@article{pmid31763193,

title = {Optimized plasma-assisted bi-layer photoresist fabrication protocol for high resolution microfabrication of thin-film metal electrodes on porous polymer membranes},

author = {Patrick Schuller and Mario Rothbauer and Christoph Eilenberger and Sebastian R A Kratz and Gregor Höll and Philipp Taus and Markus Schinnerl and Jakob Genser and Peter Ertl and Heinz Wanzenboeck},

doi = {10.1016/j.mex.2019.10.038},

issn = {2215-0161},

year  = {2019},

date = {2019-01-01},

journal = {MethodsX},

volume = {6},

pages = {2606–2613},

abstract = {Structured metal thin-film electrodes are heavily used in electrochemical assays to detect a range of analytes including toxins, biomarkers, biological contaminants and cell cultures using amperometric, voltammetric and impedance-based (bio)sensing strategies as well as separation techniques such as dielectrophoresis. Over the last decade, thin-film electrodes have been fabricated onto various durable and flexible substrates including glass, silicon and polymers. However, the combination of thin-film technology with porous polymeric substrates frequently used for biochips often results in limited resolution and poor adhesion of the metal thin-film, thus severely restricting reproducible fabrication and reliable application in e.g. organ-on-a-chip systems. To overcome common problems associated with micro-structured electrode manufacturing on porous substrates, we have optimized a bi-layer lift-off method for the fabrication of thin-film electrodes on commercial porous polyester membranes using a combination of LOR3A with AZ5214E photoresists. To demonstrate practical application of our porous electrode membranes for trans-epithelial electrical resistance measurements a tetrapolar biosensing set-up was used to eliminate the artificial resistance of the porous polymer membrane from the electrochemical recordings. Furthermore, barrier resistance of Bewo trophoblast epithelial cells was compared to a standard Transwell assay readout using a EVOM2 volt-ohm meter. •Bi-layer photo resist lift-off yields resolution down to 2.5 μm.•Argon Plasma-assisted lift-off results in improved adhesion of gold thin films and eliminates the need for chromium adhesion layers.•Membrane electrodes can be used for elimination of the porous membrane resistance during tetra-polar epithelial resistance measurements.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31975763,

title = {Mid-infrared sensing of CO at saturated absorption conditions using intracavity quartz-enhanced photoacoustic spectroscopy},

author = {Jakob Hayden and Bettina Baumgartner and Johannes P Waclawek and Bernhard Lendl},

doi = {10.1007/s00340-019-7260-6},

issn = {0946-2171},

year  = {2019},

date = {2019-01-01},

journal = {Appl Phys B},

volume = {125},

number = {9},

pages = {159},

abstract = {The sensitivity of quartz-enhanced photoacoustic spectroscopy (QEPAS) can be drastically increased using the power enhancement in high-finesse cavities. Here, low noise resonant power enhancement to 6.3 W was achieved in a linear Brewster window cavity by exploiting optical feedback locking of a quantum cascade laser. The high intracavity intensity of up to 73 W mm in between the prongs of a custom tuning fork resulted in strong optical saturation of CO at 4.59 µm. Saturated absorption is discussed theoretically and experimentally for photoacoustic measurements in general and intracavity QEPAS (I-QEPAS) in particular. The saturation intensity of CO's R9 transition was retrieved from power-dependent I-QEPAS signals. This allowed for sensing CO independently from varying degrees of saturation caused by absorption induced changes of intracavity power. Figures of merit of the I-QEPAS setup for sensing of CO and HO are compared to standard wavelength modulation QEPAS without cavity enhancement. For HO, the sensitivity was increased by a factor of 230, practically identical to the power enhancement, while the sensitivity gain for CO detection was limited to 57 by optical saturation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30574650,

title = {Surface-enhanced Raman spectroscopy of microorganisms: limitations and applicability on the single-cell level},

author = {Ruben Weiss and Márton Palatinszky and Michael Wagner and Reinhard Niessner and Martin Elsner and Michael Seidel and Natalia P Ivleva},

doi = {10.1039/c8an02177e},

issn = {1364-5528},

year  = {2019},

date = {2019-01-01},

journal = {Analyst},

volume = {144},

number = {3},

pages = {943–953},

abstract = {Detection and characterization of microorganisms is essential for both clinical diagnostics and environmental studies. An emerging technique to analyse microbes at single-cell resolution is surface-enhanced Raman spectroscopy (surface-enhanced Raman scattering: SERS). Optimised SERS procedures enable fast analytical read-outs with specific molecular information, providing insight into the chemical composition of microbiological samples. Knowledge about the origin of microbial SERS signals and parameter(s) affecting their occurrence, intensity and/or reproducibility is crucial for reliable SERS-based analyses. In this work, we explore the feasibility and limitations of the SERS approach for characterizing microbial cells and investigate the applicability of SERS for single-cell sorting as well as for three-dimensional visualization of microbial communities. Analyses of six different microbial species (an archaeon, two Gram-positive bacteria, three Gram-negative bacteria) showed that for several of these organisms distinct features in their SERS spectra were lacking. As additional confounding factor, the physiological conditions of the cells (as influenced by e.g., storage conditions or deuterium-labelling) were systematically addressed, for which we conclude that the respective SERS signal at the single-cell level is strongly influenced by the metabolic activity of the analysed cells. While this finding complicates the interpretation of SERS data, it may on the other hand enable probing of the metabolic state of individual cells within microbial populations of interest.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31275527,

title = {Nanoscale Chemical Imaging of Individual, Chemotherapeutic Cytarabine-loaded Liposomal Nanocarriers},

author = {Karin Wieland and Georg Ramer and Victor U Weiss and Guenter Allmaier and Bernhard Lendl and Andrea Centrone},

doi = {10.1007/s12274-018-2202-x},

issn = {1998-0124},

year  = {2019},

date = {2019-01-01},

journal = {Nano Res},

volume = {12},

abstract = {Dosage of chemotherapeutic drugs is a tradeoff between efficacy and side-effects. Liposomes are nanocarriers that increase therapy efficacy and minimize side-effects by delivering otherwise difficult to administer therapeutics with improved efficiency and selectivity. Still, variabilities in liposome preparation require assessing drug encapsulation efficiency at the single liposome level, an information that, for non-fluorescent therapeutic cargos, is inaccessible due to the minute drug load per liposome. Photothermal induced resonance (PTIR) provides nanoscale compositional specificity, up to now, by leveraging an atomic force microscope (AFM) tip contacting the sample to transduce the sample's photothermal expansion. However, on soft samples (e.g. liposomes) PTIR effectiveness is reduced due to the likelihood of tip-induced sample damage and inefficient AFM transduction. Here, individual liposomes loaded with the chemotherapeutic drug cytarabine are deposited intact from suspension via nES-GEMMA (nano-electrospray gas-phase electrophoretic mobility molecular analysis) collection and characterized at the nanoscale with the chemically-sensitive PTIR method. A new tapping-mode PTIR imaging paradigm based on heterodyne detection is shown to be better adapted to measure soft samples, yielding cytarabine distribution in individual liposomes and enabling classification of empty and drug-loaded liposomes. The measurements highlight PTIR capability to detect ≈ 10 cytarabine molecules (≈ 1.7 zmol) label-free and non-destructively.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31275291,

title = {A Multicolor Fluorescence Hybridization Approach Using an Extended Set of Fluorophores to Visualize Microorganisms},

author = {Michael Lukumbuzya and Markus Schmid and Petra Pjevac and Holger Daims},

doi = {10.3389/fmicb.2019.01383},

issn = {1664-302X},

year  = {2019},

date = {2019-01-01},

journal = {Front Microbiol},

volume = {10},

pages = {1383},

abstract = {Fluorescence hybridization (FISH) with rRNA-targeted oligonucleotide probes is a key method for the detection of (uncultured) microorganisms in environmental and medical samples. A major limitation of standard FISH protocols, however, is the small number of phylogenetically distinct target organisms that can be detected simultaneously. In this study, we introduce a multicolor FISH approach that uses eight fluorophores with distinct spectral properties, which can unambiguously be distinguished by confocal laser scanning microscopy combined with white light laser technology. Hybridization of rRNA-targeted DNA oligonucleotide probes, which were mono-labeled with these fluorophores, to cultures confirmed that the fluorophores did not affect probe melting behavior. Application of the new multicolor FISH method enabled the differentiation of seven (potentially up to eight) phylogenetically distinct microbial populations in an artificial community of mixed pure cultures (five bacteria, one archaeon, and one yeast strain) and in activated sludge from a full-scale wastewater treatment plant. In contrast to previously published multicolor FISH approaches, this method does not rely on combinatorial labeling of the same microorganisms with different fluorophores, which is prone to biases. Furthermore, images acquired by this method do not require elaborate post-processing prior to analysis. We also demonstrate that the newly developed multicolor FISH method is compatible with an improved cell fixation protocol for FISH targeting Gram-negative bacterial populations. This fixation approach uses agarose embedding during formaldehyde fixation to better preserve the three-dimensional structure of spatially complex samples such as biofilms and activated sludge flocs. The new multicolor FISH approach should be highly suitable for studying structural and functional aspects of microbial communities in virtually all types of samples that can be analyzed by conventional FISH methods.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31579288,

title = {Growth explains microbial carbon use efficiency across soils differing in land use and geology},

author = {Qing Zheng and Yuntao Hu and Shasha Zhang and Lisa Noll and Theresa Böckle and Andreas Richter and Wolfgang Wanek},

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

issn = {0038-0717},

year  = {2019},

date = {2019-01-01},

journal = {Soil Biol Biochem},

volume = {128},

pages = {45–55},

abstract = {The ratio of carbon (C) that is invested into microbial growth to organic C taken up is known as microbial carbon use efficiency (CUE), which is influenced by environmental factors such as soil temperature and soil moisture. How microbes will physiologically react to short-term environmental changes is not well understood, primarily due to methodological restrictions. Here we report on two independent laboratory experiments to explore short-term temperature and soil moisture effects on soil microbial physiology (i.e. respiration, growth, CUE, and microbial biomass turnover): (i) a temperature experiment with 1-day pre-incubation at 5, 15 and 25 °C at 60% water holding capacity (WHC), and (ii) a soil moisture/oxygen (O) experiment with 7-day pre-incubation at 20 °C at 30%, 60% WHC (both at 21% O) and 90% WHC at 1% O. Experiments were conducted with soils from arable, pasture and forest sites derived from both silicate and limestone bedrocks. We found that microbial CUE responded heterogeneously though overall positively to short-term temperature changes, and decreased significantly under high moisture level (90% WHC)/suboxic conditions due to strong decreases in microbial growth. Microbial biomass turnover time decreased dramatically with increasing temperature, and increased significantly at high moisture level (90% WHC)/suboxic conditions. Our findings reveal that the responses of microbial CUE and microbial biomass turnover to short-term temperature and moisture/O changes depended mainly on microbial growth responses and less on respiration responses to the environmental cues, which were consistent across soils differing in land use and geology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30645971,

title = {The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease},

author = {Lindsay Kosack and Bettina Wingelhofer and Alexandra Popa and Anna Orlova and Benedikt Agerer and Bojan Vilagos and Peter Majek and Katja Parapatics and Alexander Lercher and Anna Ringler and Johanna Klughammer and Mark Smyth and Kseniya Khamina and Hatoon Baazim and Elvin D Araujo and David A Rosa and Jisung Park and Gary Tin and Siawash Ahmar and Patrick T Gunning and Christoph Bock and Hannah V Siddle and Gregory M Woods and Stefan Kubicek and Elizabeth P Murchison and Keiryn L Bennett and Richard Moriggl and Andreas Bergthaler},

doi = {10.1016/j.ccell.2018.11.018},

issn = {1878-3686},

year  = {2019},

date = {2019-01-01},

journal = {Cancer Cell},

volume = {35},

number = {1},

pages = {125–139.e9},

abstract = {The marsupial Tasmanian devil (Sarcophilus harrisii) faces extinction due to transmissible devil facial tumor disease (DFTD). To unveil the molecular underpinnings of this transmissible cancer, we combined pharmacological screens with an integrated systems-biology characterization. Sensitivity to inhibitors of ERBB tyrosine kinases correlated with their overexpression. Proteomic and DNA methylation analyses revealed tumor-specific signatures linked to the evolutionary conserved oncogenic STAT3. ERBB inhibition blocked phosphorylation of STAT3 and arrested cancer cells. Pharmacological blockade of ERBB or STAT3 prevented tumor growth in xenograft models and restored MHC class I expression. This link between the hyperactive ERBB-STAT3 axis and major histocompatibility complex class I-mediated tumor immunosurveillance provides mechanistic insights into horizontal transmissibility and puts forward a dual chemo-immunotherapeutic strategy to save Tasmanian devils from DFTD. VIDEO ABSTRACT.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31275315,

title = {MicroRNA-155 Controls T Helper Cell Activation During Viral Infection},

author = {Eliana Goncalves-Alves and Victoria Saferding and Christopher Schliehe and Robert Benson and Mariola Kurowska-Stolarska and Julia Stefanie Brunner and Antonia Puchner and Bruno K Podesser and Josef S Smolen and Kurt Redlich and Michael Bonelli and James Brewer and Andreas Bergthaler and Günter Steiner and Stephan Blüml},

doi = {10.3389/fimmu.2019.01367},

issn = {1664-3224},

year  = {2019},

date = {2019-01-01},

journal = {Front Immunol},

volume = {10},

pages = {1367},

abstract = {MicroRNA (miR) 155 has been implicated in the regulation of innate and adaptive immunity as well as autoimmune processes. Importantly, it has been shown to regulate several antiviral responses, but its contribution to the immune response against cytopathic viruses such as vesicular stomatitis virus (VSV) infections is not known. Using transgenic/recombinant VSV expressing ovalbumin, we show that miR-155 is crucially involved in regulating the T helper cell response against this virus. Our experiments indicate that miR-155 in CD4 T cells controls their activation, proliferation, and cytokine production and upon immunization with OVA as well as during VSV viral infection. Using intravital multiphoton microscopy we analyzed the interaction of antigen presenting cells (APCs) and T cells after OVA immunization and found impaired complex formation when using miR-155 deficient CD4 T cells compared to wildtype CD4 T cells . In contrast, miR-155 was dispensable for the maturation of myeloid APCs and for their T cell stimulatory capacity. Our data provide the first evidence that miR-155 is required for efficient CD4 T cell activation during anti-viral defense by allowing robust APC-T cell interaction required for activation and cytokine production of virus specific T cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31781058,

title = {Exploring Actinobacteria Associated With Rhizosphere and Endosphere of the Native Alpine Medicinal Plant Subspecies},

author = {Martina Oberhofer and Jaqueline Hess and Marlene Leutgeb and Florian Gössnitzer and Thomas Rattei and Christoph Wawrosch and Sergey B Zotchev},

doi = {10.3389/fmicb.2019.02531},

issn = {1664-302X},

year  = {2019},

date = {2019-01-01},

journal = {Front Microbiol},

volume = {10},

pages = {2531},

abstract = {The rhizosphere of plants is enriched in nutrients facilitating growth of microorganisms, some of which are recruited as endophytes. Endophytes, especially Actinobacteria, are known to produce a plethora of bioactive compounds. We hypothesized that subsp. (Edelweiss), a rare alpine medicinal plant, may serve as yet untapped source for uncommon Actinobacteria associated with this plant. Rhizosphere soil of native Alpine plants was used, after physical and chemical pre-treatments, for isolating Actinobacteria. Isolates were selected based on morphology and identified by 16S rRNA gene-based barcoding. Resulting 77 Actinobacteria isolates represented the genera , , , , , , , and . In parallel, Edelweiss plants from the same location were surface-sterilized, separated into leaves, roots, rhizomes, and inflorescence and pooled within tissues before genomic DNA extraction. Metagenomic 16S rRNA gene amplicons confirmed large numbers of actinobacterial operational taxonomic units (OTUs) descending in diversity from roots to rhizomes, leaves and inflorescences. These metagenomic data, when queried with isolate sequences, revealed an overlap between the two datasets, suggesting recruitment of soil bacteria by the plant. Moreover, this study uncovered a profound diversity of uncultured Actinobacteria from Rubrobacteridae, Thermoleophilales, Acidimicrobiales and unclassified Actinobacteria specifically in belowground tissues, which may be exploited by a targeted isolation approach in the future.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30863368,

title = {Rapid Transfer of Plant Photosynthates to Soil Bacteria via Ectomycorrhizal Hyphae and Its Interaction With Nitrogen Availability},

author = {Stefan Gorka and Marlies Dietrich and Werner Mayerhofer and Raphael Gabriel and Julia Wiesenbauer and Victoria Martin and Qing Zheng and Bruna Imai and Judith Prommer and Marieluise Weidinger and Peter Schweiger and Stephanie A Eichorst and Michael Wagner and Andreas Richter and Arno Schintlmeister and Dagmar Woebken and Christina Kaiser},

doi = {10.3389/fmicb.2019.00168},

issn = {1664-302X},

year  = {2019},

date = {2019-01-01},

journal = {Front Microbiol},

volume = {10},

pages = {168},

abstract = {Plant roots release recent photosynthates into the rhizosphere, accelerating decomposition of organic matter by saprotrophic soil microbes ("rhizosphere priming effect") which consequently increases nutrient availability for plants. However, about 90% of all higher plant species are mycorrhizal, transferring a significant fraction of their photosynthates directly to their fungal partners. Whether mycorrhizal fungi pass on plant-derived carbon (C) to bacteria in root-distant soil areas, i.e., incite a "hyphosphere priming effect," is not known. Experimental evidence for C transfer from mycorrhizal hyphae to soil bacteria is limited, especially for ectomycorrhizal systems. As ectomycorrhizal fungi possess enzymatic capabilities to degrade organic matter themselves, it remains unclear whether they cooperate with soil bacteria by providing photosynthates, or compete for available nutrients. To investigate a possible C transfer from ectomycorrhizal hyphae to soil bacteria, and its response to changing nutrient availability, we planted young beech trees () into "split-root" boxes, dividing their root systems into two disconnected soil compartments. Each of these compartments was separated from a litter compartment by a mesh penetrable for fungal hyphae, but not for roots. Plants were exposed to a C-CO-labeled atmosphere, while N-labeled ammonium and amino acids were added to one side of the split-root system. We found a rapid transfer of recent photosynthates via ectomycorrhizal hyphae to bacteria in root-distant soil areas. Fungal and bacterial phospholipid fatty acid (PLFA) biomarkers were significantly enriched in hyphae-exclusive compartments 24 h after C-CO-labeling. Isotope imaging with nanometer-scale secondary ion mass spectrometry (NanoSIMS) allowed for the first time visualization of plant-derived C and N taken up by an extraradical fungal hypha, and in microbial cells thriving on hyphal surfaces. When N was added to the litter compartments, bacterial biomass, and the amount of incorporated C strongly declined. Interestingly, this effect was also observed in adjacent soil compartments where added N was only available for bacteria through hyphal transport, indicating that ectomycorrhizal fungi were acting on soil bacteria. Together, our results demonstrate that (i) ectomycorrhizal hyphae rapidly transfer plant-derived C to bacterial communities in root-distant areas, and (ii) this transfer promptly responds to changing soil nutrient conditions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30881364,

title = {Root Exudation of Primary Metabolites: Mechanisms and Their Roles in Plant Responses to Environmental Stimuli},

author = {Alberto Canarini and Christina Kaiser and Andrew Merchant and Andreas Richter and Wolfgang Wanek},

doi = {10.3389/fpls.2019.00157},

issn = {1664-462X},

year  = {2019},

date = {2019-01-01},

journal = {Front Plant Sci},

volume = {10},

pages = {157},

abstract = {Root exudation is an important process determining plant interactions with the soil environment. Many studies have linked this process to soil nutrient mobilization. Yet, it remains unresolved how exudation is controlled and how exactly and under what circumstances plants benefit from exudation. The majority of root exudates including primary metabolites (sugars, amino acids, and organic acids) are believed to be passively lost from the root and used by rhizosphere-dwelling microbes. In this review, we synthetize recent advances in ecology and plant biology to explain and propose mechanisms by which root exudation of primary metabolites is controlled, and what role their exudation plays in plant nutrient acquisition strategies. Specifically, we propose a novel conceptual framework for root exudates. This framework is built upon two main concepts: (1) root exudation of primary metabolites is driven by diffusion, with plants and microbes both modulating concentration gradients and therefore diffusion rates to soil depending on their nutritional status; (2) exuded metabolite concentrations can be sensed at the root tip and signals are translated to modify root architecture. The flux of primary metabolites through root exudation is mostly located at the root tip, where the lack of cell differentiation favors diffusion of metabolites to the soil. We show examples of how the root tip senses concentration changes of exuded metabolites and translates that into signals to modify root growth. Plants can modify the concentration of metabolites either by controlling source/sink processes or by expressing and regulating efflux carriers, therefore challenging the idea of root exudation as a purely unregulated passive process. Through root exudate flux, plants can locally enhance concentrations of many common metabolites, which can serve as sensors and integrators of the plant nutritional status and of the nutrient availability in the surrounding environment. Plant-associated micro-organisms also constitute a strong sink for plant carbon, thereby increasing concentration gradients of metabolites and affecting root exudation. Understanding the mechanisms of and the effects that environmental stimuli have on the magnitude and type of root exudation will ultimately improve our knowledge of processes determining soil CO emissions, ecosystem functioning, and how to improve the sustainability of agricultural production.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30418610,

title = {eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses},

author = {Jaime Huerta-Cepas and Damian Szklarczyk and Davide Heller and Ana Hernández-Plaza and Sofia K Forslund and Helen Cook and Daniel R Mende and Ivica Letunic and Thomas Rattei and Lars J Jensen and Christian Mering and Peer Bork},

doi = {10.1093/nar/gky1085},

issn = {1362-4962},

year  = {2019},

date = {2019-01-01},

journal = {Nucleic Acids Res},

volume = {47},

number = {D1},

pages = {D309–D314},

abstract = {eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. Here, we present version 5.0, featuring a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 eukaryotic organisms and 2502 viral proteomes that were selected for diversity and filtered by genome quality. In total, 4.4M orthologous groups (OGs) distributed across 379 taxonomic levels were computed together with their associated sequence alignments, phylogenies, HMM models and functional descriptors. Precomputed evolutionary analysis provides fine-grained resolution of duplication/speciation events within each OG. Our benchmarks show that, despite doubling the amount of genomes, the quality of orthology assignments and functional annotations (80% coverage) has persisted without significant changes across this update. Finally, we improved eggNOG online services for fast functional annotation and orthology prediction of custom genomics or metagenomics datasets. All precomputed data are publicly available for downloading or via API queries at http://eggnog.embl.de.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30556814,

title = {Minimum Information about an Uncultivated Virus Genome (MIUViG)},

author = {Simon Roux and Evelien M Adriaenssens and Bas E Dutilh and Eugene V Koonin and Andrew M Kropinski and Mart Krupovic and Jens H Kuhn and Rob Lavigne and J Rodney Brister and Arvind Varsani and Clara Amid and Ramy K Aziz and Seth R Bordenstein and Peer Bork and Mya Breitbart and Guy R Cochrane and Rebecca A Daly and Christelle Desnues and Melissa B Duhaime and Joanne B Emerson and François Enault and Jed A Fuhrman and Pascal Hingamp and Philip Hugenholtz and Bonnie L Hurwitz and Natalia N Ivanova and Jessica M Labonté and Kyung-Bum Lee and Rex R Malmstrom and Manuel Martinez-Garcia and Ilene Karsch Mizrachi and Hiroyuki Ogata and David Páez-Espino and Marie-Agnès Petit and Catherine Putonti and Thomas Rattei and Alejandro Reyes and Francisco Rodriguez-Valera and Karyna Rosario and Lynn Schriml and Frederik Schulz and Grieg F Steward and Matthew B Sullivan and Shinichi Sunagawa and Curtis A Suttle and Ben Temperton and Susannah G Tringe and Rebecca Vega Thurber and Nicole S Webster and Katrine L Whiteson and Steven W Wilhelm and K Eric Wommack and Tanja Woyke and Kelly C Wrighton and Pelin Yilmaz and Takashi Yoshida and Mark J Young and Natalya Yutin and Lisa Zeigler Allen and Nikos C Kyrpides and Emiley A Eloe-Fadrosh},

doi = {10.1038/nbt.4306},

issn = {1546-1696},

year  = {2019},

date = {2019-01-01},

journal = {Nat Biotechnol},

volume = {37},

number = {1},

pages = {29–37},

abstract = {We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}