Non-lethal detection of Eubothrium crassum (Cestoda) in farmed Atlantic salmon, Salmo salar, using anal swabs and real-time PCR

Detection of intestinal parasites in fish typically requires autopsy, resulting in the sacrifice of the fish. Here, we describe a non-lethal method for detecting the tapeworm Eubothrium crassum in fish using anal swabs and real-time PCR detection. Two assays were developed to detect cytochrome oxidase I (COI) mitochondrial DNA and 18S ribosomal DNA sequences of E. crassum, respectively. The assays were tested on swab samples from confirmed pathogen free Atlantic salmon (Salmo salar L.) and on samples from farmed Atlantic salmon, where the presence and intensity of parasites had been established through autopsy. The COI assay was shown to be specific to E. crassum, while the 18S assay also amplified the closely related E. salvelini, a species infecting Arctic charr (Salvelinus alpinus L.) in freshwater. The COI assay detected E. crassum in all field samples regardless of parasite load while the 18S assay failed to detect the parasite in two samples. The results thus demonstrates that this non-lethal approach can effectively detect E. crassum and can be a valuable tool in assessing the prevalence of infection in farmed salmon, aiding in treatment decisions and evaluating treatment effectiveness.

Nopadiene: A Pinene-Derived Cyclic Diene as a Styrene Substitute for Fully Biobased Thermoplastic Elastomers

The bicyclic 1,2-substituted, 1,3-diene monomer nopadiene (1R,5S)-2-ethenyl-6,6-dimethylbicyclo[3.1.1]hept-2-ene was successfully polymerized by anionic and catalytic polymerization. Nopadiene is produced either through a facile one-step synthesis from myrtenal via Wittig-olefination or via a scalable two-step reaction from nopol (10-hydroxymethylene-2-pinene). Both terpenoids originate from the renewable β-pinene. The living anionic polymerization of nopadiene in apolar and polar solvents at 25 °C using organolithium initiators resulted in homopolymers with well-controlled molar masses in the range of 5.6-103.4 kg·mol-1 (SEC, PS calibration) and low dispersities (Đ) between 1.06 and 1.18. By means of catalytic polymerization with Me4CpSi(Me)2NtBuTiCl2 and (Flu)(Pyr)CH2Lu(CH2TMS)2(THF), the 1,4 and 3,4- microstructures of nopadiene are accessible in excellent selectivity. In pronounced contrast to other 1,3-dienes, the rigid polymers of the sterically demanding nopadiene showed an elevated glass temperature, Tg,∞ = 160 °C (in the limit of very high molar mass, Mn). ABA triblock copolymers with a central polymyrcene block and myrcene content of 60-75 mol %, with molar masses of 100-200 kg/mol were prepared by living anionic polymerization of the pinene-derivable monomers nopadiene and myrcene. This diene copolymerization resulted in thermoplastic elastomers displaying nanophase separation at different molar ratios (DSC, SAXS) and an upper service temperature about 30 K higher than that for traditional petroleum-derived styrenic thermoplastic elastomers due to the high glass temperature of polynopadiene. The materials showed good thermal stability at elevated temperatures under nitrogen (TGA), promising tensile strength and ultimate elongation of up to 1600%.

Amended diagnosis, mitochondrial genome, and phylogenetic position of Sphyranura euryceae (Neodermata, Monogenea, Polystomatidae), a parasite of the Oklahoma salamander

Polystomatidae is a monogenean family whose representatives infect mainly (semi)-aquatic tetrapods. Species of Sphyranura Wright, 1879 exhibit ectoparasitism on salamander hosts, with molecular work supporting their inclusion within Polystomatidae, at an early diverging, yet unresolved, position in the clade of otherwise endoparasitic polystomatid parasites of batrachian hosts. Records of representatives of Sphyranura are scarce with genetic data only available for S. oligorchis Alvey, 1933. Based on detailed morphological examination and comparison with type material, we identified worms belonging to Sphyranura infecting Oklahoma salamander (Eurycea tynerensis) as S. euryceae Hughes & Moore, 1943. Along with an amended diagnosis of Sphyranura, we provide the first molecular data for S. euryceae in the form of a mitochondrial genome and nuclear (18S, 28S rRNA) markers. Close morphological similarity between the two species of Sphyranura is reflected in low genetic divergence. Mitochondrial level comparison reveals instances of tRNA gene rearrangements in polystomatids. Although the phylogenetic reconstruction supports Sphyranura as early branching in the lineage of polystomatid monogeneans infecting batrachians, certain nodes remain unresolved.

An insight into the functional genomics and species classification of Eudiplozoon nipponicum (Monogenea, Diplozoidae), a haematophagous parasite of the common carp Cyprinus carpio

BACKGROUND

Monogenea (Platyhelminthes, Neodermata) are the most species-rich class within the Neodermata superclass of primarily fish parasites. Despite their economic and ecological importance, monogenean research tends to focus on their morphological, phylogenetic, and population characteristics, while comprehensive omics analyses aimed at describing functionally important molecules are few and far between. We present a molecular characterisation of monogenean representative Eudiplozoon nipponicum, an obligate haematophagous parasite infecting the gills of the common carp. We report its nuclear and mitochondrial genomes, present a functional annotation of protein molecules relevant to the molecular and biochemical aspect of physiological processes involved in interactions with the fish hosts, and re-examinate the taxonomic position of Eudiplozoon species within the Diplozoidae family.

RESULTS

We have generated 50.81 Gbp of raw sequencing data (Illumina and Oxford Nanopore reads), bioinformatically processed, and de novo assembled them into a genome draft 0.94 Gbp long, consisting of 21,044 contigs (N50 = 87 kbp). The final assembly represents 57% of the estimated total genome size (~ 1.64 Gbp), whereby repetitive and low-complexity regions account for ~ 64% of the assembled length. In total, 36,626 predicted genes encode 33,031 proteins and homology-based annotation of protein-coding genes (PCGs) and proteins characterises 14,785 (44.76%) molecules. We have detected significant representation of functional proteins and known molecular functions. The numbers of peptidases and inhibitors (579 proteins), characterised GO terms (16,016 unique assigned GO terms), and identified KEGG Orthology (4,315 proteins) acting in 378 KEGG pathways demonstrate the variety of mechanisms by which the parasite interacts with hosts on a macromolecular level (immunomodulation, feeding, and development). Comparison between the newly assembled E. nipponicum mitochondrial genome (length of 17,038 bp) and other diplozoid monogeneans confirms the existence of two distinct Eudiplozoon species infecting different fish hosts: Cyprinus carpio and Carassius spp.

CONCLUSIONS

Although the amount of sequencing data and characterised molecules of monogenean parasites has recently increased, a better insight into their molecular biology is needed. The E. nipponicum nuclear genome presented here, currently the largest described genome of any monogenean parasite, represents a milestone in the study of monogeneans and their molecules but further omics research is needed to understand these parasites' biological nature.

Merging Styrene and Diene Structures to a Cyclic Diene: Anionic Polymerization of 1-Vinylcyclohexene (VCH)

We report the first anionic polymerization of 1-vinylcyclo-hexene (VCH). This structure may be considered as an intermediate between dienes and styrene. The polymerization of this cyclic 1,2-disubstituted 1,3-diene proceeded quantitatively in cyclohexane at 25 °C with sec-butyllithium as an initiator. The obtained polymers have well-controlled molecular weights in the range of 5 to 142 kg/mol, controlled by the molar ratio of monomer and initiator, with narrow molecular weight distributions (Đ < 1.07-1.20). In situ1H NMR kinetic characteri-zation revealed a weak gradient structure for the copolymers of styrene and VCH, (rSty = 2.55, rVCH = 0.39). P(VCH) obtained in cyclohexane with sec-BuLi as an initiator showed both 1,4- and 3,4-incorporation mode (ratio: 64:36). It was demonstrated that the micro-structure of the resulting P(VCH) can be altered by the addition of a modifier (THF), resulting in increasing 3,4-microstructure (up to 78%) and elevated glass-transition temperature up to 89°C. Thus, the monomer VCH polymerizes carbanionically like a diene, however leading to rigid poly-mers with high glass transition temperature, which provides interesting options for combination with other dienes to well-defined polymer architectures and materials.

Different Shades of Kale-Approaches to Analyze Kale Variety Interrelations

Brassica oleracea is a vegetable crop with an amazing morphological diversity. Among the various crops derived from B. oleracea, kale has been in the spotlight globally due to its various health-benefitting compounds and many different varieties. Knowledge of the existing genetic diversity is essential for the improved breeding of kale. Here, we analyze the interrelationships, population structures, and genetic diversity of 72 kale and cabbage varieties by extending our previous diversity analysis and evaluating the use of summed potential lengths of shared haplotypes (SPLoSH) as a new method for such analyses. To this end, we made use of the high-density Brassica 60K SNP array, analyzed SNPs included in an available Brassica genetic map, and used these resources to generate and evaluate the information from SPLoSH data. With our results we could consistently differentiate four groups of kale across all analyses: the curly kale varieties, Italian, American, and Russian varieties, as well as wild and cultivated types. The best results were achieved by using SPLoSH information, thus validating the use of this information in improving analyses of interrelations in kale. In conclusion, our definition of kale includes the curly varieties as the kales in a strict sense, regardless of their origin. These results contribute to a better understanding of the huge diversity of kale and its interrelations.

Study on the kinetics of the adsorption and desorption of NH3 on Fe/H-BEA zeolite

In this paper, a Fe/HBEA zeolite (Si/Al: 12.5), representing an effective catalyst for the NH3-SCR process, was physico-chemically characterized and investigated towards the kinetics of the adsorption and desorption of...

A local platform for user-friendly FAIR data management and reproducible analytics

Collaborative research is common practice in modern life sciences. For most projects several researchers from multiple universities collaborate on a specific topic. Frequently, these research projects produce a wealth of data that requires central and secure storage, which should also allow for easy sharing among project participants. Only under best circumstances, this comes with minimal technical overhead for the researchers. Moreover, the need for data to be analyzed in a reproducible way often poses a challenge for researchers without a data science background and thus represents an overly time-consuming process. Here, we report on the integration of CyVerse Austria (CAT), a new cyberinfrastructure for a local community of life science researchers and provide two examples how it can be used to facilitate FAIR data management and reproducible analytics for teaching and research. In particular, we describe in detail how CAT can be used (i) as a teaching platform with a defined software environment and data management/sharing possibilities, and (ii) to build a data analysis pipeline using the Docker technology tailored to the needs and interests of the researcher.

Influence of Fiber Addition on the Properties of High-Performance Concrete

High performance fiber-reinforced concrete (HPFRC) has been frequently investigated in recent years. Plenty of studies have focused on different materials and types of fibers in combination with the concrete matrix. Experimental tests show that fiber dosage improves the energy absorption capacity of concrete and enhances the robustness of concrete elements. Fiber reinforced concrete has also been illustrated to be a material for developing infrastructure sustainability in RC elements like façade plates, columns, beams, or walls. Due to increasing costs of the produced fiber reinforced concrete and to ensure the serviceability limit state of construction elements, there is a demand to analyze the necessary fiber dosage in the concrete composition. It is expected that the surface and length of used fiber in combination with their dosage influence the structure of fresh and hardened concrete. This work presents an investigation of the mechanical parameters of HPFRC with different polymer fiber dosage. Tests were carried out on a mixture with polypropylene and polyvinyl alcohol fiber with dosages of 15, 25, and 35 kg/m³ as well as with control concrete without fiber. Differences were observed in the compressive strength and in the modulus of elasticity as well as in the flexural and splitting tensile strength. The flexural tensile strength test was conducted on two different element shapes: square panel and beam samples. These mechanical properties could lead to recommendations for designers of façade elements made of HPFRC.

Expansion of frozen hybrids in the guppy ectoparasite, Gyrodactylus turnbulli

Hybridization is one of the major factors contributing to the emergence of highly successful parasites. Hybrid vigour can play an important role in this process, but subsequent rounds of recombination in the hybrid population may dilute its effects. Increased fitness of hybrids can, however, be frozen by asexual reproduction. Here, we identify invasion of a 'frozen hybrid' genotype in natural populations of Gyrodactylus turnbulli, a facultatively sexual ectoparasitic flatworm that causes significant damage to its fish host. We resequenced genomes of these parasites infecting guppies from six Trinidad and Tobago populations, and found surprisingly high discrepancy in genome-wide nucleotide diversity between islands. The elevated heterozygosity on Tobago is maintained by predominantly clonal reproduction of hybrids formed from two diverged genomes. Hybridization has been followed by spread of the hybrids across the island, implying a selective advantage compared with native genotypes. Our results thus highlight that a single outcrossing event may be independently sufficient to cause pathogen expansion.

Perioperative Management of Gastric Cancer Patients Treated With (Sub)Total Gastrectomy, Cytoreductive Surgery, and Hyperthermic Intraperitoneal Chemotherapy (HIPEC): Lessons Learned

BACKGROUND

The PERISCOPE I study was designed to assess the safety and feasibility of (sub)total gastrectomy, cytoreductive surgery (CRS), and hyperthermic intraperitoneal chemotherapy (HIPEC) with oxaliplatin and docetaxel for gastric cancer patients who have limited peritoneal dissemination. The current analysis investigated changes in perioperative management together with their impact on postoperative outcomes.

METHODS

Patients with resectable gastric cancer and limited peritoneal dissemination were administered (sub)total gastrectomy, CRS, and HIPEC with oxaliplatin (460 mg/m²) and docetaxel (escalating scheme: 0, 50, 75 mg/m²). Of the 25 patients who completed the study protocol, 14 were treated in the dose-escalation cohort and 11 were treated in the expansion cohort (to optimize perioperative management).

RESULTS

A significant proportion of the patients in the dose-escalation cohort (n = 7, 50%) had ileus-related complications. In this cohort, enteral nutrition was started immediately after surgery at 20 ml/h, which was increased on day 1 to meet nutritional needs. In the expansion cohort, enteral nutrition was administered at 10 ml/h until day 3, then restricted to 20 ml/h until day 6, supplemented with total parenteral nutrition to meet nutritional needs. Ileus-related complications occurred for two patients (18%) of the expansion cohort. The intensive care unit (ICU) readmission rate decreased from 50 (n = 7) to 9% (n = 1; p = 0.04).

CONCLUSION

The implementation of a strict nutritional protocol during the PERISCOPE I study was associated with a decrease in postoperative complications. Based on these results, a perioperative care path was described for the gastric cancer HIPEC patients in the PERISCOPE II study.

Global systematic diversity, range distributions, conservation and taxonomic assessments of graylings (Teleostei: Salmonidae; Thymallus spp.)

Graylings (Thymallus) are among the less well-studied groups of salmonid fishes, especially across their Asian distribution range. Here we perform a comprehensive global review of their phylogeography, systematic diversity and range distributions, including biogeographic reconstruction and assessment of both conservation and taxonomic status of each species. Based on a mitogenomic phylogenetic analysis, three approaches to the delineation of molecular operational units, and evaluation of 15 a-priori defined species, we provide biological support for the recognition of 13 grayling species, plus two additional species tentatively. Several instances of paraphyly and its potential effect on systematic inferences are discussed. Overall, the genus displays increasing species diversity and decreasing range size from higher to lower latitudes and ancestral trait reconstruction supports an East Asian origin for extant diversity, most likely centred in the Amur River drainage. Europe’s colonization by Thymallus took place as early as the late Miocene, at least two colonisations of North America are supported, and multiple dispersal events likely took place into Western Siberia. The conservation status for the 15 taxa was estimated to be: 6 least concern, 1 near-threatened, 2 vulnerable, 3 endangered and 3 data deficient.

Gene duplications, divergence and recombination shape adaptive evolution of the fish ectoparasite Gyrodactylus bullatarudis

Determining the molecular basis of parasite adaptation to its host is an important component in understanding host-parasite coevolution and the epidemiology of parasitic infections. Here, we investigate short- and long-term adaptive evolution in the eukaryotic parasite Gyrodactylus bullatarudis infecting Caribbean guppies (Poecilia reticulata), by comparing the reference genome of Tobagonian G. bullatarudis with other Platyhelminthes, and by analysing resequenced samples from local Trinidadian populations. At the macroevolutionary timescale, we observed duplication of G-protein and serine proteases genes, which are probably important in host-parasite arms races. Serine protease also showed strong evidence of ongoing, diversifying selection at the microevolutionary timescale. Furthermore, our analyses revealed that a hybridization event, involving two divergent genomes, followed by recombination has dramatically affected the genetic composition of Trinidadian populations. The recombinant genotypes invaded Trinidad and replaced local parasites in all populations. We localized more than 300 genes in regions fixed in local populations for variants of different origin, possibly due to diversifying selection pressure from local host populations. In addition, around 70 genes were localized in regions identified as heterozygous in some, but not all, individuals. This pattern is consistent with a very recent spread of recombinant parasites. Overall, our results are consistent with the idea that recombination between divergent genomes can result in particularly successful parasites.

Changes in low molecular weight carbohydrates in kale during development and acclimation to cold temperatures determined by chromatographic techniques coupled to mass spectrometry

Kale (Brassica oleracea) is a cool-season vegetable widely employed in the elaboration of diverse products such as tea and smoothies in USA or in the Northern German cuisine in wintertime. Besides, kale is gaining attention due to the diverse health benefits reported in the literature for its consumption, e.g. antigenotoxic and anticarcinogenic effect, protection of cardiovascular system and gastrointestinal tract. Low molecular weight carbohydrates (LMWC) are compounds directly related with kale flavour and nutritional quality. Despite different studies focusing on the chemical composition of kale, few information on LMWC is available. Thus, in this work a multianalytical approach was conducted in order to perform a comprehensive study of kale LMWC; their evolution during plant development and acclimation to cool temperatures was also evaluated. Gas chromatography coupled to mass spectrometry allowed the identification of 13 LMWC, being myo-inositol, galactinol, maltose and melibiose described for the first time in kale. Eight major LMWC were quantified in three different commercial kale cultivars using hydrophilic interaction liquid chromatography coupled to mass spectrometry to monitor possible differences in their content during plant development and as consequence of plant acclimation to cold temperatures. Overall, for all types of kales under study, the content of maltose and sucrose decreased during the plant development while the concentration of fructose, melibiose, maltose, raffinose and galactinol was increased in all kale types exposed to low temperatures. These results underline the importance of controlling the temperature during kale cultivation in order to obtain products with a high nutritional value.

Mitochondrial genomes of ancient bowhead whales (Balaena mysticetus) from Svalbard

The endangered Spitsbergen stock of bowhead whales (Balaena mysticetus) has once been large with up to estimated 100,000 individuals. Genetic diversity of the extant Spitsbergen stock is unknown. We present 10 complete mitochondrial genomes of heterochronous ancient bowhead whale samples from Svalbard (14C age estimate range: 215-8885 years) obtained via NGS of total genomic DNA extracts. The ten mitogenomes differed by nucleotide substitutions and/or indels, and there was a total of 160 variable positions. The average nucleotide diversity was π = 0.0029. There was no statistically significant correlation between genetic divergence and time.

Cytoreductive surgery and hyperthermic intraperitoneal chemotherapy versus palliative systemic chemotherapy in stomach cancer patients with peritoneal dissemination, the study protocol of a multicentre randomised controlled trial (PERISCOPE II)

BACKGROUND

At present, palliative systemic chemotherapy is the standard treatment in the Netherlands for gastric cancer patients with peritoneal dissemination. In contrast to lymphatic and haematogenous dissemination, peritoneal dissemination may be regarded as locoregional spread of disease. Administering cytotoxic drugs directly into the peritoneal cavity has an advantage over systemic chemotherapy since high concentrations can be delivered directly into the peritoneal cavity with limited systemic toxicity. The combination of a radical gastrectomy with cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) has shown promising results in patients with gastric cancer in Asia. However, the results obtained in Asian patients cannot be extrapolated to Western patients. The aim of this study is to compare the overall survival between patients with gastric cancer with limited peritoneal dissemination and/or tumour positive peritoneal cytology treated with palliative systemic chemotherapy, and those treated with gastrectomy, CRS and HIPEC after neoadjuvant systemic chemotherapy.

METHODS

In this multicentre randomised controlled two-armed phase III trial, 106 patients will be randomised (1:1) between palliative systemic chemotherapy only (standard treatment) and gastrectomy, CRS and HIPEC (experimental treatment) after 3-4 cycles of systemic chemotherapy.Patients with gastric cancer are eligible for inclusion if (1) the primary cT3-cT4 gastric tumour including regional lymph nodes is considered to be resectable, (2) limited peritoneal dissemination (Peritoneal Cancer Index < 7) and/or tumour positive peritoneal cytology are confirmed by laparoscopy or laparotomy, and (3) systemic chemotherapy was given (prior to inclusion) without disease progression.

DISCUSSION

The PERISCOPE II study will determine whether gastric cancer patients with limited peritoneal dissemination and/or tumour positive peritoneal cytology treated with systemic chemotherapy, gastrectomy, CRS and HIPEC have a survival benefit over patients treated with palliative systemic chemotherapy only.

TRIAL REGISTRATION

clinicaltrials.gov NCT03348150 ; registration date November 2017; first enrolment November 2017; expected end date December 2022; trial status: Ongoing.

Assembly of Ancient Mitochondrial Genomes Without a Closely Related Reference Sequence

Recent methodological advances have transformed the field of ancient DNA (aDNA). Basic bioinformatics skills are becoming essential requirements to process and analyze the sheer amounts of data generated by current aDNA studies and in biomedical research in general. This chapter is intended as a practical guide to the assembly of ancient mitochondrial genomes, directly from genomic DNA-derived next-generation sequencing (NGS) data, specifically in the absence of closely related reference genomes. In a hands-on tutorial suitable for readers with little to no prior bioinformatics experience, we reconstruct the mitochondrial genome of a woolly mammoth deposited ~45,000 years ago. We introduce key software tools and outline general strategies for mitogenome assembly, including the critical quality assessment of assembly results without a reference genome.

Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus)

Environmental DNA (eDNA) analysis is a rapid, cost-effective, non-invasive biodiversity monitoring tool which utilises DNA left behind in the environment by organisms for species detection. The method is used as a species-specific survey tool for rare or invasive species across a broad range of ecosystems. Recently, eDNA and "metabarcoding" have been combined to describe whole communities rather than focusing on single target species. However, whether metabarcoding is as sensitive as targeted approaches for rare species detection remains to be evaluated. The great crested newt Triturus cristatus is a flagship pond species of international conservation concern and the first UK species to be routinely monitored using eDNA. We evaluate whether eDNA metabarcoding has comparable sensitivity to targeted real-time quantitative PCR (qPCR) for T. cristatus detection. Extracted eDNA samples (N = 532) were screened for T. cristatus by qPCR and analysed for all vertebrate species using high-throughput sequencing technology. With qPCR and a detection threshold of 1 of 12 positive qPCR replicates, newts were detected in 50% of ponds. Detection decreased to 32% when the threshold was increased to 4 of 12 positive qPCR replicates. With metabarcoding, newts were detected in 34% of ponds without a detection threshold, and in 28% of ponds when a threshold (0.028%) was applied. Therefore, qPCR provided greater detection than metabarcoding but metabarcoding detection with no threshold was equivalent to qPCR with a stringent detection threshold. The proportion of T. cristatus sequences in each sample was positively associated with the number of positive qPCR replicates (qPCR score) suggesting eDNA metabarcoding may be indicative of eDNA concentration. eDNA metabarcoding holds enormous potential for holistic biodiversity assessment and routine freshwater monitoring. We advocate this community approach to freshwater monitoring to guide management and conservation, whereby entire communities can be initially surveyed to best inform use of funding and time for species-specific surveys.

Pure and Oxidized Copper Materials as Potential Antimicrobial Surfaces for Spaceflight Activities

Microbial biofilms can lead to persistent infections and degrade a variety of materials, and they are notorious for their persistence and resistance to eradication. During long-duration space missions, microbial biofilms present a danger to crew health and spacecraft integrity. The use of antimicrobial surfaces provides an alternative strategy for inhibiting microbial growth and biofilm formation to conventional cleaning procedures and the use of disinfectants. Antimicrobial surfaces contain organic or inorganic compounds, such as antimicrobial peptides or copper and silver, that inhibit microbial growth. The efficacy of wetted oxidized copper layers and pure copper surfaces as antimicrobial agents was tested by applying cultures of Escherichia coli and Staphylococcus cohnii to these metallic surfaces. Stainless steel surfaces were used as non-inhibitory control surfaces. The production of reactive oxygen species and membrane damage increased rapidly within 1 h of exposure on pure copper surfaces, but the effect on cell survival was negligible even after 2 h of exposure. However, longer exposure times of up to 4 h led to a rapid decrease in cell survival, whereby the survival of cells was additionally dependent on the exposed cell density. Finally, the release of metal ions was determined to identify a possible correlation between copper ions in suspension and cell survival. These measurements indicated a steady increase of free copper ions, which were released indirectly by cells presumably through excreted complexing agents. These data indicate that the application of antimicrobial surfaces in spaceflight facilities could improve crew health and mitigate material damage caused by microbial contamination and biofilm formation. Furthermore, the results of this study indicate that cuprous oxide layers were superior to pure copper surfaces related to the antimicrobial effect and that cell density is a significant factor that influences the time dependence of antimicrobial activity. Key Words: Contact killing-E. coli-S. cohnii-Antimicrobial copper surfaces-Copper oxide layers-Human health-Planetary protection. Astrobiology 17, 1183-1191.

The genomic basis of cichlid fish adaptation within the deepwater "twilight zone" of Lake Malawi

Deepwater environments are characterized by low levels of available light at narrow spectra, great hydrostatic pressure, and low levels of dissolved oxygen—conditions predicted to exert highly specific selection pressures. In Lake Malawi over 800 cichlid species have evolved, and this adaptive radiation extends into the “twilight zone” below 50 m. We use population‐level RAD‐seq data to investigate whether four endemic deepwater species (Diplotaxodon spp.) have experienced divergent selection within this environment. We identify candidate genes including regulators of photoreceptor function, photopigments, lens morphology, and haemoglobin, many not previously implicated in cichlid adaptive radiations. Colocalization of functionally linked genes suggests coadapted “supergene” complexes. Comparisons of Diplotaxodon to the broader Lake Malawi radiation using genome resequencing data revealed functional substitutions and signatures of positive selection in candidate genes. Our data provide unique insights into genomic adaptation within deepwater habitats, and suggest genome‐level specialization for life at depth as an important process in cichlid radiation.

Preservation Obscures Pelagic Deep-Sea Fish Diversity: Doubling the Number of Sole-Bearing Opisthoproctids and Resurrection of the Genus Monacoa (Opisthoproctidae, Argentiniformes)

The family Opisthoproctidae (barreleyes) constitutes one of the most peculiar looking and unknown deep-sea fish groups in terms of taxonomy and specialized adaptations. All the species in the family are united by the possession of tubular eyes, with one distinct lineage exhibiting also drastic shortening of the body. Two new species of the mesopelagic opisthoproctid mirrorbelly genus Monacoa are described based on pigmentation patterns of the "sole"-a unique vertebrate structure used in the reflection and control of bioluminescence in most short-bodied forms. Different pigmentation patterns of the soles, previously noted as intraspecific variations based on preserved specimens, are here shown species-specific and likely used for communication in addition to counter-illumination of down-welling sunlight. The genus Monacoa is resurrected from Opisthoproctus based on extensive morphological synaphomorphies pertaining to the anal fin and snout. Doubling the species diversity within sole-bearing opisthoproctids, including recognition of two genera, is unambiguously supported by mitogenomic DNA sequence data. Regular fixation with formalin and alcohol preservation is shown problematic concerning the retention of species-specific pigmentation patterns. Examination or photos of fresh material before formalin fixation is shown paramount for correct species recognition of sole-bearing opisthoproctids-a relatively unknown issue concerning species diversity in the deep-sea pelagic realm.

Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods

Organisms continuously release DNA into their environments via shed cells, excreta, gametes and decaying material. Analysis of this 'environmental DNA' (eDNA) is revolutionizing biodiversity monitoring. eDNA outperforms many established survey methods for targeted detection of single species, but few studies have investigated how well eDNA reflects whole communities of organisms in natural environments. We investigated whether eDNA can recover accurate qualitative and quantitative information about fish communities in large lakes, by comparison to the most comprehensive long-term gill-net data set available in the UK. Seventy-eight 2L water samples were collected along depth profile transects, gill-net sites and from the shoreline in three large, deep lakes (Windermere, Bassenthwaite Lake and Derwent Water) in the English Lake District. Water samples were assayed by eDNA metabarcoding of the mitochondrial 12S and cytochrome b regions. Fourteen of the 16 species historically recorded in Windermere were detected using eDNA, compared to four species in the most recent gill-net survey, demonstrating eDNA is extremely sensitive for detecting species. A key question for biodiversity monitoring is whether eDNA can accurately estimate abundance. To test this, we used the number of sequence reads per species and the proportion of sampling sites in which a species was detected with eDNA (i.e. site occupancy) as proxies for abundance. eDNA abundance data consistently correlated with rank abundance estimates from established surveys. These results demonstrate that eDNA metabarcoding can describe fish communities in large lakes, both qualitatively and quantitatively, and has great potential as a complementary tool to established monitoring methods.

Comparative genomics of flatworms (platyhelminthes) reveals shared genomic features of ecto- and endoparastic neodermata

The ectoparasitic Monogenea comprise a major part of the obligate parasitic flatworm diversity. Although genomic adaptations to parasitism have been studied in the endoparasitic tapeworms (Cestoda) and flukes (Trematoda), no representative of the Monogenea has been investigated yet. We present the high-quality draft genome of Gyrodactylus salaris, an economically important monogenean ectoparasite of wild Atlantic salmon (Salmo salar). A total of 15,488 gene models were identified, of which 7,102 were functionally annotated. The controversial phylogenetic relationships within the obligate parasitic Neodermata were resolved in a phylogenomic analysis using 1,719 gene models (alignment length of >500,000 amino acids) for a set of 16 metazoan taxa. The Monogenea were found basal to the Cestoda and Trematoda, which implies ectoparasitism being plesiomorphic within the Neodermata and strongly supports a common origin of complex life cycles. Comparative analysis of seven parasitic flatworm genomes identified shared genomic features for the ecto- and endoparasitic lineages, such as a substantial reduction of the core bilaterian gene complement, including the homeodomain-containing genes, and a loss of the piwi and vasa genes, which are considered essential for animal development. Furthermore, the shared loss of functional fatty acid biosynthesis pathways and the absence of peroxisomes, the latter organelles presumed ubiquitous in eukaryotes except for parasitic protozoans, were inferred. The draft genome of G. salaris opens for future in-depth analyses of pathogenicity and host specificity of poorly characterized G. salaris strains, and will enhance studies addressing the genomics of host–parasite interactions and speciation in the highly diverse monogenean flatworms.

Diversity of Kale (Brassica oleracea var. sabellica): Glucosinolate Content and Phylogenetic Relationships

Recently, kale has become popular due to nutritive components beneficial for human health. It is an important source of phytochemicals such as glucosinolates that trigger associated cancer-preventive activity. However, nutritional value varies among glucosinolates and among cultivars. Here, we start a systematic determination of the content of five glucosinolates in 25 kale varieties and 11 non-kale Brassica oleracea cultivars by HPLC-DAD-ESI-MS(n) and compare the profiles with results from the analysis of SNPs derived from a KASP genotyping assay. Our results demonstrate that the glucosinolate levels differ markedly among varieties of different origin. Comparison of the phytochemical data with phylogenetic relationships revealed that the common name kale refers to at least three different groups. German, American, and Italian kales differ morphologically and phytochemically. Landraces do not show outstanding glucosinolate levels. Our results demonstrate the diversity of kale and the importance of preserving a broad genepool for future breeding purposes.

CdTe Timepix detectors for single-photon spectroscopy and linear polarimetry of high-flux hard x-ray radiation

Single-photon spectroscopy of pulsed, high-intensity sources of hard X-rays - such as laser-generated plasmas - is often hampered by the pileup of several photons absorbed by the unsegmented, large-volume sensors routinely used for the detection of high-energy radiation. Detectors based on the Timepix chip, with a segmentation pitch of 55 μm and the possibility to be equipped with high-Z sensor chips, constitute an attractive alternative to commonly used passive solutions such as image plates. In this report, we present energy calibration and characterization measurements of such devices. The achievable energy resolution is comparable to that of scintillators for γ spectroscopy. Moreover, we also introduce a simple two-detector Compton polarimeter setup with a polarimeter quality of (98 ± 1)%. Finally, a proof-of-principle polarimetry experiment is discussed, where we studied the linear polarization of bremsstrahlung emitted by a laser-driven plasma and found an indication of the X-ray polarization direction depending on the polarization state of the incident laser pulse.

Influence of higher harmonics of the undulator in X-ray polarimetry and crystal monochromator design

The spectrum of the undulator radiation of beamline P01 at Petra III has been measured after passing a multiple reflection channel-cut polarimeter. Odd and even harmonics up to the 15th order, as well as Compton peaks which were produced by the high harmonics in the spectrum, could been measured. These additional contributions can have a tremendous influence on the performance of the polarimeter and have to be taken into account for further polarimeter designs.

Co-Speciation of the Ectoparasite Gyrodactylus teuchis (Monogenea, Platyhelminthes) and Its Salmonid Hosts

Co-speciation is a fundamental concept of evolutionary biology and intuitively appealing, yet in practice hard to demonstrate as it is often blurred by other evolutionary processes. We investigate the phylogeographic history of the monogenean ectoparasites Gyrodactylus teuchis and G. truttae on European salmonids of the genus Salmo. Mitochondrial cytochrome oxidase subunit 1 and the nuclear ribosomal internal transcribed spacer 2 were sequenced for 189 Gyrodactylus individuals collected from 50 localities, distributed across most major European river systems, from the Iberian- to the Balkan Peninsula. Despite both anthropogenic and naturally caused admixture of the principal host lineages among major river basins, co-phylogenetic analyses revealed significant global congruence for host and parasite phylogenies, providing firm support for co-speciation of G. teuchis and its salmonid hosts brown trout (S. trutta) and Atlantic salmon (S. salar). The major split within G. teuchis, coinciding with the initial divergence of the hosts was dated to ~1.5 My BP, using a Bayesian framework based on an indirect calibration point obtained from the host phylogeny. The presence of G. teuchis in Europe thus predates some of the major Pleistocene glaciations. In contrast, G. truttae exhibited remarkably low intraspecific genetic diversity. Given the direct life cycle and potentially high transmission potential of gyrodactylids, this finding is interpreted as indication for a recent emergence (<60 ky BP) of G. truttae via a host-switch. Our study thus suggests that instances of two fundamentally different mechanisms of speciation (co-speciation vs. host-switching) may have occurred on the same hosts in Europe within a time span of less than 1.5 My in two gyrodactylid ectoparasite species.

Kinetic Modelling of the Adsorption and Desorption of NH3 on Fe/BEA Zeolite

This paper deals with the kinetic modelling of the adsorption and desorption of NH3 on Fe/BEA zeolite. Fe/BEA was recently reported to show high activity for the selective catalytic reduction (SCR) of NO x by NH3. The NH3 adsorption and desorption kinetics was examined in the temperature range from 323 to 923 K using temperature programmed desorption of NH3 (NH3-TPD) and diffuse reflectance infrared fourier transform spectroscopy (DRIFTS). With these investigations an elementary kinetic mean field model of the NH3 adsorption and desorption was constructed employing Arrhenius-based rate expressions. The model differentiated molecularly bound NH3 and NH4 + surface species originated from the NH3 chemisorption. For both kinds of species, the kinetic parameters of the adsorption of NH3 were adopted from the literature, while that of the desorption were numerically fitted based upon NH3-TPD traces. The reliability of the kinetic model was evidenced by reproduction and prediction of the NH3-TPD profiles as well as thermodynamic consistency.

Full control of the spin-wave damping in a magnetic insulator using spin-orbit torque

It is demonstrated that the threshold current for damping compensation can be reached in a 5  μm diameter YIG(20  nm)|Pt(7  nm) disk. The demonstration rests upon the measurement of the ferromagnetic resonance linewidth as a function of I(dc) using a magnetic resonance force microscope (MRFM). It is shown that the magnetic losses of spin-wave modes existing in the magnetic insulator can be reduced or enhanced by at least a factor of 5 depending on the polarity and intensity of an in-plane dc current I(dc) flowing through the adjacent normal metal with strong spin-orbit interaction. Complete compensation of the damping of the fundamental mode by spin-orbit torque is reached for a current density of ∼3×10(11)  A·m(-2), in agreement with theoretical predictions. At this critical threshold the MRFM detects a small change of static magnetization, a behavior consistent with the onset of an auto-oscillation regime.

Sirolimus conversion after heart transplant: risk factors for acute rejection and predictors of renal function response

In a randomized, comparative study of cardiac transplant patients with mild-to-moderate renal insufficiency, conversion from calcineurin inhibitors (CNIs) to sirolimus improved renal function at 1 year versus continuing CNIs, with an attendant risk of biopsy-confirmed acute rejection (BCAR). Post hoc analyses were conducted to identify predictors of BCAR and GFR improvement associated with conversion. Patients with proteinuria >500 mg/day were excluded. Univariate and multivariate regression analyses tested 13 parameters for BCAR and six for GFR improvement. In 57 sirolimus-treated patients, mean daily mycophenolate mofetil (MMF) dose was lower in those with versus without BCAR (1000 vs. 1420 mg; p = 0.014). Receiver operating characteristic analysis identified MMF dose ≤1000 mg/day as the optimal cutoff to predict BCAR. Multivariate analysis confirmed low MMF dose (odds ratio: 9.94; p = 0.007) and non-white race (odds ratio: 15.3; p = 0.06) were independently associated with BCAR. GFR improvement was evaluated in intent-to-treat patients (n = 116). Significant interaction was detected between treatment effect and preexisting diabetes status (univariate p = 0.077; multivariate p = 0.022), indicating greater beneficial effect of sirolimus in those without preexisting diabetes. These findings suggest that sirolimus is more effective in improving GFR in patients without preexisting diabetes, and adequate MMF doses are needed for sirolimus conversion.

Reduced discomfort during high-definition transcutaneous stimulation using 6% benzocaine

Background: High-Definition transcranial Direct Current Stimulation (HD-tDCS) allows for non-invasive neuromodulation using an array of compact (approximately 1 cm² contact area) “High-Definition” (HD) electrodes, as compared to conventional tDCS (which uses two large pads that are approximately 35 cm²). In a previous transcutaneous study, we developed and validated designs for HD electrodes that reduce discomfort over >20 min session with 2 mA electrode current.

Objective: The purpose of this study was to investigate the use of a chemical pretreatment with 6% benzocaine (topical numbing agent) to further reduce subjective discomfort during transcutaneous stimulation and to allow for better sham controlled studies.

Methods: Pre-treatment with 6% benzocaine was compared with control (no pretreatment) for 22 min 2 mA of stimulation, with either CCNY-4 or Lectron II electroconductive gel, for both cathodal and anodal transcutaneous (forearm) stimulation (eight different combinations).

Results: Results show that for all conditions and polarities tested, stimulation with HD electrodes is safe and well tolerated and that pretreatment further reduced subjective discomfort.

Conclusion: Pretreatment with a mild analgesic reduces discomfort during HD-tDCS.

MicroRNA loci support conspecificity of Gyrodactylus salaris and Gyrodactylus thymalli (Platyhelminthes: Monogenea)

The monogenean flatworm Gyrodactylus salaris is a serious threat to wild and farmed Atlantic salmon stocks in Norway. Morphologically, the closely related but harmless Gyrodactylus thymalli on grayling can hardly be distinguished from G. salaris. Until now, molecular approaches could not resolve unambiguously whether G. salaris and G. thymalli represent just one polytypic species, two polytypic species or a complex of more than two species. In the first known genome-wide analysis utilizing 37 conserved microRNA loci, the genetic differentiation of seven populations of G. salaris and G. thymalli was assessed. The concatenated alignment spanned 21,742bp including 62 variable positions. A neighbor-joining cluster analysis did not support any host-based or mitochondrial haplotype-based grouping of strains. We conclude that a two species concept for G. salaris and G. thymalli does not reflect meaningful biological entities. Instead, G. salaris and G. thymalli are just one species comprising several pathogenic and non-pathogenic strains on various primary hosts. Following the International Code for Zoological Nomenclature, G. salaris Malmberg, 1957 is the valid species name with G. thymalli Žitňan, 1960 becoming the junior synonym. Accordingly, the range of G. salaris is significantly increased, given that formerly G. salaris-free countries such as e.g., Great Britain are now within the species' natural range. The synonymization of G. salaris and G. thymalli implies severe challenges to current disease management routines, which assume that G. salaris and G. thymalli are readily distinguishable. Protocols for reliable identification of pathogenic and non-pathogenic strains of G. salaris need to be developed.