Miracle-dz/UniFAR-FTUs huggingface dataset:
The AMPK activator A-769662 inhibits human TASK3 potassium channels in an AMPK-independent manner

Heteromeric TASK1/3 channels play a fundamental role in oxygen-sensing by carotid body type 1 cells, where hypoxia-induced inhibition of TASK3 and/or TASK1/3 potassium currents leads to depolarisation, voltage-gated calcium entry, exocytotic transmitter release and increases in carotid body afferent input responses that initiate corrective changes in breathing patterns. However, the mechanism by which hypoxia leads to TASK-1/3 channel inhibition is still debated. It had been proposed that the AMP-activated protein kinase (AMPK) might directly phosphorylate and inhibit TASK channels, in particular TASK-3, although subsequent studies on rat type I cells argued against this view. Here we report on the effects of novel, highly selective AMPK activators on recombinant human TASK-3 potassium channels. Sequence alignment identified an AMPK recognition motif in TASK-3, but not TASK-1, with Ser55 representing a potential site for AMPK-dependent phosphorylation in TASK-3. However, neither of the AMPK activators, AICAR or MK-8722, caused a significant reduction of human TASK-3 current amplitude. By contrast, high concentrations of the AMPK activator A-769662 (100-500 µM) inhibited human TASK-3 currents in a concentration-dependent manner. Importantly, A-769662 (300 µM) also inhibited human TASK-3 channels in HEK293 cells that stably over-expressed an AMPK-β1 subunit mutant (S108A) that renders AMPK insensitive to activators binding the Allosteric Drug and Metabolite (ADaM) site, such as A-769662. We therefore identify A-769662 as a novel human TASK-3 channel inhibitor and provide conclusive evidence that AMPK does not regulate TASK-3 channel currents.
Bundling and segregation affects “liking”, but not “wanting”, in an insect

Behavioural economists have identified many psychological manipulations which affect perceived value, although value in humans is not a unitary experience, with “liking” and “wanting” being neurologically separate processes. A prominent example of this is bundling, in which several small gains (or costs) are experienced as more valuable (or costly) than if the same total amount is presented together. While extensively demonstrated in humans, to our knowledge this effect has never been investigated in an animal, let alone an invertebrate. We trained individual Lasius niger workers to two of three conditions in which either costs (travel distance), gains (sucrose reward), or both were either bundled or segregated: A) both costs and gains bundled, B) both segregated, and C) only gains segregated. We recorded pheromone deposition on the ants’ return trips to the nest as measure of “liking”. After training, we offer the ants a binary choice between odours associated with the treatments, as a measure of “wanting”. While bundling treatment did not affect choice, i.e. “wanting”, it strongly influenced pheromone deposition, i.e. “liking”. Ants deposited c. 80% more pheromone when rewards were segregated but costs bundled as compared with both costs and rewards being bundled. This pattern is further complicated by the pairwise experience each animal made, and which of the treatments it experiences first during training. The current study is the first to demonstrate a bundling effect in an animal, and the first to report a dichotomy between “liking” and “wanting” in an insect. We propose that the deviation between “wanting” and “liking” in this case is due to the unique nature of distance perception in ants, which is recorded linearly, while almost all other sensory perception in animals is logarithmic.
Anterior insular cortex firing links initial and sustained encoding during aversion-resistant alcohol consumption

Compulsive-like alcohol drinking (CLAD), where intake persists despite adverse consequences, is often a core facet of alcohol use disorder. Recent work sheds light on underlying mechanisms, but much remains unknown about CLAD etiology. Previously, we showed that projections from anterior insula (aINS), a central mediator of emotion, motivation, and interoception, promote CLAD in rodents, and heavy human drinkers exhibit similar insula-circuit recruitment under compulsion-like conditions. However, global aINS inhibition also reduces alcohol-only drinking (AOD), and one major obstacle is the lack of information on aINS firing patterns that could promote different aspects of intake. Here, we recorded single-unit activity in right aINS from 15 rats during AOD or CLAD (10mg/L or 60mg/L quinine in alcohol). Neurons with a sustained-increase or sustained-decrease phenotype (SIP, SDP) showed no firing differences across drinking conditions. In contrast, aINS neurons with a phenotype of strong firing increase at initiation of responding (IRP) showed significantly greater activity across the rest of licking during CLAD versus AOD, concurring with our previous behavioral findings suggesting quick evaluation and response strategy adjustment under CLAD. There were also no condition-related differences in firing-phenotype abundance. Further, total responding only correlated with abundance of SDP cells, but SDP firing returned to baseline during pauses in licking, while IRP and SIP sustained responding through pauses in licking. Thus, only aINS cells with a particular strong firing at licking onset showd greater sustained responding under compulsion-like conditions, while other cells likely promoted drinking more generally, providing critical new information about how aINS activity could promote alcohol consumption under different drinking conditions.
O-GlcNAc transferase plays a non-catalytic role in C. elegans male fertility

Animal behavior is influenced by the competing drives to maintain energy and to reproduce. The balance between these evolutionary pressures and how nutrient signaling pathways intersect with mating drive remains unclear. The nutrient sensor O-GlcNAc transferase, which post-translationally modifies intracellular proteins with a single monosaccharide, is responsive to cellular nutrient status and regulates diverse biological processes. Though essential in most metazoans, O-GlcNAc transferase (ogt-1) is dispensable in Caenorhabditis elegans, allowing genetic analysis of its physiological roles. Compared to control, ogt-1 males have a four-fold reduction in mean offspring, with nearly two thirds producing zero progeny. Interestingly, we found that isolated ogt-1 males are less likely to engage in mate-searching, and they initiate mating less often when exposed to mates. In addition, ogt-1 males which do initiate mating are less likely to continue with subsequent steps in the mating process, resulting in fewer successful sperm transfers. Lowering barriers to mating such as immobilizing mates or allowing more mating time significantly improves ogt-1 male mating. Surprisingly, we found high fertility levels for ogt-1 mutant males with hypodermal expression of wild-type ogt-1 and by ogt-1 harboring mutations that prevent the transfer of O-GlcNAc by OGT-1. This suggests OGT-1 serves a non-catalytic function in the hypodermis impacting the male mating drive. This study builds upon research on the nutrient sensor O- GlcNAc transferase and demonstrates a role it plays in the interplay between the evolutionary drives for reproduction and survival. Author Summary Animals must make decisions on whether to engage in reproduction or conserve energy. These decisions must take into account the energy available to the animal, therefore making the nutrient sensing enzyme OGT of particular interest. In response to nutrient levels in the cell, OGT transfers the GlcNAc sugar onto proteins to regulate their function. OGT is implicated in a number of human diseases including diabetes, cancer, and X-linked intellectual disability. By deleting the gene encoding OGT in the nematode C. elegans, we show OGT is required for male fertility. We assessed the behavior of these mutant male worms and found they have a reduced mating drive. Surprisingly, restoring OGT specifically in the hypodermis was able to raise male fertility and mating drive back to normal levels. In addition, missense mutations in the OGT catalytic domain which prevent the enzyme from transferring GlcNAc do not negatively impact fertility, suggesting a different function of OGT is important in this process. Our study demonstrates that OGT is important in critical behavioral decisions and that further investigation in C. elegans may help reveal new functions of the enzyme.
Store-Operated Ca2+ Channels Mediate Microdomain Ca2+ Signals and Amplify Gq-Coupled Ca2+ Elevations in Capillary Pericytes

Pericytes are multifunctional cells of the vasculature that are vital to brain homeostasis, yet many of their fundamental physiological properties remain unexplored. Ca2+ is a ubiquitous second messenger across cell-types, where it mediates diverse functions such as contractility and gene transcription. It is therefore important to understand the cellular mechanisms underlying Ca2+ signalling in capillary pericytes. Here, we performed pharmacological and ion substitution experiments to investigate the mechanisms underlying pericyte Ca2+ signaling in acute cortical brain slices of PDGFRβ-GCaMP6f mice. We report that in mid-capillary bed pericytes (≥ 4th branch order), spontaneous microdomain Ca2+ signals are dependent on extracellular Ca2+, but largely independent of depolarization, L- and T-type voltage-gated calcium channels (VGCCs), and TRPC3/6 channels. In contrast, these microdomain signals were inhibited by multiple Orai channel blockers, including the specific antagonist GSK-7975A. Furthermore, capillary pericytes exhibited classical store operated calcium entry (SOCE) following store depletion that was sensitive to GSK-7975A and required for amplification of intracellular Ca2+ increases evoked by the vasoconstrictor endothelin-1. These results suggest that Orai SOCE mediates microdomain Ca2+ signals at rest and amplifies Gq-GPCR coupled Ca2+ elevations in capillary pericytes. Thus, SOCE is a major regulator of pericyte Ca2+ and a target for manipulating their function in health and disease.
Correlated retrograde and developmental regulons implicate multiple retrograde signals as coordinators of chloroplast development in maize

Signals emanating from chloroplasts influence nuclear gene expression, but roles of retrograde signals during chloroplast development are unclear. To address this gap, we analyzed transcriptomes of four non-photosynthetic maize mutants and interpreted them in the context of transcriptome dynamics during normal leaf development. We analyzed two albino mutants lacking plastid ribosomes and two chlorotic mutants with thylakoid targeting or plastid transcription defects. The ∼2700 differentially expressed genes fall into six major categories based on the polarity and mutant-specificity of the change. These distinct retrograde responses correlate with distinct developmental dynamics, with down-regulated genes expressed later in normal development and up-regulated genes acting early. Photosynthesis genes are down-regulated specifically in the albino mutants, whereas up-regulated genes are enriched for functions in chloroplast biogenesis and cytosolic translation. TOR signaling is elevated in plastid ribosome-deficient mutants and declines in concert with plastid ribosome buildup during leaf development. Our results implicate three plastid signals as integral players during photosynthetic differentiation. One signal requires plastid ribosomes and activates photosynthesis genes. A second signal reflects attainment of chloroplast maturity and represses chloroplast biogenesis genes. A third signal responds to nutrient consumption by developing chloroplasts and represses TOR, which down-regulates cell proliferation genes early in leaf development. One sentence summary Transcriptomes of non-photosynthetic maize mutants when interpreted in the context of normal developmental dynamics implicate three plastid signals as coordinators of photosynthetic differentiation. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (https://academic.oup.com/plcell/pages/General-Instructions) is Alice Barkan (abarkan@uoregon.edu)
How important is budding speciation for comparative studies?

The acknowledgment of evolutionary dependence among species has fundamentally changed how we ask biological questions. Phylogenetic models became the standard approach for studies with three or more lineages, in particular those using extant species. Most phylogenetic comparative methods (PCMs) translate relatedness into covariance, meaning that evolutionary changes before lineages split should be interpreted together whereas after the split lineages are expected to change independently. This clever realization has shaped decades of research. Here we discuss one element of the comparative method often ignored or assumed as unimportant: if nodes of a phylogeny represent the dissolution of the ancestral lineage into two new ones or if the ancestral lineage can survive speciation events (i.e., budding). Budding speciation is often reported in paleontological studies, due to the nature of the evidence for budding in the fossil record, but it is surprisingly absent in comparative methods. Here we show that many PCMs assume that divergence happens as a symmetric split, even if these methods don’t explicitly mention this assumption. We discuss the properties of trait evolution models for continuous and discrete traits and their adequacy under a scenario of budding speciation. We discuss the effects of budding speciation under a series of plausible evolutionary scenarios and show when and how these can influence our estimates. We also propose that long-lived lineages that have survived through a series of budding speciation events and given birth to multiple new lineages can produce evolutionary patterns that challenge our intuition about the most parsimonious history of trait changes in a clade. We hope our discussion can help bridge comparative approaches in paleontology and neontology as well as foster awareness about the assumptions we make when we use phylogenetic trees.
A Van Gogh/Vangl tyrosine phosphorylation switch regulates its interaction with core Planar Cell Polarity factors Prickle and Dishevelled

Epithelial tissues can be polarized along two axes, in addition to apical-basal polarity they are often also polarized within the plane of the epithelium, known as planar cell polarity (PCP). PCP depends upon the conserved Wnt/Frizzled (Fz) signaling factors, including Fz itself and Van Gogh (Vang/Vangl). Here, taking advantage of the complementary features of Drosophila wing and mouse skin PCP establishment, we dissect how Vang phosphorylation on a specific conserved tyrosine residue affects its interaction with two cytoplasmic core PCP factors, Dsh/Dvl and Pk. We demonstrate that Pk and Dsh/Dvl bind to Vang/Vangl in an overlapping region centered around this tyrosine. Strikingly, Vang/Vangl2 phosphorylation promotes its binding to Pk, a key effector of the Vang/Vangl complex, and inhibits its interaction with Dsh/Dvl, and thus phosphorylation of this tyrosine appears to promote the formation of the mature and stable Vang/Vangl-Pk complex during PCP establishment. Interestingly, as our single point mutations allow selective binding inhibition of either Dsh or Pk, we can demonstrate for the first time that Dsh interaction with Vang is physiologically important, as all single point mutations fail to rescue the Vang null mutant wing phenotype.
User-friendly electron microscopy protocols for the visualization of biological macromolecular complexes in three dimensions: Visualization of planta clathrin-coated vesicles at ultrastructural resolution

Biological systems are the sum of their dynamic 3-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolutions to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these protocols require specialized equipment and personnel to complete them. Here we present novel accessible protocols to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolutions, focusing on Arabidopsis clathrin-coated vesicles (CCVs) - an essential trafficking organelle lacking detailed structural characterization due to their low preservation in classical electron microscopy techniques. First, we establish a protocol to visualize CCVs in unroofed cells using scanning-transmission electron microscopy (STEM) tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this protocol in any electron microscopy lab. Secondly, we demonstrate this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis workflow to screen the ‘pseudo 3D’ morphology of CCVs imaged with 2D modalities. Overall, we present accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs.
In vivo selection reveals long non-coding RNAs implicated in colon to liver metastasis

Colorectal cancer (CRC) is the third most common malignancy in both American men and women. Most of the deaths attributed to CRC are a result of metastatic spread to the liver. In this study, colon cancer cells that highly metastasized to liver in vivo were compared to less metastatic parental cells to investigate the role for long non-coding RNAs (lncRNAs) in CRC metastasis. The highly metastatic daughter cells (LS-3B) were found to be 63-fold more metastatic than the parental cell line (LS-PAR) in vivo. A lncRNA microarray comparing LS-PAR and LS-3B cells revealed that 104 lncRNAs had fold changes > 2.0 and an FDR < 0.05. Real time PCR mediated validation revealed many lncRNAs exhibited high fold changes such as a 60-fold increase in LOC101448202, a 20-fold increase in MRPL23-AS1 and 50-fold decreases in GNAS-AS1 and LOC101928131. In vivo metastasis differences could be recapitulated in vitro as LS-3B cells closed wounds faster than their parental LS-PAR cells. However, intestinal epithelial cancer cells with robust downregulation of MRPL23-AS1, C1QTNF1-AS1, GNAS-AS1, LINCR-0002 and LOC101448202 failed to display differences in comparison to controls in in vitro migration assays. Three of the five lncRNAs with microarray probes for currently available GEO-datasets were significantly altered in liver CRC-associated tumor biopsies as compared to the primary tumor of non-metastatic CRC. Further studies on the lncRNAs identified will better define their roles in metastasis and how they might be useful if targeted therapeutically.
The structure of yeast Npl3 bound to RNA reveals a cooperative sequence-specific recognition and an RNA chaperone role in splicing

The conserved SR-like protein Npl3 promotes splicing of diverse pre-mRNAs. However, the RNA sequence(s) recognized by the RNA Recognition Motifs (RRM1 & RRM2) of Npl3 during the splicing reaction remain elusive. Here, we developed a split-iCRAC approach in yeast to uncover the consensus sequence bound to each RRM. High-resolution NMR structures show that RRM2 recognizes a 5’-GNGG-3’ motif leading to an unusual mille-feuille topology. These structures also reveal how RRM1 preferentially interacts with a CC-dinucleotide upstream of this motif, and how the inter-RRM linker and the region C-terminal to RRM2 contributes to cooperative RNA-binding. Structure-guided functional studies show that Npl3 genetically interacts with U2 snRNP specific factors and we provide evidence that Npl3 melts U2 snRNA stem-loop I, a prerequisite for U2/U6 duplex formation within the catalytic center of the Bact spliceosomal complex. Thus, our findings provide insights into an unanticipated RNA chaperoning role for Npl3 during spliceosome active site formation.
De novo lipogenesis fuels adipocyte autophagosome membrane dynamics

Autophagy is a homeostatic degradative process for cell components that enables stress resilience and can determine cellular fate and function. However, lipid sources for the rapid membrane expansions of autophagosomes, the workhorses of autophagy, are poorly understood. Here, we identify de novo lipogenesis (DNL) as a critical source of fatty acids (FA) to fuel autophagosome dynamics in adipocytes. Adipocyte fatty acid synthase (Fasn) deficiency markedly impairs autophagy, evident by autophagosome accumulation, and severely compromises degradation of the autophagic substrate p62. Autophagy dependence on FA produced by Fasn is not fully alleviated by exogenous FA in cultured adipocytes even though lipid droplet size is restored. Imaging studies reveal that Fasn colocalizes with nascent autophagosomes, while loss of Fasn decreases certain membrane phosphoinositides known to be required for autophagosome assembly. Together, our studies highlight a newly appreciated function for adipocyte DNL in autophagosome membrane formation and provide evidence that localized FA synthesis contributes to autophagosome dynamics.
Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa

While mutation rates have been extensively studied, variation in mutation rates throughout the genome is poorly understood. To understand patterns of genetic variation, it is important to understand how mutation rates vary. Chromatin modifications may be an important factor in determining variation in mutation rates in eukaryotic genomes. To study variation in mutation rates, we performed a mutation accumulation experiment in the filamentous fungus Neurospora crassa, and sequenced the genomes of the 40 MA lines that had been propagated asexually for approximately 1015 [1003, 1026] mitoses. We detected 1322 mutations in total, and observed that the mutation rate was higher in regions of low GC, in domains of H3K9 trimethylation, in centromeric regions, and in domains of H3K27 trimethylation. The rate of single nucleotide mutations in euchromatin was 2.46 [2.19, 2.77] × 10−10. In contrast, the mutation rate in H3K9me3 domains was tenfold higher: 2.43 [2.25, 2.62] × 10−9. We also observed that the spectrum of single nucleotide mutations was different between H3K9me3 and euchromatic domains. Our statistical model of mutation rate variation predicted a moderate amount of extant genetic variation, suggesting that the mutation rate is an important factor in determining levels of natural genetic variation. Furthermore, we characterized mutation rates of structural variants, complex mutations, and the effect of local sequence context on the mutation rate. Our study highlights that chromatin modifications are associated with mutation rates, and accurate evolutionary inferences should take variation in mutation rates across the genome into account.