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Jussi Helppi, Dora Schreier, Ronald Naumann, Oliver Zierau
Mouse reproductive fitness is maintained up to an ambient temperature of 28℃ when housed in individually-ventilated cages.
Lab. Anim., 50(4) 254-263 (2016)
PubMed   

Production of genetically-modified mice is strongly dependent on environmental conditions. Mice are commonly housed at 22℃, which is significantly lower than their thermoneutral zone. But, when given a choice, mice often seem to prefer higher ambient temperatures. In the current study we investigated the effect of higher ambient temperature on the production of transgenic mice, with emphasis on embryo and sperm yield and quality. Mice (C57BL/6JOlaHsd) were housed under four different ambient temperatures (22, 25, 28 and 30℃). Female mice were superovulated, and mated with males. As indicators for reproductive fitness, the success of the mating was observed, including embryo yield and quality, as well as sperm count, motility and progressivity. Female mice were found to produce high amounts of high quality embryos from 22 to 28℃. Sperm count dropped continuously from 22 to 30℃, but sperm motility and progressivity remained high from 22 to 28℃. We conclude that mice can be housed at significantly higher temperatures than is commonly recommended without compromising embryo production and quality, or sperm quality. These results could lead to fundamental changes in how mouse facilities are built and operated - especially in warmer climates whereby energy consumption and therefore costs could be significantly reduced.
@article{Helppi6308,
author={Jussi Helppi, Dora Schreier, Ronald Naumann, Oliver Zierau},
title={Mouse reproductive fitness is maintained up to an ambient temperature of 28℃ when housed in individually-ventilated cages.},
journal={Laboratory animals},
volume={50},
issue ={4},
pages={254--263},
year=2016
}

Elvan Boke, Martine Ruer, Martin Wühr, Margaret Coughlin, Regis P. Lemaitre, Steven Gygi, Simon Alberti, David N. Drechsel, Anthony Hyman, Timothy J. Mitchison
Amyloid-like Self-Assembly of a Cellular Compartment.
Cell, 166(3) 637-650 (2016)
PubMed   

Most vertebrate oocytes contain a Balbiani body, a large, non-membrane-bound compartment packed with RNA, mitochondria, and other organelles. Little is known about this compartment, though it specifies germline identity in many non-mammalian vertebrates. We show Xvelo, a disordered protein with an N-terminal prion-like domain, is an abundant constituent of Xenopus Balbiani bodies. Disruption of the prion-like domain of Xvelo, or substitution with a prion-like domain from an unrelated protein, interferes with its incorporation into Balbiani bodies in vivo. Recombinant Xvelo forms amyloid-like networks in vitro. Amyloid-like assemblies of Xvelo recruit both RNA and mitochondria in binding assays. We propose that Xenopus Balbiani bodies form by amyloid-like assembly of Xvelo, accompanied by co-recruitment of mitochondria and RNA. Prion-like domains are found in germ plasm organizing proteins in other species, suggesting that Balbiani body formation by amyloid-like assembly could be a conserved mechanism that helps oocytes function as long-lived germ cells.
@article{Boke6600,
author={Elvan Boke, Martine Ruer, Martin Wühr, Margaret Coughlin, Regis P. Lemaitre, Steven Gygi, Simon Alberti, David N. Drechsel, Anthony Hyman, Timothy J. Mitchison},
title={Amyloid-like Self-Assembly of a Cellular Compartment.},
journal={Cell},
volume={166},
issue ={3},
pages={637--650},
year=2016
}

Mark Leaver, Simone Kienle, Maria L Begasse, Ralf J Sommer, Anthony Hyman
A locus in Pristionchus pacificus that is responsible for the ability to give rise to fertile offspring at higher temperatures.
Biol Open, Art. No. doi: 10.1242/bio.018127 (2016)
  PubMed   

Temperature is a stress factor that varies temporally and spatially, and can affect the fitness of cold-blooded organisms, leading to a loss of reproductive output; however, little is understood about the genetics behind the long-term response of organisms to temperature. Here, we approach this problem in the model nematode Pristionchus pacificus by utilising a large collection of natural isolates with diverse phenotypes. From this collection we identify two strains, one from California that can give rise to fertile offspring up to 28°C and one from Japan that is fertile up to 30°C. We show that the optimum temperature and the upper temperature limit for fertility is shifted higher in the Japanese strain suggesting that there is a mechanism that controls the temperature response of fertility across a range of temperatures. By crossing the two strains, and using genetic mapping, we identify a region on chromosome V that is responsible for maintaining fertility at higher temperatures. Thus, we conclude that fitness of P. pacificus at high temperature is under genetic control, suggesting that it could be subject to natural selection.
@article{Leaver6598,
author={Mark Leaver, Simone Kienle, Maria L Begasse, Ralf J Sommer, Anthony Hyman},
title={A locus in Pristionchus pacificus that is responsible for the ability to give rise to fertile offspring at higher temperatures.},
journal={Biology open},
volume={},
issue ={},
pages={null--null},
year=2016
}

Sara Caviglia, Marko Brankatschk, Elisabeth Fischer, Suzanne Eaton, Stefan Luschnig
Staccato/Unc-13-4 controls secretory lysosome-mediated lumen fusion during epithelial tube anastomosis.
Nat Cell Biol, 18(7) 727-739 (2016)
PubMed   

A crucial yet ill-defined step during the development of tubular networks, such as the vasculature, is the formation of connections (anastomoses) between pre-existing lumenized tubes. By studying tracheal tube anastomosis in Drosophila melanogaster, we uncovered a key role of secretory lysosome-related organelle (LRO) trafficking in lumen fusion. We identified the conserved calcium-binding protein Unc-13-4/Staccato (Stac) and the GTPase Rab39 as critical regulators of this process. Stac and Rab39 accumulate on dynamic vesicles, which form exclusively in fusion tip cells, move in a dynein-dependent manner, and contain late-endosomal, lysosomal, and SNARE components characteristic of LROs. The GTPase Arl3 is necessary and sufficient for Stac LRO formation and promotes Stac-dependent intracellular fusion of juxtaposed apical plasma membranes, thereby forming a transcellular lumen. Concomitantly, calcium is released locally from ER exit sites and apical membrane-associated calcium increases. We propose that calcium-dependent focused activation of LRO exocytosis restricts lumen fusion to appropriate domains within tip cells.
@article{Caviglia6589,
author={Sara Caviglia, Marko Brankatschk, Elisabeth Fischer, Suzanne Eaton, Stefan Luschnig},
title={Staccato/Unc-13-4 controls secretory lysosome-mediated lumen fusion during epithelial tube anastomosis.},
journal={Nature cell biology},
volume={18},
issue ={7},
pages={727--739},
year=2016
}

Michael Heide, Marta Florio, Wieland B. Huttner
Die Rolle humanspezifischer Gene in der Gehirnentwicklung und -evolution
BIOspektrum, 22(4) 352-355 (2016)
 

@article{Heide6595,
author={Michael Heide, Marta Florio, Wieland B. Huttner},
title={Die Rolle humanspezifischer Gene in der Gehirnentwicklung und -evolution},
journal={BIOspektrum},
volume={22},
issue ={4},
pages={352--355},
year=2016
}

Virag Sharma, Anas Elghafari, Michael Hiller
Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation.
Nucleic Acids Res, 44(11) Art. No. e103 (2016)
  PubMed   

Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in exons that are truly conserved. To overcome these limitations, we have developed CESAR (Coding Exon-Structure Aware Realigner) that realigns coding exons, while considering reading frame and splice sites of each exon. CESAR effectively avoids spurious frameshifts in conserved genes and detects 91% of shifted splice sites. This results in the identification of thousands of additional conserved exons and 99% of the exons that lack inactivating mutations match real exons. Finally, to demonstrate the potential of using CESAR for comparative gene annotation, we applied it to 188 788 exons of 19 865 human genes to annotate human genes in 99 other vertebrates. These comparative gene annotations are available as a resource (http://bds.mpi-cbg.de/hillerlab/CESAR/). CESAR (https://github.com/hillerlab/CESAR/) can readily be applied to other alignments to accurately annotate coding genes in many other vertebrate and invertebrate genomes.
@article{Sharma6464,
author={Virag Sharma, Anas Elghafari, Michael Hiller},
title={Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation.},
journal={Nucleic acids research},
volume={44},
issue ={11},
pages={null--null},
year=2016
}

Michaela Mickoleit
Imaging and Reconstructing the beating Heart and its Morphogenesis
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2016)
 

@phdthesis{Mickoleit6566,
author = {Michaela Mickoleit},
title={Imaging and Reconstructing the beating Heart and its Morphogenesis},
school = {Technische Universität Dresden},
year=2016,
address = {Dresden, Germany},
}

Olena Steshenko, Débora M Andrade, Alf Honigmann, Veronika Mueller, Falk Schneider, Erdinc Sezgin, Stefan W Hell, Mikael Simons, Christian Eggeling
Reorganization of Lipid Diffusion by Myelin Basic Protein as Revealed by STED Nanoscopy.
Biophys J, 110(11) 2441-2450 (2016)
  PubMed   

Myelin is a multilayered membrane that ensheathes axonal fibers in the vertebrate nervous system, allowing fast propagation of nerve action potentials. It contains densely packed lipids, lacks an actin-based cytocortex, and requires myelin basic protein (MBP) as its major structural component. This protein is the basic constituent of the proteinaceous meshwork that is localized between adjacent cytoplasmic membranes of the myelin sheath. Yet, it is not clear how MBP influences the organization and dynamics of the lipid constituents of myelin. Here, we used optical stimulated emission depletion super-resolution microscopy in combination with fluorescence correlation spectroscopy to assess the characteristics of diffusion of different fluorescent lipid analogs in myelin membrane sheets of cultured oligodendrocytes and in micrometer-sized domains that were induced by MBP in live epithelial PtK2 cells. Lipid diffusion was significantly faster and less anomalous both in oligodendrocytes and inside the MBP-rich domains of PtK2 cells compared with undisturbed live PtK2 cells. Our data show that MBP reorganizes lipid diffusion, possibly by preventing the buildup of an actin-based cytocortex and by preventing most membrane proteins from entering the myelin sheath region. Yet, in contrast to myelin sheets in oligodendrocytes, the MBP-induced domains in epithelial PtK2 cells demonstrate no change in lipid order, indicating that segregation of long-chain lipids into myelin sheets is a process specific to oligodendrocytes.
@article{Steshenko6573,
author={Olena Steshenko, Débora M Andrade, Alf Honigmann, Veronika Mueller, Falk Schneider, Erdinc Sezgin, Stefan W Hell, Mikael Simons, Christian Eggeling},
title={Reorganization of Lipid Diffusion by Myelin Basic Protein as Revealed by STED Nanoscopy.},
journal={Biophysical journal},
volume={110},
issue ={11},
pages={2441--2450},
year=2016
}

Yin Ning Chiang, Kah Junn Tan, Henry Chung, Oksana Lavrynenko, Andrej Shevchenko, Joanne Y Yew
Steroid Hormone Signaling Is Essential for Pheromone Production and Oenocyte Survival.
PLoS Genet, 12(6) Art. No. e1006126 (2016)
  PubMed   

Many of the lipids found on the cuticles of insects function as pheromones and communicate information about age, sex, and reproductive status. In Drosophila, the composition of the information-rich lipid profile is dynamic and changes over the lifetime of an individual. However, the molecular basis of this change is not well understood. To identify genes that control cuticular lipid production in Drosophila, we performed a RNA interference screen and used Direct Analysis in Real Time and gas chromatography mass spectrometry to quantify changes in the chemical profiles. Twelve putative genes were identified whereby transcriptional silencing led to significant differences in cuticular lipid production. Amongst them, we characterized a gene which we name spidey, and which encodes a putative steroid dehydrogenase that has sex- and age-dependent effects on viability, pheromone production, and oenocyte survival. Transcriptional silencing or overexpression of spidey during embryonic development results in pupal lethality and significant changes in levels of the ecdysone metabolite 20-hydroxyecdysonic acid and 20-hydroxyecdysone. In contrast, inhibiting gene expression only during adulthood resulted in a striking loss of oenocyte cells and a concomitant reduction of cuticular hydrocarbons, desiccation resistance, and lifespan. Oenocyte loss and cuticular lipid levels were partially rescued by 20-hydroxyecdysone supplementation. Taken together, these results identify a novel regulator of pheromone synthesis and reveal that ecdysteroid signaling is essential for the maintenance of cuticular lipids and oenocytes throughout adulthood.
@article{Chiang6590,
author={Yin Ning Chiang, Kah Junn Tan, Henry Chung, Oksana Lavrynenko, Andrej Shevchenko, Joanne Y Yew},
title={Steroid Hormone Signaling Is Essential for Pheromone Production and Oenocyte Survival.},
journal={PLoS genetics},
volume={12},
issue ={6},
pages={null--null},
year=2016
}

Édgar Roldán, Ana Lisica, Daniel Sánchez-Taltavull, Stephan W. Grill
Stochastic resetting in backtrack recovery by RNA polymerases.
Phys Rev E, 93(6-1) Art. No. 062411 (2016)
PubMed   

Transcription is a key process in gene expression, in which RNA polymerases produce a complementary RNA copy from a DNA template. RNA polymerization is frequently interrupted by backtracking, a process in which polymerases perform a random walk along the DNA template. Recovery of polymerases from the transcriptionally inactive backtracked state is determined by a kinetic competition between one-dimensional diffusion and RNA cleavage. Here we describe backtrack recovery as a continuous-time random walk, where the time for a polymerase to recover from a backtrack of a given depth is described as a first-passage time of a random walker to reach an absorbing state. We represent RNA cleavage as a stochastic resetting process and derive exact expressions for the recovery time distributions and mean recovery times from a given initial backtrack depth for both continuous and discrete-lattice descriptions of the random walk. We show that recovery time statistics do not depend on the discreteness of the DNA lattice when the rate of one-dimensional diffusion is large compared to the rate of cleavage.
@article{Roldán6584,
author={Édgar Roldán, Ana Lisica, Daniel Sánchez-Taltavull, Stephan W. Grill},
title={Stochastic resetting in backtrack recovery by RNA polymerases.},
journal={Physical review. E},
volume={93},
issue ={6-1},
pages={null--null},
year=2016
}