@article{8402, abstract = {Background: The mitochondrial pyruvate carrier (MPC) plays a central role in energy metabolism by transporting pyruvate across the inner mitochondrial membrane. Its heterodimeric composition and homology to SWEET and semiSWEET transporters set the MPC apart from the canonical mitochondrial carrier family (named MCF or SLC25). The import of the canonical carriers is mediated by the carrier translocase of the inner membrane (TIM22) pathway and is dependent on their structure, which features an even number of transmembrane segments and both termini in the intermembrane space. The import pathway of MPC proteins has not been elucidated. The odd number of transmembrane segments and positioning of the N-terminus in the matrix argues against an import via the TIM22 carrier pathway but favors an import via the flexible presequence pathway. Results: Here, we systematically analyzed the import pathways of Mpc2 and Mpc3 and report that, contrary to an expected import via the flexible presequence pathway, yeast MPC proteins with an odd number of transmembrane segments and matrix-exposed N-terminus are imported by the carrier pathway, using the receptor Tom70, small TIM chaperones, and the TIM22 complex. The TIM9·10 complex chaperones MPC proteins through the mitochondrial intermembrane space using conserved hydrophobic motifs that are also required for the interaction with canonical carrier proteins. Conclusions: The carrier pathway can import paired and non-paired transmembrane helices and translocate N-termini to either side of the mitochondrial inner membrane, revealing an unexpected versatility of the mitochondrial import pathway for non-cleavable inner membrane proteins.}, author = {Rampelt, Heike and Sucec, Iva and Bersch, Beate and Horten, Patrick and Perschil, Inge and Martinou, Jean-Claude and van der Laan, Martin and Wiedemann, Nils and Schanda, Paul and Pfanner, Nikolaus}, issn = {1741-7007}, journal = {BMC Biology}, keywords = {Biotechnology, Plant Science, General Biochemistry, Genetics and Molecular Biology, Developmental Biology, Cell Biology, Physiology, Ecology, Evolution, Behavior and Systematics, Structural Biology, General Agricultural and Biological Sciences}, publisher = {Springer Nature}, title = {{The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments}}, doi = {10.1186/s12915-019-0733-6}, volume = {18}, year = {2020}, } @article{8767, abstract = {Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring.}, author = {Kaveh, Kamran and McAvoy, Alex and Chatterjee, Krishnendu and Nowak, Martin A.}, issn = {1553-7358}, journal = {PLOS Computational Biology}, keywords = {Ecology, Modelling and Simulation, Computational Theory and Mathematics, Genetics, Ecology, Evolution, Behavior and Systematics, Molecular Biology, Cellular and Molecular Neuroscience}, number = {11}, publisher = {Public Library of Science}, title = {{The Moran process on 2-chromatic graphs}}, doi = {10.1371/journal.pcbi.1008402}, volume = {16}, year = {2020}, } @article{12189, abstract = {Meiotic crossovers (COs) are important for reshuffling genetic information between homologous chromosomes and they are essential for their correct segregation. COs are unevenly distributed along chromosomes and the underlying mechanisms controlling CO localization are not well understood. We previously showed that meiotic COs are mis-localized in the absence of AXR1, an enzyme involved in the neddylation/rubylation protein modification pathway in Arabidopsis thaliana. Here, we report that in axr1-/-, male meiocytes show a strong defect in chromosome pairing whereas the formation of the telomere bouquet is not affected. COs are also redistributed towards subtelomeric chromosomal ends where they frequently form clusters, in contrast to large central regions depleted in recombination. The CO suppressed regions correlate with DNA hypermethylation of transposable elements (TEs) in the CHH context in axr1-/- meiocytes. Through examining somatic methylomes, we found axr1-/- affects DNA methylation in a plant, causing hypermethylation in all sequence contexts (CG, CHG and CHH) in TEs. Impairment of the main pathways involved in DNA methylation is epistatic over axr1-/- for DNA methylation in somatic cells but does not restore regular chromosome segregation during meiosis. Collectively, our findings reveal that the neddylation pathway not only regulates hormonal perception and CO distribution but is also, directly or indirectly, a major limiting pathway of TE DNA methylation in somatic cells.}, author = {Christophorou, Nicolas and She, Wenjing and Long, Jincheng and Hurel, Aurélie and Beaubiat, Sébastien and Idir, Yassir and Tagliaro-Jahns, Marina and Chambon, Aurélie and Solier, Victor and Vezon, Daniel and Grelon, Mathilde and Feng, Xiaoqi and Bouché, Nicolas and Mézard, Christine}, issn = {1553-7404}, journal = {PLOS Genetics}, keywords = {Cancer Research, Genetics (clinical), Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics}, number = {6}, publisher = {Public Library of Science (PLoS)}, title = {{AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization}}, doi = {10.1371/journal.pgen.1008894}, volume = {16}, year = {2020}, } @article{10895, abstract = {Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. }, author = {Vanneste, Steffen and Friml, Jiří}, issn = {2223-7747}, journal = {Plants}, keywords = {Plant Science, Ecology, Ecology, Evolution, Behavior and Systematics}, number = {4}, pages = {650--675}, publisher = {MDPI}, title = {{Calcium: The missing link in auxin action}}, doi = {10.3390/plants2040650}, volume = {2}, year = {2013}, } @article{11086, abstract = {Faithful execution of developmental gene expression programs occurs at multiple levels and involves many different components such as transcription factors, histone-modification enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation. Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes. In addition, we identify two modes of developmental gene regulation by NUP98 that are differentiated by the spatial localization of NUP98 target genes. Genes in the initial stage of developmental induction can associate with NUP98 that is embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores. This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs.}, author = {Liang, Yun and Franks, Tobias M. and Marchetto, Maria C. and Gage, Fred H. and HETZER, Martin W}, issn = {1553-7404}, journal = {PLoS Genetics}, keywords = {Cancer Research, Genetics (clinical), Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics}, number = {2}, publisher = {Public Library of Science}, title = {{Dynamic association of NUP98 with the human genome}}, doi = {10.1371/journal.pgen.1003308}, volume = {9}, year = {2013}, } @article{12648, abstract = {Distributed glacier melt models generally assume that the glacier surface consists of bare exposed ice and snow. In reality, many glaciers are wholly or partially covered in layers of debris that tend to suppress ablation rates. In this paper, an existing physically based point model for the ablation of debris-covered ice is incorporated in a distributed melt model and applied to Haut Glacier d'Arolla, Switzerland, which has three large patches of debris cover on its surface. The model is based on a 10 m resolution digital elevation model (DEM) of the area; each glacier pixel in the DEM is defined as either bare or debris-covered ice, and may be covered in snow that must be melted off before ice ablation is assumed to occur. Each debris-covered pixel is assigned a debris thickness value using probability distributions based on over 1000 manual thickness measurements. Locally observed meteorological data are used to run energy balance calculations in every pixel, using an approach suitable for snow, bare ice or debris-covered ice as appropriate. The use of the debris model significantly reduces the total ablation in the debris-covered areas, however the precise reduction is sensitive to the temperature extrapolation used in the model distribution because air near the debris surface tends to be slightly warmer than over bare ice. Overall results suggest that the debris patches, which cover 10% of the glacierized area, reduce total runoff from the glacierized part of the basin by up to 7%.}, author = {Reid, T. D. and Carenzo, M. and Pellicciotti, Francesca and Brock, B. W.}, issn = {0148-0227}, journal = {Journal of Geophysical Research: Atmospheres}, keywords = {Paleontology, Space and Planetary Science, Earth and Planetary Sciences (miscellaneous), Atmospheric Science, Earth-Surface Processes, Geochemistry and Petrology, Soil Science, Water Science and Technology, Ecology, Aquatic Science, Forestry, Oceanography, Geophysics}, number = {D18}, publisher = {American Geophysical Union}, title = {{Including debris cover effects in a distributed model of glacier ablation}}, doi = {10.1029/2012jd017795}, volume = {117}, year = {2012}, } @article{12651, abstract = {Temperature data from three Automatic Weather Stations and twelve Temperature Loggers are used to investigate the spatiotemporal variability of temperature over a glacier, its main atmospheric controls, the suitability of extrapolation techniques and their effect on melt modeling. We use data collected on Juncal Norte Glacier, central Chile, during one ablation season. We examine temporal and spatial variability in lapse rates (LRs), together with alternative statistical interpolation methods. The main control over the glacier thermal regime is the development of a katabatic boundary layer (KBL). Katabatic wind occurs at night and in the morning and is eroded in the afternoon. LRs reveal strong diurnal variability, with steeper LRs during the day when the katabatic wind weakens and shallower LRs during the night and morning. We suggest that temporally variable LRs should be used to account for the observed change. They tend to be steeper than equivalent constant LRs, and therefore result in a reduction in simulated melt compared to use of constant LRs when extrapolating from lower to higher elevations. In addition to the temporal variability, the temperature-elevation relationship varies also in space. Differences are evident between local LRs and including such variability in melt modeling affects melt simulations. Extrapolation methods based on the spatial variability of the observations after removal of the elevation trend, such as Inverse Distance Weighting or Kriging, do not seem necessary for simulations of gridded temperature data over a glacier.}, author = {Petersen, L. and Pellicciotti, Francesca}, issn = {0148-0227}, journal = {Journal of Geophysical Research: Atmospheres}, keywords = {Paleontology, Space and Planetary Science, Earth and Planetary Sciences (miscellaneous), Atmospheric Science, Earth-Surface Processes, Geochemistry and Petrology, Soil Science, Water Science and Technology, Ecology, Aquatic Science, Forestry, Oceanography, Geophysics}, number = {D23}, publisher = {American Geophysical Union}, title = {{Spatial and temporal variability of air temperature on a melting glacier: Atmospheric controls, extrapolation methods and their effect on melt modeling, Juncal Norte Glacier, Chile}}, doi = {10.1029/2011jd015842}, volume = {116}, year = {2011}, } @article{12658, abstract = {[1] During the ablation period 2001 a glaciometeorological experiment was carried out on Haut Glacier d'Arolla, Switzerland. Five meteorological stations were installed on the glacier, and one permanent automatic weather station in the glacier foreland. The altitudes of the stations ranged between 2500 and 3000 m a.s.l., and they were in operation from end of May to beginning of September 2001. The spatial arrangement of the stations and temporal duration of the measurements generated a unique data set enabling the analysis of the spatial and temporal variability of the meteorological variables across an alpine glacier. All measurements were taken at a nominal height of 2 m, and hourly averages were derived for the analysis. The wind regime was dominated by the glacier wind (mean value 2.8 m s−1) but due to erosion by the synoptic gradient wind, occasionally the wind would blow up the valley. A slight decrease in mean 2 m air temperatures with altitude was found, however the 2 m air temperature gradient varied greatly and frequently changed its sign. Mean relative humidity was 71% and exhibited limited spatial variation. Mean incoming shortwave radiation and albedo both generally increased with elevation. The different components of shortwave radiation are quantified with a parameterization scheme. Resulting spatial variations are mainly due to horizon obstruction and reflections from surrounding slopes, i.e., topography. The effect of clouds accounts for a loss of 30% of the extraterrestrial flux. Albedos derived from a Landsat TM image of 30 July show remarkably constant values, in the range 0.49 to 0.50, across snow covered parts of the glacier, while albedo is highly spatially variable below the zone of continuous snow cover. These results are verified with ground measurements and compared with parameterized albedo. Mean longwave radiative fluxes decreased with elevation due to lower air temperatures and the effect of upper hemisphere slopes. It is shown through parameterization that this effect would even be more pronounced without the effect of clouds. Results are discussed with respect to a similar study which has been carried out on Pasterze Glacier (Austria). The presented algorithms for interpolating, parameterizing and simulating variables and parameters in alpine regions are integrated in the software package AMUNDSEN which is freely available to be adapted and further developed by the community.}, author = {Strasser, Ulrich and Corripio, Javier and Pellicciotti, Francesca and Burlando, Paolo and Brock, Ben and Funk, Martin}, issn = {0148-0227}, journal = {Journal of Geophysical Research: Atmospheres}, keywords = {Paleontology, Space and Planetary Science, Earth and Planetary Sciences (miscellaneous), Atmospheric Science, Earth-Surface Processes, Geochemistry and Petrology, Soil Science, Water Science and Technology, Ecology, Aquatic Science, Forestry, Oceanography, Geophysics}, number = {D3}, publisher = {American Geophysical Union}, title = {{Spatial and temporal variability of meteorological variables at Haut Glacier d'Arolla (Switzerland) during the ablation season 2001: Measurements and simulations}}, doi = {10.1029/2003jd003973}, volume = {109}, year = {2004}, }