Sort by
Showing 21 to 30 of 2,331 entries
Show entries

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
}

Anna Bajur
Dynamic regulation of Crumbs at the plasma membrane during epithelial morphogenesis in Drosophila melanogaster
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2018)
 

@phdthesis{Bajur7120,
author = {Anna Bajur},
title={Dynamic regulation of Crumbs at the plasma membrane during epithelial morphogenesis in Drosophila melanogaster},
school = {Technische Universität Dresden},
year=2018,
address = {Dresden, Germany},
}

Julia Brenmoehl, Christina Walz, Marion Spitschak, Elisa Wirthgen, Michael Walz, Martina Langhammer, Armin Tuchscherer, Ronald Naumann, Andreas Hoeflich
Partial phenotype conversion and differential trait response to conditions of husbandry in mice.
J Comp Physiol B , 188(3) 527-539 (2018)
PubMed Source   

Functional genome analysis usually is performed on the level of genotype-phenotype interaction. However, phenotypes also depend on the relations between genomes and environment. In our experimental system, we observed differential response to environmental factors defined by different conditions of husbandry in a semi-barrier unit or in a SPF (specific pathogen free) barrier unit, which resulted in partial reversal of phenotypes previously observed under semi-barrier conditions. To provide an update of basic phenotypes in unselected and randomly mated controls (DUC) and long-term selected DUhTP (Dummerstorf high treadmill performance) mice in the SPF facility, we compared growth parameters, reproductive performance, the accretion of muscle and fat mass, physical activity, and running performance as well as food intake in all experimental groups. For selected parameters, the comparative analysis spans more than 30 generations. In DUC mice, under SPF conditions a more than threefold (P < 0.0001) higher subcutaneous fat mass, higher muscle mass by about 25% (P < 0.0001), but lower epididymal fat mass in DUhTP mice by about 20% (P < 0.0001) were observed. In SPF husbandry, body weight increased to a stronger extent in adult DUC mice (≈ 20%; P < 0.0001) than in DUhTP mice (≈ 8%; P = 0.001). The concentrations of IGF-1 and IGFBPs in the serum as well as the liver weights were similar in all experimental groups, indicating growth effects independent of the somatotropic axis. Under SPF conditions the litter size at birth increased in DUC mice (P < 0.001) but not in DUhTP mice. The differential effect of husbandry on body weights at day 21 and concentrations of triglycerides in the serum of our model were due to the different diets used in the semi-barrier and in the SPF facility. Our results demonstrate differential trait response to environmental factors resulting in partial phenotype conversion in our experimental system. The existence of conditional phenotypes as a result of genotype-environment interactions points to the importance of environmental factors in functional genome analysis.
@article{Brenmoehl7003,
author={Julia Brenmoehl, Christina Walz, Marion Spitschak, Elisa Wirthgen, Michael Walz, Martina Langhammer, Armin Tuchscherer, Ronald Naumann, Andreas Hoeflich},
title={Partial phenotype conversion and differential trait response to conditions of husbandry in mice.},
journal={Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology},
volume={188},
issue ={3},
pages={527--539},
year=2018
}

Lorenzo Duso, Christoph Zechner
Selected-node stochastic simulation algorithm.
J Chem Phys, 148(16) Art. No. 164108 (2018)
PubMed Source   

Stochastic simulations of biochemical networks are of vital importance for understanding complex dynamics in cells and tissues. However, existing methods to perform such simulations are associated with computational difficulties and addressing those remains a daunting challenge to the present. Here we introduce the selected-node stochastic simulation algorithm (snSSA), which allows us to exclusively simulate an arbitrary, selected subset of molecular species of a possibly large and complex reaction network. The algorithm is based on an analytical elimination of chemical species, thereby avoiding explicit simulation of the associated chemical events. These species are instead described continuously in terms of statistical moments derived from a stochastic filtering equation, resulting in a substantial speedup when compared to Gillespie's stochastic simulation algorithm (SSA). Moreover, we show that statistics obtained via snSSA profit from a variance reduction, which can significantly lower the number of Monte Carlo samples needed to achieve a certain performance. We demonstrate the algorithm using several biological case studies for which the simulation time could be reduced by orders of magnitude.
@article{Duso7118,
author={Lorenzo Duso, Christoph Zechner},
title={Selected-node stochastic simulation algorithm.},
journal={The Journal of chemical physics},
volume={148},
issue ={16},
pages={null--null},
year=2018
}

Máté Pálfy
The role of transcription factors in shaping the chromatin landscape and regulating the timing of zygotic genome activation in zebrafish
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2018)
 

@phdthesis{Pálfy7119,
author = {Máté Pálfy},
title={The role of transcription factors in shaping the chromatin landscape and regulating the timing of zygotic genome activation in zebrafish},
school = {Technische Universität Dresden},
year=2018,
address = {Dresden, Germany},
}

Akanksha Jain
Molecular, Cellular and Mechanical basis of Epithelial Morphogenesis during Tribolium Embryogenesis
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2018)
 

@phdthesis{Jain7123,
author = {Akanksha Jain},
title={Molecular, Cellular and Mechanical basis of Epithelial Morphogenesis during Tribolium Embryogenesis},
school = {Technische Universität Dresden},
year=2018,
address = {Dresden, Germany},
}

Celina Galles, Gastón M Prez, Sider Penkov, Sebastian Boland, Exequiel O J Porta, Silvia G Altabe, Guillermo R Labadie, Ulrike Schmidt, Hans-Joachim Knölker, Teymuras V. Kurzchalia, Diego Mendoza
Endocannabinoids in Caenorhabditis elegans are essential for the mobilization of cholesterol from internal reserves.
Sci Rep, 8(1) Art. No. 6398 (2018)
PubMed Source   

Proper cholesterol transport is crucial for the functionality of cells. In C. elegans, certain cholesterol derivatives called dafachronic acids (DAs) govern the entry into diapause. In their absence, worms form a developmentally arrested dauer larva. Thus, cholesterol transport to appropriate places for DA biosynthesis warrants the reproductive growth. Recently, we discovered a novel class of glycosphingolipids, PEGCs, required for cholesterol mobilization/transport from internal storage pools. Here, we identify other components involved in this process. We found that strains lacking polyunsaturated fatty acids (PUFAs) undergo increased dauer arrest when grown without cholesterol. This correlates with the depletion of the PUFA-derived endocannabinoids 2-arachidonoyl glycerol and anandamide. Feeding of these endocannabinoids inhibits dauer formation caused by PUFAs deficiency or impaired cholesterol trafficking (e.g. in Niemann-Pick C1 or DAF-7/TGF-β mutants). Moreover, in parallel to PEGCs, endocannabinoids abolish the arrest induced by cholesterol depletion. These findings reveal an unsuspected function of endocannabinoids in cholesterol trafficking regulation.
@article{Galles7113,
author={Celina Galles, Gastón M Prez, Sider Penkov, Sebastian Boland, Exequiel O J Porta, Silvia G Altabe, Guillermo R Labadie, Ulrike Schmidt, Hans-Joachim Knölker, Teymuras V. Kurzchalia, Diego Mendoza},
title={Endocannabinoids in Caenorhabditis elegans are essential for the mobilization of cholesterol from internal reserves.},
journal={Scientific reports},
volume={8},
issue ={1},
pages={null--null},
year=2018
}

Marija Matejcic
Coordination of tissue shape and size in the developing zebrafish neuroepithelium
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2018)
 

@phdthesis{Matejcic7124,
author = {Marija Matejcic},
title={Coordination of tissue shape and size in the developing zebrafish neuroepithelium},
school = {Technische Universität Dresden},
year=2018,
address = {Dresden, Germany},
}

Mengfei Gao, Riccardo Maraspini, Oliver Beutel, Amin Zehtabian, Britta Eickholt, Alf Honigmann, Helge Ewers
Expansion Stimulated Emission Depletion Microscopy (ExSTED).
ACS Nano, Art. No. doi: 10.1021/acsnano.8b00776 (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{Gao7116,
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={},
pages={1--1},
year=2018
}

Alvin Kuriakose Thomas, Robert Wieduwild, Ralf Zimmermann, Weilin Lin, Jens Friedrichs, Marc Bickle, Karim Fahmy, Carsten Werner, Yixin Zhang
Layer-by-Layer Assembly of Heparin and Peptide-Polyethylene Glycol Conjugates to Form Hybrid Nanothin Films of Biomatrices.
ACS Appl Mater Interfaces, 10(17) 14264-14270 (2018)
PubMed Source   

We investigated the utility of a heparin/peptide-polyethylene glycol conjugate system to build layer-by-layer (LbL) structures, to assemble tailored multilayer-biomatrices for cell culture. The LbL assembly balances the advantages of polyelectrolyte systems and protein-based systems. Human umbilical vein endothelial cells showed distinct responses to the film thickness and structure; the presence, density, and spatial arrangement of a cell adhesion ligand within the nanothin film; and the pretreatment of the film with morphogens. The LbL technique presents a versatile tool for modifying cell culture substrates with defined and diverse biochemical and structural features, for investigating cell-material interactions.
@article{Thomas7114,
author={Alvin Kuriakose Thomas, Robert Wieduwild, Ralf Zimmermann, Weilin Lin, Jens Friedrichs, Marc Bickle, Karim Fahmy, Carsten Werner, Yixin Zhang},
title={Layer-by-Layer Assembly of Heparin and Peptide-Polyethylene Glycol Conjugates to Form Hybrid Nanothin Films of Biomatrices.},
journal={ACS applied materials & interfaces},
volume={10},
issue ={17},
pages={14264--14270},
year=2018
}