Differences in enteric neuronal density in the NSE-Noggin mouse model across institutes

The enteric nervous system (ENS) is a large and complex part of the peripheral nervous system, and it is vital for gut homeostasis. To study the ENS, different hyper- and hypo-innervated model systems have been developed. The NSE-Noggin mouse model was described as one of the few models with a higher enteric neuronal density in the colon. However, in our hands NSE-Noggin mice did not present with a hyperganglionic phenotype. NSE-Noggin mice were phenotyped based on fur appearance, genotyped and DNA sequenced to demonstrate transgene and intact NSE-Noggin-IRES-EGFP construct presence, and RNA expression of Noggin was shown to be upregulated. Positive EGFP staining in the plexus of NSE-Noggin mice also confirmed Noggin protein expression. Myenteric plexus preparations of the colon were examined to quantify both the overall density of enteric neurons and the proportions of enteric neurons expressing specific subtype markers. The total number of enteric neurons in the colonic myenteric plexus of transgenic mice did not differ significantly from wild types, nor did the proportion of calbindin, calretinin, or serotonin immunoreactive myenteric neurons. Possible reasons as to why the hyperinnervated phenotype could not be observed in contrast with original studies using this mouse model are discussed, including study design, influence of microbiota, and other environmental variables.

Cerebral microvascular endothelial cell-derived extracellular vesicles regulate blood - brain barrier function

Autoreactive T lymphocytes crossing the blood-brain barrier (BBB) into the central nervous system (CNS) play a crucial role in the initiation of demyelination and neurodegeneration in multiple sclerosis (MS). Recently, extracellular vesicles (EV) secreted by BBB endothelial cells (BBB-EC) have emerged as a unique form of cell-to-cell communication that contributes to cerebrovascular dysfunction. However, the precise impact of different size-based subpopulations of BBB-EC-derived EV (BBB-EV) on the early stages of MS remains unclear. Therefore, our objective was to investigate the content and function of distinct BBB-EV subpopulations in regulating BBB integrity and their role in T cell transendothelial migration, both in vitro and in vivo. Our study reveals that BBB-ECs release two distinct size based EV populations, namely small EV (sEV; 30-150 nm) and large EV (lEV; 150-300 nm), with a significantly higher secretion of sEV during inflammation. Notably, the expression patterns of cytokines and adhesion markers differ significantly between these BBB-EV subsets, indicating specific functional differences in the regulation of T cell migration. Through in vitro experiments, we demonstrate that lEV, which predominantly reflect their cellular source, play a major role in BBB integrity loss and the enhanced migration of pro-inflammatory Th1 and Th17.1 cells. Conversely, sEV appear to protect BBB function by inducing an anti-inflammatory phenotype in BBB-EC. These findings align with our in vivo data, where the administration of sEV to mice with experimental autoimmune encephalomyelitis (EAE) results in lower disease severity compared to the administration of lEV, which exacerbates disease symptoms. In conclusion, our study highlights the distinct and opposing effects of BBB-EV subpopulations on the BBB, both in vitro and in vivo. These findings underscore the need for further investigation into the diagnostic and therapeutic potential of BBB-EV in the context of MS.

Gamma radiation effects on AG MP-50 cation exchange resin and sulfonated activated carbon for bismuth-213 separation

Medical 225Ac/213Bi radionuclide generators are designed to provide a local supply of the short-lived 213Bi for cancer treatment. However, radiation-induced damage to the sorbents commonly used in such radionuclide generators remains a major concern. In this study, the effects of gamma radiation on AG MP-50 cation exchange resin and sulfonated activated carbon (SAC) were studied by analyzing the changes in the morphological characteristics, functional groups, and the La3+/Bi3+ sorption performance, with La3+ being a suitable non-radioactive substitute for Ac3+. The surface sulfonic acid groups of AG MP-50 resin suffered from severe radiation-induced degradation, while the particle morphology was changed markedly after being exposed to absorbed doses of approximately 11 MGy. As a result, the sorption performance of irradiated AG MP-50 for La3+ and Bi3+ was significantly decreased with increasing absorbed doses. In contrast, no apparent changes in acquired morphological characteristics were observed for pristine and irradiated SAC based on SEM and XRD characterization. The surface oxygen content (e.g., O-C[double bond, length as m-dash]O) of irradiated SAC increased for an absorbed dose of 11 MGy due to free radical-induced oxidation. The sorption performance of pristine and irradiated SAC materials for La3+ and Bi3+ remained generally the same at pH values of 1 and 2. Furthermore, the applicability of AG MP-50 and SAC in the 225Ac/213Bi generators was illustrated in terms of their radiolytic stability. This study provides further evidence for the practical implementation of both AG MP-50 and SAC in 225Ac/213Bi radionuclide generators.

Barcoding and traditional health practitioner perspectives are informative to monitor and conserve frogs and reptiles traded for traditional medicine in urban South Africa

Previous literature suggests that Indigenous cultural practices, specifically traditional medicine, are commonplace among urban communities contrary to the general conception that such practices are restricted to rural societies. We reviewed previous literature for records of herptiles (frog and reptile species) sold by traditional health practitioners in urban South Africa, then used visual confirmation surveys, DNA barcoding and folk taxonomy to identify the herptile species that were on sale. Additionally, we interviewed 11 IsiZulu and SePedi speaking traditional health practitioners to document details of the collection and pricing of herptile specimens along with the practitioners' views of current conservation measures for traditional medicine markets. The 34 herptile species recorded in previous literature on traditional medicine markets included endangered and non-native species. Spectrophotometry measurements of the DNA we extracted from the tissue of herptiles used in traditional medicine were an unreliable predictor of whether those extractions would be suitable for further experimental work. From our initial set of 111 tissue samples, 81 sequencing reactions were successful and 55 of those sequences had species-level matches to COI reference sequences on the NCBI GenBank and/or BOLD databases. Molecular identification revealed that traditional health practitioners correctly labelled 77% of the samples that we successfully identified with DNA barcoding in this study. Our mixed methodology approach is useful for conservation planning as it updates knowledge of animal use in Indigenous remedies and can accurately identify species of high conservation priority. Furthermore, this study highlights the possibility of collaborative conservation planning with traditional health practitioners.

Tailoring Interlayer Charge Transfer Dynamics in 2D Perovskites with Electroactive Spacer Molecules

The family of hybrid organic-inorganic lead-halide perovskites are the subject of intense interest for optoelectronic applications, from light-emitting diodes to photovoltaics to X-ray detectors. Due to the inert nature of most organic molecules, the inorganic sublattice generally dominates the electronic structure and therefore the optoelectronic properties of perovskites. Here, we use optically and electronically active carbazole-based Cz-Ci molecules, where Ci indicates an alkylammonium chain and i indicates the number of CH2 units in the chain, varying from 3 to 5, as cations in the two-dimensional (2D) perovskite structure. By investigating the photophysics and charge transport characteristics of (Cz-Ci)2PbI4, we demonstrate a tunable electronic coupling between the inorganic lead-halide and organic layers. The strongest interlayer electronic coupling was found for (Cz-C3)2PbI4, where photothermal deflection spectroscopy results remarkably reveal an organic-inorganic charge transfer state. Ultrafast transient absorption spectroscopy measurements demonstrate ultrafast hole transfer from the photoexcited lead-halide layer to the Cz-Ci molecules, the efficiency of which increases by varying the chain length from i = 5 to i = 3. The charge transfer results in long-lived carriers (10-100 ns) and quenched emission, in stark contrast to the fast (sub-ns) and efficient radiative decay of bound excitons in the more conventional 2D perovskite (PEA)2PbI4, in which phenylethylammonium (PEA) acts as an inert spacer. Electrical charge transport measurements further support enhanced interlayer coupling, showing increased out-of-plane carrier mobility from i = 5 to i = 3. This study paves the way for the rational design of 2D perovskites with combined inorganic-organic electronic properties through the wide range of functionalities available in the world of organics.

Simple and flexible sign and rank-based methods for testing for differential abundance in microbiome studies

Microbiome data obtained with amplicon sequencing are considered as compositional data. It has been argued that these data can be analysed after appropriate transformation to log-ratios, but ratios and logarithms cause problems with the many zeroes in typical microbiome experiments. We demonstrate that some well chosen sign and rank transformations also allow for valid inference with compositional data, and we show how logistic regression and probabilistic index models can be used for testing for differential abundance, while inheriting the flexibility of a statistical modelling framework. The results of a simulation study demonstrate that the new methods perform better than most other methods, and that it is comparable with ANCOM-BC. These methods are implemented in an R-package 'signtrans' and can be installed from Github (https://github.com/lucp9827/signtrans).

Bacteria associated with Zn-hyperaccumulators Arabidopsis halleri and Arabidopsis arenosa from Zn-Pb-Cd waste heaps in Poland as promising tools for bioremediation

To identify metal adapted bacteria equipped with traits positively influencing the growth of two hyperaccumulator plant species Arabidopsis arenosa and Arabidopsis halleri, we isolated bacteria inhabiting rhizosphere and vegetative tissues (roots, basal and stem leaves) of plants growing on two old Zn-Pb-Cd waste heaps in Bolesław and Bukowno (S. Poland), and characterized their potential plant growth promoting (PGP) traits as well as determined metal concentrations in rhizosphere and plant tissues. To determine taxonomic position of 144 bacterial isolates, 16S rDNA Sanger sequencing was used. A metabolic characterization of isolated strains was performed in vitro using PGP tests. A. arenosa and A. halleri accumulate high amounts of Zn in their tissues, especially in stem leaves. Among in total 22 identified bacterial taxa, the highest level of the taxonomical diversity (H' = 2.01) was revealed in A. halleri basal leaf endophytes originating from Bukowno waste heap area. The 96, 98, 99, and 98% of investigated strains showed tolerant to Cd, Zn, Pb and Cu, respectively. Generally, higher percentages of bacteria could synthesize auxins, siderophores, and acetoin as well as could solubilize phosphate. Nine of waste heap origin bacterial strains were tolerant to toxic metals, showed in vitro PGP traits and are potential candidates for bioremediation.

Diversity and potential plant growth promoting capacity of seed endophytic bacteria of the holoparasite Cistanche phelypaea (Orobanchaceae)

Salt marshes are highly dynamic, biologically diverse ecosystems with a broad range of ecological functions. We investigated the endophytic bacterial community of surface sterilized seeds of the holoparasitic Cistanche phelypaea growing in coastal salt marshes of the Iberian Peninsula in Portugal. C. phelypaea is the only representative of the genus Cistanche that was reported in such habitat. Using high-throughput sequencing methods, 23 bacterial phyla and 263 different OTUs on genus level were found. Bacterial strains belonging to phyla Proteobacteria and Actinobacteriota were dominating. Also some newly classified or undiscovered bacterial phyla, unclassified and unexplored taxonomic groups, symbiotic Archaea groups inhabited the C. phelypaea seeds. γ-Proteobacteria was the most diverse phylogenetic group. Sixty-three bacterial strains belonging to Bacilli, Actinomycetes, α-, γ- and β-Proteobacteria and unclassified bacteria were isolated. We also investigated the in vitro PGP traits and salt tolerance of the isolates. Among the Actinobacteria, Micromonospora spp. showed the most promising endophytes in the seeds. Taken together, the results indicated that the seeds were inhabited by halotolerant bacterial strains that may play a role in mitigating the adverse effects of salt stress on the host plant. In future research, these bacteria should be assessed as potential sources of novel and unique bioactive compounds or as novel bacterial species.

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.

3D Perovskite Passivation with a Benzotriazole-Based 2D Interlayer for High-Efficiency Solar Cells

2H-Benzotriazol-2-ylethylammonium bromide and iodide and its difluorinated derivatives are synthesized and employed as interlayers for passivation of formamidinium lead triiodide (FAPbI₃) solar cells. In combination with PbI₂ and PbBr₂, these benzotriazole derivatives form two-dimensional (2D) Ruddlesden-Popper perovskites (RPPs) as evidenced by their crystal structures and thin film characteristics. When used to passivate n-i-p FAPbI₃ solar cells, the power conversion efficiency improves from 20% to close to 22% by enhancing the open-circuit voltage. Quasi-Fermi level splitting experiments and scanning electron microscopy cathodoluminescence hyperspectral imaging reveal that passivation provides a reduced nonradiative recombination at the interface between the perovskite and hole transport layer. Photoluminescence spectroscopy, angle-resolved grazing-incidence wide-angle X-ray scattering, and depth profiling X-ray photoelectron spectroscopy studies of the 2D/three-dimensional (3D) interface between the benzotriazole RPP and FAPbI₃ show that a nonuniform layer of 2D perovskites is enough to passivate defects, enhance charge extraction, and decrease nonradiative recombination.

Plasmon enhanced fluorescence from meticulously positioned gold nanoparticles, deposited by ultra sonic spray coating on organic light emitting diodes

Enhancement of the spontaneous emission of fluorophores aided by plasmonic nanoparticles (PNPs) prompts the growth of plasmonic organic light emitting diodes (OLEDs). Together with the spatial dependence of the fluorophore and PNPs on enhanced fluorescence, the surface coverage of the PNPs controls the charge transport in OLEDs. Hence, here, the spatial and surface coverage reliance of plasmonic gold nanoparticles is controlled by a roll-to-roll compatible ultrasonic spray coating technique. A 2-fold enhancement in the multi photon fluorescence is seen by two-photon fluorescence microscopy for a polystyrene sulfonate (PSS) stabilized gold nanoparticle located 10 nm away from the super yellow fluorophore. Fluorescence enhancement combined with ∼2% surface coverage of PNPs, provides a 33%, 20% and ∼40% increase in the electroluminescence, luminous efficacy and external quantum efficiency, respectively.

WASP: the World Archives of Species Perception

While human perception can play a role in influencing public support for species conservation, the mechanisms underlying human perception remain poorly understood. Some previous studies on perception have focused on a few specific taxa, which makes the understanding of the public perception of species at large a resource- and time-intensive task. Here, we introduce the World Archives of Species Perception project that consists of an animal survey and a plant survey to construct the first systematic database to study the human perception of the floral and faunal diversity at a global scale. We provide a description of our survey method, species selection, survey implementation and a discussion of the potential uses of our databases in multidisciplinary research. In the animal survey, we cover 1980 International Union for Conservation of Nature (IUCN)-evaluated species, representing 25 classes, 192 orders, 1037 families and 1705 genera. In the plant survey, we cover 2000 IUCN-evaluated species, representing 13 classes, 93 orders, 386 families and 1968 genera. Data from the survey will be collected and made available 24 months after the publication of the article. Database URL http://wasp-project.net/.

Entrepreneurs Can Know More Than They Can Tell: Conceptualizing and Measuring Tacit Entrepreneurial Knowledge

Organizational knowledge components dominate research on tacit knowledge. In order to overcome this dominance, we introduce Tacit Entrepreneurial Knowledge (TEK). TEK is conceptualized as one's experiential learning from past experiences and insights that result in tacit knowledge regarding entrepreneurship that is implicit, personal, and uncodified. For this study the situational judgment test (SJT) approach is adopted to overcome the common limitations in quantifying an individual's tacit knowledge. The SJT is a scenario-based measurement instrument that allows us to quantify an individual's TEK. The SJT is developed using three steps: first, scenarios were collected through interviews, followed by formulating responses to the scenarios, and finally, the effectiveness of the responses for each scenario was evaluated. The outcome of this research article is threefold; first, a comprehensive conceptualization of TEK, including delineation of its nomological network. Second, the development of a measurement instrument for TEK and subsequent scoring method. Finally, an antecedent-consequence model which includes potential contingencies associated with these relationships. In the debate on tacit knowledge, our measurement is innovative and relevant, as previous research failed to uncover an individual's tacit knowledge in the context of entrepreneurship, despite its importance in various entrepreneurial processes. This study aspires to ignite research into TEK by demonstrating important research opportunities unlocked by our conceptualization and subsequent measurement, offering future researchers a wide range of avenues to uncover the black box of tacit knowledge in entrepreneurship.

An Alliance of Trifolium repens—Rhizobium leguminosarum bv. trifolii—Mycorrhizal Fungi From an Old Zn-Pb-Cd Rich Waste Heap as a Promising Tripartite System for Phytostabilization of Metal Polluted Soils

The Bolesław waste heap in South Poland, with total soil Zn concentrations higher than 50,000 mg kg^–1, 5,000 mg Pb kg^–1, and 500 mg Cd kg^–1, is a unique habitat for metallicolous plants, such as Trifolium repens L. The purpose of this study was to characterize the association between T. repens and its microbial symbionts, i.e., Rhizobium leguminosarum bv. trifolii and mycorrhizal fungi and to evaluate its applicability for phytostabilization of metal-polluted soils. Rhizobia originating from the nutrient-poor waste heap area showed to be efficient in plant nodulation and nitrogen fixation. They demonstrated not only potential plant growth promotion traits in vitro, but they also improved the growth of T. repens plants to a similar extent as strains from a non-polluted reference area. Our results revealed that the adaptations of T. repens to high Zn-Pb-Cd concentrations are related to the storage of metals predominantly in the roots (excluder strategy) due to nodule apoplast modifications (i.e., thickening and suberization of cell walls, vacuolar storage), and symbiosis with arbuscular mycorrhizal fungi of a substantial genetic diversity. As a result, the rhizobia-mycorrhizal fungi-T. repens association appears to be a promising tool for phytostabilization of Zn-Pb-Cd-polluted soils.

Exercise Systolic Reserve and Exercise Pulmonary Hypertension Improve Diagnosis of Heart Failure With Preserved Ejection Fraction

Aims

Diastolic stress testing (DST) is recommended to confirm heart failure with preserved ejection fraction (HFpEF) in patients with exertional dyspnea, but current algorithms do not detect all patients. We aimed to identify additional echocardiographic markers of elevated pulmonary arterial wedge pressure during exercise (exPAWP) in patients referred for DST.

Methods and Results

We identified candidate parameters in 22 patients referred for exercise right heart catheterization with simultaneous echocardiography. Elevated exPAWP (≥25 mmHg) was present in 14 patients, and was best identified by peak septal systolic annular velocity <9.5 cm/s [exS', area under the receiver operating characteristic curve (AUC) 0.97, 95% confidence interval 0.92–1.0] and mean pulmonary artery pressure/cardiac output slope ≥3.2 mmHg/L [mPAP/CO, AUC 0.88 (0.72–1.0)]. We propose a decision tree to identify patients with elevated exPAWP. Applying this decision tree to 326 patients in an independent non-invasive DST cohort showed that patients labeled as “high probability of HFpEF” (n = 85) had reduced peak oxygen uptake [13.0 (10.7–15.1) mL/kg/min, p < 0.001 vs. intermediate/low probability], high H2FPEF score [53 (40–72) %, p < 0.001 vs. intermediate/low probability], and typical clinical characteristics. The diagnostic yield of DST increased from 11% using exercise E/e', to 62% using the decision tree.

Conclusion

In DST for suspected HFpEF, exS' was the most accurate echocardiographic parameter to identify elevated PAWP. We propose a decision tree including exS' and mPAP/CO for interpretation of DST. Application of this decision tree revealed typical HFpEF characteristics in patients labeled as high probability of HFpEF, and substantially reduced the number of inconclusive results.

The polymeric glyco-linker controls the signal outputs for plasmonic gold nanorod biosensors due to biocorona formation

Gold nanorods (GNRs) are a promising platform for nanoplasmonic biosensing. The localised surface plasmon resonance (LSPR) peak of GNRs is located in the near-infrared optical window and is sensitive to local binding events, enabling label-free detection of biomarkers in complex biological fluids. A key challenge in the development of such sensors is achieving target affinity and selectivity, while both minimizing non-specific binding and maintaining colloidal stability. Herein, we reveal how GNRs decorated with galactosamine-terminated polymer ligands display significantly different binding responses in buffer compared to serum, due to biocorona formation, and how biocorona displacement due to lectin binding plays a key role in their optical responses. GNRs were coated with either poly(N-(2-hydroxypropyl)methacrylamide) (PHPMA) or poly(N-hydroxyethyl acrylamide) (PHEA) prepared via reversible addition-fragmentation chain-transfer (RAFT) polymerisation and end-functionalised with galactosamine (Gal) as the lectin-targeting unit. In buffer Gal-PHEA-coated GNRs aggregated upon soybean agglutinin (SBA) addition, whereas Gal-PHPMA-coated GNRs exhibited a red-shift of the LSPR spectrum without aggregation. In contrast, when incubated in serum Gal-PHPMA-coated nanorods showed no binding response, while Gal-PHEA GNRs exhibited a dose-dependent blue-shift of the LSPR peak, which is the opposite direction (red-shift) to what was observed in buffer. This differential behaviour was attributed to biocorona formation onto both polymer-coated GNRs, shown by differential centrifugal sedimentation and nanoparticle tracking analysis. Upon addition of SBA to the Gal-PHEA coated nanorods, signal was generated due to displacement of weakly-bound biocorona components by lectin binding. However, in the case of Gal-PHPMA which had a thicker corona, attributed to lower polymer grafting densities, addition of SBA did not lead to biocorona displacement and there was no signal output. These results show that plasmonic optical responses in complex biological media can be significantly affected by biocorona formation, and that biocorona formation itself does not prevent sensing so long as its exact nature (e.g. 'hard versus soft') is tuned.

A Compositional Model to Predict the Aggregated Isotope Distribution for Average DNA and RNA Oligonucleotides

Structural modifications of DNA and RNA molecules play a pivotal role in epigenetic and posttranscriptional regulation. To characterise these modifications, more and more MS and MS/MS- based tools for the analysis of nucleic acids are being developed. To identify an oligonucleotide in a mass spectrum, it is useful to compare the obtained isotope pattern of the molecule of interest to the one that is theoretically expected based on its elemental composition. However, this is not straightforward when the identity of the molecule under investigation is unknown. Here, we present a modelling approach for the prediction of the aggregated isotope distribution of an average DNA or RNA molecule when a particular (monoisotopic) mass is available. For this purpose, a theoretical database of all possible DNA/RNA oligonucleotides up to a mass of 25 kDa is created, and the aggregated isotope distribution for the entire database of oligonucleotides is generated using the BRAIN algorithm. Since this isotope information is compositional in nature, the modelling method is based on the additive log-ratio analysis of Aitchison. As a result, a univariate weighted polynomial regression model of order 10 is fitted to predict the first 20 isotope peaks for DNA and RNA molecules. The performance of the prediction model is assessed by using a mean squared error approach and a modified Pearson's χ2 goodness-of-fit measure on experimental data. Our analysis has indicated that the variability in spectral accuracy contributed more to the errors than the approximation of the theoretical isotope distribution by our proposed average DNA/RNA model. The prediction model is implemented as an online tool. An R function can be downloaded to incorporate the method in custom analysis workflows to process mass spectral data.

A novel method for assessing climate change impacts in ecotron experiments

Ecotron facilities allow accurate control of many environmental variables coupled with extensive monitoring of ecosystem processes. They therefore require multivariate perturbation of climate variables, close to what is observed in the field and projections for the future. Here, we present a new method for creating realistic climate forcing for manipulation experiments and apply it to the UHasselt Ecotron experiment. The new methodology uses data derived from the best available regional climate model projection and consists of generating climate forcing along a gradient representative of increasingly high global mean air temperature anomalies. We first identified the best-performing regional climate model simulation for the ecotron site from the Coordinated Regional Downscaling Experiment in the European domain (EURO-CORDEX) ensemble based on two criteria: (i) highest skill compared to observations from a nearby weather station and (ii) representativeness of the multi-model mean in future projections. The time window is subsequently selected from the model projection for each ecotron unit based on the global mean air temperature of the driving global climate model. The ecotron units are forced with 3-hourly output from the projections of the 5-year period in which the global mean air temperature crosses the predefined values. With the new approach, Ecotron facilities become able to assess ecosystem responses on changing climatic conditions, while accounting for the co-variation between climatic variables and their projection in variability, well representing possible compound events. The presented methodology can also be applied to other manipulation experiments, aiming at investigating ecosystem responses to realistic future climate change.

A carcinogenic trigger to study the function of tumor suppressor genes in Schmidtea mediterranea

Planarians have been long known for their regenerative ability, which hinges on pluripotency. Recently, however, the planarian model has been successfully established for routine toxicological screens aimed to assess overproliferation, mutagenicity and tumorigenesis. In this study, we focused on planarian tumor suppressor genes (TSGs) and their role during chemically induced carcinogenic stress in Schmidtea mediterranea Combining in silico and proteomic screens with exposure to human carcinogen type 1A agent cadmium (Cd), we showed that many TSGs have a function in stem cells and that, in general, exposure to Cd accelerated the onset and increased the severity of the observed phenotype. This suggested that the interaction between environmental and genetic factors plays an important role in tumor development in S. mediterranea Therefore, we further focused on the synergistic effects of Cd exposure and p53 knockdown (KD) at the cellular and molecular levels. Cd also produced a specific proteomic landscape in homeostatic animals, with 172 proteins differentially expressed, 43 of which were downregulated. Several of these proteins have tumor suppressor function in human and other animals, namely Wilms Tumor 1 Associated Protein (WT1), Heat Shock Protein 90 (HSP90), Glioma Pathogenesis-Related Protein 1 (GLIPR1) and Matrix Metalloproteinase B (Smed-MMPB). Both Glipr1 and MmpB KD produced large outgrowths, epidermal lesions and epidermal blisters. The epidermal blisters that formed as a consequence of Smed-MmpB KD were populated by smedwi1+ cells, many of which were actively proliferating, while large outgrowths contained ectopically differentiated structures, such as photoreceptors, nervous tissue and a small pharynx. In conclusion, Smed-MmpB is a planarian TSG that prevents stem cell proliferation and differentiation outside the proper milieu.

A role for telomere length and chromosomal damage in idiopathic pulmonary fibrosis

BACKGROUND

Idiopathic pulmonary fibrosis is a fatal lung disease characterized by a progressive formation of fibroblastic foci in the interstitium. This disease is strongly associated with telomere dysfunction but the extent of telomere shortening and consequent chromosomal damage within IPF lungs and with regional disease severity remains unknown.

METHODS

Explanted IPF lungs (n = 10) were collected from transplant surgeries with six samples per lung analysed to capture the regional heterogeneity ranging from mild to severe disease. Non-used donor lungs (n = 6) were collected as "healthy" controls. Structural changes related to disease severity (microCT surface density), relative telomere length (real-time qPCR), and quantitative histology of chromosomal damage (γ-H2A.X) and extracellular matrix (elastin, total collagen, collagen 1, and collagen 3) were measured. A multivariate linear mixed-effects model controlling for subject was used to identify association of disease severity or fibrotic markers with telomere length and chromosomal damage.

RESULTS

We observed shorter telomere length (p = 0.001) and increased chromosomal damage (p = 0.018) in IPF lungs compared to controls. In IPF lungs, telomere length was associated with total collagen (p < 0.001) but not with structural changes of disease severity. Chromosomal damage was positively associated with increased elastin (p = 0.006) and negatively with structural disease severity (p = 0.046). Extensive γ-H2A.X staining was also present in airway epithelial cells.

CONCLUSIONS

Telomere length and chromosomal damage are involved in IPF with regional variation in telomere length and chromosomal damage associated with pathological changes in tissue structure and the extracellular matrix.

The first next-generation sequencing approach to the mitochondrial phylogeny of African monogenean parasites (Platyhelminthes: Gyrodactylidae and Dactylogyridae)

BACKGROUND

Monogenean flatworms are the main ectoparasites of fishes. Representatives of the species-rich families Gyrodactylidae and Dactylogyridae, especially those infecting cichlid fishes and clariid catfishes, are important parasites in African aquaculture, even more so due to the massive anthropogenic translocation of their hosts worldwide. Several questions on their evolution, such as the phylogenetic position of Macrogyrodactylus and the highly speciose Gyrodactylus, remain unresolved with available molecular markers. Also, diagnostics and population-level research would benefit from the development of higher-resolution genetic markers. We aim to offer genetic resources for work on African monogeneans by providing mitogenomic data of four species (two belonging to Gyrodactylidae, two to Dactylogyridae), and analysing their gene sequences and gene order from a phylogenetic perspective.

RESULTS

Using Illumina technology, the first four mitochondrial genomes of African monogeneans were assembled and annotated for the cichlid parasites Gyrodactylus nyanzae, Cichlidogyrus halli, Cichlidogyrus mbirizei (near-complete mitogenome) and the catfish parasite Macrogyrodactylus karibae (near-complete mitogenome). Complete nuclear ribosomal operons were also retrieved, as molecular vouchers. The start codon TTG is new for Gyrodactylus and for Dactylogyridae, as is the incomplete stop codon TA for Dactylogyridae. Especially the nad2 gene is promising for primer development. Gene order was identical for protein-coding genes and differed between the African representatives of these families only in a tRNA gene transposition. A mitochondrial phylogeny based on an alignment of nearly 12,500 bp including 12 protein-coding and two ribosomal RNA genes confirms that the Neotropical oviparous Aglaiogyrodactylus forficulatus takes a sister group position with respect to the other gyrodactylids, instead of the supposedly 'primitive' African Macrogyrodactylus. Inclusion of the African Gyrodactylus nyanzae confirms the paraphyly of Gyrodactylus. The position of the African dactylogyrid Cichlidogyrus is unresolved, although gene order suggests it is closely related to marine ancyrocephalines.

CONCLUSIONS

The amount of mitogenomic data available for gyrodactylids and dactylogyrids is increased by roughly one-third. Our study underscores the potential of mitochondrial genes and gene order in flatworm phylogenetics, and of next-generation sequencing for marker development for these non-model helminths for which few primers are available.