Correction for Zella et al., Mycoplasma promotes malignant transformation in vivo, and its DnaK, a bacterial chaperon protein, has broad oncogenic properties [Correction]
MICROBIOLOGY Correction for “Mycoplasma promotes malignant transformation in vivo, and its DnaK, a bacterial chaperon protein, has broad oncogenic properties,” by Davide Zella, Sabrina Curreli, Francesca Benedetti, Selvi Krishnan, Fiorenza Cocchi, Olga S. Latinovic, Frank Denaro, Fabio Romerio, Muhammad Djavani, Man E. Charurat, Joseph L. Bryant, Hervé Tettelin, and Robert... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Tags: Corrections Source Type: research

Correction for Terui et al., Metapopulation stability in branching river networks [Correction]
ECOLOGY Correction for “Metapopulation stability in branching river networks,” by Akira Terui, Nobuo Ishiyama, Hirokazu Urabe, Satoru Ono, Jacques C. Finlay, and Futoshi Nakamura, which was first published June 12, 2018; 10.1073/pnas.1800060115 (Proc Natl Acad Sci USA 115:E5963–E5969). The authors wish to note the following: “While extending a theoretical framework... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Tags: Corrections Source Type: research

Correction for Paluck et al., Changing climates of conflict: A social network experiment in 56 schools [Correction]
PSYCHOLOGICAL AND COGNITIVE SCIENCES Correction for “Changing climates of conflict: A social network experiment in 56 schools,” by Elizabeth Levy Paluck, Hana Shepherd, and Peter M. Aronow, which was first published January 4, 2016; 10.1073/pnas.1514483113 (Proc Natl Acad Sci USA 113:566–571). The authors note that the following statement should be... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Tags: Corrections Source Type: research

Correction for Li et al., Pressure-induced phase transitions and superconductivity in a black phosphorus single crystal [Correction]
PHYSICS Correction for “Pressure-induced phase transitions and superconductivity in a black phosphorus single crystal,” by Xiang Li, Jianping Sun, Prashant Shahi, Miao Gao, Allan H. MacDonald, Yoshiya Uwatoko, Tao Xiang, John B. Goodenough, Jinguang Cheng, and Jianshi Zhou, which was first published September 14, 2018; 10.1073/pnas.1810726115 (Proc Natl Acad Sci... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Tags: Corrections Source Type: research

Integration in emerging social networks explains academic failure and success [Social Sciences]
Academic success of students has been explained with a variety of individual and socioeconomic factors. Social networks that informally emerge within student communities can have an additional effect on their achievement. However, this effect of social ties is difficult to measure and quantify, because social networks are multidimensional and dynamically... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Christoph Stadtfeld, Andras Voros, Timon Elmer, Zsofia Boda, Isabel J. Raabe Tags: Social Sciences Source Type: research

Science and Culture: Searching for the science behind art therapy [Psychological and Cognitive Sciences]
John sat hunched over, ears red, cursing the paint under his breath. A war veteran not an artist, John (not his real name) hadn’t painted with water colors before. But he and seven other combat veterans of the Afghanistan and Iraq wars weren’t trying to master a new artistic medium.... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Carolyn Beans Tags: Science and Culture, Front Matter Source Type: research

Thermal disequilibration of ions and electrons by collisionless plasma turbulence [Physics]
Does overall thermal equilibrium exist between ions and electrons in a weakly collisional, magnetized, turbulent plasma? And, if not, how is thermal energy partitioned between ions and electrons? This is a fundamental question in plasma physics, the answer to which is also crucial for predicting the properties of far-distant astronomical... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Yohei Kawazura, Michael Barnes, Alexander A. Schekochihin Tags: Physical Sciences Source Type: research

Direct electrochemical generation of supercooled sulfur microdroplets well below their melting temperature [Physics]
Supercooled liquid sulfur microdroplets were directly generated from polysulfide electrochemical oxidation on various metal-containing electrodes. The sulfur droplets remain liquid at 155 °C below sulfur’s melting point (Tm = 115 °C), with fractional supercooling change (Tm − Tsc)/Tm larger than 0.40. In operando light microscopy captured the rapid merging and... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Nian Liu, Guangmin Zhou, Ankun Yang, Xiaoyun Yu, Feifei Shi, Jie Sun, Jinsong Zhang, Bofei Liu, Chun-Lan Wu, Xinyong Tao, Yongming Sun, Yi Cui, Steven Chu Tags: Physical Sciences Source Type: research

Conotoxin {kappa}M-RIIIJ, a tool targeting asymmetric heteromeric Kv1 channels [Neuroscience]
The vast complexity of native heteromeric K+ channels is largely unexplored. Defining the composition and subunit arrangement of individual subunits in native heteromeric K+ channels and establishing their physiological roles is experimentally challenging. Here we systematically explored this “zone of ignorance” in molecular neuroscience. Venom components, such as peptide toxins,... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Sonke Cordeiro, Rocio K. Finol–Urdaneta, David Kopfer, Anna Markushina, Jie Song, Robert J. French, Woȷciech Kopec, Bert L. de Groot, Mario J. Giacobassi, Lee S. Leavitt, Shrinivasan Raghuraman, Russell W. Teichert, Baldomero M. Olivera, Hein Tags: Biological Sciences Source Type: research

Dual inhibition of MDM2 and MDM4 in virus-positive Merkel cell carcinoma enhances the p53 response [Microbiology]
Merkel cell polyomavirus (MCV) contributes to approximately 80% of all Merkel cell carcinomas (MCCs), a highly aggressive neuroendocrine carcinoma of the skin. MCV-positive MCC expresses small T antigen (ST) and a truncated form of large T antigen (LT) and usually contains wild-type p53 (TP53) and RB (RB1). In contrast, virus-negative... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Donglim Esther Park, Jingwei Cheng, Christian Berrios, Joan Montero, Marta Cortes–Cros, Stephane Ferretti, Reety Arora, Michelle L. Tillgren, Prafulla C. Gokhale, James A. DeCaprio Tags: Biological Sciences Source Type: research

Interfacial fluid transport is a key to hydrogel bioadhesion [Medical Sciences]
Attaching hydrogels to soft internal tissues is a key to the development of a number of biomedical devices. Nevertheless, the wet nature of hydrogels and tissues renders this adhesion most difficult to achieve and control. Here, we show that the transport of fluids across hydrogel−tissue interfaces plays a central role... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Raphael Michel, Lena Poirier, Quentin van Poelvoorde, Josette Legagneux, Mathieu Manassero, Laurent Corte Tags: Physical Sciences Source Type: research

Phosphatase PP2A is essential for TH17 differentiation [Immunology and Inflammation]
Phosphatase PP2A expression levels are positively correlated to the clinical severity of systemic lupus erythematosus (SLE) and IL17A cytokine overproduction, indicating a potential role of PP2A in controlling TH17 differentiation and inflammation. By generating a mouse strain with ablation of the catalytic subunit α of PP2A in peripheral mature T... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Qin Xu, Xuexiao Jin, Mingzhu Zheng, Deepak Rohila, Guotong Fu, Zhuoyu Wen, Jun Lou, Songquan Wu, Richard Sloan, Lie Wang, Hu Hu, Xiang Gao, Linrong Lu Tags: Biological Sciences Source Type: research

RNA-binding protein YTHDF3 suppresses interferon-dependent antiviral responses by promoting FOXO3 translation [Immunology and Inflammation]
IFN–stimulated genes (ISGs) are essential effectors of the IFN-dependent antiviral immune response. Dysregulation of ISG expression can cause dysfunctional antiviral responses and autoimmune disorders. Epitranscriptomic regulation, such as N6-methyladenosine (m6A) modification of mRNAs, plays key roles in diverse biological processes. Here, we found that the m6A “reader” YT521-B homology domain-containing... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Yuan Zhang, Xin Wang, Xiao Zhang, Jiaming Wang, Yuanwu Ma, Lianfeng Zhang, Xuetao Cao Tags: Biological Sciences Source Type: research

Human RIPK1 deficiency causes combined immunodeficiency and inflammatory bowel diseases [Immunology and Inflammation]
Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) is a critical regulator of cell death and inflammation, but its relevance for human disease pathogenesis remains elusive. Studies of monogenic disorders might provide critical insights into disease mechanisms and therapeutic targeting of RIPK1 for common diseases. Here, we report on eight patients from six... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Yue Li, Marita Fuhrer, Ehsan Bahrami, Piotr Socha, Maȷa Klaudel–Dreszler, Amira Bouzidi, Yanshan Liu, Anna S. Lehle, Thomas Magg, Sebastian Hollizeck, Meino Rohlfs, Raffaele Conca, Michael Field, Neil Warner, Slae Mordechai, Eyal Shteyer, Dan Tags: Biological Sciences Source Type: research

HIV peptidome-wide association study reveals patient-specific epitope repertoires associated with HIV control [Genetics]
Genetic variation in the peptide-binding groove of the highly polymorphic HLA class I molecules has repeatedly been associated with HIV-1 control and progression to AIDS, accounting for up to 12% of the variation in HIV-1 set point viral load (spVL). This suggests a key role in disease control for HLA... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Jatin Arora, Paul J. McLaren, Nimisha Chaturvedi, Mary Carrington, Jacques Fellay, Tobias L. Lenz Tags: Biological Sciences Source Type: research

Climate-induced phenological shifts in a Batesian mimicry complex [Evolution]
Climate-induced changes in spatial and temporal occurrence of species, as well as species traits such as body size, each have the potential to decouple symbiotic relationships. Past work has focused primarily on direct interactions, particularly those between predators and prey and between plants and pollinators, but studies have rarely demonstrated... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Christopher Hassall, Jac Billington, Thomas N. Sherratt Tags: Biological Sciences Source Type: research

The genomic basis of Red Queen dynamics during rapid reciprocal host-pathogen coevolution [Evolution]
Red Queen dynamics, involving coevolutionary interactions between species, are ubiquitous, shaping the evolution of diverse biological systems. To date, information on the underlying selection dynamics and the involved genome regions is mainly available for bacteria–phage systems or only one of the antagonists of a eukaryotic host–pathogen interaction. We add to... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Andrei Papkou, Thiago Guzella, Wentao Yang, Svenȷa Koepper, Barbara Pees, Rebecca Schalkowski, Mike–Christoph Barg, Philip C. Rosenstiel, Henrique Teotonio, Hinrich Schulenburg Tags: Biological Sciences Source Type: research

Economic carbon cycle feedbacks may offset additional warming from natural feedbacks [Environmental Sciences]
As the Earth warms, carbon sinks on land and in the ocean will weaken, thereby increasing the rate of warming. Although natural mechanisms contributing to this positive climate–carbon feedback have been evaluated using Earth system models, analogous feedbacks involving human activities have not been systematically quantified. Here we conceptualize and... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Dawn L. Woodard, Steven J. Davis, James T. Randerson Tags: Physical Sciences Source Type: research

Designing combinatorial exchanges for the reallocation of resource rights [Economic Sciences]
We describe the design and implementation of a combinatorial exchange for trading catch shares in New South Wales, Australia. The exchange ended a decades-long political debate by providing a market-based response to a major policy problem faced by fisheries worldwide: the reallocation of catch shares in cap-and-trade programs designed to... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Martin Bichler, Vladimir Fux, Jacob K. Goeree Tags: Social Sciences Source Type: research

Global synthesis of conservation studies reveals the importance of small habitat patches for biodiversity [Ecology]
Island biogeography theory posits that species richness increases with island size and decreases with isolation. This logic underpins much conservation policy and regulation, with preference given to conserving large, highly connected areas, and relative ambivalence shown toward protecting small, isolated habitat patches. We undertook a global synthesis of the relationship... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Brendan A. Wintle, Heini Kujala, Amy Whitehead, Alison Cameron, Sam Veloz, Aija Kukkala, Atte Moilanen, Ascelin Gordon, Pia E. Lentini, Natasha C. R. Cadenhead, Sarah A. Bekessy Tags: Biological Sciences Source Type: research

Nanoscale infrared imaging analysis of carbonaceous chondrites to understand organic-mineral interactions during aqueous alteration [Earth, Atmospheric, and Planetary Sciences]
Organic matter in carbonaceous chondrites is distributed in fine-grained matrix. To understand pre- and postaccretion history of organic matter and its association with surrounding minerals, microscopic techniques are mandatory. Infrared (IR) spectroscopy is a useful technique, but the spatial resolution of IR is limited to a few micrometers, due to... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Yoko Kebukawa, Hanae Kobayashi, Norio Urayama, Naoki Baden, Masashi Kondo, Michael E. Zolensky, Kensei Kobayashi Tags: Physical Sciences Source Type: research

Mcm10 has potent strand-annealing activity and limits translocase-mediated fork regression [Chemistry]
The 11-subunit eukaryotic replicative helicase CMG (Cdc45, Mcm2-7, GINS) tightly binds Mcm10, an essential replication protein in all eukaryotes. Here we show that Mcm10 has a potent strand-annealing activity both alone and in complex with CMG. CMG-Mcm10 unwinds and then reanneals single strands soon after they have been unwound in... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Ryan Mayle, Lance Langston, Kelly R. Molloy, Dan Zhang, Brian T. Chait, Michael E. O’Donnell Tags: Biological Sciences Source Type: research

Inner Workings: How bacteria could help recycle electronic waste [Chemistry]
The bacterium Chromobacterium violaceum is known for producing an antimicrobial agent called violacein. But C. violaceum offers more than medical applications. The bacterium might be capable of recovering precious metals from the massive quantities of electrical and electronic waste (e-waste) generated around the world. People tossed out 44.7 million metric... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Roberta Kwok Tags: Inner Workings, Front Matter Source Type: research

Patched1-ArhGAP36-PKA-Inversin axis determines the ciliary translocation of Smoothened for Sonic Hedgehog pathway activation [Cell Biology]
The Sonic Hedgehog (Shh) pathway conducts primarily in the primary cilium and plays important roles in cell proliferation, individual development, and tumorigenesis. Shh ligand binding with its ciliary membrane-localized transmembrane receptor Patched1 results in the removal of Patched1 from and the translocation of the transmembrane oncoprotein Smoothened into the cilium,... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Boyan Zhang, Tenghan Zhuang, Qiaoyu Lin, Biying Yang, Xiaowei Xu, Guangwei Xin, Shicong Zhu, Gang Wang, Bin Yu, Tingting Zhang, Qing Jiang, Chuanmao Zhang Tags: Biological Sciences Source Type: research

Ca2+-activated Cl- current ensures robust and reliable signal amplification in vertebrate olfactory receptor neurons [Biophysics and Computational Biology]
Activation of most primary sensory neurons results in transduction currents that are carried by cations. One notable exception is the vertebrate olfactory receptor neuron (ORN), where the transduction current is carried largely by the anion Cl−. However, it remains unclear why ORNs use an anionic current for signal amplification. We... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Johannes Reisert, Jurgen Reingruber Tags: Biological Sciences Source Type: research

Arrestin-3 scaffolding of the JNK3 cascade suggests a mechanism for signal amplification [Biochemistry]
Scaffold proteins tether and orient components of a signaling cascade to facilitate signaling. Although much is known about how scaffolds colocalize signaling proteins, it is unclear whether scaffolds promote signal amplification. Here, we used arrestin-3, a scaffold of the ASK1-MKK4/7-JNK3 cascade, as a model to understand signal amplification by a... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Nicole A. Perry, Tamer S. Kaoud, Oscar O. Ortega, Ali I. Kaya, David J. Marcus, John M. Pleinis, Sandra Berndt, Qiuyan Chen, Xuanzhi Zhan, Kevin N. Dalby, Carlos F. Lopez, T. M. Iverson, Vsevolod V. Gurevich Tags: Biological Sciences Source Type: research

Structural basis for prodrug recognition by the SLC15 family of proton-coupled peptide transporters [Biochemistry]
A major challenge in drug development is the optimization of intestinal absorption and cellular uptake. A successful strategy has been to develop prodrug molecules, which hijack solute carrier (SLC) transporters for active transport into the body. The proton-coupled oligopeptide transporters, PepT1 and PepT2, have been successfully targeted using this approach.... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Gurdeep S. Minhas, Simon Newstead Tags: Biological Sciences Source Type: research

Linear variational principle for Riemann mappings and discrete conformality [Applied Mathematics]
We consider Riemann mappings from bounded Lipschitz domains in the plane to a triangle. We show that in this case the Riemann mapping has a linear variational principle: It is the minimizer of the Dirichlet energy over an appropriate affine space. By discretizing the variational principle in a natural way... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Nadav Dym, Raz Slutsky, Yaron Lipman Tags: Physical Sciences Source Type: research

Nutrition, the visceral immune system, and the evolutionary origins of pathogenic obesity [Medical Sciences]
The global obesity epidemic is the subject of an immense, diversely specialized research effort. An evolutionary analysis reveals connections among disparate findings, starting with two well-documented facts: Obesity-associated illnesses (e.g., type-2 diabetes and cardiovascular disease), are especially common in: (i) adults with abdominal obesity, especially enlargement of visceral adipose tissue... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Mary Jane West-Eberhard Tags: Perspective Source Type: research

Regulation of acetate metabolism and coordination with the TCA cycle via a processed small RNA [Microbiology]
Bacterial regulatory small RNAs act as crucial regulators in central carbon metabolism by modulating translation initiation and degradation of target mRNAs in metabolic pathways. Here, we demonstrate that a noncoding small RNA, SdhX, is produced by RNase E-dependent processing from the 3′UTR of the sdhCDAB-sucABCD operon, encoding enzymes of the... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Francois De Mets, Laurence Van Melderen, Susan Gottesman Tags: PNAS Plus Source Type: research

Herpes simplex virus 1 ICP8 mutant lacking annealing activity is deficient for viral DNA replication [Microbiology]
Most DNA viruses that use recombination-dependent mechanisms to replicate their DNA encode a single-strand annealing protein (SSAP). The herpes simplex virus (HSV) single-strand DNA binding protein (SSB), ICP8, is the central player in all stages of DNA replication. ICP8 is a classical replicative SSB and interacts physically and/or functionally with... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Savithri Weerasooriya, Katherine A. DiScipio, Anthar S. Darwish, Ping Bai, Sandra K. Weller Tags: PNAS Plus Source Type: research

Rigidification of the Escherichia coli cytoplasm by the human antimicrobial peptide LL-37 revealed by superresolution fluorescence microscopy [Microbiology]
Superresolution, single-particle tracking reveals effects of the cationic antimicrobial peptide LL-37 on the Escherichia coli cytoplasm. Seconds after LL-37 penetrates the cytoplasmic membrane, the chromosomal DNA becomes rigidified on a length scale of ∼30 nm, evidenced by the loss of jiggling motion of specific DNA markers. The diffusive motion of... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Yanyu Zhu, Sonisilpa Mohapatra, James C. Weisshaar Tags: PNAS Plus Source Type: research

Unregulated antigen-presenting cell activation by T cells breaks self tolerance [Immunology and Inflammation]
T cells proliferate vigorously following acute depletion of CD4+ Foxp3+ T regulatory cells [natural Tregs (nTregs)] and also when naive T cells are transferred to syngeneic, nTreg-deficient Rag1−/− hosts. Here, using mice raised in an antigen-free (AF) environment, we show that proliferation in these two situations is directed to self... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Jaeu Yi, Jisun Jung, Sung-Wook Hong, Jun Young Lee, Daehee Han, Kwang Soon Kim, Jonathan Sprent, Charles D. Surh Tags: PNAS Plus Source Type: research

Microglia are effector cells of CD47-SIRP{alpha} antiphagocytic axis disruption against glioblastoma [Immunology and Inflammation]
Glioblastoma multiforme (GBM) is a highly aggressive malignant brain tumor with fatal outcome. Tumor-associated macrophages and microglia (TAMs) have been found to be major tumor-promoting immune cells in the tumor microenvironment. Hence, modulation and reeducation of tumor-associated macrophages and microglia in GBM is considered a promising antitumor strategy. Resident microglia... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Gregor Hutter, Johanna Theruvath, Claus Moritz Graef, Michael Zhang, Matthew Kenneth Schoen, Eva Maria Manz, Mariko L. Bennett, Andrew Olson, Tej D. Azad, Rahul Sinha, Carmel Chan, Suzana Assad Kahn, Sharareh Gholamin, Christy Wilson, Gerald Grant, Joy He Tags: PNAS Plus Source Type: research

Binding mode of the side-by-side two-IgV molecule CD226/DNAM-1 to its ligand CD155/Necl-5 [Immunology and Inflammation]
Natural killer (NK) cells are important component of innate immunity and also contribute to activating and reshaping the adaptive immune responses. The functions of NK cells are modulated by multiple inhibitory and stimulatory receptors. Among these receptors, the activating receptor CD226 (DNAM-1) mediates NK cell activation via binding to its... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Han Wang, Jianxun Qi, Shuijun Zhang, Yan Li, Shuguang Tan, George F. Gao Tags: PNAS Plus Source Type: research

Constitutive Dicer1 phosphorylation accelerates metabolism and aging in vivo [Genetics]
DICER1 gene alterations and decreased expression are associated with developmental disorders and diseases in humans. Oscillation of Dicer1 phosphorylation and dephosphorylation regulates its function during the oocyte-to-embryo transition in Caenorhabditis elegans. Dicer1 is also phosphorylated upon FGF stimulation at conserved serines in mouse embryonic fibroblasts and HEK293 cells. However, whether... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Neeraj K. Aryal, Vinod Pant, Amanda R. Wasylishen, Jan Parker-Thornburg, Laura Baseler, Adel K. El-Naggar, Bin Liu, Awdhesh Kalia, Guillermina Lozano, Swathi Arur Tags: PNAS Plus Source Type: research

Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis [Genetics]
Computational analyses of human patient exomes aim to filter out as many nonpathogenic genetic variants (NPVs) as possible, without removing the true disease-causing mutations. This involves comparing the patient’s exome with public databases to remove reported variants inconsistent with disease prevalence, mode of inheritance, or clinical penetrance. However, variants frequent... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Patrick Maffucci, Benedetta Bigio, Franck Rapaport, Aurelie Cobat, Alessandro Borghesi, Marie Lopez, Etienne Patin, Alexandre Bolze, Lei Shang, Matthieu Bendavid, Eric M. Scott, Peter D. Stenson, Charlotte Cunningham–Rundles, David N. Cooper, Joseph Tags: PNAS Plus Source Type: research

Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora [Evolution]
Plastid genomes (plastomes) vary enormously in size and gene content among the many lineages of nonphotosynthetic plants, but key lineages remain unexplored. We therefore investigated plastome sequence and expression in the holoparasitic and morphologically bizarre Balanophoraceae. The two Balanophora plastomes examined are remarkable, exhibiting features rarely if ever seen before... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Huei-Jiun Su, Todd J. Barkman, Weilong Hao, Samuel S. Jones, Julia Naumann, Elizabeth Skippington, Eric K. Wafula, Jer-Ming Hu, Jeffrey D. Palmer, Claude W. dePamphilis Tags: PNAS Plus Source Type: research

Global-scale dispersal and connectivity in mangroves [Ecology]
Dispersal provides a key mechanism for geographical range shifts in response to changing environmental conditions. For mangroves, which are highly susceptible to climate change, the spatial scale of dispersal remains largely unknown. Here we use a high-resolution, eddy- and tide-resolving numerical ocean model to simulate mangrove propagule dispersal across the... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Tom Van der Stocken, Dustin Carroll, Dimitris Menemenlis, Marc Simard, Nico Koedam Tags: PNAS Plus Source Type: research

Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy [Developmental Biology]
Identifying functional enhancer elements in metazoan systems is a major challenge. Large-scale validation of enhancers predicted by ENCODE reveal false-positive rates of at least 70%. We used the pregrastrula-patterning network of Drosophila melanogaster to demonstrate that loss in accuracy in held-out data results from heterogeneity of functional signatures in enhancer... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Hamutal Arbel, Sumanta Basu, William W. Fisher, Ann S. Hammonds, Kenneth H. Wan, Soo Park, Richard Weiszmann, Benjamin W. Booth, Soile V. Keranen, Clara Henriquez, Omid Shams Solari, Peter J. Bickel, Mark D. Biggin, Susan E. Celniker, James B. Brown Tags: PNAS Plus Source Type: research

Different roles of E proteins in t(8;21) leukemia: E2-2 compromises the function of AETFC and negatively regulates leukemogenesis [Cell Biology]
The AML1-ETO fusion protein, generated by the t(8;21) chromosomal translocation, is causally involved in nearly 20% of acute myeloid leukemia (AML) cases. In leukemic cells, AML1-ETO resides in and functions through a stable protein complex, AML1-ETO–containing transcription factor complex (AETFC), that contains multiple transcription (co)factors. Among these AETFC components, HEB... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Na Liu, Junhong Song, Yangyang Xie, Xiao-Lin Wang, Bowen Rong, Na Man, Meng-Meng Zhang, Qunling Zhang, Fei-Fei Gao, Mei-Rong Du, Ying Zhang, Jian Shen, Chun-Hui Xu, Cheng-Long Hu, Ji-Chuan Wu, Ping Liu, Yuan-Liang Zhang, Yin-Yin Xie, , Jin-Yan Huang, Qiu- Tags: PNAS Plus Source Type: research

Single-molecule imaging of the transcription factor SRF reveals prolonged chromatin-binding kinetics upon cell stimulation [Cell Biology]
Serum response factor (SRF) mediates immediate early gene (IEG) and cytoskeletal gene expression programs in almost any cell type. So far, SRF transcriptional dynamics have not been investigated at single-molecule resolution. We provide a study of single Halo-tagged SRF molecules in fibroblasts and primary neurons. In both cell types, individual... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Lisa Hipp, Judith Beer, Oliver Kuchler, Matthias Reisser, Daniela Sinske, Jens Michaelis, J. Christof M. Gebhardt, Bernd Knoll Tags: PNAS Plus Source Type: research

Photoswitching FRET to monitor protein-protein interactions [Cell Biology]
FRET is a powerful approach to study the interactions of fluorescent molecules, and numerous methods have been developed to measure FRET in cells. Here, we present a method based on a donor molecule’s photoswitching properties, which are slower in the presence vs. the absence of an acceptor. The technique, photoswitching... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Kristin H. Rainey, George H. Patterson Tags: PNAS Plus Source Type: research

Role of domain interactions in the aggregation of full-length immunoglobulin light chains [Biophysics and Computational Biology]
Amyloid light-chain (LC) amyloidosis is a protein misfolding disease in which the aggregation of an overexpressed antibody LC from a clonal plasma cell leads to organ toxicity and patient death if left untreated. While the overall dimeric architecture of LC molecules is established, with each LC composed of variable (VL)... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Enrico Rennella, Gareth J. Morgan, Jeffery W. Kelly, Lewis E. Kay Tags: PNAS Plus Source Type: research

Two symmetric arginine residues play distinct roles in Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage [Biophysics and Computational Biology]
Bacterium Thermus thermophilus Argonaute (Ago; TtAgo) is a prokaryotic Ago (pAgo) that acts as the host defense against the uptake and propagation of foreign DNA by catalyzing the DNA cleavage reaction. The TtAgo active site consists of a plugged-in glutamate finger with two arginine residues (R545 and R486) located symmetrically... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Jinping Lei, Gang Sheng, Peter Pak-Hang Cheung, Shenglong Wang, Yu Li, Xin Gao, Yingkai Zhang, Yanli Wang, Xuhui Huang Tags: PNAS Plus Source Type: research

Biosynthesis of mycobacterial methylmannose polysaccharides requires a unique 1-O-methyltransferase specific for 3-O-methylated mannosides [Biochemistry]
Mycobacteria are a wide group of organisms that includes strict pathogens, such as Mycobacterium tuberculosis, as well as environmental species known as nontuberculous mycobacteria (NTM), some of which—namely Mycobacterium avium—are important opportunistic pathogens. In addition to a distinctive cell envelope mediating critical interactions with the host immune system and largely... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Jorge Ripoll–Rozada, Mafalda Costa, Jose A. Manso, Ana Maranha, Vanessa Miranda, Andre Sequeira, M. Rita Ventura, Sandra Macedo–Ribeiro, Pedro Jose Barbosa Pereira, Nuno Empadinhas Tags: PNAS Plus Source Type: research

ParST is a widespread toxin-antitoxin module that targets nucleotide metabolism [Biochemistry]
Toxin–antitoxin (TA) systems interfere with essential cellular processes and are implicated in bacterial lifestyle adaptations such as persistence and the biofilm formation. Here, we present structural, biochemical, and functional data on an uncharacterized TA system, the COG5654–COG5642 pair. Bioinformatic analysis showed that this TA pair is found in 2,942 of... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Frank J. Piscotta, Philip D. Jeffrey, A. James Link Tags: PNAS Plus Source Type: research

DNA damage and genome instability by G-quadruplex ligands are mediated by R loops in human cancer cells [Biochemistry]
G quadruplexes (G4s) and R loops are noncanonical DNA structures that can regulate basic nuclear processes and trigger DNA damage, genome instability, and cell killing. By different technical approaches, we here establish that specific G4 ligands stabilize G4s and simultaneously increase R-loop levels within minutes in human cancer cells. Genome-wide... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Alessio De Magis, Stefano G. Manzo, Marco Russo, Jessica Marinello, Rita Morigi, Olivier Sordet, Giovanni Capranico Tags: PNAS Plus Source Type: research

Data-driven quantitative modeling of bacterial active nematics [Physics]
Active matter comprises individual units that convert energy into mechanical motion. In many examples, such as bacterial systems and biofilament assays, constituent units are elongated and can give rise to local nematic orientational order. Such “active nematics” systems have attracted much attention from both theorists and experimentalists. However, despite intense... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: He Li, Xia–qing Shi, Mingȷi Huang, Xiao Chen, Minfeng Xiao, Chenli Liu, Hugues Chate, H. P. Zhang Tags: PNAS Plus Source Type: research

Bioactive cell-like hybrids from dendrimersomes with a human cell membrane and its components [Chemistry]
Cell-like hybrids from natural and synthetic amphiphiles provide a platform to engineer functions of synthetic cells and protocells. Cell membranes and vesicles prepared from human cell membranes are relatively unstable in vitro and therefore are difficult to study. The thicknesses of biological membranes and vesicles self-assembled from amphiphilic Janus dendrimers,... (Source: Proceedings of the National Academy of Sciences)
Source: Proceedings of the National Academy of Sciences - January 15, 2019 Category: Science Authors: Srujana S. Yadavalli, Qi Xiao, Samuel E. Sherman, William D. Hasley, Michael L. Klein, Mark Goulian, Virgil Percec Tags: PNAS Plus Source Type: research