TY - JOUR A1 - Omidbakhshfard, Mohammad Amin A1 - Proost, Sebastian A1 - Fujikura, Ushio A1 - Müller-Röber, Bernd T1 - Growth-Regulating Factors (GRFs): A Small Transcription Factor Family with Important Functions in Plant Biology JF - Molecular plant N2 - Growth-regulating factors (GRFs) are plant-specific transcription factors that were originally identified for their roles in stem and leaf development, but recent studies highlight them to be similarly important for other central developmental processes including flower and seed formation, root development, and the coordination of growth processes under adverse environmental conditions. The expression of several GRFs is controlled by microRNA miR396, and the GRF-miRNA396 regulatory module appears to be central to several of these processes. In addition, transcription factors upstream of GRFs and miR396 have been discovered, and gradually downstream target genes of GRFs are being unraveled. Here, we review the current knowledge of the biological functions performed by GRFs and survey available molecular data to illustrate how they exert their roles at the cellular level. KW - abiotic stress KW - chromatin remodeling KW - flower development KW - growth regulation KW - leaf development KW - miRNA Y1 - 2015 U6 - https://doi.org/10.1016/j.molp.2015.01.013 SN - 1674-2052 SN - 1752-9867 VL - 8 IS - 7 SP - 998 EP - 1010 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Sree, K. Sowjanya A1 - Keresztes, Aron A1 - Müller-Röber, Bernd A1 - Brandt, Ronny A1 - Eberius, Matthias A1 - Fischer, Wolfgang A1 - Appenroth, Klaus-J. T1 - Phytotoxicity of cobalt ions on the duckweed Lemna minor - Morphology, ion uptake, and starch accumulation JF - Chemosphere : chemistry, biology and toxicology as related to environmental problems N2 - Cobalt (Co2+) inhibits vegetative growth of Lemna minor gradually from 1 mu M to 100 mu M. Fronds accumulated up to 21 mg Co2+ g(-1) dry weight at 10 mu M external Co2+ indicating hyperaccumulation. Interestingly, accumulation of Co2+ did not decrease the iron (Fe) content in fronds, highlighting L. minor as a suitable system for studying effects of Co2+ undisturbed by Fe deficiency symptoms unlike most other plants. Digital image analysis revealed the size distribution of fronds after Co2+ treatment and also a reduction in pigmentation of newly formed daughter fronds unlike the mother fronds during the 7-day treatment. Neither chlorophyll nor photosystem II fluorescence changed significantly during the initial 4 d, indicating effective photosynthesis. During the later phase of the 7-day treatment, however, chlorophyll content and photosynthetic efficiency decreased in the Co2+-treated daughter fronds, indicating that Co2+ inhibits the biosynthesis of chlorophyll rather than leading to the destruction of pre-existing pigment molecules. In addition, during the first 4 d of Co2+ treatment starch accumulated in the fronds and led to the transition of chloroplasts to chloro-amyloplasts and amylo-chloroplasts, while starch levels strongly decreased thereafter. (C) 2015 Elsevier Ltd. All rights reserved. KW - Chloroplast KW - Cobalt KW - Lemnaceae KW - Lemna minor KW - Phytotoxicity KW - Starch accumulation Y1 - 2015 U6 - https://doi.org/10.1016/j.chemosphere.2015.03.008 SN - 0045-6535 SN - 1879-1298 VL - 131 SP - 149 EP - 156 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Topping, Christopher J. A1 - Alroe, Hugo Fjelsted A1 - Farrell, Katharine N. A1 - Grimm, Volker T1 - Per Aspera ad Astra: Through Complex Population Modeling to Predictive Theory JF - The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences N2 - Population models in ecology are often not good at predictions, even if they are complex and seem to be realistic enough. The reason for this might be that Occam's razor, which is key for minimal models exploring ideas and concepts, has been too uncritically adopted for more realistic models of systems. This can tic models too closely to certain situations, thereby preventing them from predicting the response to new conditions. We therefore advocate a new kind of parsimony to improve the application of Occam's razor. This new parsimony balances two contrasting strategies for avoiding errors in modeling: avoiding inclusion of nonessential factors (false inclusions) and avoiding exclusion of sometimes-important factors (false exclusions). It involves a synthesis of traditional modeling and analysis, used to describe the essentials of mechanistic relationships, with elements that arc included in a model because they have been reported to be or can arguably be assumed to be important under certain conditions. The resulting models should be able to reflect how the internal organization of populations change and thereby generate representations of the novel behavior necessary for complex predictions, including regime shifts. KW - complexity KW - error avoidance KW - agent-based models KW - model development KW - modest approach Y1 - 2015 U6 - https://doi.org/10.1086/683181 SN - 0003-0147 SN - 1537-5323 VL - 186 IS - 5 SP - 669 EP - 674 PB - Univ. of Chicago Press CY - Chicago ER - TY - JOUR A1 - Stillman, Richard A. A1 - Railsback, Steven Floyd A1 - Giske, Jarl A1 - Berger, Uta A1 - Grimm, Volker T1 - Making Predictions in a Changing World: The Benefits of Individual-Based Ecology JF - Bioscience N2 - Ecologists urgently need a better ability to predict how environmental change affects biodiversity. We examine individual-based ecology (IBE), a research paradigm that promises better a predictive ability by using individual-based models (IBMs) to represent ecological dynamics as arising from how individuals interact with their environment and with each other. A key advantage of IBMs is that the basis for predictions-fitness maximization by individual organisms-is more general and reliable than the empirical relationships that other models depend on. Case studies illustrate the usefulness and predictive success of long-term IBE programs. The pioneering programs had three phases: conceptualization, implementation, and diversification. Continued validation of models runs throughout these phases. The breakthroughs that make IBE more productive include standards for describing and validating IBMs, improved and standardized theory for individual traits and behavior, software tools, and generalized instead of system-specific IBMs. We provide guidelines for pursuing IBE and a vision for future IBE research. KW - ecology KW - fitness-maximization KW - individual-based KW - modeling KW - prediction Y1 - 2015 U6 - https://doi.org/10.1093/biosci/biu192 SN - 0006-3568 SN - 1525-3244 VL - 65 IS - 2 SP - 140 EP - 150 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Thiele, Jan C. A1 - Grimm, Volker T1 - Replicating and breaking models: good for you and good for ecology JF - Oikos N2 - There are two major limitations to the potential of computational models in ecology for producing general insights: their design is path-dependent, reflecting different underlying questions, assumptions, and data, and there is too little robustness analysis exploring where the model mechanisms explaining certain observations break down. We here argue that both limitations could be overcome if modellers in ecology would more often replicate existing models, try to break the models, and explore modifications. Replication comprises the re-implementation of an existing model and the replication of its results. Breaking models means to identify under what conditions the mechanisms represented in a model can no longer explain observed phenomena. The benefits of replication include less effort being spent to enter the iterative stage of model development and having more time for systematic robustness analysis. A culture of replication would lead to increased credibility, coherence and efficiency of computational modelling and thereby facilitate theory development. Y1 - 2015 U6 - https://doi.org/10.1111/oik.02170 SN - 0030-1299 SN - 1600-0706 VL - 124 IS - 6 SP - 691 EP - 696 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Groeneveld, Jürgen A1 - Johst, Karin A1 - Kawaguchi, So A1 - Meyer, Bettina A1 - Teschke, Mathias A1 - Grimm, Volker T1 - How biological clocks and changing environmental conditions determine local population growth and species distribution in Antarctic krill (Euphausia superba): a conceptual model JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - The Southern Ocean ecosystem is characterized by extreme seasonal changes in environmental factors such as day length, sea ice extent and food availability. The key species Antarctic krill (Euphausia superba) has evolved metabolic and behavioural seasonal rhythms to cope with these seasonal changes. We investigate the switch between a physiological less active and active period for adult krill, a rhythm which seems to be controlled by internal biological clocks. These biological clocks can be synchronized by environmental triggers such as day length and food availability. They have evolved for particular environmental regimes to synchronize predictable seasonal environmental changes with important life cycle functions of the species. In a changing environment the time when krill is metabolically active and the time of peak food availability may not overlap if krill's seasonal activity is solely determined by photoperiod (day length). This is especially true for the Atlantic sector of the Southern Ocean where the spatio-temporal ice cover dynamics are changing substantially with rising average temperatures. We developed an individual-based model for krill to explore the impact of photoperiod and food availability on the growth and demographics of krill. We simulated dynamics of local krill populations (with no movement of krill assumed) along a south-north gradient for different triggers of metabolic activity and different levels of food availability below the ice. We also observed the fate of larval krill which cannot switch to low metabolism and therefore are likely to overwinter under ice. Krill could only occupy the southern end of the gradient, where algae bloom only lasts for a short time, when alternative food supply under the ice was high and metabolic activity was triggered by photoperiod. The northern distribution was limited by lack of overwintering habitat for krill larvae due to short duration of sea ice cover even for high food content under the ice. The variability of the krill's length-frequency distributions varied for different triggers of metabolic activity, but did not depend on the sea ice extent. Our findings suggest a southward shift of krill populations due to reduction in the spatial sea ice extent, which is consistent with field observations. Overall, our results highlight the importance of the explicit consideration of spatio-temporal sea ice dynamics especially for larval krill together with temporal synchronization through internal clocks, triggered by environmental factors (photoperiod and food) in adult krill for the population modelling of krill. (C) 2015 Elsevier B.V. All rights reserved. KW - Dynamic energy budget theory KW - Individual based model KW - Southern Ocean KW - Sea ice KW - Climate change KW - Marine ecology Y1 - 2015 U6 - https://doi.org/10.1016/j.ecolmodel.2015.02.009 SN - 0304-3800 SN - 1872-7026 VL - 303 SP - 78 EP - 86 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Sundelof, Andreas A1 - Grimm, Volker A1 - Ulmestrand, Mats A1 - Fiksen, Oyvind T1 - Modelling harvesting strategies for the lobster fishery in northern Europe: the importance of protecting egg-bearing females JF - Population ecology KW - European lobster KW - Female moratorium KW - Individual-based model KW - Management KW - Minimum landing size KW - Yield per recruit (YPR) Y1 - 2015 U6 - https://doi.org/10.1007/s10144-014-0460-3 SN - 1438-3896 SN - 1438-390X VL - 57 IS - 1 SP - 237 EP - 251 PB - Springer CY - Tokyo ER - TY - JOUR A1 - Tanne, Johannes A1 - Jeoung, Jae-Hun A1 - Peng, Lei A1 - Yarman, Aysu A1 - Dietzel, Birgit A1 - Schulz, Burkhard A1 - Schad, Daniel A1 - Dobbek, Holger A1 - Wollenberger, Ursula A1 - Bier, Frank Fabian A1 - Scheller, Frieder W. T1 - Direct Electron Transfer and Bioelectrocatalysis by a Hexameric, Heme Protein at Nanostructured Electrodes JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - A nanohybrid consisting of poly(3-aminobenzenesulfonic acid-co-aniline) and multiwalled carbon nanotubes [MWCNT-P(ABS-A)]) on a gold electrode was used to immobilize the hexameric tyrosine-coordinated heme protein (HTHP). The enzyme showed direct electron transfer between the heme group of the protein and the nanostructured surface. Desorption of the noncovalently bound heme from the protein could be excluded by control measurements with adsorbed hemin on aminohexanthiol-modified electrodes. The nanostructuring and the optimised charge characteristics resulted in a higher protein coverage as compared with MUA/MU modified electrodes. The adsorbed enzyme shows catalytic activity for the cathodic H2O2 reduction and oxidation of NADH. KW - HTHP KW - Nanohybrid KW - Poylaniline KW - Multiwalled carbon nanotube Y1 - 2015 U6 - https://doi.org/10.1002/elan.201500231 SN - 1040-0397 SN - 1521-4109 VL - 27 IS - 10 SP - 2262 EP - 2267 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Hermanussen, Michael A1 - Scheffler, Christiane A1 - Groth, Detlef A1 - Aßmann, Christian T1 - Height and skeletal morphology in relation to modern life style JF - Journal of physiological anthropology N2 - Height and skeletal morphology strongly relate to life style. Parallel to the decrease in physical activity and locomotion, modern people are slimmer in skeletal proportions. In German children and adolescents, elbow breadth and particularly relative pelvic breadth (50th centile of bicristal distance divided by body height) have significantly decreased in recent years. Even more evident than the changes in pelvic morphology are the rapid changes in body height in most modern countries since the end-19th and particularly since the mid-20th century. Modern Japanese mature earlier; the age at take-off (ATO, the age at which the adolescent growth spurt starts) decreases, and they are taller at all ages. Preece-Baines modelling of six national samples of Japanese children and adolescents, surveyed between 1955 and 2000, shows that this gain in height is largely an adolescent trend, whereas height at take-off (HTO) increased by less than 3 cm since 1955; adolescent growth (height gain between ATO and adult age) increased by 6 cm. The effect of globalization on the modern post-war Japanese society ("community effect in height") on adolescent growth is discussed. KW - Pelvic breadth KW - Elbow breadth KW - Growth KW - Adult height KW - Community effect in height Y1 - 2015 U6 - https://doi.org/10.1186/s40101-015-0080-4 SN - 1880-6805 VL - 34 PB - BioMed Central CY - London ER - TY - JOUR A1 - Benina, Maria A1 - Ribeiro, Dimas Mendes A1 - Gechev, Tsanko S. A1 - Müller-Röber, Bernd A1 - Schippers, Jos H. M. T1 - A cell type-specific view on the translation of mRNAs from ROS-responsive genes upon paraquat treatment of Arabidopsis thaliana leaves JF - Plant, cell & environment : cell physiology, whole-plant physiology, community physiology N2 - Oxidative stress causes dramatic changes in the expression levels of many genes. The formation of a functional protein through successful mRNA translation is central to a coordinated cellular response. To what extent the response towards reactive oxygen species (ROS) is regulated at the translational level is poorly understood. Here we analysed leaf- and tissue-specific translatomes using a set of transgenic Arabidopsis thaliana lines expressing a FLAG-tagged ribosomal protein to immunopurify polysome-bound mRNAs before and after oxidative stress. We determined transcript levels of 171 ROS-responsive genes upon paraquat treatment, which causes formation of superoxide radicals, at the whole-organ level. Furthermore, the translation of mRNAs was determined for five cell types: mesophyll, bundle sheath, phloem companion, epidermal and guard cells. Mesophyll and bundle sheath cells showed the strongest response to paraquat treatment. Interestingly, several ROS-responsive transcription factors displayed cell type-specific translation patterns, while others were translated in all cell types. In part, cell type-specific translation could be explained by the length of the 5-untranslated region (5-UTR) and the presence of upstream open reading frames (uORFs). Our analysis reveals insights into the translational regulation of ROS-responsive genes, which is important to understanding cell-specific responses and functions during oxidative stress. The study illustrates the response of different Arabidopsis thaliana leaf cells and tissues to oxidative stress at the translational level, an aspect of reactive oxygen species (ROS) biology that has been little studied in the past. Our data reveal insights into how translational regulation of ROS-responsive genes is fine-tuned at the cellular level, a phenomenon contributing to the integrated physiological response of leaves to stresses involving changes in ROS levels. KW - Arabidopsis KW - gene regulation KW - oxidative stress KW - tissue-specific KW - translation Y1 - 2015 U6 - https://doi.org/10.1111/pce.12355 SN - 0140-7791 SN - 1365-3040 VL - 38 IS - 2 SP - 349 EP - 363 PB - Wiley-Blackwell CY - Hoboken ER -