@article{pmid31708944,

title = {A Bioinformatics Guide to Plant Microbiome Analysis},

author = {Rares Lucaciu and Claus Pelikan and Samuel M Gerner and Christos Zioutis and Stephan Köstlbacher and Harald Marx and Craig W Herbold and Hannes Schmidt and Thomas Rattei},

doi = {10.3389/fpls.2019.01313},

issn = {1664-462X},

year  = {2019},

date = {2019-01-01},

journal = {Front Plant Sci},

volume = {10},

pages = {1313},

abstract = {Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant-microbiome studies. We discuss sequencing and "omics" techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant-bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31166981,

title = {The composition of bacterial communities associated with plastic biofilms differs between different polymers and stages of biofilm succession},

author = {Maria Pinto and Teresa M Langer and Thorsten Hüffer and Thilo Hofmann and Gerhard J Herndl},

doi = {10.1371/journal.pone.0217165},

issn = {1932-6203},

year  = {2019},

date = {2019-01-01},

journal = {PLoS One},

volume = {14},

number = {6},

pages = {e0217165},

abstract = {Once in the ocean, plastics are rapidly colonized by complex microbial communities. Factors affecting the development and composition of these communities are still poorly understood. Additionally, whether there are plastic-type specific communities developing on different plastics remains enigmatic. We determined the development and succession of bacterial communities on different plastics under ambient and dim light conditions in the coastal Northern Adriatic over the course of two months using scanning electron microscopy and 16S rRNA gene analyses. Plastics used were low- and high-density polyethylene (LDPE and HDPE, respectively), polypropylene (PP) and polyvinyl chloride with two typical additives (PVC DEHP and PVC DINP). The bacterial communities developing on the plastics clustered in two groups; one group was found on PVC and the other group on all the other plastics and on glass, which was used as an inert control. Specific bacterial taxa were found on specific surfaces in essentially all stages of biofilm development and in both ambient and dim light conditions. Differences in bacterial community composition between the different plastics and light exposures were stronger after an incubation period of one week than at the later stages of the incubation. Under both ambient and dim light conditions, one part of the bacterial community was common on all plastic types, especially in later stages of the biofilm development, with families such as Flavobacteriaceae, Rhodobacteraceae, Planctomycetaceae and Phyllobacteriaceae presenting relatively high relative abundances on all surfaces. Another part of the bacterial community was plastic-type specific. The plastic-type specific fraction was variable among the different plastic types and was more abundant after one week of incubation than at later stages of the succession.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31788438,

title = {The leaching of phthalates from PVC can be determined with an infinite sink approach},

author = {Charlotte Henkel and Thorsten Hüffer and Thilo Hofmann},

doi = {10.1016/j.mex.2019.10.026},

issn = {2215-0161},

year  = {2019},

date = {2019-01-01},

journal = {MethodsX},

volume = {6},

pages = {2729–2734},

abstract = {Polyvinyl chloride (PVC) is the third most used polymer for plastic products in the European Union (+NO/ CH) and contains the highest amounts of additives, especially phthalic acid esters (phthalates). Leaching kinetics of additives from (micro-) plastics into aqueous environments are highly relevant for environmental risk assessment and modelling of the fluxes of plastics and its associated additives. Investigating the leaching of phthalates into aqueous environments in batch experiments is challenging due to their low solubility and high hydrophobicity and there are no standard methods to study release processes. Here we describe an infinite sink method to investigate the leaching of phthalates from PVC into the aqueous phase. Spiking and leaching experiments using bis(2-ethylhexyl) phthalate as a model phthalate enabled the validation and evaluation of the designed infinite sink method. The developed method offers: •a low-cost and simple approach to investigate leaching of phthalates from PVC into aqueous environments•the use of a high-surface activated carbon powder as an infinite sink•a tool to elucidate the transport fluxes of plastics and additives.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30384010,

title = {Synthesis and biological evaluation of biotin-conjugated anticancer thiosemicarbazones and their iron(III) and copper(II) complexes},

author = {Sebastian Kallus and Lukas Uhlik and Sushilla Schoonhoven and Karla Pelivan and Walter Berger and Éva A Enyedy and Thilo Hofmann and Petra Heffeter and Christian R Kowol and Bernhard K Keppler},

doi = {10.1016/j.jinorgbio.2018.10.006},

issn = {1873-3344},

year  = {2019},

date = {2019-01-01},

journal = {J Inorg Biochem},

volume = {190},

pages = {85–97},

abstract = {Triapine, the most prominent anticancer drug candidate from the substance class of thiosemicarbazones, was investigated in >30 clinical phase I and II studies. However, the results were rather disappointing against solid tumors, which can be explained (at least partially) due to inefficient delivery to the tumor site. Hence, we synthesized the first biotin-functionalized thiosemicarbazone derivatives in order to increase tumor specificity and accumulation. Additionally, for Triapine and one biotin conjugate the iron(III) and copper(II) complexes were prepared. Subsequently, the novel compounds were biologically evaluated on a cell line panel with different biotin uptake. The metal-free biotin-conjugated ligands showed comparable activity to the reference compound Triapine. However, astonishingly, the metal complexes of the biotinylated derivative showed strikingly decreased anticancer activity. To further analyze possible differences between the metal complexes, detailed physico- and electrochemical experiments were performed. However, neither lipophilicity or complex solution stability, nor the reduction potential or behavior in the presence of biologically relevant reducing agents showed strong variations between the biotinylated and non-biotinylated derivatives (only some differences in the reduction kinetics were observed). Nonetheless, the metal-free biotin-conjugate of Triapine revealed distinct activity in a colon cancer mouse model upon oral application comparable to Triapine. Therefore, this type of biotin-conjugated thiosemicarbazone is of interest for further synthetic strategies and biological studies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30559115,

title = {Functional network interactions at rest underlie individual differences in memory ability},

author = {Mariët Buuren and Isabella C Wagner and Guillén Fernández},

doi = {10.1101/lm.048199.118},

issn = {1549-5485},

year  = {2019},

date = {2019-01-01},

journal = {Learn Mem},

volume = {26},

number = {1},

pages = {9–19},

abstract = {Intrinsic network interactions may underlie individual differences in the ability to remember. The default mode network (DMN) comprises subnetworks implicated in memory, and interactions between the DMN and frontoparietal network (FPN) were shown to support mnemonic processing. However, it is unclear if such interactions during resting-state predict episodic memory ability. We investigated whether intrinsic network interactions within and between the DMN and FPN are related to individual differences in memory performance. Resting-state activity was measured using functional MRI in healthy young adults followed by a memory test for object-location associations that were studied 3 d earlier. We identified two subnetworks within the DMN, the main-DMN and the medial temporal lobe, retrosplenial cortex (MTL_RSC)-DMN. Further, we found regions forming the FPN. Memory performance was associated with lower connectivity within the MTL_RSC-DMN, and stronger connectivity between the main-DMN and FPN. Exploratory whole-brain analysis revealed stronger MTL connectivity with the left posterior parietal cortex that was related to better memory performance. Furthermore, we found increased task-evoked activation during successful retrieval within the main-DMN and FPN, but not within the MTL_RSC-DMN. In sum, lower intrinsic connectivity within the MTL_RSC-DMN, combined with stronger connectivity between the main-DMN and FPN, explain individual differences in memory ability.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wanek2019,

title = {A novel isotope pool dilution approach to quantify gross rates of key abiotic and biological processes in the soil phosphorus cycle},

author = {Wolfgang Wanek and David Zezula and Daniel Wasner and Maria Mooshammer and Judith Prommer},

doi = {10.5194/bg-16-3047-2019},

issn = {1726-4189},

year  = {2019},

date = {2019-00-00},

journal = {Biogeosciences},

volume = {16},

number = {15},

pages = {3047–3068},

publisher = {Copernicus GmbH},

abstract = {<jats:p>Abstract. Efforts to understand and model the current and future behavior of the global 

phosphorus (P) cycle are limited by the availability of global data on rates of soil P processes, as well as their environmental controls. Here, we present a novel isotope pool dilution approach using 33P labeling of live and sterile soils, which allows for high-quality data on gross fluxes of soil inorganic P (Pi) sorption and desorption, as well as of gross fluxes of organic P mineralization and microbial Pi uptake to be obtained. At the same time, net immobilization of 33Pi by soil microbes and abiotic 

sorption can be easily derived and partitioned. Compared with other approaches, we used short incubation times (up to 48 h), avoiding tracer 

remineralization, which was confirmed by the separation of organic P and Pi using isobutanol fractionation. This approach is also suitable for strongly weathered and P-impoverished soils, as the sensitivity is increased by the extraction of exchangeable bioavailable Pi (Olsen Pi; 0.5 M NaHCO3) 

followed by Pi measurement using the malachite green assay. Biotic 

processes were corrected for desorption/sorption processes using adequate 

sterile abiotic controls that exhibited negligible microbial and 

extracellular phosphatase activities. Gross rates were calculated using 

analytical solutions of tracer kinetics, which also allowed for the study of gross 

soil P dynamics under non-steady-state conditions. Finally, we present major 

environmental controls of gross P-cycle processes that were measured for 

three P-poor tropical forest and three P-rich temperate grassland soils. 

 </jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}