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Takashi Namba, Samir Vaid, Wieland Huttner
Primate neocortex development and evolution: Conserved versus evolved folding.
J Comp Neurol, 527(10) 1621-1632 (2019)
PubMed Source   

The neocortex, the seat of higher cognitive functions, exhibits a key feature across mammalian species-a highly variable degree of folding. Within the neocortex, two distinct subtypes of cortical areas can be distinguished, the isocortex and the proisocortex. Here, we have compared specific spatiotemporal aspects of folding between the proisocortex and the isocortex in 13 primates, including human, chimpanzee, and various Old World and New World monkeys. We find that folding at the boundaries of the dorsal isocortex and the proisocortex, which gives rise to the cingulate sulcus (CiS) and the lateral fissure (LF), is conserved across the primates studied and is therefore referred to as conserved folding. In contrast, the degree of folding within the dorsal isocortex exhibits huge variation across these primates, indicating that this folding, which gives rise to gyri and sulci, is subject to major changes during primate evolution. We therefore refer to the folding within the dorsal isocortex as evolved folding. Comparison of fetal neocortex development in long-tailed macaque and human reveals that the onset of conserved folding precedes the onset of evolved folding. Moreover, the analysis of infant human neocortex exhibiting lissencephaly, a developmental malformation thought to be mainly due to abnormal neuronal migration, shows that the evolved folding is perturbed more than the conserved folding. Taken together, our study presents a two-step model of folding that pertains to primate neocortex development and evolution. Specifically, our data imply that the conserved folding and the evolved folding constitute two distinct, sequential events.
@article{Namba7305,
author={Takashi Namba, Samir Vaid, Wieland Huttner},
title={Primate neocortex development and evolution: Conserved versus evolved folding.},
journal ={The Journal of comparative neurology},
volume={527},
issue ={10},
pages={1621--1632},
year=2019
}

Nereo Kalebic, Carlotta Gilardi, Barbara Stepien, Michaela Wilsch-Bräuninger, Katherine S. Long, Takashi Namba, Marta Florio, Barbara Langen, Benoit Lombardot, Anna Shevchenko, Manfred W Kilimann, Hiroshi Kawasaki, Pauline Wimberger, Wieland Huttner
Neocortical Expansion Due to Increased Proliferation of Basal Progenitors Is Linked to Changes in Their Morphology.
Cell Stem Cell, 24(4) 535-550 (2019)
PubMed Source   

The evolutionary expansion of the mammalian neocortex (Ncx) is thought to be linked to increased proliferative capacity of basal progenitors (BPs) and their neurogenic capacity. Here, by quantifying BP morphology in the developing Ncx of mouse, ferret, and human, we show that increased BP proliferative capacity is linked to an increase in BP process number. We identify human membrane-bound PALMDELPHIN (PALMD-Caax) as an underlying factor, and we show that it drives BP process growth and proliferation when expressed in developing mouse and ferret Ncx. Conversely, CRISPR/Cas9-mediated disruption of PALMD or its binding partner ADDUCIN-γ in fetal human Ncx reduces BP process numbers and proliferation. We further show that PALMD-induced processes enable BPs to receive pro-proliferative integrin-dependent signals. These findings provide a link between BP morphology and proliferation, suggesting that changes in BP morphology may have contributed to the evolutionary expansion of the Ncx.
@article{Kalebic7370,
author={Nereo Kalebic, Carlotta Gilardi, Barbara Stepien, Michaela Wilsch-Bräuninger, Katherine S. Long, Takashi Namba, Marta Florio, Barbara Langen, Benoit Lombardot, Anna Shevchenko, Manfred W Kilimann, Hiroshi Kawasaki, Pauline Wimberger, Wieland Huttner},
title={Neocortical Expansion Due to Increased Proliferation of Basal Progenitors Is Linked to Changes in Their Morphology.},
journal ={Cell stem cell},
volume={24},
issue ={4},
pages={535--550},
year=2019
}

Johannes Klaus, Sabina Kanton, Christina Kyrousi, Ane Cristina Ayo-Martin, Rossella Di Giaimo, Stephan Riesenberg, Adam C O'Neill, J Gray Camp, Chiara Tocco, Malgorzata Santel, Ejona Rusha, Micha Drukker, Mariana Schroeder, Magdalena Götz, Stephen P Robertson, Barbara Treutlein, Silvia Cappello
Altered neuronal migratory trajectories in human cerebral organoids derived from individuals with neuronal heterotopia.
Nat Med, 25(4) 561-568 (2019)
PubMed Source   

Malformations of the human cortex represent a major cause of disability1. Mouse models with mutations in known causal genes only partially recapitulate the phenotypes and are therefore not unlimitedly suited for understanding the molecular and cellular mechanisms responsible for these conditions2. Here we study periventricular heterotopia (PH) by analyzing cerebral organoids derived from induced pluripotent stem cells (iPSCs) of patients with mutations in the cadherin receptor-ligand pair DCHS1 and FAT4 or from isogenic knockout (KO) lines1,3. Our results show that human cerebral organoids reproduce the cortical heterotopia associated with PH. Mutations in DCHS1 and FAT4 or knockdown of their expression causes changes in the morphology of neural progenitor cells and result in defective neuronal migration dynamics only in a subset of neurons. Single-cell RNA-sequencing (scRNA-seq) data reveal a subpopulation of mutant neurons with dysregulated genes involved in axon guidance, neuronal migration and patterning. We suggest that defective neural progenitor cell (NPC) morphology and an altered navigation system in a subset of neurons underlie this form of PH.
@article{Klaus7369,
author={Johannes Klaus, Sabina Kanton, Christina Kyrousi, Ane Cristina Ayo-Martin, Rossella Di Giaimo, Stephan Riesenberg, Adam C O'Neill, J Gray Camp, Chiara Tocco, Malgorzata Santel, Ejona Rusha, Micha Drukker, Mariana Schroeder, Magdalena Götz, Stephen P Robertson, Barbara Treutlein, Silvia Cappello},
title={Altered neuronal migratory trajectories in human cerebral organoids derived from individuals with neuronal heterotopia.},
journal ={Nature medicine},
volume={25},
issue ={4},
pages={561--568},
year=2019
}

Saskia Lippens, Christophe D'Enfert, Lilla M. Farkas, Anna Kehres, Bernhard Korn, Mònica Morales, Rainer Pepperkok, Lavanya Premvardhan, Ralph Schlapbach, Andreas Tiran, Doris Meder, Geert Van Minnebruggen
One step ahead: Innovation in core facilities.
EMBO Rep, 20(4) Art. No. doi: 10.15252/embr.201948017 (2019)
PubMed Source  

@article{Lippens7377,
author={Saskia Lippens, Christophe D'Enfert, Lilla M. Farkas, Anna Kehres, Bernhard Korn, Mònica Morales, Rainer Pepperkok, Lavanya Premvardhan, Ralph Schlapbach, Andreas Tiran, Doris Meder, Geert Van Minnebruggen},
title={One step ahead: Innovation in core facilities.},
journal ={EMBO reports},
volume={20},
issue ={4},
pages={null--null},
year=2019
}

Lara Marrone, Hannes C A Drexler, Jie Wang, Priyanka Tripathi, Tania Distler, Patrick Heisterkamp, Eric D Anderson, Sukhleen Kour, Anastasia Moraiti, Shovamayee Maharana, Rajat Bhatnagar, T Grant Belgard, Vadreenath Tripathy, Norman Kalmbach, Zohreh Hosseinzadeh, Valeria Crippa, Masin Abo-Rady, Florian Wegner, Angelo Poletti, Dirk Troost, Eleonora Aronica, Volker Busskamp, Joachim Weis, Udai Pandey, Anthony Hyman, Simon Alberti, Anand Goswami, Jared Sterneckert
FUS pathology in ALS is linked to alterations in multiple ALS-associated proteins and rescued by drugs stimulating autophagy.
Acta Neuropathol., Art. No. doi: 10.1007/s00401-019-01998-x (2019)
PubMed Source   

Amyotrophic lateral sclerosis (ALS) is a lethal disease characterized by motor neuron degeneration and associated with aggregation of nuclear RNA-binding proteins (RBPs), including FUS. How FUS aggregation and neurodegeneration are prevented in healthy motor neurons remain critically unanswered questions. Here, we use a combination of ALS patient autopsy tissue and induced pluripotent stem cell-derived neurons to study the effects of FUS mutations on RBP homeostasis. We show that FUS' tendency to aggregate is normally buffered by interacting RBPs, but this buffering is lost when FUS mislocalizes to the cytoplasm due to ALS mutations. The presence of aggregation-prone FUS in the cytoplasm causes imbalances in RBP homeostasis that exacerbate neurodegeneration. However, enhancing autophagy using small molecules reduces cytoplasmic FUS, restores RBP homeostasis and rescues motor function in vivo. We conclude that disruption of RBP homeostasis plays a critical role in FUS-ALS and can be treated by stimulating autophagy.
@article{Marrone7376,
author={Lara Marrone, Hannes C A Drexler, Jie Wang, Priyanka Tripathi, Tania Distler, Patrick Heisterkamp, Eric D Anderson, Sukhleen Kour, Anastasia Moraiti, Shovamayee Maharana, Rajat Bhatnagar, T Grant Belgard, Vadreenath Tripathy, Norman Kalmbach, Zohreh Hosseinzadeh, Valeria Crippa, Masin Abo-Rady, Florian Wegner, Angelo Poletti, Dirk Troost, Eleonora Aronica, Volker Busskamp, Joachim Weis, Udai Pandey, Anthony Hyman, Simon Alberti, Anand Goswami, Jared Sterneckert},
title={FUS pathology in ALS is linked to alterations in multiple ALS-associated proteins and rescued by drugs stimulating autophagy.},
journal ={Acta neuropathologica},
volume={},
pages={1--1},
year=2019
}

Anwoy Kumar Mohanty, Dana Vuzman, Laurent Francioli, Christopher Cassa, Christopher null, Christopher null, Christopher null, Agnes Toth-Petroczy, Shamil Sunyaev
novoCaller: a Bayesian network approach for de novo variant calling from pedigree and population sequence data.
Bioinformatics, 35(7) 1174-1180 (2019)
PubMed Source   

De novo mutations (i.e. newly occurring mutations) are a pre-dominant cause of sporadic dominant monogenic diseases and play a significant role in the genetics of complex disorders. De novo mutation studies also inform population genetics models and shed light on the biology of DNA replication and repair. Despite the broad interest, there is room for improvement with regard to the accuracy of de novo mutation calling.
@article{Mohanty7342,
author={Anwoy Kumar Mohanty, Dana Vuzman, Laurent Francioli, Christopher Cassa, Christopher null, Christopher null, Christopher null, Agnes Toth-Petroczy, Shamil Sunyaev},
title={novoCaller: a Bayesian network approach for de novo variant calling from pedigree and population sequence data.},
journal ={Bioinformatics (Oxford, England)},
volume={35},
issue ={7},
pages={1174--1180},
year=2019
}

Shashank Rai, Maryam Arasteh, Matthew Jefferson, Timothy Pearson, Yingxue Wang, Weijiao Zhang, Bertalan Bicsak, Devina Divekar, Penny P Powell, Ronald Naumann, Naiara Beraza, Simon R Carding, Oliver Florey, Ulrike Mayer, Thomas Wileman
The ATG5-binding and coiled coil domains of ATG16L1 maintain autophagy and tissue homeostasis in mice independently of the WD domain required for LC3-associated phagocytosis.
Autophagy, 15(4) 599-612 (2019)
PubMed Source   

Macroautophagy/autophagy delivers damaged proteins and organelles to lysosomes for degradation, and plays important roles in maintaining tissue homeostasis by reducing tissue damage. The translocation of LC3 to the limiting membrane of the phagophore, the precursor to the autophagosome, during autophagy provides a binding site for autophagy cargoes, and facilitates fusion with lysosomes. An autophagy-related pathway called LC3-associated phagocytosis (LAP) targets LC3 to phagosome and endosome membranes during uptake of bacterial and fungal pathogens, and targets LC3 to swollen endosomes containing particulate material or apoptotic cells. We have investigated the roles played by autophagy and LAP in vivo by exploiting the observation that the WD domain of ATG16L1 is required for LAP, but not autophagy. Mice lacking the linker and WD domains, activate autophagy, but are deficient in LAP. The LAP-/- mice survive postnatal starvation, grow at the same rate as littermate controls, and are fertile. The liver, kidney, brain and muscle of these mice maintain levels of autophagy cargoes such as LC3 and SQSTM1/p62 similar to littermate controls, and prevent accumulation of SQSTM1 inclusions and tissue damage associated with loss of autophagy. The results suggest that autophagy maintains tissue homeostasis in mice independently of LC3-associated phagocytosis. Further deletion of glutamate E230 in the coiled-coil domain required for WIPI2 binding produced mice with defective autophagy that survived neonatal starvation. Analysis of brain lysates suggested that interactions between WIPI2 and ATG16L1 were less critical for autophagy in the brain, which may allow a low level of autophagy to overcome neonatal lethality. Abbreviations: CCD: coiled-coil domain; CYBB/NOX2: cytochrome b-245: beta polypeptide; GPT/ALT: glutamic pyruvic transaminase: soluble; LAP: LC3-associated phagocytosis; LC3: microtubule-associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; NOD: nucleotide-binding oligomerization domain; NADPH: nicotinamide adenine dinucleotide phosphate; RUBCN/Rubicon: RUN domain and cysteine-rich domain containing Beclin 1-interacting protein; SLE: systemic lupus erythematosus; SQSTM1/p62: sequestosome 1; TLR: toll-like receptor; TMEM: transmembrane protein; TRIM: tripartite motif-containing protein; UVRAG: UV radiation resistance associated gene; WD: tryptophan-aspartic acid; WIPI: WD 40 repeat domain: phosphoinositide interacting.
@article{Rai7312,
author={Shashank Rai, Maryam Arasteh, Matthew Jefferson, Timothy Pearson, Yingxue Wang, Weijiao Zhang, Bertalan Bicsak, Devina Divekar, Penny P Powell, Ronald Naumann, Naiara Beraza, Simon R Carding, Oliver Florey, Ulrike Mayer, Thomas Wileman},
title={The ATG5-binding and coiled coil domains of ATG16L1 maintain autophagy and tissue homeostasis in mice independently of the WD domain required for LC3-associated phagocytosis.},
journal ={Autophagy},
volume={15},
issue ={4},
pages={599--612},
year=2019
}

Benjamin Schmid, Philipp Tripal, Tina Fraaß, Christina Kersten, Barbara Ruder, Anika Grüneboom, Jan Huisken, Ralf Palmisano
3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax.
Nat Methods, 16(4) 278-280 (2019)
PubMed Source  

@article{Schmid7372,
author={Benjamin Schmid, Philipp Tripal, Tina Fraaß, Christina Kersten, Barbara Ruder, Anika Grüneboom, Jan Huisken, Ralf Palmisano},
title={3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax.},
journal ={Nature methods},
volume={16},
issue ={4},
pages={278--280},
year=2019
}

German Tischler-Höhle
Haplotype and repeat separation in long reads
In: Computational Intelligence Methods for Bioinformatics and Biostatistics : 14th International Meeting, CIBB 2017, Cagliari, Italy, September 7-9, 2017, Revised Selected Papers (2019)(Eds.) Massimo Bartoletti (Lecture Notes in Computer Science ;10834), Cham, Springer International Publishing (2019), 103-114
Source  

@proceedings{Tischler-Höhle7378,
title = {Haplotype and repeat separation in long reads},
year = 2019,
editor = {German Tischler-Höhle},
volume = { Computational Intelligence Methods for Bioinformatics and Biostatistics : 14th International Meeting, CIBB 2017, Cagliari, Italy, September 7-9, 2017, Revised Selected Papers},
series = {(Lecture Notes in Computer Science ;10834)},
publisher = {Springer International Publishing}
}

Regis P. Lemaitre, Aliona Bogdanova, Barbara Borgonovo, Jeffrey Woodruff, David N. Drechsel
FlexiBAC: a versatile, open-source baculovirus vector system for protein expression, secretion, and proteolytic processing.
BMC Biotechnol., 19(1) Art. No. 20 (2019)
PubMed Source   

Baculovirus-mediated expression in insect cells is a powerful approach for protein production. However, many existing methods are time-consuming, offer limited options for protein tagging, and are unsuitable for secreted proteins requiring proteolytic maturation, such as TGF-β family growth factors.
@article{Lemaitre7373,
author={Regis P. Lemaitre, Aliona Bogdanova, Barbara Borgonovo, Jeffrey Woodruff, David N. Drechsel},
title={FlexiBAC: a versatile, open-source baculovirus vector system for protein expression, secretion, and proteolytic processing.},
journal ={BMC biotechnology},
volume={19},
issue ={1},
pages={null--null},
year=2019
}