlation of the weight matrix with all past explored environments analytically. When only a small fraction of cells are place cells in any given environment, we show that the full dynamics of a recurrent network endowed with BTSP is equivalent to its projection onto a series of weakly interacting manifolds, one for each environment. Interestingly, this weak interaction, which takes the form of quenched variability, actually enhances the memory capacity by stabilizing remote memories which otherwise would be unretrievable.
Evidence for conservation of primordial ∼12-hour ultradian gene programs in humans under free-living conditions
Authors: Zhu Bokai , Liu Silvia , David Natalie L. , Dion William , Doshi Nandini K , Siegel Lauren B. , Amorim Tânia , Andrews Rosemary E. , Kumar GV Naveen , Li Hanwen , Irfan Saad , Pesaresi Tristan , Sharma Ankit X. , Sun Michelle , Fazeli Pouneh K. , Steinhauser Matthew L.
Published: May 2023

While circadian rhythms are entrained to the once daily light-dark cycle of the sun, many marine organisms exhibit ∼12h ultradian rhythms corresponding to the twice daily movement of the tides. Although human ancestors emerged from circatidal environment millions of years ago, direct evidence of ∼12h ultradian rhythms in humans is lacking. Here, we performed prospective, temporal transcriptome profiling of peripheral white blood cells and identified robust ∼12h transcriptional rhythms from three healthy participants. Pathway analysis implicated ∼12h rhythms in RNA and protein metabolism, with strong homology to the circatidal gene programs previously identified in Cnidarian marine species. We further observed ∼12h rhythms of intron retention events of genes involved in MHC class I antigen presentation, synchronized to expression of mRNA splicing genes in all three participants. Gene regulatory network inference revealed XBP1, and GABP and KLF transcription factor family members as potential transcriptional regulators of human ∼12h rhythms. These results suggest that human ∼12h biological rhythms have a primordial evolutionary origin with important implications for human health and disease.
Family-wide analysis of integrin structures predicted by AlphaFold2
Authors: Zhang Heng , Zhu Daniel S. , Zhu Jieqing
Published: May 2023

Recent advances in protein structure prediction using AlphaFold2, known for its high efficiency and accuracy, have opened new avenues for comprehensive analysis of all structures within a single protein family. In this study, we evaluated the capabilities of AphaFold2 in analyzing integrin structures. Integrins are heterodimeric cell surface receptors composed of a combination of 18 α and 8 β subunits, resulting in a family of 24 different members. Both α and β subunits consist of a large extracellular domain, a short transmembrane domain, and typically, a short cytoplasmic tail. Integrins play a pivotal role in a wide range of cellular functions by recognizing diverse ligands. Despite significant advances in integrin structural studies in recent decades, high-resolution structures have only been determined for a limited subsets of integrin members, thus limiting our understanding of the entire integrin family. Here, we first analyzed the single-chain structures of 18 α and 8 β integrins in the AlphaFold2 protein structure database. We then employed the newly developed AlphaFold2-multimer program to predict the α/β heterodimer structures of all 24 human integrins. The predicted structures show a high level of accuracy for the subdomains of both α and β subunits, offering high-resolution structure insights for all integrin heterodimers. Our comprehensive structural analysis of the entire integrin family unveils a potentially diverse range of conformations among the 24 members, providing a valuable structure database for studies related to integrin structure and function. We further discussed the potential applications and limitations of the AlphaFold2-derived integrin structures.
D2/D3 dopamine supports the precision of mental state inferences and self-relevance of joint social outcomes
Authors: Barnby J.M. , Bell V. , Deeley Q , Mehta M. , Moutoussis M.
Published: May 2023

Striatal dopamine is important in paranoid attributions, although its computational role in social inference remains elusive. We employed a simple game theoretic paradigm and computational model of intentional attributions to investigate the effects of dopamine D2/D3 antagonism on ongoing mental state inference following social outcomes. Haloperidol, compared to placebo, enhanced the impact of partner behaviour on beliefs about the harmful intent of partners, and increased learning from recent encounters. These alterations caused significant changes to model covariation and negative correlations between self-interest and harmful intent attributions. Our findings suggest haloperidol improves belief flexibility about others and simultaneously reduces the self-relevance of social observations. Our results may reflect the role of D2/D3 dopamine in supporting self-relevant mentalisation. Our data and model bridge theory between general and social accounts of value representation. We demonstrate initial evidence for the sensitivity of our model and short social paradigm to drug intervention and clinical dimensions, allowing distinctions between mechanisms that operate across traits and states.

Data Availability

All data and code are available online:

https://github.com/josephmbarnby/Barnby_etal_2023_D2D3Modelling

Graphical Abstract
Genome dynamics across the evolutionary transition to endosymbiosis
Authors: Siozios Stefanos , Jimenez Pol Nadal , Azagi Tal , Sprong Hein , Frost Crystal L , Parratt Steven R , Taylor Graeme , Brettell Laura , Liew Kwee Chin , Croft Larry , King Kayla C , Brockhurst Michael A , Hypša Václav , Novakova Eva , Darby Alistair C , Hurst Gregory DD
Published: May 2023

Endosymbiosis – where a microbe lives and replicates within a host – is an important contributor to organismal function that has accelerated evolutionary innovations and catalysed the evolution of complex life. The evolutionary processes associated with transitions to endosymbiosis, however, are poorly understood. Here, we use comparative genomics of the genusArsenophonusto reveal the complex processes that occur on evolution of an endosymbiotic lifestyle. We compared the genomes of 38 strains spanning diverse lifestyles from environmentally acquired infections to obligate inter-dependent endosymbionts. We observed recent endosymbionts had larger genome sizes than closely related environmentally acquired strains, consistent with evolutionary innovation and rapid gain of new function. Increased genome size was a consequence of prophage and plasmid acquisition including a cargo of type III effectors, and concomitant loss of CRISPR-Cas genome defence systems enabling mobile genetic element expansion. Persistent endosymbiosis was also associated with loss of type VI secretion, likely reflecting reduced microbe-microbe competition. Thereafter, the transition to stable endosymbiosis and vertical inheritance was associated with the expected relaxation of purifying selection, pseudogenisation of genes and reduction of metabolism, leading to genome reduction. However, reduced %GC that is typically considered a progressive linear process was observed only in obligate interdependent endosymbionts. We argue that a combination of the need for rapid horizontal gene transfer-mediated evolutionary innovation together with reduced phage predation in endosymbiotic niches drives loss of genome defence systems and rapid genome expansion upon adoption of endosymbiosis. These remodelling processes precede the reductive evolution traditionally associated with adaptation to endosymbiosis.
Moving Past Neonicotinoids and Honeybees: A Systematic Review of Existing Research on Other Insecticides and Bees
Authors: Dirilgen T. , Herbertsson L. , O’Reilly A. , Mahon N. , Stanley D.A.
Published: May 2023

Synthetic pesticides are used widely in agriculture to protect crops from pests, weeds and disease. However, their use also comes with a range of environmental concerns. One of which is effects of insecticides on non-target organisms such as bees, who provide pollination services for crops and wild plants. This systematic literature review quantifies the existing research on bees and insecticides broadly, and then focuses more specifically on non-neonicotinoid insecticides and non-honeybees. We find that articles on honeybees (Apis sp.)and insecticides account for 80% of all research, with all other bees combined making up 20%. Neonicotinoids were studied in 34% of articles across all bees and were the most widely studied insecticide class for non-honeybees overall, with almost three times as many studies than the second most studied class. Of non-neonicotinoid insecticide classes and non-honeybees; the most studied were pyrethroids and organophosphates followed by carbamates, and the most widely represented bee taxa were bumblebees (Bombus), followed by leaf-cutter bees (Megachile) and mason bees (Osmia). Research has taken place across several countries, with the highest numbers of articles from Brazil and the US, and with notable gaps from countries in Asia, Africa and Oceania. Mortality was the most studied effect type, while sub-lethal effects such as on behaviour were less studied. Few studies tested how insecticides were influenced by other multiple pressures, such as climate change and co-occurring pesticides (cocktail effects). As anthropogenic pressures do not occur in isolation, we suggest that future research also addresses these knowledge gaps. Given the changing global patterns in insecticide use, and the increasing inclusion of both non-honeybees and sub-lethal effects in pesticide risk assessment, there is a need for expanding research beyond current state to ensure a strong scientific evidence base for the development of risk assessment and associated policy.
Chromatin context-dependent effects of epigenetic drugs on CRISPR-Cas9 editing
Authors: Schep Ruben , Trauernicht Max , Morris Ben , Vergara Xabier , Beijersbergen Roderick L. , Steensel Bas van
Published: May 2023

The efficiency and outcome of CRISPR/Cas9 editing depends on the chromatin state at the cut site. It has been shown that changing the chromatin state can influence both the efficiency and repair outcome, and epigenetic drugs have been used to improve Cas9 editing. However, because the target proteins of these drugs are not homogeneously distributed across the genome, the efficacy of these drugs may be expected to vary from locus to locus. Here, we systematically analyzed this chromatin context-dependency for 160 epigenetic drugs. We used a human cell line with 19 stably integrated reporters to induce a double-stranded break (DSB) in different chromatin environments. We then measure Cas9 editing efficiency and repair pathway usage by sequencing the mutational signatures. We identified 67 drugs that modulate Cas9 editing efficiency and/or repair outcome dependent on the local chromatin environment. For example, we find a subset of histone deacetylase inhibitors that improve Cas9 editing efficiency throughout all types of heterochromatin (e.g., PCI-24781), while others were only effective in H3K27me3-marked regions (e.g., Vorinostat). In summary, this study reveals that most epigenetic drugs alter CRISPR editing in a chromatin-dependent manner, and provides a detailed guide to improve Cas9 editing more selectively at the desired location.

HIGHLIGHTS

A screen identifies dozens of drugs that alter Cas9 editing in a chromatin context-dependent manner

Many HDAC inhibitors boost Cas9 editing efficiency throughout all types of heterochromatin

The DNMT inhibitor Decitabine completely blocks resection-dependent repair across the genome
Hindbrain boundaries as niches of neural progenitor/stem cells regulated by the extracellular matrix proteoglycan chondroitin sulphate
Authors: Hutchings Carmel , Nuriel Yarden , Lazar Daniel , Kohl Ayelet , Muir Elizabeth , Nevo Yuval , Benyamini Hadar , Sela-Donenfeld Dalit
Published: May 2023

The interplay between neural progenitor/stem cells (NPSC) and their extracellular matrix (ECM), is a crucial regulatory mechanism that determines their behavior. Nonetheless, how the ECM dictates internal processes remains elusive. The hindbrain is valuable to examine this relationship, as cells in the hindbrain boundaries (HB), which arise between any two neighboring rhombomeres, express the NPSC-marker Sox2 while being surrounded with the ECM molecule chondroitin sulphate proteoglycan (CSPG), in chick and mouse embryos. CSPG expression was used to isolate HB/Sox2+ cells for RNA-sequencing, revealing their distinguished molecular properties as typical NPSCs, which express known and newly-identified genes relating to stem cells, cancer, matrisome and cell-cycle. In contrast, the CSPG-/non-HB cells, displayed clear neural-differentiation transcriptome. To address whether CSPG is significant for hindbrain development, its expression was manipulated in vivo and in vitro. CSPG-manipulations shifted the stem versus differentiation state of HB cells, evident by their behavior and altered gene expression. These results provide novel understanding on the uniqueness of hindbrain boundaries as repetitive pools of NPSCs in-between the rapidly-growing rhombomeres, which rely on their microenvironment to maintain undifferentiated during development.

SUMMARY:

Transcriptomic analysis of hindbrain boundaries revels them to harbor cells with neural progenitor\stem cell properties that rely on local extracellular matrix to maintain their undifferentiated state.
Automatic annotation of the bHLH gene family in plants
Authors: Thoben Corinna , Pucker Boas
Published: May 2023

Background

The bHLH transcription factor family is named after the basic helix-loop-helix (bHLH) domain that is a characteristic element of their members. Understanding the function and characteristics of this family is important for the examination of a wide range of functions. As the availability of genome sequences and transcriptome assemblies has increased significantly, the need for automated solutions that provide reliable functional annotations is emphasised.

Results

A phylogenetic approach was adapted for the automatic identification and functional annotation of the bHLH transcription factor family. The bHLH_annotator for the automated functional annotation of bHLHs was implemented in Python3. Sequences of bHLHs described in literature were collected to represent the full diversity of bHLH sequences.

Previously described orthologs form the basis for the functional annotation assignment to candidates which are also screened for bHLH-specific motifs. The pipeline was successfully deployed on the twoArabidopsis thalianaaccessions Col-0 and Nd-1, the monocot speciesDioscorea dumetorum, and a transcriptome assembly ofCroton tiglium.

Depending on the applied search parameters for the initial candidates in the pipeline, species-specific candidates or members of the bHLH family which experienced domain loss can be identified.

Conclusions

The bHLH_annotator allows a detailed and systematic investigation of the bHLH family in land plant species and classifies candidates based on bHLH-specific characteristics, which distinguishes the pipeline from other established functional annotation tools. This provides the basis for the functional annotation of the bHLH family in land plants and the systematic examination of a wide range of functions regulated by this transcription factor family.
Isoform Specific Regulation of Adenylyl Cyclase 5 by Gβγ
Authors: Yen Yu-Chen , Li Yong , Chen Chun-Liang , Klose Thomas , Watts Val J , Dessauer Carmen W , Tesmer John J. G.
Published: May 2023

The nine different membrane-anchored adenylyl cyclase isoforms (AC1-9) in mammals are stimulated by the heterotrimeric G protein Gαs, but their response to Gβγ regulation is isoform-specific. For example, AC5 is conditionally activated by Gβγ. Here, we report cryo-EM structures of ligand-free AC5 in complex with Gβγ and of a dimeric form of AC5 that could be involved in its regulation. Gβγ binds to a coiled-coil domain that links the AC transmembrane region to its catalytic core as well as to a region (C1b) that is known to be a hub for isoform-specific regulation. We confirmed the Gβγ interaction with both purified proteins and cell-based assays. The interface with Gβγ involves AC5 residues that are subject to gain-of-function mutations in humans with familial dyskinesia, indicating that the observed interaction is important for motor function. A molecular mechanism wherein Gβγ either prevents dimerization of AC5 or allosterically modulates the coiled-coil domain, and hence the catalytic core, is proposed. Because our mechanistic understanding of how individual AC isoforms are uniquely regulated is limited, studies such as this may provide new avenues for isoform-specific drug development.
Defining a critical role of an essential membrane protein in mycolic acid transport in mycobacteria
Authors: Liang Jeremy , Chen Yushu , Chng Shu-Sin
Published: May 2023

A major feature of the mycobacterial outer membrane (OM) is the presence of long, branched chain mycolic acids (MAs), which render the OM hydrophobic and impervious against various noxious substances, including antibiotics. While the biosynthesis of MA is well studied, the mechanisms governing its transport from the inner membrane to the OM remain largely elusive. In this study, we characterized the function of MSMEG_0317 inMycobacterium smegmatis, a membrane protein encoded within a conserved genetic locus that has been implicated in MA metabolism and/or transport. Using a conditional knockout mutant, we demonstrate thatmsmeg_0317is essential for mycobacterial growth. Depletingmsmeg_0317from cells blocks the formation of MA species found at the OM, establishing a critical function in MA transport across the cell envelope. We further reveal that MSMEG_0317 exists as stable dimersin vitrothat require the presence of its N- and C-terminal transmembrane helices, both of which are important for functionality in cells. Our work defines the essential role of MSMEG_0317 in MA metabolism and/or transport, and offers new insights into cell envelope biogenesis in mycobacteria.
Disease resistance gene count increases with rainfall inSilphium integrifolium
Authors: Keepers Kyle , Peterson Kelsey , Raduski Andrew , Turner Kathryn M. , Van Tassel David , Smith Kevin , Harkess Alex , Bever James D. , Brandvain Yaniv
Published: May 2023

Intracellular plant defense against pathogens is mediated by a class of disease resistance genes known as NB-LRRs or NLRs (R genes). Many of the diseases these genes protect against are more prevalent in regions of higher rainfall, which provide better growth conditions for the pathogens. As such, we expect a higher selective pressure for the maintenance and proliferation of R genes in plants adapted to wetter conditions. In this study, we enriched libraries for R genes using RenSeq from baits primarily developed from the common sunflower (Helianthus annuus) reference genome. We sequenced the R gene libraries ofSilphium integrifoliumMichx, a perennial relative of sunflower, from 12 prairie remnants across a rainfall gradient in the Central Plains of the United States, with both Illumina short-read (n=99) and PacBio long-read (n=10) approaches. We found a positive relationship between the mean effective annual precipitation of a plant’s source prairie remnant and the number of R genes in its genome, consistent with intensity of plant pathogen coevolution increasing with precipitation. We show that RenSeq can be applied to the study of ecological hypotheses in non-model relatives of model organisms.
Cup and Pan Behavioral Assays for AssessingAnopheles coluzziiLarval Volatile Responses
Authors: Liu Feng , Sun Huahua , Zwiebel Laurence J.
Published: May 2023

Larval stageAnopheles coluzziiare highly reliant on their olfactory system to locate food sources and to avoid predators and less advantageous microenvironments within their aqueous habitats. The major larval chemosensory appendage, the antenna, is a complex organ with multiple sensory components that is responsible for both gustation and olfaction, thereby facilitating the detection and of both soluble and volatile compounds of biological relevance. Such compounds include food sources, predators, and a range of environmental toxicants. Unlike other mosquitoes,Anopheles coluzziioften position themselves parallel and just under the surface of their aqueous habitats, where they can detect and respond to volatile stimuli. We describe two assays for assessing the behavioral responses of larval anophelines in response to volatile chemicals. The first is a dual-choice, water-surface, inverted-cup assay designed to behaviorally characterize the response valences (attraction, neutral, and repulsion) of anopheline larvae by monitoring and recording the distribution of larvae proximate to chemical volatiles relative to solvent controls. Second, an aqueous-based larval pan behavior assay is designed to assess the responses of mosquito larvae to soluble compounds (as well as potential headspace volatiles) that are released from a point source within larval water. Here, the response valence (attractive, neutral, and repulsive) of mosquito larvae is assessed by quantifying the numbers of larvae in predefined zones proximate to chemical sources.
The synthesis, crystal structure and Hirshfeld surface analysis of the thiophene derivatives 5-(phenylsulfonyl)-5,6-dihydrobenzo[4,5]thieno[3,2-j]phenanthridine and (E)-N-{2-[2-(benzo[b]thiophen-2-yl)ethenyl]phenyl}-N-(prop-2-yn-1-yl)benzenesulfonamide
Authors: Madhan S. , NizamMohideen M. , Pavunkumar Vinayagam , MohanaKrishnan Arasambattu K.
Published: May 2023

In both of the title compounds, C26H19NO2S2, (I), and C25H19NO2S2, (II), the benzothiophene rings are essentially planar with maximum deviations of 0.026 (1) and −0.016 (1) Å for the carbon and sulfur atoms in compounds (I) and (II), respectively. In (I), the thiophene ring system is almost orthogonal to the phenyl ring attached to the sulfonyl group, subtending a dihedral angle of 88.1 (1)°, and the dihydropyridine ring adopts a screw–boat conformation. In both compounds, the molecular structure is consolidated by weak C—H...O intramolecular interactions formed by the sulfone oxygen atoms, which generate S(5) ring motifs. In the crystal of II, molecules are linked via C—H...O hydrogen bonds, generating C(7) chains running along the [100] direction. No significant intermolecular interactions are observed in I.
Engine condition monitoring on small single engine turboprop
Authors: Šplíchal Miroslav , Červenka Miroslav , Juracka Jaroslav
Published: May 2023

Purpose

This study aims to focus on verifying the possibility of monitoring the condition of a turboprop engine using data recorded by on-board avionics Garmin G1000. This approach has potential benefits for operators without the need to invest in specialised equipment. The main focus was on the inter-turbine temperature (ITT). An unexpected increase in temperature above the usual value may indicate an issue with the engine. The problem lies in the detection of small deviations when the absolute value of the ITT is affected by several external variables.

Design/methodology/approach

The ITT is monitored by engine sensors and stored by avionics 1× per second onto an SD card. This process generates large amount of data that needs to be processed. Therefore, an algorithm was created to detect the steady states of the engine parameters. The ITT value also depends on the flight parameters and surrounding environment. As a solution to these effects, the division of data into clusters that represent the usual flight profiles was tested. This ensures a comparison at comparable ambient pressures. The dominant environmental influence then remain at the ambient air temperature (OAT). Three OAT compensation methods were tested in this study. Compensation for the standard atmosphere, compensation for the standard temperature of the given flight level and compensation for the speed of the generator, where the regression analysis proved the dependence between the ambient temperature and the speed of the generator.

Findings

The influence of ambient temperature on the corrected ITT values is noticeable. The best method for correcting the OAT appears to be the use of compensation through the revolutions of the compressor turbine NG. The speed of the generator depends on several parameters, and can refine the corrected ITT value. During the long-term follow-up, the ITT differences (delta values) were within the expected range. The tested data did not include the behaviour of the engine with a malfunction or other damage that would clearly verify this approach. Therefore, the engine monitoring will continue.

Practical implications

This study presents a possible approach to turbine engine condition monitoring using limited on board avionic data. These findings can support the development of an engine condition monitoring system with automatic abnormality detection and low operating costs.

Originality/value

This article represent a practical description of problems in monitoring the condition of a turboprop engine in an aircraft with variable flight profiles. The authors are not aware of a similar method that uses monitoring of engine parameters at defined flight levels. Described findings should limit the influence of ambient air pressure on engine parameters.