Proceedings of the Natural Academy of Sciences

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  • Clonality in virus evolution [Colloquium Paper]
    [Jul 2015]

    In the present article we examine clonality in virus evolution. Most viruses retain an active recombination machinery as a potential means to initiate new levels of genetic exploration that go beyond those attainable solely by point mutations. However, despite abundant recombination that may be linked to molecular events essential for...
    Categories: Journal Articles
  • Bacterial clonality and recombination [Colloquium Paper]
    [Jul 2015]

    Bacteria reproduce asexually and pass on a single genome copied from the parent, a reproductive mode that assures the clonal descent of progeny; however, a truly clonal bacterial species is extremely rare. The signal of clonality can be interrupted by gene uptake and exchange, initiating homologous recombination that results in...
    Categories: Journal Articles
  • Clonal reproduction in fungi [Colloquium Paper]
    [Jul 2015]

    Research over the past two decades shows that both recombination and clonality are likely to contribute to the reproduction of all fungi. This view of fungi is different from the historical and still commonly held view that a large fraction of fungi are exclusively clonal and that some fungi have...
    Categories: Journal Articles
  • Clonal evolution in Neisseria [Colloquium Paper]
    [Jul 2015]

    The three species Neisseria meningitidis, Neisseria gonorrheae, and Neisseria lactamica are often regarded as highly recombining bacteria. N. meningitidis has been considered a paradigmatic case of the “semiclonal model” or of “epidemic clonality,” demonstrating occasional bouts of clonal propagation in an otherwise recombining species. In this model, occasional clonality generates...
    Categories: Journal Articles
  • Toward an evolutionary model of cancer [Colloquium Paper]
    [Jul 2015]

    Our understanding of cancer has greatly advanced since Nordling [Nordling CO (1953) Br J Cancer 7(1):68–72] and Armitage and Doll [Armitage P, Doll R (1954) Br J Cancer 8(1):1–12] put forth the multistage model of carcinogenesis. However, a number of observations remain poorly understood from the standpoint of this paradigm...
    Categories: Journal Articles
  • Stem cells are units of natural selection [Colloquium Paper]
    [Jul 2015]

    It is obvious that natural selection operates at the level of individuals and collections of individuals. Nearly two decades ago we showed that in multi-individual colonies of protochordate colonial tunicates sharing a blood circulation, there exists an exchange of somatic stem cells and germline stem cells, resulting in somatic chimeras...
    Categories: Journal Articles
  • Clonality enhances sexual fitness [Colloquium Paper]
    [Jul 2015]

    Clonality is a pervasive feature of sessile organisms, but this form of asexual reproduction is thought to interfere with sexual fitness via the movement of gametes among the modules that comprise the clone. This within-clone movement of gametes is expected to reduce sexual fitness via mate limitation of male reproductive...
    Categories: Journal Articles
  • Cancer in the parasitic protozoans [Colloquium Paper]
    [Jul 2015]

    Cancer is a general name for more than 100 malignant diseases. It is postulated that all cancers start from a single abnormal cell that grows out of control. Untreated cancers can cause serious consequences and deaths. Great progress has been made in cancer research that has significantly improved our knowledge...
    Categories: Journal Articles
  • Ecosystem in the balance captured in a work of art [Science and Culture]
    [Jul 2015]

    As visitors approach the ominously titled sculpture Collapse, they may be puzzled by the pyramid of 455 one-gallon jars. But as they step closer, it becomes clear that most of the jars, stacked 12 feet high and 15 feet on each side, contain a multitude of exquisitely detailed marine specimens....
    Categories: Journal Articles
  • Extracting precious metals from sewage [Inner Workings]
    [Jul 2015]

    Two groups of researchers found that sewage contains precious metals potentially worth millions. Image courtesy of shutterstock/gameanna. Making a valuable, unexpected discovery while exploring an unrelated hypothesis is a classic theme in the history of science. But literally striking gold? And in sewage, of all places? That’s what actually happened...
    Categories: Journal Articles
  • Codon pair usage and dinucleotide frequencies [Biological Sciences]
    [Jul 2015]

    Shen et al. (1) describe the modification of three regions of the Dengue virus type 2 (DENV-2) genome to match the codon pair use of insect genes rather than those of mammals. We have previously shown that such recoding also modifies frequencies of CpG and UpA dinucleotides and have proposed...
    Categories: Journal Articles
  • Codon pair and dinucleotide bias not distinguished [Biological Sciences]
    [Jul 2015]

    Simmonds et al. (1) have criticized our paper (2). Two disagreements stand out. First, the authors suggest that our viruses are attenuated by increased “dinucleotide frequencies” (1, 3), but “codon pair deoptimization” they dismiss as “artefact” (3). We believe this is just semantic word juggling. When a protein is recoded,...
    Categories: Journal Articles
  • Erroneous Parkinson's biomarker identification [Biological Sciences]
    [Jul 2015]

    Santiago and Potashkin (1) propose that two RNAs in blood, hepatocyte nuclear factor 4 alpha (HNF4A) and polypyrimidine tract binding protein 1 (PTBP1), might be clinically useful biomarkers for diagnosing and tracking the progression of Parkinson’s disease (PD), even speculating that they are better than neurological examination. Many have proposed...
    Categories: Journal Articles
  • Blood biomarkers for Parkinson's disease [Biological Sciences]
    [Jul 2015]

    We are grateful for the opportunity to respond to the comments of Toker and Pavlidis (1) regarding our recent publication, in which hepatocyte nuclear factor 4 alpha (HNF4A) and polypyrimidine tract binding protein 1 (PTBP1) mRNAs are identified as potential blood biomarkers for Parkinson’s disease (PD) (2). Early diagnosis of...
    Categories: Journal Articles
  • Hydrodynamic collective effects of active proteins [Physics]
    [Jul 2015]

    The cytoplasm and biomembranes in biological cells contain large numbers of proteins that cyclically change their shapes. They are molecular machines that can function as molecular motors or carry out various other tasks in the cell. Many enzymes also undergo conformational changes within their turnover cycles. We analyze the advection...
    Categories: Journal Articles
  • Depth-resolved MRI of TIs [Physics]
    [Jul 2015]

    Considerable evidence suggests that variations in the properties of topological insulators (TIs) at the nanoscale and at interfaces can strongly affect the physics of topological materials. Therefore, a detailed understanding of surface states and interface coupling is crucial to the search for and applications of new topological phases of matter....
    Categories: Journal Articles
  • Components of a host-pathogen arms race [Agricultural Sciences]
    [Jul 2015]

    Entomopathogenic fungi and their insect hosts represent a model system for examining invertebrate-pathogen coevolutionary selection processes. Here we report the characterization of competing components of an arms race consisting of insect protective antimicrobial compounds and evolving fungal mechanisms of detoxification. The insect pathogenic fungus Beauveria bassiana has a remarkably wide...
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  • Magnetic levitation of single cells [Applied Biological Sciences]
    [Jul 2015]

    Several cellular events cause permanent or transient changes in inherent magnetic and density properties of cells. Characterizing these changes in cell populations is crucial to understand cellular heterogeneity in cancer, immune response, infectious diseases, drug resistance, and evolution. Although magnetic levitation has previously been used for macroscale objects, its use...
    Categories: Journal Articles
  • Sin3L/Rpd3L HDAC complex assembly [Biochemistry]
    [Jul 2015]

    Acetylation is correlated with chromatin decondensation and transcriptional activation, but its regulation by histone deacetylase (HDAC)-bearing corepressor complexes is poorly understood. Here, we describe the mechanism of assembly of the mammalian Sin3L/Rpd3L complex facilitated by Sds3, a conserved subunit deemed critical for proper assembly. Sds3 engages a globular, helical region...
    Categories: Journal Articles
  • Ran function is regulated by lysine acetylation [Biochemistry]
    [Jul 2015]

    Ran is a small GTP-binding protein of the Ras superfamily regulating fundamental cellular processes: nucleo-cytoplasmic transport, nuclear envelope formation and mitotic spindle assembly. An intracellular Ran•GTP/Ran•GDP gradient created by the distinct subcellular localization of its regulators RCC1 and RanGAP mediates many of its cellular effects. Recent proteomic screens identified five...
    Categories: Journal Articles