Increased risk of dementia in the aftermath of the 2011 Great East Japan Earthquake and Tsunami
Hiroyuki Hikichi, Jun Aida, Katsunori Kondo, Toru Tsuboya, Yusuke Matsuyama, S. V. Subramanian, and Ichiro Kawachi
Recovery after major disaster poses potential risks of dementia for the elderly population. However, no previous studies have examined exposure to natural disaster and changes in risk factors as predictors of deterioration in cognitive function. We prospectively examined whether housing damage and loss of relatives or friends were associated with cognitive decline in the aftermath of the 2011 Great East Japan Earthquake and Tsunami. In this study, which included 3,566 survivors who are 65 y old or older, the severity of housing damage was significantly associated with cognitive decline after controlling changes of covariates and risk factors during the follow-up period. The cognitive decline should be listed as a health risk of older survivors in the aftermath of natural disasters. (See pp. E6911–E6918.)
Polymeric nanofiber coating with tunable combinatorial antibiotic delivery prevents biofilm-associated infection in vivo
Alyssa G. Ashbaugh, Xuesong Jiang, Jesse Zheng, Andrew S. Tsai, Woo-Shin Kim, John M. Thompson, Robert J. Miller, Jonathan H. Shahbazian, Yu Wang, Carly A. Dillen, Alvaro A. Ordonez, Yong S. Chang, Sanjay K. Jain, Lynne C. Jones, Robert S. Sterling, Hai-Quan Mao, and Lloyd S. Miller
Biofilm infections are a major complication associated with implantable medical devices and prostheses, which are exceedingly difficult to treat. To date, there has been no effective clinical solution that combines antibacterial efficiency with excellent osseointegration. Here, a nanofiber-based conformal coating capable of controlled and independent local delivery of two or more combinatorial antibiotics was developed to provide optimal antimicrobial activity for the prevention of biofilm-associated infections. In a preclinical animal model of orthopedic-implant infection, this technology demonstrated complete bacterial clearance from the implant and surrounding bone/joint tissue while promoting osseointegration. This tunable nanofiber composite coating could be highly effective in preventing medical device infections in patients. (See pp. E6919–E6928.)
Chromosome-refolding model of mating-type switching in yeast
Barış Avşaroğlu, Gabriel Bronk, Kevin Li, James E. Haber, and Jane Kondev
Although many studies have shown that chromosomes are folded into cells in a nonrandom fashion, the functional significance of this spatial organization remains poorly understood. Combining theory and fluorescence microscopy, we demonstrate that the folded state of yeast chromosome III changes in response to a DNA double-strand break at the MAT locus, in agreement with previous studies. Importantly, we show that the change in the folded state of the chromosome after the break quantitatively accounts for the dynamics of homology search during DNA repair. Our study provides an example of a cell changing the folded state of one of its chromosomes in response to an internal chemical cue (DNA break), thereby affecting its function (DNA repair). (See pp. E6929–E6938.)
Probing the free energy landscapes of ALS disease mutants of SOD1 by NMR spectroscopy
Ashok Sekhar, Jessica A. O. Rumfeldt, Helen R. Broom, Colleen M. Doyle, Ryan E. Sobering, Elizabeth M. Meiering, and Lewis E. Kay
A series of amyotrophic lateral sclerosis disease-causing mutants of superoxide dismutase have been studied using NMR experiments probing sparsely populated, transiently formed protein conformers. Focusing on the most immature enzyme form, which is monomeric, metal-free, and lacking a stabilizing disulfide bond, we show that the ground states for the wild-type and disease mutant proteins are similar, with an intact eight-stranded β-barrel structure resembling the structure of the mature enzyme. In contrast, conformationally excited states can be affected by mutation, both in terms of the number and types of structures accessible to the mutant. These excited states can play roles in both maturation and aggregation processes and, in the latter case, can provide a variety of possible pathways for aberrant interactions. (See pp. E6939–E6945.)
Global mapping of antibody recognition of the hepatitis C virus E2 glycoprotein: Implications for vaccine design
Brian G. Pierce, Zhen-Yong Keck, Patrick Lau, Catherine Fauvelle, Ragul Gowthaman, Thomas F. Baumert, Thomas R. Fuerst, Roy A. Mariuzza, and Steven K. H. Foung
Hepatitis C virus is a major public health concern, infecting approximately 3% of the world’s population, with no vaccine currently available. To enable rational vaccine design for this highly diverse and dynamic virus, we performed alanine scanning of nearly all positions of the E2 envelope protein, which is the primary target of the antibody response, using a panel of 16 human monoclonal antibodies that target a broad range of epitopes. This approach provided an unprecedented global view of the determinants of E2 stability, residue connectivity, and neutralizing antibody recognition. These insights and mapping data provide a framework to engineer E2 to modulate antibody recognition and optimize its capacity to induce broadly neutralizing antibodies in the context of a vaccine. (See pp. E6946–E6954.)
Acid activation mechanism of the influenza A M2 proton channel
Ruibin Liang, Jessica M. J. Swanson, Jesper J. Madsen, Mei Hong, William F. DeGrado, and Gregory A. Voth
The influenza A M2 channel (AM2) transports protons into the influenza virus upon acid activation. It is an important pharmacological target as well as a prototypical case to study proton conduction through biological channels. The current work provides the most complete computational characterization to date of the physical basis for the acid activation mechanism of the AM2 proton channel. Our results show that lowering the pH value gradually opens the Trp41 gate and decreases the deprotonation barrier of the His37 tetrad, leading to channel activation. Our result also demonstrates that the C-terminal amphipathic helix does not significantly change the proton conduction mechanism in the AM2 transmembrane domain. (See pp. E6955–E6964.)
FASN regulates cellular response to genotoxic treatments by increasing PARP-1 expression and DNA repair activity via NF-κB and SP1
Xi Wu, Zizheng Dong, Chao J. Wang, Lincoln James Barlow, Valerie Fako, Moises A. Serrano, Yue Zou, Jing-Yuan Liu, and Jian-Ting Zhang
The findings of this study have revealed a potential molecular pathway for how fatty acid synthase (FASN) overexpression causes drug and radiation resistance and contributes to poor clinical prognosis of cancer diseases. FASN is the sole cytosolic enzyme responsible for de novo lipid synthesis, required for cancer cell survival but not for most normal nonadipose tissues. The finding that FASN regulates DNA repair by regulating specificity protein 1 and NF-κB in cancer cell responses to anticancer treatments will have a profound impact on designing future treatment strategies. It will also help establish FASN as a target for therapeutic discovery to sensitize drug and radiation resistance. (See pp. E6965–E6973.)
Differential growth triggers mechanical feedback that elevates Hippo signaling
Yuanwang Pan, Idse Heemskerk, Consuelo Ibar, Boris I. Shraiman, and Kenneth D. Irvine
To form organs of correct size and proportion, growth must be tightly controlled. Previous studies have characterized how biochemical signals influence organ growth; this report describes an interrelationship between tissue mechanics and organ growth. We show that differential growth leads to accumulation of mechanical stress within tissues and describe both theoretically and experimentally how this mechanical stress can result in reduced tension within faster-growing cells. We show how this reduced tension can increase the activity of the Hippo signaling pathway, which decreases growth rates, and show that this mechanism influences patterns of cell proliferation in vivo. Our results support and extend a theoretical model, termed “mechanical feedback,” that described the relationship between growth rates and tissue mechanics. (See pp. E6974–E6983.)
The heterocyst regulatory protein HetP and its homologs modulate heterocyst commitment in Anabaena sp. strain PCC 7120
Patrick Videau, Orion S. Rivers, Kathryn Hurd, Blake Ushijima, Reid T. Oshiro, Rachel J. Ende, Samantha M. O’Hanlon, and Loralyn M. Cozy
Terminal commitment of differentiating cells is fundamental to multicellular life but remains the least characterized phase of development. Using Anabaena, a multicellular cyanobacterium that irreversibly commits 10% of cells to specialized nitrogen-fixing heterocysts, we report the identification of four genes that regulate commitment timing and efficacy in a cyanobacterium, including two that delay commitment: a unique finding across developmental model systems. Through protein–protein interactions, cell type-specific and -nonspecific expression patterns, and epistatic relationships, we present evidence that these four genes function together in a hierarchy to control correct timing of the commitment decision. This work illustrates the importance of Anabaena as a model system for studying the genetic underpinnings controlling the process of cellular differentiation. (See pp. E6984–E6992.)
Endocytosis of Wingless via a dynamin-independent pathway is necessary for signaling in Drosophila wing discs
Anupama Hemalatha, Chaitra Prabhakara, and Satyajit Mayor
Regulated interaction of secreted morphogens with their receptors is necessary for patterning of tissues during development. The morphogen Wingless (Wg) is apically secreted at the dorso-ventral boundary of Drosophila wing imaginal discs, and its receptor, DFrizzled2 (DFz2), is localized basally in recipient cells. Here, we show that Wg is endocytosed by a dynamin-independent endocytic pathway, the CLIC/GEEC pathway, at the apical surface of the epithelium, whereas DFz2 is internalized basally via the conventional clathrin-dependent mechanism. Subsequently, Wg requires the acidic milieu of the merged endosome derived from the fusion of these two pathways to interact with DFz2 for subsequent signaling. This study provides evidence for a mechanism wherein cells leverage multiple endocytic pathways to coordinate signaling during patterning. (See pp. E6993–E7002.)
Evolutionary consequences of behavioral diversity
Alexander J. Stewart, Todd L. Parsons, and Joshua B. Plotkin
Access to a diversity of behavioral choices makes social dynamics rich and difficult to analyze. Individuals are rarely constrained to a binary choice between “cooperate” or “defect,” as many theoretical treatments assume. Here we use game theory to ask what social behaviors will emerge in populations as the number of behavioral choices grows. We show that simple strategies, where players do not vary their behavior much at all, can nonetheless be successful, and that access to a broader range of behavioral choices can cause a population to evolve toward lower levels of cooperation. Finally, we show that access to greater choice in rock–paper–scissors games inevitably leads to behavioral diversity, with players using strategies that make use of all possible choices. (See pp. E7003–E7009.)
Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation
Zhenzhen Yang, Yeting Zhang, Eric K. Wafula, Loren A. Honaas, Paula E. Ralph, Sam Jones, Christopher R. Clarke, Siming Liu, Chun Su, Huiting Zhang, Naomi S. Altman, Stephan C. Schuster, Michael P. Timko, John I. Yoder, James H. Westwood, and Claude W. dePamphilis
Horizontal gene transfer (HGT) is the nonsexual transfer and genomic integration of genetic materials between organisms. In eukaryotes, HGT appears rare, but parasitic plants may be exceptions, as haustorial feeding connections between parasites and their hosts provide intimate cellular contacts that could facilitate DNA transfer between unrelated species. Through analysis of genome-scale data, we identified >50 expressed and likely functional HGT events in one family of parasitic plants. HGT reflected parasite preferences for different host plants and was much more frequent in plants with increasing parasitic dependency. HGT was strongly biased toward expression and protein types likely to contribute to haustorial function, suggesting that functional HGT of host genes may play an important role in adaptive evolution of parasites. (See pp. E7010–E7019.)
Stable Caenorhabditis elegans chromatin domains separate broadly expressed and developmentally regulated genes
Kenneth J. Evans, Ni Huang, Przemyslaw Stempor, Michael A. Chesney, Thomas A. Down, and Julie Ahringer
Genomes are organized into domains of different structure and activity, yet our understanding of their formation and regulation is poor. We show that Caenorhabditis elegans chromatin domain organization in early embryos and third-larval stage animals is remarkably similar despite the two developmental stages containing very different cell types. Chromatin domains separate genes into those with stable versus developmentally regulated expression. Analyses of chromatin domain structure suggest that transcription regulation and germ-line chromatin regulation play roles in separating chromatin domains. Our results further our understanding of genome domain organization. (See pp. E7020–E7029.)
RNA-binding profiles of Drosophila CPEB proteins Orb and Orb2
Barbara Krystyna Stepien, Cornelia Oppitz, Daniel Gerlach, Ugur Dag, Maria Novatchkova, Sebastian Krüttner, Alexander Stark, and Krystyna Keleman
Local protein synthesis is a highly used mechanism to create functional asymmetries within cells. It underlies diverse biological processes, including the development and function of the nervous and reproductive systems. Cytoplasmic polyadenylation element-binding (CPEB) proteins regulate local translation in early development, synaptic plasticity, and long-term memory. However, their binding specificity is not fully resolved. We used a transcriptome-wide approach and established that Drosophila representatives of two CPEB subfamilies, Orb and Orb2, regulate largely overlapping target mRNAs by binding to CPE-like sequences in their 3′ UTRs, potentially with a shift in specificity for motif variants. Moreover, our data suggest that a subset of these mRNAs is translationally regulated and involved in long-term memory. (See pp. E7030–E7038.)
Optimal immunization cocktails can promote induction of broadly neutralizing Abs against highly mutable pathogens
J. Scott Shaffer, Penny L. Moore, Mehran Kardar, and Arup K. Chakraborty
The design of vaccination strategies that generate potent Abs directed against diverse strains of highly mutable pathogens, like HIV and malaria, will significantly impact global health. Such Abs are called broadly neutralizing Abs (bnAbs). Abs are produced by a Darwinian evolutionary process called affinity maturation. Induction of bnAbs will likely require vaccination with diverse mutant antigens. How affinity maturation occurs in the presence of multiple diverse antigens is not well-understood, thus hindering rational design of immunization strategies. We study this issue using computer simulations and statistical mechanical theory. Our results provide guides for the rational design of optimal vaccination strategies, and they reveal mechanistic principles at a crossroad of immunology and evolutionary biology. (See pp. E7039–E7048.)
Neurotensin stimulates sortilin and mTOR in human microglia inhibitable by methoxyluteolin, a potential therapeutic target for autism
Arti B. Patel, Irene Tsilioni, Susan E. Leeman, and Theoharis C. Theoharides
Human microglia, the resident immune cells of the brain, express only the neurotensin (NT) receptor-3/sortilin. NT significantly increases microglia synthesis and release of proinflammatory cytokine IL-1β and chemokine (C-X-C motif) ligand 8 (CXCL8), chemokine (C-C motif) ligand 2 (CCL2), and CCL5 via NTR3/sortilin. A soluble form of this receptor is secreted from stimulated microglia and is increased in the serum of children with autism spectrum disorders (ASD). These responses and the NT-stimulated increases in microglia numbers are mediated via mammalian target of rapamycin (mTOR) activation and are inhibitable by the natural flavonoids luteolin and methoxyluteolin. (See pp. E7049–E7058.)
Serum stimulation of CCR7 chemotaxis due to coagulation factor XIIa-dependent production of high-molecular-weight kininogen domain 5
Manish P. Ponda and Jan L. Breslow
We describe a mechanism of regulating immune cell chemotaxis. We identified in serum a peptide derived from domain 5 of high-molecular-weight kininogen produced by coagulation factor XIIa cleavage that accelerates C-C chemokine receptor 7-mediated chemotaxis. Thus, we present a paradigm in which a humoral peptide functions as a chemotactic cofactor that links inflammation to immunity. (See pp. E7059–E7068.)
Primate-specific miR-515 family members inhibit key genes in human trophoblast differentiation and are upregulated in preeclampsia
Ming Zhang, Sribalasubashini Muralimanoharan, Alison C. Wortman, and Carole R. Mendelson
Preeclampsia, a hypertensive disorder of pregnancy and leading cause of maternal and neonatal morbidity and mortality, is associated with defective placental implantation and vascularization. Herein, we characterized regulation and function of miR-515-5p, which belongs to the primate- and placenta-specific chromosome 19 miRNA cluster, one of the largest miRNA clusters in humans. We observed that miR-515-5p was markedly downregulated during human syncytiotrophoblast differentiation and upregulated in placentas from preeclamptic women. miR-515-5p overexpression inhibited syncytiotrophoblast differentiation. Important miR-515-5p targets were identified, including hCYP19A1/aromatase, transcription factor glial cells missing 1 and WNT receptor, frizzled 5, which share critical roles in trophoblast differentiation. Thus, miR-515-5p may serve a key role in human trophoblast differentiation and provide a marker and therapeutic target for preeclampsia. (See pp. E7069–E7076.)
Daptomycin inhibits cell envelope synthesis by interfering with fluid membrane microdomains
Anna Müller, Michaela Wenzel, Henrik Strahl, Fabian Grein, Terrens N. V. Saaki, Bastian Kohl, Tjalling Siersma, Julia E. Bandow, Hans-Georg Sahl, Tanja Schneider, and Leendert W. Hamoen
To date, simple membrane pore formation resulting in cytoplasmic leakage is the prevailing model for how membrane-active antibiotics kill bacteria and also is one of the main explanations for the activity of the membrane-binding antibiotic daptomycin. However, such models, typically derived from model membrane studies, often depict membranes as homogenous lipid bilayers. They do not take into account the complex architecture of biological membranes, with their many different membrane proteins, or the presence of microdomains with different fluidity properties. Here we report that daptomycin perturbs fluid microdomains in bacterial cell membranes, thereby interfering with membrane-bound cell wall and lipid synthesis processes. Our results add a different perspective as to how membrane-active antibiotics can kill bacteria. (See pp. E7077–E7086.)
FoxO6 affects Plxna4-mediated neuronal migration during mouse cortical development
Ricardo H. Paap, Saskia Oosterbroek, Cindy M. R. J. Wagemans, Lars von Oerthel, Raymond D. Schellevis, Annemarie J. A. Vastenhouw-van der Linden, Marian J. A. Groot Koerkamp, Marco F. M. Hoekman, and Marten P. Smidt
The molecular basis of radial migration of cortical neurons is a well-studied process showing prominent roles for axon guidance, cell adhesion, cell polarity, and cytoskeleton remodeling. Remarkably, knowledge about transcriptional control of such processes is scarce. In this study, we show that the forkhead transcription factor FoxO6 influences Plexin A4 (Plxna4) expression, a key component of the Semaphorin signaling pathway, known for its role in axonal guidance and cortical migration. FoxO6 knockdown animals show a hampered migration of embryonic day 14.5-born neurons, which can be rescued by recombinant Plxna4 expression constructs. Altogether, our data provide insights into the molecular mechanisms whereby transcriptional programs influence cortical development. (See pp. E7087–E7096.)
Neonatal isolation augments social dominance by altering actin dynamics in the medial prefrontal cortex
Hirobumi Tada, Tomoyuki Miyazaki, Kiwamu Takemoto, Kenkichi Takase, Susumu Jitsuki, Waki Nakajima, Mayu Koide, Naoko Yamamoto, Kasane Komiya, Kumiko Suyama, Akane Sano, Akiko Taguchi, and Takuya Takahashi
Social separation early in life can lead to the development of impaired interpersonal relationships and profound social disorders. However, the underlying cellular and molecular mechanisms involved are largely unknown. In a rat model of neonatal isolation, we examined social dominance in juveniles. We further investigated the relationship between actin dynamics and glutamate synaptic AMPA receptor delivery in spines of the medial prefrontal cortex (mPFC) of isolated animals. Here, we report that neonatal isolation alters spines in the mPFC by reducing actin dynamics, leading to the decrease of synaptic AMPA receptor delivery and altered social behavior later in life. Our study provides molecular and cellular mechanisms underlying the influence of social separation early in life on later social behaviors. (See pp. E7097–E7105.)
Identifying the elusive link between amino acid sequence and charge selectivity in pentameric ligand-gated ion channels
Gisela D. Cymes and Claudio Grosman
The cation-versus-anion selectivity of pentameric ligand-gated ion channels cannot always be predicted on the basis of their amino acid sequences alone. Indeed, the relationship between amino acid sequence and function contains subtle elements that have eluded prior investigation. Here, we found that ion–ion interactions between the passing ions and ionized side chains in the first turn of the M2 α-helices dominate the permeation free-energy landscape, but we also found that the mere presence of an ionized residue in the first turn of M2 does not ensure that its charge is “felt” by permeating ions. Instead, there seems to be a requirement for a proper conformation for a charged side chain to exert its effect on selectivity. (See pp. E7106–E7115.)
PDE1C deficiency antagonizes pathological cardiac remodeling and dysfunction
Walter E. Knight, Si Chen, Yishuai Zhang, Masayoshi Oikawa, Meiping Wu, Qian Zhou, Clint L. Miller, Yujun Cai, Deanne M. Mickelsen, Christine Moravec, Eric M. Small, Junichi Abe, and Chen Yan
Heart failure is the leading global cause of death; therefore developing a greater understanding of disease etiology and identifying novel therapeutic targets is critical. Here, we describe the role of the cyclic nucleotide-degrading protein phosphodiesterase 1C (PDE1C) in the context of pathological cardiac remodeling. In cardiac myocytes, we found that PDE1C regulates both cyclic AMP- and cyclic GMP-mediated signaling pathways under different conditions. In both isolated cells and mice we found that inhibition of PDE1C could potentiate protective signaling and prevent the development of many aspects of heart failure, potentially by signaling through multiple cell types. PDE1 inhibition therefore may represent a viable therapeutic strategy for treatment of heart failure. (See pp. E7116–E7125.)
Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis
Polly Yingshan Hsu, Lorenzo Calviello, Hsin-Yen Larry Wu, Fay-Wei Li, Carl J. Rothfels, Uwe Ohler, and Philip N. Benfey
Translation is the process by which ribosomes decode information in RNA to produce proteins. The resulting proteins constitute cellular structures and regulate diverse functions in all organisms. Translation also affects mRNA stability. As the final step of the central dogma, translation can alter protein production more rapidly than transcription in a changing environment. However, a robust experimental method to define the landscape of the translatome has not been established in many organisms. We developed an advanced experimental approach and used it to discover proteins missed in the annotation of the Arabidopsis genome. This study confirmed computationally predicted noncanonical translation events and uncovered unannotated small proteins that likely have important functions in plants. (See pp. E7126–E7135.)