@misc{OmranianNikoloskiGrimm2022, author = {Omranian, Sara and Nikoloski, Zoran and Grimm, Dominik G.}, title = {Computational identification of protein complexes from network interactions: Present state, challenges, and the way forward}, series = {Computational and structural biotechnology journal}, volume = {20}, journal = {Computational and structural biotechnology journal}, publisher = {Research Network of Computational and Structural Biotechnology (RNCSB)}, address = {Gotenburg}, issn = {2001-0370}, doi = {10.1016/j.csbj.2022.05.049}, pages = {2699 -- 2712}, year = {2022}, abstract = {Physically interacting proteins form macromolecule complexes that drive diverse cellular processes. Advances in experimental techniques that capture interactions between proteins provide us with protein-protein interaction (PPI) networks from several model organisms. These datasets have enabled the prediction and other computational analyses of protein complexes. Here we provide a systematic review of the state-of-the-art algorithms for protein complex prediction from PPI networks proposed in the past two decades. The existing approaches that solve this problem are categorized into three groups, including: cluster-quality-based, node affinity-based, and network embedding-based approaches, and we compare and contrast the advantages and disadvantages. We further include a comparative analysis by computing the performance of eighteen methods based on twelve well-established performance measures on four widely used benchmark protein-protein interaction networks. Finally, the limitations and drawbacks of both, current data and approaches, along with the potential solutions in this field are discussed, with emphasis on the points that pave the way for future research efforts in this field. (c) 2022 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/).}, language = {en} } @misc{ApriyantoCompartFettke2022, author = {Apriyanto, Ardha and Compart, Julia and Fettke, J{\"o}rg}, title = {A review of starch, a unique biopolymer - structure, metabolism and in planta modifications}, series = {Plant science : an international journal of experimental plant biology}, volume = {318}, journal = {Plant science : an international journal of experimental plant biology}, publisher = {Elsevier Science}, address = {Amsterdam [u.a.]}, issn = {0168-9452}, doi = {10.1016/j.plantsci.2022.111223}, pages = {8}, year = {2022}, abstract = {Starch is a complex carbohydrate polymer produced by plants and especially by crops in huge amounts. It consists of amylose and amylopectin, which have alpha-1,4-and alpha-1,6-linked glucose units. Despite this simple chemistry, the entire starch metabolism is complex, containing various (iso)enzymes/proteins. However, whose interplay is still not yet fully understood. Starch is essential for humans and animals as a source of nutrition and energy. Nowadays, starch is also commonly used in non-food industrial sectors for a variety of purposes. However, native starches do not always satisfy the needs of a wide range of (industrial) applications. This review summarizes the structural properties of starch, analytical methods for starch characterization, and in planta starch modifications.}, language = {en} } @misc{YarmanScheller2020, author = {Yarman, Aysu and Scheller, Frieder W.}, title = {How reliable is the electrochemical readout of MIP sensors?}, series = {Sensors}, volume = {20}, journal = {Sensors}, number = {9}, publisher = {MDPI}, address = {Basel}, issn = {1424-8220}, doi = {10.3390/s20092677}, pages = {23}, year = {2020}, abstract = {Electrochemical methods offer the simple characterization of the synthesis of molecularly imprinted polymers (MIPs) and the readouts of target binding. The binding of electroinactive analytes can be detected indirectly by their modulating effect on the diffusional permeability of a redox marker through thin MIP films. However, this process generates an overall signal, which may include nonspecific interactions with the nonimprinted surface and adsorption at the electrode surface in addition to (specific) binding to the cavities. Redox-active low-molecular-weight targets and metalloproteins enable a more specific direct quantification of their binding to MIPs by measuring the faradaic current. The in situ characterization of enzymes, MIP-based mimics of redox enzymes or enzyme-labeled targets, is based on the indication of an electroactive product. This approach allows the determination of both the activity of the bio(mimetic) catalyst and of the substrate concentration.}, language = {en} } @misc{Leimkuehler2020, author = {Leimk{\"u}hler, Silke}, title = {The biosynthesis of the molybdenum cofactors in Escherichia coli}, series = {Environmental microbiology}, volume = {22}, journal = {Environmental microbiology}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {1462-2912}, doi = {10.1111/1462-2920.15003}, pages = {2007 -- 2026}, year = {2020}, abstract = {The biosynthesis of the molybdenum cofactor (Moco) is highly conserved among all kingdoms of life. In all molybdoenzymes containing Moco, the molybdenum atom is coordinated to a dithiolene group present in the pterin-based 6-alkyl side chain of molybdopterin (MPT). In general, the biosynthesis of Moco can be divided into four steps in in bacteria: (i) the starting point is the formation of the cyclic pyranopterin monophosphate (cPMP) from 5 '-GTP, (ii) in the second step the two sulfur atoms are inserted into cPMP leading to the formation of MPT, (iii) in the third step the molybdenum atom is inserted into MPT to form Moco and (iv) in the fourth step bis-Mo-MPT is formed and an additional modification of Moco is possible with the attachment of a nucleotide (CMP or GMP) to the phosphate group of MPT, forming the dinucleotide variants of Moco. This review presents an update on the well-characterized Moco biosynthesis in the model organism Escherichia coli including novel discoveries from the recent years.}, language = {en} } @misc{vanReesWaylenSchmidtKloiberetal.2020, author = {van Rees, Charles B. and Waylen, Kerry A. and Schmidt-Kloiber, Astrid and Thackeray, Stephen J. and Kalinkat, Gregor and Martens, Koen and Domisch, Sami and Lillebo, Ana and Hermoso, Virgilio and Grossart, Hans-Peter and Schinegger, Rafaela and Decleer, Kris and Adriaens, Tim and Denys, Luc and Jaric, Ivan and Janse, Jan H. and Monaghan, Michael T. and De Wever, Aaike and Geijzendorffer, Ilse and Adamescu, Mihai C. and J{\"a}hnig, Sonja C.}, title = {Safeguarding freshwater life beyond 2020}, series = {Conservation letters}, volume = {14}, journal = {Conservation letters}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {1755-263X}, doi = {10.1111/conl.12771}, pages = {17}, year = {2020}, abstract = {Plans are currently being drafted for the next decade of action on biodiversity-both the post-2020 Global Biodiversity Framework of the Convention on Biological Diversity (CBD) and Biodiversity Strategy of the European Union (EU). Freshwater biodiversity is disproportionately threatened and underprioritized relative to the marine and terrestrial biota, despite supporting a richness of species and ecosystems with their own intrinsic value and providing multiple essential ecosystem services. Future policies and strategies must have a greater focus on the unique ecology of freshwater life and its multiple threats, and now is a critical time to reflect on how this may be achieved. We identify priority topics including environmental flows, water quality, invasive species, integrated water resources management, strategic conservation planning, and emerging technologies for freshwater ecosystem monitoring. We synthesize these topics with decades of first-hand experience and recent literature into 14 special recommendations for global freshwater biodiversity conservation based on the successes and setbacks of European policy, management, and research. Applying and following these recommendations will inform and enhance the ability of global and European post-2020 biodiversity agreements to halt and reverse the rapid global decline of freshwater biodiversity.}, language = {en} } @misc{CabralValenteHartig2017, author = {Cabral, Juliano Sarmento and Valente, Luis and Hartig, Florian}, title = {Mechanistic simulation models in macroecology and biogeography}, series = {Ecography : pattern and diversity in ecology}, volume = {40}, journal = {Ecography : pattern and diversity in ecology}, number = {2}, publisher = {Wiley}, address = {Hoboken}, issn = {0906-7590}, doi = {10.1111/ecog.02480}, pages = {267 -- 280}, year = {2017}, abstract = {Macroecology and biogeography are concerned with understanding biodiversity patterns across space and time. In the past, the two disciplines have addressed this question mainly with correlative approaches, despite frequent calls for more mechanistic explanations. Recent advances in computational power, theoretical understanding, and statistical tools are, however, currently facilitating the development of more system-oriented, mechanistic models. We review these models, identify different model types and theoretical frameworks, compare their processes and properties, and summarize emergent findings. We show that ecological (physiology, demographics, dispersal, biotic interactions) and evolutionary processes, as well as environmental and human-induced drivers, are increasingly modelled mechanistically; and that new insights into biodiversity dynamics emerge from these models. Yet, substantial challenges still lie ahead for this young research field. Among these, we identify scaling, calibration, validation, and balancing complexity as pressing issues. Moreover, particular process combinations are still understudied, and so far models tend to be developed for specific applications. Future work should aim at developing more flexible and modular models that not only allow different ecological theories to be expressed and contrasted, but which are also built for tight integration with all macroecological data sources. Moving the field towards such a 'systems macroecology' will test and improve our understanding of the causal pathways through which eco-evolutionary processes create diversity patterns across spatial and temporal scales.}, language = {en} } @misc{LeimkuehlerBuehningBeilschmidt2017, author = {Leimk{\"u}hler, Silke and B{\"u}hning, Martin and Beilschmidt, Lena}, title = {Shared sulfur mobilization routes for tRNA thiolation and molybdenum cofactor biosynthesis in prokaryotes and eukaryotes}, series = {Biomolecules}, volume = {7}, journal = {Biomolecules}, number = {1}, publisher = {MDPI}, address = {Basel}, issn = {2218-273X}, doi = {10.3390/biom7010005}, pages = {20}, year = {2017}, abstract = {Modifications of transfer RNA (tRNA) have been shown to play critical roles in the biogenesis, metabolism, structural stability and function of RNA molecules, and the specific modifications of nucleobases with sulfur atoms in tRNA are present in pro- and eukaryotes. Here, especially the thiomodifications xm(5)s(2)U at the wobble position 34 in tRNAs for Lys, Gln and Glu, were suggested to have an important role during the translation process by ensuring accurate deciphering of the genetic code and by stabilization of the tRNA structure. The trafficking and delivery of sulfur nucleosides is a complex process carried out by sulfur relay systems involving numerous proteins, which not only deliver sulfur to the specific tRNAs but also to other sulfur-containing molecules including iron-sulfur clusters, thiamin, biotin, lipoic acid and molybdopterin (MPT). Among the biosynthesis of these sulfur-containing molecules, the biosynthesis of the molybdenum cofactor (Moco) and the synthesis of thio-modified tRNAs in particular show a surprising link by sharing protein components for sulfur mobilization in pro- and eukaryotes.}, language = {en} } @misc{RomaoCoelhoSantosSilvaetal.2017, author = {Romao, Maria Joao and Coelho, Catarina and Santos-Silva, Teresa and Foti, Alessandro and Terao, Mineko and Garattini, Enrico and Leimk{\"u}hler, Silke}, title = {Structural basis for the role of mammalian aldehyde oxidases in the metabolism of drugs and xenobiotics}, series = {Current Opinion in Chemical Biology}, volume = {37}, journal = {Current Opinion in Chemical Biology}, publisher = {Elsevier}, address = {Oxford}, issn = {1367-5931}, doi = {10.1016/j.cbpa.2017.01.005}, pages = {39 -- 47}, year = {2017}, abstract = {Aldehyde oxidases (AOXs) are molybdo-flavoenzymes characterized by broad substrate specificity, oxidizing aromatic/aliphatic aldehydes into the corresponding carboxylic acids and hydroxylating various heteroaromatic rings. Mammals are characterized by a complement of species specific AOX isoenzymes, that varies from one in humans (AOX1) to four in rodents (AOX1, AOX2, AOX3 and AOX4). The physiological function of mammalian AOX isoenzymes is unknown, although human AOX1 is an emerging enzyme in phase-I drug metabolism. Indeed, the number of therapeutic molecules under development which act as AOX substrates is increasing. The recent crystallization and structure determination of human AOX1 as well as mouse AOX3 has brought new insights into the mechanisms underlying substrate/inhibitor binding as well as the catalytic activity of this class of enzymes.}, language = {en} } @misc{YarmanJetzschmannNeumannetal.2017, author = {Yarman, Aysu and Jetzschmann, Katharina J. and Neumann, Bettina and Zhang, Xiaorong and Wollenberger, Ulla and Cordin, Aude and Haupt, Karsten and Scheller, Frieder W.}, title = {Enzymes as Tools in MIP-Sensors}, series = {Chemosensors}, volume = {5}, journal = {Chemosensors}, publisher = {MDPI}, address = {Basel}, issn = {2227-9040}, doi = {10.3390/chemosensors5020011}, pages = {16}, year = {2017}, abstract = {Molecularly imprinted polymers (MIPs) have the potential to complement antibodies in bioanalysis, are more stable under harsh conditions, and are potentially cheaper to produce. However, the affinity and especially the selectivity of MIPs are in general lower than those of their biological pendants. Enzymes are useful tools for the preparation of MIPs for both low and high-molecular weight targets: As a green alternative to the well-established methods of chemical polymerization, enzyme-initiated polymerization has been introduced and the removal of protein templates by proteases has been successfully applied. Furthermore, MIPs have been coupled with enzymes in order to enhance the analytical performance of biomimetic sensors: Enzymes have been used in MIP-sensors as tracers for the generation and amplification of the measuring signal. In addition, enzymatic pretreatment of an analyte can extend the analyte spectrum and eliminate interferences.}, language = {en} } @misc{HasanHocher2017, author = {Hasan, Ahmed Abdallah Abdalrahman Mohamed and Hocher, Berthold}, title = {Role of soluble and membrane-bound dipeptidyl peptidase-4 in diabetic nephropathy}, series = {Journal of Molecular Endocrinology}, volume = {59}, journal = {Journal of Molecular Endocrinology}, publisher = {Bioscientifica LTD}, address = {Bristol}, issn = {0952-5041}, doi = {10.1530/JME-17-0005}, pages = {R1 -- R10}, year = {2017}, abstract = {Diabetic nephropathy is one of the most frequent, devastating and costly complications of diabetes. The available therapeutic approaches are limited. Dipeptidyl peptidase type 4 (DPP-4) inhibitors represent a new class of glucose-lowering drugs that might also have reno-protective properties. DPP-4 exists in two forms: a plasma membranebound form and a soluble form, and can exert many biological actions mainly through its peptidase activity and interaction with extracellular matrix components. The kidneys have the highest DPP-4 expression level in mammalians. DPP-4 expression and urinary activity are up-regulated in diabetic nephropathy, highlighting its role as a potential target to manage diabetic nephropathy. Preclinical animal studies and some clinical data suggest that DPP-4 inhibitors decrease the progression of diabetic nephropathy in a blood pressure-and glucose-independent manner. Many studies reported that these reno-protective effects could be due to increased half-life of DPP-4 substrates such as glucagon-like peptide-1 (GLP-1) and stromal derived factor-1 alpha (SDF-1a). However, the underlying mechanisms are far from being completely understood and clearly need further investigations.}, language = {en} } @misc{CisekTokarzKontenisetal.2018, author = {Cisek, Richard and Tokarz, Danielle and Kontenis, Lukas and Barzda, Virginijus and Steup, Martin}, title = {Polarimetric second harmonic generation microscopy}, series = {Starch-Starke}, volume = {70}, journal = {Starch-Starke}, number = {1-2}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {0038-9056}, doi = {10.1002/star.201700031}, pages = {15}, year = {2018}, abstract = {Second harmonic generation (SHG) is a nonlinear optical process that inherently generates signal in non-centrosymmetric materials, such as starch granules, and therefore can be used for label-free imaging. Both intensity and polarization of SHG are determined by material properties that are characterized by the nonlinear susceptibility tensor, ((2)). Examination of the tensor is performed for each focal volume of the image by measuring the outgoing polarization state of the SHG signal for a set of incoming laser beam polarizations. Mapping of nonlinear properties expressed as the susceptibility ratio reveals structural features including the organization of crystalline material within a single starch granule, and the distribution of structural properties in a population of granules. Isolated granules, as well as in situ starch, can be analyzed using polarimetric SHG microscopy. Due to the fast sample preparation and short imaging times, polarimetric SHG microscopy allows for a quick assessment of starch structure and permits rapid feedback for bioengineering applications. This article presents the basics of SHG theory and microscopy applications for starch-containing materials. Quantification of ultrastructural features within individual starch granules is described. New results obtained by polarization resolved SHG microscopy of starch granules are presented for various maize genotypes revealing heterogeneity within a single starch particle and between various granules.}, language = {en} } @misc{DuncanRosa2017, author = {Duncan, Susan and Rosa, Stefanie Nunes}, title = {Gaining insight into plant gene transcription using smFISH}, series = {Transcription}, volume = {9}, journal = {Transcription}, number = {3}, publisher = {Taylor \& Francis Group}, address = {Philadelphia}, issn = {2154-1264}, doi = {10.1080/21541264.2017.1372043}, pages = {166 -- 170}, year = {2017}, abstract = {Single molecule RNA fluorescent in situ hybridization (smFISH) enables gene transcription to be assessed at the cellular level. In this point of view article, we describe our recent smFISH research in the model plant Arabidopsis thaliana and discuss how this technique could further knowledge of plant gene transcription in the future.}, language = {en} } @misc{NakamuraGrebe2018, author = {Nakamura, Moritaka and Grebe, Markus}, title = {Outer, inner and planar polarity in the Arabidopsis root}, series = {Current opinion in plant biology}, volume = {41}, journal = {Current opinion in plant biology}, publisher = {Elsevier}, address = {London}, issn = {1369-5266}, doi = {10.1016/j.pbi.2017.08.002}, pages = {46 -- 53}, year = {2018}, abstract = {Plant roots control uptake of water and nutrients and cope with environmental challenges. The root epidermis provides the first selective interface for nutrient absorption, while the endodermis produces the main apoplastic diffusion barrier in the form of a structure called the Casparian strip. The positioning of root hairs on epidermal cells, and of the Casparian strip around endodermal cells, requires asymmetries along cellular axes (cell polarity). Cell polarity is termed planar polarity, when coordinated within the plane of a given tissue layer. Here, we review recent molecular advances towards understanding both the polar positioning of the proteo-lipid membrane domain instructing root hair initiation, and the cytoskeletal, trafficking and polar tethering requirements of proteins at outer or inner plasma membrane domains. Finally, we highlight progress towards understanding mechanisms of Casparian strip formation and underlying endodermal cell polarity.}, language = {en} } @misc{LauxBierHoelzel2018, author = {Laux, Eva-Maria and Bier, Frank Fabian and H{\"o}lzel, Ralph}, title = {Electrode-based AC electrokinetics of proteins}, series = {Bioelectrochemistry : official journal of the Bioelectrochemical Society ; an international journal devoted to electrochemical aspects of biology and biological aspects of electrochemistry}, volume = {120}, journal = {Bioelectrochemistry : official journal of the Bioelectrochemical Society ; an international journal devoted to electrochemical aspects of biology and biological aspects of electrochemistry}, publisher = {Elsevier B.V.}, address = {Amsterdam}, issn = {1567-5394}, doi = {10.1016/j.bioelechem.2017.11.010}, pages = {76 -- 82}, year = {2018}, abstract = {Employing electric phenomena for the spatial manipulation of bioparticles from whole cells down to dissolved molecules has become a useful tool in biotechnology and analytics. AC electrokinetic effects like dielectrophoresis and AC electroosmosis are increasingly used to concentrate, separate and immobilize DNA and proteins. With the advance of photolithographical micro- and nanofabrication methods, novel or improved bioanalytical applications benefit from concentrating analytes, signal enhancement and locally controlled immobilization by AC electrokinetic effects. In this review of AC electrokinetics of proteins, the respective studies are classified according to their different electrode geometries: individual electrode pairs, interdigitated electrodes, quadrupole electrodes, and 3D configurations of electrode arrays. Known advantages and disadvantages of each layout are discussed.}, language = {en} } @misc{AyllonGrimmAttingeretal.2018, author = {Ayllon, Daniel and Grimm, Volker and Attinger, Sabine and Hauhs, Michael and Simmer, Clemens and Vereecken, Harry and Lischeid, Gunnar}, title = {Cross-disciplinary links in environmental systems science}, series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, volume = {622}, journal = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0048-9697}, doi = {10.1016/j.scitotenv.2017.12.007}, pages = {954 -- 973}, year = {2018}, abstract = {Terrestrial environmental systems are characterised by numerous feedback links between their different compartments. However, scientific research is organized into disciplines that focus on processes within the respective compartments rather than on interdisciplinary links. Major feedback mechanisms between compartments might therefore have been systematically overlooked so far. Without identifying these gaps, initiatives on future comprehensive environmental monitoring schemes and experimental platforms might fail. We performed a comprehensive overview of feedbacks between compartments currently represented in environmental sciences and explores to what degree missing links have already been acknowledged in the literature. We focused on process models as they can be regarded as repositories of scientific knowledge that compile findings of numerous single studies. In total, 118 simulation models from 23 model types were analysed. Missing processes linking different environmental compartments were identified based on a meta-review of 346 published reviews, model inter-comparison studies, and model descriptions. Eight disciplines of environmental sciences were considered and 396 linking processes were identified and ascribed to the physical, chemical or biological domain. There were significant differences between model types and scientific disciplines regarding implemented interdisciplinary links. The most wide-spread interdisciplinary links were between physical processes in meteorology, hydrology and soil science that drive or set the boundary conditions for other processes (e.g., ecological processes). In contrast, most chemical and biological processes were restricted to links within the same compartment. Integration of multiple environmental compartments and interdisciplinary knowledge was scarce in most model types. There was a strong bias of suggested future research foci and model extensions towards reinforcing existing interdisciplinary knowledge rather than to open up new interdisciplinary pathways. No clear pattern across disciplines exists with respect to suggested future research efforts. There is no evidence that environmental research would clearly converge towards more integrated approaches or towards an overarching environmental systems theory. (c) 2017 Elsevier B.V. All rights reserved.}, language = {en} } @misc{HermanussenBoginScheffler2018, author = {Hermanussen, Michael and Bogin, Barry and Scheffler, Christiane}, title = {Stunting, starvation and refeeding}, series = {Acta paediatrica : nurturing the child}, volume = {107}, journal = {Acta paediatrica : nurturing the child}, number = {7}, publisher = {Wiley}, address = {Hoboken}, issn = {0803-5253}, doi = {10.1111/apa.14311}, pages = {1166 -- 1176}, year = {2018}, abstract = {Aim: To scrutinize to what extent modern ideas about nutrition effects on growth are supported by historic observations in European populations. Method: We reviewed 19th and early 20th century paediatric journals in the Staatsbibliothek zu Berlin, the third largest European library with an almost complete collection of the German medical literature. During a three-day visit, we inspected 15 bookshelf meters of literature not available in electronic format. Results: Late 19th and early 20th century breastfed European infants and children, independent of social strata, grew far below World Health Organisation (WHO) standards and 15-30\% of adequately-fed children would be classified as stunted by the WHO standards. Historic sources indicate that growth in height is largely independent of the extent and nature of the diet. Height catch-up after starvation was greater than catch-up reported in modern nutrition intervention studies, and allowed for unimpaired adult height. Conclusion: Historical studies are indispensable to understand why stunting does not equate with undernutrition and why modern diet interventions frequently fail to prevent stunting. Appropriateness and effect size of modern nutrition interventions on growth need revision.}, language = {en} } @misc{WozniakSicard2018, author = {Wozniak, Natalia Joanna and Sicard, Adrien}, title = {Evolvability of flower geometry}, series = {Seminars in cell \& developmental biology}, volume = {79}, journal = {Seminars in cell \& developmental biology}, publisher = {Elsevier}, address = {London}, issn = {1084-9521}, doi = {10.1016/j.semcdb.2017.09.028}, pages = {3 -- 15}, year = {2018}, abstract = {Flowers represent a key innovation during plant evolution. Driven by reproductive optimization, evolution of flower morphology has been central in boosting species diversification. In most cases, this has happened through specialized interactions with animal pollinators and subsequent reduction of gene flow between specialized morphs. While radiation has led to an enormous variability in flower forms and sizes, recurrent evolutionary patterns can be observed. Here, we discuss the targets of selection involved in major trends of pollinator-driven flower evolution. We review recent findings on their adaptive values, developmental grounds and genetic bases, in an attempt to better understand the repeated nature of pollinator-driven flower evolution. This analysis highlights how structural innovation can provide flexibility in phenotypic evolution, adaptation and speciation. (C) 2017 Elsevier Ltd. All rights reserved.}, language = {en} } @misc{MuehlenbruchGrossartEigemannetal.2018, author = {M{\"u}hlenbruch, Marco and Grossart, Hans-Peter and Eigemann, Falk and Voss, Maren}, title = {Mini-review: Phytoplankton-derived polysaccharides in the marine environment and their interactions with heterotrophic bacteria}, series = {Environmental microbiology}, volume = {20}, journal = {Environmental microbiology}, number = {8}, publisher = {Wiley}, address = {Hoboken}, issn = {1462-2912}, doi = {10.1111/1462-2920.14302}, pages = {2671 -- 2685}, year = {2018}, abstract = {Within the wealth of molecules constituting marine dissolved organic matter, carbohydrates make up the largest coherent and quantifiable fraction. Their main sources are from primary producers, which release large amounts of photosynthetic products - mainly polysaccharides - directly into the surrounding water via passive and active exudation. The organic carbon and other nutrients derived from these photosynthates enrich the 'phycosphere' and attract heterotrophic bacteria. The rapid uptake and remineralization of dissolved free monosaccharides by heterotrophic bacteria account for the barely detectable levels of these compounds. By contrast, dissolved combined polysaccharides can reach high concentrations, especially during phytoplankton blooms. Polysaccharides are too large to be taken up directly by heterotrophic bacteria, instead requiring hydrolytic cleavage to smaller oligo- or monomers by bacteria with a suitable set of exoenzymes. The release of diverse polysaccharides by various phytoplankton taxa is generally interpreted as the deposition of excess organic material. However, these molecules likely also fulfil distinct, yet not fully understood functions, as inferred from their active modulation in terms of quality and quantity when phytoplankton becomes nutrient limited or is exposed to heterotrophic bacteria. This minireview summarizes current knowledge regarding the exudation and composition of phytoplankton-derived exopolysaccharides and acquisition of these compounds by heterotrophic bacteria.}, language = {en} } @misc{FischerShaki2018, author = {Fischer, Martin H. and Shaki, Samuel}, title = {Number concepts: abstract and embodied}, series = {Philosophical transactions of the Royal Society of London : B, Biological sciences}, volume = {373}, journal = {Philosophical transactions of the Royal Society of London : B, Biological sciences}, number = {1752}, publisher = {Royal Society}, address = {London}, issn = {0962-8436}, doi = {10.1098/rstb.2017.0125}, pages = {8}, year = {2018}, abstract = {Numerical knowledge, including number concepts and arithmetic procedures, seems to be a clear-cut case for abstract symbol manipulation. Yet, evidence from perceptual and motor behaviour reveals that natural number knowledge and simple arithmetic also remain closely associated with modal experiences. Following a review of behavioural, animal and neuroscience studies of number processing, we propose a revised understanding of psychological number concepts as grounded in physical constraints, embodied in experience and situated through task-specific intentions. The idea that number concepts occupy a range of positions on the continuum between abstract and modal conceptual knowledge also accounts for systematic heuristics and biases in mental arithmetic, thus inviting psycho-logical approaches to the study of the mathematical mind.}, language = {en} } @misc{BaslerFernieNikoloski2018, author = {Basler, Georg and Fernie, Alisdair R. and Nikoloski, Zoran}, title = {Advances in metabolic flux analysis toward genome-scale profiling of higher organisms}, series = {Bioscience reports : communications and reviews in molecular and cellular biology}, volume = {38}, journal = {Bioscience reports : communications and reviews in molecular and cellular biology}, publisher = {Portland Press (London)}, address = {London}, issn = {0144-8463}, doi = {10.1042/BSR20170224}, pages = {11}, year = {2018}, abstract = {Methodological and technological advances have recently paved the way for metabolic flux profiling in higher organisms, like plants. However, in comparison with omics technologies, flux profiling has yet to provide comprehensive differential flux maps at a genome-scale and in different cell types, tissues, and organs. Here we highlight the recent advances in technologies to gather metabolic labeling patterns and flux profiling approaches. We provide an opinion of how recent local flux profiling approaches can be used in conjunction with the constraint-based modeling framework to arrive at genome-scale flux maps. In addition, we point at approaches which use metabolomics data without introduction of label to predict either non-steady state fluxes in a time-series experiment or flux changes in different experimental scenarios. The combination of these developments allows an experimentally feasible approach for flux-based large-scale systems biology studies.}, language = {en} } @misc{FritzRosaSicard2018, author = {Fritz, Michael Andre and Rosa, Stefanie and Sicard, Adrien}, title = {Mechanisms Underlying the Environmentally Induced Plasticity of Leaf Morphology}, series = {Frontiers in genetics}, volume = {9}, journal = {Frontiers in genetics}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-8021}, doi = {10.3389/fgene.2018.00478}, pages = {25}, year = {2018}, abstract = {The primary function of leaves is to provide an interface between plants and their environment for gas exchange, light exposure and thermoregulation. Leaves have, therefore a central contribution to plant fitness by allowing an efficient absorption of sunlight energy through photosynthesis to ensure an optimal growth. Their final geometry will result from a balance between the need to maximize energy uptake while minimizing the damage caused by environmental stresses. This intimate relationship between leaf and its surroundings has led to an enormous diversification in leaf forms. Leaf shape varies between species, populations, individuals or even within identical genotypes when those are subjected to different environmental conditions. For instance, the extent of leaf margin dissection has, for long, been found to inversely correlate with the mean annual temperature, such that Paleobotanists have used models based on leaf shape to predict the paleoclimate from fossil flora. Leaf growth is not only dependent on temperature but is also regulated by many other environmental factors such as light quality and intensity or ambient humidity. This raises the question of how the different signals can be integrated at the molecular level and converted into clear developmental decisions. Several recent studies have started to shed the light on the molecular mechanisms that connect the environmental sensing with organ-growth and patterning. In this review, we discuss the current knowledge on the influence of different environmental signals on leaf size and shape, their integration as well as their importance for plant adaptation.}, language = {en} } @misc{Baeurle2017, author = {B{\"a}urle, Isabel}, title = {Can't remember to forget you}, series = {Seminars in cell \& developmental biology}, volume = {83}, journal = {Seminars in cell \& developmental biology}, publisher = {Elsevier}, address = {London}, issn = {1084-9521}, doi = {10.1016/j.semcdb.2017.09.032}, pages = {133 -- 139}, year = {2017}, abstract = {In nature plants are exposed to frequent changes in their abiotic and biotic environment. While some environmental cues are used to gauge the environment and align growth and development, others are beyond the regularly encountered spectrum of a species and trigger stress responses. Such stressful conditions provide a potential threat to survival and integrity. Plants adapt to extreme environmental conditions through physiological adaptations that are usually transient and are maintained until stressful environments subside. It is increasingly appreciated that in some cases environmental cues activate a stress memory that persists for some time after the extreme condition has subsided. Recent research has shown that this stress-induced environmental memory is mediated by epigenetic and chromatin-based mechanisms and both histone methylation and nucleosome occupancy are associated with it.}, language = {en} } @misc{MacGroganMuenchdelaPompa2018, author = {MacGrogan, Donal and M{\"u}nch, Juliane and de la Pompa, Jos{\´e} Luis}, title = {Notch and interacting signalling pathways in cardiac development, disease, and regeneration}, series = {Nature Reviews Cardiology}, volume = {15}, journal = {Nature Reviews Cardiology}, number = {11}, publisher = {Nature Publ. Group}, address = {New York}, issn = {1759-5002}, doi = {10.1038/s41569-018-0100-2}, pages = {685 -- 704}, year = {2018}, abstract = {Cardiogenesis is a complex developmental process involving multiple overlapping stages of cell fate specification, proliferation, differentiation, and morphogenesis. Precise spatiotemporal coordination between the different cardiogenic processes is ensured by intercellular signalling crosstalk and tissue-tissue interactions. Notch is an intercellular signalling pathway crucial for cell fate decisions during multicellular organismal development and is aptly positioned to coordinate the complex signalling crosstalk required for progressive cell lineage restriction during cardiogenesis. In this Review, we describe the role of Notch signalling and the crosstalk with other signalling pathways during the differentiation and patterning of the different cardiac tissues and in cardiac valve and ventricular chamber development. We examine how perturbation of Notch signalling activity is linked to congenital heart diseases affecting the neonate and adult, and discuss studies that shed light on the role of Notch signalling in heart regeneration and repair after injury.}, language = {en} } @misc{BalintPfenningerGrossartetal.2018, author = {B{\´a}lint, Mikl{\´o}s and Pfenninger, Markus and Grossart, Hans-Peter and Taberlet, Pierre and Vellend, Mark and Leibold, Mathew A. and Englund, Goran and Bowler, Diana}, title = {Environmental DNA time series in ecology}, series = {Trends in ecology \& evolution}, volume = {33}, journal = {Trends in ecology \& evolution}, number = {12}, publisher = {Elsevier}, address = {London}, issn = {0169-5347}, doi = {10.1016/j.tree.2018.09.003}, pages = {945 -- 957}, year = {2018}, abstract = {Ecological communities change in time and space, but long-term dynamics at the century-to-millennia scale are poorly documented due to lack of relevant data sets. Nevertheless, understanding long-term dynamics is important for explaining present-day biodiversity patterns and placing conservation goals in a historical context. Here, we use recent examples and new perspectives to highlight how environmental DNA (eDNA) is starting to provide a powerful new source of temporal data for research questions that have so far been overlooked, by helping to resolve the ecological dynamics of populations, communities, and ecosystems over hundreds to thousands of years. We give examples of hypotheses that may be addressed by temporal eDNA biodiversity data, discuss possible research directions, and outline related challenges.}, language = {en} } @misc{QuiterioMartinsOnofreetal.2018, author = {Quiterio, Ana and Martins, Joao and Onofre, Marcos and Costa, Joao and Rodrigues, Joao Mota and Gerlach, Erin and Scheur, Claude and Herrmann, Christian}, title = {MOBAK 1 assessment in primary physical education}, series = {Perceptual \& motor skills}, volume = {125}, journal = {Perceptual \& motor skills}, number = {6}, publisher = {Sage Publ.}, address = {Thousand Oaks}, issn = {0031-5125}, doi = {10.1177/0031512518804358}, pages = {1055 -- 1069}, year = {2018}, abstract = {Children's motor competence is known to have a determinant role in learning and engaging later in complex motor skills and, thus, in physical activity. The development of adequate motor competence is a central aim of physical education, and assuring that pupils are learning and developing motor competence depends on accurate assessment protocols. The MOBAK 1 test battery is a recent instrument developed to assess motor competence in primary physical education. This study used the MOBAK 1 to explore motor competence levels and gender differences among 249 (Mage = 6.3, SD = 0.5 years; 127 girls and 122 boys) Grade 1 primary school Portuguese children. On independent sample t tests, boys presented higher object movement motor competence than girls (boys: M = 5.8, SD = 1.7; girls: M = 4.0, SD = 1.7; p < .001), while girls were more proficient among self-movement skills (girls: M = 5.1, SD = 1.8; boys: M = 4.3, SD = 1.7; p < .01). On "total motor competence," boys (M = 10.3, SD = 2.6) averaged one point ahead of girls (M = 9.1, SD = 2.9). The percentage of girls in the first quartile of object movement was 18.9\%, while, for "self movement," the percentage of boys in the first quartile was almost double that of girls (30.3\% and 17.3\%, respectively). The confirmatory model to test for construct validity confirmed the assumed theoretical two-factor structure of MOBAK 1 test items in this Portuguese sample. These results support the MOBAK 1 instrument for assessing motor competence and highlighted gender differences, of relevance to intervention efforts.}, language = {en} } @misc{PaoliniAbdelilahSeyfried2018, author = {Paolini, Alessio and Abdelilah-Seyfried, Salim}, title = {The mechanobiology of zebrafish cardiac valve leaflet formation}, series = {Current opinion in cell biology : review articles, recommended reading, bibliography of the world literature}, volume = {55}, journal = {Current opinion in cell biology : review articles, recommended reading, bibliography of the world literature}, publisher = {Elsevier}, address = {London}, issn = {0955-0674}, doi = {10.1016/j.ceb.2018.05.007}, pages = {52 -- 58}, year = {2018}, abstract = {Over a lifetime, rhythmic contractions of the heart provide a continuous flow of blood throughout the body. An essential morphogenetic process during cardiac development which ensures unidirectional blood flow is the formation of cardiac valves. These structures are largely composed of extracellular matrix and of endocardial cells, a specialized population of endothelial cells that line the interior of the heart and that are subjected to changing hemodynamic forces. Recent studies have significantly expanded our understanding of this morphogenetic process. They highlight the importance of the mechanobiology of cardiac valve formation and show how biophysical forces due to blood flow drive biochemical and electrical signaling required for the differentiation of cells to produce cardiac valves.}, language = {en} } @misc{BlockDenfeldStockwelletal.2019, author = {Block, Benjamin D. and Denfeld, Blaize A. and Stockwell, Jason D. and Flaim, Giovanna and Grossart, Hans-Peter and Knoll, Lesley B. and Maier, Dominique B. and North, Rebecca L. and Rautio, Milla and Rusak, James A. and Sadro, Steve and Weyhenmeyer, Gesa A. and Bramburger, Andrew J. and Branstrator, Donn K. and Salonen, Kalevi and Hampton, Stephanie E.}, title = {The unique methodological challenges of winter limnology}, series = {Limnology and Oceanography: Methods}, volume = {17}, journal = {Limnology and Oceanography: Methods}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {1541-5856}, doi = {10.1002/lom3.10295}, pages = {42 -- 57}, year = {2019}, abstract = {Winter is an important season for many limnological processes, which can range from biogeochemical transformations to ecological interactions. Interest in the structure and function of lake ecosystems under ice is on the rise. Although limnologists working at polar latitudes have a long history of winter work, the required knowledge to successfully sample under winter conditions is not widely available and relatively few limnologists receive formal training. In particular, the deployment and operation of equipment in below 0 degrees C temperatures pose considerable logistical and methodological challenges, as do the safety risks of sampling during the ice-covered period. Here, we consolidate information on winter lake sampling and describe effective methods to measure physical, chemical, and biological variables in and under ice. We describe variation in snow and ice conditions and discuss implications for sampling logistics and safety. We outline commonly encountered methodological challenges and make recommendations for best practices to maximize safety and efficiency when sampling through ice or deploying instruments in ice-covered lakes. Application of such practices over a broad range of ice-covered lakes will contribute to a better understanding of the factors that regulate lakes during winter and how winter conditions affect the subsequent ice-free period.}, language = {en} } @misc{RomeroMujalliJeltschTiedemann2018, author = {Romero-Mujalli, Daniel and Jeltsch, Florian and Tiedemann, Ralph}, title = {Individual-based modeling of eco-evolutionary dynamics}, series = {Regional environmental change}, volume = {19}, journal = {Regional environmental change}, number = {1}, publisher = {Springer}, address = {Heidelberg}, issn = {1436-3798}, doi = {10.1007/s10113-018-1406-7}, pages = {1 -- 12}, year = {2018}, abstract = {A challenge for eco-evolutionary research is to better understand the effect of climate and landscape changes on species and their distribution. Populations of species can respond to changes in their environment through local genetic adaptation or plasticity, dispersal, or local extinction. The individual-based modeling (IBM) approach has been repeatedly applied to assess organismic responses to environmental changes. IBMs simulate emerging adaptive behaviors from the basic entities upon which both ecological and evolutionary mechanisms act. The objective of this review is to summarize the state of the art of eco-evolutionary IBMs and to explore to what degree they already address the key responses of organisms to environmental change. In this, we identify promising approaches and potential knowledge gaps in the implementation of eco-evolutionary mechanisms to motivate future research. Using mainly the ISI Web of Science, we reveal that most of the progress in eco-evolutionary IBMs in the last decades was achieved for genetic adaptation to novel local environmental conditions. There is, however, not a single eco-evolutionary IBM addressing the three potential adaptive responses simultaneously. Additionally, IBMs implementing adaptive phenotypic plasticity are rare. Most commonly, plasticity was implemented as random noise or reaction norms. Our review further identifies a current lack of models where plasticity is an evolving trait. Future eco-evolutionary models should consider dispersal and plasticity as evolving traits with their associated costs and benefits. Such an integrated approach could help to identify conditions promoting population persistence depending on the life history strategy of organisms and the environment they experience.}, language = {en} } @misc{MachatschekSchulzLendlein2018, author = {Machatschek, Rainhard Gabriel and Schulz, Burkhard and Lendlein, Andreas}, title = {Langmuir Monolayers as Tools to Study Biodegradable Polymer Implant Materials}, series = {Macromolecular rapid communications}, volume = {40}, journal = {Macromolecular rapid communications}, number = {1}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1022-1336}, doi = {10.1002/marc.201800611}, pages = {11}, year = {2018}, abstract = {Langmuir monolayers provide a fast and elegant route to analyze the degradation behavior of biodegradable polymer materials. In contrast to bulk materials, diffusive transport of reactants and reaction products in the (partially degraded) material can be neglected at the air-water interface, allowing for the study of molecular degradation kinetics in experiments taking less than a day and in some cases just a few minutes, in contrast to experiments with bulk materials that can take years. Several aspects of the biodegradation behavior of polymer materials, such as the interaction with biomolecules and degradation products, are directly observable. Expanding the technique with surface-sensitive instrumental techniques enables evaluating the evolution of the morphology, chemical composition, and the mechanical properties of the degrading material in situ. The potential of the Langmuir monolayer degradation technique as a predictive tool for implant degradation when combined with computational methods is outlined, and related open questions and strategies to overcome these challenges are pointed out.}, language = {en} } @misc{LaitinenNikoloski2018, author = {Laitinen, Roosa A. E. and Nikoloski, Zoran}, title = {Genetic basis of plasticity in plants}, series = {Journal of experimental botany}, volume = {70}, journal = {Journal of experimental botany}, number = {3}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/ery404}, pages = {739 -- 745}, year = {2018}, abstract = {The ability of an organism to change its phenotype in response to different environments, termed plasticity, is a particularly important characteristic to enable sessile plants to adapt to rapid changes in their surroundings. Plasticity is a quantitative trait that can provide a fitness advantage and mitigate negative effects due to environmental perturbations. Yet, its genetic basis is not fully understood. Alongside technological limitations, the main challenge in studying plasticity has been the selection of suitable approaches for quantification of phenotypic plasticity. Here, we propose a categorization of the existing quantitative measures of phenotypic plasticity into nominal and relative approaches. Moreover, we highlight the recent advances in the understanding of the genetic architecture underlying phenotypic plasticity in plants. We identify four pillars for future research to uncover the genetic basis of phenotypic plasticity, with emphasis on development of computational approaches and theories. These developments will allow us to perform specific experiments to validate the causal genes for plasticity and to discover their role in plant fitness and evolution.}, language = {en} } @misc{YamamichiKlauschiesMineretal.2019, author = {Yamamichi, Masato and Klauschies, Toni and Miner, Brooks E. and van Velzen, Ellen}, title = {Modelling inducible defences in predator-prey interactions}, series = {Ecology letters}, volume = {22}, journal = {Ecology letters}, number = {2}, publisher = {Wiley}, address = {Hoboken}, issn = {1461-023X}, doi = {10.1111/ele.13183}, pages = {390 -- 404}, year = {2019}, abstract = {Inducible defences against predation are widespread in the natural world, allowing prey to economise on the costs of defence when predation risk varies over time or is spatially structured. Through interspecific interactions, inducible defences have major impacts on ecological dynamics, particularly predator-prey stability and phase lag. Researchers have developed multiple distinct approaches, each reflecting assumptions appropriate for particular ecological communities. Yet, the impact of inducible defences on ecological dynamics can be highly sensitive to the modelling approach used, making the choice of model a critical decision that affects interpretation of the dynamical consequences of inducible defences. Here, we review three existing approaches to modelling inducible defences: Switching Function, Fitness Gradient and Optimal Trait. We assess when and how the dynamical outcomes of these approaches differ from each other, from classic predator-prey dynamics and from commonly observed eco-evolutionary dynamics with evolving, but non-inducible, prey defences. We point out that the Switching Function models tend to stabilise population dynamics, and the Fitness Gradient models should be carefully used, as the difference with evolutionary dynamics is important. We discuss advantages of each approach for applications to ecological systems with particular features, with the goal of providing guidelines for future researchers to build on.}, language = {en} } @misc{LanghammerThoberLangeetal.2019, author = {Langhammer, Maria and Thober, Jule and Lange, Martin and Frank, Karin and Grimm, Volker}, title = {Agricultural landscape generators for simulation models}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {393}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2018.12.010}, pages = {135 -- 151}, year = {2019}, abstract = {There is an increasing need for an assessment of the impacts of land use and land use change (LUCC). In this context, simulation models are valuable tools for investigating the impacts of stakeholder actions or policy decisions. Agricultural landscape generators (ALGs), which systematically and automatically generate realistic but simplified representations of land cover in agricultural landscapes, can provide the input for LUCC models. We reviewed existing ALGs in terms of their objectives, design and scope. We found eight ALGs that met our definition. They were based either on generic mathematical algorithms (pattern-based) or on representations of ecological or land use processes (process-based). Most ALGs integrate only a few landscape metrics, which limits the design of the landscape pattern and thus the range of applications. For example, only a few specific farming systems have been implemented. We conclude that existing ALGs contain useful approaches that can be used for specific purposes, but ideally generic modular ALGs are developed that can be used for a wide range of scenarios, regions and model types. We have compiled features of such generic ALGs and propose a possible software architecture. Considerable joint efforts are required to develop such generic ALGs, but the benefits in terms of a better understanding and development of more efficient agricultural policies would be high.}, language = {en} } @misc{AriasAndresRojasJimenezGrossart2018, author = {Arias-Andres, Maria and Rojas-Jimenez, Keilor and Grossart, Hans-Peter}, title = {Collateral effects of microplastic pollution on aquatic microorganisms}, series = {Trends in Analytical Chemistry}, volume = {112}, journal = {Trends in Analytical Chemistry}, publisher = {Elsevier}, address = {Oxford}, issn = {0165-9936}, doi = {10.1016/j.trac.2018.11.041}, pages = {234 -- 240}, year = {2018}, abstract = {Microplastics (MP) provide a unique and extensive surface for microbial colonization in aquatic ecosystems. The formation of microorganism-microplastic complexes, such as biofilms, maximizes the degradation of organic matter and horizontal gene transfer. In this context, MP affect the structure and function of microbial communities, which in turn render the physical and chemical fate of MP. This new paradigm generates challenges for microbiology, ecology, and ecotoxicology. Dispersal of MP is concomitant with that of their associated microorganisms and their mobile genetic elements, including antibiotic resistance genes, islands of pathogenicity, and diverse metabolic pathways. Functional changes in aquatic microbiomes can alter carbon metabolism and food webs, with unknown consequences on higher organisms or human microbiomes and hence health. Here, we examine a variety of effects of MP pollution from the microbial ecology perspective, whose repercussions on aquatic ecosystems begin to be unraveled. (C) 2018 Elsevier B.V. All rights reserved.}, language = {en} } @misc{FriedrichFaivreBaeurleetal.2018, author = {Friedrich, Thomas and Faivre, Lea and B{\"a}urle, Isabel and Schubert, Daniel}, title = {Chromatin-based mechanisms of temperature memory in plants}, series = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, volume = {42}, journal = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, number = {3}, publisher = {Wiley}, address = {Hoboken}, issn = {0140-7791}, doi = {10.1111/pce.13373}, pages = {762 -- 770}, year = {2018}, abstract = {For successful growth and development, plants constantly have to gauge their environment. Plants are capable to monitor their current environmental conditions, and they are also able to integrate environmental conditions over time and store the information induced by the cues. In a developmental context, such an environmental memory is used to align developmental transitions with favourable environmental conditions. One temperature-related example of this is the transition to flowering after experiencing winter conditions, that is, vernalization. In the context of adaptation to stress, such an environmental memory is used to improve stress adaptation even when the stress cues are intermittent. A somatic stress memory has now been described for various stresses, including extreme temperatures, drought, and pathogen infection. At the molecular level, such a memory of the environment is often mediated by epigenetic and chromatin modifications. Histone modifications in particular play an important role. In this review, we will discuss and compare different types of temperature memory and the histone modifications, as well as the reader, writer, and eraser proteins involved.}, language = {en} } @misc{AntoniettiLopezSalasPrimo2018, author = {Antonietti, Markus and Lopez-Salas, Nieves and Primo, Ana}, title = {Adjusting the Structure and Electronic Properties of Carbons for Metal-Free Carbocatalysis of Organic Transformations}, series = {Advanced materials}, volume = {31}, journal = {Advanced materials}, number = {13}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {0935-9648}, doi = {10.1002/adma.201805719}, pages = {15}, year = {2018}, abstract = {Carbon nanomaterials doped with some other lightweight elements were recently described as powerful, heterogeneous, metal-free organocatalysts, adding to their high performance in electrocatalysis. Here, recent observations in traditional catalysis are reviewed, and the underlying reaction mechanisms of the catalyzed organic transformations are explored. In some cases, these are due to specific active functional sites, but more generally the catalytic activity relates to collective properties of the conjugated nanocarbon frameworks and the electron transfer from and to the catalytic centers and substrates. It is shown that the !earnings are tightly related to those of electrocatalysis; i.e., the search for better electrocatalysts also improves chemocatalysis, and vice versa. Carbon-carbon heterojunction effects and some perspectives on future possibilities are discussed at the end.}, language = {en} } @misc{JaricHegerMonzonetal.2019, author = {Jaric, Ivan and Heger, Tina and Monzon, Federico Castro and Jeschke, Jonathan M. and Kowarik, Ingo and McConkey, Kim R. and Pysek, Petr and Sagouis, Alban and Essl, Franz}, title = {Crypticity in Biological Invasions}, series = {Trends in Ecology \& Evolution}, volume = {34}, journal = {Trends in Ecology \& Evolution}, number = {4}, publisher = {Elsevier}, address = {London}, issn = {0169-5347}, doi = {10.1016/j.tree.2018.12.008}, pages = {291 -- 302}, year = {2019}, abstract = {Ecological effects of alien species can be dramatic, but management and prevention of negative impacts are often hindered by crypticity of the species or their ecological functions. Ecological functions can change dramatically over time, or manifest after long periods of an innocuous presence. Such cryptic processes may lead to an underestimation of long-term impacts and constrain management effectiveness. Here, we present a conceptual framework of crypticity in biological invasions. We identify the underlying mechanisms, provide evidence of their importance, and illustrate this phenomenon with case studies. This framework has potential to improve the recognition of the full risks and impacts of invasive species.}, language = {en} } @misc{SchellerZhangYarmanetal.2019, author = {Scheller, Frieder W. and Zhang, Xiaorong and Yarman, Aysu and Wollenberger, Ulla and Gyurcs{\´a}nyi, R{\´o}bert E.}, title = {Molecularly imprinted polymer-based electrochemical sensors for biopolymers}, series = {Current opinion in electrochemistry}, volume = {14}, journal = {Current opinion in electrochemistry}, publisher = {Elsevier}, address = {Amsterdam}, issn = {2451-9103}, doi = {10.1016/j.coelec.2018.12.005}, pages = {53 -- 59}, year = {2019}, abstract = {Electrochemical synthesis and signal generation dominate among the almost 1200 articles published annually on protein-imprinted polymers. Such polymers can be easily prepared directly on the electrode surface, and the polymer thickness can be precisely adjusted to the size of the target to enable its free exchange. In this architecture, the molecularly imprinted polymer (MIP) layer represents only one 'separation plate'; thus, the selectivity does not reach the values of 'bulk' measurements. The binding of target proteins can be detected straightforwardly by their modulating effect on the diffusional permeability of a redox marker through the thin MIP films. However, this generates an 'overall apparent' signal, which may include nonspecific interactions in the polymer layer and at the electrode surface. Certain targets, such as enzymes or redox active proteins, enables a more specific direct quantification of their binding to MIPs by in situ determination of the enzyme activity or direct electron transfer, respectively.}, language = {en} } @misc{GrossartVandenWyngaertKagamietal.2019, author = {Grossart, Hans-Peter and Van den Wyngaert, Silke and Kagami, Maiko and Wurzbacher, Christian and Cunliffe, Michael and Rojas-Jimenz, Keilor}, title = {Fungi in aquatic ecosystems}, series = {Nature reviews. Microbiology}, volume = {17}, journal = {Nature reviews. Microbiology}, number = {6}, publisher = {Nature Publ. Group}, address = {Basingstoke}, issn = {1740-1526}, doi = {10.1038/s41579-019-0175-8}, pages = {339 -- 354}, year = {2019}, abstract = {Fungi are phylogenetically and functionally diverse ubiquitous components of almost all ecosystems on Earth, including aquatic environments stretching from high montane lakes down to the deep ocean. Aquatic ecosystems, however, remain frequently overlooked as fungal habitats, although fungi potentially hold important roles for organic matter cycling and food web dynamics. Recent methodological improvements have facilitated a greater appreciation of the importance of fungi in many aquatic systems, yet a conceptual framework is still missing. In this Review, we conceptualize the spatiotemporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic food webs. We focus on currently unexplored fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats.}, language = {en} } @misc{ZupokIobbiNivolMejeanetal.2019, author = {Zupok, Arkadiusz and Iobbi-Nivol, Chantal and Mejean, Vincent and Leimk{\"u}hler, Silke}, title = {The regulation of Moco biosynthesis and molybdoenzyme gene expression by molybdenum and iron in bacteria}, series = {Metallomics : integrated biometal science}, volume = {11}, journal = {Metallomics : integrated biometal science}, number = {10}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1756-5901}, doi = {10.1039/c9mt00186g}, pages = {1602 -- 1624}, year = {2019}, abstract = {Bacterial molybdoenzymes are key enzymes involved in the global sulphur, nitrogen and carbon cycles. These enzymes require the insertion of the molybdenum cofactor (Moco) into their active sites and are able to catalyse a large range of redox-reactions. Escherichia coli harbours nineteen different molybdoenzymes that require a tight regulation of their synthesis according to substrate availability, oxygen availability and the cellular concentration of molybdenum and iron. The synthesis and assembly of active molybdoenzymes are regulated at the level of transcription of the structural genes and of translation in addition to the genes involved in Moco biosynthesis. The action of global transcriptional regulators like FNR, NarXL/QP, Fur and ArcA and their roles on the expression of these genes is described in detail. In this review we focus on what is known about the molybdenum- and iron-dependent regulation of molybdoenzyme and Moco biosynthesis genes in the model organism E. coli. The gene regulation in E. coli is compared to two other well studied model organisms Rhodobacter capsulatus and Shewanella oneidensis.}, language = {en} } @misc{BorregaardAmorimBorgesetal.2017, author = {Borregaard, Michael K. and Amorim, Isabel R. and Borges, Paulo A. V. and Cabral, Juliano Sarmento and Fernandez-Palacios, Jose M. and Field, Richard and Heaney, Lawrence R. and Kreft, Holger and Matthews, Thomas J. and Olesen, Jens M. and Price, Jonathan and Rigal, Francois and Steinbauer, Manuel J. and Triantis, Konstantinos A. and Valente, Luis and Weigelt, Patrick and Whittaker, Robert J.}, title = {Oceanic island biogeography through the lens of the general dynamic model: assessment and prospect}, series = {Biological reviews}, volume = {92}, journal = {Biological reviews}, publisher = {Wiley}, address = {Hoboken}, issn = {1464-7931}, doi = {10.1111/brv.12256}, pages = {830 -- 853}, year = {2017}, language = {en} } @misc{ColomboWackerParrishetal.2017, author = {Colombo, Stefanie M. and Wacker, Alexander and Parrish, Christopher C. and Kainz, Martin J. and Arts, Michael T.}, title = {A fundamental dichotomy in long-chain polyunsaturated fatty acid abundance between and within marine and terrestrial ecosystems}, series = {Environmental reviews = Dossiers environnement}, volume = {25}, journal = {Environmental reviews = Dossiers environnement}, publisher = {NRC Research Press}, address = {Ottawa}, issn = {1208-6053}, doi = {10.1139/er-2016-0062}, pages = {163 -- 174}, year = {2017}, abstract = {Polyunsaturated fatty acids (PUFA), especially long-chain (i.e., >= 20 carbons) polyunsaturated fatty acids (LC-PUFA), are fundamental to the health and survival of marine and terrestrial organisms. Therefore, it is imperative that we gain a better understanding of their origin, abundance, and transfer between and within these ecosystems. We evaluated the natural variation in PUFA distribution and abundance that exists between and within these ecosystems by amassing and analyzing, using multivariate and analysis of variance (ANOVA) methods, >3000 fatty acid (FA) profiles from marine and terrestrial organisms. There was a clear dichotomy in LC-PUFA abundance between organisms in marine and terrestrial ecosystems, mainly driven by the C-18 PUFA in terrestrial organisms and omega-3 (n-3) LC-PUFA in marine organisms. The PUFA content of an organism depended on both its biome (marine vs terrestrial) and taxonomic group. Within the marine biome, the PUFA content varied among taxonomic groups. PUFA content of marine organisms was dependent on both geographic zone (i.e., latitude, and thus broadly related to temperature) and trophic level (a function of diet). The contents of n-3 LC-PUFA were higher in polar and temperate marine organisms than those from the tropics. Therefore, we conclude that, on a per capita basis, high latitude marine organisms provide a disproportionately large global share of these essential nutrients to consumers, including terrestrial predators. Our analysis also hints at how climate change, and other anthropogenic stressors, might act to negatively impact the global distribution and abundance of n-3 LC-PUFA within marine ecosystems and on the terrestrial consumers that depend on these subsidies.}, language = {en} } @misc{Leimkuehler2017, author = {Leimk{\"u}hler, Silke}, title = {Shared function and moonlighting proteins in molybdenum cofactor biosynthesis}, series = {Biological chemistry}, volume = {398}, journal = {Biological chemistry}, publisher = {De Gruyter}, address = {Berlin}, issn = {1431-6730}, doi = {10.1515/hsz-2017-0110}, pages = {1009 -- 1026}, year = {2017}, abstract = {The biosynthesis of the molybdenum cofactor (Moco) is a highly conserved pathway in bacteria, archaea and eukaryotes. The molybdenum atom in Moco-containing enzymes is coordinated to the dithiolene group of a tricyclic pyranopterin monophosphate cofactor. The biosynthesis of Moco can be divided into three conserved steps, with a fourth present only in bacteria and archaea: (1) formation of cyclic pyranopterin monophosphate, (2) formation of molybdopterin (MPT), (3) insertion of molybdenum into MPT to form Mo-MPT, and (4) additional modification of Mo-MPT in bacteria with the attachment of a GMP or CMP nucleotide, forming the dinucleotide variants of Moco. While the proteins involved in the catalytic reaction of each step of Moco biosynthesis are highly conserved among the Phyla, a surprising link to other cellular pathways has been identified by recent discoveries. In particular, the pathways for FeS cluster assembly and thio-modifications of tRNA are connected to Moco biosynthesis by sharing the same protein components. Further, proteins involved in Moco biosynthesis are not only shared with other pathways, but additionally have moonlighting roles. This review gives an overview of Moco biosynthesis in bacteria and humans and highlights the shared function and moonlighting roles of the participating proteins.}, language = {en} } @misc{FrenkenAlacidBergeretal.2017, author = {Frenken, Thijs and Alacid, Elisabet and Berger, Stella A. and Bourne, Elizabeth Charlotte and Gerphagnon, Melanie and Grossart, Hans-Peter and Gsell, Alena S. and Ibelings, Bas W. and Kagami, Maiko and Kupper, Frithjof C. and Letcher, Peter M. and Loyau, Adeline and Miki, Takeshi and Nejstgaard, Jens C. and Rasconi, Serena and Rene, Albert and Rohrlack, Thomas and Rojas-Jimenez, Keilor and Schmeller, Dirk S. and Scholz, Bettina and Seto, Kensuke and Sime-Ngando, Telesphore and Sukenik, Assaf and Van de Waal, Dedmer B. and Van den Wyngaert, Silke and Van Donk, Ellen and Wolinska, Justyna and Wurzbacher, Christian and Agha, Ramsy}, title = {Integrating chytrid fungal parasites into plankton ecology: research gaps and needs}, series = {Environmental microbiology}, volume = {19}, journal = {Environmental microbiology}, publisher = {Wiley}, address = {Hoboken}, issn = {1462-2912}, doi = {10.1111/1462-2920.13827}, pages = {3802 -- 3822}, year = {2017}, abstract = {Chytridiomycota, often referred to as chytrids, can be virulent parasites with the potential to inflict mass mortalities on hosts, causing e.g. changes in phytoplankton size distributions and succession, and the delay or suppression of bloom events. Molecular environmental surveys have revealed an unexpectedly large diversity of chytrids across a wide range of aquatic ecosystems worldwide. As a result, scientific interest towards fungal parasites of phytoplankton has been gaining momentum in the past few years. Yet, we still know little about the ecology of chytrids, their life cycles, phylogeny, host specificity and range. Information on the contribution of chytrids to trophic interactions, as well as co-evolutionary feedbacks of fungal parasitism on host populations is also limited. This paper synthesizes ideas stressing the multifaceted biological relevance of phytoplankton chytridiomycosis, resulting from discussions among an international team of chytrid researchers. It presents our view on the most pressing research needs for promoting the integration of chytrid fungi into aquatic ecology.}, language = {en} } @misc{KappelCuongNguyenHuuLenhard2017, author = {Kappel, Christian and Cuong Nguyen Huu, and Lenhard, Michael}, title = {A short story gets longer: recent insights into the molecular basis of heterostyly}, series = {Journal of experimental botany}, volume = {68}, journal = {Journal of experimental botany}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/erx387}, pages = {5719 -- 5730}, year = {2017}, abstract = {Heterostyly is a fascinating adaptation to promote outbreeding and a classical paradigm of botany. In the most common type of heterostyly, plants either form flowers with long styles and short stamens, or short styles and long stamens. This reciprocal organ positioning reduces pollen wastage and promotes cross-pollination, thus increasing male fitness. In addition, in many heterostylous species selfing and the generation of unfit progeny due to inbreeding depression is limited by a self-incompatibility system, thus promoting female fitness. The two floral forms are genetically determined by the S locus as a complex supergene, namely a chromosomal region containing several individual genes that control the different traits, such as style or stamen length, and are held together by very tight linkage due to suppressed recombination. Recent molecular-genetic studies in several systems, including Turnera, Fagopyrum, Linum, and Primula have begun to identify and characterize the causal heterostyly genes residing at the S locus. An emerging theme from several families is that the dominant S haplotype represents a hemizygous region not present on the recessive s haplotype. This provides an explanation for the suppressed recombination and suggests a scenario for the chromosomal evolution of the S locus. In this review, we discuss the results from recent molecular-genetic analyses in light of the classical models on the genetics and evolution of heterostyly.}, language = {en} } @misc{LeimkuehlerIobbiNivol2016, author = {Leimk{\"u}hler, Silke and Iobbi-Nivol, Chantal}, title = {Bacterial molybdoenzymes: old enzymes for new purposes}, series = {FEMS microbiology reviews}, volume = {40}, journal = {FEMS microbiology reviews}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0168-6445}, doi = {10.1093/femsre/fuv043}, pages = {1 -- 18}, year = {2016}, abstract = {Molybdoenzymes are widespread in eukaryotic and prokaryotic organisms where they play crucial functions in detoxification reactions in the metabolism of humans and bacteria, in nitrate assimilation in plants and in anaerobic respiration in bacteria. To be fully active, these enzymes require complex molybdenum-containing cofactors, which are inserted into the apoenzymes after folding. For almost all the bacterial molybdoenzymes, molybdenum cofactor insertion requires the involvement of specific chaperones. In this review, an overview on the molybdenum cofactor biosynthetic pathway is given together with the role of specific chaperones dedicated for molybdenum cofactor insertion and maturation. Many bacteria are involved in geochemical cycles on earth and therefore have an environmental impact. The roles of molybdoenzymes in bioremediation and for environmental applications are presented.This review gives an overview of the diverse mechanisms leading to the insertion of the different forms of the molybdenum cofactor into the respective target enzymes and summarizes the roles of different molybdoenzymes in the environment.This review gives an overview of the diverse mechanisms leading to the insertion of the different forms of the molybdenum cofactor into the respective target enzymes and summarizes the roles of different molybdoenzymes in the environment.}, language = {en} } @misc{SperfeldRaubenheimerWacker2016, author = {Sperfeld, Erik and Raubenheimer, David and Wacker, Alexander}, title = {Bridging factorial and gradient concepts of resource co-limitation: towards a general framework applied to consumers}, series = {Ecology letters}, volume = {19}, journal = {Ecology letters}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1461-023X}, doi = {10.1111/ele.12554}, pages = {201 -- 215}, year = {2016}, abstract = {Organism growth can be limited either by a single resource or by multiple resources simultaneously (co-limitation). Efforts to characterise co-limitation have generated two influential approaches. One approach uses limitation scenarios of factorial growth assays to distinguish specific types of co-limitation; the other uses growth responses spanned over a continuous, multi-dimensional resource space to characterise different types of response surfaces. Both approaches have been useful in investigating particular aspects of co-limitation, but a synthesis is needed to stimulate development of this recent research area. We address this gap by integrating the two approaches, thereby presenting a more general framework of co-limitation. We found that various factorial (co-)limitation scenarios can emerge in different response surface types based on continuous availabilities of essential or substitutable resources. We tested our conceptual co-limitation framework on data sets of published and unpublished studies examining the limitation of two herbivorous consumers in a two-dimensional resource space. The experimental data corroborate the predictions, suggesting a general applicability of our co-limitation framework to generalist consumers and potentially also to other organisms. The presented framework might give insight into mechanisms that underlie co-limitation responses and thus can be a seminal starting point for evaluating co-limitation patterns in experiments and nature.}, language = {en} } @misc{HaackAbdelilahSeyfried2016, author = {Haack, Timm and Abdelilah-Seyfried, Salim}, title = {The force within: endocardial development, mechanotransduction and signalling during cardiac morphogenesis}, series = {Development : Company of Biologists}, volume = {143}, journal = {Development : Company of Biologists}, publisher = {Company of Biologists Limited}, address = {Cambridge}, issn = {0950-1991}, doi = {10.1242/dev.131425}, pages = {373 -- 386}, year = {2016}, abstract = {Endocardial cells are cardiac endothelial cells that line the interior of the heart tube. Historically, their contribution to cardiac development has mainly been considered from a morphological perspective. However, recent studies have begun to define novel instructive roles of the endocardium, as a sensor and signal transducer of biophysical forces induced by blood flow, and as an angiocrine signalling centre that is involved in myocardial cellular morphogenesis, regeneration and reprogramming. In this Review, we discuss how the endocardium develops, how endocardial-myocardial interactions influence the developing embryonic heart, and how the dysregulation of blood flowresponsive endocardial signalling can result in pathophysiological changes.}, language = {en} } @misc{YanChenKaufmann2016, author = {Yan, Wenhao and Chen, Dijun and Kaufmann, Kerstin}, title = {Molecular mechanisms of floral organ specification by MADS domain proteins}, series = {Current opinion in plant biology}, volume = {29}, journal = {Current opinion in plant biology}, publisher = {Elsevier}, address = {London}, issn = {1369-5266}, doi = {10.1016/j.pbi.2015.12.004}, pages = {154 -- 162}, year = {2016}, abstract = {Flower development is a model system to understand organ specification in plants. The identities of different types of floral organs are specified by homeotic MADS transcription factors that interact in a combinatorial fashion. Systematic identification of DNA-binding sites and target genes of these key regulators show that they have shared and unique sets of target genes. DNA binding by MADS proteins is not based on 'simple' recognition of a specific DNA sequence, but depends on DNA structure and combinatorial interactions. Homeotic MADS proteins regulate gene expression via alternative mechanisms, one of which may be to modulate chromatin structure and accessibility in their target gene promoters.}, language = {en} } @misc{deVinuesaAbdelilahSeyfriedKnausetal.2016, author = {de Vinuesa, Amaya Garcia and Abdelilah-Seyfried, Salim and Knaus, Petra and Zwijsen, An and Bailly, Sabine}, title = {BMP signaling in vascular biology and dysfunction}, series = {New journal of physics : the open-access journal for physics}, volume = {27}, journal = {New journal of physics : the open-access journal for physics}, publisher = {Elsevier}, address = {Oxford}, issn = {1359-6101}, doi = {10.1016/j.cytogfr.2015.12.005}, pages = {65 -- 79}, year = {2016}, abstract = {The vascular system is critical for developmental growth, tissue homeostasis and repair but also for tumor development. Bone morphogenetic protein (BMP) signaling has recently emerged as a fundamental pathway of the endothelium by regulating cardiovascular and lymphatic development and by being causative for several vascular dysfunctions. Two vascular disorders have been directly linked to impaired BMP signaling: pulmonary arterial hypertension and hereditary hemorrhagic telangiectasia. Endothelial BMP signaling critically depends on the cellular context, which includes among others vascular heterogeneity, exposure to flow, and the intertwining with other signaling cascades (Notch, WNT, Hippo and hypoxia). The purpose of this review is to highlight the most recent findings illustrating the clear need for reconsidering the role of BMPs in vascular biology. (C) 2015 Elsevier Ltd. All rights reserved.}, language = {en} } @misc{WoodhouseMakowerYeungetal.2016, author = {Woodhouse, Jason Nicholas and Makower, A. Katharina and Yeung, Anna C. Y. and Ongley, Sarah E. and Micallef, Melinda L. and Moffitt, Michelle C. and Neilan, Brett A.}, title = {Advances in genomics, transcriptomics and proteomics of toxin-producing cyanobacteria}, series = {Environmental microbiology reports}, volume = {8}, journal = {Environmental microbiology reports}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1758-2229}, doi = {10.1111/1758-2229.12366}, pages = {3 -- 13}, year = {2016}, abstract = {A common misconception persists that the genomes of toxic and non-toxic cyanobacterial strains are largely conserved with the exception of the presence or absence of the genes responsible for toxin production. Implementation of -omics era technologies has challenged this paradigm, with comparative analyses providing increased insight into the differences between strains of the same species. The implementation of genomic, transcriptomic and proteomic approaches has revealed distinct profiles between toxin-producing and non-toxic strains. Further, metagenomics and metaproteomics highlight the genomic potential and functional state of toxic bloom events over time. In this review, we highlight how these technologies have shaped our understanding of the complex relationship between these molecules, their producers and the environment at large within which they persist.}, language = {en} }