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Edlyn Wu, Ajay A Vashisht, Clément Chapat, Mathieu N Flamand, Emiliano Cohen, Mihail Sarov, Yuval Tabach, Nahum Sonenberg, James Wohlschlegel, Thomas F Duchaine
A continuum of mRNP complexes in embryonic microRNA-mediated silencing.
Nucleic Acids Res, 45(4) 2081-2098 (2017)
  PubMed  

@article{Wu6704,
author={Edlyn Wu, Ajay A Vashisht, Clément Chapat, Mathieu N Flamand, Emiliano Cohen, Mihail Sarov, Yuval Tabach, Nahum Sonenberg, James Wohlschlegel, Thomas F Duchaine},
title={A continuum of mRNP complexes in embryonic microRNA-mediated silencing.},
journal={Nucleic acids research},
volume={45},
issue ={4},
pages={2081--2098},
year=2017
}

Doris Höglinger, André Nadler, Per Haberkant, Joanna Kirkpatrick, Martina Schifferer, Frank Stein, Sebastian Hauke, Forbes D Porter, Carsten Schultz
Trifunctional lipid probes for comprehensive studies of single lipid species in living cells.
Proc Natl Acad Sci U.S.A., 114(7) 1566-1571 (2017)
PubMed   

Lipid-mediated signaling events regulate many cellular processes. Investigations of the complex underlying mechanisms are difficult because several different methods need to be used under varying conditions. Here we introduce multifunctional lipid derivatives to study lipid metabolism, lipid-protein interactions, and intracellular lipid localization with a single tool per target lipid. The probes are equipped with two photoreactive groups to allow photoliberation (uncaging) and photo-cross-linking in a sequential manner, as well as a click-handle for subsequent functionalization. We demonstrate the versatility of the design for the signaling lipids sphingosine and diacylglycerol; uncaging of the probe for these two species triggered calcium signaling and intracellular protein translocation events, respectively. We performed proteomic screens to map the lipid-interacting proteome for both lipids. Finally, we visualized a sphingosine transport deficiency in patient-derived Niemann-Pick disease type C fibroblasts by fluorescence as well as correlative light and electron microscopy, pointing toward the diagnostic potential of such tools. We envision that this type of probe will become important for analyzing and ultimately understanding lipid signaling events in a comprehensive manner.
@article{Höglinger6763,
author={Doris Höglinger, André Nadler, Per Haberkant, Joanna Kirkpatrick, Martina Schifferer, Frank Stein, Sebastian Hauke, Forbes D Porter, Carsten Schultz},
title={Trifunctional lipid probes for comprehensive studies of single lipid species in living cells.},
journal={Proceedings of the National Academy of Sciences of the United States of America},
volume={114},
issue ={7},
pages={1566--1571},
year=2017
}

Markus Rempfler, Jan-Hendrik Lange, Florian Jug, Corinna Blasse, Eugene W Myers, Bjoern H. Menze, Bjoern Andres
Efficient Algorithms for Moral Lineage Tracing
arXiv, Art. No. 1702.04111 (2017)
   

@article{Rempfler6771,
author={Markus Rempfler, Jan-Hendrik Lange, Florian Jug, Corinna Blasse, Eugene W Myers, Bjoern H. Menze, Bjoern Andres},
title={Efficient Algorithms for Moral Lineage Tracing},
journal={arXiv},
volume={},
pages={1--9},
year=2017
}

Jacqueline Tabler, Maggie M Rigney, Gordon J Berman, Swetha Gopalakrishnan, Eglantine Heude, Hadeel Adel Al-Lami, Basil Z Yannakoudakis, Rebecca D Fitch, Crystal N. Carter, Steven A Vokes, Karen J Liu, Shahragim Tajbakhsh, Se Roian Egnor, John Wallingford
Cilia-mediated Hedgehog signaling controls form and function in the mammalian larynx.
Elife, 6 Art. No. e19153 (2017)
  PubMed   

Acoustic communication is fundamental to social interactions among animals, including humans. In fact, deficits in voice impair the quality of life for a large and diverse population of patients. Understanding the molecular genetic mechanisms of development and function in the vocal apparatus is thus an important challenge with relevance both to the basic biology of animal communication and to biomedicine. However, surprisingly little is known about the developmental biology of the mammalian larynx. Here, we used genetic fate mapping to chart the embryological origins of the tissues in the mouse larynx, and we describe the developmental etiology of laryngeal defects in mice with disruptions in cilia-mediated Hedgehog signaling. In addition, we show that mild laryngeal defects correlate with changes in the acoustic structure of vocalizations. Together, these data provide key new insights in the molecular genetics of form and function in the mammalian vocal apparatus.
@article{Tabler6772,
author={Jacqueline Tabler, Maggie M Rigney, Gordon J Berman, Swetha Gopalakrishnan, Eglantine Heude, Hadeel Adel Al-Lami, Basil Z Yannakoudakis, Rebecca D Fitch, Crystal N. Carter, Steven A Vokes, Karen J Liu, Shahragim Tajbakhsh, Se Roian Egnor, John Wallingford},
title={Cilia-mediated Hedgehog signaling controls form and function in the mammalian larynx.},
journal={eLife},
volume={6},
pages={null--null},
year=2017
}

Ekaterina Korotkevich, Ritsuya Niwayama, Aurélien Courtois, Stefanie Friese, Nicolas Berger, Frank Buchholz, Takashi Hiiragi
The Apical Domain Is Required and Sufficient for the First Lineage Segregation in the Mouse Embryo.
Dev Cell, 40(3) 235-247 (2017)
  PubMed   

Mammalian development begins with segregation of the extra-embryonic trophectoderm from the embryonic lineage in the blastocyst. While cell polarity and adhesion play key roles, the decisive cue driving this lineage segregation remains elusive. Here, to study symmetry breaking, we use a reduced system in which isolated blastomeres recapitulate the first lineage segregation. We find that in the 8-cell stage embryo, the apical domain recruits a spindle pole to ensure its differential distribution upon division. Daughter cells that inherit the apical domain adopt trophectoderm fate. However, the fate of apolar daughter cells depends on whether their position within the embryo facilitates apical domain formation by Cdh1-independent cell contact. Finally, we develop methods for transplanting apical domains and show that acquisition of this domain is not only required but also sufficient for the first lineage segregation. Thus, we provide mechanistic understanding that reconciles previous models for symmetry breaking in mouse development.
@article{Korotkevich6774,
author={Ekaterina Korotkevich, Ritsuya Niwayama, Aurélien Courtois, Stefanie Friese, Nicolas Berger, Frank Buchholz, Takashi Hiiragi},
title={The Apical Domain Is Required and Sufficient for the First Lineage Segregation in the Mouse Embryo.},
journal={Developmental cell},
volume={40},
issue ={3},
pages={235--247},
year=2017
}

Tom Stückemann, James Cleland, Steffen Werner, Hanh Thi-Kim Vu, Robert Bayersdorf, Shang-Yun Liu, Benjamin Friedrich, Frank Jülicher, Jochen Rink
Antagonistic Self-Organizing Patterning Systems Control Maintenance and Regeneration of the Anteroposterior Axis in Planarians.
Dev Cell, 40(3) 248-263 (2017)
PubMed   

Planarian flatworms maintain their body plan in the face of constant internal turnover and can regenerate from arbitrary tissue fragments. Both phenomena require self-maintaining and self-organizing patterning mechanisms, the molecular mechanisms of which remain poorly understood. We show that a morphogenic gradient of canonical Wnt signaling patterns gene expression along the planarian anteroposterior (A/P) axis. Our results demonstrate that gradient formation likely occurs autonomously in the tail and that an autoregulatory module of Wnt-mediated Wnt expression both shapes the gradient at steady state and governs its re-establishment during regeneration. Functional antagonism between the tail Wnt gradient and an unknown head patterning system further determines the spatial proportions of the planarian A/P axis and mediates mutually exclusive molecular fate choices during regeneration. Overall, our results suggest that the planarian A/P axis is patterned by self-organizing patterning systems deployed from either end that are functionally coupled by mutual antagonism.
@article{Stückemann6773,
author={Tom Stückemann, James Cleland, Steffen Werner, Hanh Thi-Kim Vu, Robert Bayersdorf, Shang-Yun Liu, Benjamin Friedrich, Frank Jülicher, Jochen Rink},
title={Antagonistic Self-Organizing Patterning Systems Control Maintenance and Regeneration of the Anteroposterior Axis in Planarians.},
journal={Developmental cell},
volume={40},
issue ={3},
pages={248--263},
year=2017
}

Gaelle R Carrat, Ming Hu, Marie-Sophie Nguyen-Tu, Pauline Chabosseau, Kyle J Gaulton, Martijn van de Bunt, Afshan Siddiq, Mario Falchi, Matthias Thurner, Mickaël Canouil, Francois Pattou, Isabelle Leclerc, Timothy J Pullen, Matthew C Cane, Priyanka Prabhala, William Greenwald, Anke Schulte, Piero Marchetti, Mark Ibberson, Patrick E MacDonald, Jocelyn E Manning Fox, Anna L Gloyn, Philippe Froguel, Michele Solimena, Mark I McCarthy, Guy A Rutter
Decreased STARD10 Expression Is Associated with Defective Insulin Secretion in Humans and Mice.
Am J Hum Genet, 100(2) 238-256 (2017)
  PubMed   

Genetic variants near ARAP1 (CENTD2) and STARD10 influence type 2 diabetes (T2D) risk. The risk alleles impair glucose-induced insulin secretion and, paradoxically but characteristically, are associated with decreased proinsulin:insulin ratios, indicating improved proinsulin conversion. Neither the identity of the causal variants nor the gene(s) through which risk is conferred have been firmly established. Whereas ARAP1 encodes a GTPase activating protein, STARD10 is a member of the steroidogenic acute regulatory protein (StAR)-related lipid transfer protein family. By integrating genetic fine-mapping and epigenomic annotation data and performing promoter-reporter and chromatin conformational capture (3C) studies in β cell lines, we localize the causal variant(s) at this locus to a 5 kb region that overlaps a stretch-enhancer active in islets. This region contains several highly correlated T2D-risk variants, including the rs140130268 indel. Expression QTL analysis of islet transcriptomes from three independent subject groups demonstrated that T2D-risk allele carriers displayed reduced levels of STARD10 mRNA, with no concomitant change in ARAP1 mRNA levels. Correspondingly, β-cell-selective deletion of StarD10 in mice led to impaired glucose-stimulated Ca(2+) dynamics and insulin secretion and recapitulated the pattern of improved proinsulin processing observed at the human GWAS signal. Conversely, overexpression of StarD10 in the adult β cell improved glucose tolerance in high fat-fed animals. In contrast, manipulation of Arap1 in β cells had no impact on insulin secretion or proinsulin conversion in mice. This convergence of human and murine data provides compelling evidence that the T2D risk associated with variation at this locus is mediated through reduction in STARD10 expression in the β cell.
@article{Carrat6775,
author={Gaelle R Carrat, Ming Hu, Marie-Sophie Nguyen-Tu, Pauline Chabosseau, Kyle J Gaulton, Martijn van de Bunt, Afshan Siddiq, Mario Falchi, Matthias Thurner, Mickaël Canouil, Francois Pattou, Isabelle Leclerc, Timothy J Pullen, Matthew C Cane, Priyanka Prabhala, William Greenwald, Anke Schulte, Piero Marchetti, Mark Ibberson, Patrick E MacDonald, Jocelyn E Manning Fox, Anna L Gloyn, Philippe Froguel, Michele Solimena, Mark I McCarthy, Guy A Rutter},
title={Decreased STARD10 Expression Is Associated with Defective Insulin Secretion in Humans and Mice.},
journal={American journal of human genetics},
volume={100},
issue ={2},
pages={238--256},
year=2017
}

Damla Kaptan
Metabolic Transition in Caenorhabditis elegans Dauer Larva
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2017)
 

@phdthesis{Kaptan6780,
author = {Damla Kaptan},
title={Metabolic Transition in Caenorhabditis elegans Dauer Larva},
school = {Technische Universität Dresden},
year=2017,
address = {Dresden, Germany},
}

Sara Caviglia, David Flores-Benitez, Johanna Lattner, Stefan Luschnig, Marko Brankatschk
Rabs on the fly: functions of Rab GTPases during development.
Small GTPases, 0-0 (2017)
PubMed   

The organisation of intracellular transport processes is adapted specifically to different cell types, developmental stages, and physiological requirements. Some protein traffic routes are universal to all cells and constitutively active, while other routes are cell-type specific, transient, and induced under particular conditions only. Small GTPases of the Rab (Ras related in brain) subfamily are conserved across eukaryotes and regulate most intracellular transit pathways. The complete sets of Rab proteins have been identified in model organisms, and molecular principles underlying Rab functions have been uncovered. Rabs provide intracellular landmarks that define intracellular transport sequences. Nevertheless, it remains a challenge to systematically map the subcellular distribution of all Rabs and their functional interrelations. This task requires novel tools to precisely describe and manipulate the Rab machinery in vivo. Here we discuss recent findings about Rab roles during development and we consider novel approaches to investigate Rab functions in vivo.
@article{Caviglia6761,
author={Sara Caviglia, David Flores-Benitez, Johanna Lattner, Stefan Luschnig, Marko Brankatschk},
title={Rabs on the fly: functions of Rab GTPases during development.},
journal={Small GTPases},
volume={},
pages={0--0},
year=2017
}

Hernando Suarez, Bjorn Langer, Pradnya Ladde, Michael Hiller
chainCleaner improves genome alignment specificity and sensitivity.
Bioinformatics, Art. No. doi: 10.1093/bioinformatics/btx024 (2017)
  PubMed   

Accurate alignments between entire genomes are crucial for comparative genomics. However, computing sensitive and accurate genome alignments is a challenging problem, complicated by genomic rearrangements.
@article{Suarez6740,
author={Hernando Suarez, Bjorn Langer, Pradnya Ladde, Michael Hiller},
title={chainCleaner improves genome alignment specificity and sensitivity.},
journal={Bioinformatics (Oxford, England)},
volume={},
pages={1--8},
year=2017
}