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Proceedings of the National Academy of Sciences
Journal Prestige (SJR): 6.092
Citation Impact (citeScore): 9
Number of Followers: 1052  
 
  Full-text available via subscription Subscription journal
ISSN (Print) 0027-8424 - ISSN (Online) 1091-6490
Published by PNAS Homepage  [1 journal]
  • Thiol-based chemical probes exhibit antiviral activity against SARS-CoV-2
           via allosteric disulfide disruption in the spike glycoprotein
           [Microbiology]

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      Authors: Yunlong Shi; Ari Zeida, Caitlin E. Edwards, Michael L. Mallory, Santiago Sastre, Matias R. Machado, Raymond J. Pickles, Ling Fu, Keke Liu, Jing Yang, Ralph S. Baric, Richard C. Boucher, Rafael Radi, Kate S. Carroll
      Abstract: The development of small-molecules targeting different components of SARS-CoV-2 is a key strategy to complement antibody-based treatments and vaccination campaigns in managing the COVID-19 pandemic. Here, we show that two thiol-based chemical probes that act as reducing agents, P2119 and P2165, inhibit infection by human coronaviruses, including SARS-CoV-2, and decrease...
      Keywords: Microbiology, Coronavirus (COVID-19)
      PubDate: 2022-01-24T12:01:57-08:00
      DOI: 10.1073/pnas.2120419119
      Issue No: Vol. 119, No. 6 (2022)
       
  • Impact of ADAR-induced editing of minor viral RNA populations on
           replication and transmission of SARS-CoV-2 [Microbiology]

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      Authors: Johan Ringlander; Joshua Fingal, Hanna Kann, Kasthuri Prakash, Gustaf Rydell, Maria Andersson, Anna Martner, Magnus Lindh, Peter Horal, Kristoffer Hellstrand, Michael Kann
      Abstract: Adenosine deaminases acting on RNA (ADAR) are RNA-editing enzymes that may restrict viral infection. We have utilized deep sequencing to determine adenosine to guanine (A→G) mutations, signifying ADAR activity, in clinical samples retrieved from 93 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)–infected patients in the early phase of the COVID-19...
      Keywords: Microbiology, Coronavirus (COVID-19)
      PubDate: 2022-01-21T12:00:37-08:00
      DOI: 10.1073/pnas.2112663119
      Issue No: Vol. 119, No. 6 (2022)
       
  • One model for the learning of language [Psychological and Cognitive
           Sciences]

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      Authors: Yuan Yang; Steven T. Piantadosi
      Abstract: A major goal of linguistics and cognitive science is to understand what class of learning systems can acquire natural language. Until recently, the computational requirements of language have been used to argue that learning is impossible without a highly constrained hypothesis space. Here, we describe a learning system that is...
      Keywords: Psychological and Cognitive Sciences
      PubDate: 2022-01-24T12:02:00-08:00
      DOI: 10.1073/pnas.2021865119
      Issue No: Vol. 119, No. 5 (2022)
       
  • Carbon emissions reductions from Indonesia’s moratorium on forest
           concessions are cost-effective yet contribute little to Paris pledges
           [Sustainability Science]

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      Authors: Ben Groom; Charles Palmer, Lorenzo Sileci
      Abstract: International initiatives for reducing carbon emissions from deforestation and forest degradation (REDD+) could make critical, cost-effective contributions to tropical countries’ nationally determined contributions (NDCs). Norway, a key donor of such initiatives, had a REDD+ partnership with Indonesia, offering results-based payments in exchange for emissions reductions calculated against a historical baseline....
      Keywords: Sustainability Science
      PubDate: 2022-01-24T12:02:00-08:00
      DOI: 10.1073/pnas.2102613119
      Issue No: Vol. 119, No. 5 (2022)
       
  • Identification of genetic risk loci and prioritization of genes and
           pathways for myasthenia gravis: a genome-wide association study [Genetics]
           

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      Authors: Ruth Chia; Sara Saez–Atienzar, Natalie Murphy, Adriano Chio, Cornelis Blauwendraat, International Myasthenia Gravis Genomics Consortium, Ricardo H. Roda, Pentti J. Tienari, Henry J. Kaminski, Roberta Ricciardi, Melania Guida, Anna De Rosa, Loredana Petrucci, Amelia Evoli, Carlo Provenzano, Daniel B. Drachman, Bryan J. Traynor
      Abstract: Myasthenia gravis is a chronic autoimmune disease characterized by autoantibody-mediated interference of signal transmission across the neuromuscular junction. We performed a genome-wide association study (GWAS) involving 1,873 patients diagnosed with acetylcholine receptor antibody-positive myasthenia gravis and 36,370 healthy individuals to identify disease-associated genetic risk loci. Replication of the discovered loci...
      Keywords: Genetics
      PubDate: 2022-01-24T12:02:00-08:00
      DOI: 10.1073/pnas.2108672119
      Issue No: Vol. 119, No. 5 (2022)
       
  • EchidnaCSI: Engaging the public in research and conservation of the
           short-beaked echidna [Sustainability Science]

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      Authors: Tahlia Perry; Alan Stenhouse, Isabella Wilson, Imma Perfetto, Michael W. McKelvey, Michelle Coulson, Rachel A. Ankeny, Peggy D. Rismiller, Frank Grutzner
      Abstract: The short-beaked echidna is an iconic Australian animal and the most-widespread native mammal, inhabiting diverse environments. The cryptic nature of echidnas has limited research into their ecology in most areas; however, from the well-researched and endangered Kangaroo Island echidna population, we understand that the threats include habitat loss, roads, and...
      Keywords: Environmental Sciences, Sustainability Science
      PubDate: 2022-01-24T12:02:00-08:00
      DOI: 10.1073/pnas.2108826119
      Issue No: Vol. 119, No. 5 (2022)
       
  • Characterizing cell interactions at scale with made-to-order droplet
           ensembles (MODEs) [Engineering]

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      Authors: Justin L. Madrigal; Nathan G. Schoepp, Linfeng Xu, Codian S. Powell, Cyrille L. Delley, Christian A. Siltanen, Jay Danao, Maithreyan Srinivasan, Russell H. Cole, Adam R. Abate
      Abstract: Cell–cell interactions are important to numerous biological systems, including tissue microenvironments, the immune system, and cancer. However, current methods for studying cell combinations and interactions are limited in scalability, allowing just hundreds to thousands of multicell assays per experiment; this limited throughput makes it difficult to characterize interactions at biologically...
      Keywords: Engineering, Immunology and Inflammation
      PubDate: 2022-01-24T12:02:00-08:00
      DOI: 10.1073/pnas.2110867119
      Issue No: Vol. 119, No. 5 (2022)
       
  • Multitarget nociceptor sensitization by a promiscuous peptide from the
           venom of the King Baboon spider [Pharmacology]

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      Authors: Rocio K. Finol-Urdaneta; Rebekah Ziegman, Zoltan Dekan, Jeffrey R. McArthur, Stewart Heitmann, Karen Luna-Ramirez, Han-Shen Tae, Alexander Mueller, Hana Starobova, Yanni K.-Y. Chin, Joshua S. Wingerd, Eivind A. B. Undheim, Ben Cristofori-Armstrong, Adam P. Hill, Volker Herzig, Glenn F. King, Irina Vetter, Lachlan D. Rash, David J. Adams, Paul F. Alewood
      Abstract: The King Baboon spider, Pelinobius muticus, is a burrowing African tarantula. Its impressive size and appealing coloration are tempered by reports describing severe localized pain, swelling, itchiness, and muscle cramping after accidental envenomation. Hyperalgesia is the most prominent symptom after bites from P. muticus, but the molecular basis by which...
      Keywords: Pharmacology
      PubDate: 2022-01-24T12:02:00-08:00
      DOI: 10.1073/pnas.2110932119
      Issue No: Vol. 119, No. 5 (2022)
       
  • Molecular electronics sensors on a scalable semiconductor chip: A platform
           for single-molecule measurement of binding kinetics and enzyme activity
           [Applied Biological Sciences]

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      Authors: Carl W. Fuller; Pius S. Padayatti, Hadi Abderrahim, Lisa Adamiak, Nolan Alagar, Nagaraj Ananthapadmanabhan, Jihye Baek, Sarat Chinni, Chulmin Choi, Kevin J. Delaney, Rich Dubielzig, Julie Frkanec, Chris Garcia, Calvin Gardner, Daniel Gebhardt, Tim Geiser, Zachariah Gutierrez, Drew A. Hall, Andrew P. Hodges, Guangyuan Hou, Sonal Jain, Teresa Jones, Raymond Lobaton, Zsolt Majzik, Allen Marte, Prateek Mohan, Paul Mola II, Paul Mudondo, James Mullinix, Thuan Nguyen, Frederick Ollinger, Sarah Orr, Yuxuan Ouyang, Paul Pan, Namseok Park, David Porras, Keshav Prabhu, Cassandra Reese, Travers Ruel, Trevor Sauerbrey, Jaymie R. Sawyer, Prem Sinha, Jacky Tu, A. G. Venkatesh, Sushmitha VijayKumar, Le Zheng, Sungho Jin, James M. Tour, George M. Church, Paul W. Mola, Barry Merriman
      Abstract: For nearly 50 years, the vision of using single molecules in circuits has been seen as providing the ultimate miniaturization of electronic chips. An advanced example of such a molecular electronics chip is presented here, with the important distinction that the molecular circuit elements play the role of general-purpose single-molecule...
      Keywords: Applied Biological Sciences, Coronavirus Related
      PubDate: 2022-01-24T12:02:00-08:00
      DOI: 10.1073/pnas.2112812119
      Issue No: Vol. 119, No. 5 (2022)
       
  • Direct observation of reversible liquid-liquid transition in a trehalose
           aqueous solution [Chemistry]

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      Authors: Yoshiharu Suzuki
      Abstract: Water forms two glassy waters, low-density and high-density amorphs, which undergo a reversible polyamorphic transition with the change in pressure. The two glassy waters transform into the different liquids, low-density liquid (LDL) and high-density liquid (HDL), at high temperatures. It is predicted that the two liquid waters also undergo a...
      Keywords: Chemistry
      PubDate: 2022-01-24T12:02:00-08:00
      DOI: 10.1073/pnas.2113411119
      Issue No: Vol. 119, No. 5 (2022)
       
  • Convergent evolution of a blood-red nectar pigment in
           vertebrate-pollinated flowers [Plant Biology]

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      Authors: Rahul Roy; Nickolas Moreno, Stephen A. Brockman, Adam Kostanecki, Amod Zambre, Catherine Holl, Erik M. Solhaug, Anzu Minami, Emilie C. Snell-Rood, Marshall Hampton, Mark A. Bee, Ylenia Chiari, Adrian D. Hegeman, Clay J. Carter
      Abstract: Nearly 90% of flowering plants depend on animals for reproduction. One of the main rewards plants offer to pollinators for visitation is nectar. Nesocodon mauritianus (Campanulaceae) produces a blood-red nectar that has been proposed to serve as a visual attractant for pollinator visitation. Here, we show that the nectar’s red...
      Keywords: Plant Biology
      PubDate: 2022-01-24T12:02:00-08:00
      DOI: 10.1073/pnas.2114420119
      Issue No: Vol. 119, No. 5 (2022)
       
  • No sustained increase in zooarchaeological evidence for carnivory after
           the appearance of Homo erectus [Anthropology]

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      Authors: W. Andrew Barr; Briana Pobiner, John Rowan, Andrew Du, J. Tyler Faith
      Abstract: The appearance of Homo erectus shortly after 2.0 Ma is widely considered a turning point in human dietary evolution, with increased consumption of animal tissues driving the evolution of larger brain and body size and a reorganization of the gut. An increase in the size and number of zooarchaeological assemblages...
      Keywords: Anthropology
      PubDate: 2022-01-24T12:02:00-08:00
      DOI: 10.1073/pnas.2115540119
      Issue No: Vol. 119, No. 5 (2022)
       
  • The impact of a poverty reduction intervention on infant brain activity
           [Psychological and Cognitive Sciences]

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      Authors: Sonya V. Troller-Renfree; Molly A. Costanzo, Greg J. Duncan, Katherine Magnuson, Lisa A. Gennetian, Hirokazu Yoshikawa, Sarah Halpern-Meekin, Nathan A. Fox, Kimberly G. Noble
      Abstract: Early childhood poverty is a risk factor for lower school achievement, reduced earnings, and poorer health, and has been associated with differences in brain structure and function. Whether poverty causes differences in neurodevelopment, or is merely associated with factors that cause such differences, remains unclear. Here, we report estimates of...
      Keywords: Psychological and Cognitive Sciences
      PubDate: 2022-01-24T12:02:00-08:00
      DOI: 10.1073/pnas.2115649119
      Issue No: Vol. 119, No. 5 (2022)
       
  • Quantifying net carbon fixation by Tibetan alpine ecosystems should
           consider multiple anthropogenic activities [Biological Sciences]

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      Authors: Lei Ma; Hong-Chao Zuo
      Abstract: Tibetan alpine permafrost soils functioned as a significant net carbon sink during 2000 to 2010 (1), causing a negative climate–carbon feedback under a changing climate; however, the current and future fates of this sink across the Tibetan Plateau are unknown. In PNAS, Wei et al. (2) present interesting results with...
      Keywords: Earth, Atmospheric, and Planetary Sciences, Ecology, Letters
      PubDate: 2022-01-24T12:02:00-08:00
      DOI: 10.1073/pnas.2115676119
      Issue No: Vol. 119, No. 5 (2022)
       
  • Illusory faces are more likely to be perceived as male than female
           [Psychological and Cognitive Sciences]

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      Authors: Susan G. Wardle; Sanika Paranjape, Jessica Taubert, Chris I. Baker
      Abstract: Despite our fluency in reading human faces, sometimes we mistakenly perceive illusory faces in objects, a phenomenon known as face pareidolia. Although illusory faces share some neural mechanisms with real faces, it is unknown to what degree pareidolia engages higher-level social perception beyond the detection of a face. In a...
      Keywords: Psychological and Cognitive Sciences
      PubDate: 2022-01-24T12:02:00-08:00
      DOI: 10.1073/pnas.2117413119
      Issue No: Vol. 119, No. 5 (2022)
       
  • Precautions for study design and data interpretation of clinical
           metabolomics [Biological Sciences]

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      Authors: Jinping Zheng; Kaiqiang Wang, Yuefei Wang, Kefeng Li
      Abstract: Metabolomics is increasingly used in clinical research such as mechanistic elucidation, biomarker discovery, and personalized and translational medicine. In a paper in PNAS by Teruya et al. (1) on whole-blood metabolomics in dementia patients, the authors report that they have discovered 33 blood metabolites that are linked to dementia. Unlike...
      Keywords: Biochemistry, Letters
      PubDate: 2022-01-24T12:02:00-08:00
      DOI: 10.1073/pnas.2118654119
      Issue No: Vol. 119, No. 5 (2022)
       
  • Reply to Zheng et al.: Clinical metabolomics: Detailed analysis by
           nontargeted method is complementary to large-scale studies [Biological
           Sciences]

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      Authors: Hiroshi Kondoh; Takayuki Teruya, Yung-Ju Chen, Yasuhide Fukuji, Mitsuhiro Yanagida
      Abstract: Accurate, nontargeted, comprehensive analysis of metabolites provides essential information about cutting-edge clinical questions (1). Zheng et al. (2) question the legitimacy of our recent discovery of dementia markers using whole-blood metabolomics (3). First, they express concern about the sample size of our study (n = 16) (2). However, our findings...
      Keywords: Biochemistry, Letters
      PubDate: 2022-01-24T12:02:00-08:00
      DOI: 10.1073/pnas.2120693119
      Issue No: Vol. 119, No. 5 (2022)
       
  • Reply to Ma and Zuo: Ecological restoration on the Tibetan Plateau would
           benefit terrestrial CO2 uptake [Biological Sciences]

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      Authors: Da Wei; Hui Zhao, Xufeng Wang, Yongheng Gao, Xiaodan Wang
      Abstract: We welcome a new comment on our paper and appreciate the opportunity to clarify our thinking (1). We are happy that they agree with the notion of a strengthening CO2 sink of the Tibetan Plateau (TP) (2). We agree with the importance of the influence of human activities on the...
      Keywords: Earth, Atmospheric, and Planetary Sciences, Ecology, Letters
      PubDate: 2022-01-24T12:02:00-08:00
      DOI: 10.1073/pnas.2121009119
      Issue No: Vol. 119, No. 5 (2022)
       
  • The new W family reconstructs the evolution of MHC genes [Evolution]

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      Authors: Jim Kaufman
      Abstract: The importance of adaptive immunity has been highlighted by the protection afforded by vaccination in the face of the current coronavirus pandemic. Much has been learned about the origins and subsequent evolution of the antigen-specific receptors used by this crucial arm of the immune response. Among recent discoveries are the...
      Keywords: Evolution, Commentaries
      PubDate: 2022-01-24T12:02:00-08:00
      DOI: 10.1073/pnas.2122079119
      Issue No: Vol. 119, No. 5 (2022)
       
  • Edward Osborne Wilson, Naturalist (1929-2021) [Retrospectives]

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      Authors: Bert Holldobler
      Abstract: In January 1980, at the commencement of a new decade, the journal Harvard Magazine asked several Harvard professors what they consider to be the major problems for humanity in the future. Edward O. Wilson replied (1): The worst that can happen—will happen—is not energy depletion, economic collapse, limited nuclear war,...
      Keywords: Retrospectives
      PubDate: 2022-01-21T11:51:30-08:00
      DOI: 10.1073/pnas.2200201119
      Issue No: Vol. 119, No. 5 (2022)
       
  • Measuring infectious SARS-CoV-2 in clinical samples reveals a higher viral
           titer:RNA ratio for Delta and Epsilon vs. Alpha variants [Microbiology]

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      Authors: Hannah W. Despres; Margaret G. Mills, David J. Shirley, Madaline M. Schmidt, Meei-Li Huang, Pavitra Roychoudhury, Keith R. Jerome, Alexander L. Greninger, Emily A. Bruce
      Abstract: Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants pose a challenge to controlling the COVID-19 pandemic. Previous studies indicate that clinical samples collected from individuals infected with the Delta variant may contain higher levels of RNA than previous variants, but the relationship between levels of viral RNA and infectious...
      Keywords: Microbiology, Brief Reports, Coronavirus (COVID-19)
      PubDate: 2022-01-20T12:07:15-08:00
      DOI: 10.1073/pnas.2116518119
      Issue No: Vol. 119, No. 5 (2022)
       
  • Extra-pair paternity explains cooperation in a bird species [Ecology]

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      Authors: Indrikis A. Krams; Adele Mennerat, Tatȷana Krama, Ronalds Krams, Priit Joers, Didzis Elferts, Severi Luoto, Markus J. Rantala, Sigrunn Eliassen
      Abstract: In many social animals, females mate with multiple males, but the adaptive value of female extra-pair mating is not fully understood. Here, we tested whether male pied flycatchers (Ficedula hypoleuca) engaging in extra-pair copulations with neighboring females were more likely to assist their neighbors in antipredator defense. We found that...
      Keywords: Ecology
      PubDate: 2022-01-18T13:28:12-08:00
      DOI: 10.1073/pnas.2112004119
      Issue No: Vol. 119, No. 5 (2022)
       
  • Mechanical disruption of E-cadherin complexes with epidermal growth factor
           receptor actuates growth factor-dependent signaling [Biophysics and
           Computational Biology]

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      Authors: Brendan Sullivan; Taylor Light, Vinh Vu, Adrian Kapustka, Kalina Hristova, Deborah Leckband
      Abstract: Increased intercellular tension is associated with enhanced cell proliferation and tissue growth. Here, we present evidence for a force-transduction mechanism that links mechanical perturbations of epithelial (E)-cadherin (CDH1) receptors to the force-dependent activation of epidermal growth factor receptor (EGFR, ERBB1)—a key regulator of cell proliferation. Here, coimmunoprecipitation studies first show...
      Keywords: Biophysics and Computational Biology
      PubDate: 2022-01-24T13:17:31-08:00
      DOI: 10.1073/pnas.2100679119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Myeloid cell TBK1 restricts inflammatory responses [Immunology and
           Inflammation]

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      Authors: Tianxiao Gao; Ting Liu, Chun-Jung Ko, Lingyun Zhang, Donghyun Joo, Xiaoping Xie, Lele Zhu, Yanchuan Li, Xuhong Cheng, Shao-Cong Sun
      Abstract: Proinflammatory cytokine production by innate immune cells plays a crucial role in inflammatory diseases, but the molecular mechanisms controlling the inflammatory responses are poorly understood. Here, we show that TANK-binding kinase 1 (TBK1) serves as a vital regulator of proinflammatory macrophage function and protects against tissue inflammation. Myeloid cell–conditional Tbk1...
      Keywords: Immunology and Inflammation
      PubDate: 2022-01-24T13:17:31-08:00
      DOI: 10.1073/pnas.2107742119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Ultrafast atomic view of laser-induced melting and breathing motion of
           metallic liquid clusters with MeV ultrafast electron diffraction [Physics]
           

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      Authors: Jun Wu; Minxue Tang, Lingrong Zhao, Pengfei Zhu, Tao Jiang, Xiao Zou, Liang Hong, Sheng-Nian Luo, Dao Xiang, Jie Zhang
      Abstract: Under the irradiation of an ultrafast intense laser, solid materials can be driven into nonequilibrium states undergoing an ultrafast solid–liquid phase transition. Understanding such nonequilibrium states is essential for scientific research and industrial applications because they exist in various processes including laser fusion and laser machining yet challenging in the...
      Keywords: Physics
      PubDate: 2022-01-24T13:17:31-08:00
      DOI: 10.1073/pnas.2111949119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Ultrafast end-to-end protein structure prediction enables high-throughput
           exploration of uncharacterized proteins [Biophysics and Computational
           Biology]

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      Authors: Shaun M. Kandathil; Joe G. Greener, Andy M. Lau, David T. Jones
      Abstract: Deep learning-based prediction of protein structure usually begins by constructing a multiple sequence alignment (MSA) containing homologs of the target protein. The most successful approaches combine large feature sets derived from MSAs, and considerable computational effort is spent deriving these input features. We present a method that greatly reduces the...
      Keywords: Biophysics and Computational Biology
      PubDate: 2022-01-24T13:17:31-08:00
      DOI: 10.1073/pnas.2113348119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Translational control of E2f1 regulates the Drosophila cell cycle [Cell
           Biology]

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      Authors: Jan Inge Ovrebo; Mary–Rose Bradley–Gill, Norman Zielke, Minhee Kim, Marco Marchetti, Jonathan Bohlen, Megan Lewis, Monique van Straaten, Nam–Sung Moon, Bruce A. Edgar
      Abstract: E2F transcription factors are master regulators of the eukaryotic cell cycle. In Drosophila, the sole activating E2F, E2F1, is both required for and sufficient to promote G1→S progression. E2F1 activity is regulated both by binding to RB Family repressors and by posttranscriptional control of E2F1 protein levels by the EGFR...
      Keywords: Cell Biology
      PubDate: 2022-01-24T13:17:31-08:00
      DOI: 10.1073/pnas.2113704119
      Issue No: Vol. 119, No. 4 (2022)
       
  • When danger strikes: A linguistic tool for tracking America’s collective
           response to threats [Social Sciences]

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      Authors: Virginia K. Choi; Snehesh Shrestha, Xinyue Pan, Michele J. Gelfand
      Abstract: In today’s vast digital landscape, people are constantly exposed to threatening language, which attracts attention and activates the human brain’s fear circuitry. However, to date, we have lacked the tools needed to identify threatening language and track its impact on human groups. To fill this gap, we developed a threat...
      Keywords: Inaugural Articles, Social Sciences
      PubDate: 2022-01-24T13:17:31-08:00
      DOI: 10.1073/pnas.2113891119
      Issue No: Vol. 119, No. 4 (2022)
       
  • MDGA1 negatively regulates amyloid precursor protein-mediated synapse
           inhibition in the hippocampus [Neuroscience]

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      Authors: Jinhu Kim; Seungjoon Kim, Hyeonho Kim, In-Wook Hwang, Sungwon Bae, Sudeep Karki, Dongwook Kim, Roberto Ogelman, Geul Bang, Jin Young Kim, Tommi Kajander, Ji Won Um, Won Chan Oh, Jaewon Ko
      Abstract: Balanced synaptic inhibition, controlled by multiple synaptic adhesion proteins, is critical for proper brain function. MDGA1 (meprin, A-5 protein, and receptor protein-tyrosine phosphatase mu [MAM] domain-containing glycosylphosphatidylinositol anchor protein 1) suppresses synaptic inhibition in mammalian neurons, yet the molecular mechanisms underlying MDGA1-mediated negative regulation of GABAergic synapses remain unresolved. Here,...
      Keywords: Neuroscience
      PubDate: 2022-01-24T13:17:31-08:00
      DOI: 10.1073/pnas.2115326119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Conformation-driven strategy for resilient and functional protein
           materials [Biochemistry]

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      Authors: Xuan Mu, John S. K. Yuan Jr; Jaewon Choi, Yixin Zhang, Peggy Cebe, Xiaocheng Jiang, Yu Shrike Zhang, David L. Kaplan
      Abstract: The exceptional elastic resilience of some protein materials underlies essential biomechanical functions with broad interest in biomedical fields. However, molecular design of elastic resilience is restricted to amino acid sequences of a handful of naturally occurring resilient proteins such as resilin and elastin. Here, we exploit non-resilin/elastin sequences that adopt...
      Keywords: Biochemistry, Engineering
      PubDate: 2022-01-24T13:17:31-08:00
      DOI: 10.1073/pnas.2115523119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Oxidative desulfurization pathway for complete catabolism of
           sulfoquinovose by bacteria [Biochemistry]

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      Authors: Mahima Sharma; James P. Lingford, Mariȷa Petricevic, Alexander J.D. Snow, Yunyang Zhang, Michael A. Jarva, Janice W.–Y. Mui, Nichollas E. Scott, Eleanor C. Saunders, Runyu Mao, Ruwan Epa, Bruna M. da Silva, Douglas E.V. Pires, David B. Ascher, Malcolm J. McConville, Gideon J. Davies, Spencer J. Williams, Ethan D. Goddard–Borger
      Abstract: Catabolism of sulfoquinovose (SQ; 6-deoxy-6-sulfoglucose), the ubiquitous sulfosugar produced by photosynthetic organisms, is an important component of the biogeochemical carbon and sulfur cycles. Here, we describe a pathway for SQ degradation that involves oxidative desulfurization to release sulfite and enable utilization of the entire carbon skeleton of the sugar to...
      Keywords: Biochemistry, Chemistry
      PubDate: 2022-01-24T13:17:31-08:00
      DOI: 10.1073/pnas.2116022119
      Issue No: Vol. 119, No. 4 (2022)
       
  • DNA-induced spatial entrapment of general transcription machinery can
           stabilize gene expression in a nondividing cell [Developmental Biology]

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      Authors: Khayam Javed; Jerome Jullien, Gaurav Agarwal, Nicola Lawrence, Richard Butler, Pantelis Savvas Ioannou, Farhat Nazir, J. B. Gurdon
      Abstract: An important characteristic of cell differentiation is its stability. Only rarely do cells or their stem cell progenitors change their differentiation pathway. If they do, it is often accompanied by a malfunction such as cancer. A mechanistic understanding of the stability of differentiated states would allow better prospects of alleviating...
      Keywords: Developmental Biology
      PubDate: 2022-01-24T13:17:31-08:00
      DOI: 10.1073/pnas.2116091119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Sex-specific splicing of Z- and W-borne nr5a1 alleles suggests sex
           determination is controlled by chromosome conformation [Genetics]

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      Authors: Xiuwen Zhang; Susan Wagner, Clare E. Holleley, Janine E. Deakin, Kazumi Matsubara, Ira W. Deveson, Denis O’Meally, Hardip R. Patel, Tariq Ezaz, Zhao Li, Chexu Wang, Melanie Edwards, Jennifer A. Marshall Graves, Arthur Georges
      Abstract: Pogona vitticeps has female heterogamety (ZZ/ZW), but the master sex-determining gene is unknown, as it is for all reptiles. We show that nr5a1 (Nuclear Receptor Subfamily 5 Group A Member 1), a gene that is essential in mammalian sex determination, has alleles on the Z and W chromosomes (Z-nr5a1 and...
      Keywords: Genetics
      PubDate: 2022-01-24T13:17:31-08:00
      DOI: 10.1073/pnas.2116475119
      Issue No: Vol. 119, No. 4 (2022)
       
  • CHAF1A/B mediate silencing of unintegrated HIV-1 DNAs early in infection
           [Microbiology]

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      Authors: Franziska K. Geis; Yosef Sabo, Xiao Chen, Yinglu Li, Chao Lu, Stephen P. Goff
      Abstract: Early events of the retroviral life cycle are the targets of many host restriction factors that have evolved to prevent establishment of infection. Incoming retroviral DNAs are transcriptionally silenced before integration in most cell types, and efficient viral gene expression occurs only after formation of the provirus. The molecular machinery...
      Keywords: Microbiology
      PubDate: 2022-01-24T13:17:31-08:00
      DOI: 10.1073/pnas.2116735119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Disruption of MeCP2-TCF20 complex underlies distinct neurodevelopmental
           disorders [Neuroscience]

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      Authors: Jian Zhou; Hamdan Hamdan, Hari Krishna Yalamanchili, Kaifang Pang, Amy E. Pohodich, Joanna Lopez, Yingyao Shao, Juan A. Oses–Prieto, Lifang Li, Wonho Kim, Mark A. Durham, Sameer S. Baȷikar, Donna J. Palmer, Philip Ng, Michelle L. Thompson, E. Martina Bebin, Amelie J. Muller, Alma Kuechler, Antȷe Kampmeier, Tobias B. Haack, Alma L. Burlingame, Zhandong Liu, Matthew N. Rasband, Huda Y. Zoghbi
      Abstract: MeCP2 is associated with Rett syndrome (RTT), MECP2 duplication syndrome, and a number of conditions with isolated features of these diseases, including autism, intellectual disability, and motor dysfunction. MeCP2 is known to broadly bind methylated DNA, but the precise molecular mechanism driving disease pathogenesis remains to be determined. Using proximity-dependent...
      Keywords: Neuroscience
      PubDate: 2022-01-24T13:17:31-08:00
      DOI: 10.1073/pnas.2119078119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Structures of the peptidase-containing ABC transporter PCAT1 under
           equilibrium and nonequilibrium conditions [Biophysics and Computational
           Biology]

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      Authors: Virapat Kieuvongngam; Jue Chen
      Abstract: ATP-binding cassette (ABC) transporters are ubiquitous molecular pumps that transport a broad range of substrates across biological membranes. Although the structure and function of ABC transporters has been studied extensively, our understanding of their energetics and dynamics remains limited. Here, we present studies of the peptidase-containing ABC transporter 1 (PCAT1),...
      Keywords: Biophysics and Computational Biology
      PubDate: 2022-01-24T13:17:31-08:00
      DOI: 10.1073/pnas.2120534119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Correction to Supporting Information for Chen et al., Increased gene copy
           number of DEFA1/DEFA3 worsens sepsis by inducing endothelial pyroptosis
           [Medical Sciences]

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      Abstract: MEDICAL SCIENCES Correction to Supporting Information for “Increased gene copy number of DEFA1/DEFA3 worsens sepsis by inducing endothelial pyroptosis,” by QiXing Chen, Yang Yang, JinChao Hou, Qiang Shu, YiXuan Yin, WeiTao Fu, Feng Han, TingJun Hou, CongLi Zeng, Elizabeta Nemeth, Rose Linzmeier, Tomas Ganz, and XiangMing Fang, which was first...
      PubDate: 2022-01-24T13:17:31-08:00
      DOI: 10.1073/pnas.2121889119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Correction for Liu et al., HIF-1-regulated expression of calreticulin
           promotes breast tumorigenesis and progression through Wnt/{beta}-catenin
           pathway activation [Medical Sciences]

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      Abstract: MEDICAL SCIENCES Correction for “HIF-1–regulated expression of calreticulin promotes breast tumorigenesis and progression through Wnt/β-catenin pathway activation,” by Xiaoxu Liu, Peiling Xie, Na Hao, Miao Zhang, Yang Liu, Peijun Liu, Gregg L. Semenza, Jianjun He, and Huimin Zhang, which published October 27, 2021; 10.1073/pnas.2109144118 (Proc. Natl. Acad. Sci. U.S.A. 118,...
      Keywords: Medical Sciences, Corrections
      PubDate: 2022-01-24T13:17:31-08:00
      DOI: 10.1073/pnas.2121952119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Correction for Yi et al., Transcriptional suppression of AMPK{alpha}1
           promotes breast cancer metastasis upon oncogene activation [Medical
           Sciences]

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      Abstract: MEDICAL SCIENCES Correction for “Transcriptional suppression of AMPKα1 promotes breast cancer metastasis upon oncogene activation,” by Yong Yi, Deshi Chen, Juan Ao, Wenhua Zhang, Jianqiao Yi, Xiaokun Ren, Junjie Fei, Fengtian Li, Mengmeng Niu, Hu Chen, Yangkun Luo, Zhijun Luo, and Zhi-Xiong Jim Xiao, which was first published March 19,...
      Keywords: Medical Sciences, Corrections
      PubDate: 2022-01-24T13:17:31-08:00
      DOI: 10.1073/pnas.2122573119
      Issue No: Vol. 119, No. 4 (2022)
       
  • A social perspective on perceived distances reveals deep community
           structure [Applied Mathematics]

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      Authors: Kenneth S. Berenhaut; Katherine E. Moore, Ryan L. Melvin
      Abstract: Community structure, including relationships between and within groups, is foundational to our understanding of the world around us. For dissimilarity-based data, leveraging social concepts of conflict and alignment, we provide an approach for capturing meaningful structural information resulting from induced local comparisons. In particular, a measure of local (community) depth...
      Keywords: Applied Mathematics
      PubDate: 2022-01-21T12:38:00-08:00
      DOI: 10.1073/pnas.2003634119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Identification of alternative protein targets of glutamate-ureido-lysine
           associated with PSMA tracer uptake in prostate cancer cells [Biochemistry]
           

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      Authors: Martin K. Bakht; John J. Hayward, Farsheed Shahbazi-Raz, Magdalena Skubal, Ryo Tamura, Keith F. Stringer, Daniel Meister, Varadha Balaji Venkadakrishnan, Hui Xue, Adam Pillon, Mathew Stover, Adam Tronchin, Bre-Anne Fifield, Lavleen Mader, Sheng-Yu Ku, Gi Jeong Cheon, Keon Wook Kang, Yuzhuo Wang, Xuesen Dong, Himisha Beltran, Jan Grimm, Lisa A. Porter, John F. Trant
      Abstract: Prostate-specific membrane antigen (PSMA) is highly overexpressed in most prostate cancers and is clinically visualized using PSMA-specific probes incorporating glutamate-ureido-lysine (GUL). PSMA is effectively absent from certain high-mortality, treatment-resistant subsets of prostate cancers, such as neuroendocrine prostate cancer (NEPC); however, GUL-based PSMA tracers are still reported to have the potential...
      Keywords: Biochemistry, Biophysics and Computational Biology
      PubDate: 2022-01-21T12:38:00-08:00
      DOI: 10.1073/pnas.2025710119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Turning traditionally nonwetting surfaces wetting for even ultra-high
           surface energy liquids [Applied Physical Sciences]

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      Authors: Kyle L. Wilke; Zhengmao Lu, Youngsup Song, Evelyn N. Wang
      Abstract: We present a surface-engineering approach that turns all liquids highly wetting, including ultra-high surface tension fluids such as mercury. Previously, highly wetting behavior was only possible for intrinsically wetting liquid/material combinations through surface roughening to enable the so-called Wenzel and hemiwicking states, in which liquid fills the surface structures and...
      Keywords: Applied Physical Sciences
      PubDate: 2022-01-21T12:38:00-08:00
      DOI: 10.1073/pnas.2109052119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Evidence for a semisolid phase state of aerosols and droplets relevant to
           the airborne and surface survival of pathogens [Environmental Sciences]

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      Authors: Erik Huynh; Anna Olinger, David Woolley, Ravleen Kaur Kohli, Jack M. Choczynski, James F. Davies, Kaisen Lin, Linsey C. Marr, Ryan D. Davis
      Abstract: The phase state of respiratory aerosols and droplets has been linked to the humidity-dependent survival of pathogens such as SARS-CoV-2. To inform strategies to mitigate the spread of infectious disease, it is thus necessary to understand the humidity-dependent phase changes associated with the particles in which pathogens are suspended. Here,...
      Keywords: Environmental Sciences
      PubDate: 2022-01-21T12:38:00-08:00
      DOI: 10.1073/pnas.2109750119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Narratives imagined in response to instrumental music reveal
           culture-bounded intersubjectivity [Psychological and Cognitive Sciences]

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      Authors: Elizabeth H. Margulis; Patrick C. M. Wong, Cara Turnbull, Benjamin M. Kubit, J. Devin McAuley
      Abstract: The scientific literature sometimes considers music an abstract stimulus, devoid of explicit meaning, and at other times considers it a universal language. Here, individuals in three geographically distinct locations spanning two cultures performed a highly unconstrained task: they provided free-response descriptions of stories they imagined while listening to instrumental music....
      Keywords: Psychological and Cognitive Sciences
      PubDate: 2022-01-21T12:38:00-08:00
      DOI: 10.1073/pnas.2110406119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Broadcasting of amplitude- and frequency-modulated c-di-GMP signals
           facilitates cooperative surface commitment in bacterial lineages
           [Microbiology]

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      Authors: Calvin K. Lee; William C. Schmidt, Shanice S. Webster, Jonathan W. Chen, George A. O’Toole, Gerard C. L. Wong
      Abstract: Work on surface sensing in bacterial biofilms has focused on how cells transduce sensory input into cyclic diguanylate (c-di-GMP) signaling, low and high levels of which generally correlate with high-motility planktonic cells and low-motility biofilm cells, respectively. Using Granger causal inference methods, however, we find that single-cell c-di-GMP increases are...
      Keywords: Applied Physical Sciences, Microbiology
      PubDate: 2022-01-21T12:38:00-08:00
      DOI: 10.1073/pnas.2112226119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Engineering pan-HIV-1 neutralization potency through multispecific
           antibody avidity [Biophysics and Computational Biology]

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      Authors: Edurne Rujas; Hong Cui, Jonathan Burnie, Clare Burn Aschner, Tiantian Zhao, Sara Insausti, Krithika Muthuraman, Anthony Semesi, Jasper Ophel, Jose L. Nieva, Michael S. Seaman, Christina Guzzo, Bebhinn Treanor, Jean-Philippe Julien
      Abstract: Deep mining of B cell repertoires of HIV-1–infected individuals has resulted in the isolation of dozens of HIV-1 broadly neutralizing antibodies (bNAbs). Yet, it remains uncertain whether any such bNAbs alone are sufficiently broad and potent to deploy therapeutically. Here, we engineered HIV-1 bNAbs for their combination on a single...
      Keywords: Biophysics and Computational Biology
      PubDate: 2022-01-21T12:38:00-08:00
      DOI: 10.1073/pnas.2112887119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Cation reordering instead of phase transitions: Origins and implications
           of contrasting lithiation mechanisms in 1D {zeta}- and 2D {alpha}-V2O5
           [Chemistry]

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      Authors: Yuting Luo; Shahed Rezaei, David A. Santos, Yuwei Zhang, Joseph V. Handy, Luis Carrillo, Brian J. Schultz, Leonardo Gobbato, Max Pupucevski, Kamila Wiaderek, Harry Charalambous, Andrey Yakovenko, Matt Pharr, Bai-Xiang Xu, Sarbajit Banerjee
      Abstract: Substantial improvements in cycle life, rate performance, accessible voltage, and reversible capacity are required to realize the promise of Li-ion batteries in full measure. Here, we have examined insertion electrodes of the same composition (V2O5) prepared according to the same electrode specifications and comprising particles with similar dimensions and geometries...
      Keywords: Chemistry
      PubDate: 2022-01-21T12:38:00-08:00
      DOI: 10.1073/pnas.2115072119
      Issue No: Vol. 119, No. 4 (2022)
       
  • TRITHORAX-dependent arginine methylation of HSP68 mediates circadian
           repression by PERIOD in the monarch butterfly [Neuroscience]

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      Authors: Ying Zhang; Samantha E. Iiams, Jerome S. Menet, Paul E. Hardin, Christine Merlin
      Abstract: Transcriptional repression drives feedback loops that are central to the generation of circadian (∼24-h) rhythms. In mammals, circadian repression of circadian locomotor output cycles kaput, and brain and muscle ARNT-like 1 (CLOCK:BMAL1)-mediated transcription is provided by a complex formed by PERIOD (PER) and CRYPTOCHROME (CRY) proteins. PER initiates transcriptional repression...
      Keywords: Neuroscience
      PubDate: 2022-01-21T12:38:00-08:00
      DOI: 10.1073/pnas.2115711119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Synchronous inhibitory pathways create both efficiency and diversity in
           the retina [Neuroscience]

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      Authors: Mihai Manu; Lane T. McIntosh, David B. Kastner, Benjamin N. Naecker, Stephen A. Baccus
      Abstract: Sensory receptive fields combine features that originate in different neural pathways. Retinal ganglion cell receptive fields compute intensity changes across space and time using a peripheral region known as the surround, a property that improves information transmission about natural scenes. The visual features that construct this fundamental property have not...
      Keywords: Neuroscience
      PubDate: 2022-01-21T12:38:00-08:00
      DOI: 10.1073/pnas.2116589119
      Issue No: Vol. 119, No. 4 (2022)
       
  • XP-524 is a dual-BET/EP300 inhibitor that represses oncogenic KRAS and
           potentiates immune checkpoint inhibition in pancreatic cancer [Immunology
           and Inflammation]

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      Authors: Daniel R. Principe; Rui Xiong, Yangfeng Li, Thao N. D. Pham, Suneel D. Kamath, Oleksii Dubrovskyi, Kiira Ratia, Fei Huang, Jiong Zhao, Zhengnan Shen, Dinesh Thummuri, Zhou Daohong, Patrick W. Underwood, Jose Trevino, Hidayatullah G. Munshi, Gregory R. J. Thatcher, Ajay Rana
      Abstract: Pancreatic ductal adenocarcinoma (PDAC) is associated with extensive dysregulation of the epigenome and epigenetic regulators, such as bromodomain and extraterminal motif (BET) proteins, have been suggested as potential targets for therapy. However, single-agent BET inhibition has shown poor efficacy in clinical trials, and no epigenetic approaches are currently used in...
      Keywords: Immunology and Inflammation
      PubDate: 2022-01-21T12:38:00-08:00
      DOI: 10.1073/pnas.2116764119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Temperature sensing using junctions between mobile ions and mobile
           electrons [Engineering]

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      Authors: Yecheng Wang; Kun Jia, Shuwen Zhang, Hyeong Jun Kim, Yang Bai, Ryan C. Hayward, Zhigang Suo
      Abstract: Sensing technology is under intense development to enable the Internet of everything and everyone in new and useful ways. Here we demonstrate a method of stretchable and self-powered temperature sensing. The basic sensing element consists of three layers: an electrolyte, a dielectric, and an electrode. The electrolyte/dielectric interface accumulates ions,...
      Keywords: Engineering
      PubDate: 2022-01-21T12:38:00-08:00
      DOI: 10.1073/pnas.2117962119
      Issue No: Vol. 119, No. 4 (2022)
       
  • The context of the ribosome binding site in mRNAs defines specificity of
           action of kasugamycin, an inhibitor of translation initiation
           [Microbiology]

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      Authors: Yan Zhang; Nikolay A. Aleksashin, Dorota Klepacki, Caleb Anderson, Nora Vazquez–Laslop, Carol A. Gross, Alexander S. Mankin
      Abstract: Kasugamycin (KSG) is an aminoglycoside antibiotic widely used in agriculture and exhibits considerable medical potential. Previous studies suggested that KSG interferes with translation by blocking binding of canonical messenger RNA (mRNA) and initiator transfer tRNA (tRNA) to the small ribosomal subunit, thereby preventing initiation of protein synthesis. Here, by using...
      Keywords: Microbiology
      PubDate: 2022-01-21T12:38:00-08:00
      DOI: 10.1073/pnas.2118553119
      Issue No: Vol. 119, No. 4 (2022)
       
  • A large fraction of trisomy 12, 17p-, and 11q- CLL cases carry
           unidentified microdeletions of miR-15a/16-1 [Medical Sciences]

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      Authors: Felice Pepe; Laura Z. Rassenti, Yuri Pekarsky, Jadwiga Labanowska, Tatsuya Nakamura, Giovanni Nigita, Thomas J. Kipps, Veronica Balatti, Carlo M. Croce
      Abstract: Chronic lymphocytic leukemia (CLL) is the most common adult leukemia and is characterized by chromosomal aberrations including 13q, 11q, and 17p deletions and a trisomy of chromosome 12 (T12). 13q deletions are often associated with 11q and 17p deletions in aggressive cases. Conversely, T12 CLLs show a variable prognosis, and...
      Keywords: Medical Sciences
      PubDate: 2022-01-21T12:38:00-08:00
      DOI: 10.1073/pnas.2118752119
      Issue No: Vol. 119, No. 4 (2022)
       
  • The DsrD functional marker protein is an allosteric activator of the DsrAB
           dissimilatory sulfite reductase [Microbiology]

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      Authors: Delfim Ferreira; Ana C. C. Barbosa, Goncalo P. Oliveira, Teresa Catarino, Sofia S. Venceslau, Ines A. C. Pereira
      Abstract: Dissimilatory sulfur metabolism was recently shown to be much more widespread among bacteria and archaea than previously believed. One of the key pathways involved is the dsr pathway that is responsible for sulfite reduction in sulfate-, sulfur-, thiosulfate-, and sulfite-reducing organisms, sulfur disproportionators and organosulfonate degraders, or for the production...
      Keywords: Microbiology
      PubDate: 2022-01-21T12:38:00-08:00
      DOI: 10.1073/pnas.2118880119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Occasional paternal inheritance of the germline-restricted chromosome in
           songbirds [Evolution]

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      Authors: Yifan Pei; Wolfgang Forstmeier, Francisco J. Ruiz–Ruano, Jakob C. Mueller, Josefa Cabrero, Juan Pedro M. Camacho, Juan D. Alche, Andre Franke, Marc Hoeppner, Stefan Borno, Ivana Gessara, Moritz Hertel, Kim Teltscher, Ulrich Knief, Alexander Suh, Bart Kempenaers
      Abstract: Songbirds have one special accessory chromosome, the so-called germline-restricted chromosome (GRC), which is only present in germline cells and absent from all somatic tissues. Earlier work on the zebra finch (Taeniopygia guttata castanotis) showed that the GRC is inherited only through the female line—like the mitochondria—and is eliminated from the...
      Keywords: Evolution
      PubDate: 2022-01-20T12:39:07-08:00
      DOI: 10.1073/pnas.2103960119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Pseudouridine synthase 7 is an opportunistic enzyme that binds and
           modifies substrates with diverse sequences and structures [Biochemistry]

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      Authors: Meredith K. Purchal; Daniel E. Eyler, Mehmet Tardu, Monika K. Franco, Megan M. Korn, Taslima Khan, Ryan McNassor, Rachel Giles, Katherine Lev, Hari Sharma, Jeremy Monroe, Leena Mallik, Markos Koutmos, Kristin S. Koutmou
      Abstract: Pseudouridine (Ψ) is a ubiquitous RNA modification incorporated by pseudouridine synthase (Pus) enzymes into hundreds of noncoding and protein-coding RNA substrates. Here, we determined the contributions of substrate structure and protein sequence to binding and catalysis by pseudouridine synthase 7 (Pus7), one of the principal messenger RNA (mRNA) modifying enzymes....
      Keywords: Biochemistry
      PubDate: 2022-01-20T12:39:07-08:00
      DOI: 10.1073/pnas.2109708119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Phagocytosis and self-destruction break down dendrites of Drosophila
           sensory neurons at distinct steps of Wallerian degeneration [Neuroscience]
           

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      Authors: Hui Ji; Maria L. Sapar, Ankita Sarkar, Bei Wang, Chun Han
      Abstract: After injury, severed dendrites and axons expose the “eat-me” signal phosphatidylserine (PS) on their surface while they break down. The degeneration of injured axons is controlled by a conserved Wallerian degeneration (WD) pathway, which is thought to activate neurite self-destruction through Sarm-mediated nicotinamide adenine dinucleotide (NAD+) depletion. While neurite PS...
      Keywords: Neuroscience
      PubDate: 2022-01-20T12:39:07-08:00
      DOI: 10.1073/pnas.2111818119
      Issue No: Vol. 119, No. 4 (2022)
       
  • No link between population isolation and speciation rate in squamate
           reptiles [Evolution]

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      Authors: Sonal Singhal; Guarino R. Colli, Maggie R. Grundler, Gabriel C. Costa, Ivan Prates, Daniel L. Rabosky
      Abstract: Rates of species formation vary widely across the tree of life and contribute to massive disparities in species richness among clades. This variation can emerge from differences in metapopulation-level processes that affect the rates at which lineages diverge, persist, and evolve reproductive barriers and ecological differentiation. For example, populations that...
      Keywords: Evolution
      PubDate: 2022-01-20T12:39:07-08:00
      DOI: 10.1073/pnas.2113388119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Cell-free DNA profiling informs all major complications of hematopoietic
           cell transplantation [Biophysics and Computational Biology]

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      Authors: Alexandre Pellan Cheng; Matthew Pellan Cheng, Conor James Loy, Joan Sesing Lenz, Kaiwen Chen, Sami Smalling, Philip Burnham, Kaitlyn Marie Timblin, Jose Luis Oreȷas, Emily Silverman, Paz Polak, Francisco M. Marty, Jerome Ritz, Iwiȷn De Vlaminck
      Abstract: Allogeneic hematopoietic cell transplantation (HCT) provides effective treatment for hematologic malignancies and immune disorders. Monitoring of posttransplant complications is critical, yet current diagnostic options are limited. Here, we show that cell-free DNA (cfDNA) in blood is a versatile analyte for monitoring of the most important complications that occur after HCT:...
      Keywords: Systems Biology
      PubDate: 2022-01-20T12:39:07-08:00
      DOI: 10.1073/pnas.2113476118
      Issue No: Vol. 119, No. 4 (2022)
       
  • Recurrent mutations in topoisomerase II{alpha} cause a previously
           undescribed mutator phenotype in human cancers [Genetics]

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      Authors: Arnoud Boot; Mo Liu, Nicole Stantial, Viraj Shah, Willie Yu, Karin C. Nitiss, John L. Nitiss, Sue Jinks-Robertson, Steven G. Rozen
      Abstract: Topoisomerases nick and reseal DNA to relieve torsional stress associated with transcription and replication and to resolve structures such as knots and catenanes. Stabilization of the yeast Top2 cleavage intermediates is mutagenic in yeast, but whether this extends to higher eukaryotes is less clear. Chemotherapeutic topoisomerase poisons also elevate cleavage,...
      Keywords: Genetics
      PubDate: 2022-01-20T12:39:07-08:00
      DOI: 10.1073/pnas.2114024119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Understanding the local chemical environment of bioelectrocatalysis
           [Chemistry]

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      Authors: Esther Edwardes Moore; Samuel J. Cobb, Ana Margarida Coito, Ana Rita Oliveira, Ines A. C. Pereira, Erwin Reisner
      Abstract: Bioelectrochemistry employs an array of high-surface-area meso- and macroporous electrode architectures to increase protein loading and the electrochemical current response. While the local chemical environment has been studied in small-molecule and heterogenous electrocatalysis, conditions in enzyme electrochemistry are still commonly established based on bulk solution assays, without appropriate consideration of...
      Keywords: Chemistry
      PubDate: 2022-01-20T12:39:07-08:00
      DOI: 10.1073/pnas.2114097119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Pathogenic TNF-{alpha} drives peripheral nerve inflammation in an
           Aire-deficient model of autoimmunity [Immunology and Inflammation]

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      Authors: Yan Wang, Lily Guo, Xihui Yin, Ethan C. McCarthy, Mandy I. Cheng, Aline T. Hoang, Ho-Chung Chen, Anushi Y. Patel, Denise Allard Trout, Erin Xu, Natalie Yakobian, Willy Hugo, James F. Howard Jr; Katherine M. Sheu, Alexander Hoffmann, Melissa G. Lechner, Maureen A. Su
      Abstract: Immune cells infiltrate the peripheral nervous system (PNS) after injury and with autoimmunity, but their net effect is divergent. After injury, immune cells are reparative, while in inflammatory neuropathies (e.g., Guillain Barré Syndrome and chronic inflammatory demyelinating polyneuropathy), immune cells are proinflammatory and promote autoimmune demyelination. An understanding of immune...
      Keywords: Immunology and Inflammation
      PubDate: 2022-01-20T12:39:07-08:00
      DOI: 10.1073/pnas.2114406119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Engineered human antibodies for the opsonization and killing of
           Staphylococcus aureus [Microbiology]

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      Authors: Xinhai Chen; Olaf Schneewind, Dominique Missiakas
      Abstract: Gram-positive organisms with their thick envelope cannot be lysed by complement alone. Nonetheless, antibody-binding on the surface can recruit complement and mark these invaders for uptake and killing by phagocytes, a process known as opsonophagocytosis. The crystallizable fragment of immunoglobulins (Fcγ) is key for complement recruitment. The cell surface of...
      Keywords: Microbiology
      PubDate: 2022-01-20T12:39:07-08:00
      DOI: 10.1073/pnas.2114478119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Trade-offs between bycatch and target catches in static versus dynamic
           fishery closures [Sustainability Science]

    • Free pre-print version: Loading...

      Authors: Maite Pons; Jordan T. Watson, Daniel Ovando, Sandra Andraka, Stephanie Brodie, Andres Domingo, Mark Fitchett, Rodrigo Forselledo, Martin Hall, Elliott L. Hazen, Jason E. Jannot, Miguel Herrera, Sebastian Jimenez, David M. Kaplan, Sven Kerwath, Jon Lopez, Jon McVeigh, Lucas Pacheco, Liliana Rendon, Kate Richerson, Rodrigo Sant’Ana, Rishi Sharma, James A. Smith, Kayleigh Somers, Ray Hilborn
      Abstract: While there have been recent improvements in reducing bycatch in many fisheries, bycatch remains a threat for numerous species around the globe. Static spatial and temporal closures are used in many places as a tool to reduce bycatch. However, their effectiveness in achieving this goal is uncertain, particularly for highly...
      Keywords: Sustainability Science
      PubDate: 2022-01-20T12:39:07-08:00
      DOI: 10.1073/pnas.2114508119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Atomic-resolution chemical characterization of (2x)72-kDa tryptophan
           synthase via four- and five-dimensional 1H-detected solid-state NMR
           [Biophysics and Computational Biology]

    • Free pre-print version: Loading...

      Authors: Alexander Klein; Petra Rovo, Varun V. Sakhrani, Yangyang Wang, Jacob B. Holmes, Viktoriia Liu, Patricia Skowronek, Laura Kukuk, Suresh K. Vasa, Peter Guntert, Leonard J. Mueller, Rasmus Linser
      Abstract: NMR chemical shifts provide detailed information on the chemical properties of molecules, thereby complementing structural data from techniques like X-ray crystallography and electron microscopy. Detailed analysis of protein NMR data, however, often hinges on comprehensive, site-specific assignment of backbone resonances, which becomes a bottleneck for molecular weights beyond 40 to...
      Keywords: Biophysics and Computational Biology
      PubDate: 2022-01-20T12:39:07-08:00
      DOI: 10.1073/pnas.2114690119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Remodeling of lateral geniculate nucleus projections to extrastriate area
           MT following long-term lesions of striate cortex [Neuroscience]

    • Free pre-print version: Loading...

      Authors: Nafiseh Atapour; Katrina H. Worthy, Marcello G. P. Rosa
      Abstract: Here, we report on a previously unknown form of thalamocortical plasticity observed following lesions of the primary visual area (V1) in marmoset monkeys. In primates, lateral geniculate nucleus (LGN) neurons form parallel pathways to the cortex, which are characterized by the expression of different calcium-binding proteins. LGN projections to the...
      Keywords: Neuroscience
      PubDate: 2022-01-20T12:39:07-08:00
      DOI: 10.1073/pnas.2117137119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Plants protect themselves from herbivores by optimizing the distribution
           of chemical defenses [Plant Biology]

    • Free pre-print version: Loading...

      Authors: Jonathan Gershenzon; Chhana Ullah
      Abstract: Plants, as a whole, are well stocked with chemical defense compounds that function in protection against herbivores and pathogens. Within individual plants, however, there is extensive variation in the amounts of chemical defenses among different organs, tissues, and developmental stages. For example, defense compounds are typically present in greater concentrations...
      Keywords: Plant Biology, Commentaries
      PubDate: 2022-01-20T12:39:07-08:00
      DOI: 10.1073/pnas.2120277119
      Issue No: Vol. 119, No. 4 (2022)
       
  • A compensatory link between cleavage/polyadenylation and mRNA turnover
           regulates steady-state mRNA levels in yeast [Cell Biology]

    • Free pre-print version: Loading...

      Authors: Zarmik Moqtaderi; Joseph V. Geisberg, Kevin Struhl
      Abstract: Cells have compensatory mechanisms to coordinate the rates of major biological processes, thereby permitting growth in a wide variety of conditions. Here, we uncover a compensatory link between cleavage/polyadenylation in the nucleus and messenger RNA (mRNA) turnover in the cytoplasm. On a global basis, same-gene 3′ mRNA isoforms with twofold...
      Keywords: Cell Biology
      PubDate: 2022-01-20T12:39:07-08:00
      DOI: 10.1073/pnas.2121488119
      Issue No: Vol. 119, No. 4 (2022)
       
  • When kinetics plays strange tricks [Applied Physical Sciences]

    • Free pre-print version: Loading...

      Authors: Alessandro Laio
      Abstract: Nanometer-scale ionic crystals, when immersed in an appropriate salt solution, often undergo a process of ion exchange; some atoms of the crystals are replaced by atoms from the solution. Thermodynamics dictates what will happen after the system reaches equilibrium. The concentration of the guest ions should reach a steady state...
      Keywords: Applied Physical Sciences, Commentaries
      PubDate: 2022-01-20T12:39:07-08:00
      DOI: 10.1073/pnas.2122078119
      Issue No: Vol. 119, No. 4 (2022)
       
  • QnAs with Nenad Ban [QnAs]

    • Free pre-print version: Loading...

      Authors: Farooq Ahmed
      Abstract: The central dogma of molecular biology describes the flow of information in a cell from DNA to RNA and onto proteins. Key to this flow of information, ribosomes act as the site of translation, taking in genetic information and producing polypeptides made of amino acids. Although they are complex macromolecular...
      Keywords: QnAs
      PubDate: 2022-01-20T12:39:07-08:00
      DOI: 10.1073/pnas.2122359119
      Issue No: Vol. 119, No. 4 (2022)
       
  • A mitochondrial ADXR-ADX-P450 electron transport chain is essential for
           maternal gametophytic control of embryogenesis in Arabidopsis [Plant
           Biology]

    • Free pre-print version: Loading...

      Authors: Andres Martin Bellido; Ayelen Mariana Distefano, Nicolas Setzes, Maria Milagros Cascallares, Jana Oklestkova, Ondreȷ Novak, Javier Alberto Ramirez, Eduardo J. Zabaleta, Diego F. Fiol, Gabriela C. Pagnussat
      Abstract: Mitochondrial adrenodoxins (ADXs) are small iron–sulfur proteins with electron transfer properties. In animals, ADXs transfer electrons between an adrenodoxin reductase (ADXR) and mitochondrial P450s, which is crucial for steroidogenesis. Here we show that a plant mitochondrial steroidogenic pathway, dependent on an ADXR–ADX–P450 shuttle, is essential for female gametogenesis and early...
      Keywords: Plant Biology
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2000482119
      Issue No: Vol. 119, No. 4 (2022)
       
  • ISM1 protects lung homeostasis via cell-surface GRP78-mediated alveolar
           macrophage apoptosis [Immunology and Inflammation]

    • Free pre-print version: Loading...

      Authors: Terence Y. W. Lam; Ngan Nguyen, Hong Yong Peh, Mahalakshmi Shanmugasundaram, Ritu Chandna, Jong Huat Tee, Chee Bing Ong, Md. Zakir Hossain, Shruthi Venugopal, Tianyi Zhang, Simin Xu, Tao Qiu, Wan Ting Kong, Svetoslav Chakarov, Supriya Srivastava, Wupeng Liao, Jin-Soo Kim, Ming Teh, Florent Ginhoux, W. S. Fred Wong, Ruowen Ge
      Abstract: Alveolar macrophages (AMs) are critical for lung immune defense and homeostasis. They are orchestrators of chronic obstructive pulmonary disease (COPD), with their number significantly increased and functions altered in COPD. However, it is unclear how AM number and function are controlled in a healthy lung and if changes in AMs...
      Keywords: Immunology and Inflammation
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2019161119
      Issue No: Vol. 119, No. 4 (2022)
       
  • COVID-19 increased censorship circumvention and access to sensitive topics
           in China [Political Sciences]

    • Free pre-print version: Loading...

      Authors: Keng-Chi Chang; William R. Hobbs, Margaret E. Roberts, Zachary C. Steinert-Threlkeld
      Abstract: Crisis motivates people to track news closely, and this increased engagement can expose individuals to politically sensitive information unrelated to the initial crisis. We use the case of the COVID-19 outbreak in China to examine how crisis affects information seeking in countries that normally exert significant control over access to...
      Keywords: Political Sciences
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2102818119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Tuning protein half-life in mouse using sequence-defined biopolymers
           functionalized with lipids [Engineering]

    • Free pre-print version: Loading...

      Authors: Koen Vanderschuren; Pol Arranz-Gibert, Minsoo Khang, Dagan Hadar, Alice Gaudin, Fan Yang, Ewa Folta-Stogniew, W. Mark Saltzman, Miriam Amiram, Farren J. Isaacs
      Abstract: The use of biologics in the treatment of numerous diseases has increased steadily over the past decade due to their high specificities, low toxicity, and limited side effects. Despite this success, peptide- and protein-based drugs are limited by short half-lives and immunogenicity. To address these challenges, we use a genomically...
      Keywords: Applied Biological Sciences
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2103099119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Mechanistic differences between methanol and dimethyl ether in
           zeolite-catalyzed hydrocarbon synthesis [Chemistry]

    • Free pre-print version: Loading...

      Authors: Felix M. Kirchberger; Yue Liu, Philipp N. Plessow, Markus Tonigold, Felix Studt, Maricruz Sanchez-Sanchez, Johannes A. Lercher
      Abstract: Water influences critically the kinetics of the autocatalytic conversion of methanol to hydrocarbons in acid zeolites. At very low conversions but otherwise typical reaction conditions, the initiation of the reaction is delayed in presence of H2O. In absence of hydrocarbons, the main reactions are the methanol and dimethyl ether (DME)...
      Keywords: Chemistry
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2103840119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Template switching in DNA replication can create and maintain RNA hairpins
           [Evolution]

    • Free pre-print version: Loading...

      Authors: Heli A. M. Monttinen; Ari Loytynoȷa
      Abstract: The evolutionary origin of RNA stem structures and the preservation of their base pairing under a spontaneous and random mutation process have puzzled theoretical evolutionary biologists. DNA replication–related template switching is a mutation mechanism that creates reverse-complement copies of sequence regions within a genome by replicating briefly along either the...
      Keywords: Evolution
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2107005119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal
           response to nitrate [Plant Biology]

    • Free pre-print version: Loading...

      Authors: Orlando Contreras–Lopez; Elena A. Vidal, Eleodoro Riveras, Jose M. Alvarez, Tomas C. Moyano, Erin E. Sparks, Joaquin Medina, Angelo Pasquino, Philip N. Benfey, Gloria M. Coruzzi, Rodrigo A. Gutierrez
      Abstract: Nitrate is a nutrient and a potent signal that impacts global gene expression in plants. However, the regulatory factors controlling temporal and cell type–specific nitrate responses remain largely unknown. We assayed nitrate-responsive transcriptome changes in five major root cell types of the Arabidopsis thaliana root as a function of time....
      Keywords: Plant Biology
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2107879119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Universal adaptability: Target-independent inference that competes with
           propensity scoring [Statistics]

    • Free pre-print version: Loading...

      Authors: Michael P. Kim; Christoph Kern, Shafi Goldwasser, Frauke Kreuter, Omer Reingold
      Abstract: The gold-standard approaches for gleaning statistically valid conclusions from data involve random sampling from the population. Collecting properly randomized data, however, can be challenging, so modern statistical methods, including propensity score reweighting, aim to enable valid inferences when random sampling is not feasible. We put forth an approach for making...
      Keywords: Statistics
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2108097119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Quantifying the effectiveness of betaherpesvirus-vectored transmissible
           vaccines [Ecology]

    • Free pre-print version: Loading...

      Authors: Tanner J. Varrelman; Christopher H. Remien, Andrew J. Basinski, Shelley Gorman, Alec Redwood, Scott L. Nuismer
      Abstract: Transmissible vaccines have the potential to revolutionize how zoonotic pathogens are controlled within wildlife reservoirs. A key challenge that must be overcome is identifying viral vectors that can rapidly spread immunity through a reservoir population. Because they are broadly distributed taxonomically, species specific, and stable to genetic manipulation, betaherpesviruses are...
      Keywords: Ecology
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2108610119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Fundamental limitations on efficiently forecasting certain epidemic
           measures in network models [Ecology]

    • Free pre-print version: Loading...

      Authors: Daniel J. Rosenkrantz; Anil Vullikanti, S. S. Ravi, Richard E. Stearns, Simon Levin, H. Vincent Poor, Madhav V. Marathe
      Abstract: The ongoing COVID-19 pandemic underscores the importance of developing reliable forecasts that would allow decision makers to devise appropriate response strategies. Despite much recent research on the topic, epidemic forecasting remains poorly understood. Researchers have attributed the difficulty of forecasting contagion dynamics to a multitude of factors, including complex behavioral...
      Keywords: Computer Sciences, Ecology
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2109228119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Individuals with adverse childhood experiences explore less and
           underweight reward feedback [Psychological and Cognitive Sciences]

    • Free pre-print version: Loading...

      Authors: Alex Lloyd; Ryan Thomas McKay, Nicholas Furl
      Abstract: Adverse childhood experiences (ACEs) are extreme stressors that lead to negative psychosocial outcomes in adulthood. Nonhuman animals explore less after exposure to early stress. Therefore, in this preregistered study, we hypothesized that reduced exploration following ACEs would also be evident in human adults. Further, we predicted that adults with ACEs,...
      Keywords: Psychological and Cognitive Sciences
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2109373119
      Issue No: Vol. 119, No. 4 (2022)
       
  • High-throughput selection of cells based on accumulated growth and
           division using PicoShell particles [Engineering]

    • Free pre-print version: Loading...

      Authors: Mark van Zee; Joseph de Rutte, Rose Rumyan, Cayden Williamson, Trevor Burnes, Randor Radakovits, Andrew Sonico Eugenio, Sara Badih, Sohyung Lee, Dong-Hyun Lee, Maani Archang, Dino Di Carlo
      Abstract: Production of high-energy lipids by microalgae may provide a sustainable energy source that can help tackle climate change. However, microalgae engineered to produce more lipids usually grow slowly, leading to reduced overall yields. Unfortunately, culture vessels used to select cells based on growth while maintaining high biomass production, such as...
      Keywords: Applied Biological Sciences, Engineering
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2109430119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Ultrasound controlled mechanophore activation in hydrogels for cancer
           therapy [Applied Physical Sciences]

    • Free pre-print version: Loading...

      Authors: Gun Kim; Qiong Wu, James L. Chu, Emily J. Smith, Michael L. Oelze, Jeffrey S. Moore, King C. Li
      Abstract: Mechanophores are molecular motifs that respond to mechanical perturbance with targeted chemical reactions toward desirable changes in material properties. A large variety of mechanophores have been investigated, with applications focusing on functional materials, such as strain/stress sensors, nanolithography, and self-healing polymers, among others. The responses of engineered mechanophores, such as...
      Keywords: Applied Physical Sciences
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2109791119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Parkinson's disease protein PARK7 prevents metabolite and protein damage
           caused by a glycolytic metabolite [Biochemistry]

    • Free pre-print version: Loading...

      Authors: Isaac P. Heremans; Francesco Caligiore, Isabelle Gerin, Marina Bury, Marilena Lutz, Julie Graff, Vincent Stroobant, Didier Vertommen, Aurelio A. Teleman, Emile Van Schaftingen, Guido T. Bommer
      Abstract: Cells are continuously exposed to potentially dangerous compounds. Progressive accumulation of damage is suspected to contribute to neurodegenerative diseases and aging, but the molecular identity of the damage remains largely unknown. Here we report that PARK7, an enzyme mutated in hereditary Parkinson’s disease, prevents damage of proteins and metabolites caused...
      Keywords: Biochemistry
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2111338119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Multiple representations of the body schema for the same body part
           [Psychological and Cognitive Sciences]

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      Authors: Kazumichi Matsumiya
      Abstract: Purposeful motor actions depend on the brain’s representation of the body, called the body schema, and disorders of the body schema have been reported to show motor deficits. The body schema has been assumed for almost a century to be a common body representation supporting all types of motor actions,...
      Keywords: Psychological and Cognitive Sciences
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2112318119
      Issue No: Vol. 119, No. 4 (2022)
       
  • A multiscale biophysical model gives quantized metachronal waves in a
           lattice of beating cilia [Applied Mathematics]

    • Free pre-print version: Loading...

      Authors: Brato Chakrabarti; Sebastian Furthauer, Michael J. Shelley
      Abstract: Motile cilia are slender, hair-like cellular appendages that spontaneously oscillate under the action of internal molecular motors and are typically found in dense arrays. These active filaments coordinate their beating to generate metachronal waves that drive long-range fluid transport and locomotion. Until now, our understanding of their collective behavior largely...
      Keywords: Applied Mathematics
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2113539119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Probing molecular crowding in compressed tissues with Brillouin light
           scattering [Biophysics and Computational Biology]

    • Free pre-print version: Loading...

      Authors: Guqi Yan; Sylvain Monnier, Maleke Mouelhi, Thomas Dehoux
      Abstract: Volume regulation is key in maintaining important tissue functions, such as growth or healing. This is achieved by modulation of active contractility as well as water efflux that changes molecular crowding within individual cells. Local sensors have been developed to monitor stresses or forces in model tissues, but these approaches...
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2113614119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Cryptochrome proteins regulate the circadian intracellular behavior and
           localization of PER2 in mouse suprachiasmatic nucleus neurons
           [Neuroscience]

    • Free pre-print version: Loading...

      Authors: Nicola J. Smyllie; James Bagnall, Alex A. Koch, Dhevahi Niranjan, Lenka Polidarova, Johanna E. Chesham, Jason W. Chin, Carrie L. Partch, Andrew S. I. Loudon, Michael H. Hastings
      Abstract: The ∼20,000 cells of the suprachiasmatic nucleus (SCN), the master circadian clock of the mammalian brain, coordinate subordinate cellular clocks across the organism, driving adaptive daily rhythms of physiology and behavior. The canonical model for SCN timekeeping pivots around transcriptional/translational feedback loops (TTFL) whereby PERIOD (PER) and CRYPTOCHROME (CRY) clock...
      Keywords: Neuroscience
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2113845119
      Issue No: Vol. 119, No. 4 (2022)
       
  • NO rapidly mobilizes cellular heme to trigger assembly of its own receptor
           [Biochemistry]

    • Free pre-print version: Loading...

      Authors: Yue Dai; Emily M. Faul, Arnab Ghosh, Dennis J. Stuehr
      Abstract: Nitric oxide (NO) signaling in biology relies on its activating cyclic guanosine monophosphate (cGMP) production by the NO receptor soluble guanylyl cyclase (sGC). sGC must obtain heme and form a heterodimer to become functional, but paradoxically often exists as an immature heme-free form in cells and tissues. Based on our...
      Keywords: Biochemistry
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2115774119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Organic molecular dynamics and charge-carrier lifetime in lead iodide
           perovskite MAPbI3 [Physics]

    • Free pre-print version: Loading...

      Authors: Akihiro Koda; Hirotaka Okabe, Masatoshi Hiraishi, Ryosuke Kadono, Katelyn A. Dagnall, Joshua J. Choi, Seung-Hun Lee
      Abstract: The long charge carrier lifetime of the hybrid organic–inorganic perovskites (HOIPs) is the key for their remarkable performance as a solar cell material. The microscopic mechanism for the long lifetime is still in debate. Here, by using a muon spin relaxation technique that probes the fluctuation of local magnetic fields,...
      Keywords: Physics
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2115812119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Yeast cells actively tune their membranes to phase separate at
           temperatures that scale with growth temperatures [Biophysics and
           Computational Biology]

    • Free pre-print version: Loading...

      Authors: Chantelle L. Leveille; Caitlin E. Cornell, Alexey J. Merz, Sarah L. Keller
      Abstract: Membranes of vacuoles, the lysosomal organelles of Saccharomyces cerevisiae (budding yeast), undergo extraordinary changes during the cell’s normal growth cycle. The cycle begins with a stage of rapid cell growth. Then, as glucose becomes scarce, growth slows, and vacuole membranes phase separate into micrometer-scale domains of two liquid phases. Recent...
      Keywords: Biophysics and Computational Biology
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2116007119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Structure and function of an effector domain in antiviral factors and
           tumor suppressors SAMD9 and SAMD9L [Medical Sciences]

    • Free pre-print version: Loading...

      Authors: Shuxia Peng; Xiangzhi Meng, Fushun Zhang, Prabhat Kumar Pathak, Juhi Chaturvedi, Jaime Coronado, Marisol Morales, Yuanhui Mao, Shu-Bing Qian, Junpeng Deng, Yan Xiang
      Abstract: SAMD9 and SAMD9L (SAMD9/9L) are antiviral factors and tumor suppressors, playing a critical role in innate immune defense against poxviruses and the development of myeloid tumors. SAMD9/9L mutations with a gain-of-function (GoF) in inhibiting cell growth cause multisystem developmental disorders including many pediatric myelodysplastic syndromes. Predicted to be multidomain proteins...
      Keywords: Medical Sciences
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2116550119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Aluminum Cayley trees as scalable, broadband, multiresonant optical
           antennas [Applied Physical Sciences]

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      Authors: Thomas Simon; Xiaoyan Li, Jerome Martin, Dmitry Khlopin, Odile Stephan, Mathieu Kociak, Davy Gerard
      Abstract: An optical antenna can convert a propagative optical radiation into a localized excitation and the reciprocal. Although optical antennas can be readily created using resonant nanoparticles (metallic or dielectric) as elementary building blocks, the realization of antennas sustaining multiple resonances over a broad range of frequencies remains a challenging task....
      Keywords: Applied Physical Sciences
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2116833119
      Issue No: Vol. 119, No. 4 (2022)
       
  • The psychology of separation: Border walls, soft power, and international
           neighborliness [Political Sciences]

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      Authors: Diana C. Mutz; Beth A. Simmons
      Abstract: This study assesses the impact of international border walls on evaluations of countries and on beliefs about bilateral relationships between states. Using a short video, we experimentally manipulate whether a border wall image appears in a broader description of the history and culture of a little-known country. In a third...
      Keywords: Political Sciences
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2117797119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Skin-resident dendritic cells mediate postoperative pain via CCR4 on
           sensory neurons [Immunology and Inflammation]

    • Free pre-print version: Loading...

      Authors: Jaqueline Raymondi Silva; Mircea Iftinca, Francisco I. Fernandes Gomes, Julia P. Segal, Olivia M. A. Smith, Courtney A. Bannerman, Atlante Silva Mendes, Manon Defaye, Madeline E. C. Robinson, Ian Gilron, Thiago Mattar Cunha, Christophe Altier, Nader Ghasemlou
      Abstract: Inflammatory pain, such as hypersensitivity resulting from surgical tissue injury, occurs as a result of interactions between the immune and nervous systems with the orchestrated recruitment and activation of tissue-resident and circulating immune cells to the site of injury. Our previous studies identified a central role for Ly6Clow myeloid cells...
      Keywords: Immunology and Inflammation
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2118238119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Opinion: To assess marine cloud brightening's technical feasibility, we
           need to know what to study—and when to stop [Environmental Sciences]

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      Authors: Michael S. Diamond; Andrew Gettelman, Matthew D. Lebsock, Allison McComiskey, Lynn M. Russell, Robert Wood, Graham Feingold
      Abstract: To avoid the worst impacts of climate change, it’s paramount that we decarbonize the economy and preserve and restore natural ecosystems. Unfortunately, pledges made from countries thus far will not limit warming to below 1.5 °C, even after accounting for the more ambitious targets set at the recent COP26 climate...
      Keywords: Opinions, Earth, Atmospheric, and Planetary Sciences, Environmental Sciences, Front Matter
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2118379119
      Issue No: Vol. 119, No. 4 (2022)
       
  • The flagellar motor protein FliL forms a scaffold of circumferentially
           positioned rings required for stator activation [Microbiology]

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      Authors: Shoichi Tachiyama; Kar L. Chan, Xiaolin Liu, Skander Hathroubi, Briana Peterson, Mohammad F. Khan, Karen M. Ottemann, Jun Liu, Anna Roujeinikova
      Abstract: The flagellar motor stator is an ion channel nanomachine that assembles as a ring of the MotA5MotB2 units at the flagellar base. The role of accessory proteins required for stator assembly and activation remains largely enigmatic. Here, we show that one such assembly factor, the conserved protein FliL, forms an...
      Keywords: Microbiology
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2118401119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Molecular basis of differential receptor usage for naturally occurring
           CD55-binding and -nonbinding coxsackievirus B3 strains [Microbiology]

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      Authors: Qingling Wang; Qian Yang, Congcong Liu, Guoqing Wang, Hao Song, Guijun Shang, Ruchao Peng, Xiao Qu, Sheng Liu, Yingzi Cui, Peiyi Wang, Wenbo Xu, Xin Zhao, Jianxun Qi, Mengsu Yang, George F. Gao
      Abstract: Receptor usage defines cell tropism and contributes to cell entry and infection. Coxsackievirus B (CVB) engages coxsackievirus and adenovirus receptor (CAR), and selectively utilizes the decay-accelerating factor (DAF; CD55) to infect cells. However, the differential receptor usage mechanism for CVB remains elusive. This study identified VP3-234 residues (234Q/N/V/D/E) as critical...
      Keywords: Microbiology
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2118590119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Social mindfulness for global environmental sustainability' [Social
           Sciences]

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      Authors: Hikaru Komatsu; Jeremy Rappleye, Iveta Silova
      Abstract: Van Doesum et al. (1) report a positive correlation between social mindfulness and national environmental performance represented by the Environmental Performance Index (EPI), that is, a higher EPI for countries with higher scores of social mindfulness (SoMi). This result comes at a crucial time, as it highlights the relationship between...
      Keywords: Letters, Psychological and Cognitive Sciences
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2118710118
      Issue No: Vol. 119, No. 4 (2022)
       
  • Development and quantitative analysis of a biosensor based on the
           Arabidopsis SWEET1 sugar transporter [Biochemistry]

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      Authors: Jihyun Park; Taylor M. Chavez, Jordan A. Guistwhite, Sojeong Gwon, Wolf B. Frommer, Lily S. Cheung
      Abstract: SWEETs are transporters with homologs in Archeae, plants, some fungi, and animals. As the only transporters known to facilitate the cellular release of sugars in plants, SWEETs play critical roles in the allocation of sugars from photosynthetic leaves to storage tissues in seeds, fruits, and tubers. Here, we report the...
      Keywords: Biochemistry
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2119183119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Ca2+ leak through ryanodine receptor 1 regulates thermogenesis in resting
           skeletal muscle [Physiology]

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      Authors: Aldo Meizoso-Huesca; Luke Pearce, Christopher J. Barclay, Bradley S. Launikonis
      Abstract: Mammals rely on nonshivering thermogenesis (NST) from skeletal muscle so that cold temperatures can be tolerated. NST results from activity of the sarcoplasmic reticulum (SR) Ca2+ pump in skeletal muscle, but the mechanisms that regulate this activity are unknown. Here, we develop a single-fiber assay to investigate the role of...
      Keywords: Physiology
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2119203119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Is there solid evidence of widespread landscape disturbance in the Azores
           before the arrival of the Portuguese' [Biological Sciences]

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      Authors: Rui B. Elias; Simon E. Connor, Carlos A. Gois–Marques, Hanno Schaefer, Luis Silva, Miguel M. Sequeira, Monica Moura, Paulo A. V. Borges, Rosalina Gabriel
      Abstract: Raposeiro et al. (1) conclude that human occupation of the Azores islands began between 700 and 850 CE, causing widespread landscape disturbance and raising doubts about the islands’ presumed pristine nature when the Portuguese arrived. However, previous paleoecological studies from Flores, Pico, and São Miguel Islands (Table 1) show that...
      Keywords: Earth, Atmospheric, and Planetary Sciences, Environmental Sciences, Letters
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2119218119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Reply to Komatsu et al.: From local social mindfulness to global
           sustainability efforts' [Social Sciences]

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      Authors: Niels J. Van Doesum; Ryan O. Murphy, Marcello Gallucci, Efrat Aharonov–Maȷar, Ursula Athenstaedt, Wing Tung Au, Liying Bai, Robert Bohm, Inna Bovina, Nancy R. Buchan, Xiao–Ping Chen, Kitty B. Dumont, Jan B. Engelmann, Kimmo Eriksson, Hyun Euh, Susann Fiedler, Justin Friesen, Simon Gachter, Camilo Garcia, Roberto Gonzalez, Sylvie Graf, Katarzyna Growiec, Serge Guimond, Martina Hřebičkova, Elizabeth Immer–Bernold, Jeff Joireman, Gokhan Karagonlar, Kerry Kawakami, Toko Kiyonari, Yu Kou, Alexandros–Andreas Kyrtsis, Siugmin Lay, Geoffrey J. Leonardelli, Norman P. Li, Yang Li, Boris Macieȷovsky, Zoi Manesi, Ali Mashuri, Aurelia Mok, Karin S. Moser, Ladislav Motak, Adrian Netedu, Michael J. Platow, Karolina Raczka–Winkler, Christopher P. Reinders Folmer, Cecilia Reyna, Angelo Romano, Shaul Shalvi, Claudia Simao, Adam W. Stivers, Pontus Strimling, Yannis Tsirbas, Sonȷa Utz, Leander van der Meiȷ, Sven Waldzus, Yiwen Wang, Bernd Weber, Ori Weisel, Tim Wildschut, Fabian Winter, Junhui Wu, Jose C. Yong, Paul A. M. Van Lange
      Abstract: Komatsu et al. (1) argue that Van Doesum et al. (2) may have overlooked the role of GDP in reporting a positive association between social mindfulness (SoMi) and the Environmental Performance Index (EPI) at country level. Although the relationship between EPI and SoMi is relatively weaker for countries with higher...
      Keywords: Letters, Psychological and Cognitive Sciences
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2119303118
      Issue No: Vol. 119, No. 4 (2022)
       
  • Carcinomas assemble a filamentous CXCL12-keratin-19 coating that
           suppresses T cell-mediated immune attack [Immunology and Inflammation]

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      Authors: Zhikai Wang; Philip Moresco, Ran Yan, Jiayun Li, Ya Gao, Daniele Biasci, Min Yao, Jordan Pearson, Jaclyn F. Hechtman, Tobias Janowitz, Raza M. Zaidi, Matthew J. Weiss, Douglas T. Fearon
      Abstract: Cancer immunotherapy frequently fails because most carcinomas have few T cells, suggesting that cancers can suppress T cell infiltration. Here, we show that cancer cells of human pancreatic ductal adenocarcinoma (PDA), colorectal cancer, and breast cancer are coated with transglutaminase-2 (TGM2)–dependent covalent CXCL12–keratin-19 (KRT19) heterodimers that are organized as filamentous...
      Keywords: Immunology and Inflammation
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2119463119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Larger images are better remembered during naturalistic encoding
           [Psychological and Cognitive Sciences]

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      Authors: Shaimaa Masarwa; Olga Kreichman, Sharon Gilaie-Dotan
      Abstract: We are constantly exposed to multiple visual scenes, and while freely viewing them without an intentional effort to memorize or encode them, only some are remembered. It has been suggested that image memory is influenced by multiple factors, such as depth of processing, familiarity, and visual category. However, this is...
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2119614119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Cellular and molecular architecture of submucosal glands in wild-type and
           cystic fibrosis pigs [Cell Biology]

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      Authors: Wenjie Yu; Thomas O. Moninger, Andrew L. Thurman, Yuliang Xie, Akansha Jain, Keyan Zarei, Linda S. Powers, Alejandro A. Pezzulo, David A. Stoltz, Michael J. Welsh
      Abstract: Submucosal glands (SMGs) protect lungs but can also contribute to disease. For example, in cystic fibrosis (CF), SMGs produce abnormal mucus that disrupts mucociliary transport. CF is an ion transport disease, yet knowledge of the ion transporters expressed by SMG acini, which produce mucus, and SMG ducts that carry it...
      Keywords: Cell Biology
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2119759119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Reply to Elias et al.: Multiproxy evidence of widespread landscape
           disturbance in multiple Azorean lakes before the Portuguese arrival
           [Biological Sciences]

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      Authors: Pedro M. Raposeiro; Armand Hernandez, Sergi Pla–Rabes, Vitor Goncalves, Roberto Bao, Alberto Saez, Timothy Shanahan, Mario Benavente, Erik J. de Boer, Nora Richter, Veronica Gordon, Helena Marques, Pedro M. Sousa, Martin Souto, Miguel G. Matias, Nicole Aguiar, Catia Pereira, Catarina Ritter, Maria Jesus Rubio, Marina Salcedo, David Vazquez–Loureiro, Olga Margalef, Linda A. Amaral–Zettler, Ana Cristina Costa, Yongsong Huang, Jacqueline F. N. van Leeuwen, Pere Masque, Ricardo Prego, Ana Carolina Ruiz–Fernandez, Joan–Albert Sanchez–Cabeza, Ricardo Trigo, Santiago Giralt
      Abstract: Despite the multidisciplinary and comprehensive approach taken in ref. 1, we acknowledge that there are still open questions that require further research. We emphasize that our study relies on multiple records that show the synchronous arrival of humans on multiple islands before ca. 1400 CE. Elias et al. (2) raise...
      Keywords: Earth, Atmospheric, and Planetary Sciences, Environmental Sciences, Letters
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2120107119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Injectable amnion hydrogel-mediated delivery of adipose-derived stem cells
           for osteoarthritis treatment [Applied Biological Sciences]

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      Authors: Maumita Bhattacharjee; Jorge L. Escobar Ivirico, Ho-Man Kan, Shiv Shah, Takayoshi Otsuka, Rosalie Bordett, Mohammed Barajaa, Naveen Nagiah, Rishikesh Pandey, Lakshmi S. Nair, Cato T. Laurencin
      Abstract: Current treatment strategies for osteoarthritis (OA) predominantly address symptoms with limited disease-modifying potential. There is a growing interest in the use of adipose-derived stem cells (ADSCs) for OA treatment and developing biomimetic injectable hydrogels as cell delivery systems. Biomimetic injectable hydrogels can simulate the native tissue microenvironment by providing appropriate...
      Keywords: Applied Biological Sciences, Engineering
      PubDate: 2022-01-19T12:58:09-08:00
      DOI: 10.1073/pnas.2120968119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Rapid radiation in a highly diverse marine environment [Evolution]

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      Authors: Kosmas Hench; Martin Helmkampf, W. Owen McMillan, Oscar Puebla
      Abstract: Rapid diversification is often observed when founding species invade isolated or newly formed habitats that provide ecological opportunity for adaptive radiation. However, most of the Earth’s diversity arose in diverse environments where ecological opportunities appear to be more constrained. Here, we present a striking example of a rapid radiation in...
      Keywords: Evolution
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2020457119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Difficult climate-adaptive decisions in forests as complex
           social-ecological systems [Ecology]

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      Authors: Kieran Findlater; Robert Kozak, Shannon Hagerman
      Abstract: Climate change threatens the social, ecological, and economic benefits enjoyed by forest-dependent communities worldwide. Climate-adaptive forest management strategies such as genomics-based assisted migration (AM) may help protect many of these threatened benefits. However, such novel technological interventions in complex social–ecological systems will generate new risks, benefits, and uncertainties that interact...
      Keywords: Ecology, Sustainability Science
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2108326119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Surrogate gradients for analog neuromorphic computing [Neuroscience]

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      Authors: Benȷamin Cramer; Sebastian Billaudelle, Simeon Kanya, Aron Leibfried, Andreas Grubl, Vitali Karasenko, Christian Pehle, Korbinian Schreiber, Yannik Stradmann, Johannes Weis, Johannes Schemmel, Friedemann Zenke
      Abstract: To rapidly process temporal information at a low metabolic cost, biological neurons integrate inputs as an analog sum, but communicate with spikes, binary events in time. Analog neuromorphic hardware uses the same principles to emulate spiking neural networks with exceptional energy efficiency. However, instantiating high-performing spiking networks on such hardware...
      Keywords: Computer Sciences, Neuroscience
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2109194119
      Issue No: Vol. 119, No. 4 (2022)
       
  • An endemic pathway to sheep and goat domestication at Aşıklı Hoyuk
           (Central Anatolia, Turkey) [Anthropology]

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      Authors: Mary C. Stiner; Natalie D. Munro, Hiȷlke Buitenhuis, Guneş Duru, Mihriban Ozbaşaran
      Abstract: Sheep and goats (caprines) were domesticated in Southwest Asia in the early Holocene, but how and in how many places remain open questions. This study investigates the initial conditions and trajectory of caprine domestication at Aşıklı Höyük, which preserves an unusually high-resolution record of the first 1,000 y of Neolithic...
      Keywords: Anthropology
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2110930119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Circumpolar ocean stability on Mars 3 Gy ago [Earth, Atmospheric, and
           Planetary Sciences]

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      Authors: Frederic Schmidt; Michael J. Way, Francois Costard, Sylvain Bouley, Antoine Seȷourne, Igor Aleinov
      Abstract: What was the nature of the Late Hesperian climate, warm and wet or cold and dry' Formulated this way the question leads to an apparent paradox since both options seem implausible. A warm and wet climate would have produced extensive fluvial erosion but few valley networks have been observed at...
      Keywords: Earth, Atmospheric, and Planetary Sciences
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2112930118
      Issue No: Vol. 119, No. 4 (2022)
       
  • Dissection of brain-wide resting-state and functional somatosensory
           circuits by fMRI with optogenetic silencing [Neuroscience]

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      Authors: Won Beom Jung; Haiyan Jiang, Soohyun Lee, Seong-Gi Kim
      Abstract: To further advance functional MRI (fMRI)–based brain science, it is critical to dissect fMRI activity at the circuit level. To achieve this goal, we combined brain-wide fMRI with neuronal silencing in well-defined regions. Since focal inactivation suppresses excitatory output to downstream pathways, intact input and suppressed output circuits can be...
      Keywords: Neuroscience
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2113313119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Climate and agronomy, not genetics, underpin recent maize yield gains in
           favorable environments [Agricultural Sciences]

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      Authors: Gonzalo Rizzo; Juan Pablo Monzon, Fatima A. Tenorio, Reka Howard, Kenneth G. Cassman, Patricio Grassini
      Abstract: Quantitative understanding of factors driving yield increases of major food crops is essential for effective prioritization of research and development. Yet previous estimates had limitations in distinguishing among contributing factors such as changing climate and new agronomic and genetic technologies. Here, we distinguished the separate contribution of these factors to...
      Keywords: Agricultural Sciences
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2113629119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Rad54 and Rdh54 prevent Srs2-mediated disruption of Rad51 presynaptic
           filaments [Biochemistry]

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      Authors: Aviv Meir; J. Brooks Crickard, Youngho Kwon, Patrick Sung, Eric C. Greene
      Abstract: Srs2 is a superfamily 1 (SF1) helicase that participates in several pathways necessary for the repair of damaged DNA. Srs2 regulates formation of early homologous recombination (HR) intermediates by actively removing the recombinase Rad51 from single-stranded DNA (ssDNA). It is not known whether and how Srs2 itself is down-regulated to...
      Keywords: Biochemistry
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2113871119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Integrated genome and transcriptome analyses reveal the mechanism of
           genome instability in ataxia with oculomotor apraxia 2 [Cell Biology]

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      Authors: Radhakrishnan Kanagaraj; Richard Mitter, Theodoros Kantidakis, Matthew M. Edwards, Anaid Benitez, Probir Chakravarty, Beiyuan Fu, Olivier Becherel, Fengtang Yang, Martin F. Lavin, Amnon Koren, Aengus Stewart, Stephen C. West
      Abstract: Mutations in the SETX gene, which encodes Senataxin, are associated with the progressive neurodegenerative diseases ataxia with oculomotor apraxia 2 (AOA2) and amyotrophic lateral sclerosis 4 (ALS4). To identify the causal defect in AOA2, patient-derived cells and SETX knockouts (human and mouse) were analyzed using integrated genomic and transcriptomic approaches....
      Keywords: Cell Biology
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2114314119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Yeast has evolved to minimize protein resource cost for synthesizing amino
           acids [Systems Biology]

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      Authors: Yu Chen; Jens Nielsen
      Abstract: Proteins, as essential biomolecules, account for a large fraction of cell mass, and thus the synthesis of the complete set of proteins (i.e., the proteome) represents a substantial part of the cellular resource budget. Therefore, cells might be under selective pressures to optimize the resource costs for protein synthesis, particularly...
      Keywords: Systems Biology, Brief Reports
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2114622119
      Issue No: Vol. 119, No. 4 (2022)
       
  • The Earth BioGenome Project 2020: Starting the clock [Evolution]

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      Authors: Harris A. Lewin; Stephen Richards, Erez Lieberman Aiden, Miguel L. Allende, John M. Archibald, Miklos Balint, Katharine B. Barker, Bridget Baumgartner, Katherine Belov, Giorgio Bertorelle, Mark L. Blaxter, Jing Cai, Nicolette D. Caperello, Keith Carlson, Juan Carlos Castilla–Rubio, Shu–Miaw Chaw, Lei Chen, Anna K. Childers, Jonathan A. Coddington, Dalia A. Conde, Montserrat Corominas, Keith A. Crandall, Andrew J. Crawford, Federica DiPalma, Richard Durbin, ThankGod E. Ebenezer, Scott V. Edwards, Olivier Fedrigo, Paul Flicek, Giulio Formenti, Richard A. Gibbs, M. Thomas P. Gilbert, Melissa M. Goldstein, Jennifer Marshall Graves, Henry T. Greely, Igor V. Grigoriev, Kevin J. Hackett, Neil Hall, David Haussler, Kristofer M. Helgen, Carolyn J. Hogg, Sachiko Isobe, Kȷetill Sigurd Jakobsen, Axel Janke, Erich D. Jarvis, Warren E. Johnson, Steven J. M. Jones, Elinor K. Karlsson, Paul J. Kersey, Jin–Hyoung Kim, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, James H. Leebens–Mack, Xueyan Li, Kerstin Lindblad–Toh, Xin Liu, Jose V. Lopez, Tomas Marques–Bonet, Sophie Mazard, Jonna A. K. Mazet, Camila J. Mazzoni, Eugene W. Myers, Rachel J. O’Neill, Sadye Paez, Hyun Park, Gene E. Robinson, Cristina Roquet, Oliver A. Ryder, Jamal S. M. Sabir, H. Bradley Shaffer, Timothy M. Shank, Jacob S. Sherkow, Pamela S. Soltis, Boping Tang, Leho Tedersoo, Marcela Uliano–Silva, Kun Wang, Xiaofeng Wei, Regina Wetzer, Julia L. Wilson, Xun Xu, Huanming Yang, Anne D. Yoder, Guoȷie Zhang
      Abstract: November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project’s goals,...
      Keywords: Evolution, Introductions, The Earth BioGenome Project: The Launch of a Moonshot for Biology
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2115635118
      Issue No: Vol. 119, No. 4 (2022)
       
  • Why sequence all eukaryotes' [Evolution]

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      Authors: Mark Blaxter; John M. Archibald, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Federica Di Palma, Richard Durbin, Scott V. Edwards, Jennifer A. M. Graves, Kevin J. Hackett, Neil Hall, Erich D. Jarvis, Rebecca N. Johnson, Elinor K. Karlsson, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, Kerstin Lindblad-Toh, Jose V. Lopez, Nancy A. Moran, Gene E. Robinson, Oliver A. Ryder, Beth Shapiro, Pamela S. Soltis, Tandy Warnow, Guojie Zhang, Harris A. Lewin
      Abstract: Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing...
      Keywords: Evolution, Perspectives, The Earth BioGenome Project: The Launch of a Moonshot for Biology
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2115636118
      Issue No: Vol. 119, No. 4 (2022)
       
  • Standards recommendations for the Earth BioGenome Project [Evolution]

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      Authors: Mara K. N. Lawniczak; Richard Durbin, Paul Flicek, Kerstin Lindblad–Toh, Xiaofeng Wei, John M. Archibald, William J. Baker, Katherine Belov, Mark L. Blaxter, Tomas Marques Bonet, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Andrew J. Crawford, Robert P. Davey, Federica Di Palma, Qi Fang, Wilfried Haerty, Neil Hall, Katharina J. Hoff, Kerstin Howe, Erich D. Jarvis, Warren E. Johnson, Rebecca N. Johnson, Paul J. Kersey, Xin Liu, Jose Victor Lopez, Eugene W. Myers, Olga Vinnere Pettersson, Adam M. Phillippy, Monica F. Poelchau, Kim D. Pruitt, Arang Rhie, Juan Carlos Castilla–Rubio, Sunil Kumar Sahu, Nicholas A. Salmon, Pamela S. Soltis, David Swarbreck, Francoise Thibaud–Nissen, Sibo Wang, Jill L. Wegrzyn, Guoȷie Zhang, He Zhang, Harris A. Lewin, Stephen Richards
      Abstract: A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample...
      Keywords: Evolution, Perspectives, The Earth BioGenome Project: The Launch of a Moonshot for Biology
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2115639118
      Issue No: Vol. 119, No. 4 (2022)
       
  • Green plant genomes: What we know in an era of rapidly expanding
           opportunities [Plant Biology]

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      Authors: W. John Kress; Douglas E. Soltis, Paul J. Kersey, Jill L. Wegrzyn, James H. Leebens-Mack, Morgan R. Gostel, Xin Liu, Pamela S. Soltis
      Abstract: Green plants play a fundamental role in ecosystems, human health, and agriculture. As de novo genomes are being generated for all known eukaryotic species as advocated by the Earth BioGenome Project, increasing genomic information on green land plants is essential. However, setting standards for the generation and storage of the...
      Keywords: Plant Biology, Perspectives, The Earth BioGenome Project: The Launch of a Moonshot for Biology
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2115640118
      Issue No: Vol. 119, No. 4 (2022)
       
  • EBP-Colombia and the bioeconomy: Genomics in the service of biodiversity
           conservation and sustainable development [Social Sciences]

    • Free pre-print version: Loading...

      Authors: Joseph E. A. Huddart; Andrew J. Crawford, Arturo L. Luna-Tapia, Silvia Restrepo, Federica Di Palma
      Abstract: The 2016 Peace Agreement has increased access to Colombia’s unique ecosystems, which remain understudied and increasingly under threat. The Colombian government has recently announced its National Bioeconomic Strategy (NBS), founded on the sustainable characterization, management, and conservation of the nation's biodiversity as a means to achieve sustainability and peace. Molecular...
      Keywords: Evolution, Perspectives, The Earth BioGenome Project: The Launch of a Moonshot for Biology, Sustainability Science
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2115641119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Sequence locally, think globally: The Darwin Tree of Life Project
           [Evolution]

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      Abstract: The goals of the Earth Biogenome Project—to sequence the genomes of all eukaryotic life on earth—are as daunting as they are ambitious. The Darwin Tree of Life Project was founded to demonstrate the credibility of these goals and to deliver at-scale genome sequences of unprecedented quality for a biogeographic region:...
      Keywords: Evolution, Perspectives, The Earth BioGenome Project: The Launch of a Moonshot for Biology
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2115642118
      Issue No: Vol. 119, No. 4 (2022)
       
  • Threatened Species Initiative: Empowering conservation action using
           genomic resources [Genetics]

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      Authors: Carolyn J. Hogg; Kym Ottewell, Peter Latch, Maurizio Rossetto, James Biggs, Andrew Gilbert, Sarah Richmond, Katherine Belov
      Abstract: Globally, 15,521 animal species are listed as threatened by the International Union for the Conservation of Nature, and of these less than 3% have genomic resources that can inform conservation management. To combat this, global genome initiatives are developing genomic resources, yet production of a reference genome alone does not...
      Keywords: Genetics, Perspectives, The Earth BioGenome Project: The Launch of a Moonshot for Biology
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2115643118
      Issue No: Vol. 119, No. 4 (2022)
       
  • Darwinian genomics and diversity in the tree of life [Evolution]

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      Authors: Taylorlyn Stephan; Shawn M. Burgess, Hans Cheng, Charles G. Danko, Clare A. Gill, Erich D. Jarvis, Klaus-Peter Koepfli, James E. Koltes, Eric Lyons, Pamela Ronald, Oliver A. Ryder, Lynn M. Schriml, Pamela Soltis, Sue VandeWoude, Huaijun Zhou, Elaine A. Ostrander, Elinor K. Karlsson
      Abstract: Genomics encompasses the entire tree of life, both extinct and extant, and the evolutionary processes that shape this diversity. To date, genomic research has focused on humans, a small number of agricultural species, and established laboratory models. Fewer than 18,000 of ∼2,000,000 eukaryotic species (
      Keywords: Evolution, Perspectives, The Earth BioGenome Project: The Launch of a Moonshot for Biology
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2115644119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Depleted carbon isotope compositions observed at Gale crater, Mars [Earth,
           Atmospheric, and Planetary Sciences]

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      Authors: Christopher H. House; Gregory M. Wong, Christopher R. Webster, Gregory J. Flesch, Heather B. Franz, Jennifer C. Stern, Alex Pavlov, Sushil K. Atreya, Jennifer L. Eigenbrode, Alexis Gilbert, Amy E. Hofmann, Maeva Millan, Andrew Steele, Daniel P. Glavin, Charles A. Malespin, Paul R. Mahaffy
      Abstract: Obtaining carbon isotopic information for organic carbon from Martian sediments has long been a goal of planetary science, as it has the potential to elucidate the origin of such carbon and aspects of Martian carbon cycling. Carbon isotopic values (δ13CVPDB) of the methane released during pyrolysis of 24 powder samples...
      Keywords: Earth, Atmospheric, and Planetary Sciences
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2115651119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Ethical, legal, and social issues in the Earth BioGenome Project [Social
           Sciences]

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      Authors: Jacob S. Sherkow; Katharine B. Barker, Irus Braverman, Robert Cook-Deegan, Richard Durbin, Carla L. Easter, Melissa M. Goldstein, Maui Hudson, W. John Kress, Harris A. Lewin, Debra J. H. Mathews, Catherine McCarthy, Ann M. McCartney, Manuela da Silva, Andrew W. Torrance, Henry T. Greely
      Abstract: The Earth BioGenome Project (EBP) is an audacious endeavor to obtain whole-genome sequences of representatives from all eukaryotic species on Earth. In addition to the project’s technical and organizational challenges, it also faces complicated ethical, legal, and social issues. This paper, from members of the EBP’s Ethical, Legal, and Social...
      Keywords: Evolution, Political Sciences, Perspectives, The Earth BioGenome Project: The Launch of a Moonshot for Biology
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2115859119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Balancing openness with Indigenous data sovereignty: An opportunity to
           leave no one behind in the journey to sequence all of life [Evolution]

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      Authors: Ann M. Mc Cartney; Jane Anderson, Libby Liggins, Maui L. Hudson, Matthew Z. Anderson, Ben TeAika, Janis Geary, Robert Cook-Deegan, Hardip R. Patel, Adam M. Phillippy
      Abstract: The field of genomics has benefited greatly from its “openness” approach to data sharing. However, with the increasing volume of sequence information being created and stored and the growing number of international genomics efforts, the equity of openness is under question. The United Nations Convention of Biodiversity aims to develop...
      Keywords: Evolution, Perspectives, The Earth BioGenome Project: The Launch of a Moonshot for Biology
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2115860119
      Issue No: Vol. 119, No. 4 (2022)
       
  • V-CARMA: A tool for the detection and modification of antigen-specific T
           cells [Immunology and Inflammation]

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      Authors: Xi-zhi J. Guo; Stephen J. Elledge
      Abstract: T cells promote our body’s ability to battle cancers and infectious diseases but can act pathologically in autoimmunity. The recognition of peptides presented by major histocompatibility complex (pMHC) molecules by T cell receptors (TCRs) enables T cell–mediated responses. To modify disease-relevant T cells, new tools to genetically modify T cells...
      Keywords: Immunology and Inflammation
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2116277119
      Issue No: Vol. 119, No. 4 (2022)
       
  • The time complexity of self-assembly [Biophysics and Computational
           Biology]

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      Authors: Florian M. Gartner; Isabella R. Graf, Erwin Frey
      Abstract: Time efficiency of self-assembly is crucial for many biological processes. Moreover, with the advances of nanotechnology, time efficiency in artificial self-assembly becomes ever more important. While structural determinants and the final assembly yield are increasingly well understood, kinetic aspects concerning the time efficiency, however, remain much more elusive. In computer...
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2116373119
      Issue No: Vol. 119, No. 4 (2022)
       
  • A theory of entropic bonding [Applied Physical Sciences]

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      Authors: Thi Vo; Sharon C. Glotzer
      Abstract: Entropy alone can self-assemble hard nanoparticles into colloidal crystals of remarkable complexity whose structures are the same as atomic and molecular crystals, but with larger lattice spacings. Molecular simulation is a powerful tool used extensively to study the self-assembly of ordered phases from disordered fluid phases of atoms, molecules, or...
      Keywords: Applied Physical Sciences
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2116414119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Evidence of magnetism-induced topological protection in the axion
           insulator candidate EuSn2P2 [Physics]

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      Authors: Gian Marco Pierantozzi; Alessandro De Vita, Chiara Bigi, Xin Gui, Hung-Ju Tien, Debashis Mondal, Federico Mazzola, Jun Fujii, Ivana Vobornik, Giovanni Vinai, Alessandro Sala, Cristina Africh, Tien-Lin Lee, Giorgio Rossi, Tay-Rong Chang, Weiwei Xie, Robert J. Cava, Giancarlo Panaccione
      Abstract: We unravel the interplay of topological properties and the layered (anti)ferromagnetic ordering in EuSn2P2, using spin and chemical selective electron and X-ray spectroscopies supported by first-principle calculations. We reveal the presence of in-plane long-range ferromagnetic order triggering topological invariants and resulting in the multiple protection of topological Dirac states. We...
      Keywords: Physics
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2116575119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Fast response times signal social connection in conversation
           [Psychological and Cognitive Sciences]

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      Authors: Emma M. Templeton; Luke J. Chang, Elizabeth A. Reynolds, Marie D. Cone LeBeaumont, Thalia Wheatley
      Abstract: Clicking is one of the most robust metaphors for social connection. But how do we know when two people "click"' We asked pairs of friends and strangers to talk with each other and rate their felt connection. For both friends and strangers, speed in response was a robust predictor of...
      Keywords: Psychological and Cognitive Sciences
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2116915119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Longitudinal clonal dynamics of HIV-1 latent reservoirs measured by
           combination quadruplex polymerase chain reaction and sequencing
           [Microbiology]

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      Authors: Alice Cho; Christian Gaebler, Thiago Olveira, Victor Ramos, Marwa Saad, Julio C. C. Lorenzi, Anna Gazumyan, Susan Moir, Marina Caskey, Tae-Wook Chun, Michel C. Nussenzweig
      Abstract: HIV-1 infection produces a long-lived reservoir of latently infected CD4+ T cells that represents the major barrier to HIV-1 cure. The reservoir contains both intact and defective proviruses, but only the proviruses that are intact can reinitiate infection upon cessation of antiretroviral therapy (ART). Here we combine four-color quantitative PCR...
      Keywords: Microbiology
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2117630119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Multiscale X-ray study of Bacillus subtilis biofilms reveals interlinked
           structural hierarchy and elemental heterogeneity [Biophysics and
           Computational Biology]

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      Authors: David N. Azulay; Oliver Spaeker, Mnar Ghrayeb, Michaela Wilsch–Brauninger, Ernesto Scoppola, Manfred Burghammer, Ivo Zizak, Luca Bertinetti, Yael Politi, Liraz Chai
      Abstract: Biofilms are multicellular microbial communities that encase themselves in an extracellular matrix (ECM) of secreted biopolymers and attach to surfaces and interfaces. Bacterial biofilms are detrimental in hospital and industrial settings, but they can be beneficial, for example, in agricultural as well as in food technology contexts. An essential property...
      Keywords: Microbiology
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2118107119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Neuronal identities derived by misexpression of the POU IV sensory
           determinant in a protovertebrate [Developmental Biology]

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      Authors: Prakriti Paul Chacha; Ryoko Horie, Takehiro G. Kusakabe, Yasunori Sasakura, Mona Singh, Takeo Horie, Michael Levine
      Abstract: The protovertebrate Ciona intestinalis type A (sometimes called Ciona robusta) contains a series of sensory cell types distributed across the head–tail axis of swimming tadpoles. They arise from lateral regions of the neural plate that exhibit properties of vertebrate placodes and neural crest. The sensory determinant POU IV/Brn3 is known...
      Keywords: Developmental Biology
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2118817119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Dynamic multifunctional devices enabled by ultrathin metal nanocoatings
           with optical/photothermal and morphological versatility [Applied Physical
           Sciences]

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      Authors: Songshan Zeng; Zhuoran Yang, Zaili Hou, Cheonjin Park, Michael D. Jones, Hao Ding, Kuangyu Shen, Andrew T. Smith, Henry X. Jin, Bing Wang, Han Jiang, Luyi Sun
      Abstract: Inspired by the intriguing adaptivity of natural life, such as squids and flowers, we propose a series of dynamic and responsive multifunctional devices based on multiscale structural design, which contain metal nanocoating layers overlaid with other micro-/nanoscale soft or rigid layers. Since the optical/photothermal properties of a metal nanocoating are...
      Keywords: Applied Physical Sciences
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2118991119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Lipid membranes modulate the activity of RNA through sequence-dependent
           interactions [Biochemistry]

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      Authors: Tomasz Czerniak; James P. Saenz
      Abstract: RNA is a ubiquitous biomolecule that can serve as both catalyst and information carrier. Understanding how RNA bioactivity is controlled is crucial for elucidating its physiological roles and potential applications in synthetic biology. Here, we show that lipid membranes can act as RNA organization platforms, introducing a mechanism for riboregulation....
      Keywords: Biochemistry
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2119235119
      Issue No: Vol. 119, No. 4 (2022)
       
  • CMG helicase can use ATP{gamma}S to unwind DNA: Implications for the
           rate-limiting step in the reaction mechanism [Biochemistry]

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      Authors: Nina Y. Yao; Dan Zhang, Olga Yurieva, Michael E. O’Donnell
      Abstract: The adenosine triphosphate (ATP) analog ATPγS often greatly slows or prevents enzymatic ATP hydrolysis. The eukaryotic CMG (Cdc45, Mcm2 to 7, GINS) replicative helicase is presumed unable to hydrolyze ATPγS and thus unable to perform DNA unwinding, as documented for certain other helicases. Consequently, ATPγS is often used to “preload”...
      Keywords: Biochemistry
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2119580119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Atomic structure of Lanreotide nanotubes revealed by cryo-EM [Biophysics
           and Computational Biology]

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      Authors: Laura Pieri; Fengbin Wang, Ana–Andreea Arteni, Matthiȷn Vos, Jean–Marie Winter, Marie–Helene Le Du, Franck Artzner, Frederic Gobeaux, Pierre Legrand, Yves Boulard, Stephane Bressanelli, Edward H. Egelman, Maite Paternostre
      Abstract: Functional and versatile nano- and microassemblies formed by biological molecules are found at all levels of life, from cell organelles to full organisms. Understanding the chemical and physicochemical determinants guiding the formation of these assemblies is crucial not only to understand the biological processes they carry out but also to...
      Keywords: Biophysics and Computational Biology
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2120346119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Using big data to track major shifts in human cognition [Psychological and
           Cognitive Sciences]

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      Authors: Simon DeDeo
      Abstract: Scheffer et al.’s (1) exciting new work reports an historic rearrangement, occurring in the late 20th century, of the balance between reason and emotion. Its approach is part of a new trend in the psychological sciences that uses extremely large volumes of text to study basic patterns of human cognition....
      Keywords: Psychological and Cognitive Sciences, Commentaries
      PubDate: 2022-01-18T13:32:53-08:00
      DOI: 10.1073/pnas.2121300119
      Issue No: Vol. 119, No. 4 (2022)
       
  • Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes
           [Biophysics and Computational Biology]

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      Authors: Juan Rodriguez-Rivas; Giancarlo Croce, Maureen Muscat, Martin Weigt
      Abstract: The emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major concern given their potential impact on the transmissibility and pathogenicity of the virus as well as the efficacy of therapeutic interventions. Here, we predict the mutability of all positions in SARS-CoV-2 protein domains to...
      Keywords: Coronavirus (COVID-19)
      PubDate: 2022-01-12T12:53:29-08:00
      DOI: 10.1073/pnas.2113118119
      Issue No: Vol. 119, No. 4 (2022)
       
  • SNX27 suppresses SARS-CoV-2 infection by inhibiting viral lysosome/late
           endosome entry [Microbiology]

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      Authors: Bo Yang; Yuanyuan Jia, Yumin Meng, Ying Xue, Kefang Liu, Yan Li, Shichao Liu, Xiaoxiong Li, Kaige Cui, Lina Shang, Tianyou Cheng, Zhichao Zhang, Yingxiang Hou, Xiaozhu Yang, Hong Yan, Liqiang Duan, Zhou Tong, Changxin Wu, Zhida Liu, Shan Gao, Shu Zhuo, Weijin Huang, George Fu Gao, Jianxun Qi, Guijun Shang
      Abstract: After binding to its cell surface receptor angiotensin converting enzyme 2 (ACE2), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters the host cell through directly fusing with plasma membrane (cell surface pathway) or undergoing endocytosis traveling to lysosome/late endosome for membrane fusion (endocytic pathway). However, the endocytic entry regulation by...
      Keywords: Microbiology, Coronavirus (COVID-19)
      PubDate: 2022-01-12T12:53:29-08:00
      DOI: 10.1073/pnas.2117576119
      Issue No: Vol. 119, No. 4 (2022)
       
  • In This Issue [This Week in PNAS]

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      Abstract: PLANT BIOLOGY Eucalyptus trees. Image credit: pixabay/ekaterinvor. MicroRNA molecules mediate plant–fungus merger Mutualistic and pathogenic microbes can transfer small RNA molecules, such as microRNAs, to plant hosts to help sustain symbiosis or infection. However, the role of cross-kingdom RNA transfer in establishing mutualistic mycorrhizal relationships, between fungi and plants, is...
      Keywords: In This Issue
      PubDate: 2022-01-18T10:35:27-08:00
      DOI: 10.1073/iti0322119
      Issue No: Vol. 119, No. 3 (2022)
       
  • A tribute to Eddy Fischer (April 6, 1920-August 27, 2021): Passionate
           biochemist and mentor [Retrospectives]

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      Authors: Susan S. Taylor; Tony Hunter, Jean-Pierre Changeux
      Abstract: Edmond (Eddy) Fischer was one of the great biochemists of the 20th and 21st centuries. He was also a gifted pianist, an avid mountain climber, and a pilot, a true man of the world who lived on three continents and spoke many languages fluently. Having spent his childhood in China...
      Keywords: Retrospectives
      PubDate: 2022-01-18T10:35:27-08:00
      DOI: 10.1073/pnas.2121815119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Celebrating 20 years of live single-actin-filament studies with five
           golden rules [Biochemistry]

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      Authors: Hugo Wioland; Antoine Jegou, Guillaume Romet–Lemonne
      Abstract: The precise assembly and disassembly of actin filaments is required for several cellular processes, and their regulation has been scrutinized for decades. Twenty years ago, a handful of studies marked the advent of a new type of experiment to study actin dynamics: using optical microscopy to look at individual events,...
      Keywords: Biochemistry, Perspectives
      PubDate: 2022-01-18T10:35:27-08:00
      DOI: 10.1073/pnas.2109506119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Mitoribosomal small subunit maturation involves formation of
           initiation-like complexes [Biochemistry]

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      Authors: Tea Lenarčič; Moritz Niemann, David J. F. Ramrath, Salvatore Calderaro, Timo Flugel, Martin Saurer, Marc Leibundgut, Daniel Boehringer, Celine Prange, Elke K. Horn, Andre Schneider, Nenad Ban
      Abstract: Mitochondrial ribosomes (mitoribosomes) play a central role in synthesizing mitochondrial inner membrane proteins responsible for oxidative phosphorylation. Although mitoribosomes from different organisms exhibit considerable structural variations, recent insights into mitoribosome assembly suggest that mitoribosome maturation follows common principles and involves a number of conserved assembly factors. To investigate the steps...
      Keywords: Inaugural Articles, Biochemistry
      PubDate: 2022-01-18T10:35:27-08:00
      DOI: 10.1073/pnas.2114710118
      Issue No: Vol. 119, No. 3 (2022)
       
  • Double-layer structure of the Pt(111)-aqueous electrolyte interface
           [Chemistry]

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      Authors: Kasinath Ojha; Katharina Doblhoff-Dier, Marc T. M. Koper
      Abstract: We present detailed measurements of the double-layer capacitance of the Pt(111)–electrolyte interface close to the potential of zero charge (PZC) in the presence of several different electrolytes consisting of anions and cations that are considered to be nonspecifically adsorbed. For low electrolyte concentrations, we show strong deviations from traditional Gouy–Chapman–Stern...
      Keywords: Chemistry
      PubDate: 2022-01-18T10:35:27-08:00
      DOI: 10.1073/pnas.2116016119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Genomic and transcriptomic analyses of the subterranean termite
           Reticulitermes speratus: Gene duplication facilitates social evolution
           [Evolution]

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      Authors: Shuji Shigenobu; Yoshinobu Hayashi, Dai Watanabe, Gaku Tokuda, Masaru Y. Hojo, Kouhei Toga, Ryota Saiki, Hajime Yaguchi, Yudai Masuoka, Ryutaro Suzuki, Shogo Suzuki, Moe Kimura, Masatoshi Matsunami, Yasuhiro Sugime, Kohei Oguchi, Teruyuki Niimi, Hiroki Gotoh, Masaru K. Hojo, Satoshi Miyazaki, Atsushi Toyoda, Toru Miura, Kiyoto Maekawa
      Abstract: Termites are model social organisms characterized by a polyphenic caste system. Subterranean termites (Rhinotermitidae) are ecologically and economically important species, including acting as destructive pests. Rhinotermitidae occupies an important evolutionary position within the clade representing a transitional taxon between the higher (Termitidae) and lower (other families) termites. Here, we report...
      Keywords: Evolution
      PubDate: 2022-01-18T10:35:27-08:00
      DOI: 10.1073/pnas.2110361119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Radiotherapy transiently reduces the sensitivity of cancer cells to
           lymphocyte cytotoxicity [Immunology and Inflammation]

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      Authors: Karoliina Tuomela; Debayan Mukherȷee, Ashley R. Ambrose, Ashish Harikrishnan, Holly Mole, Adam Hurlstone, Bȷorn Onfelt, Jamie Honeychurch, Daniel M. Davis
      Abstract: The impact of radiotherapy on the interaction between immune cells and cancer cells is important not least because radiotherapy can be used alongside immunotherapy as a cancer treatment. Unexpectedly, we found that X-ray irradiation of cancer cells induced significant resistance to natural killer (NK) cell killing. This was true across...
      Keywords: Immunology and Inflammation
      PubDate: 2022-01-18T10:35:27-08:00
      DOI: 10.1073/pnas.2111900119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Eosinophils regulate intra-adipose axonal plasticity [Immunology and
           Inflammation]

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      Authors: Xia Meng; Xinmin Qian, Xiaofan Ding, Wenjing Wang, Xia Yin, Guanglei Zhuang, Wenwen Zeng
      Abstract: Sympathetic innervation regulates energy balance, and the nerve density in the adipose tissues changes under various metabolic states, resulting in altered neuronal control and conferring resilience to metabolic challenges. However, the impact of the immune milieu on neuronal innervation is not known. Here, we examined the regulatory role on nerve...
      Keywords: Immunology and Inflammation
      PubDate: 2022-01-18T10:35:27-08:00
      DOI: 10.1073/pnas.2112281119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Politicians polarize and experts depolarize public support for COVID-19
           management policies across countries [Psychological and Cognitive
           Sciences]

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      Authors: Alexandra Flores; Jennifer C. Cole, Stephan Dickert, Kimin Eom, Gabriela M. Jiga–Boy, Tehila Kogut, Riley Loria, Marcus Mayorga, Eric J. Pedersen, Beatriz Pereira, Enrico Rubaltelli, David K. Sherman, Paul Slovic, Daniel Vastfȷall, Leaf Van Boven
      Abstract: Political polarization impeded public support for policies to reduce the spread of COVID-19, much as polarization hinders responses to other contemporary challenges. Unlike previous theory and research that focused on the United States, the present research examined the effects of political elite cues and affective polarization on support for policies...
      Keywords: Psychological and Cognitive Sciences, Coronavirus Related
      PubDate: 2022-01-18T10:35:27-08:00
      DOI: 10.1073/pnas.2117543119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Correction for KaramiNejadRanjbar et al., Consequences of resistance
           evolution in a Cas9-based sex conversion-suppression gene drive for insect
           pest management [Applied Biological Sciences]

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      Abstract: APPLIED BIOLOGICAL SCIENCES Correction for “Consequences of resistance evolution in a Cas9-based sex conversion-suppression gene drive for insect pest management,” by Mohammad KaramiNejadRanjbar, Kolja N. Eckermann, Hassan M. M. Ahmed, Héctor M. Sánchez C., Stefan Dippel, John M. Marshall, and Ernst A. Wimmer, which was first published May 29, 2018;...
      Keywords: Applied Biological Sciences, Corrections
      PubDate: 2022-01-18T10:35:27-08:00
      DOI: 10.1073/pnas.2121101118
      Issue No: Vol. 119, No. 3 (2022)
       
  • Correction for Molimau-Samasoni et al., Functional genomics and
           metabolomics advance the ethnobotany of the Samoan traditional medicine
           “matalafi” [Plant Biology]

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      Abstract: PLANT BIOLOGY, SOCIAL SCIENCES Correction for “Functional genomics and metabolomics advance the ethnobotany of the Samoan traditional medicine “matalafi”,” by Seeseei Molimau-Samasoni, Victoria Helen Woolner, Su’emalo Talie Foliga, Katharina Robichon, Vimal Patel, Sarah K. Andreassend, Jeffrey P. Sheridan, Tama Te Kawa, David Gresham, Darach Miller, Daniel J. Sinclair, Anne C....
      Keywords: Plant Biology, Social Sciences, Corrections
      PubDate: 2022-01-18T10:35:27-08:00
      DOI: 10.1073/pnas.2121327119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Correction to Supporting Information for Mehlhoff et al., Collateral
           fitness effects of mutations [Evolution]

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      Abstract: EVOLUTION Correction to Supporting Information for “Collateral fitness effects of mutations,” by Jacob D. Mehlhoff, Frank W. Stearns, Dahlia Rohm, Buheng Wang, Erh-Yeh Tsou, Nisita Dutta, Meng-Hsuan Hsiao, Courtney E. Gonzalez, Alan F. Rubin, and Marc Ostermeier, which was first published May 8, 2020; 10.1073/pnas.1918680117 (Proc. Natl. Acad. Sci. U.S.A....
      PubDate: 2022-01-18T10:35:27-08:00
      DOI: 10.1073/pnas.2121396119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Correction for Lu et al., Robust high-temperature potassium-ion batteries
           enabled by carboxyl functional group energy storage [Chemistry]

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      Abstract: CHEMISTRY Correction for “Robust high-temperature potassium-ion batteries enabled by carboxyl functional group energy storage,” by Xianlu Lu, Xuenan Pan, Dongdong Zhang, Zhi Fang, Shang Xu, Yu Ma, Qiao Liu, Gang Shao, Dingfa Fu, Jie Teng, and Weiyou Yang, which published August 24, 2021; 10.1073/pnas.2110912118 (Proc. Natl. Acad. Sci. U.S.A. 118,...
      Keywords: Chemistry, Corrections
      PubDate: 2022-01-18T10:35:27-08:00
      DOI: 10.1073/pnas.2121880119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Inhibition of EZH2 transactivation function sensitizes solid tumors to
           genotoxic stress [Medical Sciences]

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      Authors: Yiȷi Liao; Chen–Hao Chen, Tengfei Xiao, Barbara de la Pena Avalos, Eloise V. Dray, Changmeng Cai, Shuai Gao, Neel Shah, Zhao Zhang, Avery Feit, Pengya Xue, Zhiȷie Liu, Mei Yang, Ji Hoon Lee, Han Xu, Wei Li, Shenglin Mei, Roodolph S. Pierre, Shaokun Shu, Teng Fei, Melissa Duarte, Jin Zhao, James E. Bradner, Kornelia Polyak, Philip W. Kantoff, Henry Long, Steven P. Balk, X. Shirley Liu, Myles Brown, Kexin Xu
      Abstract: Drugs that block the activity of the methyltransferase EZH2 are in clinical development for the treatment of non-Hodgkin lymphomas harboring EZH2 gain-of-function mutations that enhance its polycomb repressive function. We have previously reported that EZH2 can act as a transcriptional activator in castration-resistant prostate cancer (CRPC). Now we show that...
      Keywords: Medical Sciences
      PubDate: 2022-01-14T11:49:04-08:00
      DOI: 10.1073/pnas.2105898119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Regional synapse gain and loss accompany memory formation in larval
           zebrafish [Neuroscience]

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      Authors: William P. Dempsey; Zhuowei Du, Anna Nadtochiy, Colton D. Smith, Karl Czajkowski, Andrey Andreev, Drew N. Robson, Jennifer M. Li, Serina Applebaum, Thai V. Truong, Carl Kesselman, Scott E. Fraser, Don B. Arnold
      Abstract: Defining the structural and functional changes in the nervous system underlying learning and memory represents a major challenge for modern neuroscience. Although changes in neuronal activity following memory formation have been studied [B. F. Grewe et al., Nature 543, 670–675 (2017); M. T. Rogan, U. V. Stäubli, J. E. LeDoux,...
      Keywords: Neuroscience
      PubDate: 2022-01-14T11:49:04-08:00
      DOI: 10.1073/pnas.2107661119
      Issue No: Vol. 119, No. 3 (2022)
       
  • CD169+ macrophages in lymph node and spleen critically depend on dual RANK
           and LTbetaR signaling [Immunology and Inflammation]

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      Authors: Abdouramane Camara; Alice C. Lavanant, Jun Abe, Henri Lee Desforges, Yannick O. Alexandre, Erika Girardi, Zinaida Igamberdieva, Kenichi Asano, Masato Tanaka, Thomas Hehlgans, Klaus Pfeffer, Sebastien Pfeffer, Scott N. Mueller, Jens V. Stein, Christopher G. Mueller
      Abstract: CD169+ macrophages reside in lymph node (LN) and spleen and play an important role in the immune defense against pathogens. As resident macrophages, they are responsive to environmental cues to shape their tissue-specific identity. We have previously shown that LN CD169+ macrophages require RANKL for formation of their niche and...
      Keywords: Immunology and Inflammation
      PubDate: 2022-01-14T11:49:04-08:00
      DOI: 10.1073/pnas.2108540119
      Issue No: Vol. 119, No. 3 (2022)
       
  • A functional division of Drosophila sweet taste neurons that is
           value-based and task-specific [Neuroscience]

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      Authors: Hsueh-Ling Chen; Dorsa Motevalli, Ulrich Stern, Chung-Hui Yang
      Abstract: Sucrose is an attractive feeding substance and a positive reinforcer for Drosophila. But Drosophila females have been shown to robustly reject a sucrose-containing option for egg-laying when given a choice between a plain and a sucrose-containing option in specific contexts. How the sweet taste system of Drosophila promotes context-dependent devaluation...
      Keywords: Neuroscience
      PubDate: 2022-01-14T11:49:04-08:00
      DOI: 10.1073/pnas.2110158119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Targeted vaccination and the speed of SARS-CoV-2 adaptation [Evolution]

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      Authors: Sylvain Gandon; Sebastien Lion
      Abstract: The limited supply of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) raises the question of targeted vaccination. Many countries have opted to vaccinate older and more sensitive hosts first to minimize the disease burden. However, what are the evolutionary consequences of targeted vaccination' We clarify the consequences of...
      Keywords: Evolution, Coronavirus Related
      PubDate: 2022-01-14T11:49:04-08:00
      DOI: 10.1073/pnas.2110666119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Volatile-consuming reactions fracture rocks and self-accelerate fluid flow
           in the lithosphere [Earth, Atmospheric, and Planetary Sciences]

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      Authors: Masaoki Uno; Kodai Koyanagawa, Hisamu Kasahara, Atsushi Okamoto, Noriyoshi Tsuchiya
      Abstract: Hydration and carbonation reactions within the Earth cause an increase in solid volume by up to several tens of vol%, which can induce stress and rock fracture. Observations of naturally hydrated and carbonated peridotite suggest that permeability and fluid flow are enhanced by reaction-induced fracturing. However, permeability enhancement during solid-volume–increasing...
      Keywords: Earth, Atmospheric, and Planetary Sciences
      PubDate: 2022-01-14T11:49:04-08:00
      DOI: 10.1073/pnas.2110776118
      Issue No: Vol. 119, No. 3 (2022)
       
  • A new angle on odor trail tracking [Biophysics and Computational Biology]

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      Authors: Siddharth Jayakumar; Venkatesh N. Murthy
      Abstract: Animals navigate by making a series of decisions using external stimuli and any internal model (or map) of the world they may have formed. Many animals, including ants, dogs, and rodents, spontaneously track scent trails, which are chemical cues that form navigational guides that allow animals to locate food, mates,...
      Keywords: Commentaries
      PubDate: 2022-01-14T11:49:04-08:00
      DOI: 10.1073/pnas.2121332119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Genome-wide screens identify specific drivers of mutant hTERT promoters
           [Cell Biology]

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      Authors: Raghuvaran Shanmugam; Mert Burak Ozturk, Joo-Leng Low, Semih Can Akincilar, Joelle Yi Heng Chua, Matan Thangavelu Thangavelu, Giridharan Periyasamy, Ramanuj DasGupta, Vinay Tergaonkar
      Abstract: Cancer-specific hTERT promoter mutations reported in 19% of cancers result in enhanced telomerase activity. Understanding the distinctions between transcriptional regulation of wild-type (WT) and mutant (Mut) hTERT promoters may open up avenues for development of inhibitors which specially block hTERT expression in cancer cells. To comprehensively identify physiological regulators of...
      Keywords: Cell Biology
      PubDate: 2022-01-13T12:15:47-08:00
      DOI: 10.1073/pnas.2105171119
      Issue No: Vol. 119, No. 3 (2022)
       
  • The redundancy and diversity between two novel PKC isotypes that regulate
           learning in Caenorhabditis elegans [Neuroscience]

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      Authors: Shingo Hiroki; Yuichi Iino
      Abstract: The nematode Caenorhabditis elegans learns the concentration of NaCl and moves toward the previously experienced concentration. In this behavior, the history of NaCl concentration change is reflected in the level of diacylglycerol and the activity of protein kinase C, PKC-1, in the gustatory sensory neuron ASER and determines the direction...
      Keywords: Neuroscience
      PubDate: 2022-01-13T12:15:47-08:00
      DOI: 10.1073/pnas.2106974119
      Issue No: Vol. 119, No. 3 (2022)
       
  • A connectivity-constrained computational account of topographic
           organization in primate high-level visual cortex [Neuroscience]

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      Authors: Nicholas M. Blauch; Marlene Behrmann, David C. Plaut
      Abstract: Inferotemporal (IT) cortex in humans and other primates is topographically organized, containing multiple hierarchically organized areas selective for particular domains, such as faces and scenes. This organization is commonly viewed in terms of evolved domain-specific visual mechanisms. Here, we develop an alternative, domain-general and developmental account of IT cortical organization....
      Keywords: Neuroscience
      PubDate: 2022-01-13T12:15:47-08:00
      DOI: 10.1073/pnas.2112566119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Ribosomally derived lipopeptides containing distinct fatty acyl moieties
           [Biochemistry]

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      Authors: Florian Hubrich; Nina M. Bosch, Clara Chepkirui, Brandon I. Morinaka, Michael Rust, Muriel Gugger, Serina L. Robinson, Anna L. Vagstad, Jorn Piel
      Abstract: Lipopeptides represent a large group of microbial natural products that include important antibacterial and antifungal drugs and some of the most-powerful known biosurfactants. The vast majority of lipopeptides comprise cyclic peptide backbones N-terminally equipped with various fatty acyl moieties. The known compounds of this type are biosynthesized by nonribosomal peptide...
      Keywords: Biochemistry
      PubDate: 2022-01-13T12:15:47-08:00
      DOI: 10.1073/pnas.2113120119
      Issue No: Vol. 119, No. 3 (2022)
       
  • PDGF-D-PDGFR{beta} signaling enhances IL-15-mediated human natural killer
           cell survival [Immunology and Inflammation]

    • Free pre-print version: Loading...

      Authors: Shoubao Ma; Tingting Tang, Xiaojin Wu, Anthony G. Mansour, Ting Lu, Jianying Zhang, Li-Shu Wang, Michael A. Caligiuri, Jianhua Yu
      Abstract: The axis of platelet-derived growth factor (PDGF) and PDGF receptor-beta (PDGFRβ) plays prominent roles in cell growth and motility. In addition, PDGF-D enhances human natural killer (NK) cell effector functions when binding to the NKp44 receptor. Here, we report an additional but previously unknown role of PDGF-D, whereby it mediates...
      Keywords: Immunology and Inflammation
      PubDate: 2022-01-13T12:15:47-08:00
      DOI: 10.1073/pnas.2114134119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Discovery of a dual-action small molecule that improves neuropathological
           features of Alzheimer’s disease mice [Neuroscience]

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      Authors: Min Hee Park; Kang Ho Park, Byung Jo Choi, Wan Hui Han, Hee Ji Yoon, Hye Yoon Jung, Jihoon Lee, Im-Sook Song, Dong Yu Lim, Min-Koo Choi, Yang-Ha Lee, Cheol-Min Park, Ming Wang, Jihoon Jo, Hee-Jin Kim, Seung Hyun Kim, Edward H. Schuchman, Hee Kyung Jin, Jae-sung Bae
      Abstract: Alzheimer’s disease (AD) is characterized by complex, multifactorial neuropathology, suggesting that small molecules targeting multiple neuropathological factors are likely required to successfully impact clinical progression. Acid sphingomyelinase (ASM) activation has been recognized as an important contributor to these neuropathological features in AD, leading to the concept of using ASM inhibitors...
      Keywords: Neuroscience
      PubDate: 2022-01-13T12:15:47-08:00
      DOI: 10.1073/pnas.2115082119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Intestinal commensal microbiota and cytokines regulate Fut2+ Paneth cells
           for gut defense [Immunology and Inflammation]

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      Authors: Mariko Kamioka; Yoshiyuki Goto, Kiminori Nakamura, Yuki Yokoi, Rina Sugimoto, Shuya Ohira, Yosuke Kurashima, Shingo Umemoto, Shintaro Sato, Jun Kunisawa, Yu Takahashi, Steven E. Domino, Jean-Christophe Renauld, Susumu Nakae, Yoichiro Iwakura, Peter B. Ernst, Tokiyoshi Ayabe, Hiroshi Kiyono
      Abstract: Paneth cells are intestinal epithelial cells that release antimicrobial peptides, such as α-defensin as part of host defense. Together with mesenchymal cells, Paneth cells provide niche factors for epithelial stem cell homeostasis. Here, we report two subtypes of murine Paneth cells, differentiated by their production and utilization of fucosyltransferase 2...
      Keywords: Immunology and Inflammation
      PubDate: 2022-01-13T12:15:47-08:00
      DOI: 10.1073/pnas.2115230119
      Issue No: Vol. 119, No. 3 (2022)
       
  • The role of ATXR6 expression in modulating genome stability and
           transposable element repression in Arabidopsis [Genetics]

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      Authors: Magdalena E. Potok; Zhenhui Zhong, Colette L. Picard, Qikun Liu, Truman Do, Cassidy E. Jacobsen, Ocean Sakr, Bilguudei Naranbaatar, Ruwan Thilakaratne, Zhanna Khnkoyan, Megan Purl, Harrison Cheng, Helena Vervaet, Suhua Feng, Shima Rayatpisheh, James A. Wohlschlegel, Ronan C. O’Malley, Joseph R. Ecker, Steven E. Jacobsen
      Abstract: ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements (TEs), chromocenter decompaction, and genomic instability characterized by accumulation of...
      Keywords: Genetics
      PubDate: 2022-01-13T12:15:47-08:00
      DOI: 10.1073/pnas.2115570119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Why postmortems fail [Political Sciences]

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      Authors: Robert Jervis
      Abstract: Most high-profile disasters are followed by demands for an investigation into what went wrong. Even before they start, calls for finding the missed warning signs and an explanation for why people did not “connect the dots” will be common. Unfortunately, however, the same combination of political pressures and the failure...
      Keywords: Inaugural Articles, Political Sciences
      PubDate: 2022-01-13T12:15:47-08:00
      DOI: 10.1073/pnas.2116638118
      Issue No: Vol. 119, No. 3 (2022)
       
  • Floxed exon (Flexon): A flexibly positioned stop cassette for
           recombinase-mediated conditional gene expression [Genetics]

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      Authors: Justin M. Shaffer; Iva Greenwald
      Abstract: Conditional gene expression is a powerful tool for genetic analysis of biological phenomena. In the widely used “lox-stop-lox” approach, insertion of a stop cassette consisting of a series of stop codons and polyadenylation signals flanked by lox sites into the 5′ untranslated region (UTR) of a gene prevents expression until...
      Keywords: Genetics
      PubDate: 2022-01-13T12:15:47-08:00
      DOI: 10.1073/pnas.2117451119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Cobalt: A must-have element for life and livelihood [Chemistry]

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      Authors: Michael J. Russell
      Abstract: Cobalt is in the news—demanded by life’s metabolisms and seemingly irreplaceable in our technological world, yet the element averages only 25 ppm in Earth’s crust. So, impending deficiency for both life and technology is always looming. For humans and other animals, cobalt is the active center of vitamin B12 involved...
      Keywords: Chemistry, Commentaries
      PubDate: 2022-01-13T12:15:47-08:00
      DOI: 10.1073/pnas.2121307119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Stem-loop formation drives RNA folding in mechanical unzipping experiments
           [Biophysics and Computational Biology]

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      Authors: Paolo Rissone; Cristiano V. Bizarro, Felix Ritort
      Abstract: Accurate knowledge of RNA hybridization is essential for understanding RNA structure and function. Here we mechanically unzip and rezip a 2-kbp RNA hairpin and derive the 10 nearest-neighbor base pair (NNBP) RNA free energies in sodium and magnesium with 0.1 kcal/mol precision using optical tweezers. Notably, force–distance curves (FDCs) exhibit...
      Keywords: Biophysics and Computational Biology
      PubDate: 2022-01-12T12:51:49-08:00
      DOI: 10.1073/pnas.2025575119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Spurious normativity enhances learning of compliance and enforcement
           behavior in artificial agents [Social Sciences]

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      Authors: Raphael Koster; Dylan Hadfield–Menell, Richard Everett, Laura Weidinger, Gillian K. Hadfield, Joel Z. Leibo
      Abstract: How do societies learn and maintain social norms' Here we use multiagent reinforcement learning to investigate the learning dynamics of enforcement and compliance behaviors. Artificial agents populate a foraging environment and need to learn to avoid a poisonous berry. Agents learn to avoid eating poisonous berries better when doing so...
      Keywords: Social Sciences
      PubDate: 2022-01-12T12:51:49-08:00
      DOI: 10.1073/pnas.2106028118
      Issue No: Vol. 119, No. 3 (2022)
       
  • SHORT-ROOT paralogs mediate feedforward regulation of D-type cyclin to
           promote nodule formation in soybean [Developmental Biology]

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      Authors: Chunhua Wang; Meng Li, Yang Zhao, Nengsong Liang, Haiyang Li, Pengxue Li, Liling Yang, Mengyuan Xu, Xinxin Bian, Mengxue Wang, Shasha Wu, Xufang Niu, Mengyao Wang, Xinxin Li, Yi Sang, Wentao Dong, Ertao Wang, Kimberly L. Gallagher, Shuang Wu
      Abstract: Nitrogen fixation in soybean takes place in root nodules that arise from de novo cell divisions in the root cortex. Although several early nodulin genes have been identified, the mechanism behind the stimulation of cortical cell division during nodulation has not been fully resolved. Here we provide evidence that two...
      Keywords: Developmental Biology
      PubDate: 2022-01-12T12:51:49-08:00
      DOI: 10.1073/pnas.2108641119
      Issue No: Vol. 119, No. 3 (2022)
       
  • LRRTM3 regulates activity-dependent synchronization of synapse properties
           in topographically connected hippocampal neural circuits [Neuroscience]

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      Authors: Jinhu Kim; Dongseok Park, Na-Young Seo, Taek-Han Yoon, Gyu Hyun Kim, Sang-Hoon Lee, Jinsoo Seo, Ji Won Um, Kea Joo Lee, Jaewon Ko
      Abstract: Synaptic cell-adhesion molecules (CAMs) organize the architecture and properties of neural circuits. However, whether synaptic CAMs are involved in activity-dependent remodeling of specific neural circuits is incompletely understood. Leucine-rich repeat transmembrane protein 3 (LRRTM3) is required for the excitatory synapse development of hippocampal dentate gyrus (DG) granule neurons. Here, we...
      Keywords: Neuroscience
      PubDate: 2022-01-12T12:51:49-08:00
      DOI: 10.1073/pnas.2110196119
      Issue No: Vol. 119, No. 3 (2022)
       
  • GATOR2 complex-mediated amino acid signaling regulates brain myelination
           [Neuroscience]

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      Authors: Zongyan Yu; Zhiwen Yang, Guoru Ren, Yingjie Wang, Xiang Luo, Feiyan Zhu, Shouyang Yu, Lanlan Jia, Mina Chen, Paul F. Worley, Bo Xiao
      Abstract: Amino acids are essential for cell growth and metabolism. Amino acid and growth factor signaling pathways coordinately regulate the mechanistic target of rapamycin complex 1 (mTORC1) kinase in cell growth and organ development. While major components of amino acid signaling mechanisms have been identified, their biological functions in organ development...
      Keywords: Neuroscience
      PubDate: 2022-01-12T12:51:49-08:00
      DOI: 10.1073/pnas.2110917119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Reciprocal modulation of long noncoding RNA EMS and p53 regulates
           tumorigenesis [Cell Biology]

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      Authors: Chenfeng Wang; Yang Yang, Xianning Wu, Jingxin Li, Kaiyue Liu, Debao Fang, Bingyan Li, Ge Shan, Xinyu Mei, Fang Wang, Yide Mei
      Abstract: p53 plays a central role in tumor suppression. Emerging evidence suggests long noncoding RNA (lncRNA) as an important class of regulatory molecules that control the p53 signaling. Here, we report that the oncogenic lncRNA E2F1 messenger RNA (mRNA) stabilizing factor (EMS) and p53 mutually repress each other’s expression. EMS is...
      Keywords: Cell Biology
      PubDate: 2022-01-12T12:51:49-08:00
      DOI: 10.1073/pnas.2111409119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Reevaluation of the role of LIP-1 as an ERK/MPK-1 dual specificity
           phosphatase in the C. elegans germline [Developmental Biology]

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      Authors: Debabrata Das; Jacob Seemann, David Greenstein, Tim Schedl, Swathi Arur
      Abstract: The fidelity of a signaling pathway depends on its tight regulation in space and time. Extracellular signal-regulated kinase (ERK) controls wide-ranging cellular processes to promote organismal development and tissue homeostasis. ERK activation depends on a reversible dual phosphorylation on the TEY motif in its active site by ERK kinase (MEK)...
      Keywords: Developmental Biology
      PubDate: 2022-01-12T12:51:49-08:00
      DOI: 10.1073/pnas.2113649119
      Issue No: Vol. 119, No. 3 (2022)
       
  • RNA polymerase II trapped on a molecular treadmill: Structural basis of
           persistent transcriptional arrest by a minor groove DNA binder
           [Biochemistry]

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      Authors: Juntaek Oh; Tiezheng Jia, Jun Xu, Jenny Chong, Peter B. Dervan, Dong Wang
      Abstract: Elongating RNA polymerase II (Pol II) can be paused or arrested by a variety of obstacles. These obstacles include DNA lesions, DNA-binding proteins, and small molecules. Hairpin pyrrole-imidazole (Py-Im) polyamides bind to the minor groove of DNA in a sequence-specific manner and induce strong transcriptional arrest. Remarkably, this Py-Im–induced Pol...
      Keywords: Biochemistry
      PubDate: 2022-01-12T12:51:49-08:00
      DOI: 10.1073/pnas.2114065119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Functional communication between IP3R and STIM2 at subthreshold stimuli is
           a critical checkpoint for initiation of SOCE [Physiology]

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      Authors: Moaz Ahmad; Hwei Ling Ong, Hassan Saadi, Ga-Yeon Son, Zahra Shokatian, Lara E. Terry, Mohamed Trebak, David I. Yule, Indu Ambudkar
      Abstract: Stromal interaction molecules, STIM1 and STIM2, sense decreases in the endoplasmic reticulum (ER) [Ca2+] ([Ca2+]ER) and cluster in ER–plasma membrane (ER–PM) junctions where they recruit and activate Orai1. While STIM1 responds when [Ca2+]ER is relatively low, STIM2 displays constitutive clustering in the junctions and is suggested to regulate basal Ca2+...
      Keywords: Physiology
      PubDate: 2022-01-12T12:51:49-08:00
      DOI: 10.1073/pnas.2114928118
      Issue No: Vol. 119, No. 3 (2022)
       
  • Microscopic mechanisms of cooperative communications within single
           nanocatalysts [Chemistry]

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      Authors: Bhawakshi Punia; Srabanti Chaudhury, Anatoly B. Kolomeisky
      Abstract: Catalysis is a method of accelerating chemical reactions that is critically important for fundamental research as well as for industrial applications. It has been recently discovered that catalytic reactions on metal nanoparticles exhibit cooperative effects. The mechanism of these observations, however, remains not well understood. In this work, we present...
      Keywords: Chemistry
      PubDate: 2022-01-12T12:51:49-08:00
      DOI: 10.1073/pnas.2115135119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Expanding quasiperiodicity in soft matter: Supramolecular decagonal
           quasicrystals by binary giant molecule blends [Chemistry]

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      Authors: Yuchu Liu; Tong Liu, Xiao-Yun Yan, Qing-Yun Guo, Huanyu Lei, Zongwu Huang, Rui Zhang, Yu Wang, Jing Wang, Feng Liu, Feng-Gang Bian, E.W. Meijer, Takuzo Aida, Mingjun Huang, Stephen Z.D. Cheng
      Abstract: The quasiperiodic structures in metal alloys have been known to depend on the existence of icosahedral order in the melt. Among different phases observed in intermetallics, decagonal quasicrystal (DQC) structures have been identified in many glass-forming alloys yet remain inaccessible in bulk-state condensed soft matters. Via annealing the mixture of...
      Keywords: Chemistry
      PubDate: 2022-01-12T12:51:49-08:00
      DOI: 10.1073/pnas.2115304119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Insight into the symbiotic lifestyle of DPANN archaea revealed by
           cultivation and genome analyses [Microbiology]

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      Authors: Hiroyuki D. Sakai; Naswandi Nur, Shingo Kato, Masahiro Yuki, Michiru Shimizu, Takashi Itoh, Moriya Ohkuma, Antonius Suwanto, Norio Kurosawa
      Abstract: Decades of culture-independent analyses have resulted in proposals of many tentative archaeal phyla with no cultivable representative. Members of DPANN (an acronym of the names of the first included phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota, and Nanoarchaeota), an archaeal superphylum composed of at least 10 of these tentative phyla, are generally...
      Keywords: Microbiology
      PubDate: 2022-01-12T12:51:49-08:00
      DOI: 10.1073/pnas.2115449119
      Issue No: Vol. 119, No. 3 (2022)
       
  • The PCY-SAG14 phytocyanin module regulated by PIFs and miR408 promotes
           dark-induced leaf senescence in Arabidopsis [Plant Biology]

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      Authors: Chen Hao; Yanzhi Yang, Jianmei Du, Xing Wang Deng, Lei Li
      Abstract: Leaf senescence is a critical process in plants and has a direct impact on many important agronomic traits. Despite decades of research on senescence-altered mutants via forward genetics and functional assessment of senescence-associated genes (SAGs) via reverse genetics, the senescence signal and the molecular mechanism that perceives and transduces the...
      Keywords: Plant Biology
      PubDate: 2022-01-12T12:51:49-08:00
      DOI: 10.1073/pnas.2116623119
      Issue No: Vol. 119, No. 3 (2022)
       
  • B cell-derived IL-27 promotes control of persistent LCMV infection
           [Immunology and Inflammation]

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      Authors: Isaraphorn Pratumchai; Jaroslav Zak, Zhe Huang, Booki Min, Michael B. A. Oldstone, John R. Teijaro
      Abstract: Recent studies have identified a critical role for B cell–produced cytokines in regulating both humoral and cellular immunity. Here, we show that B cells are an essential source of interleukin-27 (IL-27) during persistent lymphocytic choriomeningitis virus (LCMV) clone 13 (Cl-13) infection. By using conditional knockout mouse models with specific IL-27p28...
      Keywords: Immunology and Inflammation
      PubDate: 2022-01-12T12:51:49-08:00
      DOI: 10.1073/pnas.2116741119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Role of smooth muscle activation in the static and dynamic mechanical
           characterization of human aortas [Engineering]

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      Authors: Giulio Franchini; Ivan D. Breslavsky, Francesco Giovanniello, Ali Kassab, Gerhard A. Holzapfel, Marco Amabili
      Abstract: Experimental data and a suitable material model for human aortas with smooth muscle activation are not available in the literature despite the need for developing advanced grafts; the present study closes this gap. Mechanical characterization of human descending thoracic aortas was performed with and without vascular smooth muscle (VSM) activation....
      Keywords: Engineering
      PubDate: 2022-01-12T12:51:49-08:00
      DOI: 10.1073/pnas.2117232119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Inner Workings: Astronomers uncover new way to measure the speed of stars
           [Astronomy]

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      Authors: Ken Croswell
      Abstract: As an ambulance speeds toward you, its sirens scream at a high pitch. That pitch suddenly drops when the vehicle rushes by and races away. The change in pitch arises from a well-known phenomenon called the Doppler shift. However, the effect is more than just an amusing oddity. For more...
      Keywords: Inner Workings, Astronomy, Front Matter
      PubDate: 2022-01-12T12:51:49-08:00
      DOI: 10.1073/pnas.2122586119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Role of helical structure and dynamics in oligoadenylate synthetase 1
           (OAS1) mismatch tolerance and activation by short dsRNAs [Biochemistry]

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      Authors: Samantha L. Schwartz; Debayan Dey, Julia Tanquary, Camden R. Bair, Anice C. Lowen, Graeme L. Conn
      Abstract: The 2’-5’-oligoadenylate synthetases (OAS) are innate immune sensors of cytosolic double-stranded RNA (dsRNA) that play a critical role in limiting viral infection. How these proteins are able to avoid aberrant activation by cellular RNAs is not fully understood, but adenosine-to-inosine (A-to-I) editing has been proposed to limit accumulation of endogenous...
      Keywords: Biochemistry
      PubDate: 2022-01-11T12:17:52-08:00
      DOI: 10.1073/pnas.2107111119
      Issue No: Vol. 119, No. 3 (2022)
       
  • A guaranteed immediate payout reduces impatience of financially
           constrained individuals [Social Sciences]

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      Authors: Kimberley van der Heijden; Anouk Festjens, Caroline Goukens, Tom Meyvis
      Abstract: A large stream of literature found that individuals who experience financial strain are particularly concerned about their present needs—that is, they are more likely to choose smaller immediate payoffs over larger future payoffs. In contrast, some recent findings suggest that financially constrained individuals may be more concerned about future needs...
      Keywords: Social Sciences
      PubDate: 2022-01-11T12:17:52-08:00
      DOI: 10.1073/pnas.2108832119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Electrophysiological measures from human iPSC-derived neurons are
           associated with schizophrenia clinical status and predict individual
           cognitive performance [Neuroscience]

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      Authors: Stephanie Cerceo Page; Srinidhi Rao Sripathy, Federica Farinelli, Zengyou Ye, Yanhong Wang, Daniel J. Hiler, Elizabeth A. Pattie, Claudia V. Nguyen, Madhavi Tippani, Rebecca L. Moses, Huei-Ying Chen, Matthew Nguyen Tran, Nicholas J. Eagles, Joshua M. Stolz, Joseph L. Catallini II, Olivia R. Soudry, Dwight Dickinson, Karen F. Berman, Jose A. Apud, Daniel R. Weinberger, Keri Martinowich, Andrew E. Jaffe, Richard E. Straub, Brady J. Maher
      Abstract: Neurons derived from human induced pluripotent stem cells (hiPSCs) have been used to model basic cellular aspects of neuropsychiatric disorders, but the relationship between the emergent phenotypes and the clinical characteristics of donor individuals has been unclear. We analyzed RNA expression and indices of cellular function in hiPSC-derived neural progenitors...
      Keywords: Neuroscience
      PubDate: 2022-01-11T12:17:52-08:00
      DOI: 10.1073/pnas.2109395119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Microestimates of wealth for all low- and middle-income countries
           [Sustainability Science]

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      Authors: Guanghua Chi; Han Fang, Sourav Chatterjee, Joshua E. Blumenstock
      Abstract: Many critical policy decisions, from strategic investments to the allocation of humanitarian aid, rely on data about the geographic distribution of wealth and poverty. Yet many poverty maps are out of date or exist only at very coarse levels of granularity. Here we develop microestimates of the relative wealth and...
      Keywords: Economic Sciences, Sustainability Science
      PubDate: 2022-01-11T12:17:52-08:00
      DOI: 10.1073/pnas.2113658119
      Issue No: Vol. 119, No. 3 (2022)
       
  • An ultrafast and facile nondestructive strategy to convert various
           inefficient commercial nanocarbons to highly active Fenton-like catalysts
           [Engineering]

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      Authors: Junhui Wang; Qi Fu, Jiaxing Yu, Huangsheng Yang, Zhengping Hao, Fang Zhu, Gangfeng Ouyang
      Abstract: The Fenton-like process catalyzed by metal-free materials presents one of the most promising strategies to deal with the ever-growing environmental pollution. However, to develop improved catalysts with adequate activity, complicated preparation/modification processes and harsh conditions are always needed. Herein, we proposed an ultrafast and facile strategy to convert various inefficient...
      Keywords: Engineering
      PubDate: 2022-01-11T12:17:52-08:00
      DOI: 10.1073/pnas.2114138119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Exon-skipping antisense oligonucleotides for cystic fibrosis therapy
           [Genetics]

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      Authors: Young Jin Kim; Nicole Sivetz, Jessica Layne, Dillon M. Voss, Lucia Yang, Qian Zhang, Adrian R. Krainer
      Abstract: Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF), and the CFTR-W1282X nonsense mutation causes a severe form of CF. Although Trikafta and other CFTR-modulation therapies benefit most CF patients, targeted therapy for patients with the W1282X mutation is lacking. The CFTR-W1282X protein has residual...
      Keywords: Genetics
      PubDate: 2022-01-11T12:17:52-08:00
      DOI: 10.1073/pnas.2114858118
      Issue No: Vol. 119, No. 3 (2022)
       
  • Open reading frame correction using splice-switching antisense
           oligonucleotides for the treatment of cystic fibrosis [Cell Biology]

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      Authors: Wren E. Michaels; Cecilia Pena-Rasgado, Rusudan Kotaria, Robert J. Bridges, Michelle L. Hastings
      Abstract: CFTR gene mutations that result in the introduction of premature termination codons (PTCs) are common in cystic fibrosis (CF). This mutation type causes a severe form of the disease, likely because of low CFTR messenger RNA (mRNA) expression as a result of nonsense-mediated mRNA decay, as well as the production...
      Keywords: Cell Biology
      PubDate: 2022-01-11T12:17:52-08:00
      DOI: 10.1073/pnas.2114886119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Thermodynamic controls on rates of iron oxide reduction by extracellular
           electron shuttles [Environmental Sciences]

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      Authors: Meret Aeppli; Sebastien Giroud, Sanȷa Vranic, Andreas Voegelin, Thomas B. Hofstetter, Michael Sander
      Abstract: Anaerobic microbial respiration in suboxic and anoxic environments often involves particulate ferric iron (oxyhydr-)oxides as terminal electron acceptors. To ensure efficient respiration, a widespread strategy among iron-reducing microorganisms is the use of extracellular electron shuttles (EES) that transfer two electrons from the microbial cell to the iron oxide surface. Yet,...
      Keywords: Environmental Sciences
      PubDate: 2022-01-11T12:17:52-08:00
      DOI: 10.1073/pnas.2115629119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Heterologous vaccination interventions to reduce pandemic morbidity and
           mortality: Modeling the US winter 2020 COVID-19 wave [Biophysics and
           Computational Biology]

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      Authors: Nathaniel Hupert; Daniela Marin–Hernandez, Bo Gao, Ricardo Aguas, Douglas F. Nixon
      Abstract: COVID-19 remains a stark health threat worldwide, in part because of minimal levels of targeted vaccination outside high-income countries and highly transmissible variants causing infection in vaccinated individuals. Decades of theoretical and experimental data suggest that nonspecific effects of non–COVID-19 vaccines may help bolster population immunological resilience to new pathogens....
      Keywords: Medical Sciences, Coronavirus (COVID-19)
      PubDate: 2022-01-10T12:03:12-08:00
      DOI: 10.1073/pnas.2025448119
      Issue No: Vol. 119, No. 3 (2022)
       
  • The ectomycorrhizal fungus Pisolithus microcarpus encodes a microRNA
           

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      Authors: Johanna Wong-Bajracharya; Vasanth R. Singan, Remo Monti, Krista L. Plett, Vivian Ng, Igor V. Grigoriev, Francis M. Martin, Ian C. Anderson, Jonathan M. Plett
      Abstract: Small RNAs (sRNAs) are known to regulate pathogenic plant–microbe interactions. Emerging evidence from the study of these model systems suggests that microRNAs (miRNAs) can be translocated between microbes and plants to facilitate symbiosis. The roles of sRNAs in mutualistic mycorrhizal fungal interactions, however, are largely unknown. In this study, we...
      Keywords: Plant Biology
      PubDate: 2022-01-10T12:03:12-08:00
      DOI: 10.1073/pnas.2103527119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Biosafety of human environments can be supported by effective use of
           renewable biomass [Sustainability Science]

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      Authors: Fengbo Yu; Wei Zhao, Tao Qin, Wang Zhao, Yulian Chen, Xinyu Miao, Litao Lin, Hua Shang, Guodong Sui, Daxin Peng, Yi Yang, Yongguan Zhu, Shicheng Zhang, Xiangdong Zhu
      Abstract: Preventing pathogenic viral and bacterial transmission in the human environment is critical, especially in potential outbreaks that may be caused by the release of ancient bacteria currently trapped in the permafrost. Existing commercial disinfectants present issues such as a high carbon footprint. This study proposes a sustainable alternative, a bioliquid...
      Keywords: Environmental Sciences, Brief Reports, Sustainability Science
      PubDate: 2022-01-10T12:03:12-08:00
      DOI: 10.1073/pnas.2106843119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Conservation of magnetite biomineralization genes in all domains of life
           and implications for magnetic sensing [Applied Physical Sciences]

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      Authors: M. Renee Bellinger; Jiandong Wei, Uwe Hartmann, Herve Cadiou, Michael Winklhofer, Michael A. Banks
      Abstract: Animals use geomagnetic fields for navigational cues, yet the sensory mechanism underlying magnetic perception remains poorly understood. One idea is that geomagnetic fields are physically transduced by magnetite crystals contained inside specialized receptor cells, but evidence for intracellular, biogenic magnetite in eukaryotes is scant. Certain bacteria produce magnetite crystals inside...
      Keywords: Applied Physical Sciences, Evolution
      PubDate: 2022-01-10T12:03:12-08:00
      DOI: 10.1073/pnas.2108655119
      Issue No: Vol. 119, No. 3 (2022)
       
  • A genetic switch for male UV iridescence in an incipient species pair of
           sulphur butterflies [Evolution]

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      Authors: Vincent Ficarrotta; Joseph J. Hanly, Ling S. Loh, Caroline M. Francescutti, Anna Ren, Kalle Tunstrom, Christopher W. Wheat, Adam H. Porter, Brian A. Counterman, Arnaud Martin
      Abstract: Mating cues evolve rapidly and can contribute to species formation and maintenance. However, little is known about how sexual signals diverge and how this variation integrates with other barrier loci to shape the genomic landscape of reproductive isolation. Here, we elucidate the genetic basis of ultraviolet (UV) iridescence, a courtship...
      Keywords: Evolution
      PubDate: 2022-01-10T12:03:12-08:00
      DOI: 10.1073/pnas.2109255118
      Issue No: Vol. 119, No. 3 (2022)
       
  • Global evidence on the selfish rich inequality hypothesis [Economic
           Sciences]

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      Authors: Ingvild Almas; Alexander W. Cappelen, Erik O. Sorensen, Bertil Tungodden
      Abstract: We report on a study of whether people believe that the rich are richer than the poor because they have been more selfish in life, using data from more than 26,000 individuals in 60 countries. The findings show a strong belief in the selfish rich inequality hypothesis at the global...
      Keywords: Economic Sciences
      PubDate: 2022-01-10T12:03:12-08:00
      DOI: 10.1073/pnas.2109690119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Ship traffic connects Antarctica’s fragile coasts to worldwide
           ecosystems [Ecology]

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      Authors: Arlie H. McCarthy; Lloyd S. Peck, David C. Aldridge
      Abstract: Antarctica, an isolated and long considered pristine wilderness, is becoming increasingly exposed to the negative effects of ship-borne human activity, and especially the introduction of invasive species. Here, we provide a comprehensive quantitative analysis of ship movements into Antarctic waters and a spatially explicit assessment of introduction risk for nonnative...
      Keywords: Ecology
      PubDate: 2022-01-10T12:03:12-08:00
      DOI: 10.1073/pnas.2110303118
      Issue No: Vol. 119, No. 3 (2022)
       
  • Direct visualization of polaron formation in the thermoelectric SnSe
           [Physics]

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      Authors: Laurent P. Rene de Cotret; Martin R. Otto, Jan–Hendrik Pohls, Zhongzhen Luo, Mercouri G. Kanatzidis, Bradley J. Siwick
      Abstract: SnSe is a layered material that currently holds the record for bulk thermoelectric efficiency. The primary determinant of this high efficiency is thought to be the anomalously low thermal conductivity resulting from strong anharmonic coupling within the phonon system. Here we show that the nature of the carrier system in...
      Keywords: Physics
      PubDate: 2022-01-10T12:03:12-08:00
      DOI: 10.1073/pnas.2113967119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Increasing instability of a rocky intertidal meta-ecosystem [Ecology]

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      Authors: Bruce A. Menge; Sarah A. Gravem, Angela Johnson, Jonathan W. Robinson, Brittany N. Poirson
      Abstract: Climate change threatens to destabilize ecological communities, potentially moving them from persistently occupied “basins of attraction” to different states. Increasing variation in key ecological processes can signal impending state shifts in ecosystems. In a rocky intertidal meta-ecosystem consisting of three distinct regions spread across 260 km of the Oregon coast,...
      Keywords: Ecology
      PubDate: 2022-01-10T12:03:12-08:00
      DOI: 10.1073/pnas.2114257119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Unraveling the origin of extra strengthening in gradient nanotwinned
           metals [Engineering]

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      Authors: Zhao Cheng; Linfeng Bu, Yin Zhang, HengAn Wu, Ting Zhu, Huajian Gao, Lei Lu
      Abstract: Materials containing heterogeneous nanostructures hold great promise for achieving superior mechanical properties. However, the strengthening effect due to plastically inhomogeneous deformation in heterogeneous nanostructures has not been clearly understood. Here, we investigate a prototypical heterogeneous nanostructured material of gradient nanotwinned (GNT) Cu to unravel the origin of its extra strength...
      Keywords: Engineering
      PubDate: 2022-01-10T12:03:12-08:00
      DOI: 10.1073/pnas.2116808119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Multivalency enables unidirectional switch-like competition between
           intrinsically disordered proteins [Biophysics and Computational Biology]

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      Authors: Rebecca B. Berlow; H. Jane Dyson, Peter E. Wright
      Abstract: Intrinsically disordered proteins must compete for binding to common regulatory targets to carry out their biological functions. Previously, we showed that the activation domains of two disordered proteins, the transcription factor HIF-1α and its negative regulator CITED2, function as a unidirectional, allosteric molecular switch to control transcription of critical adaptive...
      Keywords: Biophysics and Computational Biology
      PubDate: 2022-01-10T12:03:12-08:00
      DOI: 10.1073/pnas.2117338119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Dengue virus infection modifies mosquito blood-feeding behavior to
           increase transmission to the host [Microbiology]

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      Authors: Benȷamin Wong Wei Xiang; Wilfried A. A. Saron, James C. Stewart, Arthur Hain, Varsha Walvekar, Dorothee Misse, Frederic Thomas, R. Manȷunatha Kini, Benȷamin Roche, Adam Claridge–Chang, Ashley L. St. John, Julien Pompon
      Abstract: Mosquito blood-feeding behavior is a key determinant of the epidemiology of dengue viruses (DENV), the most-prevalent mosquito-borne viruses. However, despite its importance, how DENV infection influences mosquito blood-feeding and, consequently, transmission remains unclear. Here, we developed a high-resolution, video-based assay to observe the blood-feeding behavior of Aedes aegypti mosquitoes on...
      Keywords: Microbiology
      PubDate: 2022-01-10T12:03:12-08:00
      DOI: 10.1073/pnas.2117589119
      Issue No: Vol. 119, No. 3 (2022)
       
  • Early antitumor activity of oral Langerhans cells is compromised by a
           carcinogen [Immunology and Inflammation]

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      Authors: Yasmin Saba; Itay Aizenbud, Daniela Matanes, Noam Koren, Or Barel, Khalid Zubeidat, Tal Capucha, Eyal David, Luba Eli-Berchoer, Patrizia Stoitzner, Asaf Wilensky, Ido Amit, Rakefet Czerninski, Simon Yona, Avi-Hai Hovav
      Abstract: Early diagnosis of oral squamous cell carcinoma (OSCC) remains an unmet clinical need. Therefore, elucidating the initial events of OSCC preceding tumor development could benefit OSCC prognosis. Here, we define the Langerhans cells (LCs) of the tongue and demonstrate that LCs protect the epithelium from carcinogen-induced OSCC by rapidly priming...
      Keywords: Immunology and Inflammation
      PubDate: 2022-01-10T12:03:12-08:00
      DOI: 10.1073/pnas.2118424119
      Issue No: Vol. 119, No. 3 (2022)
       
  • How migratory birds might have tracked past climate change [Ecology]

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      Authors: Benjamin M. Van Doren
      Abstract: Organisms’ responses to past climatic extremes provide a useful perspective for understanding the impacts of ongoing and increasingly rapid climate change. Volant organisms can disperse long distances, allowing them to find and colonize new habitats during periods of change. However, the ability to move long distances does not necessarily imply...
      Keywords: Ecology, Commentaries
      PubDate: 2022-01-10T12:03:12-08:00
      DOI: 10.1073/pnas.2121738119
      Issue No: Vol. 119, No. 3 (2022)
       
  • North American tree migration paced by climate in the West, lagging in the
           East [Ecology]

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      Authors: Shubhi Sharma; Robert Andrus, Yves Bergeron, Michal Bogdziewicz, Don C. Bragg, Dale Brockway, Natalie L. Cleavitt, Benoit Courbaud, Adrian J. Das, Michael Dietze, Timothy J. Fahey, Jerry F. Franklin, Gregory S. Gilbert, Cathryn H. Greenberg, Qinfeng Guo, Janneke Hille Ris Lambers, Ines Ibanez, Jill F. Johnstone, Christopher L. Kilner, Johannes M. H. Knops, Walter D. Koenig, Georges Kunstler, Jalene M. LaMontagne, Diana Macias, Emily Moran, Jonathan A. Myers, Robert Parmenter, Ian S. Pearse, Renata Poulton-Kamakura, Miranda D. Redmond, Chantal D. Reid, Kyle C. Rodman, C. Lane Scher, William H. Schlesinger, Michael A. Steele, Nathan L. Stephenson, Jennifer J. Swenson, Margaret Swift, Thomas T. Veblen, Amy V. Whipple, Thomas G. Whitham, Andreas P. Wion, Christopher W. Woodall, Roman Zlotin, James S. Clark
      Abstract: Tree fecundity and recruitment have not yet been quantified at scales needed to anticipate biogeographic shifts in response to climate change. By separating their responses, this study shows coherence across species and communities, offering the strongest support to date that migration is in progress with regional limitations on rates. The...
      Keywords: Ecology
      PubDate: 2022-01-04T12:56:55-08:00
      DOI: 10.1073/pnas.2116691118
      Issue No: Vol. 119, No. 3 (2022)
       
 
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