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Antje Janosch, Carolin Kaffka, Marc Bickle
Unbiased Phenotype Detection Using Negative Controls
Pending, 1-1 (2018)
Supplementary Website  

@article{Janosch7217,
author={Antje Janosch, Carolin Kaffka, Marc Bickle},
title={Unbiased Phenotype Detection Using Negative Controls},
journal ={Pending},
volume={},
pages={1--1},
year=2018
}

David Jebb, Michael Hiller
Recurrent loss of HMGCS2 shows that ketogenesis is not essential for the evolution of large mammalian brains
Elife, in press 1-1 (2018)
 

@article{Jebb7221,
author={David Jebb, Michael Hiller},
title={Recurrent loss of HMGCS2 shows that ketogenesis is not essential for the evolution of large mammalian brains},
journal ={eLife},
volume={in press},
pages={1--1},
year=2018
}

Madina Karimova, Oliver Baker, Aylin Camgoz, Ronald Naumann, Frank Buchholz, Konstantinos Anastassiadis
A single reporter mouse line for Vika, Flp, Dre, and Cre-recombination.
Sci Rep, 8(1) Art. No. 14453 (2018)
PubMed Source   

Site-specific recombinases (SSR) are utilized as important genome engineering tools to precisely modify the genome of mice and other model organisms. Reporter mice that mark cells that at any given time had expressed the enzyme are frequently used for lineage tracing and to characterize newly generated mice expressing a recombinase from a chosen promoter. With increasing sophistication of genome alteration strategies, the demand for novel SSR systems that efficiently and specifically recombine their targets is rising and several SSR-systems are now used in combination to address complex biological questions in vivo. Generation of reporter mice for each one of these recombinases is cumbersome and increases the number of mouse lines that need to be maintained in animal facilities. Here we present a multi-reporter mouse line for loci-of-recombination (X) (MuX) that streamlines the characterization of mice expressing prominent recombinases. MuX mice constitutively express nuclear green fluorescent protein after recombination by either Cre, Flp, Dre or Vika recombinase, rationalizing the number of animal lines that need to be maintained. We also pioneer the use of the Vika/vox system in mice, illustrating its high efficacy and specificity, thereby facilitating future designs of sophisticated recombinase-based in vivo genome engineering strategies.
@article{Karimova7224,
author={Madina Karimova, Oliver Baker, Aylin Camgoz, Ronald Naumann, Frank Buchholz, Konstantinos Anastassiadis},
title={A single reporter mouse line for Vika, Flp, Dre, and Cre-recombination.},
journal ={Scientific reports},
volume={8},
issue ={1},
pages={null--null},
year=2018
}

Björn Langer, Juliana Roscito, Michael Hiller
REforge associates transcription factor binding site divergence in regulatory elements with phenotypic differences between species.
Mol Biol Evol, Art. No. doi: 10.1093/molbev/msy187 (2018)
  PubMed Source   

Elucidating the genomic determinants of morphological differences between species is key to understanding how morphological diversity evolved. While differences in cis-regulatory elements are an important genetic source for morphological evolution, it remains challenging to identify regulatory elements involved in phenotypic differences. Here, we present Regulatory Element forward genomics (REforge), a computational approach that detects associations between transcription factor binding site divergence in putative regulatory elements and phenotypic differences between species. By simulating regulatory element evolution in silico, we show that this approach has substantial power to detect such associations. To validate REforge on real data, we used known binding motifs for eye-related transcription factors and identified significant binding site divergence in vision-impaired subterranean mammals in 1% of all conserved non-coding elements. We show that these genomic regions are significantly enriched in regulatory elements that are specifically active in mouse eye tissues, and that several of them are located near genes, which are required for eye development and photoreceptor function and are implicated in human eye disorders. Thus, our genome-wide screen detects widespread divergence of eye-regulatory elements and highlights regulatory regions that likely contributed to eye degeneration in subterranean mammals. REforge has broad applicability to detect regulatory elements that could be involved in many other phenotypes, which will help to reveal the genomic basis of morphological diversity.
@article{Langer7220,
author={Björn Langer, Juliana Roscito, Michael Hiller},
title={REforge associates transcription factor binding site divergence in regulatory elements with phenotypic differences between species.},
journal ={Molecular biology and evolution},
volume={},
pages={1--1},
year=2018
}

Jun Hoe Lee, Kevin M Lewis, Timothy W Moural, Bogdan Kirilenko, Barbara Borgonovo, Gisa Prange, Manfred Koessl, Stefan Huggenberger, ChulHee Kang, Michael Hiller
Molecular parallelism in fast-twitch muscle proteins in echolocating mammals
Sci Adv, 4(9) Art. No. eaat9660 (2018)
  Source  

@article{Lee7203,
author={Jun Hoe Lee, Kevin M Lewis, Timothy W Moural, Bogdan Kirilenko, Barbara Borgonovo, Gisa Prange, Manfred Koessl, Stefan Huggenberger, ChulHee Kang, Michael Hiller},
title={Molecular parallelism in fast-twitch muscle proteins in echolocating mammals},
journal ={Science Advances},
volume={4},
issue ={9},
pages={null--null},
year=2018
}

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
}