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Mohammad A Rahman, Cordula Reuther, Frida W Lindberg, Martina Mengoni, Aseem Salhotra, Georg Heldt, Heiner Linke, Stefan Diez, Alf Månsson
Regeneration of Assembled, Molecular-Motor-Based Bionanodevices.
Nano Lett, 19(10) 7155-7163 (2019)
PubMed Source   

The guided gliding of cytoskeletal filaments, driven by biomolecular motors on nano/microstructured chips, enables novel applications in biosensing and biocomputation. However, expensive and time-consuming chip production hampers the developments. It is therefore important to establish protocols to regenerate the chips, preferably without the need to dismantle the assembled microfluidic devices which contain the structured chips. We here describe a novel method toward this end. Specifically, we use the small, nonselective proteolytic enzyme, proteinase K to cleave all surface-adsorbed proteins, including myosin and kinesin motors. Subsequently, we apply a detergent (5% SDS or 0.05% Triton X100) to remove the protein remnants. After this procedure, fresh motor proteins and filaments can be added for new experiments. Both, silanized glass surfaces for actin-myosin motility and pure glass surfaces for microtubule-kinesin motility were repeatedly regenerated using this approach. Moreover, we demonstrate the applicability of the method for the regeneration of nano/microstructured silicon-based chips with selectively functionalized areas for supporting or suppressing gliding motility for both motor systems. The results substantiate the versatility and a promising broad use of the method for regenerating a wide range of protein-based nano/microdevices.
@article{Rahman7517,
author={Mohammad A Rahman, Cordula Reuther, Frida W Lindberg, Martina Mengoni, Aseem Salhotra, Georg Heldt, Heiner Linke, Stefan Diez, Alf Månsson},
title={Regeneration of Assembled, Molecular-Motor-Based Bionanodevices.},
journal ={Nano letters},
volume={19},
issue ={10},
pages={7155--7163},
year=2019
}

Iskra Yanakieva, Anna Erzberger, Marija Matejčić, Carl D. Modes, Caren Norden
Cell and tissue morphology determine actin-dependent nuclear migration mechanisms in neuroepithelia.
J Cell Biol, 218(10) 3272-3289 (2019)
PubMed Source   

Correct nuclear position is crucial for cellular function and tissue development. Depending on cell context, however, the cytoskeletal elements responsible for nuclear positioning vary. While these cytoskeletal mechanisms have been intensely studied in single cells, how nuclear positioning is linked to tissue morphology is less clear. Here, we compare apical nuclear positioning in zebrafish neuroepithelia. We find that kinetics and actin-dependent mechanisms of nuclear positioning vary in tissues of different morphology. In straight neuroepithelia, nuclear positioning is controlled by Rho-ROCK-dependent myosin contractility. In contrast, in basally constricted neuroepithelia, a novel formin-dependent pushing mechanism is found for which we propose a proof-of-principle force generation theory. Overall, our data suggest that correct nuclear positioning is ensured by the adaptability of the cytoskeleton to cell and tissue shape. This in turn leads to robust epithelial maturation across geometries. The conclusion that different nuclear positioning mechanisms are favored in tissues of different morphology highlights the importance of developmental context for the execution of intracellular processes.
@article{Yanakieva7484,
author={Iskra Yanakieva, Anna Erzberger, Marija Matejčić, Carl D. Modes, Caren Norden},
title={Cell and tissue morphology determine actin-dependent nuclear migration mechanisms in neuroepithelia.},
journal ={The Journal of cell biology},
volume={218},
issue ={10},
pages={3272--3289},
year=2019
}

Juliana G. Roscito, Michael Hiller
Methods to Detect and Associate Divergence in Cis-Regulatory Elements to Phenotypic Divergence.
In: Evolution, Origin of Life, Concepts and Methods . (Eds.) Pierre Pontarotti,Cham,Springer International Publishing (2019),113-134 Ch. 6
Source   

Understanding which genomic changes are responsible for morphological differences between species is a long-standing question in biology. While evolutionary theory predicts that morphology largely evolves by changing expression of important developmental genes, finding the underlying regulatory mutations is inherently difficult. Here, we discuss how the integration of comparative and functional genomics has provided valuable insights into the regulatory changes involved in morphological changes. By comparing genomes of species exhibiting differences in a morphological trait, comparative genomic methods enable the systematic detection of regulatory elements with divergence in sequence or transcription factor binding sites. To narrow this set of diverged elements down to those that likely contribute to differences in the trait of interest, one can leverage knowledge about gene function to assess which elements are associated with genes known to control the development of this trait. In addition, functional genomics can further prioritize diverged genomic regions based on overlap with experimentally determined regulatory elements that are active in tissues relevant for the trait. Further experiments can then evaluate whether sequence or binding site divergence translates into regulatory differences and affects the development of the trait. Thus, combining comparative and functional genomic approaches provide a widely applicable strategy to reveal regulatory changes contributing to morphological differences, which will enhance our understanding of how nature’s spectacular phenotypic diversity evolved.

Hannes Mutschler, Tom Robinson, T-Y Dora Tang, Seraphine Wegner
Special Issue on Bottom-Up Synthetic Biology.
Chembiochem, Art. No. doi: 10.1002/cbic.201900507 (2019)
PubMed Source   

Bottom-up synthetic biology uses both biological and artificial chemical building blocks to create biomimetic systems, including artificial cells. Existing and new technologies such as microfluidics are being developed and applied to the assembly processes. In this special issue, experts present and review the latest progress in this rapidly expanding and diverse field.
@article{Mutschler7518,
author={Hannes Mutschler, Tom Robinson, T-Y Dora Tang, Seraphine Wegner},
title={Special Issue on Bottom-Up Synthetic Biology.},
journal ={Chembiochem : a European journal of chemical biology},
volume={},
pages={null--null},
year=2019
}

Aaron M Wenger, Paul Peluso, William J Rowell, Pi-Chuan Chang, Richard J Hall, Gregory T Concepcion, Jana Ebler, Arkarachai Fungtammasan, Alexey Kolesnikov, Nathan D Olson, Armin Töpfer, Michael Alonge, Medhat Mahmoud, Yufeng Qian, Chen-Shan Chin, Adam M Phillippy, Michael C Schatz, Gene Myers, Mark A DePristo, Jue Ruan, Tobias Marschall, Fritz J Sedlazeck, Justin M Zook, Heng Li, Sergey Koren, Andrew Carroll, David R Rank, Michael W Hunkapiller
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
Nat Biotechnol, 37(10) 1155-1162 (2019)
PubMed Source   

The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5 kilobases (kb). We applied our approach to sequence the well-characterized human HG002/NA24385 genome and obtained precision and recall rates of at least 99.91% for single-nucleotide variants (SNVs), 95.98% for insertions and deletions <50 bp (indels) and 95.99% for structural variants. Our CCS method matches or exceeds the ability of short-read sequencing to detect small variants and structural variants. We estimate that 2,434 discordances are correctable mistakes in the 'genome in a bottle' (GIAB) benchmark set. Nearly all (99.64%) variants can be phased into haplotypes, further improving variant detection. De novo genome assembly using CCS reads alone produced a contiguous and accurate genome with a contig N50 of >15 megabases (Mb) and concordance of 99.997%, substantially outperforming assembly with less-accurate long reads.
@article{Wenger7504,
author={Aaron M Wenger, Paul Peluso, William J Rowell, Pi-Chuan Chang, Richard J Hall, Gregory T Concepcion, Jana Ebler, Arkarachai Fungtammasan, Alexey Kolesnikov, Nathan D Olson, Armin Töpfer, Michael Alonge, Medhat Mahmoud, Yufeng Qian, Chen-Shan Chin, Adam M Phillippy, Michael C Schatz, Gene Myers, Mark A DePristo, Jue Ruan, Tobias Marschall, Fritz J Sedlazeck, Justin M Zook, Heng Li, Sergey Koren, Andrew Carroll, David R Rank, Michael W Hunkapiller},
title={Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.},
journal ={Nature biotechnology},
volume={37},
issue ={10},
pages={1155--1162},
year=2019
}

Yuko Sato, Lennart Hilbert, Haruka Oda, Yinan Wan, John M Heddleston, Teng-Leong Chew, Vasily Zaburdaev, Philipp Keller, Timothee Lionnet, Nadine Vastenhouw, Hiroshi Kimura
Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live-cell analysis.
Development, 146(19) Art. No. dev179127 (2019)
PubMed Source   

Histone post-translational modifications are key gene expression regulators, but their rapid dynamics during development remain difficult to capture. We applied a Fab-based live endogenous modification labeling technique to monitor the changes in histone modification levels during zygotic genome activation (ZGA) in living zebrafish embryos. Among various histone modifications, H3 Lys27 acetylation (H3K27ac) exhibited most drastic changes, accumulating in two nuclear foci in the 64- to 1k-cell-stage embryos. The elongating form of RNA polymerase II, which is phosphorylated at Ser2 in heptad repeats within the C-terminal domain (RNAP2 Ser2ph), and miR-430 transcripts were also concentrated in foci closely associated with H3K27ac. When treated with α-amanitin to inhibit transcription or JQ-1 to inhibit binding of acetyl-reader proteins, H3K27ac foci still appeared but RNAP2 Ser2ph and miR-430 morpholino were not concentrated in foci, suggesting that H3K27ac precedes active transcription during ZGA. We anticipate that the method presented here could be applied to a variety of developmental processes in any model and non-model organisms.
@article{Sato7520,
author={Yuko Sato, Lennart Hilbert, Haruka Oda, Yinan Wan, John M Heddleston, Teng-Leong Chew, Vasily Zaburdaev, Philipp Keller, Timothee Lionnet, Nadine Vastenhouw, Hiroshi Kimura},
title={Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live-cell analysis.},
journal ={Development (Cambridge, England)},
volume={146},
issue ={19},
pages={null--null},
year=2019
}

Rubina Tabassum, Joel T Rämö, Pietari Ripatti, Jukka T Koskela, Mitja Kurki, Juha Karjalainen, Priit Palta, Shabbeer Hassan, Javier Nunez-Fontarnau, Tuomo T J Kiiskinen, Sanni Söderlund, Niina Matikainen, Mathias J. Gerl, Michal Surma, Christian Klose, Nathan O Stitziel, Hannele Laivuori, Aki S Havulinna, Susan K Service, Veikko Salomaa, Matti Pirinen, Matti null, M Jauhiainen, Mark J Daly, Nelson B Freimer, Aarno Palotie, Marja-Riitta Taskinen, Kai Simons, Samuli Ripatti
Genetic architecture of human plasma lipidome and its link to cardiovascular disease.
Nat Commun, 10(1) Art. No. 4329 (2019)
PubMed Source   

Understanding genetic architecture of plasma lipidome could provide better insights into lipid metabolism and its link to cardiovascular diseases (CVDs). Here, we perform genome-wide association analyses of 141 lipid species (n = 2,181 individuals), followed by phenome-wide scans with 25 CVD related phenotypes (n = 511,700 individuals). We identify 35 lipid-species-associated loci (P <5 ×10-8), 10 of which associate with CVD risk including five new loci-COL5A1, GLTPD2, SPTLC3, MBOAT7 and GALNT16 (false discovery rate<0.05). We identify loci for lipid species that are shown to predict CVD e.g., SPTLC3 for CER(d18:1/24:1). We show that lipoprotein lipase (LPL) may more efficiently hydrolyze medium length triacylglycerides (TAGs) than others. Polyunsaturated lipids have highest heritability and genetic correlations, suggesting considerable genetic regulation at fatty acids levels. We find low genetic correlations between traditional lipids and lipid species. Our results show that lipidomic profiles capture information beyond traditional lipids and identify genetic variants modifying lipid levels and risk of CVD.
@article{Tabassum7515,
author={Rubina Tabassum, Joel T Rämö, Pietari Ripatti, Jukka T Koskela, Mitja Kurki, Juha Karjalainen, Priit Palta, Shabbeer Hassan, Javier Nunez-Fontarnau, Tuomo T J Kiiskinen, Sanni Söderlund, Niina Matikainen, Mathias J. Gerl, Michal Surma, Christian Klose, Nathan O Stitziel, Hannele Laivuori, Aki S Havulinna, Susan K Service, Veikko Salomaa, Matti Pirinen, Matti null, M Jauhiainen, Mark J Daly, Nelson B Freimer, Aarno Palotie, Marja-Riitta Taskinen, Kai Simons, Samuli Ripatti},
title={Genetic architecture of human plasma lipidome and its link to cardiovascular disease.},
journal ={Nature communications},
volume={10},
issue ={1},
pages={null--null},
year=2019
}

Natalie Dye, Ali Mahmoud, K. Venkatesan Iyer, Ivona Mateska, Suhrid Ghosh, Ioannis Nellas, Romina Piscitello-Gómez, Salma Ahmed Zeidan, Jana Fuhrmann, Allison Lewis, Abhijeet Krishna
Suzanne Eaton (1959-2019) Obituary
Dev Cell, 50(6) 680-682 (2019)
Source  

@article{Dye7522,
author={Natalie Dye, Ali Mahmoud, K. Venkatesan Iyer, Ivona Mateska, Suhrid Ghosh, Ioannis Nellas, Romina Piscitello-Gómez, Salma Ahmed Zeidan, Jana Fuhrmann, Allison Lewis, Abhijeet Krishna},
title={Suzanne Eaton (1959-2019) Obituary},
journal ={Developmental cell},
volume={50},
issue ={6},
pages={680--682},
year=2019
}

Kai Schuhmann, HongKee Moon, Henrik Thomas, Jacobo Miranda Ackerman, Michael Groessl, Nicolai Wagner, Markus Kellmann, Ian Henry, André Nadler, Andrej Shevchenko
Quantitative Fragmentation Model for Bottom-Up Shotgun Lipidomics.
Anal Chem, 91(18) 12085-12093 (2019)
PubMed Source   

Quantitative bottom-up shotgun lipidomics relies on molecular species-specific "signature" fragments consistently detectable in tandem mass spectra of analytes and standards. Molecular species of glycerophospholipids are typically quantified using carboxylate fragments of their fatty acid moieties produced by higher-energy collisional dissociation of their molecular anions. However, employing standards whose fatty acids moieties are similar, yet not identical, to the target lipids could severely compromise their quantification. We developed a generic and portable fragmentation model implemented in the open-source LipidXte software that harmonizes the abundances of carboxylate anion fragments originating from fatty acid moieties having different sn-1/2 positions at the glycerol backbone, length of the hydrocarbon chain, and number and location of double bonds. The postacquisition adjustment enables unbiased absolute (molar) quantification of glycerophospholipid species independent of instrument settings, collision energy, and employed internal standards.
@article{Schuhmann7481,
author={Kai Schuhmann, HongKee Moon, Henrik Thomas, Jacobo Miranda Ackerman, Michael Groessl, Nicolai Wagner, Markus Kellmann, Ian Henry, André Nadler, Andrej Shevchenko},
title={Quantitative Fragmentation Model for Bottom-Up Shotgun Lipidomics.},
journal ={Analytical chemistry},
volume={91},
issue ={18},
pages={12085--12093},
year=2019
}

Mario Ivankovic, Radmila Haneckova, Albert Thommen, Markus Grohme, Miquel Vila-Farré, Steffen Werner, Jochen Rink
Model systems for regeneration: planarians.
Development, 146(17) Art. No. dev167684 (2019)
PubMed Source   

Planarians are a group of flatworms. Some planarian species have remarkable regenerative abilities, which involve abundant pluripotent adult stem cells. This makes these worms a powerful model system for understanding the molecular and evolutionary underpinnings of regeneration. By providing a succinct overview of planarian taxonomy, anatomy, available tools and the molecular orchestration of regeneration, this Primer aims to showcase both the unique assets and the questions that can be addressed with this model system.
@article{Ivankovic7514,
author={Mario Ivankovic, Radmila Haneckova, Albert Thommen, Markus Grohme, Miquel Vila-Farré, Steffen Werner, Jochen Rink},
title={Model systems for regeneration: planarians.},
journal ={Development (Cambridge, England)},
volume={146},
issue ={17},
pages={null--null},
year=2019
}