Multi-omics data integration reveals link between epigenetic modifications and gene expression in sugar beet (Beta vulgaris subsp. vulgaris) in response to cold.

BACKGROUND: DNA methylation is thought to influence the expression of genes, especially in response to changing environmental conditions and developmental changes. Sugar beet (Beta vulgaris ssp. vulgaris), and other biennial or perennial plants are inevitably exposed to fluctuating temperatures throughout their lifecycle and might even require such stimulus to acquire floral competence. Therefore, plants such as beets, need to fine-tune their epigenetic makeup to ensure phenotypic plasticity towards changing environmental conditions while at the same time steering essential developmental processes. Different crop species may show opposing reactions towards the same abiotic stress, or, vice versa, identical species may respond differently depending on the specific kind of stress. RESULTS: In this study, we investigated common effects of cold treatment on genome-wide DNA methylation and gene expression of two Beta vulgaris accessions via multi-omics data analysis. Cold exposure resulted in a pronounced reduction of DNA methylation levels, which particularly affected methylation in CHH context (and to a lesser extent CHG) and was accompanied by transcriptional downregulation of the chromomethyltransferase CMT2 and strong upregulation of several genes mediating active DNA demethylation. CONCLUSION: Integration of methylomic and transcriptomic data revealed that, rather than methylation having directly influenced expression, epigenetic modifications correlated with changes in expression of known players involved in DNA (de)methylation. In particular, cold triggered upregulation of genes putatively contributing to DNA demethylation via the ROS1 pathway. Our observations suggest that these transcriptional responses precede the cold-induced global DNA-hypomethylation in non-CpG, preparing beets for additional transcriptional alterations necessary for adapting to upcoming environmental changes.

Vernalization Alters Sink and Source Identities and Reverses Phloem Translocation from Taproots to Shoots in Sugar Beet.

During their first year of growth, overwintering biennial plants transport Suc through the phloem from photosynthetic source tissues to storage tissues. In their second year, they mobilize carbon from these storage tissues to fuel new growth and reproduction. However, both the mechanisms driving this shift and the link to reproductive growth remain unclear. During vegetative growth, biennial sugar beet (Beta vulgaris) maintains a steep Suc concentration gradient between the shoot (source) and the taproot (sink). To shift from vegetative to generative growth, they require a chilling phase known as vernalization. We studied sugar beet sink-source dynamics upon vernalization and showed that before flowering, the taproot underwent a reversal from a sink to a source of carbohydrates. This transition was induced by transcriptomic and functional reprogramming of sugar beet tissue, resulting in a reversal of flux direction in the phloem. In this transition, the vacuolar Suc importers and exporters TONOPLAST SUGAR TRANSPORTER2;1 and SUCROSE TRANSPORTER4 were oppositely regulated, leading to the mobilization of sugars from taproot storage vacuoles. Concomitant changes in the expression of floral regulator genes suggest that these processes are a prerequisite for bolting. Our data will help both to dissect the metabolic and developmental triggers for bolting and to identify potential targets for genome editing and breeding.

Specificity and reproducibility of nasal biomarkers in patients with allergic rhinitis after allergen challenge chamber exposure.

BACKGROUND: Allergic rhinitis is an inflammatory disease that causes cellular influx and mediator release in the nose. These inflammatory changes might be used as nasal biomarkers to assess the efficacy of novel anti-allergic treatments. OBJECTIVE: To assess the specificity and reproducibility of nasal biomarkers in patients with allergic rhinitis after grass pollen exposure in an allergen challenge chamber. METHODS: In a monocenter pilot study, 15 patients with allergic rhinitis and 19 healthy individuals underwent two 4-hour Dactylis glomerate pollen challenges in the challenge chamber with an interval of 21 days. Before challenge, on exit, and after 2 and 22 hours, a nasal lavage was performed and nasal secretions were collected on filter paper to determine a wide panel of cells and mediators. Furthermore, total nasal symptom score, nasal flow, and nasal nitric oxide were measured. RESULTS: Pollen exposure significantly increased eosinophil, interleukin (IL) 5, IL-6, IL-13, and macrophage inflammatory protein 1ß levels in allergic patients but not in healthy individuals. The effect could be reproduced for eosinophils, IL-5, IL-6, and macrophage inflammatory protein 1ß after the second allergen challenge. By contrast, the IL-13 levels were higher and eotaxin levels first increased after repetitive allergen challenge. There was no correlation between total nasal symptom score and elevated cell or cytokine levels. Nasal nitric oxide levels were nonspecifically elevated in both patients with allergy and healthy controls. CONCLUSION: A subset of cellular and soluble biomarkers in nasal lavage and secretion reveals specificity and reproducibility in patients with allergic rhinitis. These can be used to measure the immunologic efficacy of antiallergic treatments in an allergen challenge chamber. Carryover effects attributable to priming must be considered when designing cross-over studies. TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT00297843.

Functional testing of an inhalable nanoparticle based influenza vaccine using a human precision cut lung slice technique.

Annual outbreaks of influenza infections, caused by new influenza virus subtypes and high incidences of zoonosis, make seasonal influenza one of the most unpredictable and serious health threats worldwide. Currently available vaccines, though the main prevention strategy, can neither efficiently be adapted to new circulating virus subtypes nor provide high amounts to meet the global demand fast enough. New influenza vaccines quickly adapted to current virus strains are needed. In the present study we investigated the local toxicity and capacity of a new inhalable influenza vaccine to induce an antigen-specific recall response at the site of virus entry in human precision-cut lung slices (PCLS). This new vaccine combines recombinant H1N1 influenza hemagglutinin (HAC1), produced in tobacco plants, and a silica nanoparticle (NP)-based drug delivery system. We found no local cellular toxicity of the vaccine within applicable concentrations. However higher concentrations of NP (≥10(3) µg/ml) dose-dependently decreased viability of human PCLS. Furthermore NP, not the protein, provoked a dose-dependent induction of TNF-α and IL-1ß, indicating adjuvant properties of silica. In contrast, we found an antigen-specific induction of the T cell proliferation and differentiation cytokine, IL-2, compared to baseline level (152±49 pg/mg vs. 22±5 pg/mg), which could not be seen for the NP alone. Additionally, treatment with 10 µg/ml HAC1 caused a 6-times higher secretion of IFN-γ compared to baseline (602±307 pg/mg vs. 97±51 pg/mg). This antigen-induced IFN-γ secretion was further boosted by the adjuvant effect of silica NP for the formulated vaccine to a 12-fold increase (97±51 pg/mg vs. 1226±535 pg/mg). Thus we were able to show that the plant-produced vaccine induced an adequate innate immune response and re-activated an established antigen-specific T cell response within a non-toxic range in human PCLS at the site of virus entry.

Pollen starch granules in bronchial inflammation.

BACKGROUND: Pollen grains with a diameter of more than 10 µm preferentially deposit in the upper airways. Their contribution to lower airway inflammation is unclear. One hypothesis is that lower airway inflammation is mainly caused by allergen containing pollen starch granules, which are released from the pollen grains and can easily enter the peripheral airways because of their smaller size. OBJECTIVE: To investigate the differential effect of pollen grains and pollen starch granules on nasal symptoms and lower airway inflammation. METHODS: In a 2-period crossover design, 30 patients with allergic rhinitis and mild intermittent asthma underwent 2 allergen challenges on consecutive days in an environmental challenge chamber with either a mixture of pollen grains plus starch granules or starch granules only. End points were the total nasal symptom score (TNSS), nasal secretion weight, nasal flow, spirometry, and exhaled nitric oxide (eNO). RESULTS: The presence of pollen grains had a significant and considerable effect on increase in TNSS and secretion weight and on decrease in nasal flow. Starch granules alone only had minimal effects on nasal symptoms. Challenges with starch granules significantly increased eNO. Pollen had no effect on eNO. CONCLUSION: Pollen grains cause nasal symptoms but do not augment lower airway inflammation, whereas starch granules trigger lower airway inflammation but hardly induce nasal symptoms.

Impact of food and herbal medication on calcineurin inhibitor dose in renal transplant patients: a cross-sectional study.

The incidence and severity of interactions of herbal products with calcineurin inhibitor (CNI) metabolism in renal transplant recipients have not been systematically investigated. These patients have a high rate of herbal product consumption, including products interfering with CNI metabolism. The study aimed at identifying an impact of herbs and foods on CNI metabolism in a cohort of renal transplant recipients by conducting dietary interviews (1) in patients with very low and high CNI maintenance dose requirements and (2) by retrospective analysis of unexplained marked deviations from CNI baseline trough levels. Of 73 renal transplant recipients, 59 were treated with a CNI-based immunosuppressive regimen. Seven patients with an exceptionally high or low CNI dose were interviewed. Five of these seven patients had not consumed any plant product with known influence on CNI metabolism. In one patient chicory-coffee and bitter chocolate had been suspected as contributing to high CNI dose requirement, but the dose could not be lowered after discontinuation of these foods. Participating nephrologists reported three as yet unexplained temporary deviations from baseline CNI trough levels, of which two could be linked to newly started consumption of high volumes of herbal teas and the other to St. John's wort. Consumption of herbal products within the study cohort had no detectable impact on maintenance doses of CNI. However, herbal products, and specifically teas when consumed by the liter, could be linked to temporary strong deviations from CNI trough levels. The study demonstrates that as yet unnoticed herbal interactions with CNI can be detected by detailed dietary analysis, but that the overall impact on maintenance doses of CNI appears to be low.

Complementary and alternative medications consumed by renal patients in southern Germany.

BACKGROUND: Complementary and alternative medicine (CAM) is frequently used in the general population, yet scant data are available regarding the prevalence of these medications in patients with end-stage renal disease (ESRD). OBJECTIVE: To survey patients with ESRD regarding their use of CAM and health foods. METHODS: Consecutive patients treated with dialysis or renal transplantation for ESRD were approached by nephrologists of 5 renal centers to report their usage of and knowledge on CAM and health foods by answering a questionnaire. Of 180 approached patients, 164 returned completed questionnaires for analysis. RESULTS: Fifty-seven percent of dialysis patients and 49% of transplant patients reported to be regular CAM-consumers. CAM consumption was positively associated with female sex and negatively with diabetes as comorbidity. Forty-one different CAM products had been named, with mineral supplements and vitamins ranking first. Besides CAM, many renal patients had regularly consumed herbal teas and citrus-juices (50% and 35%, respectively). Close to 40% of the documented CAM/health food consumptions have potential risks for patients because of constituents that either accumulate in renal failure or interact with pharmaceutical medication. However, only about 50% of dialysis patients, but 73% of transplant patients used to inform their physicians about CAM consumption (P = .005). Awareness about interaction risks linked to CAM was especially low in dialysis patients when compared to transplant patients (39% versus 78%, P < .0001) and increased when physicians had routinely questioned patients about their CAM consumption. Currently, however, patients reported that only a minority of physicians had taken an active interest into consumption of these substances. CONCLUSION: Consumption of CAM and health food is common among renal patients. Physicians are currently not adequately informed about CAM consumption by their patients. Because many products are at risk to either accumulate or cause interactions with medication, physicians should take an active role to inform themselves.

Reduced amino acid content in transgenic potato tubers due to antisense inhibition of the leaf H+/amino acid symporter StAAP1.

Transport processes across the plasma membrane of leaf vascular tissue are essential for transport and distribution of assimilates. In potato, leaves are the predominant sites for nitrate reduction and amino acid biosynthesis. From there, assimilated amino acids are exported through the phloem to supply tubers with organic nitrogen. To study the role of amino acid transporters in long-distance transport and allocation of organic nitrogen in potato plants, a gene encoding a functional, leaf-expressed amino acid permease StAAP1 was isolated. Similar to the sucrose transporter SUT1, StAAP1 expression was induced during the sink-to-source transition, indicating a role in phloem loading. To test the role of StAAP1, expression was inhibited by an antisense approach. Transgenic plants with reduced StAAP1 expression were phenotypically indistinguishable from wild type, as were photosynthetic capacity and tuber yield. However, tubers from antisense StAAP1 plants showed up to 50% reduction in free amino acid contents. In comparison, starch content was not affected or tended to increase relative to wild type. The reduction in all amino acids except aspartate in the antisense plants is consistent with the properties of amino acid permeases (AAPs) found in heterologous systems. The results demonstrate an important role for StAAP1 in long-distance transport of amino acids and highlight the importance of plasma membrane transport for nutrient distribution in plants.