On the complex dynamics of savanna landscapes
Jonathan David Touboul, Ann Carla Staver, and Simon Asher Levin
This paper makes a significant contribution both to ecological theory and to an understanding more generally regarding how complex dynamics can emerge in mathematical models from quite simple underlying assumptions. Empirical and theoretical work has suggested that savanna–forest systems exhibit bistability, potentially flipping from one state to another in the face of environmental change. Here, we show that the dynamics of those systems may be much more complicated (periodic and endogenously driven) and present surprising responses to environmental variability. From a mathematical point of view, the models that we explore exhibit a rich array of behaviors and responses to random perturbations, and we suggest that such dynamics may arise in a variety of contexts. (See pp. E1336–E1345.)
RNA force field with accuracy comparable to state-of-the-art protein force fields
Dazhi Tan, Stefano Piana, Robert M. Dirks, and David E. Shaw
The complex and often highly dynamic 3D structures of RNA molecules are central to their diverse cellular functions. Molecular dynamics (MD) simulations have played a major role in characterizing the structure and dynamics of proteins, but the physical models (“force fields”) used for simulating nucleic acids are substantially less accurate overall than those used in protein simulations, creating a major challenge for MD studies of RNA. Here, we report an RNA force field capable of describing the structural and thermodynamic properties of RNA molecules with accuracy comparable to state-of-the-art protein force fields. This force field should facilitate the use of MD simulation as a tool for the study of biologically significant RNA molecules and protein–RNA complexes. (See pp. E1346–E1355.)
Landau–Ginzburg theory of cortex dynamics: Scale-free avalanches emerge at the edge of synchronization
Serena di Santo, Pablo Villegas, Raffaella Burioni, and Miguel A. Muñoz
The human cortex operates in a state of restless activity, the meaning and functionality of which are still not understood. A fascinating, though controversial, hypothesis, partially backed by empirical evidence, suggests that the cortex might work at the edge of a phase transition, from which important functional advantages stem. However, the nature of such a transition remains elusive. Here, we adopt ideas from the physics of phase transitions to construct a general (Landau–Ginzburg) theory of cortical networks, allowing us to analyze their possible collective phases and phase transitions. We conclude that the empirically reported scale-invariant avalanches can possibly come about if the cortex operated at the edge of a synchronization phase transition, at which neuronal avalanches and incipient oscillations coexist. (See pp. E1356–E1365.)
Superresolution imaging of individual replication forks reveals unexpected prodrug resistance mechanism
Therese Triemer, Alessandra Messikommer, Stella M. K. Glasauer, Jawad Alzeer, Miriam H. Paulisch, and Nathan W. Luedtke
The pharmacophore of a clinically important prodrug, cytarabine (ara-C), was directly modified with an azide group that had little or no impact on its potency or mode of action. This “clickable” anticancer drug mimic unexpectedly revealed that the efficient incorporation of ara-C into DNA was associated with drug resistance rather than drug sensitivity. Our results therefore challenge a long-standing perception regarding the cell-type selectivity of nucleoside-based drugs. The mediators of ara-C resistance, DNA replication foci, were characterized using superresolution microscopy. In addition to providing detailed glimpses of individual replication forks in cells, these results suggest that new theranostic candidates for blood-cell analysis can be generated by introducing a bioorthogonal functional group directly into the pharmacophore of a Food and Drug Administration-approved drug. (See pp. E1366–E1373.)
Wireless optoelectronic photometers for monitoring neuronal dynamics in the deep brain
Luyao Lu, Philipp Gutruf, Li Xia, Dionnet L. Bhatti, Xinying Wang, Abraham Vazquez-Guardado, Xin Ning, Xinru Shen, Tian Sang, Rongxue Ma, Grace Pakeltis, Gabriel Sobczak, Hao Zhang, Dong-oh Seo, Mantian Xue, Lan Yin, Debashis Chanda, Xing Sheng, Michael R. Bruchas, and John A. Rogers
Wireless systems for imaging/recording neuronal activity in untethered, freely behaving animals have broad relevance to neuroscience research. Here, we demonstrate a thin, flexible probe that combines light sources and photodetectors into a platform with submillimeter dimensions, capable of direct insertion into targeted regions of the deep brain. This system allows wireless stimulation and recording of fluorescence associated with genetically encoded calcium indicators, with unique capabilities in visualizing neuronal activity. Studies using unconstrained, freely moving animal models in two different behavioral assays demonstrate the robust, reliable operation of these devices and allow comparisons to traditional photometry systems based on fiber-optic tethers to external light sources and detectors. (See pp. E1374–E1383.)
Auxetic metamaterials from disordered networks
Daniel R. Reid, Nidhi Pashine, Justin M. Wozniak, Heinrich M. Jaeger, Andrea J. Liu, Sidney R. Nagel, and Juan J. de Pablo
Recent work indicates that selective pruning of disordered networks of nodes connected by bonds can generate materials with nontrivial mechanical properties, including auxetic networks having a negative Poisson's ratio ν. Until now, auxetic networks created based on this strategy have not been successfully realized in experiment. Here a model that includes angle-bending forces and the experimental boundary conditions is introduced for pruning-based design of auxetic materials. By pruning the appropriate bonds, ν can be tuned to values approaching the lower mechanical limit of –1, and the corresponding laboratory networks exhibit good agreement with model predictions. Optimization algorithms are then used to show that highly auxetic materials can be engineered from inhomogeneous bonds and nodes that exhibit distinct mechanical characteristics. (See pp. E1384–E1390.)
Light-enabled reversible self-assembly and tunable optical properties of stable hairy nanoparticles
Yihuang Chen, Zewei Wang, Yanjie He, Young Jun Yoon, Jaehan Jung, Guangzhao Zhang, and Zhiqun Lin
This work reports a versatile and robust strategy for creating monodisperse plasmonic nanoparticles (NPs) intimately and permanently capped with photoresponsive polymers via capitalizing on amphiphilic star-like diblock copolymer nanoreactors. The reversibly assembled nanostructures comprising photoresponsive NPs may exhibit a broad range of new attributes, functions, and applications as a direct consequence of size-dependent physical property from individual NP and the collective property originated from the NP interaction due to their close proximity within nanostructure. (See pp. E1391–E1400.)
K63 ubiquitylation triggers proteasomal degradation by seeding branched ubiquitin chains
Fumiaki Ohtake, Hikaru Tsuchiya, Yasushi Saeki, and Keiji Tanaka
Posttranslational modification of proteins by ubiquitylation regulates numerous biological processes. Polyubiquitin chain linkages are critical determinants that direct substrates to distinct pathways, a concept referred to as the ubiquitin code. Lysine-63 (K63)-linked polyubiquitin chains are the second most abundant linkage type in cells, and are known to regulate proteasome-independent pathways such as signal transduction and endocytosis. We report that K63-linked polyubiquitylation of the proapoptotic regulator TXNIP by the ubiquitin ligase ITCH triggers proteasome-mediated protein degradation. K63 ubiquitin chains facilitate subsequent assembly of K48/K63 branched ubiquitin chains through recruitment of ubiquitin ligases assembling K48 chains, thereby directing substrates to the proteasome. These results reveal an unappreciated ubiquitin-dependent pathway leading to the proteasome. (See pp. E1401–E1408.)
Identification of Wiskott-Aldrich syndrome protein (WASP) binding sites on the branched actin filament nucleator Arp2/3 complex
Qing Luan, Alex Zelter, Michael J. MacCoss, Trisha N. Davis, and Brad J. Nolen
Arp2/3 complex is a macromolecular machine that nucleates branched actin filaments in response to cellular signals. WASP family proteins regulate the nucleation activity of Arp2/3 complex, providing a way for cells to assemble branched actin filament networks with the spatiotemporal precision required to orchestrate cellular processes such as cellular motility and endocytosis. Despite its importance, how WASP activates filament nucleation by Arp2/3 complex is still unknown, largely because it has been uncertain how WASP binds to Arp2/3 complex. Here we use a combination of biophysical, biochemical, and computational methods to map the binding of WASP to the complex. These results have important implications for understanding how cells regulate the assembly of actin filaments. (See pp. E1409–E1418.)
Molecular basis for the recognition of the human AAUAAA polyadenylation signal
Yadong Sun, Yixiao Zhang, Keith Hamilton, James L. Manley, Yongsheng Shi, Thomas Walz, and Liang Tong
The AAUAAA polyadenylation signal (PAS) was identified more than 40 years ago, but it has remained a mystery how this signal is recognized at the molecular level, which is required for the 3′-end processing of nearly all eukaryotic messenger RNA precursors. We have determined the cryo-electron microscopy structure of a quaternary complex of human CPSF-160, WDR33, CPSF-30, and an AAUAAA RNA at 3.4-Å resolution. The AAUAAA PAS assumes an unusual conformation and is recognized directly by both CPSF-30 and WDR33. CPSF-160 functions as an essential scaffold and preorganizes CPSF-30 and WDR33 for high-affinity binding to AAUAAA. Our findings provide an elegant molecular explanation for how PAS sequences are recognized for mRNA 3′-end formation. (See pp. E1419–E1428.)
High integrin αVβ6 affinity reached by hybrid domain deletion slows ligand-binding on-rate
Xianchi Dong, Bo Zhao, Fu-Yang Lin, Chafen Lu, Bruce N. Rogers, and Timothy A. Springer
Integrins are complex multidomain adhesion molecules. We study how their affinity and binding kinetics for extracellular ligands are regulated, which is essential to enable integrins to communicate with the cytoskeleton. We show that the hybrid domain, which interfaces with the βI domain, strongly regulates affinity for ligand, which binds to a distal face of the βI domain. At high integrin affinity, the ligand binding on-rate goes down. We propose that integrins bind ligand in their low-affinity state, which has a wider ligand-binding pocket, and then convert to their high-affinity state, which has a tighter pocket. (See pp. E1429–E1436.)
Structures and mechanism of dipeptidyl peptidases 8 and 9, important players in cellular homeostasis and cancer
Breyan Ross, Stephan Krapp, Martin Augustin, Reiner Kierfersauer, Marcelino Arciniega, Ruth Geiss-Friedlander, and Robert Huber
Cells require specific molecular entities to regulate biological processes, which are often out of balance in diseases. Once identified, their activities may be modulated by specific ligands. DPP4 protein is an example of a target to successfully treat type II diabetes by small molecule ligands. Besides DPP4, other members of this protein family, DPP8 and DPP9 are similarly interesting and relevant in immune response and cancer. It is crucial to understand their structures and enzymatic mechanism to enable structure-based drug development. Here we unveil the crystallographic structures of DPP8 and DPP9, whereby we observe a different active site architecture and substrate binding mechanism in this family. These discoveries open new options for drug development targeting DPP8 and DPP9. (See pp. E1437–E1445.)
Mechanism of inhibition of retromer transport by the bacterial effector RidL
Jialin Yao, Fan Yang, Xiaodong Sun, Shen Wang, Ninghai Gan, Qi Liu, Dingdong Liu, Xia Zhang, Dawen Niu, Yuquan Wei, Cong Ma, Zhao-Qing Luo, Qingxiang Sun, and Da Jia
Intracellular pathogens hijack many host processes, including the vesicle trafficking pathway, to help their survival and replication. Legionella pneumophila is the causative agent of Legionnaires’ disease, which utilizes numerous effector proteins, including RidL during infection. RidL suppresses retromer transport activity, but the exact mechanism for this has remained unclear. Using a combination of structural, biochemical, and cellular approaches, we show how retromer specifically targets to retromer subunit VPS29. The RidL–VPS29 interaction is necessary for the proper localization and function of RidL. Mechanistically, RidL inhibits retromer activity by direct competition with TBC1d5, an essential retromer regulator. Our study highlights the beauty of studying host–pathogen interaction in the discovery of novel aspects of host cell biology. (See pp. E1446–E1454.)
Structure of the fission yeast actomyosin ring during constriction
Matthew T. Swulius, Lam T. Nguyen, Mark S. Ladinsky, Davi R. Ortega, Samya Aich, Mithilesh Mishra, and Grant J. Jensen
Many eukaryotic cells divide using a contractile actomyosin ring, but its structure is unknown. Here we use new specimen preparation methods and electron cryotomography to image constricting rings directly in 3D, in a near-native state in the model organism Schizosaccharomyces pombe. Our images reveal the arrangement of individual actin filaments within the contracting actomyosin ring. (See pp. E1455–E1464.)
LncRNA IDH1-AS1 links the functions of c-Myc and HIF1α via IDH1 to regulate the Warburg effect
Shaoxun Xiang, Hao Gu, Lei Jin, Rick F. Thorne, Xu Dong Zhang, and Mian Wu
We report in this article that c-Myc-mediated repression of lncRNA IDH1-AS1 sustains activation of the Warburg effect by HIF1α under normoxic conditions. IDH1-AS1 would otherwise enhance IDH1 enzymatic activity through promoting its homodimerization, leading to increased production of α-KG, which, along with decreases in ROS levels similarly resulting from increased IDH1 activity, causes down-regulation of HIF1a and a reduction in glycolysis. Collectively, our results have identified a signaling axis c-Myc-(IDH1-AS1)-IDH1-αKG/ROS-HIF1α that is important for activation of the Warburg effect under normoxia. Moreover, the results reveal IDH1 as a member of c-Myc-responsive metabolic enzymes and demonstrate that c-Myc plays an important part in balancing mitochondrial respiration and glycolysis to ensure glycolysis be executed efficiently in cancer cells under normoxia. (See pp. E1465–E1474.)
RGMb protects against acute kidney injury by inhibiting tubular cell necroptosis via an MLKL-dependent mechanism
Wenjing Liu, Binbin Chen, Yang Wang, Chenling Meng, Huihui Huang, Xiao-Ru Huang, Jinzhong Qin, Shrikant R. Mulay, Hans-Joachim Anders, Andong Qiu, Baoxue Yang, Gordon J. Freeman, Hua Jenny Lu, Herbert Y. Lin, Zhi-Hua Zheng, Hui-Yao Lan, Yu Huang, and Yin Xia
Necroptosis is critically involved in the development of acute kidney injury (AKI), but it has not been well demonstrated that necroptosis occurs in renal tubular epithelial cells in vivo during AKI. Now, we provide evidence that renal proximal tubular cells undergo necroptosis during ischemia/reperfusion injury or oxalate nephropathy. Repulsive guidance molecule-b protects against AKI by inhibiting mixed lineage kinase domain-like membrane association and necroptosis in proximal tubular cells. (See pp. E1475–E1484.)
Arabidopsis mRNA decay landscape arises from specialized RNA decay substrates, decapping-mediated feedback, and redundancy
Reed S. Sorenson, Malia J. Deshotel, Katrina Johnson, Frederick R. Adler, and Leslie E. Sieburth
Gene expression is governed by the opposing forces of transcription and decay. How RNA decay modulates the transcriptome is largely unknown, including whether the three major cytoplasmic degradative pathways (mRNA decapping, the RNA exosome, and SOV/DIS3L2) act on specific sets of RNAs. We used maximum likelihood mathematical modeling and RNAseq to analyze mRNA decay in wild-type and Arabidopsis RNA decay mutants. We demonstrate that mRNA decapping contributes broadly to mRNA decay (68% of RNAs), and is especially important for short-lived RNAs. SOV deficiency caused slower decay of few transcripts, but also elicited broad feedback: Many RNAs decayed faster, and required mRNA decapping for this faster rate. Despite altered turnover, these RNAs were maintained at near-wild-type abundance. (See pp. E1485–E1494.)
Effects of rapamycin on growth hormone receptor knockout mice
Yimin Fang, Cristal M. Hill, Justin Darcy, Adriana Reyes-Ordoñez, Edwin Arauz, Samuel McFadden, Chi Zhang, Jared Osland, John Gao, Tian Zhang, Stuart J. Frank, Martin A. Javors, Rong Yuan, John J. Kopchick, Liou Y. Sun, Jie Chen, and Andrzej Bartke
In various animal species, including mammals, longevity can be extended by rapamycin, an inhibitor of mTOR (mechanistic target of rapamycin). mTOR acts through two complexes: mTORC1 and mTORC2. Antiaging effects of rapamycin are mediated by suppression of mTORC1, while the role of mTORC2 in aging remains to be elucidated. Here, we report that mTORC2 plays a positive role in regulating longevity via maintenance, or enhancement, of whole-body homeostasis. When mTORC2-mediated homeostasis was disrupted by rapamycin in the remarkably long-lived GHR-KO mice (in which mTORC1 signaling is low, while mTORC2 signaling is elevated), their life span was shortened. Hence, a selective approach toward mTORC1 inhibition without impairing mTORC2 is important in devising a strategy for slowing aging. (See pp. E1495–E1503.)
Farming the mitochondrial ancestor as a model of endosymbiotic establishment by natural selection
István Zachar, András Szilágyi, Szabolcs Számadó, and Eörs Szathmáry
The origin of mitochondria is a challenging and intensely debated issue. Mitochondria are ancestrally present in eukaryotes, and their endosymbiotic inclusion was an extremely important step during the transition from prokaryotes to eukaryotes. However, because of the unknown order of eukaryotic inventions (e.g., cytoskeleton, phagocytosis, and endomembranes), it is unknown whether they led to or followed the acquisition of mitochondria. According to the farming hypothesis, the mitochondrial ancestor was captured by a phagocytotic host, but the advantage was not direct metabolic help provided by the symbiont; rather, it was provisioning captured prey to farmers in poor times, like humans farm pigs. Our analytical and computational models prove that farming could lead to stable endosymbiosis without any further benefit assumed between partners. (See pp. E1504–E1510.)
Loss of Capicua alters early T cell development and predisposes mice to T cell lymphoblastic leukemia/lymphoma
Qiumin Tan (谭秋敏), Lorenzo Brunetti, Maxime W. C. Rousseaux, Hsiang-Chih Lu, Ying-Wooi Wan, Jean-Pierre Revelli, Zhandong Liu, Margaret A. Goodell, and Huda Y. Zoghbi
Capicua (CIC) is a protein that regulates gene transcription, and its dysfunction leads to several neurological diseases. CIC is frequently mutated in several cancers, but mechanistic studies on its tumor suppressor function have been limited. Here, we showed that deletion of Cic in mice causes T cell acute lymphoblastic leukemia/lymphoma (T-ALL) and disrupts early T cell development. We also found that loss of CIC up-regulates the oncogenic RAS program, both before and after the onset of T-ALL. Moreover, we detected activation of the NOTCH1 and MYC transcriptional programs, which we propose cooperate with the RAS pathway to drive tumor development. Our study demonstrates that CIC is a tumor suppressor for lymphoid malignancies and elucidates the tumorigenic events upon loss of CIC. (See pp. E1511–E1519.)
Male-specific IL-33 expression regulates sex-dimorphic EAE susceptibility
Abigail E. Russi, Mark E. Ebel, Yuchen Yang, and Melissa A. Brown
Women are much more likely to develop autoimmune diseases, such as systemic lupus erythematous, rheumatoid arthritis, and multiple sclerosis. Sex hormones, including estrogen and testosterone, clearly influence disease susceptibility, but the precise cellular and molecular targets of these hormones have remained unexplained. While most studies have focused on what causes the damaging inflammation in females, there is also much to be learned by studying the factors that confer protection to males. Using a mouse model of multiple sclerosis, a CNS demyelinating disease, we identified a testosterone-driven pathway mediated by mast cell-dependent IL-33 expression that limits the development of a destructive immune response in males. The identification of such pathways has important therapeutic implications. (See pp. E1520–E1529.)
OLT1177, a β-sulfonyl nitrile compound, safe in humans, inhibits the NLRP3 inflammasome and reverses the metabolic cost of inflammation
Carlo Marchetti, Benjamin Swartzwelter, Fabia Gamboni, Charles P. Neff, Katrin Richter, Tania Azam, Sonia Carta, Isak Tengesdal, Travis Nemkov, Angelo D’Alessandro, Curtis Henry, Gerald S. Jones, Scott A. Goodrich, Joseph P. St. Laurent, Terry M. Jones, Curtis L. Scribner, Robert B. Barrow, Roy D. Altman, Damaris B. Skouras, Marco Gattorno, Veronika Grau, Sabina Janciauskiene, Anna Rubartelli, Leo A. B. Joosten, and Charles A. Dinarello
The NLRP3 inflammasome is an intracellular oligomer regulating the activation of caspase-1 for the processing and secretion of IL-1β and IL-18. Although there is growing evidence to substantiate inflammasome inhibition as a therapeutic option for the treatment of inflammatory diseases, to date, there are no approved humans agents. OLT1177, a β-sulfonyl nitrile molecule, shown to be safe in humans, is a selective inhibitor of the NLRP3 inflammasome, with unique properties to reverse the metabolic costs of inflammation and to treat IL-1β– and IL-18–mediated diseases. (See pp. E1530–E1539.)
Anti–PD-1/anti–CTLA-4 efficacy in melanoma brain metastases depends on extracranial disease and augmentation of CD8+ T cell trafficking
David Taggart, Tereza Andreou, Karen J. Scott, Jennifer Williams, Nora Rippaus, Rebecca J. Brownlie, Elizabeth J. Ilett, Robert J. Salmond, Alan Melcher, and Mihaela Lorger
Brain metastases are an unmet clinical need with high frequency in melanoma patients. With immune checkpoint inhibitors targeting programmed death 1 (PD-1) and cytotoxic T lymphocyte-associated protein 4 (CTLA-4) becoming a frontline therapy in melanoma, it is critical to understand how this therapy works in the “immune-specialized” brain microenvironment. Our study shows that in the absence of extracranial tumor, melanoma tumors growing in the brain escape anti–PD-1/anti–CTLA-4 therapy. A synergy between immune checkpoint inhibition and extracranial tumor is required to put a break on brain metastases by enhancing CD8+ T cell recruitment to the brain via peripheral expansion of effector cells and upregulation of T cell entry receptors on tumor blood vessels. Augmentation of these processes could be explored to enhance the efficacy of immunotherapy in brain metastases. (See pp. E1540–E1549.)
Platelets release pathogenic serotonin and return to circulation after immune complex-mediated sequestration
Nathalie Cloutier, Isabelle Allaeys, Genevieve Marcoux, Kellie R. Machlus, Benoit Mailhot, Anne Zufferey, Tania Levesque, Yann Becker, Nicolas Tessandier, Imene Melki, Huiying Zhi, Guy Poirier, Matthew T. Rondina, Joseph E. Italiano, Louis Flamand, Steven E. McKenzie, Francine Cote, Bernhard Nieswandt, Waliul I. Khan, Matthew J. Flick, Peter J. Newman, Steve Lacroix, Paul R. Fortin, and Eric Boilard
Immune complexes (ICs) form when antibodies encounter their antigens. ICs are present in blood in multiple pathological conditions. Given the abundance of platelets in blood and that they express a receptor for ICs, called Fcγ receptor IIA (FcγRIIA), we examined the impact of ICs in blood in a mouse model. We found that circulating ICs induced systemic shock, characterized by loss of consciousness, by activating platelet FcγRIIA. Shock was mediated by the liberation of serotonin, a molecule better known for its role in the brain, from platelet granules. During shock, platelets were sequestered in the lungs and brain and returned to the blood circulation after their degranulation. Platelets are thus crucial in response to ICs. (See pp. E1550–E1559.)
E-cigarette smoke damages DNA and reduces repair activity in mouse lung, heart, and bladder as well as in human lung and bladder cells
Hyun-Wook Lee, Sung-Hyun Park, Mao-wen Weng, Hsiang-Tsui Wang, William C. Huang, Herbert Lepor, Xue-Ru Wu, Lung-Chi Chen, and Moon-shong Tang
E-cigarette smoke (ECS) delivers nicotine through aerosols without burning tobacco. ECS is promoted as noncarcinogenic. We found that ECS induces DNA damage in mouse lung, bladder, and heart and reduces DNA-repair functions and proteins in lung. Nicotine and its nitrosation product 4-(methylnitrosamine)-1-(3-pyridyl)-1-butanone can cause the same effects as ECS and enhance mutations and tumorigenic cell transformation in cultured human lung and bladder cells. These results indicate that nicotine nitrosation occurs in the lung, bladder, and heart, and that its products are further metabolized into DNA damaging agents. We propose that ECS, through damaging DNA and inhibiting DNA repair, might contribute to human lung and bladder cancer as well as to heart disease, although further studies are required to substantiate this proposal. (See pp. E1560–E1569.)
Disruption of the anaphase-promoting complex confers resistance to TTK inhibitors in triple-negative breast cancer
K. L. Thu, J. Silvester, M. J. Elliott, W. Ba-alawi, M. H. Duncan, A. C. Elia, A. S. Mer, P. Smirnov, Z. Safikhani, B. Haibe-Kains, T. W. Mak, and D. W. Cescon
Using functional genomic screens, we have identified resistance mechanisms to the clinical TTK protein kinase inhibitor (TTKi) CFI-402257 in breast cancer. As this and other TTKi are currently in clinical trials, understanding determinants of tumor drug response could permit rational selection of patients for treatment. We found that TTKi resistance is conferred by impairing anaphase-promoting complex/cyclosome (APC/C) function to minimize the lethal effects of mitotic segregation errors. Discovery of this mechanism in aneuploid cancer cells builds on previous reports indicating that weakening the APC/C promotes tolerance of chromosomal instability in diploid cells. Our work suggests that APC/C functional capacity may serve as a clinically useful biomarker of tumor response to TTKi that warrants investigation in ongoing clinical trials. (See pp. E1570–E1577.)
Pyruvate cycle increases aminoglycoside efficacy and provides respiratory energy in bacteria
Yu-bin Su, Bo Peng, Hui Li, Zhi-xue Cheng, Tian-tuo Zhang, Jia-xin Zhu, Dan Li, Min-yi Li, Jin-zhou Ye, Chao-chao Du, Song Zhang, Xian-liang Zhao, Man-jun Yang, and Xuan-xian Peng
Exogenous metabolites have been documented to potentiate antibiotics to kill multidrug-resistant pathogens, but the mechanisms are largely unknown. The work presented here shows that intermetabolites from the TCA cycle and the phosphoenolpyruvate (PEP)-pyruvate-AcCoA pathway have the potential to improve targeting of these resistant microorganisms. The enzymes that connect the PEP-pyruvate-AcCoA pathway to the TCA cycle are essential for this potentiation, indicating both pathway and cycle can be merged to be considered a pyruvate cycle (P cycle). The P cycle operates routinely as a general mechanism for energy production and regulating the TCA cycle in Escherichia coli and Edwardsiella tarda. The results reported here provide insights into metabolite-facilitated targeting by antibiotics as well as bacterial energy metabolism and homeostasis. (See pp. E1578–E1587.)
Superior colliculus neuronal ensemble activity signals optimal rather than subjective confidence
Brian Odegaard, Piercesare Grimaldi, Seong Hah Cho, Megan A. K. Peters, Hakwan Lau, and Michele A. Basso
Previously, the neuronal correlates of perceptual confidence have been identified in neural circuits responsible for deciding what an animal sees. However, behaviorally, confidence and perceptual decision accuracy are confounded; we are usually more confident about perceptual decisions when they are accurate. To tease them apart, we introduced a task with stimulus conditions that produced similar decision accuracy but different reports of subjective confidence. We decoded decision performance from neuronal signals in nonhuman primates in a subcortical region involved in decision-making, the superior colliculus (SC), and found that SC ensemble activity tracks decision accuracy, but not subjective confidence. These results challenge current ideas about how to measure subjective confidence in experiments and inspire ways to study its neuronal mechanisms. (See pp. E1588–E1597.)
Heterogeneity within the frontoparietal control network and its relationship to the default and dorsal attention networks
Matthew L. Dixon, Alejandro De La Vega, Caitlin Mills, Jessica Andrews-Hannac, R. Nathan Spreng, Michael W. Cole, and Kalina Christoff
The frontoparietal control network (FPCN) contributes to executive control, the ability to deliberately guide action based on goals. While the FPCN is often viewed as a unitary domain general system, it is possible that the FPCN contains a finegrained internal organization, with separate zones involved in different types of executive control. Here, we use graph theory and meta-analytic functional profiling to demonstrate that the FPCN is composed of two separate subsystems: FPCNA is connected to the default network and is involved in the regulation of introspective processes, whereas FPCNB is connected to the dorsal attention network and is involved in the regulation of perceptual attention. These findings offer a distinct perspective on the systems-level circuitry underlying cognitive control. (See pp. E1598–E1607.)
Effects of the ecto-ATPase apyrase on microglial ramification and surveillance reflect cell depolarization, not ATP depletion
Christian Madry, I. Lorena Arancibia-Cárcamo, Vasiliki Kyrargyri, Victor T. T. Chan, Nicola B. Hamilton, and David Attwell
ATP mediates interactions between cells in many tissues, but is particularly important for microglia, the brain’s immune cells, which constantly survey the brain to detect infection and regulate the brain’s wiring during development. It is controversial whether the ceaseless movement of microglia is driven by ATP release from brain cells. We show that an enzyme (apyrase) widely used to manipulate ATP levels is contaminated with K+ ions which inhibit microglial surveillance, and that no ATP release is needed to drive microglial process movement. Thus, all conclusions about a role of ATP in signaling based on applying apyrase need reexamining, and brain immune surveillance is not regulated by ATP release. (See pp. E1608–E1617.)
Restoring GABAergic inhibition rescues memory deficits in a Huntington’s disease mouse model
Zahra Dargaei, Jee Yoon Bang, Vivek Mahadevan, C. Sahara Khademullah, Simon Bedard, Gustavo Morrone Parfitt, Jun Chul Kim, and Melanie A. Woodin
Huntington’s disease (HD) is a fatal neurodegenerative disorder that currently has no cure. Although HD is classically considered a motor disorder, HD patients experience learning and memory deficits years before the onset of motor symptoms, and these deficits resemble those observed in HD mouse models. In this work, using transgenic mouse models of HD, we demonstrate that the action of the neurotransmitter GABA has switched from inhibitory to excitatory. By treating HD mice with a clinically used diuretic (bumetanide), which restores inhibitory GABA, we rescued the learning and memory deficits. Our data suggest a potential therapeutic approach for the treatment of the cognitive deficits in early HD that can improve patient quality of life and reduce caregiver burden. (See pp. E1618–E1626.)
Entorhinal fast-spiking speed cells project to the hippocampus
Jing Ye, Menno P. Witter, May-Britt Moser, and Edvard I. Moser
Our location in space is represented by a spectrum of space and direction-responsive cell types in medial entorhinal cortex and hippocampus. Many cells in these areas respond also to running speed. The presence of local speed-tuned cells is considered a requirement for position to be encoded in a self-motion–dependent manner; however, whether and how speed-responsive cells in entorhinal cortex and hippocampus are functionally connected have not been determined. The present study shows that a large proportion of entorhinal speed cells are fast-spiking with properties similar to those of GABAergic interneurons and that outputs from a subset of these cells, particularly the parvalbumin-expressing subset, form a component of the medial entorhinal input to the hippocampus. (See pp. E1627–E1636.)
Path integration in place cells of developing rats
Tale L. Bjerknes, Nenitha C. Dagslott, Edvard I. Moser, and May-Britt Moser
The mammalian brain has neurons that specifically represent the animal’s location in the environment. Place cells in the hippocampus encode position, whereas grid cells in the medial entorhinal cortex, one synapse away, also express information about the distance and direction that the animal is moving. In this study, we show that, in 2.5–3-wk-old rat pups, place cells have firing fields whose positions depend on distance travelled, despite the immature state of grid fields at this age. The results suggest that place fields can be generated from self-motion–induced distance information in the absence of fully matured grid patterns. (See pp. E1637–E1646.)
Brain-state dependent astrocytic Ca2+ signals are coupled to both positive and negative BOLD-fMRI signals
Maosen Wang, Yi He, Terrence J. Sejnowski, and Xin Yu
The role of astrocytes on brain function is controversial in many aspects. It remains challenging to specify the in vivo functional impact of astrocytic calcium signal when mediating vasodilation/constriction at varied physiological or pathophysiological conditions. Here, we applied simultaneous fMRI and GCaMP-mediated Ca2+ optical fiber recording to detect distinct astrocytic Ca2+ signals (evoked vs. intrinsic) coupled to positive and negative blood-oxygen-level-dependent signals, respectively and concurrently, with unique spatial and temporal patterns. Not only did we demonstrate the distinct neurovascular coupling events coupled to the evoked and intrinsic astrocytic calcium signals, but also revealed the thalamic regulation mechanism underlying the astrocytic calcium-mediated brain state switch. This astrocytic-relevant regulatory mechanism could underlie numerous brain disorder and injury models relevant to gliovascular disruption. (See pp. E1647–E1656.)
TRPV1 channels and the progesterone receptor Sig-1R interact to regulate pain
Miguel Ortíz-Rentería, Rebeca Juárez-Contreras, Ricardo González-Ramírez, León D. Islas, Félix Sierra-Ramírez, Itzel Llorente, Sidney A. Simon, Marcia Hiriart, Tamara Rosenbaum, and Sara L. Morales-Lázaro
The TRPV1 ion channel has been widely associated with the generation of painful responses. The responses of cells expressing this ion channel and, presumably, the overall pain response of an organism may be regulated by controlling the amount of TRPV1 channels in the plasma membrane. TRPV1 levels can be regulated by its interaction with intracellular proteins, but there are no studies describing TRPV1 or any other mammalian TRP channel’s association with chaperones or how these interactions may affect the perception of pain. Here, we show that TRPV1-dependent pain is decreased through Sig-1R antagonism by progesterone and determine the presence of a physical interaction between these two proteins that may reduce pain under physiological conditions such as pregnancy. (See pp. E1657–E1666.)
Phosphatidylinositol-(4, 5)-bisphosphate regulates calcium gating of small-conductance cation channel TMEM16F
Wenlei Ye, Tina W. Han, Layla M. Nassar, Mario Zubia, Yuh Nung Jan, and Lily Yeh Jan
TMEM16F, a small-conductance Ca2+-activated cation channel that permeates Ca2+, is required for the Ca2+-activated phospholipid scramblase activity. The Ca2+-activated Ca2+-conductance mediated by TMEM16F constitutes positive feedback, with potentially deleterious outcomes if not tightly regulated. We performed electrophysiological recordings to show that Ca2+-gating of TMEM16F depends on TMEM16F interaction with PIP2, a minor yet functionally significant phospholipid constituent in the plasma membrane. Elevated intracellular Ca2+ promotes PIP2 hydrolysis by membrane-tethered phospholipases, thereby causing TMEM16F inactivation and likely rendering protection from Ca2+-overloading and cytotoxicity. Given that TMEM16F plays significant roles in blood coagulation and immune responses, our study will help reveal how signaling pathways involving phosphoinositides could potentially contribute to these physiological processes. (See pp. E1667–E1674.)
AtCAP2 is crucial for lytic vacuole biogenesis during germination by positively regulating vacuolar protein trafficking
Yun Kwon, Jinbo Shen, Myoung Hui Lee, Kyoung Rok Geem, Liwen Jiang, and Inhwan Hwang
Plant cells contain two types of vacuoles: the lytic vacuole (LV) and protein storage vacuole (PSV). During embryogenesis, the LV is degenerated and PSVs are produced. Thus, embryonic cells in seeds contain PSVs but not LVs. The situation is reversed during germination, and vegetative cells contain the LV. Recent studies showed that vacuolar trafficking is crucial for LV biogenesis during germination. We identified AtCAP2 as a crucial factor for the vacuole transition during germination. AtCAP2 functions as a positive regulator of the vacuolar trafficking via prevacuolar compartment recruitment of GAPC2, an isoform of glyceraldehyde 3-phosphate dehydrogenases (GAPDHs), well-known metabolic enzymes involved in energy production via glycolysis. Thus, our study provides a connection between vacuolar trafficking and energy metabolism. (See pp. E1675–E1683.)
Projecting one’s own spatial bias onto others during a theory-of-mind task
Branden J. Bio, Taylor W. Webb, and Michael S. A. Graziano
Most people have an intrinsic spatial bias—many are better at processing objects to the left, whereas some are biased to the right. Here, we found that this subtle bias in one’s own awareness is mirrored in one’s ability to process what is likely to be in other people’s minds. If you are biased toward processing your own right side of space, then you may be faster at recognizing when someone else processes an object to his or her right side. One possible interpretation is that we process the space around us, and understand how others process the space around them, using at least partially shared mechanisms. (See pp. E1684–E1689.)
Stimulus generalization as a mechanism for learning to trust
Oriel FeldmanHall, Joseph E. Dunsmoor, Alexa Tompary, Lindsay E. Hunter, Alexander Todorov, and Elizabeth A. Phelps
Humans can learn to trust through direct social experiences. In our everyday lives, however, we constantly meet new people where judgments of trustworthiness are blind to reputation. In these cases, what drives decisions to trust? We find a simple learning mechanism observed across species—stimulus generalization—is deployed in complex social learning environments: Individuals distrust strangers who implicitly resemble those known to be untrustworthy. These behavioral findings were mirrored at the neural level, revealing that the amygdala and caudate selectively encode the transfer of social value during moral learning. The results demonstrate a mechanism that draws on prior learning to reduce the uncertainty associated with strangers, ultimately facilitating potentially adaptive decisions to trust, or withhold trust from, unfamiliar others. (See pp. E1690–E1697.)