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Malte Lehmann, Elisabeth Knust, Sarita Hebbar
Drosophila melanogaster: A Valuable Genetic Model Organism to Elucidate the Biology of Retinitis Pigmentosa.
Methods Mol Biol, 1834 221-249 (2019)
PubMed Source   

Retinitis pigmentosa (RP) is a complex inherited disease. It is associated with mutations in a wide variety of genes with many different functions. These mutations impact the integrity of rod photoreceptors and ultimately result in the progressive degeneration of rods and cone photoreceptors in the retina, leading to complete blindness. A hallmark of this disease is the variable degree to which symptoms are manifest in patients. This is indicative of the influence of the environment, and/or of the distinct genetic makeup of the individual.The fruit fly, Drosophila melanogaster, has effectively proven to be a great model system to better understand interconnected genetic networks. Unraveling genetic interactions and thereby different cellular processes is relatively easy because more than a century of research on flies has enabled the creation of sophisticated genetic tools to perturb gene function. A remarkable conservation of disease genes across evolution and the similarity of the general organization of the fly and vertebrate photoreceptor cell had prompted research on fly retinal degeneration. To date six fly models for RP, including RP4, RP11, RP12, RP14, RP25, and RP26, have been established, and have provided useful information on RP disease biology. In this chapter, an outline of approaches and experimental specifications are described to enable utilizing or developing new fly models of RP.
@article{Lehmann7271,
author={Malte Lehmann, Elisabeth Knust, Sarita Hebbar},
title={Drosophila melanogaster: A Valuable Genetic Model Organism to Elucidate the Biology of Retinitis Pigmentosa.},
journal ={Methods in molecular biology (Clifton, N.J.)},
volume={1834},
pages={221--249},
year=2019
}

Monalisa Mishra, Elisabeth Knust
Analysis of the Drosophila Compound Eye with Light and Electron Microscopy.
Methods Mol Biol, 1834 345-364 (2019)
PubMed Source   

The Drosophila compound eye is composed of about 750 units, called ommatidia, which are arranged in a highly regular pattern. Eye development proceeds in a stereotypical fashion, where epithelial cells of the eye imaginal discs are specified, recruited, and differentiated in a sequential order that leads to the highly precise structure of an adult eye. Even small perturbations, for example in signaling pathways that control proliferation, cell death, or differentiation, can impair the regular structure of the eye, which can be easily detected and analyzed. In addition, the Drosophila eye has proven to be an ideal model for studying the genetic control of neurodegeneration, since the eye is not essential for viability. Several human neurodegeneration diseases have been modeled in the fly, leading to a better understanding of the function/misfunction of the respective gene. In many cases, the genes involved and their functions are conserved between flies and human. More strikingly, when ectopically expressed in the fly eye some human genes, even those without a Drosophila counterpart, can induce neurodegeneration, detectable by aberrant phototaxis, impaired electrophysiology, or defects in eye morphology and retinal histology. These defects are often rather subtle alteration in shape, size, or arrangement of the cells, and can be easily scored at the ultrastructural level. This chapter aims to provide an overview regarding the analysis of the retina by light and electron microscopy.
@article{Mishra7270,
author={Monalisa Mishra, Elisabeth Knust},
title={Analysis of the Drosophila Compound Eye with Light and Electron Microscopy.},
journal ={Methods in molecular biology (Clifton, N.J.)},
volume={1834},
pages={345--364},
year=2019
}

Giorgio Fracasso, Yvonne Körner, David Thomas Gonzales, T-Y Dora Tang
In vitro gene expression and detergent free reconstitution of active proteorhodopsin in lipid vesicles
Experimental Biology and Medicine, in press 1-1 (2018)
 

@article{Fracasso7286,
author={Giorgio Fracasso, Yvonne Körner, David Thomas Gonzales, T-Y Dora Tang},
title={In vitro gene expression and detergent free reconstitution of active proteorhodopsin in lipid vesicles},
journal ={Experimental Biology and Medicine},
volume={in press},
pages={1--1},
year=2018
}

Björn Langer, Juliana Roscito, Michael Hiller
REforge Associates Transcription Factor Binding Site Divergence in Regulatory Elements with Phenotypic Differences between Species.
Mol Biol Evol, 35(12) 3027-3040 (2018)
  PubMed Source   

Elucidating the genomic determinants of morphological differences between species is key to understanding how morphological diversity evolved. While differences in cis-regulatory elements are an important genetic source for morphological evolution, it remains challenging to identify regulatory elements involved in phenotypic differences. Here, we present Regulatory Element forward genomics (REforge), a computational approach that detects associations between transcription factor binding site divergence in putative regulatory elements and phenotypic differences between species. By simulating regulatory element evolution in silico, we show that this approach has substantial power to detect such associations. To validate REforge on real data, we used known binding motifs for eye-related transcription factors and identified significant binding site divergence in vision-impaired subterranean mammals in 1% of all conserved noncoding elements. We show that these genomic regions are significantly enriched in regulatory elements that are specifically active in mouse eye tissues, and that several of them are located near genes, which are required for eye development and photoreceptor function and are implicated in human eye disorders. Thus, our genome-wide screen detects widespread divergence of eye-regulatory elements and highlights regulatory regions that likely contributed to eye degeneration in subterranean mammals. REforge has broad applicability to detect regulatory elements that could be involved in many other phenotypes, which will help to reveal the genomic basis of morphological diversity.
@article{Langer7220,
author={Björn Langer, Juliana Roscito, Michael Hiller},
title={REforge Associates Transcription Factor Binding Site Divergence in Regulatory Elements with Phenotypic Differences between Species.},
journal ={Molecular biology and evolution},
volume={35},
issue ={12},
pages={3027--3040},
year=2018
}

Hiroo Tanaka, Mitsunobu Imasato, Yuji Yamazaki, Kengo Matsumoto, Koshi Kunimoto, Julien Delpierre, Kirstin Meyer, Marino Zerial, Naho Kitamura, Mitsuhiro Watanabe, Atsushi Tamura, Sachiko Tsukita
Claudin-3 regulates bile canalicular paracellular barrier and cholesterol gallstone core formation in mice.
J Hepatol, 69(6) 1308-1316 (2018)
PubMed Source   

Most cholesterol gallstones have a core consisting of inorganic and/or organic calcium salts, although the mechanisms of core formation are poorly understood. We examined whether the paracellular permeability of ions at hepatic tight junctions is involved in the core formation of cholesterol gallstones, with particular interest in the role of phosphate ion, a common food additive and preservative.
@article{Tanaka7241,
author={Hiroo Tanaka, Mitsunobu Imasato, Yuji Yamazaki, Kengo Matsumoto, Koshi Kunimoto, Julien Delpierre, Kirstin Meyer, Marino Zerial, Naho Kitamura, Mitsuhiro Watanabe, Atsushi Tamura, Sachiko Tsukita},
title={Claudin-3 regulates bile canalicular paracellular barrier and cholesterol gallstone core formation in mice.},
journal ={Journal of hepatology},
volume={69},
issue ={6},
pages={1308--1316},
year=2018
}

Frederic Berndt, Gopi Shah, Rory M Power, Jan Brugués, Jan Huisken
Dynamic and non-contact 3D sample rotation for microscopy
Nat Commun, 9 Art. No. 5025 (2018)
Source  

@article{Berndt7285,
author={Frederic Berndt, Gopi Shah, Rory M Power, Jan Brugués, Jan Huisken},
title={Dynamic and non-contact 3D sample rotation for microscopy},
journal ={Nature communications},
volume={9},
pages={null--null},
year=2018
}

Nereo Kalebic, Carlotta Gilardi, Mareike Albert, Takashi Namba, Katherine S. Long, Milos Kostic, Barbara Langen, Wieland Huttner
Human-specific ARHGAP11B induces hallmarks of neocortical expansion in developing ferret neocortex.
Elife, 7 Art. No. e41241 (2018)
PubMed Source   

The evolutionary increase in size and complexity of the primate neocortex is thought to underlie the higher cognitive abilities of humans. ARHGAP11B is a human-specific gene that, based on its expression pattern in fetal human neocortex and progenitor effects in embryonic mouse neocortex, has been proposed to have a key function in the evolutionary expansion of the neocortex. Here, we study the effects of ARHGAP11B expression in the developing neocortex of the gyrencephalic ferret. In contrast to its effects in mouse, ARHGAP11B markedly increases proliferative basal radial glia, a progenitor cell type thought to be instrumental for neocortical expansion, and results in extension of the neurogenic period and an increase in upper-layer neurons. Consequently, the postnatal ferret neocortex exhibits increased neuron density in the upper cortical layers and expands in both the radial and tangential dimensions. Thus, human-specific ARHGAP11B can elicit hallmarks of neocortical expansion in the developing ferret neocortex.
@article{Kalebic7283,
author={Nereo Kalebic, Carlotta Gilardi, Mareike Albert, Takashi Namba, Katherine S. Long, Milos Kostic, Barbara Langen, Wieland Huttner},
title={Human-specific ARHGAP11B induces hallmarks of neocortical expansion in developing ferret neocortex.},
journal ={eLife},
volume={7},
pages={null--null},
year=2018
}

Björn Langer, Michael Hiller
TFforge utilizes large-scale binding site divergence to identify transcriptional regulators involved in phenotypic differences.
Nucleic Acids Res, Art. No. doi: 10.1093/nar/gky1200 (2018)
PubMed Source   

Changes in gene regulation are important for phenotypic and in particular morphological evolution. However, it remains challenging to identify the transcription factors (TFs) that contribute to differences in gene regulation and thus to phenotypic differences between species. Here, we present TFforge (Transcription Factor forward genomics), a computational method to identify TFs that are involved in the loss of phenotypic traits. TFforge screens an input set of regulatory genomic regions to detect TFs that exhibit a significant binding site divergence signature in species that lost a particular phenotypic trait. Using simulated data of modular and pleiotropic regulatory elements, we show that TFforge can identify the correct TFs for many different evolutionary scenarios. We applied TFforge to available eye regulatory elements to screen for TFs that exhibit a significant binding site decay signature in subterranean mammals. This screen identified interacting and co-binding eye-related TFs, and thus provides new insights into which TFs likely contribute to eye degeneration in these species. TFforge has broad applicability to identify the TFs that contribute to phenotypic changes between species, and thus can help to unravel the gene-regulatory differences that underlie phenotypic evolution.
@article{Langer7252,
author={Björn Langer, Michael Hiller},
title={TFforge utilizes large-scale binding site divergence to identify transcriptional regulators involved in phenotypic differences.},
journal ={Nucleic acids research},
volume={},
pages={null--null},
year=2018
}

Andrei Rozanski, HongKee Moon, Holger Brandl, José M Martín-Durán, Markus Grohme, Katja Hüttner, Kerstin Bartscherer, Ian Henry, Jochen Rink
PlanMine 3.0-improvements to a mineable resource of flatworm biology and biodiversity.
Nucleic Acids Res, Art. No. doi: 10.1093/nar/gky1070 (2018)
PubMed Source   

Flatworms (Platyhelminthes) are a basally branching phylum that harbours a wealth of fascinating biology, including planarians with their astonishing regenerative abilities and the parasitic tape worms and blood flukes that exert a massive impact on human health. PlanMine (http://planmine.mpi-cbg.de/) has the mission objective of providing both a mineable sequence repository for planarians and also a resource for the comparative analysis of flatworm biology. While the original PlanMine release was entirely based on transcriptomes, the current release transitions to a more genomic perspective. Building on the recent availability of a high quality genome assembly of the planarian model species Schmidtea mediterranea, we provide a gene prediction set that now assign existing transcripts to defined genomic coordinates. The addition of recent single cell and bulk RNA-seq datasets greatly expands the available gene expression information. Further, we add transcriptomes from a broad range of other flatworms and provide a phylogeny-aware interface that makes evolutionary species comparisons accessible to non-experts. At its core, PlanMine continues to utilize the powerful InterMine framework and consistent data annotations to enable meaningful inter-species comparisons. Overall, PlanMine 3.0 thus provides a host of new features that makes the fascinating biology of flatworms accessible to the wider research community.
@article{Rozanski7279,
author={Andrei Rozanski, HongKee Moon, Holger Brandl, José M Martín-Durán, Markus Grohme, Katja Hüttner, Kerstin Bartscherer, Ian Henry, Jochen Rink},
title={PlanMine 3.0-improvements to a mineable resource of flatworm biology and biodiversity.},
journal ={Nucleic acids research},
volume={},
pages={null--null},
year=2018
}

Juliana Roscito, Katrin Sameith, Martin Pippel, Kees-Jan Francoijs, Sylke Winkler, Andreas Dahl, Georg Papoutsoglou, Gene Myers, Michael Hiller
The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly.
GigaScience, Art. No. doi: 10.1093/gigascience/giy141 (2018)
PubMed Source   

Reptiles are a species-rich group with great phenotypic and life history diversity, but are highly underrepresented among the vertebrate species with sequenced genomes.
@article{Roscito7206,
author={Juliana Roscito, Katrin Sameith, Martin Pippel, Kees-Jan Francoijs, Sylke Winkler, Andreas Dahl, Georg Papoutsoglou, Gene Myers, Michael Hiller},
title={The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly.},
journal ={GigaScience},
volume={},
pages={null--null},
year=2018
}