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Björn Drobot, Juan M Iglesias-Artola, Kristian Le Vay, Viktoria Mayr, Mrityunjoy Kar, Moritz Kreysing, Hannes Mutschler, T-Y Dora Tang
Compartmentalised RNA catalysis in membrane-free coacervate protocells.
Nat Commun, 9(1) Art. No. 3643 (2018)
Supplementary Website PubMed Source   

Phase separation of mixtures of oppositely charged polymers provides a simple and direct route to compartmentalisation via complex coacervation, which may have been important for driving primitive reactions as part of the RNA world hypothesis. However, to date, RNA catalysis has not been reconciled with coacervation. Here we demonstrate that RNA catalysis is viable within coacervate microdroplets and further show that these membrane-free droplets can selectively retain longer length RNAs while permitting transfer of lower molecular weight oligonucleotides.
@article{Drobot7196,
author={Björn Drobot, Juan M Iglesias-Artola, Kristian Le Vay, Viktoria Mayr, Mrityunjoy Kar, Moritz Kreysing, Hannes Mutschler, T-Y Dora Tang},
title={Compartmentalised RNA catalysis in membrane-free coacervate protocells.},
journal={Nature communications},
volume={9},
issue ={1},
pages={null--null},
year=2018
}

J Gray Camp, Damian Wollny, Barbara Treutlein
Single-cell genomics to guide human stem cell and tissue engineering.
Nat Methods, 15(9) 661-667 (2018)
PubMed Source   

To understand human development and disease, as well as to regenerate damaged tissues, scientists are working to engineer certain cell types in vitro and to create 3D microenvironments in which cells behave physiologically. Single-cell genomics (SCG) technologies are being applied to primary human organs and to engineered cells and tissues to generate atlases of cell diversity in these systems at unparalleled resolution. Moving beyond atlases, SCG methods are powerful tools for gaining insight into the engineering and disease process. Here we discuss how scientists can use single-cell sequencing to optimize human cell and tissue engineering by measuring precision, detecting inefficiencies, and assessing accuracy. We also provide a perspective on how emerging SCG methods can be used to reverse-engineer human cells and tissues and unravel disease mechanisms.
@article{Camp7215,
author={J Gray Camp, Damian Wollny, Barbara Treutlein},
title={Single-cell genomics to guide human stem cell and tissue engineering.},
journal={Nature methods},
volume={15},
issue ={9},
pages={661--667},
year=2018
}

Matthäus Mittasch
Light-driven intracellular flow perturbations reveal physical principles of cell organization
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2018)
 

@phdthesis{Mittasch7214,
author = {Matthäus Mittasch},
title={Light-driven intracellular flow perturbations reveal physical principles of cell organization},
school = {Technische Universität Dresden},
year=2018,
address = {Dresden, Germany},
}

Katherine S. Long, Ben Newland, Marta Florio, Nereo Kalebic, Barbara Langen, Anna Kolterer, Pauline Wimberger, Wieland Huttner
Extracellular Matrix Components HAPLN1, Lumican, and Collagen I Cause Hyaluronic Acid-Dependent Folding of the Developing Human Neocortex.
Neuron, 99(4) 702-719 (2018)
PubMed Source   

Neocortical expansion, thought to underlie the cognitive traits unique to humans, is accompanied by cortical folding. This folding starts around gestational week (GW) 20, but what causes it remains largely unknown. Extracellular matrix (ECM) has been previously implicated in neocortical expansion and here we investigate the potential role of ECM in the formation of neocortical folds. We focus on three specific ECM components localized in the human fetal cortical plate (CP): hyaluronan and proteoglycan link protein 1 (HAPLN1), lumican and collagen I (collectively, HLC). Addition of HLC to cultures of human fetal neocortex (11-22 GW) caused local changes in tissue stiffness, induced CP folding, increased CP hyaluronic acid (HA), and required the HA-receptor CD168 and downstream ERK signaling. Importantly, loss of HA reduced HLC-induced and 22 GW physiological nascent folds. This was altered in samples with neurodevelopmental disorders, indicating it may be a useful system to study such disorders.
@article{Long7198,
author={Katherine S. Long, Ben Newland, Marta Florio, Nereo Kalebic, Barbara Langen, Anna Kolterer, Pauline Wimberger, Wieland Huttner},
title={Extracellular Matrix Components HAPLN1, Lumican, and Collagen I Cause Hyaluronic Acid-Dependent Folding of the Developing Human Neocortex.},
journal={Neuron},
volume={99},
issue ={4},
pages={702--719},
year=2018
}

Oskar Knittelfelder, Sofia Traikov, Olga Vvedenskaya, Andrea Schuhmann, Sandra Segeletz, Anna Shevchenko, Andrej Shevchenko
Shotgun Lipidomics Combined with Laser Capture Microdissection: A Tool To Analyze Histological Zones in Cryosections of Tissues.
Anal Chem, 90(16) 9868-9878 (2018)
PubMed Source   

Shotgun analysis provides a quantitative snapshot of the lipidome composition of cells, tissues, or model organisms; however, it does not elucidate the spatial distribution of lipids. Here we demonstrate that shotgun analysis could quantify low-picomole amounts of lipids isolated by laser capture microdissection (LCM) of hundred micrometer-sized histological zones visualized at the cryosections of tissues. We identified metabolically distinct periportal (pp) and pericentral (pc) zones by immunostaining of 20 μm thick cryosections of a healthy mouse liver. LCM was used to ablate, catapult, and collect the tissue material from 10 to 20 individual zones covering a total area of 0.3-0.5 mm2 and containing ca. 500 cells. Top-down shotgun profiling relying upon computational stitching of 61 targeted selective ion monitoring ( t-SIM) spectra quantified more than 200 lipid species from 17 lipid classes including glycero- and glycerophospholipids, sphingolipids, cholesterol esters, and cholesterol. Shotgun LCM revealed the overall commonality of the full lipidome composition of pp and pc zones along with significant ( p < 0.001) difference in the relative abundance of 13 lipid species. Follow-up proteomics analyses of pellets recovered from an aqueous phase saved after the lipid extraction identified 13 known and 7 new protein markers exclusively present in pp or in pc zones and independently validated the specificity of their visualization, isolation, and histological assignment.
@article{Knittelfelder7190,
author={Oskar Knittelfelder, Sofia Traikov, Olga Vvedenskaya, Andrea Schuhmann, Sandra Segeletz, Anna Shevchenko, Andrej Shevchenko},
title={Shotgun Lipidomics Combined with Laser Capture Microdissection: A Tool To Analyze Histological Zones in Cryosections of Tissues.},
journal={Analytical chemistry},
volume={90},
issue ={16},
pages={9868--9878},
year=2018
}

Bo Burla, Makoto Arita, Makoto Arita, Anne K Bendt, Amaury Cazenave-Gassiot, Edward A Dennis, Kim Ekroos, Xianlin Han, Kazutaka Ikeda, Gerhard Liebisch, Michelle I Lin, Tze Ping Loh, Peter J Meikle, Matej Orešič, Oswald Quehenberger, Andrej Shevchenko, Federico Torta, Michael J O Wakelam, Craig E Wheelock, Markus R Wenk
MS-based lipidomics of human blood plasma - a community-initiated position paper to develop accepted guidelines.
J Lipid Res, Art. No. doi: 10.1194/jlr.S087163 (2018)
PubMed Source   

Human blood is a self-regenerating, lipid-rich biologic fluid that is routinely collected in hospital settings. The inventory of lipid molecules found in blood plasma (plasma lipidome) offers insights into individual metabolism and physiology in health and disease. Disturbances in lipid metabolism also occur in conditions that are not directly linked to lipid metabolism; therefore, plasma lipidomics based on mass spectrometry (MS) is an emerging tool in an array of clinical diagnostics and disease management. However, challenges exist in the translation of such lipidomic data to clinical applications. These relate to the reproducibility, accuracy, and precision of lipid quantitation, study design, sample handling, and data sharing. This position paper emerged from a workshop that initiated a community-led process to elaborate and define a set of generally accepted guidelines for quantitative MS-based lipidomics of blood plasma or serum, with harmonization of data acquired on different instrumentation platforms in independent laboratories across laboratories as an ultimate goal. We hope that other fields may benefit from and follow such a precedent.
@article{Burla7205,
author={Bo Burla, Makoto Arita, Makoto Arita, Anne K Bendt, Amaury Cazenave-Gassiot, Edward A Dennis, Kim Ekroos, Xianlin Han, Kazutaka Ikeda, Gerhard Liebisch, Michelle I Lin, Tze Ping Loh, Peter J Meikle, Matej Orešič, Oswald Quehenberger, Andrej Shevchenko, Federico Torta, Michael J O Wakelam, Craig E Wheelock, Markus R Wenk},
title={MS-based lipidomics of human blood plasma - a community-initiated position paper to develop accepted guidelines.},
journal={Journal of lipid research},
volume={},
pages={1--1},
year=2018
}

Katrin Daniel, Jaroslav Icha, Cindy Horenburg, Doris Müller, Caren Norden, Jorg Mansfeld
Conditional control of fluorescent protein degradation by an auxin-dependent nanobody
Nat Commun, Art. No. doi: 10.1038/s41467-018-05855-5 (2018)
 

@article{Daniel7197,
author={Katrin Daniel, Jaroslav Icha, Cindy Horenburg, Doris Müller, Caren Norden, Jorg Mansfeld},
title={Conditional control of fluorescent protein degradation by an auxin-dependent nanobody },
journal={Nature communications},
volume={},
pages={1--1},
year=2018
}

Elena Bonzón-Kulichenko, Eduardo Moltó, Cristina Pintado, Alejandro Fernández, Carmen Arribas, Dominik Schwudke, Nilda Gallardo, Andrej Shevchenko, Antonio Andrés
Changes in Visceral Adipose Tissue Plasma Membrane Lipid Composition in Old Rats Are Associated With Adipocyte Hypertrophy With Aging.
J Gerontol A Biol Sci Med Sci, 73(9) 1139-1146 (2018)
PubMed Source   

Increased adiposity, through adipocyte hypertrophy, and/or hyperplasia, characterizes aging and obesity. Both are leptin-resistant states, associated with disturbed lipid metabolism, reduced insulin sensitivity and inflammation. Nevertheless, fat tissue dysfunction appears earlier in obesity than in normal aging. In contrast, lipodystrophy is accompanied by diabetes, and improving the fat cell capacity to expand rescues the diabetic phenotype. Fat tissue dysfunction is extensively studied in the diet-induced obesity, but remains relatively neglected in the aging-associated obesity. In the Wistar rat, as occurs in humans, early or middle aging is accompanied by an increase in adiposity. Using this experimental model, we describe the molecular mechanisms contributing to the white adipose tissue (WAT) hypertrophy. WAT from middle-old age rats is characterized by decreased basal lipogenesis and lipolysis, increased esterification, as demonstrated by the higher TAG and cholesterol content in visceral WAT, and the maintenance of total ceramide levels within normal values. In addition, we describe alterations in the adipose tissue plasma membrane lipid composition, as increased total ether-phosphatidylcholine, sphingomyelin, and free cholesterol levels that favor an enlarged fat cell size with aging. All these metabolic changes may be regarded as a survival advantage that prevents the aged rats from becoming overtly diabetic.
@article{Bonzón-Kulichenko7117,
author={Elena Bonzón-Kulichenko, Eduardo Moltó, Cristina Pintado, Alejandro Fernández, Carmen Arribas, Dominik Schwudke, Nilda Gallardo, Andrej Shevchenko, Antonio Andrés},
title={Changes in Visceral Adipose Tissue Plasma Membrane Lipid Composition in Old Rats Are Associated With Adipocyte Hypertrophy With Aging.},
journal={The journals of gerontology. Series A, Biological sciences and medical sciences},
volume={73},
issue ={9},
pages={1139--1146},
year=2018
}

Marija Matejčić, Guillaume Salbreux, Caren Norden
A non-cell-autonomous actin redistribution enables isotropic retinal growth.
PLoS Biol, 16(8) Art. No. 2006018 (2018)
PubMed Source   

Tissue shape is often established early in development and needs to be scaled isotropically during growth. However, the cellular contributors and ways by which cells interact tissue-wide to enable coordinated isotropic tissue scaling are not yet understood. Here, we follow cell and tissue shape changes in the zebrafish retinal neuroepithelium, which forms a cup with a smooth surface early in development and maintains this architecture as it grows. By combining 3D analysis and theory, we show how a global increase in cell height can maintain tissue shape during growth. Timely cell height increase occurs concurrently with a non-cell-autonomous actin redistribution. Blocking actin redistribution and cell height increase perturbs isotropic scaling and leads to disturbed, folded tissue shape. Taken together, our data show how global changes in cell shape enable isotropic growth of the developing retinal neuroepithelium, a concept that could also apply to other systems.
@article{Matejčić7193,
author={Marija Matejčić, Guillaume Salbreux, Caren Norden},
title={A non-cell-autonomous actin redistribution enables isotropic retinal growth.},
journal={PLoS biology},
volume={16},
issue ={8},
pages={null--null},
year=2018
}

Neil O Carragher, Filippo Piccinini, Anna Tesei, O Joseph Trask Jr, Marc Bickle, Peter Horvath
Concerns, challenges and promises of high-content analysis of 3D cellular models.
Nat Rev Drug Discov, 17(8) Art. No. 606 (2018)
PubMed Source  

@article{Carragher7192,
author={Neil O Carragher, Filippo Piccinini, Anna Tesei, O Joseph Trask Jr, Marc Bickle, Peter Horvath},
title={Concerns, challenges and promises of high-content analysis of 3D cellular models.},
journal={Nature reviews. Drug discovery},
volume={17},
issue ={8},
pages={null--null},
year=2018
}