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Ivan Ivanov, Rafael B. Lira, T-Y Dora Tang, Titus Franzmann, Adam Klosin, Lucas Caire da Silva, Anthony Hyman, Katharina Landfester, Reinhard Lipowsky, Kai Sundmacher, Rumiana Dimova
Directed Growth of Biomimetic Microcompartments
Adv. Biosys., Art. No. doi: 10.1002/adbi.201800314 (2019)
Source  

@article{Ivanov7328,
author={Ivan Ivanov, Rafael B. Lira, T-Y Dora Tang, Titus Franzmann, Adam Klosin, Lucas Caire da Silva, Anthony Hyman, Katharina Landfester, Reinhard Lipowsky, Kai Sundmacher, Rumiana Dimova},
title={Directed Growth of Biomimetic Microcompartments},
journal ={Advanced Biosystems},
volume={},
pages={null--null},
year=2019
}

Nikolai Hecker, Virag Sharma, Michael Hiller
Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores.
Proc Natl Acad Sci U.S.A., Art. No. doi: 10.1073/pnas.1818504116 (2019)
PubMed Source   

The repeated evolution of dietary specialization represents a hallmark of mammalian ecology. To detect genomic changes that are associated with dietary adaptations, we performed a systematic screen for convergent gene losses associated with an obligate herbivorous or carnivorous diet in 31 placental mammals. For herbivores, our screen discovered the repeated loss of the triglyceride lipase inhibitor PNLIPRP1, suggesting enhanced triglyceride digestion efficiency. Furthermore, several herbivores lost the pancreatic exocytosis factor SYCN, providing an explanation for continuous pancreatic zymogen secretion in these species. For carnivores, we discovered the repeated loss of the hormone-receptor pair INSL5-RXFP4 that regulates appetite and glucose homeostasis, which likely relates to irregular feeding patterns and constant gluconeogenesis. Furthermore, reflecting the reduced need to metabolize plant-derived xenobiotics, several carnivores lost the xenobiotic receptors NR1I3 and NR1I2 Finally, the carnivore-associated loss of the gastrointestinal host defense gene NOX1 could be related to a reduced gut microbiome diversity. By revealing convergent gene losses associated with differences in dietary composition, feeding patterns, and gut microbiomes, our study contributes to understanding how similar dietary specializations evolved repeatedly in mammals.
@article{Hecker7300,
author={Nikolai Hecker, Virag Sharma, Michael Hiller},
title={Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores.},
journal ={Proceedings of the National Academy of Sciences of the United States of America},
volume={},
pages={null--null},
year=2019
}

Frida W Lindberg, Till Korten, Anette Löfstrand, Mohammad A Rahman, Mariusz Graczyk, Alf Mansson, Heiner Linke, Ivan Maximov
Design and development of nanoimprint-enabled structures for molecular motor devices
Mater. Res. Express, 6(2) Art. No. 025057 (2019)
 

@article{Lindberg7307,
author={Frida W Lindberg, Till Korten, Anette Löfstrand, Mohammad A Rahman, Mariusz Graczyk, Alf Mansson, Heiner Linke, Ivan Maximov},
title={Design and development of nanoimprint-enabled structures for molecular motor devices},
journal ={Materials Research Express},
volume={6},
issue ={2},
pages={null--null},
year=2019
}

Elodie Prince, Benjamin Kroeger, Dragan Gligorov, Clive Wilson, Suzanne Eaton, François Karch, Marko Brankatschk, Robert K Maeda
Rab-mediated trafficking in the secondary cells of Drosophila male accessory glands and its role in fecundity.
Traffic, 20(2) 137-151 (2019)
PubMed Source   

The male seminal fluid contains factors that affect female post-mating behavior and physiology. In Drosophila, most of these factors are secreted by the two epithelial cell types that make up the male accessory gland: the main and secondary cells. Although secondary cells represent only ~4% of the cells of the accessory gland, their contribution to the male seminal fluid is essential for sustaining the female post-mating response. To better understand the function of the secondary cells, we investigated their molecular organization, particularly with respect to the intracellular membrane transport machinery. We determined that large vacuole-like structures found in the secondary cells are trafficking hubs labeled by Rab6, 7, 11 and 19. Furthermore, these organelles require Rab6 for their formation and many are essential in the process of creating the long-term postmating behavior of females. In order to better serve the intracellular membrane and protein trafficking communities, we have created a searchable, online, open-access imaging resource to display our complete findings regarding Rab localization in the accessory gland.
@article{Prince7290,
author={Elodie Prince, Benjamin Kroeger, Dragan Gligorov, Clive Wilson, Suzanne Eaton, François Karch, Marko Brankatschk, Robert K Maeda},
title={Rab-mediated trafficking in the secondary cells of Drosophila male accessory glands and its role in fecundity.},
journal ={Traffic (Copenhagen, Denmark)},
volume={20},
issue ={2},
pages={137--151},
year=2019
}

Ioannis Giannios, Ioannis Serafimidis, Vivian Anastasiou, Daniela Pezzolla, Mathias Lesche, Cordula Andree, Marc Bickle, Anthony Gavalas
Protein Methyltransferase Inhibition Decreases Endocrine Specification Through the Upregulation of Aldh1b1 Expression.
Stem Cells, Art. No. doi: 10.1002/stem.2979 (2019)
PubMed Source   

Understanding the mechanisms that promote the specification of pancreas progenitors and regulate their self-renewal and differentiation will help to maintain and expand pancreas progenitor cells derived from human pluripotent stem (hPS) cells. This will improve the efficiency of current differentiation protocols of hPS cells into β cells and bring such cells closer to clinical applications for the therapy of diabetes. Aldehyde dehydrogenase 1b1 (Aldh1b1) is a mitochondrial enzyme expressed specifically in progenitor cells during mouse pancreas development and we have shown that its functional inactivation leads to accelerated differentiation and deficient β cells. In this report, we aimed to identify small molecules inducers of Aldh1b1 expression taking advantage of a mouse embryonic stem (mES) cell Aldh1b1 lacZ reporter line and a pancreas differentiation protocol directing mES cells into pancreatic progenitors. We identified AMI-5, a protein methyltransferase inhibitor, as an Aldh1b1 inducer and showed that it can maintain Aldh1b1 expression in embryonic pancreas explants. This led to a selective reduction in endocrine specification. This effect was due to a downregulation of Ngn3 and it was mediated through Aldh1b1 since the effect was abolished in Aldh1b1 null pancreata. The findings implicated methyltransferase activity in the regulation of endocrine differentiation and showed that methyltransferases can act through specific regulators during pancreas differentiation. SIGNIFICANCE STATEMENT: Recent advances in the directed differentiation of human pluripotent stem cells into ß like cells have brought the prospect of diabetes cell therapy using this approach closer. However, the very large number of endocrine cells required for a single infusion to diabetic patients remains as a key challenge. Expansion of intermediate pancreas progenitors would address this issue. We have found that protein methyltransferase activity promotes endocrine specification through the dowregulation of Aldh1b1, a gene implicated in the maintenance of pancreatic progenitors and necessary for ß cell functionality in the mouse. These findings suggest that specific, reversible protein methyltransferase inhibitors may delay differentiation of pancreas progenitors. © AlphaMed Press 2019.
@article{Giannios7322,
author={Ioannis Giannios, Ioannis Serafimidis, Vivian Anastasiou, Daniela Pezzolla, Mathias Lesche, Cordula Andree, Marc Bickle, Anthony Gavalas},
title={Protein Methyltransferase Inhibition Decreases Endocrine Specification Through the Upregulation of Aldh1b1 Expression.},
journal ={Stem cells (Dayton, Ohio)},
volume={},
pages={null--null},
year=2019
}

Dimitrios Papadopoulos, Kassiani Skouloudaki, Ylva Engström, Lars Terenius, Rudolf Rigler, Christoph Zechner, Vladana Vukojević, Pavel Tomancak
Control of Hox transcription factor concentration and cell-to-cell variability by an auto-regulatory switch.
Development, 146(12) Art. No. dev168179 (2019)
PubMed Source   

The variability in transcription factor concentration among cells is an important developmental determinant, yet how variability is controlled remains poorly understood. Studies of variability have focused predominantly on monitoring mRNA production noise. Little information exists about transcription factor protein variability, as this requires the use of quantitative methods with single-molecule sensitivity. Using Fluorescence Correlation Spectroscopy (FCS), we have characterized the concentration and variability of 14 endogenously tagged TFs in live Drosophila imaginal discs. For the Hox TF Antennapedia, we investigated whether protein variability results from random stochastic events or is developmentally regulated. We found that Antennapedia transitioned from low concentration/high variability early, to high concentration/low variability later, in development. FCS and temporally resolved genetic studies uncovered that Antennapedia itself is necessary and sufficient to drive a developmental regulatory switch from auto-activation to auto-repression, thereby reducing variability. This switch is controlled by progressive changes in relative concentrations of preferentially activating and repressing Antennapedia isoforms, which bind chromatin with different affinities. Mathematical modeling demonstrated that the experimentally supported auto-regulatory circuit can explain the increase of Antennapedia concentration and suppression of variability over time.
@article{Papadopoulos7275,
author={Dimitrios Papadopoulos, Kassiani Skouloudaki, Ylva Engström, Lars Terenius, Rudolf Rigler, Christoph Zechner, Vladana Vukojević, Pavel Tomancak},
title={Control of Hox transcription factor concentration and cell-to-cell variability by an auto-regulatory switch.},
journal ={Development (Cambridge, England)},
volume={146},
issue ={12},
pages={null--null},
year=2019
}

Simon Alberti, Amy Gladfelter, Tanja Mittag
Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates.
Cell, 176(3) 419-434 (2019)
PubMed Source   

Evidence is now mounting that liquid-liquid phase separation (LLPS) underlies the formation of membraneless compartments in cells. This realization has motivated major efforts to delineate the function of such biomolecular condensates in normal cells and their roles in contexts ranging from development to age-related disease. There is great interest in understanding the underlying biophysical principles and the specific properties of biological condensates with the goal of bringing insights into a wide range of biological processes and systems. The explosion of physiological and pathological contexts involving LLPS requires clear standards for their study. Here, we propose guidelines for rigorous experimental characterization of LLPS processes in vitro and in cells, discuss the caveats of common experimental approaches, and point out experimental and theoretical gaps in the field.
@article{Alberti7315,
author={Simon Alberti, Amy Gladfelter, Tanja Mittag},
title={Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates.},
journal ={Cell},
volume={176},
issue ={3},
pages={419--434},
year=2019
}

Cem Emre Akbas, Vladimir Ulman, Martin Maska, Florian Jug, Michal Kozubek
Automatic Fusion of Segmentation and Tracking Labels
In: Computer Vision – ECCV 2018 Workshops : Munich, Germany, September 8-14, 2018, Proceedings, Part VI (2019)(Eds.) Laura Leal-Taixé Lecture Notes in Computer Science ; 11134, Cham, Springer International Publishing (2019), 446-454
Source   

Labeled training images of high quality are required for developing well-working analysis pipelines. This is, of course, also true for biological image data, where such labels are usually hard to get. We distinguish human labels (gold corpora) and labels generated by computer algorithms (silver corpora). A naturally arising problem is to merge multiple corpora into larger bodies of labeled training datasets. While fusion of labels in static images is already an established field, dealing with labels in time-lapse image data remains to be explored. Obtaining a gold corpus for segmentation is usually very time-consuming and hence expensive. For this reason, gold corpora for object tracking often use object detection markers instead of dense segmentations. If dense segmentations of tracked objects are desired later on, an automatic merge of the detection-based gold corpus with (silver) corpora of the individual time points for segmentation will be necessary. Here we present such an automatic merging system and demonstrate its utility on corpora from the Cell Tracking Challenge. We additionally release all label fusion algorithms as freely available and open plugins for Fiji (https://github.com/xulman/CTC-FijiPlugins).
@proceedings{Akbas7320,
title = {Automatic Fusion of Segmentation and Tracking Labels},
year = 2019,
editor = {Cem Emre Akbas, Vladimir Ulman, Martin Maska, Florian Jug, Michal Kozubek},
volume = {Computer Vision – ECCV 2018 Workshops : Munich, Germany, September 8-14, 2018, Proceedings, Part VI },
series = {Lecture Notes in Computer Science ; 11134},
publisher = {Springer International Publishing}
}

Mark S Springer, Christopher A Emerling, John Gatesy, Jason Randall, Matthew A Collin, Nikolai Hecker, Michael Hiller, Frédéric Delsuc
Odontogenic ameloblast-associated (ODAM) is inactivated in toothless/enamelless placental mammals and toothed whales.
BMC Evol Biol, 19(1) Art. No. 31 (2019)
PubMed Source   

The gene for odontogenic ameloblast-associated (ODAM) is a member of the secretory calcium-binding phosphoprotein gene family. ODAM is primarily expressed in dental tissues including the enamel organ and the junctional epithelium, and may also have pleiotropic functions that are unrelated to teeth. Here, we leverage the power of natural selection to test competing hypotheses that ODAM is tooth-specific versus pleiotropic. Specifically, we compiled and screened complete protein-coding sequences, plus sequences for flanking intronic regions, for ODAM in 165 placental mammals to determine if this gene contains inactivating mutations in lineages that either lack teeth (baleen whales, pangolins, anteaters) or lack enamel on their teeth (aardvarks, sloths, armadillos), as would be expected if the only essential functions of ODAM are related to tooth development and the adhesion of the gingival junctional epithelium to the enamel tooth surface.
@article{Springer7323,
author={Mark S Springer, Christopher A Emerling, John Gatesy, Jason Randall, Matthew A Collin, Nikolai Hecker, Michael Hiller, Frédéric Delsuc},
title={Odontogenic ameloblast-associated (ODAM) is inactivated in toothless/enamelless placental mammals and toothed whales.},
journal ={BMC evolutionary biology},
volume={19},
issue ={1},
pages={null--null},
year=2019
}

Kassiani Skouloudaki, Dimitrios Papadopoulos, Pavel Tomancak, Elisabeth Knust
The apical protein Apnoia interacts with Crumbs to regulate tracheal growth and inflation.
PLoS Genet, 15(1) Art. No. e1007852 (2019)
PubMed Source   

Most organs of multicellular organisms are built from epithelial tubes. To exert their functions, tubes rely on apico-basal polarity, on junctions, which form a barrier to separate the inside from the outside, and on a proper lumen, required for gas or liquid transport. Here we identify apnoia (apn), a novel Drosophila gene required for tracheal tube elongation and lumen stability at larval stages. Larvae lacking Apn show abnormal tracheal inflation and twisted airway tubes, but no obvious defects in early steps of tracheal maturation. apn encodes a transmembrane protein, primarily expressed in the tracheae, which exerts its function by controlling the localization of Crumbs (Crb), an evolutionarily conserved apical determinant. Apn physically interacts with Crb to control its localization and maintenance at the apical membrane of developing airways. In apn mutant tracheal cells, Crb fails to localize apically and is trapped in retromer-positive vesicles. Consistent with the role of Crb in apical membrane growth, RNAi-mediated knockdown of Crb results in decreased apical surface growth of tracheal cells and impaired axial elongation of the dorsal trunk. We conclude that Apn is a novel regulator of tracheal tube expansion in larval tracheae, the function of which is mediated by Crb.
@article{Skouloudaki7281,
author={Kassiani Skouloudaki, Dimitrios Papadopoulos, Pavel Tomancak, Elisabeth Knust},
title={The apical protein Apnoia interacts with Crumbs to regulate tracheal growth and inflation.},
journal ={PLoS genetics},
volume={15},
issue ={1},
pages={null--null},
year=2019
}