Extended automated quantification algorithm (AQuA) for targeted 1H NMR metabolomics of highly complex samples: application to plant root exudates

INTRODUCTION

The Automated Quantification Algorithm (AQuA) is a rapid and efficient method for targeted NMR-based metabolomics, currently optimised for blood plasma. AQuA quantifies metabolites from 1D-1H NMR spectra based on the height of only one signal per metabolite, which minimises the computational time and workload of the method without compromising the quantification accuracy.

OBJECTIVES

To develop a fast and computationally efficient extension of AQuA for quantification of selected metabolites in highly complex samples, with minimal prior sample preparation. In particular, the method should be capable of handling interferences caused by broad background signals.

METHODS

An automatic baseline correction function was combined with AQuA into an automated workflow, the extended AQuA, for quantification of metabolites in plant root exudate NMR spectra that contained broad background signals and baseline distortions. The approach was evaluated using simulations as well as a spike-in experiment in which known metabolite amounts were added to a complex sample matrix.

RESULTS

The extended AQuA enables accurate quantification of metabolites in 1D-1H NMR spectra with varying complexity. The method is very fast (< 1 s per spectrum) and can be fully automated.

CONCLUSIONS

The extended AQuA is an automated quantification method intended for 1D-1H NMR spectra containing broad background signals and baseline distortions. Although the method was developed for plant root exudates, it should be readily applicable to any NMR spectra displaying similar issues as it is purely computational and applied to NMR spectra post-acquisition.

Planned dose of intensity modulated proton beam therapy versus volumetric modulated arch therapy to tooth-bearing regions

BACKGROUND

Intensity modulated proton beam therapy (IMPT) for head and neck cancer offers dosimetric benefits for the organs at risk when compared to photon-based volumetric modulated arch therapy (VMAT). However, limited data exists about the potential benefits of IMPT for tooth-bearing regions. The aim of this study was to compare the IMPT and VMAT radiation dosimetrics of the tooth-bearing regions in head and neck cancer patients. Also, we aimed to identify prognostic factors for a cumulative radiation dose of ≥40 Gy on the tooth-bearing areas, which is considered the threshold dose for prophylactic dental extractions.

METHODS

A total of 121 head and neck cancer patients were included in this retrospective analysis of prospectively collected data. We compared the average Dmean values of IMPT versus VMAT of multiple tooth-bearing regions in the same patients. Multivariate logistic regression analysis was performed for receiving a cumulative radiation dose of ≥40 Gy to the tooth-bearing regions (primary endpoint) in both VMAT and IMPT.

RESULTS

A lower Dmean was seen after applying IMPT to the tooth-bearing tumour regions (p < 0.001). Regarding VMAT, oral cavity tumours, T3-T4 tumours, molar regions in the mandible, and regions ipsilateral to the tumour were risk factors for receiving a cumulative radiation dose of ≥40 Gy.

CONCLUSIONS

IMPT significantly reduces the radiation dose to the tooth-bearing regions.

International multicentre observational study to assess the efficacy and safety of a 0·5 mg kg-1 per day starting dose of oral corticosteroids to treat bullous pemphigoid

BACKGROUND

European guidelines propose a 0·5 mg kg^-1 per day dose of oral prednisone as initial treatment for bullous pemphigoid (BP). We assessed the safety and efficacy of this regimen depending on BP extent and general condition of the patients.

METHODS

In a prospective international study, we consecutively included all patients diagnosed with BP. Patients received a 0·5 mg kg^-1 per day dose of prednisone, which was then gradually tapered 15 days after disease control, with the aim of stopping prednisone or maintaining minimal treatment (0·1 mg kg^-1 per day) within 6 months after the start of treatment. The two coprimary endpoints were control of disease activity at day 21 and 1-year overall survival. Disease severity was assessed according to the Bullous Pemphigoid Disease Area Index (BPDAI) score.

RESULTS

In total, 198 patients were included between 2015 and 2017. The final analysis comprised 190 patients with a mean age of 80·9 (SD 9·1) years. Control of disease activity was achieved at day 21 in 119 patients [62·6%, 95% confidence interval (CI) 55·3-69.5]; 18 of 24 patients (75%, 95% CI 53·3-90·2), 75 of 110 patients (68·8%, 95% CI 59·2-77·3) and 26 of 56 patients (46.4%, 95% CI 33·0-60·3) had mild, moderate and severe BP, respectively (P = 0·0218). A total of 30 patients died during the study. The overall Kaplan-Meier 1-year survival was 82·6% (95% CI 76·3-87·4) corresponding to 90·9%, 83·0% and 80·0% rates in patients with mild, moderate and severe BP, respectively (P = 0·5). Thresholds of 49 points for BPDAI score and 70 points for Karnofsky score yielded maximal Youden index values with respect to disease control at day 21 and 1-year survival, respectively.

CONCLUSIONS

A 0·5 mg kg^-1 per day dose of prednisone is a valuable therapeutic option in patients with mild or moderate BP whose general condition allows them to be autonomous.

Broad Diversity of Near-Infrared Single-Photon Emitters in Silicon

We report the detection of individual emitters in silicon belonging to seven different families of optically active point defects. These fluorescent centers are created by carbon implantation of a commercial silicon-on-insulator wafer usually employed for integrated photonics. Single photon emission is demonstrated over the 1.1-1.55  μm range, spanning the O and C telecom bands. We analyze their photoluminescence spectra, dipolar emissions, and optical relaxation dynamics at 10 K. For a specific family, we show a constant emission intensity at saturation from 10 K to temperatures well above the 77 K liquid nitrogen temperature. Given the advanced control over nanofabrication and integration in silicon, these individual artificial atoms are promising systems to investigate for Si-based quantum technologies.

Fluorine-based color centers in diamond

We report on the creation and characterization of the luminescence properties of high-purity diamond substrates upon F ion implantation and subsequent thermal annealing. Their room-temperature photoluminescence emission consists of a weak emission line at 558 nm and of intense bands in the 600–750 nm spectral range. Characterization at liquid He temperature reveals the presence of a structured set of lines in the 600–670 nm spectral range. We discuss the dependence of the emission properties of F-related optical centers on different experimental parameters such as the operating temperature and the excitation wavelength. The correlation of the emission intensity with F implantation fluence, and the exclusive observation of the afore-mentioned spectral features in F-implanted and annealed samples provides a strong indication that the observed emission features are related to a stable F-containing defective complex in the diamond lattice.

Vectorial calibration of superconducting magnets with a quantum magnetic sensor

Cryogenic vector magnet systems make it possible to study the anisotropic magnetic properties of materials without mechanically rotating the sample but by electrically tilting and turning the magnetic field. Vector magnetic fields generated inside superconducting vector magnets are generally measured with three Hall sensors. These three probes must be calibrated over a range of temperatures, and the temperature-dependent calibrations cannot be easily carried out inside an already magnetized superconducting magnet because of remaining magnetic fields. A single magnetometer based on an ensemble of nitrogen vacancy (NV) centers in diamond is proposed to overcome these limitations. The quenching of the photoluminescence intensity emitted by NV centers can determine the field in the remanent state of the solenoids and allows an easy and fast canceling of the residual magnetic field. Once the field is reset to zero, the calibration of this magnetometer can be performed in situ by a single measurement of an optically detected magnetic resonance spectrum. Thereby, these magnetometers do not require any additional temperature-dependent calibrations outside the magnet and offer the possibility to measure vector magnetic fields in three dimensions with a single sensor. Its axial alignment is given by the crystal structure of the diamond host, which increases the accuracy of the field orientation measured with this sensor, compared to the classical arrangement of three Hall sensors. It is foreseeable that the magnetometer described here has the potential to be applied in various fields in the future, such as the characterization of ferromagnetic core solenoids or other magnetic arrangements.

Genetic, Epigenetic and Phenotypic Diversity of Four Bacillus velezensis Strains Used for Plant Protection or as Probiotics

Bacillus velezensis strains are applied as ecologically safe biopesticides, plant growth promoting rhizobacteria (PGPR), and in veterinary probiotics. They are abundant in various environments including soil, plants, marine habitats, the intestinal micro-flora, etc. The mechanisms underlying this adaptive plasticity and bioactivity are not well understood, nor is it clear why several strains outperform other same species isolates by their bioactivities. The main objective of this work was to demonstrate versatility of bioactivities and lifestyle strategies of the selected B. velezensis strains suitable to serve as model organisms in future studies. Here, we performed a comparative study of newly sequenced genomes of four B. velezensis isolates with distinct phenotypes and isolation origin, which were assessed by RNA sequencing under the effect of root exudate stimuli and profiled by epigenetic modifications of chromosomal DNA. Among the selected strains, UCMB5044 is an oligotrophic PGPR strain adapted to nutrient poor desert soils. UCMB5113 and At1 are endophytes that colonize plants and require nutrient rich media. In contrast, the probiotic strain, UCMB5007, is a copiotroph, which shows no propensity to colonize plants. PacBio and Illumina sequencing approaches were used to generate complete genome assemblies, tracing epigenetic modifications, and determine gene expression profiles. All sequence data was deposited at NCBI. The strains, UCMB5113 and At1, show 99% sequence identity and similar phenotypes despite being isolated from geographically distant regions. UCMB5007 and UCMB5044 represent another group of organisms with almost identical genomes but dissimilar phenotypes and plant colonization propensity. The two plant associated strains, UCMB5044 and UCMB5113, share 398 genes putatively associated with root colonization, which are activated by exposure to maize root exudates. In contrast, UCMB5007 did not respond to root exudate stimuli. It was hypothesized that alterations in the global methylation pattern and some other epigenetic modifications enable adaptation of strains to different habitats and therefore may be of importance in terms of the biotechnological applicability of these bacteria. Contrary, the ability to grow on root exudates as a sole source of nutrients or a strong antagonism against phytopathogens showed by the strains in vitro cannot be considered as good predictors of PGPR activities.

Bacillus velezensis 5113 Induced Metabolic and Molecular Reprogramming during Abiotic Stress Tolerance in Wheat

Abiotic stresses are main limiting factors for agricultural production around the world. Plant growth promoting rhizobacteria (PGPR) have been shown to improve abiotic stress tolerance in several plants. However, the molecular and physiological changes connected with PGPR priming of stress management are poorly understood. The present investigation aimed to explore major metabolic and molecular changes connected with the ability of Bacillus velezensis 5113 to mediate abiotic stress tolerance in wheat. Seedlings treated with Bacillus were exposed to heat, cold/freezing or drought stress. Bacillus improved wheat survival in all stress conditions. SPAD readings showed higher chlorophyll content in 5113-treated stressed seedlings. Metabolite profiling using NMR and ESI-MS provided evidences for metabolic reprograming in 5113-treated seedlings and showed that several common stress metabolites were significantly accumulated in stressed wheat. Two-dimensional gel electrophoresis of wheat leaves resolved more than 300 proteins of which several were differentially expressed between different treatments and that cold stress had a stronger impact on the protein pattern compared to heat and drought. Peptides maps or sequences were used for database searches which identified several homologs. The present study suggests that 5113 treatment provides systemic effects that involve metabolic and regulatory functions supporting both growth and stress management.

Identifying potential molecular factors involved in Bacillus amyloliquefaciens 5113 mediated abiotic stress tolerance in wheat

Abiotic stressors are main limiting factors for agricultural production around the world. Plant growth-promoting bacteria have been successfully used to improve abiotic stress tolerance in several crops including wheat. However, the molecular changes involved in the improvement of stress management are poorly understood. The present investigation addressed some molecular factors involved in bacterially induced plant abiotic stress responses by identifying differentially expressed genes in wheat (Triticum aestivum) seedlings treated with the beneficial bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5113 prior to challenge with abiotic stress conditions such as heat, cold or drought. cDNA-AFLP analysis revealed differential expression of more than 200 transcript-derived fragments (TDFs) in wheat leaves. Expression of selected TDFs was confirmed using RT-PCR. DNA sequencing of 31 differentially expressed TDFs revealed significant homology with both known and unknown genes in database searches. Virus-induced gene silencing of two abscisic acid-related TDFs showed different effects upon heat and drought stress. We conclude that treatment with B. amyloliquefaciens 5113 caused molecular modifications in wheat in order to induce tolerance against heat, cold and drought stress. Bacillus treatment provides systemic effects that involve metabolic and regulatory functions supporting both growth and stress management.

Characterization of aluminum, aluminum oxide and titanium dioxide nanomaterials using a combination of methods for particle surface and size analysis

The application of appropriate analytical techniques is essential for nanomaterial (NM) characterization. In this study, we compared different analytical techniques for NM analysis. Regarding possible adverse health effects, ionic and particulate NM effects have to be taken into account. As NMs behave quite differently in physiological media, special attention was paid to techniques which are able to determine the biosolubility and complexation behavior of NMs. Representative NMs of similar size were selected: aluminum (Al⁰) and aluminum oxide (Al₂O₃), to compare the behavior of metal and metal oxides. In addition, titanium dioxide (TiO₂) was investigated. Characterization techniques such as dynamic light scattering (DLS) and nanoparticle tracking analysis (NTA) were evaluated with respect to their suitability for fast characterization of nanoparticle dispersions regarding a particle's hydrodynamic diameter and size distribution. By application of inductively coupled plasma mass spectrometry in the single particle mode (SP-ICP-MS), individual nanoparticles were quantified and characterized regarding their size. SP-ICP-MS measurements were correlated with the information gained using other characterization techniques, i.e. transmission electron microscopy (TEM) and small angle X-ray scattering (SAXS). The particle surface as an important descriptor of NMs was analyzed by X-ray diffraction (XRD). NM impurities and their co-localization with biomolecules were determined by ion beam microscopy (IBM) and confocal Raman microscopy (CRM). We conclude advantages and disadvantages of the different techniques applied and suggest options for their complementation. Thus, this paper may serve as a practical guide to particle characterization techniques.

The application of appropriate analytical techniques is essential for nanomaterial (NM) characterization.

Insights into the molecular basis of biocontrol of Brassica pathogens by Bacillus amyloliquefaciens UCMB5113 lipopeptides

BACKGROUND AND AIMS

Certain micro-organisms can improve plant protection against pathogens. The protective effect may be direct, e.g. due to antibiotic compounds, or indirect, by priming of plant defence as induced systemic resistance (ISR). The plant growth-promoting rhizobacterium Bacillus amyloliquefaciens UCMB5113 shows potential for disease management of oilseed rape. To investigate the mode of action of this protection, especially in relation to jasmonic acid-dependent ISR, Bacillus UCMB5113 was tested with Arabidopsis thaliana mutants and several important fungal pathogens of Brassica species.

METHODS

Secreted lipopeptide fractions from Bacillus UCMB5113, together with synthetic peptide mimics, were evaluated for their effects on fungal phytopathogens and A. thaliana . The structures of secreted lipopeptides were analysed using mass spectrometry. Plant mutants and reporter lines were used to identify signalling steps involved in disease suppression by lipopeptides.

KEY RESULTS

In plate tests Bacillus UCMB5113 and lipopeptide extracts suppressed growth of several fungal pathogens infecting Brassica plants. Separation of secreted lipopeptides using reversed-phase high-performance liquid chromatography revealed several fractions that inhibited fungal growth. Analysis by mass spectrometry identified the most potent compounds as novel linear forms of antifungal fengycins, with synthetic peptide mimics confirming the biological activity. Application of the lipopeptide extracts on Arabidopsis roots provided systemic protection against Alternaria brassicicola on leaves. Arabidopsis signalling mutants and PDF1.2 and VSP2 promoter-driven GUS lines indicated that the lipopeptide fraction involved jasmonic-acid-dependent host responses for suppression of fungal growth indicative of ISR.

CONCLUSIONS

The ability of Bacillus UCMB5113 to counteract pathogens using both antagonistic lipopeptides and through ISR provides a promising tool for sustainable crop production.

Analysis of plant growth-promoting properties of Bacillus amyloliquefaciens UCMB5113 using Arabidopsis thaliana as host plant

MAIN CONCLUSION

This study showed that Bacillus amyloliquefaciens UCMB5113 colonizing Arabidopsis roots changed root structure and promoted growth implying the usability of this strain as a novel tool to support sustainable crop production. Root architecture plays a crucial role for plants to ensure uptake of water, minerals and nutrients and to provide anchorage in the soil. The root is a dynamic structure with plastic growth and branching depending on the continuous integration of internal and environmental factors. The rhizosphere contains a complex microbiota, where some microbes can colonize plant roots and support growth and stress tolerance. Here, we report that the rhizobacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5113 stimulated the growth of Arabidopsis thaliana Col-0 by increased lateral root outgrowth and elongation and root-hair formation, although primary root elongation was inhibited. In addition, the growth of the above ground tissues was stimulated by UCMB5113. Specific hormone reporter gene lines were tested which suggested a role for at least auxin and cytokinin signaling during rhizobacterial modulation of Arabidopsis root architecture. UCMB5113 produced cytokinins and indole-3-acetic acid, and the formation of the latter was stimulated by root exudates and tryptophan. The plant growth promotion effect by UCMB5113 did not appear to depend on jasmonic acid in contrast to the disease suppression effect in plants. UCMB5113 exudates inhibited primary root growth, while a semi-purified lipopeptide fraction did not and resulted in the overall growth promotion indicating an interplay of many different bacterial compounds that affect the root growth of the host plant. This study illustrates that beneficial microbes interact with plants in root development via classic and novel signals.

Study of the negative magneto-resistance of single proton-implanted lithium-doped ZnO microwires

The magneto-transport properties of single proton-implanted ZnO and of Li(7%)-doped ZnO microwires have been studied. The as-grown microwires were highly insulating and not magnetic. After proton implantation the Li(7%) doped ZnO microwires showed a non-monotonous behavior of the negative magneto-resistance (MR) at temperature above 150 K. This is in contrast to the monotonous NMR observed below 50 K for proton-implanted ZnO. The observed difference in the transport properties of the wires is related to the amount of stable Zn vacancies created at the near surface region by the proton implantation and Li doping. The magnetic field dependence of the resistance might be explained by the formation of a magnetic/non-magnetic heterostructure in the wire after proton implantation.

Publisher's note. Identification of a novel synonymous mutation in the human β-ureidopropionase gene UPB1 affecting pre-mRNA splicing

β-Ureidopropionase is the third enzyme of the pyrimidine degradation pathway and it catalyzes the conversion of N-carbamyl-β-alanine and N-carbamyl-β-aminoisobutyric acid to β-alanine and β-aminoisobutyric acid, respectively, and ammonia and CO2. To date, only 16 genetically confirmed patients with a complete ß-ureidopropionase deficiency have been reported. Here, we report the clinical, biochemical, and molecular analysis of a newly identified patient with β-ureidopropionase deficiency. Mutation analysis of the UPB1 gene showed that the patient was compound heterozygous for a novel synonymous mutation c.93C>T (p.Gly31Gly) in exon 1 and a previously described missense mutation c.977G>A (p.Arg326Gln) in exon 9. The in silico predicted effect of the synonymous mutation p.Gly31Gly on pre-mRNA splicing was investigated using a minigene approach. Wild-type and the mutated minigene constructs, containing the entire exon 1, intron 1, and exon 2 of UPB1, yielded different splicing products after expression in HEK293 cells. The c.93C>T (p.Gly31Gly) mutation resulted in altered pre-mRNA splicing of the UPB1 minigene construct and a deletion of the last 13 nucleotides of exon 1. This deletion (r.92 104delGCAAGGAACTCAG) results in a frame shift and the generation of a premature stop codon (p.Lys32SerfsX31). Using a minigene approach, we have thus identified the first synonymous mutation in the UPB1 gene, creating a cryptic splice-donor site affecting pre-mRNA splicing.

Spectroscopy of surface-induced noise using shallow spins in diamond

We report on the noise spectrum experienced by few nanometer deep nitrogen-vacancy centers in diamond as a function of depth, surface coating, magnetic field and temperature. Analysis reveals a double-Lorentzian noise spectrum consistent with a surface electronic spin bath in the low frequency regime, along with a faster noise source attributed to surface-modified phononic coupling. These results shed new light on the mechanisms responsible for surface noise affecting shallow spins at semiconductor interfaces, and suggests possible directions for further studies. We demonstrate dynamical decoupling from the surface noise, paving the way to applications ranging from nanoscale NMR to quantum networks.

RETRACTED: Single-proton spin detection by diamond magnetometry

Extending magnetic resonance imaging to the atomic scale has been a long-standing aspiration, driven by the prospect of directly mapping atomic positions in molecules with three-dimensional spatial resolution. We report detection of individual, isolated proton spins by a nitrogen-vacancy (NV) center in a diamond chip covered by an inorganic salt. The single-proton identity was confirmed by the Zeeman effect and by a quantum coherent rotation of the weakly coupled nuclear spin. Using the hyperfine field of the NV center as an imaging gradient, we determined proton-NV distances of less than 1 nm.

Nuclear magnetic resonance spectroscopy with single spin sensitivity

Nuclear magnetic resonance spectroscopy and magnetic resonance imaging at the ultimate sensitivity limit of single molecules or single nuclear spins requires fundamentally new detection strategies. The strong coupling regime, when interaction between sensor and sample spins dominates all other interactions, is one such strategy. In this regime, classically forbidden detection of completely unpolarized nuclei is allowed, going beyond statistical fluctuations in magnetization. Here we realize strong coupling between an atomic (nitrogen-vacancy) sensor and sample nuclei to perform nuclear magnetic resonance on four (29)Si spins. We exploit the field gradient created by the diamond atomic sensor, in concert with compressed sensing, to realize imaging protocols, enabling individual nuclei to be located with Angstrom precision. The achieved signal-to-noise ratio under ambient conditions allows single nuclear spin sensitivity to be achieved within seconds.

Genome analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management

The Bacillus amyloliquefaciens subsp. plantarum strain UCMB5113 is a Gram-positive rhizobacterium that can colonize plant roots and stimulate plant growth and defense based on unknown mechanisms. This reinforcement of plants may provide protection to various forms of biotic and abiotic stress. To determine the genetic traits involved in the mechanism of plant-bacteria association, the genome sequence of UCMB5113 was obtained by assembling paired-end Illumina reads. The assembled chromosome of 3,889,532 bp was predicted to encode 3,656 proteins. Genes that potentially contribute to plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis and siderophore production were identified. Moreover, annotation identified putative genes responsible for non-ribosomal synthesis of secondary metabolites and genes supporting environment fitness of UCMB5113 including drug and metal resistance. A large number of genes encoding a diverse set of secretory proteins, enzymes of primary and secondary metabolism and carbohydrate active enzymes were found which reflect a high capacity to degrade various rhizosphere macromolecules. Additionally, many predicted membrane transporters provides the bacterium with efficient uptake capabilities of several nutrients. Although, UCMB5113 has the possibility to produce antibiotics and biosurfactants, the protective effect of plants to pathogens seems to be indirect and due to priming of plant induced systemic resistance. The availability of the genome enables identification of genes and their function underpinning beneficial interactions of UCMB5113 with plants.

Optimal strategies to identify aberrant intra-epithelial lymphocytes in refractory coeliac disease

INTRODUCTION

Different strategies have been developed to identify those refractory celiac disease (RCD) patients who are at risk to develop an enteropathy associated T-cell lymphoma (EATL). Flow cytometric analysis of intra-epithelial lymphocytes (IEL) with an aberrant phenotype is considered the golden standard but is not widely available. Immunohistochemistry (IHC) and T-cell receptor (TCR) rearrangement studies are commonly available but may lack sensitivity and specificity. Here, we compared the three different methods in the workup of patients suspected for RCD.

METHODS

Duodenal biopsies from control patient (n = 5), RCD patients with moderately increased aberrant IEL populations (20-50 %: n = 14), and RCD patients with high numbers of aberrant IEL (>50 %: n = 5) as determined by flow cytometry were analysed by IHC and TCR-γ chain rearrangement analysis. Three pathologists scored the slides independently.

RESULTS

Sensitivity of IHC and TCR-γ rearrangement analysis in RCD patients with high numbers of aberrant IELs was 100 and 71 %, respectively. RCD patients with aberrant cells between 25 and 50 % however, were missed by IHC and TCR in 50 and 57 % of cases, respectively. In addition, inter-rater reliability analysis of the IHC scoring revealed coder-pair Kappa coefficients between 0.28 and 0.85.

CONCLUSION

Immunohistochemistry and to a lesser extent TCR-γ clonality analysis are sensitive in identifying patients with high numbers of aberrant IEL populations, yet miss half of RCD patients with moderately increased numbers. In addition, IHC has a high inter-observer variability. Therefore, patients suspected for RCD should undergo flow cytometric analysis of the duodenum.

Identification of a novel synonymous mutation in the human β -Ureidopropionase Gene UPB1 affecting pre-mRNA splicing

β-Ureidopropionase is the third enzyme of the pyrimidine degradation pathway and it catalyzes the conversion of N-carbamyl-β-alanine and N-carbamyl-β-aminoisobutyric acid to β-alanine and β-aminoisobutyric acid, respectively, and ammonia and CO2. To date, only 16 genetically confirmed patients with a complete ß-ureidopropionase deficiency have been reported. Here, we report the clinical, biochemical, and molecular analysis of a newly identified patient with β-ureidopropionase deficiency. Mutation analysis of the UPB1 gene showed that the patient was compound heterozygous for a novel synonymous mutation c.93C >T (p.Gly31Gly) in exon 1 and a previously described missense mutation c.977G >A (p.Arg326Gln) in exon 9. The in silico predicted effect of the synonymous mutation p.Gly31Gly on pre-mRNA splicing was investigated using a minigene approach. Wild-type and the mutated minigene constructs, containing the entire exon 1, intron 1, and exon 2 of UPB1, yielded different splicing products after expression in HEK293 cells. The c.93C >T (p.Gly31Gly) mutation resulted in altered pre-mRNA splicing of the UPB1 minigene construct and a deletion of the last 13 nucleotides of exon 1. This deletion (r.92_104delGCAAGGAACTCAG) results in a frame shift and the generation of a premature stop codon (p.Lys32SerfsX31). Using a minigene approach, we have thus identified the first synonymous mutation in the UPB1 gene, creating a cryptic splice-donor site affecting pre-mRNA splicing.

Complete genome sequence of a plant associated bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5033

Bacillus amyloliquefaciens subsp. plantarum UCMB5033 is of special interest for its ability to promote host plant growth through production of stimulating compounds and suppression of soil borne pathogens by synthesizing antibacterial and antifungal metabolites or priming plant defense as induced systemic resistance. The genome of B. amyloliquefaciens UCMB5033 comprises a 4,071,167 bp long circular chromosome that consists of 3,912 protein-coding genes, 86 tRNA genes and 10 rRNA operons.

Impact of bacterial priming on some stress tolerance mechanisms and growth of cold stressed wheat seedlings

The potential to enhance growth of cold stressed wheat by seed treatment (priming) with the beneficial bacteria <em>Bacillus</em> <em>amyloliquefaciens</em> 5113 and <em>Azospirillum</em> <em>brasilense</em> NO40 were tested. Results showed an improved ability of bacteria-treated seedlings to survive at −5°C up to 12 h. Cold stress increased transcript levels of three stress marker genes and increased activity for the ascorbate-glutathione redox enzymes. However, primed and stressed seedlings generally showed smaller effects on the stress markers correlating with better growth and improved stress tolerance. Bacterial priming to improve crop plant performance at low temperature seems a useful strategy to explore further.

Somatic copy number changes in DPYD are associated with lower risk of recurrence in triple-negative breast cancers

BACKGROUND

Genomic rearrangements at the fragile site FRA1E may disrupt the dihydropyrimidine dehydrogenase gene (DPYD) which is involved in 5-fluorouracil (5-FU) catabolism. In triple-negative breast cancer (TNBC), a subtype of breast cancer frequently deficient in DNA repair, we have investigated the susceptibility to acquire copy number variations (CNVs) in DPYD and evaluated their impact on standard adjuvant treatment.

METHODS

DPYD CNVs were analysed in 106 TNBC tumour specimens using multiplex ligation-dependent probe amplification (MLPA) analysis. Dihydropyrimidine dehydrogenase (DPD) expression was determined by immunohistochemistry in 146 tumour tissues.

RESULTS

In TNBC, we detected 43 (41%) tumour specimens with genomic deletions and/or duplications within DPYD which were associated with higher histological grade (P=0.006) and with rearrangements in the DNA repair gene BRCA1 (P=0.007). Immunohistochemical analysis revealed low, moderate and high DPD expression in 64%, 29% and 7% of all TNBCs, and in 40%, 53% and 7% of TNBCs with DPYD CNVs, respectively. Irrespective of DPD protein levels, the presence of CNVs was significantly related to longer time to progression in patients who had received 5-FU- and/or anthracycline-based polychemotherapy (hazard ratio=0.26 (95% CI: 0.07-0.91), log-rank P=0.023; adjusted for tumour stage: P=0.037).

CONCLUSION

Genomic rearrangements in DPYD, rather than aberrant DPD protein levels, reflect a distinct tumour profile associated with prolonged time to progression upon first-line chemotherapy in TNBC.

Glycoalkaloid and calystegine levels in table potato cultivars subjected to wounding, light, and heat treatments

Potato tubers naturally contain a number of defense substances, some of which are of major concern for food safety. Among these substances are the glycoalkaloids and calystegines. We have here analyzed levels of glycoalkaloids (α-chaconine and α-solanine) and calystegines (A₃, B₂, and B₄) in potato tubers subjected to mechanical wounding, light exposure, or elevated temperature: stress treatments that are known or anticipated to induce glycoalkaloid levels. Basal glycoalkaloid levels in tubers varied between potato cultivars. Wounding and light exposure, but not heat, increased tuber glycoalkaloid levels, and the relative response differed among the cultivars. Also, calystegine levels varied between cultivars, with calystegine B4 showing the most marked variation. However, the total calystegine level was not affected by wounding or light exposure. The results demonstrate a strong variation among potato cultivars with regard to postharvest glycoalkaloid increases, and they suggest that the biosynthesis of glycoalkaloids and calystegines occurs independently of each other.

Nuclear magnetic resonance spectroscopy on a (5-nanometer)3 sample volume

Application of nuclear magnetic resonance (NMR) spectroscopy to nanoscale samples has remained an elusive goal, achieved only with great experimental effort at subkelvin temperatures. We demonstrated detection of NMR signals from a (5-nanometer)(3) voxel of various fluid and solid organic samples under ambient conditions. We used an atomic-size magnetic field sensor, a single nitrogen-vacancy defect center, embedded ~7 nanometers under the surface of a bulk diamond to record NMR spectra of various samples placed on the diamond surface. Its detection volume consisted of only 10(4) nuclear spins with a net magnetization of only 10(2) statistically polarized spins.

ML3: a novel regulator of herbivory-induced responses in Arabidopsis thaliana

ML (MD2-related lipid recognition) proteins are known to enhance innate immune responses in mammals. This study reports the analysis of the putative ML gene family in Arabidopsis thaliana and suggests a role for the ML3 gene in herbivory-associated responses in plants. Feeding by larvae of the Lepidopteran generalist herbivore Spodoptera littoralis and larvae of the specialist herbivore Plutella xylostella activated ML3 transcription in leaf tissues. ML3 loss-of-function Arabidopsis plants were compromised in the upregulation of herbivory-induced genes and displayed a semi-dwarf phenotype. Herbivory bioassays showed that larvae of S. littoralis fed on ml3 mutant plants gained more weight compared to larvae fed on wild-type plants while larvae of P. xylostella did not show any significant difference. Virus-induced gene silencing of ML3 expression in plants compromised in jasmonic acid (JA) and salicylic acid (SA) signalling revealed a complex role of ML3 in JA/defence signalling affecting both JA- and SA-dependent responses. The data suggest that ML3 is involved in herbivory-mediated responses in Arabidopsis and that it has a potential role in herbivory-associated molecular pattern recognition.

Age at onset of non-affective psychosis in relation to cannabis use, other drug use and gender

BACKGROUND

Cannabis use is associated with an earlier age at onset of psychotic illness. The aim of the present study was to examine whether this association is confounded by gender or other substance use in a large cohort of patients with a non-affective psychotic disorder.

METHOD

In 785 patients with a non-affective psychotic disorder, regression analysis was used to investigate the independent effects of gender, cannabis use and other drug use on age at onset of first psychosis.

RESULTS

Age at onset was 1.8 years earlier in cannabis users compared to non-users, controlling for gender and other possible confounders. Use of other drugs did not have an additional effect on age at onset when cannabis use was taken into account. In 63.5% of cannabis-using patients, age at most intense cannabis use preceded the age at onset of first psychosis. In males, the mean age at onset was 1.3 years lower than in females, controlling for cannabis use and other confounders.

CONCLUSIONS

Cannabis use and gender are independently associated with an earlier onset of psychotic illness. Our findings also suggest that cannabis use may precipitate psychosis. More research is needed to clarify the neurobiological factors that make people vulnerable to this precipitating effect of cannabis.

Optical detection of a single rare-earth ion in a crystal

Rare-earth-doped laser materials show strong prospects for quantum information storage and processing, as well as for biological imaging, due to their high-Q 4f↔4f optical transitions. However, the inability to optically detect single rare-earth dopants has prevented these materials from reaching their full potential. Here we detect a single photostable Pr(3+) ion in yttrium aluminium garnet nanocrystals with high contrast photon antibunching by using optical upconversion of the excited state population of the 4f↔4f optical transition into ultraviolet fluorescence. We also demonstrate on-demand creation of Pr(3+) ions in a bulk yttrium aluminium garnet crystal by patterned ion implantation. Finally, we show generation of local nanophotonic structures and cell death due to photochemical effects caused by upconverted ultraviolet fluorescence of praseodymium-doped yttrium aluminium garnet in the surrounding environment. Our study demonstrates versatile use of rare-earth atomic-size ultraviolet emitters for nanoengineering and biotechnological applications.

Cognitive alterations in patients with non-affective psychotic disorder and their unaffected siblings and parents

OBJECTIVE

The purpose of this study was to examine a range of cognitive measures as candidate phenotypic liability markers for psychosis in a uniquely large sample of patients with psychosis, their unaffected relatives and control subjects.

METHOD

Patients with non-affective psychosis (n = 1093), their unaffected siblings (n = 1044), parents (n = 911), and controls (n = 587) completed a comprehensive cognitive test battery. Cognitive functioning was compared using tests of verbal learning and memory, attention/vigilance, working memory, processing speed, reasoning and problem solving, acquired knowledge, and social cognition. Age- and gender-adjusted z-scores were compared between groups using mixed-model analyses of covariance. Clinically relevant impairment (-1 and -2 SD from control mean) was compared between subject groups.

RESULTS

Patients performed significantly worse than controls in all cognitive domains (z-range -0.26 to -1.34). Siblings and parents showed alterations for immediate verbal learning, processing speed, reasoning and problem solving, acquired knowledge, and working memory (z-range -0.22 to -0.98). Parents showed additional alterations for social cognition. Prevalence of clinically relevant impairment in relatives ranged from 50% (-1 SD criterion) to 10% (-2 SD criterion).

CONCLUSION

Cognitive functioning is a candidate intermediate phenotype given significant small to large alterations in patients and intermediate alterations in first-degree relatives.

Characterization of a novel β-thioglucosidase CpTGG1 in Carica papaya and its substrate-dependent and ascorbic acid-independent O-β-glucosidase activity

Plant thioglucosidases are the only known S-glycosidases in the large superfamily of glycosidases. These enzymes evolved more recently and are distributed mainly in Brassicales. Thioglucosidase research has focused mainly on the cruciferous crops due to their economic importance and cancer preventive benefits. In this study, we cloned a novel myrosinase gene, CpTGG1, from Carica papaya Linnaeus. and showed that it was expressed in the aboveground tissues in planta. The recombinant CpTGG1 expressed in Pichia pastoris catalyzed the hydrolysis of both sinigrin and glucotropaeolin (the only thioglucoside present in papaya), showing that CpTGG1 was indeed a functional myrosinase gene. Sequence alignment analysis indicated that CpTGG1 contained all the motifs conserved in functional myrosinases from crucifers, except for two aglycon-binding motifs, suggesting substrate priority variation of the non-cruciferous myrosinases. Using sinigrin as substrate, the apparent K(m) and V(max) values of recombinant CpTGG1 were 2.82 mM and 59.9 μmol min⁻¹ mg protein⁻¹ , respectively. The K(cat) /K(m) value was 23 s⁻¹ mM⁻¹ . O-β-glucosidase activity towards a variety of substrates were tested, CpTGG1 displayed substrate-dependent and ascorbic acid-independent O-β-glucosidase activity towards 2-nitrophenyl-β-D-glucopyranoside and 4-nitrophenyl-β-D-glucopyranoside, but was inactive towards glucovanillin and n-octyl-β-D-glucopyranoside. Phylogenetic analysis indicated CpTGG1 belongs to the MYR II subfamily of myrosinases.

Identification of purine nucleoside phosphorylase deficiency in dried blood spots by a non-radiochemical assay using reversed-phase high-performance liquid chromatography

Purine nucleoside phosphorylase (PNP) deficiency results in severe T cell dysfunction and hypouricemia. An assay to measure PNP activity in dried blood spots was developed using reversed-phase HPLC. The assay was linear with reaction times between 5 and 12.5 minutes, and protein concentrations ranging from 0.4 to 1.8 mg/ml. The intra-assay CV and the inter-assay CV for the complete assay was <3.6%. The PNP activity in a control blood spot, stored at 4 degrees C, remained stable for at least one year. In a patient suffering from a PNP deficiency, the residual PNP activity was only 0.3% compared to that observed in controls (1431 +/- 238 nmol/mg/h, n = 114). The PNP activity (483 +/- 35 nmol/mg/h, n = 3) in heterozygotes for the c.614A > C mutation (p.E205A) in the PNP gene was 34% compared to controls. Thus, the analysis of the PNP activity in blood spots can readily detect patients with a PNP deficiency.

Determination of adenosine deaminase activity in dried blood spots by a nonradiochemical assay using reversed-phase high-performance liquid chromatography

Adenosine deaminase (ADA) deficiency is a rare metabolic disease causing severe combined immunodeficiency (SCID). An assay to determine ADA activity in dried blood spots was developed using reversed-phase HPLC. The assay was linear with reaction times up to at least 4 hours, and protein concentrations up to at least 2.2 mg/ml. The intra-assay CV and the inter-assay CV for the complete assay was 3.5 and 8.4%, respectively. The ADA activity in a control blood spot, stored at 4 degrees C, remained stable for at least one year. Only a slightly decreased ADA activity (35 +/- 13 nmol/mg/h, n = 4) was observed in heterozygotes for a c.704G > A mutation in the ADA gene when compared to that observed in controls (41 +/- 13 nmol/mg/h, n = 108). In addition, increased ADA activity as found in a rare form of congenital anemia can be assessed, as observed in a bloodspot from a patient diagnosed with Diamond Blackfan anemia (ADA activity 150 nmol/mg/h).

Dihydropyrimidine dehydrogenase deficiency caused by a novel genomic deletion c.505_513del of DPYD

Dihydropyrimidine dehydrogenase (DPD) deficiency is an autosomal recessive disorder of the pyrimidine degradation pathway. In a patient presenting with convulsions, psychomotor retardation and Reye like syndrome, strongly elevated levels of uracil and thymine were detected in urine. No DPD activity could be detected in peripheral blood mononuclear cells. Analysis of the gene encoding DPD (DPYD) showed that the patient was homozygous for a novel c.505_513del (p.169_171del) mutation in exon 6 of DPYD.