Proceedings of the Natural Academy of Sciences

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  • Lateral root formation requires a carotenoid [Plant Biology]
    [Apr 2014]

    In plants, continuous formation of lateral roots (LRs) facilitates efficient exploration of the soil environment. Roots can maximize developmental capacity in variable environmental conditions through establishment of sites competent to form LRs. This LR prepattern is established by a periodic oscillation in gene expression near the root tip. The spatial...
    Categories: Journal Articles
  • Suppression disrupts unconscious memories [Psychological and Cognitive Sciences]
    [Apr 2014]

    Suppressing retrieval of unwanted memories reduces their later conscious recall. It is widely believed, however, that suppressed memories can continue to exert strong unconscious effects that may compromise mental health. Here we show that excluding memories from awareness not only modulates medial temporal lobe regions involved in explicit retention, but...
    Categories: Journal Articles
  • Entropic forces on constrained sequences [Systems Biology]
    [Apr 2014]

    We outline a theory to quantify the interplay of entropic and selective forces on nucleotide organization and apply it to the genomes of single-stranded RNA viruses. We quantify these forces as intensive variables that can easily be compared between sequences, outline a computationally efficient transfer-matrix method for their calculation, and...
    Categories: Journal Articles
  • Correction for Fanelli and Ioannidis, Reply to Nuijten et al.: Reanalyses actually confirm that US studies overestimate effects in softer research [Correction]
    [Apr 2014]

    LETTER TO THE EDITOR Correction for “Reply to Nuijten et al.: Reanalyses actually confirm that US studies overestimate effects in softer research,” by Daniele Fanelli and John P. A. Ioannidis, which appeared in issue 7, February 18, 2014, of Proc Natl Acad Sci USA (111:E714–E715; first published February 4, 2014;...
    Categories: Journal Articles
  • Correction for Burgess et al., High-precision timeline for Earth's most severe extinction [Correction]
    [Apr 2014]

    EARTH, ATMOSPHERIC, AND PLANETARY SCIENCES Correction for “High-precision timeline for Earth’s most severe extinction,” by Seth D. Burgess, Samuel Bowring, and Shu-zhong Shen, which appeared in issue 9, March 4, 2014, of Proc Natl Acad Sci USA (111:3316–3321; first published February 10, 2014; 10.1073/pnas.1317692111). The authors note that Fig. 3...
    Categories: Journal Articles
  • Correction for Tran et al., Vaccine-elicited primate antibodies use a distinct approach to the HIV-1 primary receptor binding site informing vaccine redesign [Correction]
    [Apr 2014]

    IMMUNOLOGY Correction for “Vaccine-elicited primate antibodies use a distinct approach to the HIV-1 primary receptor binding site informing vaccine redesign,” by Karen Tran, Christian Poulsen, Javier Guenaga, Natalia de Val Alda, Richard Wilson, Christopher Sundling, Yuxing Li, Robyn L. Stanfield, Ian A. Wilson, Andrew B. Ward, Gunilla B. Karlsson Hedestam,...
    Categories: Journal Articles
  • Correction for Khafizov et al., Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative [Correction]
    [Apr 2014]

    BIOPHYSICS AND COMPUTATIONAL BIOLOGY Correction for “Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative,” by Kamil Khafizov, Carlos Madrid-Aliste, Steven C. Almo, and Andras Fiser, which appeared in issue 10, March 11, 2014, of Proc Natl Acad Sci USA (111:3733–3738; first published...
    Categories: Journal Articles
  • Membrane bHLH TF involved in nodule development [Agricultural Sciences]
    [Apr 2014]

    Glycine max symbiotic ammonium transporter 1 was first documented as a putative ammonium (NH4+) channel localized to the symbiosome membrane of soybean root nodules. We show that Glycine max symbiotic ammonium transporter 1 is actually a membrane-localized basic helix–loop–helix (bHLH) DNA-binding transcription factor now renamed Glycine max bHLH membrane 1...
    Categories: Journal Articles
  • Collective action, social networks, and health in the Andes [Anthropology]
    [Apr 2014]

    Several theories have emerged to explain how group cooperation (collective action) can arise and be maintained in the face of incentives to engage in free riding. Explanations focusing on reputational benefits and partner choice have particular promise for cases in which punishment is absent or insufficient to deter free riding....
    Categories: Journal Articles
  • Origins and dispersal of Polynesian chickens [Anthropology]
    [Apr 2014]

    The human colonization of Remote Oceania remains one of the great feats of exploration in history, proceeding east from Asia across the vast expanse of the Pacific Ocean. Human commensal and domesticated species were widely transported as part of this diaspora, possibly as far as South America. We sequenced mitochondrial...
    Categories: Journal Articles
  • Direct evidence for selection on pigmentation [Anthropology]
    [Apr 2014]

    Pigmentation is a polygenic trait encompassing some of the most visible phenotypic variation observed in humans. Here we present direct estimates of selection acting on functional alleles in three key genes known to be involved in human pigmentation pathways—HERC2, SLC45A2, and TYR—using allele frequency estimates from Eneolithic, Bronze Age, and...
    Categories: Journal Articles
  • Engineered bacteria sense and record gut chemicals [Applied Biological Sciences]
    [Apr 2014]

    The mammalian gut is a dynamic community of symbiotic microbes that interact with the host to impact health, disease, and metabolism. We constructed engineered bacteria that survive in the mammalian gut and sense, remember, and report on their experiences. Based on previous genetic memory systems, we constructed a two-part system...
    Categories: Journal Articles
  • Bacterial holo-translocon [Biochemistry]
    [Apr 2014]

    The SecY/61 complex forms the protein-channel component of the ubiquitous protein secretion and membrane protein insertion apparatus. The bacterial version SecYEG interacts with the highly conserved YidC and SecDF–YajC subcomplex, which facilitates translocation into and across the membrane. Together, they form the holo-translocon (HTL), which we have successfully overexpressed and...
    Categories: Journal Articles
  • H3K4me3 regulates H2A variant exchange by Tip60 [Biochemistry]
    [Apr 2014]

    Histone H3 lysine 4 trimethylation (H3K4me3) and the acetylated H2A variant, H2A.Z/v (H2Avac), are enriched at promoters of highly transcribed loci including the stress response genes. Using the inducible Drosophila hsp70 loci as a model, we study here the roles of the dSet1 and dTip60 complexes in the generation of...
    Categories: Journal Articles
  • Toxoplasma gliding adhesin structures [Biophysics and Computational Biology]
    [Apr 2014]

    Micronemal protein 2 (MIC2) is the key adhesin that supports gliding motility and host cell invasion by Toxoplasma gondii. With a von Willebrand factor A (VWA) domain and six thrombospondin repeat domains (TSR1–6) in its ectodomain, MIC2 connects to the parasite actomyosin system through its cytoplasmic tail. MIC2-associated protein (M2AP)...
    Categories: Journal Articles
  • Effects of {gamma}1-subunits on BK channels [Biophysics and Computational Biology]
    [Apr 2014]

    Many K+ channels are oligomeric complexes with intrinsic structural symmetry arising from the homo-tetrameric core of their pore-forming subunits. Allosteric regulation of tetramerically symmetric proteins, whether by intrinsic sensing domains or associated auxiliary subunits, often mirrors the fourfold structural symmetry. Here, through patch-clamp recordings of channel population ensembles and also...
    Categories: Journal Articles
  • Polymer effects of IDPs in crowded environments [Biophysics and Computational Biology]
    [Apr 2014]

    Intrinsically disordered proteins (IDPs) are involved in a wide range of regulatory processes in the cell. Owing to their flexibility, their conformations are expected to be particularly sensitive to the crowded cellular environment. Here we use single-molecule Förster resonance energy transfer to quantify the effect of crowding as mimicked by...
    Categories: Journal Articles
  • Directed cargo transport by an ATPase gradient [Cell Biology]
    [Apr 2014]

    The faithful segregation of duplicated genetic material into daughter cells is critical to all organisms. In many bacteria, the segregation of chromosomes involves transport of “centromere-like” loci over the main body of the chromosome, the nucleoid, mediated by a two-protein partition system: a nonspecific DNA-binding ATPase, ParA, and an ATPase...
    Categories: Journal Articles
  • EPHB3 silencing in colorectal cancer [Cell Biology]
    [Apr 2014]

    The protein tyrosine kinase Ephrin type-B receptor 3 (EPHB3) counteracts tumor-cell dissemination by regulating intercellular adhesion and repulsion and acts as tumor/invasion suppressor in colorectal cancer. This protective mechanism frequently collapses at the adenoma–carcinoma transition due to EPHB3 transcriptional silencing. Here, we identify a transcriptional enhancer at the EPHB3 gene...
    Categories: Journal Articles
  • Genomic activity of unliganded ER{alpha} [Cell Biology]
    [Apr 2014]

    Estrogen receptor-α (ERα) has central role in hormone-dependent breast cancer and its ligand-induced functions have been extensively characterized. However, evidence exists that ERα has functions that are independent of ligands. In the present work, we investigated the binding of ERα to chromatin in the absence of ligands and its functions...
    Categories: Journal Articles