• PNAS Front Matter Portal
  • Science Sessions: The PNAS Podcast Program

PNAS Plus Significance Statements

Intrusion and extrusion of water in hydrophobic nanopores

Antonio Tinti, Alberto Giacomello, Yaroslav Grosu, and Carlo Massimo Casciola

Molecular springs, constituted by nanoporous materials immersed in a nonwetting liquid, are compact, economical, and efficient means of storing energy, owing to their enormous surface area. Surface energy is accumulated during liquid intrusion inside the pores and released by decreasing liquid pressure and thus triggering confined cavitation. State-of-the-art atomistic simulations shed light on the intrusion and extrusion of water in hydrophobic nanopores, revealing conspicuous deviations from macroscopic theories, which include accelerated cavitation, increased intrusion pressure, and reversible intrusion and extrusion processes. Understanding these nanoscale phenomena is the key to a better design of molecular springs as it allows relating the characteristics of the materials to the overall properties of the devices, e.g., their operational pressure and efficiency. (See pp. E10266–E10273.)

Parallel magnetic field suppresses dissipation in superconducting nanostrips

Yong-Lei Wang, Andreas Glatza, Gregory J. Kimmel, Igor S. Aranson, Laxman R. Thoutam, Zhi-Li Xiao, Golibjon R. Berdiyorov, Fran?ois M. Peeters, George W. Crabtree, and Wai-Kwong Kwok

Absolute zero resistance of superconducting materials is difficult to achieve in practice due to the motion of microscopic Abrikosov vortices, especially when external currents are applied. Even a partial resistance reduction via vortex immobilization by microscopic material imperfections is the holy grail of superconductivity research. It is commonly believed that the dissipation increases with applied magnetic field since the number of vortices increases as well. Through the example of molybdenum–germanium superconducting nanostrips, we show that resistive losses due to vortex motion can actually be decreased by applying an increasing applied magnetic field parallel to the current. This surprising recovery of superconductivity is achieved through “vortex crowding”: The increased number of vortices impedes their mutual motion, resulting in straight, untwisted vortices. (See pp. E10274–E10280.)

Closed-loop control of targeted ultrasound drug delivery across the blood–brain/tumor barriers in a rat glioma model

Tao Sun, Yongzhi Zhang, Chanikarn Power, Phillip M. Alexander, Jonathan T. Sutton, Muna Aryal, Natalia Vykhodtseva, Eric L. Miller, and Nathan J. McDannold

Focused ultrasound is currently the only method of reversible blood–brain barrier disruption for targeted drug delivery without incision or radiation. A significant challenge for its clinical translation is a lack of reliable real-time treatment control. Here a closed-loop, real-time control paradigm is shown capable of sustaining stable microbubble oscillations at a preset level while minimizing microbubble behavior that may result in vascular damage. Tested at clinically relevant frequency in healthy and tumor-bearing rats, our approach enables targeted delivery of predefined drug concentrations within a therapeutically effective range in both normal tissue and glioma, while maintaining a safe exposure level. It can be readily implemented clinically for delivering chemotherapeutics or other agents and potentially applied to other cavitation-enhanced ultrasound therapies. (See pp. E10281–E10290.)

Social preferences of future physicians

Jing Li, William H. Dow, and Shachar Kariv

This paper advances scientific understanding of social preference—a topic of longstanding cross-disciplinary interest—by studying the preferences of future physicians. In making treatment decisions, physicians make fundamental tradeoffs between their own (financial) self-interest, patient benefit, and stewardship of social resources. These tradeoffs affect patient health, adoption of new scientific medical technologies, and the equity and efficiency of our health care system. Understanding physicians' decisions about these tradeoffs requires understanding the social preferences that are behind them. Our main finding that future physicians are substantially less altruistic and more efficiency focused than the average American challenges notions of physician altruism, the fundamental feature of medical professionalism, and has potential implications for policy in a host of health care areas. (See pp. E10291–E10300.)

Nutritional and greenhouse gas impacts of removing animals from US agriculture

Robin R. White and Mary Beth Hall

US agriculture was modeled to determine impacts of removing farmed animals on food supply adequacy and greenhouse gas (GHG) emissions. The modeled system without animals increased total food production (23%), altered foods available for domestic consumption, and decreased agricultural US GHGs (28%), but only reduced total US GHG by 2.6 percentage units. Compared with systems with animals, diets formulated for the US population in the plants-only systems had greater excess of dietary energy and resulted in a greater number of deficiencies in essential nutrients. The results give insights into why decisions on modifications to agricultural systems must be made based on a description of direct and indirect effects of change and on a dietary, rather than an individual nutrient, basis. (See pp. E10301–E10308.)

Early Neolithic wine of Georgia in the South Caucasus

Patrick McGovern, Mindia Jalabadze, Stephen Batiuk, Michael P. Callahan, Karen E. Smith, Gretchen R. Hall, Eliso Kvavadze, David Maghradze, Nana Rusishvili, Laurent Bouby, Osvaldo Failla, Gabriele Cola, Luigi Mariani, Elisabetta Boaretto, Roberto Bacilieri, Patrice This, Nathan Wales, and David Lordkipanidze

The earliest biomolecular archaeological and archaeobotanical evidence for grape wine and viniculture from the Near East, ca. 6,000–5,800 BC during the early Neolithic Period, was obtained by applying state-of-the-art archaeological, archaeobotanical, climatic, and chemical methods to newly excavated materials from two sites in Georgia in the South Caucasus. Wine is central to civilization as we know it in the West. As a medicine, social lubricant, mind-altering substance, and highly valued commodity, wine became the focus of religious cults, pharmacopoeias, cuisines, economies, and society in the ancient Near East. This wine culture subsequently spread around the globe. Viniculture illustrates human ingenuity in developing horticultural and winemaking techniques, such as domestication, propagation, selection of desirable traits, wine presses, suitable containers and closures, and so on. (See pp. E10309–E10318.)

Specific inhibition of GPCR-independent G protein signaling by a rationally engineered protein

Anthony Leyme, Arthur Marivin, Marcin Maziarz, Vincent DiGiacomo, Maria P. Papakonstantinou, Prachi P. Patel, Juan B. Blanco-Canosa, Isha A. Walawalkar, Gonzalo Rodriguez-Davila, Isabel Dominguez, and Mikel Garcia-Marcos

Dysregulation of signaling via heterotrimeric G proteins leads to pathogenesis. Thus, developing an efficient armamentarium to study G protein regulation is crucial for understanding the molecular basis of disease. The classical view of G protein activation as an exclusive function of G protein-coupled receptors has been challenged by the discovery of nonreceptor G protein activators. Dysregulation of a family of such nonreceptor activators has been linked to human disorders like cancer or birth defects, but the underlying mechanisms remain poorly understood due to the lack of experimental tools. Here, we use protein engineering to rationally design a genetically encoded inhibitor of these G protein activators and demonstrate its usefulness to block aberrant signaling in cancer cells and abrogate developmental malformations in animal embryos. (See pp. E10319–E10328.)

Proteome-wide modulation of degradation dynamics in response to growth arrest

Tian Zhang, Clara Wolfe, Andrew Pierle, Kevin A. Welle, Jennifer R. Hryhorenko, and Sina Ghaemmaghami

In dividing cells, long-lived proteins are continuously diluted by being partitioned into newly formed daughter cells. Conversely, short-lived proteins are cleared from a cell primarily by proteolysis rather than cell division. Thus, when a cell stops dividing, there is a natural tendency for long-lived proteins to accumulate relative to short-lived proteins. This effect is disruptive to cells and leads to the accumulation of aged and damaged proteins over time. Here, we analyzed the degradation of thousands of proteins in dividing and nondividing (quiescent) skin cells. Our results demonstrate that quiescent cells avoid the accumulation of long-lived proteins by enhancing their degradation through pathways involving the lysosome. This mechanism may be important for promotion of protein homeostasis in aged organisms. (See pp. E10329–E10338.)

Insights into functions of the H channel of cytochrome c oxidase from atomistic molecular dynamics simulations

Vivek Sharma, Pablo G. Jambrina, Markus Kaukonen, Edina Rosta, and Peter R. Rich

Cytochrome oxidase is a widespread respiratory enzyme that conserves energy released when oxygen is reduced by pumping protons across the membrane in which it is located. Here, we use atomistic simulations of the whole bovine enzyme to investigate properties of the H channel, a structure that has been proposed to provide the pathway for pumped protons in mammalian forms of the enzyme. These studies show that although parts of the structure could function in this manner, a gap persists. This gap could be bridged only if a buried histidine becomes protonated. Based on these simulations, we propose that the H channel acts as a dielectric well, modulating effects of buried charge changes. (See pp. E10339–E10348.)

RNA stem structure governs coupling of dicing and gene silencing in RNA interference

Hye Ran Koh, Amirhossein Ghanbariniaki, and Sua Myong

RNAi is an RNA-induced gene-silencing pathway that is shared among various organisms. Better understanding of RNAi is urgently needed to improve our knowledge of RNA-mediated gene regulation and to advance the field of functional genomics and its application to gene therapy. We counted with high precision the number of transcripts in each cell’s nucleus and cytoplasm as a function of silencing time to investigate the role of small RNA secondary structures such as loop length and stem mismatches. We screened various structural features of small RNAs and discovered a distinct role of each structural element that contributes to gene-silencing kinetics. We provide a helpful guideline for designing small RNAs for more efficient gene silencing. (See pp. E10349–E10358.)

Analysis of high-resolution 3D intrachromosomal interactions aided by Bayesian network modeling

Xizhe Zhang, Sergio Branciamore, Grigoriy Gogoshin, Andrei S. Rodin, and Arthur D. Riggs

We report here that a recently developed Bayesian network (BN) methodology and software platform yield useful information when applied to the analysis of intrachromosomal interaction datasets combined with Encyclopedia of DNA Elements publicly available datasets for the B-lymphocyte cell line GM12878. Of 106 variables analyzed, interaction strength between DNA segments was found to be directly dependent on only four types of variables: distance, Rad21 or SMC3 (cohesin components), transcription at transcription start sites, and the number of CCCTC-binding factor (CTCF)–cohesin complexes between interacting DNA segments. The importance of directionally oriented ctcf motifs was confirmed not only for loops but also for enhancer–promoter interactions. Purely data-driven BN analyses also identified known critical, lineage-determining transcription factors (TFs) as well as some potentially new dependencies between TFs. (See pp. E10359–E10368.)

Recovery of taste organs and sensory function after severe loss from Hedgehog/Smoothened inhibition with cancer drug sonidegib

Archana Kumari, Alexandre N. Ermilov, Marina Grachtchouk, Andrzej A. Dlugosz, Benjamin L. Allen, Robert M. Bradley, and Charlotte M. Mistretta

Hedgehog pathway-inhibitor drugs effectively treat basal cell carcinoma, a common skin cancer. However, many patients taking such drugs report severe taste disturbances that impair their quality of life. To understand the biology behind these adverse effects, we studied the consequences of Hedgehog pathway inhibition on taste organs and neural sensation in mice. Taste bud progenitor-cell proliferation and differentiation were altered, resulting in taste bud loss. Nerve responses to lingual taste stimuli were also eliminated, while responses to touch and cold stimuli remained. After stopping Hedgehog pathway inhibition, taste buds and sensory responses recovered. This study advances our understanding of Hedgehog signaling in taste homeostasis and the reported taste recovery after clinical treatments with Hedgehog pathway-inhibiting drugs. (See pp. E10369–E10378.)

In vivo measurements of interindividual differences in DNA glycosylases and APE1 activities

Isaac A. Chaim, Zachary D. Nagel, Jennifer J. Jordan, Patrizia Mazzucato, Le P. Ngo, and Leona D. Samson

The DNA in each cell is damaged thousands of times daily. Consequently, a battery of DNA repair pathways exist that allow repair of this damage. Failure to repair can lead to devastating diseases, including cancer and neurodegeneration. Each individual’s DNA repair capacity (DRC) is inherently different. Being able to measure an individual’s DRC could contribute to a personalized approach to prevent and treat disease. Here we present powerful tools for measuring in vivo base excision repair capacity for five distinct DNA lesions. We use these methods to predict the cellular responses to a variety of DNA damaging agents, and to monitor differences in DRC in primary human lymphocytes. Additionally, we unveil previously unknown transcriptional mutagenesis induced by DNA lesions. (See pp. E10379–E10388.)

Dual function for Tango1 in secretion of bulky cargo and in ER-Golgi morphology

L. D. Ríos-Barrera, S. Sigurbj?rnsdóttir, M. Baer, and M. Leptin

Exporting bulky molecules poses challenges for cells, since the membrane vesicles that transport normal-sized molecules may not be sufficiently large. The protein Tango1 allows transport vesicles to grow much larger to accommodate bulky cargo. It has been puzzling why many smaller cargos also fail to be transported when Tango1 is absent. We show that this is because bulky cargos “clog up” the transport system, resulting in a general traffic jam. Once the blocking, large cargo is removed, the jam resulting from missing Tango1 is resolved, and other cellular stress signals also subside. However, structural defects in the transport system remain, showing that these are due to a direct requirement for Tango1, independent of its function in transport as such. (See pp. E10389–E10398.)

Human resistin protects against endotoxic shock by blocking LPS–TLR4 interaction

Jessica C. Jang, Jiang Li, Luca Gambini, Hashini M. Batugedara, Sandeep Sati, Mitchell A. Lazar, Li Fan, Maurizio Pellecchia, and Meera G. Nair

Gram-negative bacterial sepsis is a life-threatening disease that is exacerbated by an uncontrolled immune response to the endotoxin lipopolysaccharide (LPS). Human resistin is a highly expressed cytokine in sepsis, where it is hypothesized to exacerbate inflammation. We identify an unexpected protective role for resistin in endotoxic shock. We use human resistin-expressing transgenic mice and human immune cell assays to show that resistin prevents LPS-induced mortality by blocking LPS binding to its receptor Toll-like receptor 4 (TLR4) and by promoting anti-inflammatory signaling. Helminth infection-induced resistin and treatment with recombinant resistin or resistin N-terminal peptides also inhibited LPS function. These studies report a protective function for resistin and identify the therapeutic potential of resistin-mediated anti-inflammatory pathways or resistin-based reagents in sepsis. (See pp. E10399–E10408.)

T cell receptor sequencing of early-stage breast cancer tumors identifies altered clonal structure of the T cell repertoire

John F. Beausang, Amanda J. Wheeler, Natalie H. Chan, Violet R. Hanft, Frederick M. Dirbas, Stefanie S. Jeffrey, and Stephen R. Quake

The recent advances in cancer immunotherapy motivated us to investigate the clonal structure of the T cell receptor repertoire in breast tumors, normal breast, and blood in the same individuals. We found quantitatively distinct clonal structures in all three tissues, which enabled us to predict whether tissue is normal or tumor solely by comparing the repertoire of the tissue with blood. T cell receptor sequences shared between patients’ tumors are rare and, in general, do not appear to be specific to the cancer. (See pp. E10409–E10417.)

Resident macrophages of pancreatic islets have a seminal role in the initiation of autoimmune diabetes of NOD mice

Javier A. Carrero, Derrick P. McCarthy, Stephen T. Ferris, Xiaoxiao Wan, Hao Hu, Bernd H. Zinselmeyer, Anthony N. Vomund, and Emil R. Unanue

Our studies indicate that the resident macrophages of the pancreatic islets of Langerhans have a seminal role in the initiation and progression of autoimmune diabetes in NOD mice. In this study, islet macrophages were depleted by administration of a monoclonal antibody to the CSF-1 receptor. Macrophage depletion, either at the start of the autoimmune process or when diabetogenesis is active, leads to a significant reduction in diabetes incidence. Depletion of the islet macrophages reduces the entrance of T cells into islets and results in the absence of antigen presentation. Concordantly, a regulatory pathway develops that controls diabetes progression. We conclude that treatments that target the islet macrophages may have important clinical relevance for the control of autoimmune type 1 diabetes. (See pp. E10418–E10427.)

Role of estrogen receptor beta in neural differentiation of mouse embryonic stem cells

Mukesh K. Varshney, José Inzunza, Diana Lupu, Vaidheeswaran Ganapathy, Per Antonson, Jo?lle Rüegg, Ivan Nalvarte, and Jan-?ke Gustafsson

Controlling the proliferation and proper fate acquisition of pluripotent stem cells is a major challenge in regenerative therapies today. Our study reveals that the estrogen receptor beta (ERβ) is an important factor in maintaining the neuroepithelial and midbrain stem cell pools by repressing proliferation and early nonneuronal fate acquisition. We report on the factors that underlie these effects of ERβ. Further, we report that ERβ facilitates midbrain dopaminergic fate and function. The data presented in this study suggest that ERβ is a factor to be considered in designing regenerative therapies for example neurodegenerative diseases such as Parkinson’s disease. (See pp. E10428–E10437.)

Structural basis for antibody recognition of the NANP repeats in Plasmodium falciparum circumsporozoite protein

David Oyen, Jonathan L. Torres, Ulrike Wille-Reece, Christian F. Ockenhouse, Daniel Emerling, Jacob Glanville, Wayne Volkmuth, Yevel Flores-Garcia, Fidel Zavala, Andrew B. Ward, C. Richter King, and Ian A. Wilson

The Plasmodium falciparum circumsporozoite protein (CSP) has been studied for decades as a potential immunogen, but little structural information is available on how antibodies recognize the immunodominant NANP repeats within CSP. The most advanced vaccine candidate is RTS,S, which includes multiple NANP repeats. Here, we analyzed two functional antibodies from an RTS,S trial and determined the number of repeats that interact with the antibody Fab fragments using isothermal titration calorimetry and X-ray crystallography. Using negative-stain electron microscopy, we also established how the antibody binds to the NANP repeat region in a recombinant CSP construct. The structural features outlined here provide a rationale for structure-based immunogen design to improve upon the efficacy of the current RTS,S vaccine. (See pp. E10438–E10445.)

Multiple Legionella pneumophila effector virulence phenotypes revealed through high-throughput analysis of targeted mutant libraries

Stephanie R. Shames, Luying Liu, James C. Havey, Whitman B. Schofield, Andrew L. Goodman, and Craig R. Roy

The contribution of individual effectors to Legionella pneumophila virulence has not been systematically examined. This study employed a parallel high-throughput transposon insertion sequencing technique called INSeq to probe the L. pneumophila effector repertoire and identified multiple effectors that contribute to virulence in several host organisms, including an animal model of Legionnaires’ disease. Importantly, this study demonstrates that effector proteins contribute to host virulence both positively and negatively by controlling intracellular replication and influencing host immune responses, which demonstrates that the subtle alterations in the effector repertoire of a single L. pneumophila strain can greatly impact host pathogenicity. (See pp. E10446–E10454.)

Microbial pathway for anaerobic 5′-methylthioadenosine metabolism coupled to ethylene formation

Justin A. North, Anthony R. Miller, John A. Wildenthal, Sarah J. Young, and F. Robert Tabita

Sulfur is an essential element required by all organisms. Therefore, salvage of wasteful, sulfur-containing cellular by-products can be critical. Methionine salvage pathways for organisms living in oxic environments are well established. However, if and by what mechanisms organisms living in anoxic environments can regenerate methionine from such by-products remain largely unknown. This work identifies a strictly anaerobic methionine salvage pathway, the key genes for which appear to be widespread among obligate and facultatively anaerobic bacteria. Strikingly, this pathway also results in the formation of ethylene gas, a key plant hormone and signaling molecule. Anoxic environments routinely accumulate biologically produced ethylene at significant levels, but the organisms and mechanisms responsible have been slow to emerge. This study provides one possible route. (See pp. E10455–E10464.)

Sparsity enables estimation of both subcortical and cortical activity from MEG and EEG

Pavitra Krishnaswamy, Gabriel Obregon-Henao, Jyrki Ahveninen, Sheraz Khan, Behtash Babadi, Juan Eugenio Iglesias, Matti S. H?m?l?inen, and Patrick L. Purdon

Subcortical structures play a critical role in brain functions such as sensory perception, memory, emotion, and consciousness. There are limited options for assessing neuronal dynamics within subcortical structures in humans. Magnetoencephalography and electroencephalography can measure electromagnetic fields generated by subcortical activity. But localizing the sources of these fields is very difficult, because the fields generated by subcortical structures are small and cannot be distinguished from distributed cortical activity. We show that cortical and subcortical fields can be distinguished if the cortical sources are sparse. We then describe an algorithm that uses sparsity in a hierarchical fashion to jointly localize cortical and subcortical sources. Our work offers alternative perspectives and tools for assessing subcortical brain dynamics in humans. (See pp. E10465–E10474.)

Intact hemisphere and corpus callosum compensate for visuomotor functions after early visual cortex damage

Alessia Celeghin, Matteo Diano, Beatrice de Gelder, Lawrence Weiskrantz, Carlo A. Marzi, and Marco Tamietto

The brain is resilient to injury and the possibility to promote recovery rests with our ability to understand the nature of postlesional plasticity. After damage to the visual cortex some patients with clinical blindness still react to unseen stimuli with appropriate motor responses, a phenomenon known as “blindsight.” Our findings in one patient with early primary visual cortex damage suggest that this nonconscious visuomotor ability depends partly on the compensatory activity of the intact hemisphere, which can be dynamically recruited through the corpus callosum. Functional interactions between the damaged and intact hemisphere are subserved by changes in the underlying anatomical connections. These observations provide a framework for future investigations of functional recovery after brain damage and on mechanisms that mediate nonconscious abilities. (See pp. E10475–E10483.)

Gap junctional coupling between retinal amacrine and ganglion cells underlies coherent activity integral to global object perception

Kaushambi Roy, Sandeep Kumar, and Stewart A. Bloomfield

Neuron ensembles in the brain visual system often show correlated responses, but the sensory information encoded by this activity remains unclear. Here, we show that widely separated ganglion cells in the mouse retina show correlated activity when presented with a large, contiguous object, but not when the object is disjointed. We show that these long-range correlations are produced by electrical coupling via gap junctions made with polyaxonal amacrine cells, which can span distances greater than a millimeter. Blockade or ablation of these gap junctions eliminates correlations between distant ganglion cells and, moreover, diminishes an animal’s ability to discriminate large, solid objects from disjointed ones. Our findings indicate that long-range correlated activity in the retina encodes visual information critical for global object perception. (See pp. E10484–E10493.)

Dopamine reward prediction error signal codes the temporal evaluation of a perceptual decision report

Stefania Sarno, Victor de Lafuente, Ranulfo Romo, and Néstor Parga

How do animals learn to take correct actions based on uncertain observations? Although dopamine neurons can guide learning in conditioning experiments, their role in decision-making tasks is poorly understood. How can they code reward prediction errors and simultaneously exhibit decision-making processes and beliefs about the state of the environment? Using modeling work and analysis of data recorded from monkeys detecting weak stimuli delivered at uncertain times, we propose some answers to these questions. Specifically, we explain how the certainty about the presence of a stimulus is communicated to midbrain dopamine neurons through transient cortical events and why that certainty becomes visible in their response to a relevant task event. (See pp. E10494–E10503.)

Online Impact

  • 864971864 2018-01-22
  • 258841863 2018-01-22
  • 957295862 2018-01-22
  • 553518861 2018-01-22
  • 983792860 2018-01-22
  • 539694859 2018-01-22
  • 956115858 2018-01-22
  • 730379857 2018-01-22
  • 346624856 2018-01-22
  • 201609855 2018-01-22
  • 72549854 2018-01-21
  • 795928853 2018-01-21
  • 752345852 2018-01-21
  • 566508851 2018-01-21
  • 615722850 2018-01-21
  • 689612849 2018-01-21
  • 846903848 2018-01-21
  • 674896847 2018-01-21
  • 11197846 2018-01-21
  • 986896845 2018-01-21