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Ewa A Miendlarzewska, Sara Ciucci, Carlo Vittorio Cannistraci, Daphne Bavelier, Sophie Schwartz
Reward-enhanced encoding improves relearning of forgotten associations.
Sci Rep, 8(1) 8557-8557 (2018)
PubMed Source   

Research on human memory has shown that monetary incentives can enhance hippocampal memory consolidation and thereby protect memory traces from forgetting. However, it is not known whether initial reward may facilitate the recovery of already forgotten memories weeks after learning. Here, we investigated the influence of monetary reward on later relearning. Nineteen healthy human participants learned object-location associations, for half of which we offered money. Six weeks later, most of these associations had been forgotten as measured by a test of declarative memory. Yet, relearning in the absence of any reward was faster for the originally rewarded associations. Thus, associative memories encoded in a state of monetary reward motivation may persist in a latent form despite the failure to retrieve them explicitly. Alternatively, such facilitation could be analogous to the renewal effect observed in animal conditioning, whereby a reward-associated cue can reinstate anticipatory arousal, which would in turn modulate relearning. This finding has important implications for learning and education, suggesting that even when learned information is no longer accessible via explicit retrieval, the enduring effects of a past prospect of reward could facilitate its recovery.
@article{Miendlarzewska7143,
author={Ewa A Miendlarzewska, Sara Ciucci, Carlo Vittorio Cannistraci, Daphne Bavelier, Sophie Schwartz},
title={Reward-enhanced encoding improves relearning of forgotten associations.},
journal={Scientific reports},
volume={8},
issue ={1},
pages={8557--8557},
year=2018
}

Steven Boeynaems, Simon Alberti, Nicolas L Fawzi, Tanja Mittag, Magdalini Polymenidou, Frederic Rousseau, Joost Schymkowitz, James Shorter, Benjamin Wolozin, Ludo Van Den Bosch, Peter Tompa, Monika Fuxreiter
Protein Phase Separation: A New Phase in Cell Biology.
Trends Cell Biol, 28(6) 420-435 (2018)
PubMed Source   

Cellular compartments and organelles organize biological matter. Most well-known organelles are separated by a membrane boundary from their surrounding milieu. There are also many so-called membraneless organelles and recent studies suggest that these organelles, which are supramolecular assemblies of proteins and RNA molecules, form via protein phase separation. Recent discoveries have shed light on the molecular properties, formation, regulation, and function of membraneless organelles. A combination of techniques from cell biology, biophysics, physical chemistry, structural biology, and bioinformatics are starting to help establish the molecular principles of an emerging field, thus paving the way for exciting discoveries, including novel therapeutic approaches for the treatment of age-related disorders.
@article{Boeynaems7100,
author={Steven Boeynaems, Simon Alberti, Nicolas L Fawzi, Tanja Mittag, Magdalini Polymenidou, Frederic Rousseau, Joost Schymkowitz, James Shorter, Benjamin Wolozin, Ludo Van Den Bosch, Peter Tompa, Monika Fuxreiter},
title={Protein Phase Separation: A New Phase in Cell Biology.},
journal={Trends in cell biology},
volume={28},
issue ={6},
pages={420--435},
year=2018
}

Alessandro Muscoloni, Carlo Vittorio Cannistraci
A nonuniform popularity-similarity optimization (nPSO) model to efficiently generate realistic complex networks with communities
New J Phys, 20 Art. No. doi: 10.1088/1367-2630/aac06f (2018)
Source  

@article{Muscoloni7149,
author={Alessandro Muscoloni, Carlo Vittorio Cannistraci},
title={A nonuniform popularity-similarity optimization (nPSO) model to efficiently generate realistic complex networks with communities},
journal={New Journal of Physics},
volume={20},
pages={null--null},
year=2018
}

Richard Wheeler, Anthony Hyman
Controlling compartmentalization by non-membrane-bound organelles.
Philos Trans R Soc Lond B Biol Sci, 373(1747) Art. No. 20170193 (2018)
PubMed Source   

Compartmentalization is a characterizing feature of complexity in cells, used to organize their biochemistry. Membrane-bound organelles are most widely known, but non-membrane-bound liquid organelles also exist. These have recently been shown to form by phase separation of specific types of proteins known as scaffolds. This forms two phases: a condensate that is enriched in scaffold protein separated by a phase boundary from the cytoplasm or nucleoplasm with a low concentration of the scaffold protein. Phase separation is well known for synthetic polymers, but also appears important in cells. Here, we review the properties of proteins important for forming these non-membrane-bound organelles, focusing on the energetically favourable interactions that drive condensation. On this basis we make qualitative predictions about how cells may control compartmentalization by condensates; the partition of specific molecules to a condensate; the control of condensation and dissolution of condensates; and the regulation of condensate nucleation. There are emerging data supporting many of these predictions, although future results may prove incorrect. It appears that many molecules may have the ability to modulate condensate formation, making condensates a potential target for future therapeutics. The emerging properties of condensates are fundamentally unlike the properties of membrane-bound organelles. They have the capacity to rapidly integrate cellular events and act as a new class of sensors for internal and external environments.This article is part of the theme issue 'Self-organization in cell biology'.
@article{Wheeler7109,
author={Richard Wheeler, Anthony Hyman},
title={Controlling compartmentalization by non-membrane-bound organelles.},
journal={Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume={373},
issue ={1747},
pages={null--null},
year=2018
}

Mengfei Gao, Riccardo Maraspini, Oliver Beutel, Amin Zehtabian, Britta Eickholt, Alf Honigmann, Helge Ewers
Expansion Stimulated Emission Depletion Microscopy (ExSTED).
ACS Nano, 12(5) 4178-4185 (2018)
PubMed Source   

Stimulated emission depletion (STED) microscopy is routinely used to resolve the ultrastructure of cells with a ∼10-fold higher resolution compared to diffraction limited imaging. While STED microscopy is based on preparing the excited state of fluorescent probes with light, the recently developed expansion microscopy (ExM) provides subdiffraction resolution by physically enlarging the sample before microscopy. The expansion of the fixed cells by cross-linking and swelling of hydrogels easily enlarges the sample ∼4-fold and hence increases the effective optical resolution by this factor. To overcome the current limits of these complementary approaches, we combined ExM with STED (ExSTED) and demonstrated an increase in resolution of up to 30-fold compared to conventional microscopy (<10 nm lateral and ∼50 nm isotropic). While the increase in resolution is straightforward, we found that high-fidelity labeling via multi-epitopes is required to obtain emitter densities that allow ultrastructural details with ExSTED to be resolved. Our work provides a robust template for super-resolution microscopy of entire cells in the ten nanometer range.
@article{Gao7144,
author={Mengfei Gao, Riccardo Maraspini, Oliver Beutel, Amin Zehtabian, Britta Eickholt, Alf Honigmann, Helge Ewers},
title={Expansion Stimulated Emission Depletion Microscopy (ExSTED).},
journal={ACS nano},
volume={12},
issue ={5},
pages={4178--4185},
year=2018
}

Alessandro Muscoloni, Carlo Vittorio Cannistraci
Leveraging the nonuniform PSO network model as a benchmark for performance evaluation in community detection and link prediction
New J Phys, Art. No. doi: 10.1088/1367-2630/aac6f9 (2018)
Source  

@article{Muscoloni7148,
author={Alessandro Muscoloni, Carlo Vittorio Cannistraci},
title={Leveraging the nonuniform PSO network model as a benchmark for performance evaluation in community detection and link prediction},
journal={New Journal of Physics},
volume={},
pages={null--null},
year=2018
}

Anastasia Felker, Karin D Prummel, Anne M Merks, Michaela Mickoleit, Eline C Brombacher, Jan Huisken, Daniela Panáková, Christian Mosimann
Continuous addition of progenitors forms the cardiac ventricle in zebrafish.
Nat Commun, 9(1) Art. No. 2001 (2018)
PubMed Source   

The vertebrate heart develops from several progenitor lineages. After early-differentiating first heart field (FHF) progenitors form the linear heart tube, late-differentiating second heart field (SHF) progenitors extend the atrium and ventricle, and form inflow and outflow tracts (IFT/OFT). However, the position and migration of late-differentiating progenitors during heart formation remains unclear. Here, we track zebrafish heart development using transgenics based on the cardiopharyngeal gene tbx1. Live imaging uncovers a tbx1 reporter-expressing cell sheath that continuously disseminates from the lateral plate mesoderm towards the forming heart tube. High-speed imaging and optogenetic lineage tracing corroborates that the zebrafish ventricle forms through continuous addition from the undifferentiated progenitor sheath followed by late-phase accrual of the bulbus arteriosus (BA). FGF inhibition during sheath migration reduces ventricle size and abolishes BA formation, refining the window of FGF action during OFT formation. Our findings consolidate previous end-point analyses and establish zebrafish ventricle formation as a continuous process.
@article{Felker7136,
author={Anastasia Felker, Karin D Prummel, Anne M Merks, Michaela Mickoleit, Eline C Brombacher, Jan Huisken, Daniela Panáková, Christian Mosimann},
title={Continuous addition of progenitors forms the cardiac ventricle in zebrafish.},
journal={Nature communications},
volume={9},
issue ={1},
pages={null--null},
year=2018
}

Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching.
Nucleic Acids Res, Art. No. doi: 10.1093/nar/gky329 (2018)
PubMed Source   

The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and comprehensive result visualization for efficient command line tools. The webserver includes RNA-RNA interaction prediction (IntaRNA, CopraRNA, metaMIR), sRNA homology search (GLASSgo), sequence-structure alignments (LocARNA, MARNA, CARNA, ExpaRNA), CRISPR repeat classification (CRISPRmap), sequence design (antaRNA, INFO-RNA, SECISDesign), structure aberration evaluation of point mutations (RaSE), and RNA/protein-family models visualization (CMV), and other methods. Open education resources offer interactive visualizations of RNA structure and RNA-RNA interaction prediction as well as basic and advanced sequence alignment algorithms. The services are freely available at http://rna.informatik.uni-freiburg.de.
@article{Raden7140,
author={Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, Rolf Backofen},
title={Freiburg RNA tools: a central online resource for RNA-focused research and teaching.},
journal={Nucleic acids research},
volume={},
pages={1--1},
year=2018
}

David Oriola, Daniel Needleman, Jan Brugués
The Physics of the Metaphase Spindle.
Ann Rev Biophys, 47 655-673 (2018)
PubMed Source   

The assembly of the mitotic spindle and the subsequent segregation of sister chromatids are based on the self-organized action of microtubule filaments, motor proteins, and other microtubule-associated proteins, which constitute the fundamental force-generating elements in the system. Many of the components in the spindle have been identified, but until recently it remained unclear how their collective behaviors resulted in such a robust bipolar structure. Here, we review the current understanding of the physics of the metaphase spindle that is only now starting to emerge.
@article{Oriola7133,
author={David Oriola, Daniel Needleman, Jan Brugués},
title={The Physics of the Metaphase Spindle.},
journal={Annual review of biophysics},
volume={47},
pages={655--673},
year=2018
}

Bruce Alberts, Tony Hyman, Christopher L. Pickett, Shirley Tilghman, Harold Varmus
Improving support for young biomedical scientists.
Science, 360(6390) 716-718 (2018)
PubMed Source  

@article{Alberts7116,
author={Bruce Alberts, Tony Hyman, Christopher L. Pickett, Shirley Tilghman, Harold Varmus},
title={Improving support for young biomedical scientists.},
journal={Science (New York, N.Y.)},
volume={360},
issue ={6390},
pages={716--718},
year=2018
}