TY - JOUR A1 - Woodhouse, Jason Nicholas A1 - Makower, A. Katharina A1 - Yeung, Anna C. Y. A1 - Ongley, Sarah E. A1 - Micallef, Melinda L. A1 - Moffitt, Michelle C. A1 - Neilan, Brett A. T1 - Advances in genomics, transcriptomics and proteomics of toxin-producing cyanobacteria JF - Environmental microbiology reports N2 - 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. Y1 - 2016 U6 - https://doi.org/10.1111/1758-2229.12366 SN - 1758-2229 VL - 8 SP - 3 EP - 13 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Rajasundaram, Dhivyaa A1 - Selbig, Joachim T1 - analysis JF - Current opinion in plant biology N2 - The development of ‘omics’ technologies has progressed to address complex biological questions that underlie various plant functions thereby producing copious amounts of data. The need to assimilate large amounts of data into biologically meaningful interpretations has necessitated the development of statistical methods to integrate multidimensional information. Throughout this review, we provide examples of recent outcomes of ‘omics’ data integration together with an overview of available statistical methods and tools. Y1 - 2016 U6 - https://doi.org/10.1016/j.pbi.2015.12.010 SN - 1369-5266 SN - 1879-0356 VL - 30 SP - 57 EP - 61 PB - Elsevier CY - London ER - TY - JOUR A1 - Großart, Hans-Peter A1 - Rojas-Jimenez, Keilor T1 - Aquatic fungi: targeting the forgotten in microbial ecology JF - Current opinion in microbiology N2 - Fungi constitute important and conspicuous components of aquatic microbial communities, but their diversity and functional roles remain poorly characterized. New methods and conceptual frameworks are required to accurately describe their ecological roles, involvement in global cycling processes, and utility for human activities, considering both cultivation independent techniques as well as experiments in laboratory and in natural ecosystems. Here we highlight recent developments and extant knowledge gaps in aquatic mycology, and provide a conceptual model to expose the importance of fungi in aquatic food webs and related biogeochemical processes. Y1 - 2016 U6 - https://doi.org/10.1016/j.mib.2016.03.016 SN - 1369-5274 SN - 1879-0364 VL - 31 SP - 140 EP - 145 PB - Elsevier CY - London ER - TY - JOUR A1 - Marce, Rafael A1 - George, Glen A1 - Buscarinu, Paola A1 - Deidda, Melania A1 - Dunalska, Julita A1 - de Eyto, Elvira A1 - Flaim, Giovanna A1 - Grossart, Hans-Peter A1 - Istvanovics, Vera A1 - Lenhardt, Mirjana A1 - Moreno-Ostos, Enrique A1 - Obrador, Biel A1 - Ostrovsky, Ilia A1 - Pierson, Donald C. A1 - Potuzak, Jan A1 - Poikane, Sandra A1 - Rinke, Karsten A1 - Rodriguez-Mozaz, Sara A1 - Staehr, Peter A. A1 - Sumberova, Katerina A1 - Waajen, Guido A1 - Weyhenmeyer, Gesa A. A1 - Weathers, Kathleen C. A1 - Zion, Mark A1 - Ibelings, Bas W. A1 - Jennings, Eleanor T1 - Automatic High Frequency Monitoring for Improved Lake and Reservoir Management JF - Frontiers in plant science N2 - Recent technological developments have increased the number of variables being monitored in lakes and reservoirs using automatic high frequency monitoring (AHFM). However, design of AHFM systems and posterior data handling and interpretation are currently being developed on a site-by-site and issue-by-issue basis with minimal standardization of protocols or knowledge sharing. As a result, many deployments become short-lived or underutilized, and many new scientific developments that are potentially useful for water management and environmental legislation remain underexplored. This Critical Review bridges scientific uses of AHFM with their applications by providing an overview of the current AHFM capabilities, together with examples of successful applications. We review the use of AHFM for maximizing the provision of ecosystem services supplied, by lakes and reservoirs (consumptive and non consumptive uses, food production, and recreation), and for reporting lake status in the EU Water Framework Directive. We also highlight critical issues to enhance the application of AHFM, and suggest the establishment of appropriate networks to facilitate knowledge sharing and technological transfer between potential users. Finally, we give advice on how modern sensor technology can successfully be applied on a larger scale to the management of lakes and reservoirs and maximize the ecosystem services they provide. Y1 - 2016 U6 - https://doi.org/10.1021/acs.est.6b01604 SN - 0013-936X SN - 1520-5851 VL - 50 SP - 10780 EP - 10794 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Leimkühler, Silke A1 - Iobbi-Nivol, Chantal T1 - Bacterial molybdoenzymes: old enzymes for new purposes JF - FEMS microbiology reviews N2 - 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. KW - molybdenum cofactor KW - specific chaperons KW - TorD family KW - XdhC KW - molybdoenzyme maturation KW - bioremediation Y1 - 2016 U6 - https://doi.org/10.1093/femsre/fuv043 SN - 0168-6445 SN - 1574-6976 VL - 40 SP - 1 EP - 18 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Speller, Camilla A1 - van den Hurk, Youri A1 - Charpentier, Anne A1 - Rodrigues, Ana A1 - Gardeisen, Armelle A1 - Wilkens, Barbara A1 - McGrath, Krista A1 - Rowsell, Keri A1 - Spindler, Luke A1 - Collins, Matthew J. A1 - Hofreiter, Michael T1 - Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans JF - Philosophical transactions of the Royal Society of London : B, Biological sciences KW - ancient DNA KW - archaeozoology KW - cetaceans KW - collagen peptide mass fingerprinting KW - species identification KW - zooarchaeology by mass spectrometry Y1 - 2016 U6 - https://doi.org/10.1098/rstb.2015.0332 SN - 0962-8436 SN - 1471-2970 VL - 371 PB - Royal Society CY - London ER - TY - JOUR A1 - de Vinuesa, Amaya Garcia A1 - Abdelilah-Seyfried, Salim A1 - Knaus, Petra A1 - Zwijsen, An A1 - Bailly, Sabine T1 - BMP signaling in vascular biology and dysfunction JF - New journal of physics : the open-access journal for physics N2 - 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. KW - Bone morphogenetic proteins (BMP) KW - Signaling KW - Vasculature KW - Development KW - Disease Y1 - 2016 U6 - https://doi.org/10.1016/j.cytogfr.2015.12.005 SN - 1359-6101 SN - 1879-0305 VL - 27 SP - 65 EP - 79 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Sperfeld, Erik A1 - Raubenheimer, David A1 - Wacker, Alexander T1 - Bridging factorial and gradient concepts of resource co-limitation: towards a general framework applied to consumers JF - Ecology letters N2 - 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. KW - Consumer KW - essential nutrient KW - factorial design KW - food quality KW - growth rate KW - multi-nutrient limitation KW - nutritional ecology KW - performance landscape KW - substitutable resource KW - synergistic effect Y1 - 2016 U6 - https://doi.org/10.1111/ele.12554 SN - 1461-023X SN - 1461-0248 VL - 19 SP - 201 EP - 215 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Reverey, Florian A1 - Großart, Hans-Peter A1 - Premke, Katrin A1 - Lischeid, Gunnar T1 - Carbon and nutrient cycling in kettle hole sediments depending on hydrological dynamics: a review JF - Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica N2 - Kettle holes as a specific group of isolated, small lentic freshwater systems (LFS) often are (i) hot spots of biogeochemical cycling and (ii) exposed to frequent sediment desiccation and rewetting. Their ecological functioning is greatly determined by immanent carbon and nutrient transformations. The objective of this review is to elucidate effects of a changing hydrological regime (i.e., dry-wet cycles) on carbon and nutrient cycling in kettle hole sediments. Generally, dry-wet cycles have the potential to increase C and N losses as well as P availability. However, their duration and frequency are important controlling factors regarding direction and intensity of biogeochemical and microbiological responses. To evaluate drought impacts on sediment carbon and nutrient cycling in detail requires the context of the LFS hydrological history. For example, frequent drought events induce physiological adaptation of exposed microbial communities and thus flatten metabolic responses, whereas rare events provoke unbalanced, strong microbial responses. Different potential of microbial resilience to drought stress can irretrievably change microbial communities and functional guilds, gearing cascades of functional responses. Hence, dry-wet events can shift the biogeochemical cycling of organic matter and nutrients to a new equilibrium, thus affecting the dynamic balance between carbon burial and mineralization in kettle holes. KW - Drought KW - Rewetting KW - Temporary pond KW - Kettle hole KW - Organic matter KW - Nitrogen KW - Phosphorus Y1 - 2016 U6 - https://doi.org/10.1007/s10750-016-2715-9 SN - 0018-8158 SN - 1573-5117 VL - 775 SP - 1 EP - 20 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Erdossy, Julia A1 - Horvath, Viola A1 - Yarman, Aysu A1 - Scheller, Frieder W. A1 - Gyurcsanyi, Robert E. T1 - Electrosynthesized molecularly imprinted polymers for protein recognition JF - Trends in Analytical Chemistry N2 - Molecularly imprinted polymers (MIPs) for the recognition of proteins are expected to possess high affinity through the establishment of multiple interactions between the polymer matrix and the large number of functional groups of the target. However, while highly affine recognition sites need building blocks rich in complementary functionalities to their target, such units are likely to generate high levels of nonspecific binding. This paradox, that nature solved by evolution for biological receptors, needs to be addressed by the implementation of new concepts in molecular imprinting of proteins. Additionally, the structural variability, large size and incompatibility with a range of monomers made the development of protein MIPs to take a slow start. While the majority of MIP preparation methods are variants of chemical polymerization, the polymerization of electroactive functional monomers emerged as a particularly advantageous approach for chemical sensing application. Electropolymerization can be performed from aqueous solutions to preserve the natural conformation of the protein templates, with high spatial resolution and electrochemical control of the polymerization process. This review compiles the latest results, identifying major trends and providing an outlook on the perspectives of electrosynthesised protein-imprinted MIPs for chemical sensing. (C) 2016 Elsevier B.V. All rights reserved. KW - Molecularly imprinted polymers KW - Proteins KW - Surface imprinting KW - Electropolymerization KW - Nanostructuring KW - Hybrid nanofilms Y1 - 2016 U6 - https://doi.org/10.1016/j.trac.2015.12.018 SN - 0165-9936 SN - 1879-3142 VL - 79 SP - 179 EP - 190 PB - Elsevier CY - Oxford ER -