Category Archives: Proc Natl Acad Sci U S A

Chromosome segregation drives division site selection in Streptococcus pneumoniae.






Chromosome segregation drives division site selection in Streptococcus pneumoniae.
Proc Natl Acad Sci U S A. 2017 Jul 03;:
Authors: van Raaphorst R, Kjos M, Veening JW
Abstract
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Disentangling mechanisms involved in collagen pyridinoline cross-linking: The immunophilin FKBP65 is critical for dimerization of lysyl hydroxylase 2.






Disentangling mechanisms involved in collagen pyridinoline cross-linking: The immunophilin FKBP65 is critical for dimerization of lysyl hydroxylase 2.

Proc Natl Acad Sci U S A. 2016 Jun 13;

Authors: Gjaltema RA, van der Stoel MM, Boersema M, Bank RA

Abstract
Collagens are subjected to extensive posttranslational modifications, such as lysine hydroxylation. Bruck syndrome (BS) is a connective tissue disorder characterized at the molecular level by a loss of telopeptide lysine hydroxylation, resulting in reduced collagen pyridinoline cross-linking. BS results from mutations in the genes coding for lysyl hydroxylase (LH) 2 or peptidyl-prolyl cis-trans isomerase (PPIase) FKBP65. Given that the immunophilin FKBP65 does not exhibit LH activity, it is likely that LH2 activity is somehow dependent on FKPB65. In this report, we provide insights regarding the interplay between LH2 and FKBP65. We found that FKBP65 forms complexes with LH2 splice variants LH2A and LH2B but not with LH1 and LH3. Ablating the catalytic activity of FKBP65 or LH2 did not affect complex formation. Both depletion of FKBP65 and inhibition of FKBP65 PPIase activity reduced the dimeric (active) form of LH2 but did not affect the binding of monomeric (inactive) LH2 to procollagen Iα1. Furthermore, we show that LH2A and LH2B cannot form heterodimers with each other but are able to form heterodimers with LH1 and LH3. Collectively, our results indicate that FKBP65 is linked to pyridinoline cross-linking by specifically mediating the dimerization of LH2. Moreover, FKBP65 does not interact with LH1 and LH3, explaining why in BS triple-helical hydroxylysines are not affected. Our results provide a mechanistic link between FKBP65 and the loss of pyridinolines and may hold the key to future treatments for diseases related to collagen cross-linking anomalies, such as fibrosis and cancer.

PMID: 27298363 [PubMed – as supplied by publisher]

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Dutch research funding, gender bias, and Simpson’s paradox.






Dutch research funding, gender bias, and Simpson’s paradox.

Proc Natl Acad Sci U S A. 2015 Dec 3;

Authors: Albers CJ

PMID: 26635232 [PubMed – as supplied by…

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A haploid genetic screen identifies the G1/S regulatory machinery as a determinant of Wee1 inhibitor sensitivity.






A haploid genetic screen identifies the G1/S regulatory machinery as a determinant of Wee1 inhibitor sensitivity.

Proc Natl Acad Sci U S A. 2015 Nov 23;

Authors: Heijink AM, Blomen VA, Bisteau X, Degener F, Matsushita FY, Kaldis P, Foijer F, van Vugt MA

Abstract
The Wee1 cell cycle checkpoint kinase prevents premature mitotic entry by inhibiting cyclin-dependent kinases. Chemical inhibitors of Wee1 are currently being tested clinically as targeted anticancer drugs. Wee1 inhibition is thought to be preferentially cytotoxic in p53-defective cancer cells. However, TP53 mutant cancers do not respond consistently to Wee1 inhibitor treatment, indicating the existence of genetic determinants of Wee1 inhibitor sensitivity other than TP53 status. To optimally facilitate patient selection for Wee1 inhibition and uncover potential resistance mechanisms, identification of these currently unknown genes is necessary. The aim of this study was therefore to identify gene mutations that determine Wee1 inhibitor sensitivity. We performed a genome-wide unbiased functional genetic screen in TP53 mutant near-haploid KBM-7 cells using gene-trap insertional mutagenesis. Insertion site mapping of cells that survived long-term Wee1 inhibition revealed enrichment of G1/S regulatory genes, including SKP2, CUL1, and CDK2. Stable depletion of SKP2, CUL1, or CDK2 or chemical Cdk2 inhibition rescued the γ-H2AX induction and abrogation of G2 phase as induced by Wee1 inhibition in breast and ovarian cancer cell lines. Remarkably, live cell imaging showed that depletion of SKP2, CUL1, or CDK2 did not rescue the Wee1 inhibition-induced karyokinesis and cytokinesis defects. These data indicate that the activity of the DNA replication machinery, beyond TP53 mutation status, determines Wee1 inhibitor sensitivity, and could serve as a selection criterion for Wee1-inhibitor eligible patients. Conversely, loss of the identified S-phase genes could serve as a mechanism of acquired resistance, which goes along with development of severe genomic instability.

PMID: 26598692 [PubMed – as supplied by publisher]

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Facilitation shifts paradigms and can amplify coastal restoration efforts.






Facilitation shifts paradigms and can amplify coastal restoration efforts.
Proc Natl Acad Sci U S A. 2015 Nov 17;112(46):14295-14300
Authors: Silliman BR, Schrack E, He Q, Cope R, Santoni A, van der Heide T, Jacobi R… Continue reading






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Science for a wilder Anthropocene: Synthesis and future directions for trophic rewilding research.






Science for a wilder Anthropocene: Synthesis and future directions for trophic rewilding research.

Proc Natl Acad Sci U S A. 2015 Oct 26;

Authors: Svenning JC, Pedersen PB, Donlan CJ, Ejrnæs R, Faurby S, Galetti M, Hansen DM, Sandel B, Sandom CJ, Terborgh JW, Vera FW

Abstract
Trophic rewilding is an ecological restoration strategy that uses species introductions to restore top-down trophic interactions and associated trophic cascades to promote self-regulating biodiverse ecosystems. Given the importance of large animals in trophic cascades and their widespread losses and resulting trophic downgrading, it often focuses on restoring functional megafaunas. Trophic rewilding is increasingly being implemented for conservation, but remains controversial. Here, we provide a synthesis of its current scientific basis, highlighting trophic cascades as the key conceptual framework, discussing the main lessons learned from ongoing rewilding projects, systematically reviewing the current literature, and highlighting unintentional rewilding and spontaneous wildlife comebacks as underused sources of information. Together, these lines of evidence show that trophic cascades may be restored via species reintroductions and ecological replacements. It is clear, however, that megafauna effects may be affected by poorly understood trophic complexity effects and interactions with landscape settings, human activities, and other factors. Unfortunately, empirical research on trophic rewilding is still rare, fragmented, and geographically biased, with the literature dominated by essays and opinion pieces. We highlight the need for applied programs to include hypothesis testing and science-based monitoring, and outline priorities for future research, notably assessing the role of trophic complexity, interplay with landscape settings, land use, and climate change, as well as developing the global scope for rewilding and tools to optimize benefits and reduce human-wildlife conflicts. Finally, we recommend developing a decision framework for species selection, building on functional and phylogenetic information and with attention to the potential contribution from synthetic biology.

PMID: 26504218 [PubMed – as supplied by publisher]

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Combining paleo-data and modern exclosure experiments to assess the impact of megafauna extinctions on woody vegetation.






Combining paleo-data and modern exclosure experiments to assess the impact of megafauna extinctions on woody vegetation.
Proc Natl Acad Sci U S A. 2015 Oct 26;
Authors: Bakker ES, Gill JL, Johnson CN, Vera FW, Sandom… Continue reading






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Development of a diverse human T-cell repertoire despite stringent restriction of hematopoietic clonality in the thymus.






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Development of a diverse human T-cell repertoire despite stringent restriction of hematopoietic clonality in the thymus.

Proc Natl Acad Sci U S A. 2015 Oct 19;

Authors: Brugman MH, Wiekmeijer AS, van Eggermond M, Wolvers-Tettero I, Langerak AW, de Haas EF, Bystrykh LV, van Rood JJ, de Haan G, Fibbe WE, Staal FJ

Abstract
The fate and numbers of hematopoietic stem cells (HSC) and their progeny that seed the thymus constitute a fundamental question with important clinical implications. HSC transplantation is often complicated by limited T-cell reconstitution, especially when HSC from umbilical cord blood are used. Attempts to improve immune reconstitution have until now been unsuccessful, underscoring the need for better insight into thymic reconstitution. Here we made use of the NOD-SCID-IL-2Rγ(-/-) xenograft model and lentiviral cellular barcoding of human HSCs to study T-cell development in the thymus at a clonal level. Barcoded HSCs showed robust (>80% human chimerism) and reproducible myeloid and lymphoid engraftment, with T cells arising 12 wk after transplantation. A very limited number of HSC clones (<10) repopulated the xenografted thymus, with further restriction of the number of clones during subsequent development. Nevertheless, T-cell receptor rearrangements were polyclonal and showed a diverse repertoire, demonstrating that a multitude of T-lymphocyte clones can develop from a single HSC clone. Our data imply that intrathymic clonal fitness is important during T-cell development. As a consequence, immune incompetence after HSC transplantation is not related to the transplantation of limited numbers of HSC but to intrathymic events.

PMID: 26483497 [PubMed – as supplied by publisher]

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Socially mediated induction and suppression of antibiosis during bacterial coexistence.






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Socially mediated induction and suppression of antibiosis during bacterial coexistence.
Proc Natl Acad Sci U S A. 2015 Jul 27;
Authors: Abrudan MI, Smakman F, Grimbergen AJ, Westhoff S, Miller EL, van… Continue reading






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Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multidrug resistance.






Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multidrug resistance.
Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):E2874-83
Authors: Moreno-Gamez S, Hill AL, Rosenbloom DI, Petrov DA, N… Continue reading






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New chronology for Ksâr ‘Akil (Lebanon) supports Levantine route of modern human dispersal into Europe.






New chronology for Ksâr ‘Akil (Lebanon) supports Levantine route of modern human dispersal into Europe.

Proc Natl Acad Sci U S A. 2015 Jun 1;

Authors: Bosch MD, Mannino…

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Rate, spectrum, and evolutionary dynamics of spontaneous epimutations.






Rate, spectrum, and evolutionary dynamics of spontaneous epimutations.

Proc Natl Acad Sci U S A. 2015 May 11;

Authors: van der Graaf A, Wardenaar R, Neumann DA, Taudt A, Shaw RG, Jansen RC, Schmitz RJ, Colomé-Tatché M, Johannes F

Abstract
Stochastic changes in cytosine methylation are a source of heritable epigenetic and phenotypic diversity in plants. Using the model plant Arabidopsis thaliana, we derive robust estimates of the rate at which methylation is spontaneously gained (forward epimutation) or lost (backward epimutation) at individual cytosines and construct a comprehensive picture of the epimutation landscape in this species. We demonstrate that the dynamic interplay between forward and backward epimutations is modulated by genomic context and show that subtle contextual differences have profoundly shaped patterns of methylation diversity in A. thaliana natural populations over evolutionary timescales. Theoretical arguments indicate that the epimutation rates reported here are high enough to rapidly uncouple genetic from epigenetic variation, but low enough for new epialleles to sustain long-term selection responses. Our results provide new insights into methylome evolution and its population-level consequences.

PMID: 25964364 [PubMed – as supplied by publisher]

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The membrane remodeling protein Pex11p activates the GTPase Dnm1p during peroxisomal fission.






The membrane remodeling protein Pex11p activates the GTPase Dnm1p during peroxisomal fission.

Proc Natl Acad Sci U S A. 2015 May 4;

Authors: Williams C, Opalinski L, Landgraf C, Costello J, Schrader M, Krikken AM, Knoops K, Kram AM, Volkmer R, van der Klei IJ

Abstract
The initial phase of peroxisomal fission requires the peroxisomal membrane protein Peroxin 11 (Pex11p), which remodels the membrane, resulting in organelle elongation. Here, we identify an additional function for Pex11p, demonstrating that Pex11p also plays a crucial role in the final step of peroxisomal fission: dynamin-like protein (DLP)-mediated membrane scission. First, we demonstrate that yeast Pex11p is necessary for the function of the GTPase Dynamin-related 1 (Dnm1p) in vivo. In addition, our data indicate that Pex11p physically interacts with Dnm1p and that inhibiting this interaction compromises peroxisomal fission. Finally, we demonstrate that Pex11p functions as a GTPase activating protein (GAP) for Dnm1p in vitro. Similar observations were made for mammalian Pex11β and the corresponding DLP Drp1, indicating that DLP activation by Pex11p is conserved. Our work identifies a previously unknown requirement for a GAP in DLP function.

PMID: 25941407 [PubMed – as supplied by publisher]

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Reverse switching of surface roughness in a self-organized polydomain liquid crystal coating.






Reverse switching of surface roughness in a self-organized polydomain liquid crystal coating.
Proc Natl Acad Sci U S A. 2015 Mar 9;
Authors: Liu D, Liu L, Onck PR, Broer DJ
Abstract
In this work we pr… Continue reading






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Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession.






Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession.
Proc Natl Acad Sci U S A. 2015 Mar 2;
Authors: Dini-Andreote F, Stegen JC, van Elsas JD, Salle… Continue reading






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Focus on the success of others leads to selfish behavior.






Focus on the success of others leads to selfish behavior.
Proc Natl Acad Sci U S A. 2015 Feb 17;
Authors: van den Berg P, Molleman L, Weissing FJ
Abstract
It has often been argued that the spectacular… Continue reading






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Oxalic acid and diacylglycerol 36:3 are cross-species markers of sleep debt.






Oxalic acid and diacylglycerol 36:3 are cross-species markers of sleep debt.
Proc Natl Acad Sci U S A. 2015 Feb 9;
Authors: Weljie AM, Meerlo P, Goel N, Sengupta A, Kayser MS, Abel T, Birnbaum MJ, Dinges DF, Sehgal A… Continue reading






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Single liposome analysis of peptide translocation by the ABC transporter TAPL.






Single liposome analysis of peptide translocation by the ABC transporter TAPL.

Proc Natl Acad Sci U S A. 2015 Feb 2;

Authors: Zollmann T, Moiset G, Tumulka F, Tampé R, Poolman B, Abele R

Abstract
ATP-binding cassette (ABC) transporters use ATP to drive solute transport across biological membranes. Members of this superfamily have crucial roles in cell physiology, and some of the transporters are linked to severe diseases. However, understanding of the transport mechanism, especially of human ABC exporters, is scarce. We reconstituted the human lysosomal polypeptide ABC transporter TAPL, expressed in Pichia pastoris, into lipid vesicles (liposomes) and performed explicit transport measurements. We analyzed solute transport at the single liposome level by monitoring the coincident fluorescence of solutes and proteoliposomes in the focal volume of a confocal microscope. We determined a turnover number of eight peptides per minute, which is two orders of magnitude higher than previously estimated from macroscopic measurements. Moreover, we show that TAPL translocates peptides against a large concentration gradient. Maximal filling is not limited by an electrochemical gradient but by trans-inhibition. Countertransport and reversibility studies demonstrate that peptide translocation is a strictly unidirectional process. Altogether, these data are included in a refined model of solute transport by ABC exporters.

PMID: 25646430 [PubMed – as supplied by publisher]

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Thermotropic liquid crystals from biomacromolecules.






Thermotropic liquid crystals from biomacromolecules.

Proc Natl Acad Sci U S A. 2014 Dec 15;

Authors: Liu K, Chen D, Marcozzi A, Zheng L, Su J, Pesce D, Zajaczkowski W, Kolbe A, Pisula W, Müllen K, Clark NA, Herrmann A

Abstract
Complexation of biomacromolecules (e.g., nucleic acids, proteins, or viruses) with surfactants containing flexible alkyl tails, followed by dehydration, is shown to be a simple generic method for the production of thermotropic liquid crystals. The anhydrous smectic phases that result exhibit biomacromolecular sublayers intercalated between aliphatic hydrocarbon sublayers at or near room temperature. Both this and low transition temperatures to other phases enable the study and application of thermotropic liquid crystal phase behavior without thermal degradation of the biomolecular components.

PMID: 25512508 [PubMed – as supplied by publisher]

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Evolutionary tipping points in the capacity to adapt to environmental change.






Evolutionary tipping points in the capacity to adapt to environmental change.
Proc Natl Acad Sci U S A. 2014 Nov 24;
Authors: Botero CA, Weissing FJ, Wright J, Rubenstein DR
Abstract
In an era of rapi… Continue reading






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