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  • Island of hope for the threatened Nassau grouper [Commentaries]
    PNAS (IF 9.580) Pub Date : 2020-01-22
    Yvonne Sadovy de Mitcheson

    In January 1971, a young biologist braved strong currents to dive on a massive spawning aggregation (gathering of reproductive adults) of Nassau grouper (family Epinephelidae) at Cat Cay in The Bahamas. The paper he published was the first-ever eye-witness account in the scientific literature describing a spectacular gathering of 30,000 to 100,000 large adult Nassau grouper (Epinephelus striatus) preparing to spawn (1). Historically, this grouper was among the most important fishery species in the tropical western Atlantic, with earlier accounts also documenting abundance during its reproductive season (2⇓⇓⇓–6). In 2003, barely 30 y after Lavett-Smith’s (1) account, the species was listed as threatened on the International Union for Conservation of Nature (IUCN) Red List. By 2016 it was included on the United States Endangered Species List and in 2017 was added to Annex III of the Specially Protected Areas and Wildlife (SPAW) protocol. All listings were unusual for a commercial reef fish and highlighted the growing crisis for this iconic species brought about by uncontrolled fishing on its spawning aggregations and a many-hundredfold decline in production from historic levels.

    更新日期:2020-01-23
  • Requirement for epithelial p38{alpha} in KRAS-driven lung tumor progression [Medical Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-22
    Jessica Vitos-Faleato, Sebastián M. Real, Nuria Gutierrez-Prat, Alberto Villanueva, Elisabet Llonch, Matthias Drosten, Mariano Barbacid, Angel R. Nebreda

    Malignant transformation entails important changes in the control of cell proliferation through the rewiring of selected signaling pathways. Cancer cells then become very dependent on the proper function of those pathways, and their inhibition offers therapeutic opportunities. Here we identify the stress kinase p38α as a nononcogenic signaling molecule that enables the progression of KrasG12V-driven lung cancer. We demonstrate in vivo that, despite acting as a tumor suppressor in healthy alveolar progenitor cells, p38α contributes to the proliferation and malignization of lung cancer epithelial cells. We show that high expression levels of p38α correlate with poor survival in lung adenocarcinoma patients, and that genetic or chemical inhibition of p38α halts tumor growth in lung cancer mouse models. Moreover, we reveal a lung cancer epithelial cell-autonomous function for p38α promoting the expression of TIMP-1, which in turn stimulates cell proliferation in an autocrine manner. Altogether, our results suggest that epithelial p38α promotes KrasG12V-driven lung cancer progression via maintenance of cellular self-growth stimulatory signals.

    更新日期:2020-01-23
  • Plasmodium falciparum evades immunity of anopheline mosquitoes by interacting with a Pfs47 midgut receptor [Microbiology]
    PNAS (IF 9.580) Pub Date : 2020-01-22
    Alvaro Molina-Cruz, Gaspar E. Canepa, Thiago Luiz Alves e Silva, Adeline E. Williams, Simardeep Nagyal, Lampouguin Yenkoidiok-Douti, Bianca M. Nagata, Eric Calvo, John Andersen, Martin J. Boulanger, Carolina Barillas-Mury

    The surface protein Pfs47 allows Plasmodium falciparum parasites to survive and be transmitted by making them “undetectable” to the mosquito immune system. P. falciparum parasites express Pfs47 haplotypes compatible with their sympatric vectors, while those with incompatible haplotypes are eliminated by the mosquito. We proposed that Pfs47 serves as a “key” that mediates immune evasion by interacting with a mosquito receptor “the lock,” which differs in evolutionarily divergent anopheline mosquitoes. Recombinant Pfs47 (rPfs47) was used to identify the mosquito Pfs47 receptor protein (P47Rec) using far-Western analysis. rPfs47 bound to a single 31-kDa band and the identity of this protein was determined by mass spectrometry. The mosquito P47Rec has two natterin-like domains and binds to Pfs47 with high affinity (17 to 32 nM). P47Rec is a highly conserved protein with submicrovillar localization in midgut cells. It has structural homology to a cytoskeleton-interacting protein and accumulates at the site of ookinete invasion. Silencing P47Rec expression reduced P. falciparum infection, indicating that the interaction of Pfs47 with the receptor is critical for parasite survival. The binding specificity of P47Rec from distant anophelines (Anopheles gambiae, Anopheles dirus, and Anopheles albimanus) with Pfs47-Africa (GB4) and Pfs47-South America (7G8) haplotypes was evaluated, and it is in agreement with the previously documented compatibility between P. falciparum parasites expressing different Pfs47 haplotypes and these three anopheline species. Our findings give further support to the role of Pfs47 in the adaptation of P. falciparum to different vectors.

    更新日期:2020-01-23
  • Arrhythmogenic late Ca2+ sparks in failing heart cells and their control by action potential configuration [Physiology]
    PNAS (IF 9.580) Pub Date : 2020-01-22
    Ewan D. Fowler, Nan Wang, Melanie Hezzell, Guillaume Chanoit, Jules C. Hancox, Mark B. Cannell

    Sudden death in heart failure patients is a major clinical problem worldwide, but it is unclear how arrhythmogenic early afterdepolarizations (EADs) are triggered in failing heart cells. To examine EAD initiation, high-sensitivity intracellular Ca2+ measurements were combined with action potential voltage clamp techniques in a physiologically relevant heart failure model. In failing cells, the loss of Ca2+ release synchrony at the start of the action potential leads to an increase in number of microscopic intracellular Ca2+ release events (“late” Ca2+ sparks) during phase 2–3 of the action potential. These late Ca2+ sparks prolong the Ca2+ transient that activates contraction and can trigger propagating microscopic Ca2+ ripples, larger macroscopic Ca2+ waves, and EADs. Modification of the action potential to include steps to different potentials revealed the amount of current generated by these late Ca2+ sparks and their (subsequent) spatiotemporal summation into Ca2+ ripples/waves. Comparison of this current to the net current that causes action potential repolarization shows that late Ca2+ sparks provide a mechanism for EAD initiation. Computer simulations confirmed that this forms the basis of a strong oscillatory positive feedback system that can act in parallel with other purely voltage-dependent ionic mechanisms for EAD initiation. In failing heart cells, restoration of the action potential to a nonfailing phase 1 configuration improved the synchrony of excitation–contraction coupling, increased Ca2+ transient amplitude, and suppressed late Ca2+ sparks. Therapeutic control of late Ca2+ spark activity may provide an additional approach for treating heart failure and reduce the risk for sudden cardiac death.

    更新日期:2020-01-23
  • Guided transition waves in multistable mechanical metamaterials [Engineering]
    PNAS (IF 9.580) Pub Date : 2020-01-22
    Lishuai Jin, Romik Khajehtourian, Jochen Mueller, Ahmad Rafsanjani, Vincent Tournat, Katia Bertoldi, Dennis M. Kochmann

    Transition fronts, moving through solids and fluids in the form of propagating domain or phase boundaries, have recently been mimicked at the structural level in bistable architectures. What has been limited to simple one-dimensional (1D) examples is here cast into a blueprint for higher dimensions, demonstrated through 2D experiments and described by a continuum mechanical model that draws inspiration from phase transition theory in crystalline solids. Unlike materials, the presented structural analogs admit precise control of the transition wave’s direction, shape, and velocity through spatially tailoring the underlying periodic network architecture (locally varying the shape or stiffness of the fundamental building blocks, and exploiting interactions of transition fronts with lattice defects such as point defects and free surfaces). The outcome is a predictable and programmable strongly nonlinear metamaterial motion with potential for, for example, propulsion in soft robotics, morphing surfaces, reconfigurable devices, mechanical logic, and controlled energy absorption.

    更新日期:2020-01-23
  • Dynamical control by water at a molecular level in protein dimer association and dissociation [Chemistry]
    PNAS (IF 9.580) Pub Date : 2020-01-22
    Puja Banerjee, Biman Bagchi

    Water, often termed as the “lubricant of life,” is expected to play an active role in navigating protein dissociation–association reactions. In order to unearth the molecular details, we first compute the free-energy surface (FES) of insulin dimer dissociation employing metadynamics simulation, and then carry out analyses of insulin dimerization and dissociation using atomistic molecular-dynamics simulation in explicit water. We select two sets of initial configurations from 1) the dissociated state and 2) the transition state, and follow time evolution using several long trajectories (∼1–2 μs). During the process we not only monitor configuration of protein monomers, but also the properties of water. Although the equilibrium structural properties of water between the two monomers approach bulklike characteristics at a separation distance of ∼5 nm, the dynamics differ considerably. The complex association process is observed to be accompanied by several structural and dynamical changes of the system, such as large-scale correlated water density fluctuations, coupled conformational fluctuation of protein monomers, a dewettinglike transition with the change of intermonomeric distance RMM from ∼4 to ∼2 nm, orientation of monomers and hydrophobic hydration in the monomers. A quasistable, solvent-shared, protein monomer pair (SSPMP) forms at around 2 nm during association process which is a local free-energy minimum having ∼50–60% of native contacts. Simulations starting with arrangements sampled from the transition state (TS) of the dimer dissociation reveal that the final outcome depends on relative orientation of the backbone in the “hotspot” region.

    更新日期:2020-01-23
  • Identifying determinants of bacterial fitness in a model of human gut microbial succession [Microbiology]
    PNAS (IF 9.580) Pub Date : 2020-01-22
    Lihui Feng, Arjun S. Raman, Matthew C. Hibberd, Jiye Cheng, Nicholas W. Griffin, Yangqing Peng, Semen A. Leyn, Dmitry A. Rodionov, Andrei L. Osterman, Jeffrey I. Gordon

    Human gut microbiota development has been associated with healthy growth but understanding the determinants of community assembly and composition is a formidable challenge. We cultured bacteria from serially collected fecal samples from a healthy infant; 34 sequenced strains containing 103,102 genes were divided into two consortia representing earlier and later stages in community assembly during the first six postnatal months. The two consortia were introduced alone (singly), or sequentially in different order, or simultaneously into young germ-free mice fed human infant formula. The pattern of fitness of bacterial strains observed across the different colonization conditions indicated that later-phase strains substantially outcompete earlier-phase strains, although four early-phase members persist. Persistence was not determined by order of introduction, suggesting that priority effects are not prominent in this model. To characterize succession in the context of the metabolic potential of consortium members, we performed in silico reconstructions of metabolic pathways involved in carbohydrate utilization and amino acid and B-vitamin biosynthesis, then quantified the fitness (abundance) of strains in serially collected fecal samples and their transcriptional responses to different histories of colonization. Applying feature-reduction methods disclosed a set of metabolic pathways whose presence and/or expression correlates with strain fitness and that enable early-stage colonizers to survive during introduction of later colonizers. The approach described can be used to test the magnitude of the contribution of identified metabolic pathways to fitness in different community contexts, study various ecological processes thought to govern community assembly, and facilitate development of microbiota-directed therapeutics.

    更新日期:2020-01-23
  • Tool-using puffins prickle the puzzle of cognitive evolution [Commentaries]
    PNAS (IF 9.580) Pub Date : 2020-01-22
    Auguste M. P. von Bayern, Ivo Jacobs, Mathias Osvath

    In PNAS, Fayet et al. (1) report on two cases of tool use in a seabird. In two distant populations they recorded Arctic puffins (Fratercula arctica) using sticks to scratch themselves (Fig. 1). The documentation of tool use in this species expands the ever-growing list of tool-using birds through rare observations under natural conditions. Although it is neither the first observation of tool use in wild seabirds, nor the first of stick-tool use outside of a foraging context in wild birds, these findings contribute to the debate on the evolutionary and cognitive origins of tool use.

    更新日期:2020-01-23
  • Correction for Hu et al., Structural bases for F plasmid conjugation and F pilus biogenesis in Escherichia coli [Correction]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    National Academy of Sciences

    MICROBIOLOGY Correction for “Structural bases for F plasmid conjugation and F pilus biogenesis in Escherichia coli,” …

    更新日期:2020-01-22
  • Correction for Porter et al., Epithelial to mesenchymal plasticity and differential response to therapies in pancreatic ductal adenocarcinoma [Corrections]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    National Academy of Sciences

    MEDICAL SCIENCES Correction for “Epithelial to mesenchymal plasticity and differential response to therapies in pancreatic ductal adenocarcinoma,” by Rebecca L. Porter, Neelima K. C. Magnus, Vishal Thapar, Robert Morris, Annamaria Szabolcs, Azfar Neyaz, Anupriya S. Kulkarni, Eric Tai, Abhijit Chougule, Alessandra Hillis, Gabriel Golczer, …

    更新日期:2020-01-22
  • Correction for Mann, Core Concept: To improve weather and climate models, researchers are chasing atmospheric gravity waves [Corrections]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    National Academy of Sciences

    CORE CONCEPTS Correction for “Core Concept: To improve weather and climate models, researchers are chasing atmospheric gravity waves,” by Adam Mann, …

    更新日期:2020-01-22
  • Correction for Perkins, Core Concept: Albedo is a simple concept that plays complicated roles in climate and astronomy [Corrections]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    National Academy of Sciences

    CORE CONCEPTS Correction for “Core Concept: Albedo is a simple concept that plays complicated roles in climate and …

    更新日期:2020-01-22
  • A randomized trial of a lab-embedded discourse intervention to improve research ethics
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Dena K. Plemmons, Erica N. Baranski, Kyle Harp, David D. Lo, Courtney K. Soderberg, Timothy M. Errington, Brian A. Nosek, Kevin M. Esterling

    We report a randomized trial of a research ethics training intervention designed to enhance ethics communication in university science and engineering laboratories, focusing specifically on authorship and data management. The intervention is a project-based research ethics curriculum that was designed to enhance the ability of science and engineering research laboratory members to engage in reason giving and interpersonal communication necessary for ethical practice. The randomized trial was fielded in active faculty-led laboratories at two US research-intensive institutions. Here, we show that laboratory members perceived improvements in the quality of discourse on research ethics within their laboratories and enhanced awareness of the relevance and reasons for that discourse for their work as measured by a survey administered over 4 mo after the intervention. This training represents a paradigm shift compared with more typical module-based or classroom ethics instruction that is divorced from the everyday workflow and practices within laboratories and is designed to cultivate a campus culture of ethical science and engineering research in the very work settings where laboratory members interact.

    更新日期:2020-01-22
  • Scientists’ incentives and attitudes toward public communication
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Kathleen M. Rose, Ezra M. Markowitz, Dominique Brossard

    In an era of large-scale science-related challenges and rapid advancements in groundbreaking science with major societal implications, communicating about science is critical. The profile of science communication has increased over the last few decades, with multiple sectors calling for such activities. As scientists respond to calls for public-facing communication, we need to evaluate where the scientific community stands. We conducted a unique census of science faculty at land-grant universities across the United States intended to spur the next generation of science communicators and research. Despite scientists’ strong approval of science communication efforts, potential areas of tension, attributable to lack of institutional support and confidence in communication skills, constrain these efforts.

    更新日期:2020-01-22
  • The rhizobial autotransporter determines the symbiotic nitrogen fixation activity of Lotus japonicus in a host-specific manner [Plant Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Yoshikazu Shimoda, Yuki Nishigaya, Hiroko Yamaya-Ito, Noritoshi Inagaki, Yosuke Umehara, Hideki Hirakawa, Shusei Sato, Toshimasa Yamazaki, Makoto Hayashi

    Leguminous plants establish endosymbiotic associations with rhizobia and form root nodules in which the rhizobia fix atmospheric nitrogen. The host plant and intracellular rhizobia strictly control this symbiotic nitrogen fixation. We recently reported a Lotus japonicus Fix− mutant, apn1 (aspartic peptidase nodule-induced 1), that impairs symbiotic nitrogen fixation. APN1 encodes a nodule-specific aspartic peptidase involved in the Fix− phenotype in a rhizobial strain-specific manner. This host-strain specificity implies that some molecular interactions between host plant APN1 and rhizobial factors are required, although the biological function of APN1 in nodules and the mechanisms governing the interactions are unknown. To clarify how rhizobial factors are involved in strain-specific nitrogen fixation, we explored transposon mutants of Mesorhizobium loti strain TONO, which normally form Fix− nodules on apn1 roots, and identified TONO mutants that formed Fix+ nodules on apn1. The identified causal gene encodes an autotransporter, part of a protein secretion system of Gram-negative bacteria. Expression of the autotransporter gene in M. loti strain MAFF3030399, which normally forms Fix+ nodules on apn1 roots, resulted in Fix− nodules. The autotransporter of TONO functions to secrete a part of its own protein (a passenger domain) into extracellular spaces, and the recombinant APN1 protein cleaved the passenger protein in vitro. The M. loti autotransporter showed the activity to induce the genes involved in nodule senescence in a dose-dependent manner. Therefore, we conclude that the nodule-specific aspartic peptidase, APN1, suppresses negative effects of the rhizobial autotransporter in order to maintain effective symbiotic nitrogen fixation in root nodules.

    更新日期:2020-01-22
  • The maize heterotrimeric G protein {beta} subunit controls shoot meristem development and immune responses [Plant Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Qingyu Wu, Fang Xu, Lei Liu, Si Nian Char, Yezhang Ding, Byoung Il Je, Eric Schmelz, Bing Yang, David Jackson

    Heterotrimeric G proteins are important transducers of receptor signaling, functioning in plants with CLAVATA receptors in controlling shoot meristem size and with pathogen-associated molecular pattern receptors in basal immunity. However, whether specific members of the heterotrimeric complex potentiate cross-talk between development and defense, and the extent to which these functions are conserved across species, have not yet been addressed. Here we used CRISPR/Cas9 to knock out the maize G protein β subunit gene (Gβ) and found that the mutants are lethal, differing from those in Arabidopsis, in which homologous mutants have normal growth and fertility. We show that lethality is caused not by a specific developmental arrest, but by autoimmunity. We used a genetic diversity screen to suppress the lethal Gβ phenotype and also identified a maize Gβ allele with weak autoimmune responses but strong development phenotypes. Using these tools, we show that Gβ controls meristem size in maize, acting epistatically with G protein α subunit gene (Gα), suggesting that Gβ and Gα function in a common signaling complex. Furthermore, we used an association study to show that natural variation in Gβ influences maize kernel row number, an important agronomic trait. Our results demonstrate the dual role of Gβ in immunity and development in a cereal crop and suggest that it functions in cross-talk between these competing signaling networks. Therefore, modification of Gβ has the potential to optimize the trade-off between growth and defense signaling to improve agronomic production.

    更新日期:2020-01-22
  • Specialized stellate cells offer a privileged route for rapid water flux in Drosophila renal tubule [Physiology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Pablo Cabrero, Selim Terhzaz, Anthony J. Dornan, Saurav Ghimire, Heather L. Holmes, Daniel R. Turin, Michael F. Romero, Shireen A. Davies, Julian A. T. Dow

    Insects are highly successful, in part through an excellent ability to osmoregulate. The renal (Malpighian) tubules can secrete fluid faster on a per-cell basis than any other epithelium, but the route for these remarkable water fluxes has not been established. In Drosophila melanogaster, we show that 4 genes of the major intrinsic protein family are expressed at a very high level in the fly renal tissue: the aquaporins (AQPs) Drip and Prip and the aquaglyceroporins Eglp2 and Eglp4. As predicted from their structure, and by their transport function by expressing these proteins in Xenopus oocytes, Drip, Prip, and Eglp2 show significant and specific water permeability, whereas Eglp2 and Eglp4 show very high permeability to glycerol and urea. Knockdowns of any of these genes result in impaired hormone-induced fluid secretion. The Drosophila tubule has 2 main secretory cell types: active cation-transporting principal cells, wherein the aquaglyceroporins localize to opposite plasma membranes, and small stellate cells, the site of the chloride shunt conductance, with these AQPs localizing to opposite plasma membranes. This suggests a model in which osmotically obliged water flows through the stellate cells. Consistent with this model, fluorescently labeled dextran, an in vivo marker of membrane water permeability, is trapped in the basal infoldings of the stellate cells after kinin diuretic peptide stimulation, confirming that these cells provide the major route for transepithelial water flux. The spatial segregation of these components of epithelial water transport may help to explain the unique success of the higher insects in regulating their internal environments.

    更新日期:2020-01-22
  • Internal fluid pressure influences muscle contractile force [Physiology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    David A. Sleboda, Thomas J. Roberts

    Fluid fills intracellular, extracellular, and capillary spaces within muscle. During normal physiological activity, intramuscular fluid pressures develop as muscle exerts a portion of its developed force internally. These pressures, typically ranging between 10 and 250 mmHg, are rarely considered in mechanical models of muscle but have the potential to affect performance by influencing force and work produced during contraction. Here, we test a model of muscle structure in which intramuscular pressure directly influences contractile force. Using a pneumatic cuff, we pressurize muscle midcontraction at 260 mmHg and report the effect on isometric force. Pressurization reduced isometric force at short muscle lengths (e.g., −11.87% of P0 at 0.9 L0), increased force at long lengths (e.g., +3.08% of P0 at 1.25 L0), but had no effect at intermediate muscle lengths ∼1.1–1.15 L0. This variable response to pressurization was qualitatively mimicked by simple physical models of muscle morphology that displayed negative, positive, or neutral responses to pressurization depending on the orientation of reinforcing fibers representing extracellular matrix collagen. These findings show that pressurization can have immediate, significant effects on muscle contractile force and suggest that forces transmitted to the extracellular matrix via pressurized fluid may be important, but largely unacknowledged, determinants of muscle performance in vivo.

    更新日期:2020-01-22
  • Optimizing Brownian escape rates by potential shaping [Physics]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Marie Chupeau, Jannes Gladrow, Alexei Chepelianskii, Ulrich F. Keyser, Emmanuel Trizac

    Brownian escape is key to a wealth of physico-chemical processes, including polymer folding and information storage. The frequency of thermally activated energy barrier crossings is assumed to generally decrease exponentially with increasing barrier height. Here, we show experimentally that higher, fine-tuned barrier profiles result in significantly enhanced escape rates, in breach of the intuition relying on the above scaling law, and address in theory the corresponding conditions for maximum speed-up. Importantly, our barriers end on the same energy on which they start. For overdamped dynamics, the achievable boost of escape rates is, in principle, unbounded so that the barrier optimization has to be regularized. We derive optimal profiles under 2 different regularizations and uncover the efficiency of N-shaped barriers. We then demonstrate the viability of such a potential in automated microfluidic Brownian dynamics experiments using holographic optical tweezers and achieve a doubling of escape rates compared to unhindered Brownian motion. Finally, we show that this escape rate boost extends into the low-friction inertial regime.

    更新日期:2020-01-22
  • Microglial IRF5-IRF4 regulatory axis regulates neuroinflammation after cerebral ischemia and impacts stroke outcomes [Neuroscience]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Abdullah Al Mamun, Anjali Chauhan, Shaohua Qi, Conelius Ngwa, Yan Xu, Romana Sharmeen, Amy L. Hazen, Jun Li, Jaroslaw A. Aronowski, Louise D. McCullough, Fudong Liu

    Microglial activation plays a central role in poststroke inflammation and causes secondary neuronal damage; however, it also contributes in debris clearance and chronic recovery. Microglial pro- and antiinflammatory responses (or so-called M1-M2 phenotypes) coexist and antagonize each other throughout the disease progress. As a result of this balance, poststroke immune responses alter stroke outcomes. Our previous study found microglial expression of interferon regulatory factor 5 (IRF5) and IRF4 was related to pro- and antiinflammatory responses, respectively. In the present study, we genetically modified the IRF5 and IRF4 signaling to explore their roles in stroke. Both in vitro and in vivo assays were utilized; IRF5 or IRF4 small interfering RNA (siRNA), lentivirus, and conditional knockout (CKO) techniques were employed to modulate IRF5 or IRF4 expression in microglia. We used a transient middle cerebral artery occlusion model to induce stroke and examined both acute and chronic stroke outcomes. Poststroke inflammation was evaluated with flow cytometry, RT-PCR, MultiPlex, and immunofluorescence staining. An oscillating pattern of the IRF5-IRF4 regulatory axis function was revealed. Down-regulation of IRF5 signaling by siRNA or CKO resulted in increased IRF4 expression, enhanced M2 activation, quenched proinflammatory responses, and improved stroke outcomes, whereas down-regulation of IRF4 led to increased IRF5 expression, enhanced M1 activation, exacerbated proinflammatory responses, and worse functional recovery. Up-regulation of IRF4 or IRF5 by lentivirus induced similar results. We conclude that the IRF5-IRF4 regulatory axis is a key determinant in microglial activation. The IRF5-IRF4 regulatory axis is a potential therapeutic target for neuroinflammation and ischemic stroke.

    更新日期:2020-01-22
  • Robust hepatitis E virus infection and transcriptional response in human hepatocytes [Microbiology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Daniel Todt, Martina Friesland, Nora Moeller, Dimas Praditya, Volker Kinast, Yannick Brüggemann, Leonard Knegendorf, Thomas Burkard, Joerg Steinmann, Rani Burm, Lieven Verhoye, Avista Wahid, Toni Luise Meister, Michael Engelmann, Vanessa M. Pfankuche, Christina Puff, Florian W. R. Vondran, Wolfgang Baumgärtner, Philip Meuleman, Patrick Behrendt, Eike Steinmann

    Hepatitis E virus (HEV) is the causative agent of hepatitis E in humans and the leading cause for acute viral hepatitis worldwide. The virus is classified as a member of the genus Orthohepevirus A within the Hepeviridae family. Due to the absence of a robust cell culture model for HEV infection, the analysis of the viral life cycle, the development of effective antivirals and a vaccine is severely limited. In this study, we established a protocol based on the HEV genotype 3 p6 (Kernow C-1) and the human hepatoma cell lines HepG2 and HepG2/C3A with different media conditions to produce intracellular HEV cell culture-derived particles (HEVcc) with viral titers between 105 and 106 FFU/mL. Viral titers could be further enhanced by an HEV variant harboring a mutation in the RNA-dependent RNA polymerase. These HEVcc particles were characterized in density gradients and allowed the trans-complementation of subgenomic reporter HEV replicons. In addition, in vitro produced intracellular-derived particles were infectious in liver-humanized mice with high RNA copy numbers detectable in serum and feces. Efficient infection of primary human and swine hepatocytes using the developed protocol could be observed and was inhibited by ribavirin. Finally, RNA sequencing studies of HEV-infected primary human hepatocytes demonstrated a temporally structured transcriptional defense response. In conclusion, this robust cell culture model of HEV infection provides a powerful tool for studying viral–host interactions that should facilitate the discovery of antiviral drugs for this important zoonotic pathogen.

    更新日期:2020-01-22
  • A promiscuous inflammasome sparks replication of a common tumor virus [Microbiology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Eric M. Burton, Raphaela Goldbach-Mansky, Sumita Bhaduri-McIntosh

    Viruses activate inflammasomes but then subvert resulting inflammatory responses to avoid elimination. We asked whether viruses could instead use such activated or primed inflammasomes to directly aid their propagation and spread. Since herpesviruses are experts at coopting cellular functions, we investigated whether Epstein−Barr virus (EBV), an oncoherpesvirus, exploits inflammasomes to activate its replicative or lytic phase. Indeed, our experiments reveal that EBV exploits several inflammasome sensors to actually activate its replicative phase from quiescence/latency. In particular, TXNIP, a key inflammasome intermediary, causes assembly of the NLRP3 inflammasome, resulting in caspase-1−mediated depletion of the heterochromatin-inducing epigenetic repressor KAP1/TRIM28 in a subpopulation of cells. As a result, only TXNIPhiKAP1lo cells, that is, in a primed/prolytic state, turn expression of the replication/lytic/reactivation switch protein on to enter the replicative phase. Our findings 1) demonstrate that EBV dovetails its escape strategy to a key cellular danger-sensing mechanism, 2) indicate that transcription may be regulated by KAP1 abundance aside from canonical regulation through its posttranslational modification, 3) mechanistically link diabetes, which frequently activates the NLRP3 inflammasome, to deregulation of a tumor virus, and 4) demonstrate that B lymphocytes from NOMID (neonatal onset multisystem inflammatory disease) patients who have NLRP3 mutations and suffer from hyperactive innate responses are defective in controlling a herpesvirus.

    更新日期:2020-01-22
  • Mitochondrial dysfunctions trigger the calcium signaling-dependent fungal multidrug resistance [Microbiology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Yeqi Li, Yuanwei Zhang, Chi Zhang, Hongchen Wang, Xiaolei Wei, Peiying Chen, Ling Lu

    Drug resistance in fungal pathogens has risen steadily over the past decades due to long-term azole therapy or triazole usage in agriculture. Modification of the drug target protein to prevent drug binding is a major recognized route to induce drug resistance. However, mechanisms for nondrug target-induced resistance remain only loosely defined. Here, we explore the molecular mechanisms of multidrug resistance resulted from an efficient adaptation strategy for survival in drug environments in the human pathogen Aspergillus fumigatus. We show that mutants conferring multidrug resistance are linked with mitochondrial dysfunction induced by defects in heme A biosynthesis. Comparison of the gene expression profiles between the drug-resistant mutants and the parental wild-type strain shows that multidrug-resistant transporters, chitin synthases, and calcium-signaling-related genes are significantly up-regulated, while scavenging mitochondrial reactive oxygen species (ROS)-related genes are significantly down-regulated. The up-regulated-expression genes share consensus calcium-dependent serine threonine phosphatase-dependent response elements (the binding sites of calcium-signaling transcription factor CrzA). Accordingly, drug-resistant mutants show enhanced cytosolic Ca2+ transients and persistent nuclear localization of CrzA. In comparison, calcium chelators significantly restore drug susceptibility and increase azole efficacy either in laboratory-derived or in clinic-isolated A. fumigatus strains. Thus, the mitochondrial dysfunction as a fitness cost can trigger calcium signaling and, therefore, globally up-regulate a series of embedding calcineurin-dependent–response-element genes, leading to antifungal resistance. These findings illuminate how fitness cost affects drug resistance and suggest that disruption of calcium signaling might be a promising therapeutic strategy to fight against nondrug target-induced drug resistance.

    更新日期:2020-01-22
  • Bile acids and ceramide overcome the entry restriction for GII.3 human norovirus replication in human intestinal enteroids [Microbiology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Kosuke Murakami, Victoria R. Tenge, Umesh C. Karandikar, Shih-Ching Lin, Sasirekha Ramani, Khalil Ettayebi, Sue E. Crawford, Xi-Lei Zeng, Frederick H. Neill, B. Vijayalakshmi Ayyar, Kazuhiko Katayama, David Y. Graham, Erhard Bieberich, Robert L. Atmar, Mary K. Estes

    Human noroviruses (HuNoVs) cause sporadic and epidemic outbreaks of gastroenteritis in all age groups worldwide. We previously reported that stem cell-derived human intestinal enteroid (HIE) cultures support replication of multiple HuNoV strains and that some strains (e.g., GII.3) replicate only in the presence of bile. Heat- and trypsin-treatment of bile did not reduce GII.3 replication, indicating a nonproteinaceous component in bile functions as an active factor. Here we show that bile acids (BAs) are critical for GII.3 replication and replication correlates with BA hydrophobicity. Using the highly effective BA, glycochenodeoxycholic acid (GCDCA), we show BAs act during the early stage of infection, BA-dependent replication in HIEs is not mediated by detergent effects or classic farnesoid X receptor or Takeda G protein-coupled receptor 5 signaling but involves another G protein-coupled receptor, sphingosine-1-phosphate receptor 2, and BA treatment of HIEs increases particle uptake. We also demonstrate that GCDCA induces multiple cellular responses that promote GII.3 replication in HIEs, including enhancement of 1) endosomal uptake, 2) endosomal acidification and subsequent activity of endosomal/lysosomal enzyme acid sphingomyelinase (ASM), and 3) ceramide levels on the apical membrane. Inhibitors of endosomal acidification or ASM reduce GII.3 infection and exogenous addition of ceramide alone permits infection. Furthermore, inhibition of lysosomal exocytosis of ASM, which is required for ceramide production at the apical surface, decreases GII.3 infection. Together, our results support a model where GII.3 exploits rapid BA-mediated cellular endolysosomal dynamic changes and cellular ceramide to enter and replicate in jejunal HIEs.

    更新日期:2020-01-22
  • Expansion, in vivo-ex vivo cycling, and genetic manipulation of primary human hepatocytes [Medical Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Eleftherios Michailidis, Koen Vercauteren, Liliana Mancio-Silva, Linda Andrus, Cyprien Jahan, Inna Ricardo-Lax, Chenhui Zou, Mohammad Kabbani, Paul Park, Corrine Quirk, Christina Pyrgaki, Brandon Razooky, Lieven Verhoye, Irene Zoluthkin, Wei-Yu Lu, Stuart J. Forbes, Luis Chiriboga, Neil D. Theise, Roland W. Herzog, Hiroshi Suemizu, William M. Schneider, Amir Shlomai, Philip Meuleman, Sangeeta N. Bhatia, Charles M. Rice, Ype P. de Jong

    Primary human hepatocytes (PHHs) are an essential tool for modeling drug metabolism and liver disease. However, variable plating efficiencies, short lifespan in culture, and resistance to genetic manipulation have limited their use. Here, we show that the pyrrolizidine alkaloid retrorsine improves PHH repopulation of chimeric mice on average 10-fold and rescues the ability of even poorly plateable donor hepatocytes to provide cells for subsequent ex vivo cultures. These mouse-passaged (mp) PHH cultures overcome the marked donor-to-donor variability of cryopreserved PHH and remain functional for months as demonstrated by metabolic assays and infection with hepatitis B virus and Plasmodium falciparum. mpPHH can be efficiently genetically modified in culture, mobilized, and then recultured as spheroids or retransplanted to create highly humanized mice that carry a genetically altered hepatocyte graft. Together, these advances provide flexible tools for the study of human liver disease and evaluation of hepatocyte-targeted gene therapy approaches.

    更新日期:2020-01-22
  • High-dose ascorbic acid synergizes with anti-PD1 in a lymphoma mouse model [Medical Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Rebecca A. Luchtel, Tushar Bhagat, Kith Pradhan, William R. Jacobs, Mark Levine, Amit Verma, Niraj Shenoy

    Major efforts are underway to identify agents that can potentiate effects of immune checkpoint inhibition. Here, we show that ascorbic acid (AA) treatment caused genomewide demethylation and enhanced expression of endogenous retroviral elements in lymphoma cells. AA also increased 5-hydroxymethylcytosine (5hmC) levels of CD8+ T cells and enhanced their cytotoxic activity in a lymphoma coculture system. High-dose AA treatment synergized with anti-PD1 therapy in a syngeneic lymphoma mouse model, resulting in marked inhibition of tumor growth compared with either agent alone. Analysis of the intratumoral epigenome revealed increased 5hmC with AA treatment, consistent with in vitro findings. Analysis of the tumor immune microenvironment revealed that AA strikingly increased intratumoral infiltration of CD8+ T cells and macrophages, suggesting enhanced tumor immune recognition. The combination treatment markedly enhanced intratumoral infiltration of macrophages and CD8+ T lymphocytes, granzyme B production by cytotoxic cells (cytotoxic T cells and natural killer cells), and interleukin 12 production by antigen-presenting cells compared with single-agent anti-PD1. These data indicate that AA potentiates anti-PD1 checkpoint inhibition through synergistic mechanisms. The study provides compelling rationale for testing combinations of high-dose AA and anti-PD1 agents in patients with aggressive B cell lymphoma as well as in preclinical models of other malignancies.

    更新日期:2020-01-22
  • Identification and characterization of extrachromosomal circular DNA in maternal plasma [Medical Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Sarah T. K. Sin, Peiyong Jiang, Jiaen Deng, Lu Ji, Suk Hang Cheng, Anindya Dutta, Tak Y. Leung, K. C. Allen Chan, Rossa W. K. Chiu, Y. M. Dennis Lo

    We explored the presence of extrachromosomal circular DNA (eccDNA) in the plasma of pregnant women. Through sequencing following either restriction enzyme or Tn5 transposase treatment, we identified eccDNA molecules in the plasma of pregnant women. These eccDNA molecules showed bimodal size distributions peaking at ∼202 and ∼338 bp with distinct 10-bp periodicity observed throughout the size ranges within both peaks, suggestive of their nucleosomal origin. Also, the predominance of the 338-bp peak of eccDNA indicated that eccDNA had a larger size distribution than linear DNA in human plasma. Moreover, eccDNA of fetal origin were shorter than the maternal eccDNA. Genomic annotation of the overall population of eccDNA molecules revealed a preference of these molecules to be generated from 5′-untranslated regions (5′-UTRs), exonic regions, and CpG island regions. Two sets of trinucleotide repeat motifs flanking the junctional sites of eccDNA supported multiple possible models for eccDNA generation. This work highlights the topologic analysis of plasma DNA, which is an emerging direction for circulating nucleic acid research and applications.

    更新日期:2020-01-22
  • Host protein glycosylation in nucleic acid vaccines as a potential hurdle in vaccine design for nonviral pathogens [Immunology and Inflammation]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Ahmet Ozdilek, Amy V. Paschall, Michelle Dookwah, Michael Tiemeyer, Fikri Y. Avci

    Nucleic acid vaccines introduce the genetic materials encoding antigenic proteins into host cells. If these proteins are directed into the secretory pathway with a signal/leader sequence, they will be exposed to the host’s glycosylation machinery, and, if their amino acid sequences contain consensus sequons for N-linked glycosylation, they may become glycosylated. The presence of host glycans on the proteins of microbial origin may prevent a strong protective immune response either through hindering access to key epitopes by lymphocytes or through altering immune responses by binding to immunoregulatory glycan-binding receptors on immune cells. Ag85A expressed by Mycobacterium tuberculosis (Mtb) is a bacterial surface protein that is commonly used in nucleic acid vaccines in multiple clinical trials. Here we show that, when Ag85A is expressed in mammalian cells, it is glycosylated, does not induce a strong humoral immune response in mice, and does not activate Ag85A-specific lymphocytes as highly as Ag85A natively expressed by the bacterium. Our study indicates that host glycosylation of the vaccine target can impede its antigenicity and immunogenicity. Glycosylation of the antigenic protein targets therefore must be carefully evaluated in designing nucleic acid vaccines.

    更新日期:2020-01-22
  • Large-scale contractions of Friedreich’s ataxia GAA repeats in yeast occur during DNA replication due to their triplex-forming ability [Genetics]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Alexandra N. Khristich, Jillian F. Armenia, Robert M. Matera, Anna A. Kolchinski, Sergei M. Mirkin

    Friedreich’s ataxia (FRDA) is a human hereditary disease caused by the presence of expanded (GAA)n repeats in the first intron of the FXN gene [V. Campuzano et al., Science 271, 1423–1427 (1996)]. In somatic tissues of FRDA patients, (GAA)n repeat tracts are highly unstable, with contractions more common than expansions [R. Sharma et al., Hum. Mol. Genet. 11, 2175–2187 (2002)]. Here we describe an experimental system to characterize GAA repeat contractions in yeast and to conduct a genetic analysis of this process. We found that large-scale contraction is a one-step process, resulting in a median loss of ∼60 triplet repeats. Our genetic analysis revealed that contractions occur during DNA replication, rather than by various DNA repair pathways. Repeats contract in the course of lagging-strand synthesis: The processivity subunit of DNA polymerase δ, Pol32, and the catalytic domain of Rev1, a translesion polymerase, act together in the same pathway to counteract contractions. Accumulation of single-stranded DNA (ssDNA) in the lagging-strand template greatly increases the probability that (GAA)n repeats contract, which in turn promotes repeat instability in rfa1, rad27, and dna2 mutants. Finally, by comparing contraction rates for homopurine-homopyrimidine repeats differing in their mirror symmetry, we found that contractions depend on a repeat’s triplex-forming ability. We propose that accumulation of ssDNA in the lagging-strand template fosters the formation of a triplex between the nascent and fold-back template strands of the repeat. Occasional jumps of DNA polymerase through this triplex hurdle, result in repeat contractions in the nascent lagging strand.

    更新日期:2020-01-22
  • Cystic fibrosis carriers are at increased risk for a wide range of cystic fibrosis-related conditions [Genetics]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Aaron C. Miller, Alejandro P. Comellas, Douglas B. Hornick, David A. Stoltz, Joseph E. Cavanaugh, Alicia K. Gerke, Michael J. Welsh, Joseph Zabner, Philip M. Polgreen

    Autosomal recessive diseases, such as cystic fibrosis (CF), require inheritance of 2 mutated genes. However, some studies indicate that CF carriers are at increased risk for some conditions associated with CF. These investigations focused on single conditions and included small numbers of subjects. Our goal was to determine whether CF carriers are at increased risk for a range of CF-related conditions. Using the Truven Health MarketScan Commercial Claims database (2001–2017), we performed a population-based retrospective matched-cohort study. We identified 19,802 CF carriers and matched each carrier with 5 controls. The prevalence of 59 CF-related diagnostic conditions was evaluated in each cohort. Odds ratios for each condition were computed for CF carriers relative to controls. All 59 CF-related conditions were more prevalent among carriers compared with controls, with significantly increased risk (P < 0.05) for 57 conditions. Risk was increased for some conditions previously linked to CF carriers (e.g., pancreatitis, male infertility, bronchiectasis), as well as some conditions not previously reported (e.g., diabetes, constipation, cholelithiasis, short stature, failure to thrive). We compared our results with 23,557 subjects with CF, who were also matched with controls; as the relative odds of a given condition increased among subjects with CF, so did the corresponding relative odds for carriers (P < 0.001). Although individual-level risk remained low for most conditions, because there are more than 10 million carriers in the US, population-level morbidity attributable to the CF carrier state is likely substantial. Genetic testing may inform prevention, diagnosis, and treatment for a broad range of CF carrier-related conditions.

    更新日期:2020-01-22
  • Fin ray patterns at the fin-to-limb transition [Evolution]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Thomas A. Stewart, Justin B. Lemberg, Natalia K. Taft, Ihna Yoo, Edward B. Daeschler, Neil H. Shubin

    The fin-to-limb transition was marked by the origin of digits and the loss of dermal fin rays. Paleontological research into this transformation has focused on the evolution of the endoskeleton, with little attention paid to fin ray structure and function. To address this knowledge gap, we study the dermal rays of the pectoral fins of 3 key tetrapodomorph taxa—Sauripterus taylori (Rhizodontida), Eusthenopteron foordi (Tristichopteridae), and Tiktaalik roseae (Elpistostegalia)—using computed tomography. These data show several trends in the lineage leading to digited forms, including the consolidation of fin rays (e.g., reduced segmentation and branching), reduction of the fin web, and unexpectedly, the evolution of asymmetry between dorsal and ventral hemitrichia. In Eusthenopteron, dorsal rays cover the preaxial endoskeleton slightly more than ventral rays. In Tiktaalik, dorsal rays fully cover the third and fourth mesomeres, while ventral rays are restricted distal to these elements, suggesting the presence of ventralized musculature at the fin tip analogous to a fleshy “palm.” Asymmetry is also observed in cross-sectional areas of dorsal and ventral rays. Eusthenopteron dorsal rays are slightly larger than ventral rays; by contrast, Tiktaalik dorsal rays can be several times larger than ventral rays, and degree of asymmetry appears to be greater at larger sizes. Analysis of extant osteichthyans suggests that cross-sectional asymmetry in the dermal rays of paired fins is plesiomorphic to crown group osteichthyans. The evolution of dermal rays in crownward stem tetrapods reflects adaptation for a fin-supported elevated posture and resistance to substrate-based loading prior to the origin of digits.

    更新日期:2020-01-22
  • Evidence of tool use in a seabird [Evolution]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Annette L. Fayet, Erpur Snær Hansen, Dora Biro

    Documenting novel cases of tool use in wild animals can inform our understanding of the evolutionary drivers of the behavior’s emergence in the natural world. We describe a previously unknown tool-use behavior for wild birds, so far only documented in the wild in primates and elephants. We observed 2 Atlantic puffins at their breeding colonies, one in Wales and the other in Iceland (the latter captured on camera), spontaneously using a small wooden stick to scratch their bodies. The importance of these observations is 3-fold. First, while to date only a single form of body-care-related tool use has been recorded in wild birds (anting), our finding shows that the wild avian tool-use repertoire is wider than previously thought and extends to contexts other than food extraction. Second, we expand the taxonomic breadth of tool use to include another group of birds, seabirds, and a different suborder (Lari). Third, our independent observations span a distance of more than 1,700 km, suggesting that occasional tool use may be widespread in this group, and that seabirds’ physical cognition may have been underestimated.

    更新日期:2020-01-22
  • High productivity in hybrid-poplar plantations without isoprene emission to the atmosphere [Environmental Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Russell K. Monson, Barbro Winkler, Todd N. Rosenstiel, Katja Block, Juliane Merl-Pham, Steven H. Strauss, Kori Ault, Jason Maxfield, David J. P. Moore, Nicole A. Trahan, Amberly A. Neice, Ian Shiach, Greg A. Barron-Gafford, Peter Ibsen, Joel T. McCorkel, Jörg Bernhardt, Joerg-Peter Schnitzler

    Hybrid-poplar tree plantations provide a source for biofuel and biomass, but they also increase forest isoprene emissions. The consequences of increased isoprene emissions include higher rates of tropospheric ozone production, increases in the lifetime of methane, and increases in atmospheric aerosol production, all of which affect the global energy budget and/or lead to the degradation of air quality. Using RNA interference (RNAi) to suppress isoprene emission, we show that this trait, which is thought to be required for the tolerance of abiotic stress, is not required for high rates of photosynthesis and woody biomass production in the agroforest plantation environment, even in areas with high levels of climatic stress. Biomass production over 4 y in plantations in Arizona and Oregon was similar among genetic lines that emitted or did not emit significant amounts of isoprene. Lines that had substantially reduced isoprene emission rates also showed decreases in flavonol pigments, which reduce oxidative damage during extremes of abiotic stress, a pattern that would be expected to amplify metabolic dysfunction in the absence of isoprene production in stress-prone climate regimes. However, compensatory increases in the expression of other proteomic components, especially those associated with the production of protective compounds, such as carotenoids and terpenoids, and the fact that most biomass is produced prior to the hottest and driest part of the growing season explain the observed pattern of high biomass production with low isoprene emission. Our results show that it is possible to reduce the deleterious influences of isoprene on the atmosphere, while sustaining woody biomass production in temperate agroforest plantations.

    更新日期:2020-01-22
  • Channelization cascade in landscape evolution [Environmental Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Sara Bonetti, Milad Hooshyar, Carlo Camporeale, Amilcare Porporato

    The hierarchy of channel networks in landscapes displays features that are characteristic of nonequilibrium complex systems. Here we show that a sequence of increasingly complex ridge and valley networks is produced by a system of partial differential equations coupling landscape evolution dynamics with a specific catchment area equation. By means of a linear stability analysis we identify the critical conditions triggering channel formation and the emergence of characteristic valley spacing. The ensuing channelization cascade, described by a dimensionless number accounting for diffusive soil creep, runoff erosion, and tectonic uplift, is reminiscent of the subsequent instabilities in fluid turbulence, while the structure of the simulated patterns is indicative of a tendency to evolve toward optimal configurations, with anomalies similar to dislocation defects observed in pattern-forming systems. The choice of specific geomorphic transport laws and boundary conditions strongly influences the channelization cascade, underlying the nonlocal and nonlinear character of its dynamics.

    更新日期:2020-01-22
  • Infrared optical and thermal properties of microstructures in butterfly wings [Engineering]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Anirudh Krishna, Xiao Nie, Andrew D. Warren, Jorge E. Llorente-Bousquets, Adriana D. Briscoe, Jaeho Lee

    While surface microstructures of butterfly wings have been extensively studied for their structural coloration or optical properties within the visible spectrum, their properties in infrared wavelengths with potential ties to thermoregulation are relatively unknown. The midinfrared wavelengths of 7.5 to 14 µm are particularly important for radiative heat transfer in the ambient environment, because of the overlap with the atmospheric transmission window. For instance, a high midinfrared emissivity can facilitate surface cooling, whereas a low midinfrared emissivity can minimize heat loss to surroundings. Here we find that the midinfrared emissivity of butterfly wings from warmer climates such as Archaeoprepona demophoon (Oaxaca, Mexico) and Heliconius sara (Pichincha, Ecuador) is up to 2 times higher than that of butterfly wings from cooler climates such as Celastrina echo (Colorado) and Limenitis arthemis (Florida), using Fourier-transform infrared (FTIR) spectroscopy and infrared thermography. Our optical computations using a unit cell approach reproduce the spectroscopy data and explain how periodic microstructures play a critical role in the midinfrared. The emissivity spectrum governs the temperature of butterfly wings, and we demonstrate that C. echo wings heat up to 8 °C more than A. demophoon wings under the same sunlight in the clear sky of Irvine, CA. Furthermore, our thermal computations show that butterfly wings in their respective habitats can maintain a moderate temperature range through a balance of solar absorption and infrared emission. These findings suggest that the surface microstructures of butterfly wings potentially contribute to thermoregulation and provide an insight into butterflies' survival.

    更新日期:2020-01-22
  • Recovery of critically endangered Nassau grouper (Epinephelus striatus) in the Cayman Islands following targeted conservation actions [Ecology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Lynn Waterhouse, Scott A. Heppell, Christy V. Pattengill-Semmens, Croy McCoy, Phillippe Bush, Bradley C. Johnson, Brice X. Semmens

    Many large-bodied marine fishes that form spawning aggregations, such as the Nassau grouper (Epinephelus striatus), have suffered regional overfishing due to exploitation during spawning. In response, marine resource managers in many locations have established marine protected areas or seasonal closures to recover these overfished stocks. The challenge in assessing management effectiveness lies largely in the development of accurate estimates to track stock size through time. For the past 15 y, the Cayman Islands government has taken a series of management actions aimed at recovering collapsed stocks of Nassau grouper. Importantly, the government also partnered with academic and nonprofit organizations to establish a research and monitoring program (Grouper Moon) aimed at documenting the impacts of conservation action. Here, we develop an integrated population model of 2 Cayman Nassau grouper stocks based on both diver-collected mark–resight observations and video censuses. Using both data types across multiple years, we fit parameters for a state–space model for population growth. We show that over the last 15 y the Nassau grouper population on Little Cayman has more than tripled in response to conservation efforts. Census data from Cayman Brac, while more sparse, show a similar pattern. These findings demonstrate that spatial and seasonal closures aimed at rebuilding aggregation-based fisheries can foster conservation success.

    更新日期:2020-01-22
  • Scaling the risk landscape drives optimal life-history strategies and the evolution of grazing [Ecology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Uttam Bhat, Christopher P. Kempes, Justin D. Yeakel

    Consumers face numerous risks that can be minimized by incorporating different life-history strategies. How much and when a consumer adds to its energetic reserves or invests in reproduction are key behavioral and physiological adaptations that structure communities. Here we develop a theoretical framework that explicitly accounts for stochastic fluctuations of an individual consumer’s energetic reserves while foraging and reproducing on a landscape with resources that range from uniformly distributed to highly clustered. First, we show that the selection of alternative life histories depends on both the mean and variance of resource availability, where depleted and more stochastic environments promote investment in each reproductive event at the expense of future fitness as well as more investment per offspring. We then show that if resource variance scales with body size due to landscape clustering, consumers that forage for clustered foods are susceptible to strong Allee effects, increasing extinction risk. Finally, we show that the proposed relationship between resource distributions, consumer body size, and emergent demographic risk offers key ecological insights into the evolution of large-bodied grazing herbivores from small-bodied browsing ancestors.

    更新日期:2020-01-22
  • Land-use history impacts functional diversity across multiple trophic groups [Ecology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Gaëtane Le Provost, Isabelle Badenhausser, Yoann Le Bagousse-Pinguet, Yann Clough, Laura Henckel, Cyrille Violle, Vincent Bretagnolle, Marilyn Roncoroni, Peter Manning, Nicolas Gross

    Land-use change is a major driver of biodiversity loss worldwide. Although biodiversity often shows a delayed response to land-use change, previous studies have typically focused on a narrow range of current landscape factors and have largely ignored the role of land-use history in shaping plant and animal communities and their functional characteristics. Here, we used a unique database of 220,000 land-use records to investigate how 20-y of land-use changes have affected functional diversity across multiple trophic groups (primary producers, mutualists, herbivores, invertebrate predators, and vertebrate predators) in 75 grassland fields with a broad range of land-use histories. The effects of land-use history on multitrophic trait diversity were as strong as other drivers known to impact biodiversity, e.g., grassland management and current landscape composition. The diversity of animal mobility and resource-acquisition traits was lower in landscapes where much of the land had been historically converted from grassland to crop. In contrast, functional biodiversity was higher in landscapes containing old permanent grasslands, most likely because they offer a stable and high-quality habitat refuge for species with low mobility and specialized feeding niches. Our study shows that grassland-to-crop conversion has long-lasting impacts on the functional biodiversity of agricultural ecosystems. Accordingly, land-use legacy effects must be considered in conservation programs aiming to protect agricultural biodiversity. In particular, the retention of permanent grassland sanctuaries within intensive landscapes may offset ecological debts.

    更新日期:2020-01-22
  • Geographically divergent evolutionary and ecological legacies shape mammal biodiversity in the global tropics and subtropics [Earth, Atmospheric, and Planetary Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    John Rowan, Lydia Beaudrot, Janet Franklin, Kaye E. Reed, Irene E. Smail, Andrew Zamora, Jason M. Kamilar

    Studies of the factors governing global patterns of biodiversity are key to predicting community responses to ongoing and future abiotic and biotic changes. Although most research has focused on present-day climate, a growing body of evidence indicates that modern ecological communities may be significantly shaped by paleoclimatic change and past anthropogenic factors. However, the generality of this pattern is unknown, as global analyses are lacking. Here we quantify the phylogenetic and functional trait structure of 515 tropical and subtropical large mammal communities and predict their structure from past and present climatic and anthropogenic factors. We find that the effects of Quaternary paleoclimatic change are strongest in the Afrotropics, with communities in the Indomalayan realm showing mixed effects of modern climate and paleoclimate. Malagasy communities are poorly predicted by any single factor, likely due to the atypical history of the island compared with continental regions. Neotropical communities are mainly codetermined by modern climate and prehistoric and historical human impacts. Overall, our results indicate that the factors governing tropical and subtropical mammalian biodiversity are complex, with the importance of past and present factors varying based on the divergent histories of the world’s biogeographic realms and their native biotas. Consideration of the evolutionary and ecological legacies of both the recent and ancient past are key to understanding the forces shaping global patterns of present-day biodiversity and its response to ongoing and future abiotic and biotic changes in the 21st century.

    更新日期:2020-01-22
  • Fast oxidation of sulfur dioxide by hydrogen peroxide in deliquesced aerosol particles [Earth, Atmospheric, and Planetary Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Tengyu Liu, Simon L. Clegg, Jonathan P. D. Abbatt

    Atmospheric sulfate aerosols have important impacts on air quality, climate, and human and ecosystem health. However, current air-quality models generally underestimate the rate of conversion of sulfur dioxide (SO2) to sulfate during severe haze pollution events, indicating that our understanding of sulfate formation chemistry is incomplete. This may arise because the air-quality models rely upon kinetics studies of SO2 oxidation conducted in dilute aqueous solutions, and not at the high solute strengths of atmospheric aerosol particles. Here, we utilize an aerosol flow reactor to perform direct investigation on the kinetics of aqueous oxidation of dissolved SO2 by hydrogen peroxide (H2O2) using pH-buffered, submicrometer, deliquesced aerosol particles at relative humidity of 73 to 90%. We find that the high solute strength of the aerosol particles significantly enhances the sulfate formation rate for the H2O2 oxidation pathway compared to the dilute solution. By taking these effects into account, our results indicate that the oxidation of SO2 by H2O2 in the liquid water present in atmospheric aerosol particles can contribute to the missing sulfate source during severe haze episodes.

    更新日期:2020-01-22
  • Australasian impact crater buried under the Bolaven volcanic field, Southern Laos [Earth, Atmospheric, and Planetary Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Kerry Sieh, Jason Herrin, Brian Jicha, Dayana Schonwalder Angel, James D. P. Moore, Paramesh Banerjee, Weerachat Wiwegwin, Vanpheng Sihavong, Brad Singer, Tawachai Chualaowanich, Punya Charusiri

    The crater and proximal effects of the largest known young meteorite impact on Earth have eluded discovery for nearly a century. We present 4 lines of evidence that the 0.79-Ma impact crater of the Australasian tektites lies buried beneath lavas of a long-lived, 910-km3 volcanic field in Southern Laos: 1) Tektite geochemistry implies the presence of young, weathered basalts at the site at the time of the impact. 2) Geologic mapping and 40Ar-39Ar dates confirm that both pre- and postimpact basaltic lavas exist at the proposed impact site and that postimpact basalts wholly cover it. 3) A gravity anomaly there may also reflect the presence of a buried ∼17 × 13-km crater. 4) The nature of an outcrop of thick, crudely layered, bouldery sandstone and mudstone breccia 10–20 km from the center of the impact and fractured quartz grains within its boulder clasts support its being part of the proximal ejecta blanket.

    更新日期:2020-01-22
  • The role of saltwater and waves in continental shelf formation with seaward migrating clinoform [Earth, Atmospheric, and Planetary Sciences]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Toshiki Iwasaki, Gary Parker

    Continental shelves have generally been interpreted as drowned coastal plains associated with the allogenic effect of sea-level variation. Here, without disputing this mechanism we describe an alternative autogenic mechanism for subaqueous shelf formation, driven by the presence of dissolved salt in seawater and surface waves. We use a numerical model describing flow hydrodynamics, sediment transport, and morphodynamics in order to do this. More specifically, we focus on two major aspects: 1) the role of saltwater in the subaqueous construction of continental shelves and 2) the transformation of these shelves into seaward-migrating clinoforms under the condition of repeated pulses of water and sediment input and steady wave effects, but no allogenic forcing such as sea-level change. In the case for which the receiving basin contains fresh water of the same density as the sediment-laden river water, the hyperpycnal river water plunges to form a turbidity current that can run out to deep water. In the case for which the receiving basin contains sea water but the river contains sediment-laden fresh water, the hypopycnal river water forms a surface plume that deposits sediment proximally. This proximate proto-shelf can then grow to wave base, after which wave-supported turbidity currents can extend it seaward. The feature we refer to is synonymous with near-shore mud belts.

    更新日期:2020-01-22
  • Global shape of Toll activation is determined by wntD enhancer properties [Developmental Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Neta Rahimi, Shari Carmon, Inna Averbukh, Farzaneh Khajouei, Saurabh Sinha, Eyal D. Schejter, Naama Barkai, Ben-Zion Shilo

    Buffering variability in morphogen distribution is essential for reproducible patterning. A theoretically proposed class of mechanisms, termed “distal pinning,” achieves robustness by combining local sensing of morphogen levels with global modulation of gradient spread. Here, we demonstrate a critical role for morphogen sensing by a gene enhancer, which ultimately determines the final global distribution of the morphogen and enables reproducible patterning. Specifically, we show that, while the pattern of Toll activation in the early Drosophila embryo is robust to gene dosage of its locally produced regulator, WntD, it is sensitive to a single-nucleotide change in the wntD enhancer. Thus, enhancer properties of locally produced WntD directly impinge on the global morphogen profile.

    更新日期:2020-01-22
  • Designing cyclic competence-stimulating peptide (CSP) analogs with pan-group quorum-sensing inhibition activity in Streptococcus pneumoniae [Chemistry]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Yifang Yang, Jingjun Lin, Anthony Harrington, Gabriel Cornilescu, Gee W. Lau, Yftah Tal-Gan

    Streptococcus pneumoniae is an opportunistic human pathogen that utilizes the competence regulon, a quorum-sensing circuitry, to acquire antibiotic resistance genes and initiate its attack on the human host. Interception of the competence regulon can therefore be utilized to study S. pneumoniae cell−cell communication and behavioral changes, as well as attenuate S. pneumoniae infectivity. Herein we report the design and synthesis of cyclic dominant negative competence-stimulating peptide (dnCSP) analogs capable of intercepting the competence regulon in both S. pneumoniae specificity groups with activities at the low nanomolar range. Structural analysis of lead analogs provided important insights as to the molecular mechanism that drives CSP receptor binding and revealed that the pan-group cyclic CSPs exhibit a chimeric hydrophobic patch conformation that resembles the hydrophobic patches required for both ComD1 and ComD2 binding. Moreover, the lead cyclic dnCSP, CSP1-E1A-cyc(Dap6E10), was found to possess superior pharmacological properties, including improved resistance to enzymatic degradation, while remaining nontoxic. Lastly, CSP1-E1A-cyc(Dap6E10) was capable of attenuating mouse mortality during acute pneumonia caused by both group 1 and group 2 S. pneumoniae strains. This cyclic pan-group dnCSP is therefore a promising drug lead scaffold against S. pneumoniae infections that could be administered individually or utilized in combination therapy to augment the effects of current antimicrobial agents.

    更新日期:2020-01-22
  • A unified machine-learning protocol for asymmetric catalysis as a proof of concept demonstration using asymmetric hydrogenation [Chemistry]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Sukriti Singh, Monika Pareek, Avtar Changotra, Sayan Banerjee, Bangaru Bhaskararao, P. Balamurugan, Raghavan B. Sunoj

    Design of asymmetric catalysts generally involves time- and resource-intensive heuristic endeavors. In view of the steady increase in interest toward efficient catalytic asymmetric reactions and the rapid growth in the field of machine learning (ML) in recent years, we envisaged dovetailing these two important domains. We selected a set of quantum chemically derived molecular descriptors from five different asymmetric binaphthyl-derived catalyst families with the propensity to impact the enantioselectivity of asymmetric hydrogenation of alkenes and imines. The predictive power of the random forest (RF) built using the molecular parameters of a set of 368 substrate–catalyst combinations is found to be impressive, with a root-mean-square error (rmse) in the predicted enantiomeric excess (%ee) of about 8.4 ± 1.8 compared to the experimentally known values. The accuracy of RF is found to be superior to other ML methods such as convolutional neural network, decision tree, and eXtreme gradient boosting as well as stepwise linear regression. The proposed method is expected to provide a leap forward in the design of catalysts for asymmetric transformations.

    更新日期:2020-01-22
  • Highly efficient binary copper-iron catalyst for photoelectrochemical carbon dioxide reduction toward methane [Chemistry]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Baowen Zhou, Pengfei Ou, Nick Pant, Shaobo Cheng, Srinivas Vanka, Sheng Chu, Roksana Tonny Rashid, Gianluigi Botton, Jun Song, Zetian Mi

    A rational design of an electrocatalyst presents a promising avenue for solar fuels synthesis from carbon dioxide (CO2) fixation but is extremely challenging. Herein, we use density functional theory calculations to study an inexpensive binary copper−iron catalyst for photoelectrochemical CO2 reduction toward methane. The calculations of reaction energetics suggest that Cu and Fe in the binary system can work in synergy to significantly deform the linear configuration of CO2 and reduce the high energy barrier by stabilizing the reaction intermediates, thus spontaneously favoring CO2 activation and conversion for methane synthesis. Experimentally, the designed CuFe catalyst exhibits a high current density of −38.3 mA⋅cm−2 using industry-ready silicon photoelectrodes with an impressive methane Faradaic efficiency of up to 51%, leading to a distinct turnover frequency of 2,176 h−1 under air mass 1.5 global (AM 1.5G) one-sun illumination.

    更新日期:2020-01-22
  • An anticancer gold(III)-activated porphyrin scaffold that covalently modifies protein cysteine thiols [Chemistry]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Ka-Chung Tong, Chun-Nam Lok, Pui-Ki Wan, Di Hu, Yi Man Eva Fung, Xiao-Yong Chang, Song Huang, Haibo Jiang, Chi-Ming Che

    Cysteine thiols of many cancer-associated proteins are attractive targets of anticancer agents. Herein, we unequivocally demonstrate a distinct thiol-targeting property of gold(III) mesoporphyrin IX dimethyl ester (AuMesoIX) and its anticancer activities. While the binding of cysteine thiols with metal complexes usually occurs via M–S bond formation, AuMesoIX is unique in that the meso-carbon atom of the porphyrin ring is activated by the gold(III) ion to undergo nucleophilic aromatic substitution with thiols. AuMesoIX was shown to modify reactive cysteine residues and inhibit the activities of anticancer protein targets including thioredoxin, peroxiredoxin, and deubiquitinases. Treatment of cancer cells with AuMesoIX resulted in the formation of gold-bound sulfur-rich protein aggregates, oxidative stress-mediated cytotoxicity, and accumulation of ubiquitinated proteins. Importantly, AuMesoIX exhibited effective antitumor activity in mice. Our study has uncovered a gold(III)-induced ligand scaffold reactivity for thiol targeting that can be exploited for anticancer applications.

    更新日期:2020-01-22
  • The clock gene Bmal1 inhibits macrophage motility, phagocytosis, and impairs defense against pneumonia [Cell Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Gareth B. Kitchen, Peter S. Cunningham, Toryn M. Poolman, Mudassar Iqbal, Robert Maidstone, Matthew Baxter, James Bagnall, Nicola Begley, Ben Saer, Tracy Hussell, Laura C. Matthews, David H. Dockrell, Hannah J. Durrington, Julie E. Gibbs, John F. Blaikley, Andrew S. Loudon, David W. Ray

    The circadian clock regulates many aspects of immunity. Bacterial infections are affected by time of day, but the mechanisms involved remain undefined. Here we show that loss of the core clock protein BMAL1 in macrophages confers protection against pneumococcal pneumonia. Infected mice show both reduced weight loss and lower bacterial burden in circulating blood. In vivo studies of macrophage phagocytosis reveal increased bacterial ingestion following Bmal1 deletion, which was also seen in vitro. BMAL1−/− macrophages exhibited marked differences in actin cytoskeletal organization, a phosphoproteome enriched for cytoskeletal changes, with reduced phosphocofilin and increased active RhoA. Further analysis of the BMAL1−/− macrophages identified altered cell morphology and increased motility. Mechanistically, BMAL1 regulated a network of cell movement genes, 148 of which were within 100 kb of high-confidence BMAL1 binding sites. Links to RhoA function were identified, with 29 genes impacting RhoA expression or activation. RhoA inhibition restored the phagocytic phenotype to that seen in control macrophages. In summary, we identify a surprising gain of antibacterial function due to loss of BMAL1 in macrophages, associated with a RhoA-dependent cytoskeletal change, an increase in cell motility, and gain of phagocytic function.

    更新日期:2020-01-22
  • Quantitative microscopy reveals dynamics and fate of clustered IRE1{alpha} [Cell Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Vladislav Belyy, Ngoc-Han Tran, Peter Walter

    The endoplasmic reticulum (ER) membrane-resident stress sensor inositol-requiring enzyme 1 (IRE1) governs the most evolutionarily conserved branch of the unfolded protein response. Upon sensing an accumulation of unfolded proteins in the ER lumen, IRE1 activates its cytoplasmic kinase and ribonuclease domains to transduce the signal. IRE1 activity correlates with its assembly into large clusters, yet the biophysical characteristics of IRE1 clusters remain poorly characterized. We combined superresolution microscopy, single-particle tracking, fluorescence recovery, and photoconversion to examine IRE1 clustering quantitatively in living human and mouse cells. Our results revealed that: 1) In contrast to qualitative impressions gleaned from microscopic images, IRE1 clusters comprise only a small fraction (∼5%) of the total IRE1 in the cell; 2) IRE1 clusters have complex topologies that display features of higher-order organization; 3) IRE1 clusters contain a diffusionally constrained core, indicating that they are not phase-separated liquid condensates; 4) IRE1 molecules in clusters remain diffusionally accessible to the free pool of IRE1 molecules in the general ER network; 5) when IRE1 clusters disappear at later time points of ER stress as IRE1 signaling attenuates, their constituent molecules are released back into the ER network and not degraded; 6) IRE1 cluster assembly and disassembly are mechanistically distinct; and 7) IRE1 clusters’ mobility is nearly independent of cluster size. Taken together, these insights define the clusters as dynamic assemblies with unique properties. The analysis tools developed for this study will be widely applicable to investigations of clustering behaviors in other signaling proteins.

    更新日期:2020-01-22
  • Loss of TSC complex enhances gluconeogenesis via upregulation of Dlk1-Dio3 locus miRNAs [Cell Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Dritan Liko, Andrzej Rzepiela, Vanja Vukojevic, Mihaela Zavolan, Michael N. Hall

    Loss of the tumor suppressor tuberous sclerosis complex 1 (Tsc1) in the liver promotes gluconeogenesis and glucose intolerance. We asked whether this could be attributed to aberrant expression of small RNAs. We performed small-RNA sequencing on liver of Tsc1-knockout mice, and found that miRNAs of the delta-like homolog 1 (Dlk1)–deiodinase iodothyronine type III (Dio3) locus are up-regulated in an mTORC1-dependent manner. Sustained mTORC1 signaling during development prevented CpG methylation and silencing of the Dlk1-Dio3 locus, thereby increasing miRNA transcription. Deletion of miRNAs encoded by the Dlk1-Dio3 locus reduced gluconeogenesis, glucose intolerance, and fasting blood glucose levels. Thus, miRNAs contribute to the metabolic effects observed upon loss of TSC1 and hyperactivation of mTORC1 in the liver. Furthermore, we show that miRNA is a downstream effector of hyperactive mTORC1 signaling.

    更新日期:2020-01-22
  • A cell atlas of the adult Drosophila midgut [Cell Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Ruei-Jiun Hung, Yanhui Hu, Rory Kirchner, Yifang Liu, Chiwei Xu, Aram Comjean, Sudhir Gopal Tattikota, Fangge Li, Wei Song, Shannan Ho Sui, Norbert Perrimon

    Studies of the adult Drosophila midgut have led to many insights in our understanding of cell-type diversity, stem cell regeneration, tissue homeostasis, and cell fate decision. Advances in single-cell RNA sequencing provide opportunities to identify new cell types and molecular features. We used single-cell RNA sequencing to characterize the transcriptome of midgut epithelial cells and identified 22 distinct clusters representing intestinal stem cells, enteroblasts, enteroendocrine cells (EEs), and enterocytes. This unbiased approach recovered most of the known intestinal stem cells/enteroblast and EE markers, highlighting the high quality of the dataset, and led to insights on intestinal stem cell biology, cell type-specific organelle features, the roles of new transcription factors in progenitors and regional variation along the gut, 5 additional EE gut hormones, EE hormonal expression diversity, and paracrine function of EEs. To facilitate mining of this rich dataset, we provide a web-based resource for visualization of gene expression in single cells. Altogether, our study provides a comprehensive resource for addressing functions of genes in the midgut epithelium.

    更新日期:2020-01-22
  • A compartment size-dependent selective threshold limits mutation accumulation in hierarchical tissues [Biophysics and Computational Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Dániel Grajzel, Imre Derényi, Gergely J. Szöllősi

    Cancer is a genetic disease fueled by somatic evolution. Hierarchical tissue organization can slow somatic evolution by two qualitatively different mechanisms: by cell differentiation along the hierarchy “washing out” harmful mutations and by limiting the number of cell divisions required to maintain a tissue. Here we explore the effects of compartment size on somatic evolution in hierarchical tissues by considering cell number regulation that acts on cell division rates such that the number of cells in the tissue has the tendency to return to its desired homeostatic value. Introducing mutants with a proliferative advantage, we demonstrate the existence of a third fundamental mechanism by which hierarchically organized tissues are able to slow down somatic evolution. We show that tissue size regulation leads to the emergence of a threshold proliferative advantage, below which mutants cannot persist. We find that the most significant determinant of the threshold selective advantage is compartment size, with the threshold being higher the smaller the compartment. Our results demonstrate that, in sufficiently small compartments, even mutations that confer substantial proliferative advantage cannot persist, but are expelled from the tissue by differentiation along the hierarchy. The resulting selective barrier can significantly slow down somatic evolution and reduce the risk of cancer by limiting the accumulation of mutations that increase the proliferation of cells.

    更新日期:2020-01-22
  • Improved protein structure prediction using predicted interresidue orientations [Biophysics and Computational Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker

    The prediction of interresidue contacts and distances from coevolutionary data using deep learning has considerably advanced protein structure prediction. Here, we build on these advances by developing a deep residual network for predicting interresidue orientations, in addition to distances, and a Rosetta-constrained energy-minimization protocol for rapidly and accurately generating structure models guided by these restraints. In benchmark tests on 13th Community-Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP13)- and Continuous Automated Model Evaluation (CAMEO)-derived sets, the method outperforms all previously described structure-prediction methods. Although trained entirely on native proteins, the network consistently assigns higher probability to de novo-designed proteins, identifying the key fold-determining residues and providing an independent quantitative measure of the “ideality” of a protein structure. The method promises to be useful for a broad range of protein structure prediction and design problems.

    更新日期:2020-01-22
  • Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps [Biophysics and Computational Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Amir Bitran, William M. Jacobs, Xiadi Zhai, Eugene Shakhnovich

    Many large proteins suffer from slow or inefficient folding in vitro. It has long been known that this problem can be alleviated in vivo if proteins start folding cotranslationally. However, the molecular mechanisms underlying this improvement have not been well established. To address this question, we use an all-atom simulation-based algorithm to compute the folding properties of various large protein domains as a function of nascent chain length. We find that for certain proteins, there exists a narrow window of lengths that confers both thermodynamic stability and fast folding kinetics. Beyond these lengths, folding is drastically slowed by nonnative interactions involving C-terminal residues. Thus, cotranslational folding is predicted to be beneficial because it allows proteins to take advantage of this optimal window of lengths and thus avoid kinetic traps. Interestingly, many of these proteins’ sequences contain conserved rare codons that may slow down synthesis at this optimal window, suggesting that synthesis rates may be evolutionarily tuned to optimize folding. Using kinetic modeling, we show that under certain conditions, such a slowdown indeed improves cotranslational folding efficiency by giving these nascent chains more time to fold. In contrast, other proteins are predicted not to benefit from cotranslational folding due to a lack of significant nonnative interactions, and indeed these proteins’ sequences lack conserved C-terminal rare codons. Together, these results shed light on the factors that promote proper protein folding in the cell and how biomolecular self-assembly may be optimized evolutionarily.

    更新日期:2020-01-22
  • Structures of cofilin-induced structural changes reveal local and asymmetric perturbations of actin filaments [Biophysics and Computational Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Andrew R. Huehn, Jeffrey P. Bibeau, Anthony C. Schramm, Wenxiang Cao, Enrique M. De La Cruz, Charles V. Sindelar

    Members of the cofilin/ADF family of proteins sever actin filaments, increasing the number of filament ends available for polymerization or depolymerization. Cofilin binds actin filaments with positive cooperativity, forming clusters of contiguously bound cofilin along the filament lattice. Filament severing occurs preferentially at boundaries between bare and cofilin-decorated (cofilactin) segments and is biased at 1 side of a cluster. A molecular understanding of cooperative binding and filament severing has been impeded by a lack of structural data describing boundaries. Here, we apply methods for analyzing filament cryo-electron microscopy (cryo-EM) data at the single subunit level to directly investigate the structure of boundaries within partially decorated cofilactin filaments. Subnanometer resolution maps of isolated, bound cofilin molecules and an actin-cofilactin boundary indicate that cofilin-induced actin conformational changes are local and limited to subunits directly contacting bound cofilin. An isolated, bound cofilin compromises longitudinal filament contacts of 1 protofilament, consistent with a single cofilin having filament-severing activity. An individual, bound phosphomimetic (S3D) cofilin with weak severing activity adopts a unique binding mode that does not perturb actin structure. Cofilin clusters disrupt both protofilaments, consistent with a higher severing activity at boundaries compared to single cofilin. Comparison of these structures indicates that this disruption is substantially greater at pointed end sides of cofilactin clusters than at the barbed end. These structures, with the distribution of bound cofilin clusters, suggest that maximum binding cooperativity is achieved when 2 cofilins occupy adjacent sites. These results reveal the structural origins of cooperative cofilin binding and actin filament severing.

    更新日期:2020-01-22
  • Braiding topology and the energy landscape of chromosome organization proteins [Biophysics and Computational Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Dana Krepel, Aram Davtyan, Nicholas P. Schafer, Peter G. Wolynes, José N. Onuchic

    Assemblies of structural maintenance of chromosomes (SMC) proteins and kleisin subunits are essential to chromosome organization and segregation across all kingdoms of life. While structural data exist for parts of the SMC−kleisin complexes, complete structures of the entire complexes have yet to be determined, making mechanistic studies difficult. Using an integrative approach that combines crystallographic structural information about the globular subdomains, along with coevolutionary information and an energy landscape optimized force field (AWSEM), we predict atomic-scale structures for several tripartite SMC−kleisin complexes, including prokaryotic condensin, eukaryotic cohesin, and eukaryotic condensin. The molecular dynamics simulations of the SMC−kleisin protein complexes suggest that these complexes exist as a broad conformational ensemble that is made up of different topological isomers. The simulations suggest a critical role for the SMC coiled-coil regions, where the coils intertwine with various linking numbers. The twist and writhe of these braided coils are coupled with the motion of the SMC head domains, suggesting that the complexes may function as topological motors. Opening, closing, and translation along the DNA of the SMC−kleisin protein complexes would allow these motors to couple to the topology of DNA when DNA is entwined with the braided coils.

    更新日期:2020-01-22
  • Intermediate states of molecular self-assembly from liquid-cell electron microscopy [Biophysics and Computational Biology]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Huan Wang, Bo Li, Ye-Jin Kim, Oh-Hoon Kwon, Steve Granick

    Traditional single-molecule methods do not report whole-molecule kinetic conformations, and their adaptive shape changes during the process of self-assembly. Here, using graphene liquid-cell electron microscopy with electrons of low energy at low dose, we show that this approach resolves the time dependence of conformational adaptations of macromolecules for times up to minutes, the resolution determined by motion blurring, with DNA as the test case. Single-stranded DNA molecules are observed in real time as they hybridize near the solid surface to form double-stranded helices; we contrast molecules the same length but differing in base-pair microstructure (random, blocky, and palindromic hairpin) whose key difference is that random sequences possess only one stable final state, but the others offer metastable intermediate structures. Hybridization is observed to couple with enhanced translational mobility and torsion-induced rotation of the molecule. Prevalent transient loops are observed in error-correction processes. Transient melting and other failed encounters are observed in the competitive binding of multiple single-stranded molecules. Among the intermediate states reported here, some were predicted but not observed previously, and the high incidence of looping and enhanced mobility come as surprises. The error-producing mechanisms, failed encounters, and transient intermediate states would not be easily resolved by traditional single-molecule methods. The methods generalize to visualize motions and interactions of other organic macromolecules.

    更新日期:2020-01-22
  • Long-range interdomain communications in eIF5B regulate GTP hydrolysis and translation initiation [Biochemistry]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Bridget Y. Huang, Israel S. Fernández

    Translation initiation controls protein synthesis by regulating the delivery of the first aminoacyl-tRNA to messenger RNAs (mRNAs). In eukaryotes, initiation is sophisticated, requiring dozens of protein factors and 2 GTP-regulated steps. The GTPase eIF5B gates progression to elongation during the second GTP-regulated step. Using electron cryomicroscopy (cryo-EM), we imaged an in vitro initiation reaction which is set up with purified yeast components and designed to stall with eIF5B and a nonhydrolyzable GTP analog. A high-resolution reconstruction of a “dead-end” intermediate at 3.6 Å allowed us to visualize eIF5B in its ribosome-bound conformation. We identified a stretch of residues in eIF5B, located close to the γ-phosphate of GTP and centered around the universally conserved tyrosine 837 (Saccharomyces cerevisiae numbering), that contacts the catalytic histidine of eIF5B (H480). Site-directed mutagenesis confirmed the essential role that these residues play in regulating ribosome binding, GTP hydrolysis, and translation initiation both in vitro and in vivo. Our results illustrate how eIF5B transmits the presence of a properly delivered initiator aminoacyl-tRNA at the P site to the distant GTPase center through interdomain communications and underscore the importance of the multidomain architecture in translation factors to sense and communicate ribosomal states.

    更新日期:2020-01-22
  • A de novo peroxidase is also a promiscuous yet stereoselective carbene transferase [Biochemistry]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Richard Stenner, Jack W. Steventon, Annela Seddon, J. L. Ross Anderson

    By constructing an in vivo-assembled, catalytically proficient peroxidase, C45, we have recently demonstrated the catalytic potential of simple, de novo-designed heme proteins. Here, we show that C45’s enzymatic activity extends to the efficient and stereoselective intermolecular transfer of carbenes to olefins, heterocycles, aldehydes, and amines. Not only is this a report of carbene transferase activity in a completely de novo protein, but also of enzyme-catalyzed ring expansion of aromatic heterocycles via carbene transfer by any enzyme.

    更新日期:2020-01-22
  • Activation by substoichiometric inhibition [Biochemistry]
    PNAS (IF 9.580) Pub Date : 2020-01-21
    Melisa Merdanovic, Steven G. Burston, Anna Laura Schmitz, Steffen Köcher, Stefan Knapp, Tim Clausen, Markus Kaiser, Robert Huber, Michael Ehrmann

    Startling reports described the paradoxical triggering of the human mitogen-activated protein kinase pathway when a small-molecule inhibitor specifically inactivates the BRAF V600E protein kinase but not wt-BRAF. We performed a conceptual analysis of the general phenomenon “activation by inhibition” using bacterial and human HtrA proteases as models. Our data suggest a clear explanation that is based on the classic biochemical principles of allostery and cooperativity. Although substoichiometric occupancy of inhibitor binding sites results in partial inhibition, this effect is overrun by a concomitant activation of unliganded binding sites. Therefore, when an inhibitor of a cooperative enzyme does not reach saturating levels, a common scenario during drug administration, it may cause the contrary of the desired effect. The implications for drug development are discussed.

    更新日期:2020-01-22
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