TY  - JOUR
A1  - Brzezinka, Krzysztof
A1  - Altmann, Simone
A1  - Czesnick, Hjördis
A1  - Nicolas, Philippe
A1  - Gorka, Michal
A1  - Benke, Eileen
A1  - Kabelitz, Tina
A1  - Jähne, Felix
A1  - Graf, Alexander
A1  - Kappel, Christian
A1  - Bäurle, Isabel
T1  - Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling
JF  - eLife
N2  - Plants as sessile organisms can adapt to environmental stress to mitigate its adverse effects. As part of such adaptation they maintain an active memory of heat stress for several days that promotes a more efficient response to recurring stress. We show that this heat stress memory requires the activity of the FORGETTER1 (FGT1) locus, with fgt1 mutants displaying reduced maintenance of heat-induced gene expression. FGT1 encodes the Arabidopsis thaliana orthologue of Strawberry notch (Sno), and the protein globally associates with the promoter regions of actively expressed genes in a heat-dependent fashion. FGT1 interacts with chromatin remodelers of the SWI/ SNF and ISWI families, which also display reduced heat stress memory. Genomic targets of the BRM remodeler overlap significantly with FGT1 targets. Accordingly, nucleosome dynamics at loci with altered maintenance of heat-induced expression are affected in fgt1. Together, our results suggest that by modulating nucleosome occupancy, FGT1 mediates stress-induced chromatin memory.
Y1  - 2016
U6  - https://doi.org/10.7554/eLife.17061
SN  - 2050-084X
VL  - 5
PB  - eLife Sciences Publications
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Schlägel, Ulrike E.
A1  - Lewis, Mark A.
T1  - A framework for analyzing the robustness of movement models to variable step discretization
JF  - Journal of mathematical biology
N2  - When sampling animal movement paths, the frequency at which location measurements are attempted is a critical feature for data analysis. Important quantities derived from raw data, e.g. travel distance or sinuosity, can differ largely based on the temporal resolution of the data. Likewise, when movement models are fitted to data, parameter estimates have been demonstrated to vary with sampling rate. Thus, biological statements derived from such analyses can only be made with respect to the resolution of the underlying data, limiting extrapolation of results and comparison between studies. To address this problem, we investigate whether there are models that are robust against changes in temporal resolution. First, we propose a mathematically rigorous framework, in which we formally define robustness as a model property. We then use the framework for a thorough assessment of a range of basic random walk models, in which we also show how robustness relates to other probabilistic concepts. While we found robustness to be a strong condition met by few models only, we suggest a new method to extend models so as to make them robust. Our framework provides a new systematic, mathematically founded approach to the question if, and how, sampling rate of movement paths affects statistical inference.
KW  - Animal movement
KW  - Random walk
KW  - Sampling rate
KW  - Discretization
KW  - GPS data
KW  - Parameter estimation
Y1  - 2016
U6  - https://doi.org/10.1007/s00285-016-0969-5
SN  - 0303-6812
SN  - 1432-1416
VL  - 73
SP  - 815
EP  - 845
PB  - Springer
CY  - Heidelberg
ER  - 
TY  - JOUR
A1  - Schlägel, Ulrike E.
A1  - Lewis, Mark A.
T1  - Robustness of movement models: can models bridge the gap between temporal scales of data sets and behavioural processes?
JF  - Journal of mathematical biology
KW  - Animal movement
KW  - Sampling rate
KW  - Resource selection
KW  - GPS data
KW  - Parameter estimation
KW  - Markov model
Y1  - 2016
U6  - https://doi.org/10.1007/s00285-016-1005-5
SN  - 0303-6812
SN  - 1432-1416
VL  - 73
SP  - 1691
EP  - 1726
PB  - Springer
CY  - Heidelberg
ER  - 
TY  - JOUR
A1  - Lamanna, Francesco
A1  - Kirschbaum, Frank
A1  - Ernst, Anja R. R.
A1  - Feulner, Philine G. D.
A1  - Mamonekene, Victor
A1  - Paul, Christiane
A1  - Tiedemann, Ralph
T1  - Species delimitation and phylogenetic relationships in a genus of African weakly-electric fishes (Osteoglossiformes, Mormyridae, Campylomormyrus)
JF  - Molecular phylogenetics and evolution
N2  - African weakly-electric fishes (Mormyridae) are able to communicate through species-specific electric signals; this feature might have favoured the evolutionary radiation observed in this family (over 200 species) by acting as an effective pre-zygotic isolation mechanism. In the present study we used mitochondria((cytb) and nuclear (rps7, scn4aa) markers in order to reconstruct a species-phylogeny and identify species boundaries for the genus Campylomormyrus, by applying inference methods based on the multispecies coalescent model. Additionally, we employed 16 microsatellite markers, landmark-based morphometric measurements, and electro-physiological analyses as independent lines of evidence to the results obtained from the sequence data. The results show that groups that are morphologically different are also significantly divergent at the genetic level, whereas morphologically similar groups, displaying dissimilar electric signals, do not show enough genetic diversity to be considered separate species. Furthermore, the data confirm the presence of a yet undescribed species within the genus Campylomormyrus. (C) 2016 Elsevier Inc. All rights reserved.
KW  - Mormyridae
KW  - Multispecies-coalescent
KW  - Campylomormyrus
KW  - Geometric morphometrics
KW  - Microsatellites
KW  - Species-delimitation
Y1  - 2016
U6  - https://doi.org/10.1016/j.ympev.2016.04.035
SN  - 1055-7903
SN  - 1095-9513
VL  - 101
SP  - 8
EP  - 18
PB  - Elsevier
CY  - San Diego
ER  - 
TY  - JOUR
A1  - Paul, Christiane
A1  - Kirschbaum, Frank
A1  - Mamonekene, Victor
A1  - Tiedemann, Ralph
T1  - Evidence for Non-neutral Evolution in a Sodium Channel Gene in African Weakly Electric Fish (Campylomormyrus, Mormyridae)
JF  - Journal of molecular evolution
N2  - Voltage-gated sodium channels, Nav1, play a crucial role in the generation and propagation of action potentials and substantially contribute to the shape of their rising phase. The electric organ discharge (EOD) of African weakly electric fish (Mormyroidea) is the sum of action potentials fired from all electrocytes of the electric organ at the same time and hence voltage-gated sodium channels are one factor—together with the electrocyte’s morphology and innervation pattern—that determines the properties of these EODs. Due to the fish-specific genome duplication, teleost fish possess eight copies of sodium channel genes (SCN), which encode for Nav1 channels. In mormyroids, SCN4aa is solely expressed in the electrocytes of the adult electric organ. In this study, we compared entire SCN4aa sequences of six species of the genus Campylomormyrus and identified nonsynonymous substitutions among them. SCN4aa in Campylomormyrus exhibits a much higher evolutionary rate compared to its paralog SCN4ab, whose expression is not restricted to the electric organ. We also found evidence for strong positive selection on the SCN4aa gene within Mormyridae and along the lineage ancestral to the Mormyridae. We have identified sites at which all nonelectric teleosts are monomorphic in their amino acid, but mormyrids have different amino acids. Our findings confirm the crucial role of SCN4aa in EOD evolution among mormyrid weakly electric fish. The inferred positive selection within Mormyridae makes this gene a prime candidate for further investigation of the divergent evolution of pulse-type EODs among closely related species.
KW  - Mormyridae
KW  - Mormyroidea
KW  - Campylomormyrus
KW  - SCN4aa
KW  - Voltage-gated sodium channel
KW  - Positive selection
Y1  - 2016
U6  - https://doi.org/10.1007/s00239-016-9754-8
SN  - 0022-2844
SN  - 1432-1432
VL  - 83
SP  - 61
EP  - 77
PB  - Springer
CY  - New York
ER  - 
TY  - JOUR
A1  - Hartmann, Bianca
A1  - Wai, Timothy
A1  - Hu, Hao
A1  - MacVicar, Thomas
A1  - Musante, Luciana
A1  - Fischer-Zirnsak, Björn
A1  - Stenzel, Werner
A1  - Gräf, Ralph
A1  - van den Heuvel, Lambert
A1  - Ropers, Hans-Hilger
A1  - Wienker, Thomas F.
A1  - Hübner, Christoph
A1  - Langer, Thomas
A1  - Kaindl, Angela M.
T1  - Homozygous YME1L1 Mutation Causes Mitochondriopathy with Optic Atrophy and Mitochondrial Network Fragmentation
JF  - eLife
N2  - Mitochondriopathies often present clinically as multisystemic disorders of primarily high-energy consuming organs. Assembly, turnover, and surveillance of mitochondrial proteins are essential for mitochondrial function and a key task of AAA family members of metalloproteases. We identified a homozygous mutation in the nuclear encoded mitochondrial escape 1-like 1 gene YME1L1, member of the AAA protease family, as a cause of a novel mitochondriopathy in a consanguineous pedigree of Saudi Arabian descent. The homozygous missense mutation, located in a highly conserved region in the mitochondrial pre-sequence, inhibits cleavage of YME1L1 by the mitochondrial processing peptidase, which culminates in the rapid degradation of YME1L1 precursor protein. Impaired YME1L1 function causes a proliferation defect and mitochondrial network fragmentation due to abnormal processing of OPA1. Our results identify mutations in YME1L1 as a cause of a mitochondriopathy with optic nerve atrophy highlighting the importance of YME1L1 for mitochondrial functionality in humans.
KW  - YME1L1
KW  - mitochondriopathy
KW  - intellectual disability
KW  - optic atrophy
KW  - OPA1
KW  - mitochondrial fragmentation
Y1  - 2016
U6  - https://doi.org/10.7554/eLife.16078
SN  - 2050-084X
VL  - 5
SP  - 1156
EP  - 1165
PB  - eLife Sciences Publications
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Putzler, Sascha
A1  - Meyer, Irene
A1  - Gräf, Ralph
T1  - CP91 is a component of the Dictyostelium centrosome involved in centrosome biogenesis
JF  - European journal of cell biology
N2  - The Dictyostelium centrosome is a model for acentriolar centrosomes and it consists of a three-layered core structure surrounded by a corona harboring microtubule nucleation complexes. Its core structure duplicates once per cell cycle at the G2/M transition. Through proteomic analysis of isolated centrosomes we have identified CP91, a 91-kDa coiled coil protein that was localized at the centrosomal core structure. While GFP-CP91 showed almost no mobility in FRAP experiments during interphase, both GFP-CP91 and endogenous CP91 dissociated during mitosis and were absent from spindle poles from late prophase to anaphase. Since this behavior correlates with the disappearance of the central layer upon centrosome duplication, CP91 is a putative component of this layer. When expressed as GFP-fusions, CP91 fragments corresponding to the central coiled coil domain and the preceding N-terminal part (GFP-CP91cc and GFP-CP91N, respectively) also localized to the centrosome but did not show the mitotic redistribution of the full length protein suggesting a regulatory role of the C-terminal domain. Expression of all GFP-fusion proteins suppressed expression of endogenous CP91 and elicited supernumerary centrosomes. This was also very prominent upon depletion of CP91 by RNAi. Additionally, CP91-RNAi cells exhibited heavily increased ploidy due to severe defects in chromosome segregation along with increased cell size and defects in the abscission process during cytokinesis. Our results indicate that CP91 is a central centrosomal core component required for centrosomal integrity, proper centrosome biogenesis and, independently, for abscission during cytokinesis. (c) 2016 Elsevier GmbH. All rights reserved.
KW  - Dictyostelium
KW  - Mitosis
KW  - Microtubules
KW  - Centrosome
KW  - Nucleus
Y1  - 2016
U6  - https://doi.org/10.1016/j.ejcb.2016.03.001
SN  - 0171-9335
SN  - 1618-1298
VL  - 95
SP  - 124
EP  - 135
PB  - Royal Society
CY  - Jena
ER  - 
TY  - JOUR
A1  - Batsios, Petros
A1  - Ren, Xiang
A1  - Baumann, Otto
A1  - Larochelle, Denis A.
A1  - Gräf, Ralph
T1  - Src1 is a Protein of the Inner Nuclear Membrane Interacting with the Dictyostelium Lamin NE81
JF  - Cells
N2  - The nuclear envelope (NE) consists of the outer and inner nuclear membrane (INM), whereby the latter is bound to the nuclear lamina. Src1 is a Dictyostelium homologue of the helix-extension-helix family of proteins, which also includes the human lamin-binding protein MAN1. Both endogenous Src1 and GFP-Src1 are localized to the NE during the entire cell cycle. Immuno-electron microscopy and light microscopy after differential detergent treatment indicated that Src1 resides in the INM. FRAP experiments with GFP-Src1 cells suggested that at least a fraction of the protein could be stably engaged in forming the nuclear lamina together with the Dictyostelium lamin NE81. Both a BioID proximity assay and mis-localization of soluble, truncated mRFP-Src1 at cytosolic clusters consisting of an intentionally mis-localized mutant of GFP-NE81 confirmed an interaction of Src1 and NE81. Expression GFP-Src11–646, a fragment C-terminally truncated after the first transmembrane domain, disrupted interaction of nuclear membranes with the nuclear lamina, as cells formed protrusions of the NE that were dependent on cytoskeletal pulling forces. Protrusions were dependent on intact microtubules but not actin filaments. Our results indicate that Src1 is required for integrity of the NE and highlight Dictyostelium as a promising model for the evolution of nuclear architecture.
KW  - Dictyostelium
KW  - lamin
KW  - nuclear lamina
KW  - nucleus
KW  - nucleolus
KW  - HeH-protein
KW  - LEM-domain protein
Y1  - 2016
U6  - https://doi.org/10.3390/cells5010013
SN  - 2073-4409
VL  - 5
IS  - 1
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Edlich, Alexander
A1  - Gerecke, Christian
A1  - Giulbudagian, Michael
A1  - Neumann, Falko
A1  - Hedtrich, Sarah
A1  - Schaefer-Korting, Monika
A1  - Ma, Nan
A1  - Calderon, Marcelo
A1  - Kleuser, Burkhard
T1  - Specific uptake mechanisms of well-tolerated thermoresponsive polyglycerol-based nanogels in antigen-presenting cells of the skin
JF  - European Journal of Pharmaceutics and Biopharmaceutics
N2  - Engineered nanogels are of high value for a targeted and controlled transport of compounds due to the ability to change their chemical properties by external stimuli. As it has been indicated that nanogels possess a high ability to penetrate the stratum corneum, it cannot be excluded that nanogels interact with dermal dendritic cells, especially in diseased skin. In this study the potential crosstalk of the thermore-sponsive nanogels (tNGs) with the dendritic cells of the skin was investigated with the aim to determine the immunotoxicological properties of the nanogels. The investigated tNGs were made of dendritic polyglycerol (dPG) and poly(glycidyl methyl ether-co-ethyl glycidyl ether) (p(GME-co-EGE)), as polymer conferring thermoresponsive properties. Although the tNGs were taken up, they displayed neither cytotoxic and genotoxic effects nor any induction of reactive oxygen species in the tested cells. Interestingly, specific uptake mechanisms of the tNGs by the dendritic cells were depending on the nanogels cloud point temperature (Tcp), which determines the phase transition of the nanoparticle. The study points to caveolae-mediated endocytosis as being the major tNGs uptake mechanism at 37 degrees C, which is above the Tcp of the tNGs. Remarkably, an additional uptake mechanism, beside caveolae-mediated endocytosis, was observed at 29 degrees C, which is the Tcp of the tNGs. At this temperature, which is characterized by two different states of the tNGs, macropinocytosis was involved as well. In summary, our study highlights the impact of thermoresponsivity on the cellular uptake mechanisms which has to be taken into account if the tNGs are used as a drug delivery system.
KW  - Dendritic cells
KW  - Drug delivery systems
KW  - Nanogel
KW  - Nanoparticle
KW  - Nanoparticle uptake
KW  - Nanotoxicology
Y1  - 2017
U6  - https://doi.org/10.1016/j.ejpb.2016.12.016
SN  - 0939-6411
SN  - 1873-3441
VL  - 116
SP  - 155
EP  - 163
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Heinze, Johannes
A1  - Gensch, Sabine
A1  - Weber, Ewald
A1  - Joshi, Jasmin Radha
T1  - Soil temperature modifies effects of soil biota on plant growth
JF  - Journal of plant ecology
N2  - Aims Plants directly and indirectly interact with many abiotic and biotic soil components. Research so far mostly focused on direct, individual abiotic or biotic effects on plant growth, but only few studies tested the indirect effects of abiotic soil factors on plant growth. Therefore, we investigated how abiotic soil conditions affect plant performance, via changes induced by soil biota. Methods In a full-factorial experiment, we grew the widespread grass Dactylis glomerata either with or without soil biota and investigated the impact of soil temperature, fertility and moisture on the soil biota effects on plant growth. We measured biomass production, root traits and colonization by arbuscular mycorrhizal fungi as well as microbial respiration. Important Findings We found significant interaction effects between abiotic soil conditions and soil biota on plant growth for fertility, but especially for soil temperature, as an increase of 10 degrees C significantly changed the soil biota effects on plant growth from positive to neutral. However, if tested individually, an increase in soil temperature and fertility per se positively affected plant biomass production, whereas soil biota per se did not affect overall plant growth, but both influenced root architecture. By affecting soil microbial activity and root architecture, soil temperature might influence both mutualistic and pathogenic interactions between plants and soil biota. Such soil temperature effects should be considered in soil feedback studies to ensure greater transferability of results from artificial and experimental conditions to natural environmental conditions.
KW  - plant-soil interaction
KW  - soil biota
KW  - abiotic soil factors
KW  - root traits
KW  - plant growth
Y1  - 2016
U6  - https://doi.org/10.1093/jpe/rtw097
SN  - 1752-9921
SN  - 1752-993X
VL  - 10
SP  - 808
EP  - 821
PB  - Oxford Univ. Press
CY  - Oxford
ER  -