Search results

Title: Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture.
Creator: Darrow, Emily M, Huntley, Miriam H, Dudchenko, Olga, Stamenova, Elena K, Durand, Neva C, Sun, Zhuo, Huang, Su-Chen, Sanborn, Adrian L, Machol, Ido, Shamim, Muhammad, Seberg,...
Show moreDarrow, Emily M, Huntley, Miriam H, Dudchenko, Olga, Stamenova, Elena K, Durand, Neva C, Sun, Zhuo, Huang, Su-Chen, Sanborn, Adrian L, Machol, Ido, Shamim, Muhammad, Seberg, Andrew P, Lander, Eric S, Chadwick, Brian P, Aiden, Erez Lieberman
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Abstract/Description: During interphase, the inactive X chromosome (Xi) is largely transcriptionally silent and adopts an unusual 3D configuration known as the "Barr body." Despite the importance of X chromosome inactivation, little is known about this 3D conformation. We recently showed that in humans the Xi chromosome exhibits three structural features, two of which are not shared by other chromosomes. First, like the chromosomes of many species, Xi forms compartments. Second, Xi is partitioned into two huge...
Show moreDuring interphase, the inactive X chromosome (Xi) is largely transcriptionally silent and adopts an unusual 3D configuration known as the "Barr body." Despite the importance of X chromosome inactivation, little is known about this 3D conformation. We recently showed that in humans the Xi chromosome exhibits three structural features, two of which are not shared by other chromosomes. First, like the chromosomes of many species, Xi forms compartments. Second, Xi is partitioned into two huge intervals, called "superdomains," such that pairs of loci in the same superdomain tend to colocalize. The boundary between the superdomains lies near DXZ4, a macrosatellite repeat whose Xi allele extensively binds the protein CCCTC-binding factor. Third, Xi exhibits extremely large loops, up to 77 megabases long, called "superloops." DXZ4 lies at the anchor of several superloops. Here, we combine 3D mapping, microscopy, and genome editing to study the structure of Xi, focusing on the role of DXZ4 We show that superloops and superdomains are conserved across eutherian mammals. By analyzing ligation events involving three or more loci, we demonstrate that DXZ4 and other superloop anchors tend to colocate simultaneously. Finally, we show that deleting DXZ4 on Xi leads to the disappearance of superdomains and superloops, changes in compartmentalization patterns, and changes in the distribution of chromatin marks. Thus, DXZ4 is essential for proper Xi packaging.
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Date Issued: 2016-08-02
Identifier: FSU_pmch_27432957, 10.1073/pnas.1609643113, PMC4978254, 27432957, 27432957, 1609643113
Format: Citation

Title: Wavy membranes and the growth rate of a planar chemical garden: Enhanced diffusion and bioenergetics..
Creator: Ding, Yang, Batista, Bruno, Steinbock, Oliver, Cartwright, Julyan H E, Cardoso, Silvana S S
Abstract/Description: To model ion transport across protocell membranes in Hadean hydrothermal vents, we consider both theoretically and experimentally the planar growth of a precipitate membrane formed at the interface between two parallel fluid streams in a 2D microfluidic reactor. The growth rate of the precipitate is found to be proportional to the square root of time, which is characteristic of diffusive transport. However, the dependence of the growth rate on the concentrations of hydroxide and metal ions is...
Show moreTo model ion transport across protocell membranes in Hadean hydrothermal vents, we consider both theoretically and experimentally the planar growth of a precipitate membrane formed at the interface between two parallel fluid streams in a 2D microfluidic reactor. The growth rate of the precipitate is found to be proportional to the square root of time, which is characteristic of diffusive transport. However, the dependence of the growth rate on the concentrations of hydroxide and metal ions is approximately linear and quadratic, respectively. We show that such a difference in ionic transport dynamics arises from the enhanced transport of metal ions across a thin gel layer present at the surface of the precipitate. The fluctuations in transverse velocity in this wavy porous gel layer allow an enhanced transport of the cation, so that the effective diffusivity is about one order of magnitude higher than that expected from molecular diffusion alone. Our theoretical predictions are in excellent agreement with our laboratory measurements of the growth of a manganese hydroxide membrane in a microfluidic channel, and this enhanced transport is thought to have been needed to account for the bioenergetics of the first single-celled organisms.
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Date Issued: 2016-08-16
Identifier: FSU_pmch_27486248, 10.1073/pnas.1607828113, PMC4995959, 27486248, 27486248, 1607828113
Format: Citation

Title: Low rates of nitrogen fixation in eastern tropical South Pacific surface waters.
Creator: Knapp, Angela N, Casciotti, Karen L, Berelson, William M, Prokopenko, Maria G, Capone, Douglas G
Abstract/Description: An extensive region of the Eastern Tropical South Pacific (ETSP) Ocean has surface waters that are nitrate-poor yet phosphate-rich. It has been proposed that this distribution of surface nutrients provides a geochemical niche favorable for N2fixation, the primary source of nitrogen to the ocean. Here, we present results from two cruises to the ETSP where rates of N2fixation and its contribution to export production were determined with a suite of geochemical and biological measurements....
Show moreAn extensive region of the Eastern Tropical South Pacific (ETSP) Ocean has surface waters that are nitrate-poor yet phosphate-rich. It has been proposed that this distribution of surface nutrients provides a geochemical niche favorable for N2fixation, the primary source of nitrogen to the ocean. Here, we present results from two cruises to the ETSP where rates of N2fixation and its contribution to export production were determined with a suite of geochemical and biological measurements. N2fixation was only detectable using nitrogen isotopic mass balances at two of six stations, and rates ranged from 0 to 23 µmol N m(-2)d(-1)based on sediment trap fluxes. Whereas the fractional importance of N2fixation did not change, the N2-fixation rates at these two stations were several-fold higher when scaled to other productivity metrics. Regardless of the choice of productivity metric these N2-fixation rates are low compared with other oligotrophic locations, and the nitrogen isotope budgets indicate that N2fixation supports no more than 20% of export production regionally. Although euphotic zone-integrated short-term N2-fixation rates were higher, up to 100 µmol N m(-2)d(-1), and detected N2fixation at all six stations, studies of nitrogenase gene abundance and expression from the same cruises align with the geochemical data and together indicate that N2fixation is a minor source of new nitrogen to surface waters of the ETSP. This finding is consistent with the hypothesis that, despite a relative abundance of phosphate, iron may limit N2fixation in the ETSP.
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Date Issued: 2016-04-19
Identifier: FSU_pmch_26976587, 10.1073/pnas.1515641113, PMC4843426, 26976587, 26976587, 1515641113
Format: Citation

Title: Saharan dust nutrients promote Vibrio bloom formation in marine surface waters.
Creator: Westrich, Jason R, Ebling, Alina M, Landing, William M, Joyner, Jessica L, Kemp, Keri M, Griffin, Dale W, Lipp, Erin K
Abstract/Description: Vibrio is a ubiquitous genus of marine bacteria, typically comprising a small fraction of the total microbial community in surface waters, but capable of becoming a dominant taxon in response to poorly characterized factors. Iron (Fe), often restricted by limited bioavailability and low external supply, is an essential micronutrient that can limit Vibrio growth. Vibrio species have robust metabolic capabilities and an array of Fe-acquisition mechanisms, and are able to respond rapidly to...
Show moreVibrio is a ubiquitous genus of marine bacteria, typically comprising a small fraction of the total microbial community in surface waters, but capable of becoming a dominant taxon in response to poorly characterized factors. Iron (Fe), often restricted by limited bioavailability and low external supply, is an essential micronutrient that can limit Vibrio growth. Vibrio species have robust metabolic capabilities and an array of Fe-acquisition mechanisms, and are able to respond rapidly to nutrient influx, yet Vibrio response to environmental pulses of Fe remains uncharacterized. Here we examined the population growth of Vibrio after natural and simulated pulses of atmospherically transported Saharan dust, an important and episodic source of Fe to tropical marine waters. As a model for opportunistic bacterial heterotrophs, we demonstrated that Vibrio proliferate in response to a broad range of dust-Fe additions at rapid timescales. Within 24 h of exposure, strains of Vibrio cholerae and Vibrio alginolyticus were able to directly use Saharan dust-Fe to support rapid growth. These findings were also confirmed with in situ field studies; arrival of Saharan dust in the Caribbean and subtropical Atlantic coincided with high levels of dissolved Fe, followed by up to a 30-fold increase of culturable Vibrio over background levels within 24 h. The relative abundance of Vibrio increased from ∼1 to ∼20% of the total microbial community. This study, to our knowledge, is the first to describe Vibrio response to Saharan dust nutrients, having implications at the intersection of marine ecology, Fe biogeochemistry, and both human and environmental health.
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Date Issued: 2016-05-24
Identifier: FSU_pmch_27162369, 10.1073/pnas.1518080113, PMC4889353, 27162369, 27162369, 1518080113
Format: Citation

Title: Open chromatin reveals the functional maize genome.
Creator: Rodgers-Melnick, Eli, Vera, Daniel L, Bass, Hank W, Buckler, Edward S
Abstract/Description: Cellular processes mediated through nuclear DNA must contend with chromatin. Chromatin structural assays can efficiently integrate information across diverse regulatory elements, revealing the functional noncoding genome. In this study, we use a differential nuclease sensitivity assay based on micrococcal nuclease (MNase) digestion to discover open chromatin regions in the maize genome. We find that maize MNase-hypersensitive (MNase HS) regions localize around active genes and within...
Show moreCellular processes mediated through nuclear DNA must contend with chromatin. Chromatin structural assays can efficiently integrate information across diverse regulatory elements, revealing the functional noncoding genome. In this study, we use a differential nuclease sensitivity assay based on micrococcal nuclease (MNase) digestion to discover open chromatin regions in the maize genome. We find that maize MNase-hypersensitive (MNase HS) regions localize around active genes and within recombination hotspots, focusing biased gene conversion at their flanks. Although MNase HS regions map to less than 1% of the genome, they consistently explain a remarkably large amount (∼40%) of heritable phenotypic variance in diverse complex traits. MNase HS regions are therefore on par with coding sequences as annotations that demarcate the functional parts of the maize genome. These results imply that less than 3% of the maize genome (coding and MNase HS regions) may give rise to the overwhelming majority of phenotypic variation, greatly narrowing the scope of the functional genome.
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Date Issued: 2016-05-31
Identifier: FSU_pmch_27185945, 10.1073/pnas.1525244113, PMC4896728, 27185945, 27185945, 1525244113
Format: Citation

Title: 1.1-billion-year-old Porphyrins Establish A Marine Ecosystem Dominated By Bacterial Primary Producers.
Creator: Gueneli, N., McKenna, A. M., Ohkouchi, N., Boreham, C. J., Beghin, J., Javaux, E. J., Brocks, J. J.
Abstract/Description: The average cell size of marine phytoplankton is critical for the flow of energy and nutrients from the base of the food web to higher trophic levels. Thus, the evolutionary succession of primary producers through Earth's history is important for our understanding of the radiation of modern protists similar to 800 million years ago and the emergence of eumetazoan animals similar to 200 million years later. Currently, it is difficult to establish connections between primary production and the...
Show moreThe average cell size of marine phytoplankton is critical for the flow of energy and nutrients from the base of the food web to higher trophic levels. Thus, the evolutionary succession of primary producers through Earth's history is important for our understanding of the radiation of modern protists similar to 800 million years ago and the emergence of eumetazoan animals similar to 200 million years later. Currently, it is difficult to establish connections between primary production and the proliferation of large and complex organisms because the mid-Proterozoic (similar to 1,800-800 million years ago) rock record is nearly devoid of recognizable phytoplankton fossils. We report the discovery of intact porphyrins, the molecular fossils of chlorophylls, from 1,100-million-year-old marine black shales of the Taoudeni Basin (Mauritania), 600 million years older than previous findings. The porphyrin nitrogen isotopes (delta N-15(por) = 5.6-10.2 parts per thousand) are heavier than in younger sedimentary sequences, and the isotopic offset between sedimentary bulk nitrogen and porphyrins (epsilon(por) = -5.1 to -0.5 parts per thousand) points to cyanobacteria as dominant primary producers. Based on fossil carotenoids, anoxygenic green (Chlorobiacea) and purple sulfur bacteria (Chromatiaceae) also contributed to photosynthate. The low epsilon(por) values, in combination with a lack of diagnostic eukaryotic steranes in the time interval of 1,600-1,000 million years ago, demonstrate that algae played an insignificant role in mid-Proterozoic oceans. The paucity of algae and the small cell size of bacterial phytoplankton may have curtailed the flow of energy to higher trophic levels, potentially contributing to a diminished evolutionary pace toward complex eukaryotic ecosystems and large and active organisms.
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Date Issued: 2018-07-24
Identifier: FSU_libsubv1_wos_000439574700004, 10.1073/pnas.1803866115
Format: Citation

Title: Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination.
Creator: Pulivarthy, Sandhya R, Lion, Mattia, Kuzu, Guray, Matthews, Adam G W, Borowsky, Mark L, Morris, John, Kingston, Robert E, Dennis, Jonathan H, Tolstorukov, Michael Y, Oettinger,...
Show morePulivarthy, Sandhya R, Lion, Mattia, Kuzu, Guray, Matthews, Adam G W, Borowsky, Mark L, Morris, John, Kingston, Robert E, Dennis, Jonathan H, Tolstorukov, Michael Y, Oettinger, Marjorie A
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Abstract/Description: We show that the physical distribution of nucleosomes at antigen receptor loci is subject to regulated cell type-specific and lineage-specific positioning and correlates with the accessibility of these gene segments to recombination. At the Ig heavy chain locus (IgH), a nucleosome in pro-B cells is generally positioned over each IgH variable (VH) coding segment, directly adjacent to the recombination signal sequence (RSS), placing the RSS in a position accessible to the recombination...
Show moreWe show that the physical distribution of nucleosomes at antigen receptor loci is subject to regulated cell type-specific and lineage-specific positioning and correlates with the accessibility of these gene segments to recombination. At the Ig heavy chain locus (IgH), a nucleosome in pro-B cells is generally positioned over each IgH variable (VH) coding segment, directly adjacent to the recombination signal sequence (RSS), placing the RSS in a position accessible to the recombination activating gene (RAG) recombinase. These changes result in establishment of a specific chromatin organization at the RSS that facilitates accessibility of the genomic DNA for the RAG recombinase. In contrast, in mouse embryonic fibroblasts the coding segment is depleted of nucleosomes, which instead cover the RSS, thereby rendering it inaccessible. Pro-T cells exhibit a pattern intermediate between pro-B cells and mouse embryonic fibroblasts. We also find large-scale variations of nucleosome density over hundreds of kilobases, delineating chromosomal domains within IgH, in a cell type-dependent manner. These findings suggest that developmentally regulated changes in nucleosome location and occupancy, in addition to the known chromatin modifications, play a fundamental role in regulating V(D)J recombination. Nucleosome positioning-which has previously been observed to vary locally at individual enhancers and promoters-may be a more general mechanism by which cells can regulate the accessibility of the genome during development, at scales ranging from several hundred base pairs to many kilobases.
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Date Issued: 2016-10-18
Identifier: FSU_pmch_27698124, 10.1073/pnas.1605543113, PMC5081657, 27698124, 27698124, 1605543113
Format: Citation

Title: Parasite stress and pathogen avoidance relate to distinct dimensions of political ideology across 30 nations.
Creator: Tybur, Joshua M, Inbar, Yoel, Aarøe, Lene, Barclay, Pat, Barlow, Fiona Kate, de Barra, Mícheál, Becker, D Vaughn, Borovoi, Leah, Choi, Incheol, Choi, Jong An, Consedine, Nathan...
Show moreTybur, Joshua M, Inbar, Yoel, Aarøe, Lene, Barclay, Pat, Barlow, Fiona Kate, de Barra, Mícheál, Becker, D Vaughn, Borovoi, Leah, Choi, Incheol, Choi, Jong An, Consedine, Nathan S, Conway, Alan, Conway, Jane Rebecca, Conway, Paul, Adoric, Vera Cubela, Demirci, Dilara Ekin, Fernández, Ana María, Ferreira, Diogo Conque Seco, Ishii, Keiko, Jakšić, Ivana, Ji, Tingting, van Leeuwen, Florian, Lewis, David M G, Li, Norman P, McIntyre, Jason C, Mukherjee, Sumitava, Park, Justin H, Pawlowski, Boguslaw, Petersen, Michael Bang, Pizarro, David, Prodromitis, Gerasimos, Prokop, Pavol, Rantala, Markus J, Reynolds, Lisa M, Sandin, Bonifacio, Sevi, Bariş, De Smet, Delphine, Srinivasan, Narayanan, Tewari, Shruti, Wilson, Cameron, Yong, Jose C, Žeželj, Iris
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Abstract/Description: People who are more avoidant of pathogens are more politically conservative, as are nations with greater parasite stress. In the current research, we test two prominent hypotheses that have been proposed as explanations for these relationships. The first, which is an intragroup account, holds that these relationships between pathogens and politics are based on motivations to adhere to local norms, which are sometimes shaped by cultural evolution to have pathogen-neutralizing properties. The...
Show morePeople who are more avoidant of pathogens are more politically conservative, as are nations with greater parasite stress. In the current research, we test two prominent hypotheses that have been proposed as explanations for these relationships. The first, which is an intragroup account, holds that these relationships between pathogens and politics are based on motivations to adhere to local norms, which are sometimes shaped by cultural evolution to have pathogen-neutralizing properties. The second, which is an intergroup account, holds that these same relationships are based on motivations to avoid contact with outgroups, who might pose greater infectious disease threats than ingroup members. Results from a study surveying 11,501 participants across 30 nations are more consistent with the intragroup account than with the intergroup account. National parasite stress relates to traditionalism (an aspect of conservatism especially related to adherence to group norms) but not to social dominance orientation (SDO; an aspect of conservatism especially related to endorsements of intergroup barriers and negativity toward ethnic and racial outgroups). Further, individual differences in pathogen-avoidance motives (i.e., disgust sensitivity) relate more strongly to traditionalism than to SDO within the 30 nations.
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Date Issued: 2016-11-01
Identifier: FSU_pmch_27791090, 10.1073/pnas.1607398113, PMC5098626, 27791090, 27791090, 1607398113
Format: Citation

Title: Unidirectional allostery in the regulatory subunit RIα facilitates efficient deactivation of protein kinase A.
Creator: Guo, Cong, Zhou, Huan-Xiang
Abstract/Description: The holoenzyme complex of protein kinase A is in an inactive state; activation involves ordered cAMP binding to two tandem domains of the regulatory subunit and release of the catalytic subunit. Deactivation has been less studied, during which the two cAMPs unbind from the regulatory subunit to allow association of the catalytic subunit to reform the holoenzyme complex. Unbinding of the cAMPs appears ordered as indicated by a large difference in unbinding rates from the two sites, but the...
Show moreThe holoenzyme complex of protein kinase A is in an inactive state; activation involves ordered cAMP binding to two tandem domains of the regulatory subunit and release of the catalytic subunit. Deactivation has been less studied, during which the two cAMPs unbind from the regulatory subunit to allow association of the catalytic subunit to reform the holoenzyme complex. Unbinding of the cAMPs appears ordered as indicated by a large difference in unbinding rates from the two sites, but the cause has remained elusive given the structural similarity of the two tandem domains. Even more intriguingly, NMR data show that allosteric communication between the two domains is unidirectional. Here, we present a mechanism for the unidirectionality, developed from extensive molecular dynamics simulations of the tandem domains in different cAMP-bound forms. Disparate responses to cAMP releases from the two sites (A and B) in conformational flexibility and chemical shift perturbation confirmed unidirectional allosteric communication. Community analysis revealed that the A-site cAMP, by forming across-domain interactions, bridges an essential pathway for interdomain communication. The pathway is impaired when this cAMP is removed but remains intact when only the B-site cAMP is removed. Specifically, removal of the A-site cAMP leads to the separation of the two domains, creating room for binding the catalytic subunit. Moreover, the A-site cAMP, by maintaining interdomain coupling, retards the unbinding of the B-site cAMP and stalls an unproductive pathway of cAMP release. Our work expands the perspective on allostery and implicates functional importance for the directionality of allostery.
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Date Issued: 2016-11-01
Identifier: FSU_pmch_27791125, 10.1073/pnas.1610142113, PMC5098638, 27791125, 27791125, 1610142113
Format: Citation

Title: Magnetic phase diagram of underdoped YBaCuO inferred from torque magnetization and thermal conductivity.
Creator: Yu, Fan, Hirschberger, Max, Loew, Toshinao, Li, Gang, Lawson, Benjamin J, Asaba, Tomoya, Kemper, J B, Liang, Tian, Porras, Juan, Boebinger, Gregory S, Singleton, John, Keimer,...
Show moreYu, Fan, Hirschberger, Max, Loew, Toshinao, Li, Gang, Lawson, Benjamin J, Asaba, Tomoya, Kemper, J B, Liang, Tian, Porras, Juan, Boebinger, Gregory S, Singleton, John, Keimer, Bernhard, Li, Lu, Ong, N Phuan
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Abstract/Description: Strong evidence for charge-density correlation in the underdoped phase of the cuprate YBaCuO was obtained by NMR and resonant X-ray scattering. The fluctuations were found to be enhanced in strong magnetic fields. Recently, 3D charge-density-wave (CDW) formation with long-range order (LRO) was observed by X-ray diffraction in [Formula: see text] 15 T. To elucidate how the CDW transition impacts the pair condensate, we have used torque magnetization to 45 T and thermal conductivity [Formula:...
Show moreStrong evidence for charge-density correlation in the underdoped phase of the cuprate YBaCuO was obtained by NMR and resonant X-ray scattering. The fluctuations were found to be enhanced in strong magnetic fields. Recently, 3D charge-density-wave (CDW) formation with long-range order (LRO) was observed by X-ray diffraction in [Formula: see text] 15 T. To elucidate how the CDW transition impacts the pair condensate, we have used torque magnetization to 45 T and thermal conductivity [Formula: see text] to construct the magnetic phase diagram in untwinned crystals with hole density = 0.11. We show that the 3D CDW transitions appear as sharp features in the susceptibility and [Formula: see text] at the fields [Formula: see text] and [Formula: see text], which define phase boundaries in agreement with spectroscopic techniques. From measurements of the melting field [Formula: see text] of the vortex solid, we obtain evidence for two vortex solid states below 8 K. At 0.5 K, the pair condensate appears to adjust to the 3D CDW by a sharp transition at 24 T between two vortex solids with very different shear moduli. At even higher (41 T), the second vortex solid melts to a vortex liquid which survives to fields well above 41 T. de Haas-van Alphen oscillations appear at fields 24-28 T, below the lower bound for the upper critical field [Formula: see text].
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Date Issued: 2016-11-08
Identifier: FSU_pmch_27791146, 10.1073/pnas.1612591113, PMC5111645, 27791146, 27791146, 1612591113
Format: Citation

Title: Essential roles of CKIdelta and CKIepsilon in the mammalian circadian clock.
Creator: Lee, Hyeongmin, Chen, Rongmin, Lee, Yongjin, Yoo, Seunghee, Lee, Choogon
Abstract/Description: Circadian rhythms in mammals are generated by a negative transcriptional feedback loop in which PERIOD (PER) is rate-limiting for feedback inhibition. Casein kinases Idelta and Iepsilon (CKIdelta/epsilon) can regulate temporal abundance/activity of PER by phosphorylation-mediated degradation and cellular localization. Despite their potentially crucial effects on PER, it has not been demonstrated in a mammalian system that these kinases play essential roles in circadian rhythm generation as...
Show moreCircadian rhythms in mammals are generated by a negative transcriptional feedback loop in which PERIOD (PER) is rate-limiting for feedback inhibition. Casein kinases Idelta and Iepsilon (CKIdelta/epsilon) can regulate temporal abundance/activity of PER by phosphorylation-mediated degradation and cellular localization. Despite their potentially crucial effects on PER, it has not been demonstrated in a mammalian system that these kinases play essential roles in circadian rhythm generation as does their homolog in Drosophila. To disrupt both CKIdelta/epsilon while avoiding the embryonic lethality of CKIdelta disruption in mice, we used CKIdelta-deficient Per2(Luc) mouse embryonic fibroblasts (MEFs) and overexpressed a dominant-negative mutant CKIepsilon (DN-CKIepsilon) in the mutant MEFs. CKIdelta-deficient MEFs exhibited a robust circadian rhythm, albeit with a longer period, suggesting that the cells possess a way to compensate for CKIdelta loss. When CKIepsilon activity was disrupted by the DN-CKIepsilon in the mutant MEFs, circadian bioluminescence rhythms were eliminated and rhythms in endogenous PER abundance and phosphorylation were severely compromised, demonstrating that CKIdelta/epsilon are indeed essential kinases for the clockwork. This is further supported by abolition of circadian rhythms when physical interaction between PER and CKIdelta/epsilon was disrupted by overexpressing the CKIdelta/epsilon binding domain of PER2 (CKBD-P2). Interestingly, CKBD-P2 overexpression led to dramatically low levels of endogenous PER, while PER-binding, kinase-inactive DN-CKIepsilon did not, suggesting that CKIdelta/epsilon may have a non-catalytic role in stabilizing PER. Our results show that an essential role of CKIdelta/epsilon is conserved between Drosophila and mammals, but CKIdelta/epsilon and DBT may have divergent non-catalytic functions in the clockwork as well.
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Date Issued: 2009-12-15
Identifier: FSU_pmch_19948962, 10.1073/pnas.0906651106, PMC2795500, 19948962, 19948962, 0906651106
Format: Citation

Title: Pds1/Esp1-dependent and -independent sister chromatid separation in mutants defective for protein phosphatase 2A.
Creator: Tang, Xianying, Wang, Yanchang
Abstract/Description: Spindle disruption or DNA damage prevents sister chromatid separation through the activation of checkpoint pathways that inhibit anaphase entry by stabilizing the anaphase inhibitor Pds1. Mutation of CDC55, which encodes a B regulatory subunit of protein phosphatase 2A (PP2A), results in precocious sister chromatid separation when spindle is disrupted. Here we report that decreased Pds1 levels in Deltacdc55 mutants contribute to sister chromatid separation in the presence of nocodazole, a...
Show moreSpindle disruption or DNA damage prevents sister chromatid separation through the activation of checkpoint pathways that inhibit anaphase entry by stabilizing the anaphase inhibitor Pds1. Mutation of CDC55, which encodes a B regulatory subunit of protein phosphatase 2A (PP2A), results in precocious sister chromatid separation when spindle is disrupted. Here we report that decreased Pds1 levels in Deltacdc55 mutants contribute to sister chromatid separation in the presence of nocodazole, a microtubule-depolymerizing drug. However, in the presence of DNA damage, Deltacdc55 mutant cells separate sister chromatids without noticeable decrease of Pds1 or cohesin Mcd1/Scc1 levels. Further analysis demonstrates that Deltacdc55 mutants lose cohesion along the entire chromosomes when the spindle is disrupted. In contrast, separation of sister chromatids is limited to the centromeric regions in Deltacdc55 cells after DNA damage. Moreover, mutation of TPD3, which encodes the A regulatory subunit of PP2A, also results in sister chromatid separation in DNA- or spindle-damage-arrested cells. These data suggest that PP2A regulates sister chromatid cohesion in Pds1-dependent and -independent manners.
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Date Issued: 2006-10-31
Identifier: FSU_pmch_17050679, 10.1073/pnas.0607856103, PMC1637575, 17050679, 17050679, 0607856103
Format: Citation

Title: Overexplaining or underexplaining methane's role in climate change.
Creator: Prather, Michael J, Holmes, Christopher D
Date Issued: 2017-05-23
Identifier: FSU_pmch_28507153, 10.1073/pnas.1704884114, PMC5448169, 28507153, 28507153, 1704884114
Format: Citation

Title: OCD candidate gene /EAAT3 impacts basal ganglia-mediated activity and stereotypic behavior.
Creator: Zike, Isaac D, Chohan, Muhammad O, Kopelman, Jared M, Krasnow, Emily N, Flicker, Daniel, Nautiyal, Katherine M, Bubser, Michael, Kellendonk, Christoph, Jones, Carrie K, Stanwood...
Show moreZike, Isaac D, Chohan, Muhammad O, Kopelman, Jared M, Krasnow, Emily N, Flicker, Daniel, Nautiyal, Katherine M, Bubser, Michael, Kellendonk, Christoph, Jones, Carrie K, Stanwood, Gregg, Tanaka, Kenji Fransis, Moore, Holly, Ahmari, Susanne E, Veenstra-VanderWeele, Jeremy
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Abstract/Description: Obsessive-compulsive disorder (OCD) is a chronic, disabling condition with inadequate treatment options that leave most patients with substantial residual symptoms. Structural, neurochemical, and behavioral findings point to a significant role for basal ganglia circuits and for the glutamate system in OCD. Genetic linkage and association studies in OCD point to , which encodes the neuronal glutamate/aspartate/cysteine transporter excitatory amino acid transporter 3 (EAAT3)/excitatory amino...
Show moreObsessive-compulsive disorder (OCD) is a chronic, disabling condition with inadequate treatment options that leave most patients with substantial residual symptoms. Structural, neurochemical, and behavioral findings point to a significant role for basal ganglia circuits and for the glutamate system in OCD. Genetic linkage and association studies in OCD point to , which encodes the neuronal glutamate/aspartate/cysteine transporter excitatory amino acid transporter 3 (EAAT3)/excitatory amino acid transporter 1 (EAAC1). However, no previous studies have investigated EAAT3 in basal ganglia circuits or in relation to OCD-related behavior. Here, we report a model of loss based on an excisable STOP cassette that yields successful ablation of EAAT3 expression and function. Using amphetamine as a probe, we found that EAAT3 loss prevents expected increases in () locomotor activity, () stereotypy, and () immediate early gene induction in the dorsal striatum following amphetamine administration. Further, -STOP mice showed diminished grooming in an SKF-38393 challenge experiment, a pharmacologic model of OCD-like grooming behavior. This reduced grooming is accompanied by reduced dopamine D receptor binding in the dorsal striatum of -STOP mice. -STOP mice also exhibit reduced extracellular dopamine concentrations in the dorsal striatum both at baseline and following amphetamine challenge. Viral-mediated restoration of /EAAT3 expression in the midbrain but not in the striatum results in partial rescue of amphetamine-induced locomotion and stereotypy in -STOP mice, consistent with an impact of EAAT3 loss on presynaptic dopaminergic function. Collectively, these findings indicate that the most consistently associated OCD candidate gene impacts basal ganglia-dependent repetitive behaviors.
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Date Issued: 2017-05-30
Identifier: FSU_pmch_28507136, 10.1073/pnas.1701736114, PMC5465902, 28507136, 28507136, 1701736114
Format: Citation

Title: Dinosaur incubation periods directly determined from growth-line counts in embryonic teeth show reptilian-grade development.
Creator: Erickson, Gregory M, Zelenitsky, Darla K, Kay, David Ian, Norell, Mark A
Abstract/Description: Birds stand out from other egg-laying amniotes by producing relatively small numbers of large eggs with very short incubation periods (average 11-85 d). This aspect promotes high survivorship by limiting exposure to predation and environmental perturbation, allows for larger more fit young, and facilitates rapid attainment of adult size. Birds are living dinosaurs; their rapid development has been considered to reflect the primitive dinosaurian condition. Here, nonavian dinosaurian incubation...
Show moreBirds stand out from other egg-laying amniotes by producing relatively small numbers of large eggs with very short incubation periods (average 11-85 d). This aspect promotes high survivorship by limiting exposure to predation and environmental perturbation, allows for larger more fit young, and facilitates rapid attainment of adult size. Birds are living dinosaurs; their rapid development has been considered to reflect the primitive dinosaurian condition. Here, nonavian dinosaurian incubation periods in both small and large ornithischian taxa are empirically determined through growth-line counts in embryonic teeth. Our results show unexpectedly slow incubation (2.8 and 5.8 mo) like those of outgroup reptiles. Developmental and physiological constraints would have rendered tooth formation and incubation inherently slow in other dinosaur lineages and basal birds. The capacity to determine incubation periods in extinct egg-laying amniotes has implications for dinosaurian embryology, life history strategies, and survivorship across the Cretaceous-Paleogene mass extinction event.
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Date Issued: 2017-01-17
Identifier: FSU_pmch_28049837, 10.1073/pnas.1613716114, PMC5255600, 28049837, 28049837, 1613716114
Format: Citation

Title: The signaling network that silences the spindle assembly checkpoint upon the establishment of chromosome bipolar attachment.
Creator: Jin, Fengzhi, Wang, Yanchang
Abstract/Description: Improper kinetochore attachments activate the spindle assembly checkpoint (SAC) to prevent anaphase onset, but it is poorly understood how this checkpoint is silenced to allow anaphase onset. Chromosome bipolar attachment applies tension on sister kinetochores, and the lack of tension delays anaphase onset. In budding yeast, the delay induced by tension defects depends on the intact SAC as well as increase in ploidy (Ipl1)/Aurora kinase and a centromere-associated protein ShuGOshin (Sgo1)....
Show moreImproper kinetochore attachments activate the spindle assembly checkpoint (SAC) to prevent anaphase onset, but it is poorly understood how this checkpoint is silenced to allow anaphase onset. Chromosome bipolar attachment applies tension on sister kinetochores, and the lack of tension delays anaphase onset. In budding yeast, the delay induced by tension defects depends on the intact SAC as well as increase in ploidy (Ipl1)/Aurora kinase and a centromere-associated protein ShuGOshin (Sgo1). Here we provide evidence indicating that Ipl1-dependent phosphorylation of the kinetochore protein Duo1 and Mps1 interacting (Dam1) prevents SAC silencing when tension is absent. The nonphosphorylatable dam1 mutant cells, as well as sgo1 mutant cells, are competent in SAC activation but unable to prevent SAC silencing in response to tension defects. We further found that phosphomimetic dam1 mutants exhibited delayed anaphase onset mainly due to the failure in SAC silencing, but destabilized kinetochore attachment likely plays a minor role in this delay. Because the tension resulting from bipolar attachment triggers the dephosphorylation of Dam1 by protein phosphatase 1, this dephosphorylation likely coordinates SAC silencing with chromosome bipolar attachment. Therefore, Sgo1, Ipl1 kinase, Dam1, and protein phosphatase 1 comprise the SAC silencing network that ensures the correct timing for anaphase onset.
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Date Issued: 2013-12-24
Identifier: FSU_pmch_24324173, 10.1073/pnas.1307595111, PMC3876237, 24324173, 24324173, 1307595111
Format: Citation

Title: The period of the circadian oscillator is primarily determined by the balance between casein kinase 1 and protein phosphatase 1.
Creator: Lee, Hyeong-min, Chen, Rongmin, Kim, Hyukmin, Etchegaray, Jean-Pierre, Weaver, David R, Lee, Choogon
Abstract/Description: Mounting evidence suggests that PERIOD (PER) proteins play a central role in setting the speed (period) and phase of the circadian clock. Pharmacological and genetic studies have shown that changes in PER phosphorylation kinetics are associated with changes in circadian rhythm period and phase, which can lead to sleep disorders such as Familial Advanced Sleep Phase Syndrome in humans. We and others have shown that casein kinase 1δ and ε (CK1δ/ε) are essential PER kinases, but it is clear that...
Show moreMounting evidence suggests that PERIOD (PER) proteins play a central role in setting the speed (period) and phase of the circadian clock. Pharmacological and genetic studies have shown that changes in PER phosphorylation kinetics are associated with changes in circadian rhythm period and phase, which can lead to sleep disorders such as Familial Advanced Sleep Phase Syndrome in humans. We and others have shown that casein kinase 1δ and ε (CK1δ/ε) are essential PER kinases, but it is clear that additional, unknown mechanisms are also crucial for regulating the kinetics of PER phosphorylation. Here we report that circadian periodicity is determined primarily through PER phosphorylation kinetics set by the balance between CK1δ/ε and protein phosphatase 1 (PP1). In CK1δ/ε-deficient cells, PER phosphorylation is severely compromised and nonrhythmic, and the PER proteins are constitutively cytoplasmic. However, when PP1 is disrupted, PER phosphorylation is dramatically accelerated; the same effect is not seen when PP2A is disrupted. Our work demonstrates that the speed and rhythmicity of PER phosphorylation are controlled by the balance between CK1δ/ε and PP1, which in turn determines the period of the circadian oscillator. Thus, our findings provide clear insights into the molecular basis of how the period and phase of our daily rhythms are determined.
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Date Issued: 2011-09-27
Identifier: FSU_pmch_21930935, 10.1073/pnas.1107178108, PMC3182690, 21930935, 21930935, 1107178108
Format: Citation

Title: Global patterns of kelp forest change over the past half-century.
Creator: Krumhansl, Kira A, Okamoto, Daniel K, Rassweiler, Andrew, Novak, Mark, Bolton, John J, Cavanaugh, Kyle C, Connell, Sean D, Johnson, Craig R, Konar, Brenda, Ling, Scott D,...
Show moreKrumhansl, Kira A, Okamoto, Daniel K, Rassweiler, Andrew, Novak, Mark, Bolton, John J, Cavanaugh, Kyle C, Connell, Sean D, Johnson, Craig R, Konar, Brenda, Ling, Scott D, Micheli, Fiorenza, Norderhaug, Kjell M, Pérez-Matus, Alejandro, Sousa-Pinto, Isabel, Reed, Daniel C, Salomon, Anne K, Shears, Nick T, Wernberg, Thomas, Anderson, Robert J, Barrett, Nevell S, Buschmann, Alejandro H, Carr, Mark H, Caselle, Jennifer E, Derrien-Courtel, Sandrine, Edgar, Graham J, Edwards, Matt, Estes, James A, Goodwin, Claire, Kenner, Michael C, Kushner, David J, Moy, Frithjof E, Nunn, Julia, Steneck, Robert S, Vásquez, Julio, Watson, Jane, Witman, Jon D, Byrnes, Jarrett E K
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Abstract/Description: Kelp forests (Order Laminariales) form key biogenic habitats in coastal regions of temperate and Arctic seas worldwide, providing ecosystem services valued in the range of billions of dollars annually. Although local evidence suggests that kelp forests are increasingly threatened by a variety of stressors, no comprehensive global analysis of change in kelp abundances currently exists. Here, we build and analyze a global database of kelp time series spanning the past half-century to assess...
Show moreKelp forests (Order Laminariales) form key biogenic habitats in coastal regions of temperate and Arctic seas worldwide, providing ecosystem services valued in the range of billions of dollars annually. Although local evidence suggests that kelp forests are increasingly threatened by a variety of stressors, no comprehensive global analysis of change in kelp abundances currently exists. Here, we build and analyze a global database of kelp time series spanning the past half-century to assess regional and global trends in kelp abundances. We detected a high degree of geographic variation in trends, with regional variability in the direction and magnitude of change far exceeding a small global average decline (instantaneous rate of change = -0.018 y). Our analysis identified declines in 38% of ecoregions for which there are data (-0.015 to -0.18 y), increases in 27% of ecoregions (0.015 to 0.11 y), and no detectable change in 35% of ecoregions. These spatially variable trajectories reflected regional differences in the drivers of change, uncertainty in some regions owing to poor spatial and temporal data coverage, and the dynamic nature of kelp populations. We conclude that although global drivers could be affecting kelp forests at multiple scales, local stressors and regional variation in the effects of these drivers dominate kelp dynamics, in contrast to many other marine and terrestrial foundation species.
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Date Issued: 2016-11-29
Identifier: FSU_pmch_27849580, 10.1073/pnas.1606102113, PMC5137772, 27849580, 27849580, 1606102113
Format: Citation

Title: High-pressure phase of brucite stable at Earth's mantle transition zone and lower mantle conditions.
Creator: Hermann, Andreas, Mookherjee, Mainak
Abstract/Description: We investigate the high-pressure phase diagram of the hydrous mineral brucite, Mg(OH), using structure search algorithms and ab initio simulations. We predict a high-pressure phase stable at pressure and temperature conditions found in cold subducting slabs in Earth's mantle transition zone and lower mantle. This prediction implies that brucite can play a much more important role in water transport and storage in Earth's interior than hitherto thought. The predicted high-pressure phase,...
Show moreWe investigate the high-pressure phase diagram of the hydrous mineral brucite, Mg(OH), using structure search algorithms and ab initio simulations. We predict a high-pressure phase stable at pressure and temperature conditions found in cold subducting slabs in Earth's mantle transition zone and lower mantle. This prediction implies that brucite can play a much more important role in water transport and storage in Earth's interior than hitherto thought. The predicted high-pressure phase, stable in calculations between 20 and 35 GPa and up to 800 K, features MgO octahedral units arranged in the anatase-TiO structure. Our findings suggest that brucite will transform from a layered to a compact 3D network structure before eventual decomposition into periclase and ice. We show that the high-pressure phase has unique spectroscopic fingerprints that should allow for straightforward detection in experiments. The phase also has distinct elastic properties that might make its direct detection in the deep Earth possible with geophysical methods.
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Date Issued: 2016-12-06
Identifier: FSU_pmch_27872307, 10.1073/pnas.1611571113, PMC5150419, 27872307, 27872307, 1611571113
Format: Citation

Title: Experimental Support for the Evolution of Symmetric Protein Architecture from a Simple Peptide Motif.
Creator: Lee, Jihun, Blaber, Michael
Abstract/Description: The majority of protein architectures exhibit elements of structural symmetry, and "gene duplication and fusion" is the evolutionary mechanism generally hypothesized to be responsible for their emergence from simple peptide motifs. Despite the central importance of the gene duplication and fusion hypothesis, experimental support for a plausible evolutionary pathway for a specific protein architecture has yet to be effectively demonstrated. To address this question, a unique "top-down...
Show moreThe majority of protein architectures exhibit elements of structural symmetry, and "gene duplication and fusion" is the evolutionary mechanism generally hypothesized to be responsible for their emergence from simple peptide motifs. Despite the central importance of the gene duplication and fusion hypothesis, experimental support for a plausible evolutionary pathway for a specific protein architecture has yet to be effectively demonstrated. To address this question, a unique "top-down symmetric deconstruction" strategy was utilized to successfully identify a simple peptide motif capable of recapitulating, via gene duplication and fusion processes, a symmetric protein architecture (the threefold symmetric β-trefoil fold). The folding properties of intermediary forms in this deconstruction agree precisely with a previously proposed "conserved architecture" model for symmetric protein evolution. Furthermore, a route through foldable sequence-space between the simple peptide motif and extant protein fold is demonstrated. These results provide compelling experimental support for a plausible evolutionary pathway of symmetric protein architecture via gene duplication and fusion processes.
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Date Issued: 2011
Identifier: FSU_migr_biomed_faculty_publications-0020, 10.1073/pnas.1015032108, PMC3017207
Format: Citation

Title: Mesoscale ocean fronts enhance carbon export due to gravitational sinking and subduction.
Creator: Stukel, Michael R, Aluwihare, Lihini I, Barbeau, Katherine A, Chekalyuk, Alexander M, Goericke, Ralf, Miller, Arthur J, Ohman, Mark D, Ruacho, Angel, Song, Hajoon, Stephens,...
Show moreStukel, Michael R, Aluwihare, Lihini I, Barbeau, Katherine A, Chekalyuk, Alexander M, Goericke, Ralf, Miller, Arthur J, Ohman, Mark D, Ruacho, Angel, Song, Hajoon, Stephens, Brandon M, Landry, Michael R
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Abstract/Description: Enhanced vertical carbon transport (gravitational sinking and subduction) at mesoscale ocean fronts may explain the demonstrated imbalance of new production and sinking particle export in coastal upwelling ecosystems. Based on flux assessments from U:Th disequilibrium and sediment traps, we found 2 to 3 times higher rates of gravitational particle export near a deep-water front (305 mg C⋅m⋅d) compared with adjacent water or to mean (nonfrontal) regional conditions. Elevated particle flux at...
Show moreEnhanced vertical carbon transport (gravitational sinking and subduction) at mesoscale ocean fronts may explain the demonstrated imbalance of new production and sinking particle export in coastal upwelling ecosystems. Based on flux assessments from U:Th disequilibrium and sediment traps, we found 2 to 3 times higher rates of gravitational particle export near a deep-water front (305 mg C⋅m⋅d) compared with adjacent water or to mean (nonfrontal) regional conditions. Elevated particle flux at the front was mechanistically linked to Fe-stressed diatoms and high mesozooplankton fecal pellet production. Using a data assimilative regional ocean model fit to measured conditions, we estimate that an additional ∼225 mg C⋅m⋅d was exported as subduction of particle-rich water at the front, highlighting a transport mechanism that is not captured by sediment traps and is poorly quantified by most models and in situ measurements. Mesoscale fronts may be responsible for over a quarter of total organic carbon sequestration in the California Current and other coastal upwelling ecosystems.
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Date Issued: 2017-02-07
Identifier: FSU_pmch_28115723, 10.1073/pnas.1609435114, PMC5307443, 28115723, 28115723, 1609435114
Format: Citation

Title: Directional memory arises from long-lived cytoskeletal asymmetries in polarized chemotactic cells.
Creator: Prentice-Mott, Harrison V, Meroz, Yasmine, Carlson, Andreas, Levine, Michael A, Davidson, Michael W, Irimia, Daniel, Charras, Guillaume T, Mahadevan, L, Shah, Jagesh V
Abstract/Description: Chemotaxis, the directional migration of cells in a chemical gradient, is robust to fluctuations associated with low chemical concentrations and dynamically changing gradients as well as high saturating chemical concentrations. Although a number of reports have identified cellular behavior consistent with a directional memory that could account for behavior in these complex environments, the quantitative and molecular details of such a memory process remain unknown. Using microfluidics to...
Show moreChemotaxis, the directional migration of cells in a chemical gradient, is robust to fluctuations associated with low chemical concentrations and dynamically changing gradients as well as high saturating chemical concentrations. Although a number of reports have identified cellular behavior consistent with a directional memory that could account for behavior in these complex environments, the quantitative and molecular details of such a memory process remain unknown. Using microfluidics to confine cellular motion to a 1D channel and control chemoattractant exposure, we observed directional memory in chemotactic neutrophil-like cells. We modeled this directional memory as a long-lived intracellular asymmetry that decays slower than observed membrane phospholipid signaling. Measurements of intracellular dynamics revealed that moesin at the cell rear is a long-lived element that when inhibited, results in a reduction of memory. Inhibition of ROCK (Rho-associated protein kinase), downstream of RhoA (Ras homolog gene family, member A), stabilized moesin and directional memory while depolymerization of microtubules (MTs) disoriented moesin deposition and also reduced directional memory. Our study reveals that long-lived polarized cytoskeletal structures, specifically moesin, actomyosin, and MTs, provide a directional memory in neutrophil-like cells even as they respond on short time scales to external chemical cues.
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Date Issued: 2016-02-02
Identifier: FSU_pmch_26764383, 10.1073/pnas.1513289113, PMC4747767, 26764383, 26764383, 1513289113
Format: Citation

Title: Phonon mechanism in the most dilute superconductor n-type SrTiO3.
Creator: Gor'kov, Lev P
Abstract/Description: Superconductivity of n-doped SrTiO3, which remained enigmatic for half a century, is treated as a particular case of nonadiabatic phonon pairing. Motivated by experiment, we suggest the existence of the mobility edge at some dopant concentration. The itinerant part of the spectrum consists of three conduction bands filling by electrons successively. Each subband contributes to the superconducting instability and exhibits a gap in its energy spectrum at low temperatures. We argue that...
Show moreSuperconductivity of n-doped SrTiO3, which remained enigmatic for half a century, is treated as a particular case of nonadiabatic phonon pairing. Motivated by experiment, we suggest the existence of the mobility edge at some dopant concentration. The itinerant part of the spectrum consists of three conduction bands filling by electrons successively. Each subband contributes to the superconducting instability and exhibits a gap in its energy spectrum at low temperatures. We argue that superconductivity of n-doped SrTiO3 results from the interaction of electrons with several longitudinal (LO) optical phonons with frequencies much larger than the Fermi energy. Immobile charges under the mobility edge threshold increase the "optical" dielectric constant far above that in clean SrTiO3 placing control on the electron-LO phonon interaction. TC initially grows as density of states at the Fermi surface increases with doping, but the accumulating charges reduce the electrons-polar-phonon interaction by screening the longitudinal electric fields. The theory predicts maxima in the TC-concentration dependence indeed observed experimentally. Having reached a maximum in the third band, the transition temperature finally decreases, rounding out the TC (n) dome, the three maxima with accompanying superconducting gaps emerging consecutively as electrons fill successive bands. This arises from attributes of the LO optical phonon pairing of electrons. The mechanism of LO phonons opens the path to increasing superconducting transition temperature in bulk transition-metal oxides and other polar crystals, and in charged 2D layers at the LaAaO3/SrTiO3 interfaces and on the SrTiO3 substrates.
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Date Issued: 2016-04-26
Identifier: FSU_pmch_27078108, 10.1073/pnas.1604145113, PMC4855613, 27078108, 27078108, 1604145113
Format: Citation

Title: Sustained deposition of contaminants from the Deepwater Horizon spill.
Creator: Yan, Beizhan, Passow, Uta, Chanton, Jeffrey P, Nöthig, Eva-Maria, Asper, Vernon, Sweet, Julia, Pitiranggon, Masha, Diercks, Arne, Pak, Dorothy
Abstract/Description: The 2010 Deepwater Horizon oil spill resulted in 1.6-2.6 × 10(10) grams of petrocarbon accumulation on the seafloor. Data from a deep sediment trap, deployed 7.4 km SW of the well between August 2010 and October 2011, disclose that the sinking of spill-associated substances, mediated by marine particles, especially phytoplankton, continued at least 5 mo following the capping of the well. In August/September 2010, an exceptionally large diatom bloom sedimentation event coincided with elevated...
Show moreThe 2010 Deepwater Horizon oil spill resulted in 1.6-2.6 × 10(10) grams of petrocarbon accumulation on the seafloor. Data from a deep sediment trap, deployed 7.4 km SW of the well between August 2010 and October 2011, disclose that the sinking of spill-associated substances, mediated by marine particles, especially phytoplankton, continued at least 5 mo following the capping of the well. In August/September 2010, an exceptionally large diatom bloom sedimentation event coincided with elevated sinking rates of oil-derived hydrocarbons, black carbon, and two key components of drilling mud, barium and olefins. Barium remained in the water column for months and even entered pelagic food webs. Both saturated and polycyclic aromatic hydrocarbon source indicators corroborate a predominant contribution of crude oil to the sinking hydrocarbons. Cosedimentation with diatoms accumulated contaminants that were dispersed in the water column and transported them downward, where they were concentrated into the upper centimeters of the seafloor, potentially leading to sustained impact on benthic ecosystems.
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Date Issued: 2016-06-14
Identifier: FSU_pmch_27247393, 10.1073/pnas.1513156113, PMC4914201, 27247393, 27247393, 1513156113
Format: Citation

Title: Conserved mechanism for coordinating replication fork helicase assembly with phosphorylation of the helicase.
Creator: Bruck, Irina, Kaplan, Daniel L
Abstract/Description: Dbf4-dependent kinase (DDK) phosphorylates minichromosome maintenance 2 (Mcm2) during S phase in yeast, and Sld3 recruits cell division cycle 45 (Cdc45) to minichromosome maintenance 2-7 (Mcm2-7). We show here DDK-phosphoryled Mcm2 preferentially interacts with Cdc45 in vivo, and that Sld3 stimulates DDK phosphorylation of Mcm2 by 11-fold. We identified a mutation of the replication initiation factor Sld3, Sld3-m16, that is specifically defective in stimulating DDK phosphorylation of Mcm2....
Show moreDbf4-dependent kinase (DDK) phosphorylates minichromosome maintenance 2 (Mcm2) during S phase in yeast, and Sld3 recruits cell division cycle 45 (Cdc45) to minichromosome maintenance 2-7 (Mcm2-7). We show here DDK-phosphoryled Mcm2 preferentially interacts with Cdc45 in vivo, and that Sld3 stimulates DDK phosphorylation of Mcm2 by 11-fold. We identified a mutation of the replication initiation factor Sld3, Sld3-m16, that is specifically defective in stimulating DDK phosphorylation of Mcm2. Wild-type expression levels of sld3-m16 result in severe growth and DNA replication defects. Cells expressing sld3-m16 exhibit no detectable Mcm2 phosphorylation in vivo, reduced replication protein A-ChIP signal at an origin, and diminished Go, Ichi, Ni, and San association with Mcm2-7. Treslin, the human homolog of Sld3, stimulates human DDK phosphorylation of human Mcm2 by 15-fold. DDK phosphorylation of human Mcm2 decreases the affinity of Mcm5 for Mcm2, suggesting a potential mechanism for helicase ring opening. These data suggest a conserved mechanism for replication initiation: Sld3/Treslin coordinates Cdc45 recruitment to Mcm2-7 with DDK phosphorylation of Mcm2 during S phase.
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Date Issued: 2015-09-08
Identifier: FSU_pmch_26305950, 10.1073/pnas.1509608112, PMC4568703, 26305950, 26305950, 1509608112
Format: Citation

Title: Thallium Isotopes Reveal Protracted Anoxia During The Toarcian (early Jurassic) Associated With Volcanism, Carbon Burial, And Mass Extinction.
Creator: Them, Theodore R., Gill, Benjamin C., Caruthers, Andrew H., Gerhardt, Angela M., Grocke, Darren R., Lyons, Timothy W., Marroquin, Selva M., Nielsen, Sune G., Alexandre, Joao P....
Show moreThem, Theodore R., Gill, Benjamin C., Caruthers, Andrew H., Gerhardt, Angela M., Grocke, Darren R., Lyons, Timothy W., Marroquin, Selva M., Nielsen, Sune G., Alexandre, Joao P. Trabucho, Owens, Jeremy D.
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Abstract/Description: For this study, we generated thallium (TI) isotope records from two anoxic basins to track the earliest changes in global bottom water oxygen contents over the Toarcian Oceanic Anoxic Event (TOAE; similar to 183 Ma) of the Early Jurassic. The T-OAE, like other Mesozoic OAEs, has been interpreted as an expansion of marine oxygen depletion based on indirect methods such as organic-rich facies, carbon isotope excursions, and biological turnover. Our TI isotope data, however, reveal explicit...
Show moreFor this study, we generated thallium (TI) isotope records from two anoxic basins to track the earliest changes in global bottom water oxygen contents over the Toarcian Oceanic Anoxic Event (TOAE; similar to 183 Ma) of the Early Jurassic. The T-OAE, like other Mesozoic OAEs, has been interpreted as an expansion of marine oxygen depletion based on indirect methods such as organic-rich facies, carbon isotope excursions, and biological turnover. Our TI isotope data, however, reveal explicit evidence for earlier global marine deoxygenation of ocean water, some 600 ka before the classically defined T-OAE. This antecedent deoxygenation occurs at the Pliensbachian/Toarcian boundary and is coeval with the onset of initial large igneous province (LIP) volcanism and the initiation of a marine mass extinction. Thallium isotopes are also perturbed during the T-OAE interval, as defined by carbon isotopes, reflecting a second deoxygenation event that coincides with the acme of elevated marine mass extinctions and the main phase of LIP volcanism. This suggests that the duration of widespread anoxic bottom waters was at least 1 million years in duration and spanned early to middle Toarcian time. Thus, the TI data reveal a more nuanced record of marine oxygen depletion and its links to biological change during a period of climatic warming in Earth's past and highlight the role of oxygen depletion on past biological evolution.
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Date Issued: 2018-06-26
Identifier: FSU_libsubv1_wos_000436245000051, 10.1073/pnas.1803478115
Format: Citation

Title: Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein.
Creator: Longo, Liam M, Lee, Jihun, Blaber, Michael
Abstract/Description: A compendium of different types of abiotic chemical syntheses identifies a consensus set of 10 "prebiotic" α-amino acids. Before the emergence of biosynthetic pathways, this set is the most plausible resource for protein formation (i.e., proteogenesis) within the overall process of abiogenesis. An essential unsolved question regarding this prebiotic set is whether it defines a "foldable set"--that is, does it contain sufficient chemical information to permit cooperatively folding polypeptides...
Show moreA compendium of different types of abiotic chemical syntheses identifies a consensus set of 10 "prebiotic" α-amino acids. Before the emergence of biosynthetic pathways, this set is the most plausible resource for protein formation (i.e., proteogenesis) within the overall process of abiogenesis. An essential unsolved question regarding this prebiotic set is whether it defines a "foldable set"--that is, does it contain sufficient chemical information to permit cooperatively folding polypeptides? If so, what (if any) characteristic properties might such polypeptides exhibit? To investigate these questions, two "primitive" versions of an extant protein fold (the β-trefoil) were produced by top-down symmetric deconstruction, resulting in a reduced alphabet size of 12 or 13 amino acids and a percentage of prebiotic amino acids approaching 80%. These proteins show a substantial acidification of pI and require high salt concentrations for cooperative folding. The results suggest that the prebiotic amino acids do comprise a foldable set within the halophile environment.
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Date Issued: 2013-02-05
Identifier: FSU_pmch_23341608, 10.1073/pnas.1219530110, PMC3568330, 23341608, 23341608, 1219530110
Format: Citation

Title: Temporal control of the dephosphorylation of Cdk substrates by mitotic exit pathways in budding yeast.
Creator: Jin, Fengzhi, Liu, Hong, Liang, Fengshan, Rizkallah, Raed, Hurt, Myra M, Wang, Yanchang
Abstract/Description: The temporal phosphorylation of cell cycle-related proteins by cyclin-dependent kinases (Cdks) is critical for the correct order of cell cycle events. In budding yeast, CDC28 encodes the only Cdk and its association with various cyclins governs the temporal phosphorylation of Cdk substrates. S-phase Cdk substrates are phosphorylated earlier than mitotic Cdk substrates, which ensures the sequential order of DNA synthesis and mitosis. However, it remains unclear whether Cdk substrates are...
Show moreThe temporal phosphorylation of cell cycle-related proteins by cyclin-dependent kinases (Cdks) is critical for the correct order of cell cycle events. In budding yeast, CDC28 encodes the only Cdk and its association with various cyclins governs the temporal phosphorylation of Cdk substrates. S-phase Cdk substrates are phosphorylated earlier than mitotic Cdk substrates, which ensures the sequential order of DNA synthesis and mitosis. However, it remains unclear whether Cdk substrates are dephosphorylated in temporally distinct windows. Cdc14 is a conserved protein phosphatase responsible for the dephosphorylation of Cdk substrates. In budding yeast, FEAR (Cdc14 early anaphase release) and MEN (mitotic exit network) activate phosphatase Cdc14 by promoting its release from the nucleolus in early and late anaphase, respectively. Here, we show that the sequential Cdc14 release and the distinct degradation timing of different cyclins provides the molecular basis for the differential dephosphorylation windows of S-phase and mitotic cyclin substrates. Our data also indicate that FEAR-induced dephosphorylation of S-phase Cdk substrates facilitates anaphase progression, revealing an extra layer of mitotic regulation.
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Date Issued: 2008-10-21
Identifier: FSU_pmch_18845678, 10.1073/pnas.0808719105, PMC2570984, 18845678, 18845678, 0808719105
Format: Citation

Title: Offshore Aquaculture In The United States: Untapped Potential In Need Of Smart Policy.
Creator: Lester, Sarah E., Gentry, Rebecca R., Kappel, Carrie V., White, Crow, Gaines, Steven D.
Date Issued: 2018-07-10
Identifier: FSU_libsubv1_wos_000438050900038, 10.1073/pnas.1808737115
Format: Citation

Title: High Fire-derived Nitrogen Deposition On Central African Forests.
Creator: Bauters, Marijn, Drake, Travis W., Verbeeck, Hans, Bode, Samuel, Herve-Fernandez, Pedro, Zito, Phoebe, Podgorski, David C., Boyemba, Faustin, Makelele, Isaac, Ntaboba, Landry...
Show moreBauters, Marijn, Drake, Travis W., Verbeeck, Hans, Bode, Samuel, Herve-Fernandez, Pedro, Zito, Phoebe, Podgorski, David C., Boyemba, Faustin, Makelele, Isaac, Ntaboba, Landry Cizungu, Spencer, Robert G. M., Boeckx, Pascal
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Abstract/Description: Atmospheric nitrogen (N) deposition is an important determinant of N availability for natural ecosystems worldwide. Increased anthropogenic N deposition shifts the stoichiometric equilibrium of ecosystems, with direct and indirect impacts on ecosystem functioning and biogeochemical cycles. Current simulation data suggest that remote tropical forests still receive low atmospheric N deposition due to a lack of proximate industry, low rates of fossil fuel combustion, and absence of intensive...
Show moreAtmospheric nitrogen (N) deposition is an important determinant of N availability for natural ecosystems worldwide. Increased anthropogenic N deposition shifts the stoichiometric equilibrium of ecosystems, with direct and indirect impacts on ecosystem functioning and biogeochemical cycles. Current simulation data suggest that remote tropical forests still receive low atmospheric N deposition due to a lack of proximate industry, low rates of fossil fuel combustion, and absence of intensive agriculture. We present field-based N deposition data for forests of the central Congo Basin, and use ultrahigh-resolution mass spectrometry to characterize the organic N fraction. Additionally, we use satellite data and modeling for atmospheric N source apportionment. Our results indicate that these forests receive 18.2 kg N hectare(-1) years(-1) as wet deposition, with dry deposition via canopy interception adding considerably to this flux. We also show that roughly half of the N deposition is organic, which is often ignored in N deposition measurements and simulations. The source of atmospheric N is predominantly derived from intensive seasonal burning of biomass on the continent. This high N deposition has important implications for the ecology of the Congo Basin and for global biogeochemical cycles more broadly.
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Date Issued: 2018-01-16
Identifier: FSU_libsubv1_wos_000423091400050, 10.1073/pnas.1714597115
Format: Citation

Title: Neural Preservation Underlies Speech Improvement From Auditory Deprivation In Young Cochlear Implant Recipients.
Creator: Feng, Gangyi, Ingvalson, Erin M., Grieco-Calub, Tina M., Roberts, Megan Y., Ryan, Maura E., Birmingham, Patrick, Burrowes, Delilah, Young, Nancy M., Wong, Patrick C. M.
Abstract/Description: Although cochlear implantation enables some children to attain age-appropriate speech and language development, communicative delays persist in others, and outcomes are quite variable and difficult to predict, even for children implanted early in life. To understand the neurobiological basis of this variability, we used presurgical neural morphological data obtained from MRI of individual pediatric cochlear implant (CI) candidates implanted younger than 3.5 years to predict variability of...
Show moreAlthough cochlear implantation enables some children to attain age-appropriate speech and language development, communicative delays persist in others, and outcomes are quite variable and difficult to predict, even for children implanted early in life. To understand the neurobiological basis of this variability, we used presurgical neural morphological data obtained from MRI of individual pediatric cochlear implant (CI) candidates implanted younger than 3.5 years to predict variability of their speech-perception improvement after surgery. We first compared neuroanatomical density and spatial pattern similarity of CI candidates to that of age-matched children with normal hearing, which allowed us to detail neuroanatomical networks that were either affected or unaffected by auditory deprivation. This information enables us to build machine-learning models to predict the individual children's speech development following CI. We found that regions of the brain that were unaffected by auditory deprivation, in particular the auditory association and cognitive brain regions, produced the highest accuracy, specificity, and sensitivity in patient classification and the most precise prediction results. These findings suggest that brain areas unaffected by auditory deprivation are critical to developing closer to typical speech outcomes. Moreover, the findings suggest that determination of the type of neural reorganization caused by auditory deprivation before implantation is valuable for predicting post-CI language outcomes for young children.
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Date Issued: 2018-01-30
Identifier: FSU_libsubv1_wos_000423728800019, 10.1073/pnas.1717603115
Format: Citation

Title: Implications of life-history strategies for obesity.
Creator: Maner, Jon K, Dittmann, Andrea, Meltzer, Andrea L, McNulty, James K
Abstract/Description: The association between low socioeconomic status (SES) and obesity is well documented. In the current research, a life history theory (LHT) framework provided an explanation for this association. Derived from evolutionary behavioral science, LHT emphasizes how variability in exposure to unpredictability during childhood gives rise to individual differences in a range of social psychological processes across the life course. Consistent with previous LHT research, the current findings suggest...
Show moreThe association between low socioeconomic status (SES) and obesity is well documented. In the current research, a life history theory (LHT) framework provided an explanation for this association. Derived from evolutionary behavioral science, LHT emphasizes how variability in exposure to unpredictability during childhood gives rise to individual differences in a range of social psychological processes across the life course. Consistent with previous LHT research, the current findings suggest that exposure to unpredictability during childhood (a characteristic common to low SES environments) is associated with the adoption of a fast life-history strategy, one marked by impulsivity and a focus on short-term goals. We demonstrate that a fast life-history strategy, in turn, was associated with dysregulated weight-management behaviors (i.e., eating even in the absence of hunger), which were predictive of having a high body mass index (BMI) and being obese. In both studies, findings held while controlling for participants' current socioeconomic status, suggesting that obesity is rooted in childhood experiences. A serial mediation model in study 2 confirmed that effects of childhood SES on adult BMI and obesity can be explained in part by exposure to unpredictability, the adoption of a fast life-history strategy, and dysregulated-eating behaviors. These findings suggest that weight problems in adulthood may be rooted partially in early childhood exposure to unpredictable events and environments. LHT provides a valuable explanatory framework for understanding the root causes of obesity.
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Date Issued: 2017-08-08
Identifier: FSU_pmch_28739939, 10.1073/pnas.1620482114, PMC5558992, 28739939, 28739939, 1620482114
Format: Citation

Title: 3'-UTR and microRNA-24 regulate circadian rhythms by repressing PERIOD2 protein accumulation.
Creator: Yoo, Seung-Hee, Kojima, Shihoko, Shimomura, Kazuhiro, Koike, Nobuya, Buhr, Ethan D, Furukawa, Tadashi, Ko, Caroline H, Gloston, Gabrielle, Ayoub, Christopher, Nohara, Kazunari,...
Show moreYoo, Seung-Hee, Kojima, Shihoko, Shimomura, Kazuhiro, Koike, Nobuya, Buhr, Ethan D, Furukawa, Tadashi, Ko, Caroline H, Gloston, Gabrielle, Ayoub, Christopher, Nohara, Kazunari, Reyes, Bryan A, Tsuchiya, Yoshiki, Yoo, Ook-Joon, Yagita, Kazuhiro, Lee, Choogon, Chen, Zheng, Yamazaki, Shin, Green, Carla B, Takahashi, Joseph S
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Abstract/Description: We previously created two PER2::LUCIFERASE (PER2::LUC) circadian reporter knockin mice that differ only in the 3'-UTR region: , which retains the endogenous 3'-UTR and , where the endogenous 3'-UTR was replaced by an SV40 late poly(A) signal. To delineate the in vivo functions of 3'-UTR, we analyzed circadian rhythms of mice. Interestingly, mice displayed more than threefold stronger amplitude in bioluminescence rhythms than mice, and also exhibited lengthened free-running periods (∼24.0 h),...
Show moreWe previously created two PER2::LUCIFERASE (PER2::LUC) circadian reporter knockin mice that differ only in the 3'-UTR region: , which retains the endogenous 3'-UTR and , where the endogenous 3'-UTR was replaced by an SV40 late poly(A) signal. To delineate the in vivo functions of 3'-UTR, we analyzed circadian rhythms of mice. Interestingly, mice displayed more than threefold stronger amplitude in bioluminescence rhythms than mice, and also exhibited lengthened free-running periods (∼24.0 h), greater phase delays following light pulse, and enhanced temperature compensation relative to Analysis of the 3'-UTR sequence revealed that miR-24, and to a lesser degree miR-30, suppressed PER2 protein translation, and the reversal of this inhibition in augmented PER2::LUC protein level and oscillatory amplitude. Interestingly, mRNA and protein oscillatory amplitude as well as CRY1 protein oscillation were increased in mice, suggesting rhythmic overexpression of PER2 enhances expression of and other core clock genes. Together, these studies provide important mechanistic insights into the regulatory roles of 3'-UTR, miR-24, and PER2 in expression and core clock function.
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Date Issued: 2017-10-17
Identifier: FSU_pmch_28973913, 10.1073/pnas.1706611114, PMC5651750, 28973913, 28973913, 1706611114
Format: Citation

Title: Phase diagram of URu Fe Si in high magnetic fields.
Creator: Ran, Sheng, Jeon, Inho, Pouse, Naveen, Breindel, Alexander J, Kanchanavatee, Noravee, Huang, Kevin, Gallagher, Andrew, Chen, Kuan-Wen, Graf, David, Baumbach, Ryan E, Singleton,...
Show moreRan, Sheng, Jeon, Inho, Pouse, Naveen, Breindel, Alexander J, Kanchanavatee, Noravee, Huang, Kevin, Gallagher, Andrew, Chen, Kuan-Wen, Graf, David, Baumbach, Ryan E, Singleton, John, Maple, M Brian
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Abstract/Description: Electrical transport measurements were performed on URu Fe Si single-crystal specimens in high magnetic fields up to 45 T (DC fields) and 60 T (pulsed fields). We observed a systematic evolution of the critical fields for both the hidden-order (HO) and large-moment antiferromagnetic (LMAFM) phases and established the 3D phase diagram of In the HO phase, / scales with / and collapses onto a single curve. However, in the LMAFM phase, this single scaling relation is not satisfied. Within a...
Show moreElectrical transport measurements were performed on URu Fe Si single-crystal specimens in high magnetic fields up to 45 T (DC fields) and 60 T (pulsed fields). We observed a systematic evolution of the critical fields for both the hidden-order (HO) and large-moment antiferromagnetic (LMAFM) phases and established the 3D phase diagram of In the HO phase, / scales with / and collapses onto a single curve. However, in the LMAFM phase, this single scaling relation is not satisfied. Within a certain range of values, the HO phase reenters after the LMAFM phase is suppressed by the magnetic field, similar to the behavior observed for URuSi within a certain range of pressures.
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Date Issued: 2017-09-12
Identifier: FSU_pmch_28847927, 10.1073/pnas.1710192114, PMC5604036, 28847927, 28847927, 1710192114
Format: Citation

Title: Across the tree of life, radiation resistance is governed by antioxidant Mn, gauged by paramagnetic resonance.
Creator: Sharma, Ajay, Gaidamakova, Elena K, Grichenko, Olga, Matrosova, Vera Y, Hoeke, Veronika, Klimenkova, Polina, Conze, Isabel H, Volpe, Robert P, Tkavc, Rok, Gostinčar, Cene, Gunde...
Show moreSharma, Ajay, Gaidamakova, Elena K, Grichenko, Olga, Matrosova, Vera Y, Hoeke, Veronika, Klimenkova, Polina, Conze, Isabel H, Volpe, Robert P, Tkavc, Rok, Gostinčar, Cene, Gunde-Cimerman, Nina, DiRuggiero, Jocelyne, Shuryak, Igor, Ozarowski, Andrew, Hoffman, Brian M, Daly, Michael J
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Abstract/Description: Despite concerted functional genomic efforts to understand the complex phenotype of ionizing radiation (IR) resistance, a genome sequence cannot predict whether a cell is IR-resistant or not. Instead, we report that absorption-display electron paramagnetic resonance (EPR) spectroscopy of nonirradiated cells is highly diagnostic of IR survival and repair efficiency of DNA double-strand breaks (DSBs) caused by exposure to gamma radiation across archaea, bacteria, and eukaryotes, including fungi...
Show moreDespite concerted functional genomic efforts to understand the complex phenotype of ionizing radiation (IR) resistance, a genome sequence cannot predict whether a cell is IR-resistant or not. Instead, we report that absorption-display electron paramagnetic resonance (EPR) spectroscopy of nonirradiated cells is highly diagnostic of IR survival and repair efficiency of DNA double-strand breaks (DSBs) caused by exposure to gamma radiation across archaea, bacteria, and eukaryotes, including fungi and human cells. IR-resistant cells, which are efficient at DSB repair, contain a high cellular content of manganous ions (Mn) in high-symmetry (H) antioxidant complexes with small metabolites (e.g., orthophosphate, peptides), which exhibit narrow EPR signals (small zero-field splitting). In contrast, Mn ions in IR-sensitive cells, which are inefficient at DSB repair, exist largely as low-symmetry (L) complexes with substantially broadened spectra seen with enzymes and strongly chelating ligands. The fraction of cellular Mn present as H-complexes (H-Mn), as measured by EPR of live, nonirradiated Mn-replete cells, is now the strongest known gauge of biological IR resistance between and within organisms representing all three domains of life: Antioxidant H-Mn complexes, not antioxidant enzymes (e.g., Mn superoxide dismutase), govern IR survival. As the pool of intracellular metabolites needed to form H-Mn complexes depends on the nutritional status of the cell, we conclude that IR resistance is predominantly a metabolic phenomenon. In a cross-kingdom analysis, the vast differences in taxonomic classification, genome size, and radioresistance between cell types studied here support that IR resistance is not controlled by the repertoire of DNA repair and antioxidant enzymes.
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Date Issued: 2017-10-31
Identifier: FSU_pmch_29042516, 10.1073/pnas.1713608114, PMC5676931, 29042516, 29042516, 1713608114
Format: Citation

Title: High fire-derived nitrogen deposition on central African forests.
Creator: Bauters, Marijn, Drake, Travis W, Verbeeck, Hans, Bodé, Samuel, Hervé-Fernández, Pedro, Zito, Phoebe, Podgorski, David C, Boyemba, Faustin, Makelele, Isaac, Cizungu Ntaboba,...
Show moreBauters, Marijn, Drake, Travis W, Verbeeck, Hans, Bodé, Samuel, Hervé-Fernández, Pedro, Zito, Phoebe, Podgorski, David C, Boyemba, Faustin, Makelele, Isaac, Cizungu Ntaboba, Landry, Spencer, Robert G M, Boeckx, Pascal
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Abstract/Description: Atmospheric nitrogen (N) deposition is an important determinant of N availability for natural ecosystems worldwide. Increased anthropogenic N deposition shifts the stoichiometric equilibrium of ecosystems, with direct and indirect impacts on ecosystem functioning and biogeochemical cycles. Current simulation data suggest that remote tropical forests still receive low atmospheric N deposition due to a lack of proximate industry, low rates of fossil fuel combustion, and absence of intensive...
Show moreAtmospheric nitrogen (N) deposition is an important determinant of N availability for natural ecosystems worldwide. Increased anthropogenic N deposition shifts the stoichiometric equilibrium of ecosystems, with direct and indirect impacts on ecosystem functioning and biogeochemical cycles. Current simulation data suggest that remote tropical forests still receive low atmospheric N deposition due to a lack of proximate industry, low rates of fossil fuel combustion, and absence of intensive agriculture. We present field-based N deposition data for forests of the central Congo Basin, and use ultrahigh-resolution mass spectrometry to characterize the organic N fraction. Additionally, we use satellite data and modeling for atmospheric N source apportionment. Our results indicate that these forests receive 18.2 kg N hectare years as wet deposition, with dry deposition via canopy interception adding considerably to this flux. We also show that roughly half of the N deposition is organic, which is often ignored in N deposition measurements and simulations. The source of atmospheric N is predominantly derived from intensive seasonal burning of biomass on the continent. This high N deposition has important implications for the ecology of the Congo Basin and for global biogeochemical cycles more broadly.
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Date Issued: 2018-01-16
Identifier: FSU_pmch_29295919, 10.1073/pnas.1714597115, PMC5776982, 29295919, 29295919, 1714597115
Format: Citation

Title: Neural preservation underlies speech improvement from auditory deprivation in young cochlear implant recipients.
Creator: Feng, Gangyi, Ingvalson, Erin M, Grieco-Calub, Tina M, Roberts, Megan Y, Ryan, Maura E, Birmingham, Patrick, Burrowes, Delilah, Young, Nancy M, Wong, Patrick C M
Abstract/Description: Although cochlear implantation enables some children to attain age-appropriate speech and language development, communicative delays persist in others, and outcomes are quite variable and difficult to predict, even for children implanted early in life. To understand the neurobiological basis of this variability, we used presurgical neural morphological data obtained from MRI of individual pediatric cochlear implant (CI) candidates implanted younger than 3.5 years to predict variability of...
Show moreAlthough cochlear implantation enables some children to attain age-appropriate speech and language development, communicative delays persist in others, and outcomes are quite variable and difficult to predict, even for children implanted early in life. To understand the neurobiological basis of this variability, we used presurgical neural morphological data obtained from MRI of individual pediatric cochlear implant (CI) candidates implanted younger than 3.5 years to predict variability of their speech-perception improvement after surgery. We first compared neuroanatomical density and spatial pattern similarity of CI candidates to that of age-matched children with normal hearing, which allowed us to detail neuroanatomical networks that were either affected or unaffected by auditory deprivation. This information enables us to build machine-learning models to predict the individual children's speech development following CI. We found that regions of the brain that were unaffected by auditory deprivation, in particular the auditory association and cognitive brain regions, produced the highest accuracy, specificity, and sensitivity in patient classification and the most precise prediction results. These findings suggest that brain areas unaffected by auditory deprivation are critical to developing closer to typical speech outcomes. Moreover, the findings suggest that determination of the type of neural reorganization caused by auditory deprivation before implantation is valuable for predicting post-CI language outcomes for young children.
Show less
Date Issued: 2018-01-30
Identifier: FSU_pmch_29339512, 10.1073/pnas.1717603115, PMC5798370, 29339512, 29339512, 1717603115
Format: Citation

Title: Spin susceptibility of charge-ordered YBaCuO across the upper critical field.
Creator: Zhou, Rui, Hirata, Michihiro, Wu, Tao, Vinograd, Igor, Mayaffre, Hadrien, Krämer, Steffen, Reyes, Arneil P, Kuhns, Philip L, Liang, Ruixing, Hardy, W N, Bonn, D A, Julien, Marc...
Show moreZhou, Rui, Hirata, Michihiro, Wu, Tao, Vinograd, Igor, Mayaffre, Hadrien, Krämer, Steffen, Reyes, Arneil P, Kuhns, Philip L, Liang, Ruixing, Hardy, W N, Bonn, D A, Julien, Marc-Henri
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Abstract/Description: The value of the upper critical field , a fundamental characteristic of the superconducting state, has been subject to strong controversy in high- copper oxides. Since the issue has been tackled almost exclusively by macroscopic techniques so far, there is a clear need for local-probe measurements. Here, we use O NMR to measure the spin susceptibility [Formula: see text] of the CuO planes at low temperature in charge-ordered YBaCuO We find that [Formula: see text] increases (most likely...
Show moreThe value of the upper critical field , a fundamental characteristic of the superconducting state, has been subject to strong controversy in high- copper oxides. Since the issue has been tackled almost exclusively by macroscopic techniques so far, there is a clear need for local-probe measurements. Here, we use O NMR to measure the spin susceptibility [Formula: see text] of the CuO planes at low temperature in charge-ordered YBaCuO We find that [Formula: see text] increases (most likely linearly) with magnetic field and saturates above field values ranging from 20 T to 40 T. This result is consistent with the lowest values claimed previously and with the interpretation that the charge density wave (CDW) reduces in underdoped YBaCuO Furthermore, the absence of marked deviation in [Formula: see text] at the onset of long-range CDW order indicates that this [Formula: see text] reduction and the Fermi-surface reconstruction are primarily rooted in the short-range CDW order already present in zero field, not in the field-induced long-range CDW order. Above [Formula: see text], the relatively low values of [Formula: see text] at [Formula: see text] K show that the pseudogap is a ground-state property, independent of the superconducting gap.
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Date Issued: 2017-12-12
Identifier: FSU_pmch_29183974, 10.1073/pnas.1711445114, PMC5740678, 29183974, 29183974, 1711445114
Format: Citation

Title: DNA replication timing alterations identify common markers between distinct progeroid diseases.
Creator: Rivera-Mulia, Juan Carlos, Desprat, Romain, Trevilla-Garcia, Claudia, Cornacchia, Daniela, Schwerer, Hélène, Sasaki, Takayo, Sima, Jiao, Fells, Tyler, Studer, Lorenz, Lemaitre,...
Show moreRivera-Mulia, Juan Carlos, Desprat, Romain, Trevilla-Garcia, Claudia, Cornacchia, Daniela, Schwerer, Hélène, Sasaki, Takayo, Sima, Jiao, Fells, Tyler, Studer, Lorenz, Lemaitre, Jean-Marc, Gilbert, David M
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Abstract/Description: Progeroid syndromes are rare genetic disorders that phenotypically resemble natural aging. Different causal mutations have been identified, but no molecular alterations have been identified that are in common to these diseases. DNA replication timing (RT) is a robust cell type-specific epigenetic feature highly conserved in the same cell types from different individuals but altered in disease. Here, we characterized DNA RT program alterations in Hutchinson-Gilford progeria syndrome (HGPS) and...
Show moreProgeroid syndromes are rare genetic disorders that phenotypically resemble natural aging. Different causal mutations have been identified, but no molecular alterations have been identified that are in common to these diseases. DNA replication timing (RT) is a robust cell type-specific epigenetic feature highly conserved in the same cell types from different individuals but altered in disease. Here, we characterized DNA RT program alterations in Hutchinson-Gilford progeria syndrome (HGPS) and Rothmund-Thomson syndrome (RTS) patients compared with natural aging and cellular senescence. Our results identified a progeroid-specific RT signature that is common to cells from three HGPS and three RTS patients and distinguishes them from healthy individuals across a wide range of ages. Among the RT abnormalities, we identified the tumor protein p63 gene () as a gene marker for progeroid syndromes. By using the redifferentiation of four patient-derived induced pluripotent stem cells as a model for the onset of progeroid syndromes, we tracked the progression of RT abnormalities during development, revealing altered RT of the gene as an early event in disease progression of both HGPS and RTS. Moreover, the RT abnormalities in progeroid patients were associated with altered isoform expression of Our findings demonstrate the value of RT studies to identify biomarkers not detected by other methods, reveal abnormal RT as an early event in progeroid disease progression, and suggest gene regulation as a potential therapeutic target.
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Date Issued: 2017-12-19
Identifier: FSU_pmch_29196523, 10.1073/pnas.1711613114, PMC5754778, 29196523, 29196523, 1711613114
Format: Citation

Title: Opinion: Offshore aquaculture in the United States.
Creator: Lester, Sarah E, Gentry, Rebecca R, Kappel, Carrie V, White, Crow, Gaines, Steven D
Date Issued: 2018-07-10
Identifier: FSU_pmch_29991573, 10.1073/pnas.1808737115, PMC6048495, 29991573, 29991573, 1808737115
Format: Citation

Title: Fractional Coalescent.
Creator: Mashayekhi, Somayeh, Beerli, Peter
Abstract/Description: An approach to the coalescent, the fractional coalescent (f-coalescent), is introduced. The derivation is based on the discretetime Cannings population model in which the variance of the number of offspring depends on the parameter alpha. This additional parameter alpha affects the variability of the patterns of the waiting times; values of alpha
Show moreAn approach to the coalescent, the fractional coalescent (f-coalescent), is introduced. The derivation is based on the discretetime Cannings population model in which the variance of the number of offspring depends on the parameter alpha. This additional parameter alpha affects the variability of the patterns of the waiting times; values of alpha < 1 lead to an increase of short time intervals, but occasionally allow for very long time intervals. When alpha = 1, the f-coalescent and the Kingman's n-coalescent are equivalent. The distribution of the time to the most recent common ancestor and the probability that n genes descend from m ancestral genes in a time interval of length T for the f-coalescent are derived. The f-coalescent has been implemented in the population genetic model inference software MIGRATE. Simulation studies suggest that it is possible to accurately estimate alpha values from data that were generated with known alpha values and that the f-coalescent can detect potential environmental heterogeneity within a population. Bayes factor comparisons of simulated data with alpha < 1 and real data (H1N1 influenza and malaria parasites) showed an improved model fit of the f-coalescent over the n-coalescent. The development of the f-coalescent and its inclusion into the inference program MIGRATE facilitates testing for deviations from the n-coalescent.
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Date Issued: ue Mar 26 00:00:00 ED
Identifier: FSU_libsubv1_wos_000462382800066, 10.1073/pnas.1810239116
Format: Citation

Department of Biomedical Sciences (10)	+ -
National High Magnetic Field Laboratory (9)	+ -
Department of Earth, Ocean and Atmospheric Science (8)	+ -
Department of Biological Science (6)	+ -
Center for Genomics and Personalized Medicine (2)	+ -

Department of Geography (2)	+ -
Department of Physics (2)	+ -
Department of Psychology (2)	+ -
School of Communication Science and Disorders (2)	+ -
Department of Chemistry and Biochemistry (1)	+ -
Department of Scientific Computing (1)	+ -
Institute of Molecular Biophysics (1)	+ -
Program in Neuroscience (1)	+ -

Humans (11)	+ -
Animals (8)	+ -
Female (5)	+ -
Mice (5)	+ -
Cell Cycle Proteins/metabolism (4)	+ -

Phosphorylation (4)	+ -
Protein Binding (4)	+ -
Cell Cycle Proteins/genetics (3)	+ -
Cell Line (3)	+ -
Chromatin/genetics (3)	+ -
Male (3)	+ -
Mutation (3)	+ -
Nuclear Proteins/metabolism (3)	+ -
Period Circadian Proteins/metabolism (3)	+ -
Saccharomyces cerevisiae Proteins/metabolism (3)	+ -
Adult (2)	+ -
Blotting, Western (2)	+ -
Child (2)	+ -
Chromatin/metabolism (2)	+ -
Chromosome Mapping (2)	+ -
Circadian Rhythm (2)	+ -
Climate Change (2)	+ -
DNA-Binding Proteins/genetics (2)	+ -
Ecosystem (2)	+ -
Forests (2)	+ -
Gene Deletion (2)	+ -
Mice, Inbred C57BL (2)	+ -
Mice, Knockout (2)	+ -
Mice, Transgenic (2)	+ -
Models, Molecular (2)	+ -

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