Genomics Approaches to the Study of Diversity and Function of Aquatic Fungi

The kingdom of fungi comprises an enormous range of live styles and genetic variability. Different genomics approaches offer possibilities to investigate species diversity and ecological function of fungi. In this thesis I present improvements of metabarcoding methods for aquatic fungi and the application of whole genome sequencing and transcriptome sequencing to an exclusively aquatic fungus. Beside the standard metabarcoding marker for fungi, the ITS (internal transcribed spacer) region, the eukaryotic rRNA operon contains two other markers, the SSU (small subunit) and LSU (large subunit), that are also often used for metabarcoding. When choosing a metabarcode there is a tradeoff between high variability for fine grain species delineation and high conservation for good primer binding and high level classification of novel species, which are not represented in reference databases. In the work presented in chapter III, we investigated the possibility to use the information from the more conserved 5.8S sequence, that is part of many amplicons used for ITS2 sequencing. It is normally discarded, but we used it as a complementary marker to ITS2 and showed that it can improve classification of novel species with an incomplete reference database. In chapter IV this is taken one step further by using third generation sequencing to sequence the full ITS region together with the more conserved SSU and LSU in the same amplicon. This gives us the option to use different markers with different databases for classification in parallel and to circumvent the trade-off between high variability and high conservation. Fungi are ecologically very important decomposers of lignocellulose from plant biomass. The occurrence and expression of gene families for the degradation of lignin from lignocellulose has been extensively studied with whole genome and transcriptome sequencing in terrestrial, but not in aquatic fungi. In the work presented in chapter V, we used whole genome and transcriptome sequencing to investigate differential gene expression in the exclusively aquatic fungus Clavariopsis aquatica when grown on media with more and less lignin rich carbon sources and investigated the expression patterns of peroxidases, laccases and other protein families involved in plant biomass degradation. This observed up-regulation of laccases, peroxidases and genes from the cytochrome P450 super-family, as well as other gene families involved in cellulose and hemicellulose degradation, strongly suggests that C. aquatica is able to modify lignin to some extent; perhaps in order to facilitate the utilization of lignocellulose as a carbon and energy source

Optical coherence tomography-guided versus angiography-guided implantation of everolimus-eluting bioresorbable vascular scaffolds: Comparison of coverage, apposition and clinical outcome. The ALSTER-OCT ABSORB registry

Background: Suboptimal implantation of everolimus-eluting bioresorbable vascular scaffolds (EE-BVS) leading to strut malapposition and lack of neointima coverage has been hypothesized to be linked to late BVS-thrombosis. Optical coherence tomography (OCT) allows assessing subtle differences in BVS-healing. We aimed to link 6-months OCT-data on EE-BVS coverage and malapposition to implantation technique and clinical outcome. Methods: Twenty-nine consecutive EE-BVS-patients were included. EE-BVS-implantation was guided by angiography in the first 17 patients (group 1). Vessel sizing prior to implantation and implantation result was assessed by OCT in the 12 following patients (group 2). EE-BVS-implantation was performed in both groups with adequate lesion preparation, sizing and systematic high-pressure post-dilatation. All patients received 6-months invasive control including OCT-analysis and clinical follow-up for 2 years. Results: The rate of uncovered struts was group 1: 10.8 ± 10.0%; group 2: 10.6 ± 8.2%, p = 0.934. Target lesion failure due to BVS-thrombosis occurred in 2/17 patients at 9 and 18 months (11.8%, group 1), and no patients in group 2 (p = 0.218). Conclusions: Optical coherence tomography analysis at 6-months following EE-BVS-implantation finds almost 90% of struts to be covered. No difference between OCT vs. angiography-guided EE-BVS-implantation was observed. OCT at 6-months was not able to predict late BVS-thrombosis of EE-BVS

Evidence for Lignocellulose-Decomposing Enzymes in the Genome and Transcriptome of the Aquatic Hyphomycete Clavariopsis aquatica

Fungi are ecologically outstanding decomposers of lignocellulose. Fungal lignocellulose degradation is prominent in saprotrophic Ascomycota and Basidiomycota of the subkingdom Dikarya. Despite ascomycetes dominating the Dikarya inventory of aquatic environments, genome and transcriptome data relating to enzymes involved in lignocellulose decay remain limited to terrestrial representatives of these phyla. We sequenced the genome of an exclusively aquatic ascomycete (the aquatic hyphomycete Clavariopsis aquatica), documented the presence of genes for the modification of lignocellulose and its constituents, and compared differential gene expression between C. aquatica cultivated on lignocellulosic and sugar-rich substrates. We identified potential peroxidases, laccases, and cytochrome P450 monooxygenases, several of which were differentially expressed when experimentally grown on different substrates. Additionally, we found indications for the regulation of pathways for cellulose and hemicellulose degradation. Our results suggest that C. aquatica is able to modify lignin to some extent, detoxify aromatic lignin constituents, or both. Such characteristics would be expected to facilitate the use of carbohydrate components of lignocellulose as carbon and energy sources

Nitrogen Gain and Loss Along an Ecosystem Sequence: From Semi-desert to Rainforest

Plants and microorganisms, besides the climate, drive nitrogen (N) cycling in ecosystems. Our objective was to investigate N losses and N acquisition strategies along a unique ecosystem-sequence (ecosequence) ranging from arid shrubland through Mediterranean woodland to temperate rainforest. These ecosystems differ in mean annual precipitation, mean annual temperate, and vegetation cover, but developed on similar granitoid soil parent material, were addressed using a combination of molecular biology and soil biogeochemical tools. Soil N and carbon (C) contents, δ15N signatures, activities of N acquiring extracellular enzymes as well as the abundance of soil bacteria and fungi, and diazotrophs in bulk topsoil and rhizosphere were determined. Relative fungal abundance in the rhizosphere was higher under woodland and forest than under shrubland. This indicates toward plants' higher C investment into fungi in the Mediterranean and temperate rainforest sites than in the arid site. Fungi are likely to decompose lignified forest litter for efficient recycling of litter-derived N and further nutrients. Rhizosphere—a hotspot for the N fixation—was enriched in diazotrophs (factor 8 to 16 in comparison to bulk topsoil) emphasizing the general importance of root/microbe association in N cycle. These results show that the temperate rainforest is an N acquiring ecosystem, whereas N in the arid shrubland is strongly recycled. Simultaneously, the strongest 15N enrichment with decreasing N content with depth was detected in the Mediterranean woodland, indicating that N mineralization and loss is highest (and likely the fastest) in the woodland across the continental transect. Higher relative aminopeptidase activities in the woodland than in the forest enabled a fast N mineralization. Relative aminopeptidase activities were highest in the arid shrubland. The highest absolute chitinase activities were observed in the forest. This likely demonstrates that (a) plants and microorganisms in the arid shrubland invest largely into mobilization and reutilization of organically bound N by exoenzymes, and (b) that the ecosystem N nutrition shifts from a peptide-based N in the arid shrubland to a peptide- and chitin-based N nutrition in the temperate rainforest, where the high N demand is complemented by intensive N fixation in the rhizosphere

Whole genome sequencing and methylome analysis of the wild guinea pig

Abstract Background: DNA methylation is a heritable mechanism that acts in response to environmental changes, lifestyle and diseases by influencing gene expression in eukaryotes. Epigenetic studies of wild organisms are mandatory to understand their role in e.g. adaptational processes in the great variety of ecological niches. However, strategies to address those questions on a methylome scale are widely missing. In this study we present such a strategy and describe a whole genome sequence and methylome analysis of the wild guinea pig

A New Perceptual Bias Reveals Suboptimal Population Decoding of Sensory Responses

Several studies have reported optimal population decoding of sensory responses in two-alternative visual discrimination tasks. Such decoding involves integrating noisy neural responses into a more reliable representation of the likelihood that the stimuli under consideration evoked the observed responses. Importantly, an ideal observer must be able to evaluate likelihood with high precision and only consider the likelihood of the two relevant stimuli involved in the discrimination task. We report a new perceptual bias suggesting that observers read out the likelihood representation with remarkably low precision when discriminating grating spatial frequencies. Using spectrally filtered noise, we induced an asymmetry in the likelihood function of spatial frequency. This manipulation mainly affects the likelihood of spatial frequencies that are irrelevant to the task at hand. Nevertheless, we find a significant shift in perceived grating frequency, indicating that observers evaluate likelihoods of a broad range of irrelevant frequencies and discard prior knowledge of stimulus alternatives when performing two-alternative discrimination

Long-Baseline Neutrino Facility (LBNF) and Deep Underground Neutrino Experiment (DUNE) Conceptual Design Report Volume 2: The Physics Program for DUNE at LBNF

The Physics Program for the Deep Underground Neutrino Experiment (DUNE) at the Fermilab Long-Baseline Neutrino Facility (LBNF) is described

Pretransplant CSF-1 therapy expands recipient macrophages and ameliorates GVHD after allogeneic hematopoietic cell transplantation

Host macrophages protect against graft-versus-host disease in part by engulfing donor T cells and inhibiting their proliferation

Nanooptics of molecular-shunted plasmonic nanojunctions.

Gold nanoparticles are separated above a planar gold film by 1.1 nm thick self-assembled molecular monolayers of different conductivities. Incremental replacement of the nonconductive molecules with a chemically equivalent conductive version differing by only one atom produces a strong 50 nm blue-shift of the coupled plasmon. With modeling this gives a conductance of 0.17G(0) per biphenyl-4,4'-dithiol molecule and a total conductance across the plasmonic junction of 30G(0). Our approach provides a reliable tool quantifying the number of molecules in each plasmonic hotspot, here <200.We acknowledge financial support from EPSRC grant EP/ G060649/1, EP/I012060/1, EP/L027151/1, EP/K028510/1, ERC grant LINASS 320503. F.B. acknowledges support from the Winton Programme for the Physics of Sustainability. C.T. and J.A. acknowledge financial support from Project FIS2013- 41184-P from MINECO, ETORTEK 2014-15 of the Basque Department of Industry and IT756-13 from the Basque consolidated groups.This paper was originally published in Nano Letters under a CC-BY licence (F Benz, C Tserkezis, LO Herrmann, B de Nijs, A Sanders, DO Sigle, L Pukenas, SD Evans, J Aizpurua, JJ Baumberg, Nano Letters 2015, 15, 669−674

Low-Energy Physics in Neutrino LArTPCs

In this white paper, we outline some of the scientific opportunities and challenges related to detection and reconstruction of low-energy (less than 100 MeV) signatures in liquid argon time-projection chamber (LArTPC) detectors. Key takeaways are summarized as follows. 1) LArTPCs have unique sensitivity to a range of physics and astrophysics signatures via detection of event features at and below the few tens of MeV range. 2) Low-energy signatures are an integral part of GeV-scale accelerator neutrino interaction final states, and their reconstruction can enhance the oscillation physics sensitivities of LArTPC experiments. 3) BSM signals from accelerator and natural sources also generate diverse signatures in the low-energy range, and reconstruction of these signatures can increase the breadth of BSM scenarios accessible in LArTPC-based searches. 4) Neutrino interaction cross sections and other nuclear physics processes in argon relevant to sub-hundred-MeV LArTPC signatures are poorly understood. Improved theory and experimental measurements are needed. Pion decay-at-rest sources and charged particle and neutron test beams are ideal facilities for experimentally improving this understanding. 5) There are specific calibration needs in the low-energy range, as well as specific needs for control and understanding of radiological and cosmogenic backgrounds. 6) Novel ideas for future LArTPC technology that enhance low-energy capabilities should be explored. These include novel charge enhancement and readout systems, enhanced photon detection, low radioactivity argon, and xenon doping. 7) Low-energy signatures, whether steady-state or part of a supernova burst or larger GeV-scale event topology, have specific triggering, DAQ and reconstruction requirements that must be addressed outside the scope of conventional GeV-scale data collection and analysis pathways