Proceedings of the Natural Academy of Sciences

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  • Freeze-mediated expansion of mangroves [Biological Sciences]
    [Apr 2014]

    Giri and Long (1) agree with our conclusion (2) that the expansion of mangroves from 1984 to 2011 near their range limit on the Atlantic coast of Florida is a threshold response to fewer days below −4 °C. However, they suggest that our conclusions would have been “substantially different” had...
    Categories: Journal Articles
  • Strong evidence for protein epistasis [Biological Sciences]
    [Apr 2014]

    A recent paper by Ashenberg et al. (1) reports protein stability measurements and computational simulations that they claim contradict the results of our previous paper describing a “Stokes shift” in protein evolution (2). They make strong assertions that coevolutionary interactions among amino acids due to effects on stability do not...
    Categories: Journal Articles
  • CD133 and kidney repair [Biological Sciences]
    [Apr 2014]

    Kusaba et al. provide additional evidence using genetic lineage analysis that epithelial cell dedifferentiation is responsible for repair of proximal tubules after injury in mouse (1). These data challenge the hypothesis of the implication of scattered stem cells in such a process or highlight a potential distinction between rodent and...
    Categories: Journal Articles
  • Dedifferentiation and multipotency [Biological Sciences]
    [Apr 2014]

    We thank Corbeil et al. for raising important points (1) regarding our recent article (2) describing the role of epithelial dedifferentiation in kidney repair. We agree that the forward primer we used to detect CD133 mRNA is in fact not directed against the CD133 transcript. This error resulted from the...
    Categories: Journal Articles
  • Compound facial expressions of emotion [Computer Sciences]
    [Apr 2014]

    Understanding the different categories of facial expressions of emotion regularly used by us is essential to gain insights into human cognition and affect as well as for the design of computational models and perceptual interfaces. Past research on facial expressions of emotion has focused on the study of six basic...
    Categories: Journal Articles
  • Differential membrane PS recognition by Tim4 [Biophysics and Computational Biology]
    [Apr 2014]

    Recognition of phosphatidylserine (PS) lipids exposed on the extracellular leaflet of plasma membranes is implicated in both apoptotic cell removal and immune regulation. The PS receptor T cell immunoglobulin and mucin-domain-containing molecule 4 (Tim4) regulates T-cell immunity via phagocytosis of both apoptotic (high PS exposure) and nonapoptotic (intermediate PS exposure)...
    Categories: Journal Articles
  • Conformational ensemble of a DNA bulge [Biophysics and Computational Biology]
    [Apr 2014]

    Direct experimental measurements of conformational ensembles are critical for understanding macromolecular function, but traditional biophysical methods do not directly report the solution ensemble of a macromolecule. Small-angle X-ray scattering interferometry has the potential to overcome this limitation by providing the instantaneous distance distribution between pairs of gold-nanocrystal probes conjugated to...
    Categories: Journal Articles
  • Protein aggregation inhibits endocytosis [Cell Biology]
    [Apr 2014]

    Protein conformational diseases exhibit complex pathologies linked to numerous molecular defects. Aggregation of a disease-associated protein causes the misfolding and aggregation of other proteins, but how this interferes with diverse cellular pathways is unclear. Here, we show that aggregation of neurodegenerative disease-related proteins (polyglutamine, huntingtin, ataxin-1, and superoxide dismutase-1) inhibits...
    Categories: Journal Articles
  • Centrioles regulate a checkpoint in the mouse [Developmental Biology]
    [Apr 2014]

    Centrosomes are the microtubule-organizing centers of animal cells that organize interphase microtubules and mitotic spindles. Centrioles are the microtubule-based structures that organize centrosomes, and a defined set of proteins, including spindle assembly defective-4 (SAS4) (CPAP/CENPJ), is required for centriole biogenesis. The biological functions of centrioles and centrosomes vary among animals,...
    Categories: Journal Articles
  • Epidermal Wnt regulates adipocyte differentiation [Developmental Biology]
    [Apr 2014]

    It has long been recognized that the hair follicle growth cycle and oscillation in the thickness of the underlying adipocyte layer are synchronized. Although factors secreted by adipocytes are known to regulate the hair growth cycle, it is unclear whether the epidermis can regulate adipogenesis. We show that inhibition of...
    Categories: Journal Articles
  • Deepwater Horizon impacts on pelagic fish embryos [Environmental Sciences]
    [Apr 2014]

    The Deepwater Horizon disaster released more than 636 million L of crude oil into the northern Gulf of Mexico. The spill oiled upper surface water spawning habitats for many commercially and ecologically important pelagic fish species. Consequently, the developing spawn (embryos and larvae) of tunas, swordfish, and other large predators...
    Categories: Journal Articles
  • DENND1A.V2 produces a PCOS phenotype [Medical Sciences]
    [Apr 2014]

    Polycystic ovary syndrome (PCOS), characterized by increased ovarian androgen biosynthesis, anovulation, and infertility, affects 5–7% of reproductive-age women. Genome-wide association studies identified PCOS candidate loci that were replicated in subsequent reports, including DENND1A, which encodes a protein associated with clathrin-coated pits where cell-surface receptors reside. However, these studies provided no...
    Categories: Journal Articles
  • HIV-1 reactivation requires Hsp90 [Microbiology]
    [Apr 2014]

    Latency allows HIV-1 to persist in long-lived cellular reservoirs, preventing virus eradication. We have previously shown that the heat shock protein 90 (Hsp90) is required for HIV-1 gene expression and mediates greater HIV-1 replication in conditions of hyperthermia. Here we report that specific inhibitors of Hsp90 such as 17-(N-allylamino)-17-demethoxygeldanamycin and...
    Categories: Journal Articles
  • Lifespan extension in active, nondividing yeast [Microbiology]
    [Apr 2014]

    Studies of replicative and chronological lifespan in Saccharomyces cerevisiae have advanced understanding of longevity in all eukaryotes. Chronological lifespan in this species is defined as the age-dependent viability of nondividing cells. To date this parameter has only been estimated under calorie restriction, mimicked by starvation. Because postmitotic cells in higher...
    Categories: Journal Articles
  • Analysis of V. cholerae outer membrane vesicles [Microbiology]
    [Apr 2014]

    Outer membrane vesicles (OMVs) produced by Gram-negative bacteria provide an interesting research material for defining cell-envelope proteins without experimental cell disruption. OMVs are also promising immunogenic platforms and may play important roles in bacterial survival and pathogenesis. We used in-solution trypsin digestion coupled to mass spectrometry to identify 90 proteins...
    Categories: Journal Articles
  • Mangrove reemergence in eastern Florida [Biological Sciences]
    [Apr 2014]

    Cavanaugh et al. (1) report conclusive evidence of poleward expansion of mangroves at the northern limit of their historic range on the east coast of Florida and associate the expansion to a reduction in the frequency of extreme cold events. We agree with their assertion that mangrove expansion has occurred...
    Categories: Journal Articles
  • Traits predict tropical forest dynamics [Ecology]
    [Apr 2014]

    Interspecific differences in relative fitness can cause local dominance by a single species. However, stabilizing interspecific niche differences can promote local diversity. Understanding these mechanisms requires that we simultaneously quantify their effects on demography and link these effects to community dynamics. Successional forests are ideal systems for testing assembly theory...
    Categories: Journal Articles
  • Ecological differentiation in marine bacteria [Ecology]
    [Apr 2014]

    Although competition–dispersal tradeoffs are commonly invoked to explain species coexistence for animals and plants in spatially structured environments, such mechanisms for coexistence remain unknown for microorganisms. Here we show that two recently speciated marine bacterioplankton populations pursue different behavioral strategies to exploit nutrient particles in adaptation to the landscape of...
    Categories: Journal Articles
  • Deoxygenation of the Baltic Sea [Ecology]
    [Apr 2014]

    Deoxygenation is a global problem in coastal and open regions of the ocean, and has led to expanding areas of oxygen minimum zones and coastal hypoxia. The recent expansion of hypoxia in coastal ecosystems has been primarily attributed to global warming and enhanced nutrient input from land and atmosphere. The...
    Categories: Journal Articles
  • A mechanism for integral feedback [Engineering]
    [Apr 2014]

    Sensory feedback is a ubiquitous feature of guidance systems in both animals and engineered vehicles. For example, a common strategy for moving along a straight path is to turn such that the measured rate of rotation is zero. This task can be accomplished by using a feedback signal that is...
    Categories: Journal Articles