Phase separation of chromatin and small RNA pathways in plants

Gene expression can be modulated by epigenetic mechanisms, including chromatin modifications and small regulatory RNAs. These pathways are unevenly distributed within a cell and usually take place in specific intracellular regions. Unfortunately, the fundamental driving force and biological relevance of such spatial differentiation is largely unknown. Liquid–liquid phase separation (LLPS) is a natural propensity of demixing liquid phases and has been recently suggested to mediate the formation of biomolecular condensates that are relevant to diverse cellular processes. LLPS provides a mechanistic explanation for the self-assembly of subcellular structures by which the efficiency and specificity of certain cellular reactions are achieved. In plants, LLPS has been observed for several key factors in the chromatin and small RNA pathways. For example, the formation of facultative and obligate heterochromatin involves the LLPS of multiple relevant factors. In addition, phase separation is observed in a set of proteins acting in microRNA biogenesis and the small interfering RNA pathway. In this Focused Review, we highlight and discuss the recent findings regarding phase separation in the epigenetic mechanisms of plants.     

Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation

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Cigarette smoke inhibits BAFF expression and mucosal immunoglobulin A responses in the lung during influenza virus infection

Background

It is incompletely understood how cigarette smoke (CS) exposure affects lung mucosal immune responses during viral respiratory infections. B cell activating factor belonging to the tumor necrosis factor family (BAFF) plays an important role in the induction of secretory immunoglobulin A (S-IgA) which is the main effector of the mucosal immune system. We therefore investigated the effects of CS exposure on BAFF expression and S-IgA responses in the lung during influenza virus infection.

Methods

Mice were exposed to CS and/or infected with influenza virus. Bronchoalveolar lavage fluid and lung compartments were analyzed for BAFF expression, influenza-specific S-IgA level and histological changes. Lung B cells were isolated and the activation-induced cytidine deaminase (Aicda) expression was determined. BEAS-2B cells were treated with CS extract (CSE), influenza virus, interferon beta or N-acetylcysteine and BAFF expression was measured.

Results

CS inhibited BAFF expression in the lung, particularly after long-term exposure. BAFF and S-IgA levels were increased during influenza virus infection. Three-month CS exposure prior to influenza virus infection resulted in reduced BAFF and S-IgA levels in the lung as well as augmented pulmonary inflammation on day 7 after infection. Prior CS exposure also caused decreased Aicda expression in lung B cells during infection. Neutralization of BAFF in the lung resulted in reduced S-IgA levels during influenza virus infection. CSE inhibited virus-mediated BAFF induction in a dose-dependent manner in BEAS-2B cells, while this inhibition of BAFF by CSE was prevented by pretreatment with the antioxidant N-acetylcysteine.

Conclusions

Our findings indicate that CS may hinder early mucosal IgA responses in the lung during influenza virus infection through oxidative inhibition of BAFF, which might contribute to the increased incidence and severity of viral infections in smokers.

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-015-0201-y) contains supplementary material, which is available to authorized users.     

Free radicals in exhaled breath condensate in cystic fibrosis and healthy subjects

Many markers of airway inflammation and oxidative stress can be measured non-invasively in exhaled breath condensate (EBC). However, no attempt has been made to directly detect free radicals using electron paramagnetic resonance (EPR) spectroscopy. Condensate was collected in 14 children with cystic fibrosis (CF) and seven healthy subjects. Free radicals were trapped by 5,5-dimethyl-1-pyrroline-N-oxide. EPR spectra were recorded using a Bruker EMX^® spectrometer. Secondly, to study the source of oxygen centered radical formation, catalase or hydrogen peroxide was added to the condensate. Radicals were detected in 18 out of 21 condensate samples. Analysis of spectra indicated that both oxygen and carbon centered radicals were trapped. Within-subject reproducibility was good in all but one subject. Quantitatively, there was a trend towards higher maximal peak heights of both oxygen and carbon centered radicals in the children with CF. Catalase completely suppressed the signals in condensate. Addition of hydrogen peroxide resulted in increased radical signal intensity. Detection of free radicals in EBC of children with CF and healthy subjects is feasible using EPR spectroscopy.     

ReviewBiomarkers in Breath Condensate: A promising New Non-invasive Technique in Free Radical Research

Oxidative stress is associated with a range of inflammatory lung diseases including asthma, adult respiratory distress syndrome, idiopathic pulmonary fibrosis, pneumonia, lung transplantation, chronic obstructive pulmonary disease, cystic fibrosis, bronchiectasis and lung cancer. Increased concentrations of reactive oxygen species (ROS) in the airways of such patients are reflected by elevated concentrations of oxidative stress markers in the breath, airways, lung tissue and blood. Traditionally, the measurement of these biomarkers has involved invasive procedures to procure the samples, or examine the compartments. As a consequence, there is a need for less invasive approaches to measure oxidative stress. Analysis of breath hydrocarbons has partly fulfilled this need, however only gas phase volatile constituents can be assessed by this approach. The collection of exhaled breath condensate (EBC) is a simple, non-invasive approach, which comprehensively samples the lower respiratory tract. It is currently used as a research and diagnostic tool in the free radical field, yielding information on redox disturbance and the degree and type of inflammation in the lung. With further technical developments, such an approach may ultimately have a role in the clinic, in helping to diagnose specific lung diseases. EBC can be exploited to assess a spectrum of potential biomarkers, thus generating a “finger print” characteristic of the disease. By assessing the nature of oxidative stress in this manner, the most appropriate therapy can be selected and the response to treatment monitored.     

Tobacco smoke is a likely source of lead and cadmium in settled house dust

IntroductionEnvironmental exposure to lead (Pb) and cadmium (Cd) are risk factors for adverse health outcomes in children and adults. This study examined whether thirdhand smoke residue contributes to Pb and Cd in settled house dust.MethodsParticipants were 60 multiunit housing residents in San Diego, California. All had indoor smoking bans during the study period, and 55 were nonsmokers. Wipe samples from different surfaces and vacuum floor dust samples were analyzed for nicotine, a marker of thirdhand smoke, and for Pb and Cd using liquid chromatography-triple quadrupole mass spectrometry and inductively coupled plasma-mass spectrometry, respectively.ResultsExamined in each sample type separately, Pb and Cd loadings were significantly correlated (r = 0.73, vacuum floor dust; 0.52, floor wipes; 0.72, window sill/trough wipes; all p < 0.0025). Pb and Cd loadings from different sample types were not correlated (all p > 0.30). Nicotine loading in dust was significantly correlated with Pb and Cd loading in dust (r = 0.49 for Pb; r = 0.39 for Cd, all p < 0.0025). Pb and Cd loadings on floor or window surfaces, showed no association with nicotine loading in dust, on floors, or on furniture (all p < 0.30).ConclusionsTobacco smoke is a likely source of Pb and Cd that accumulates in settled house dust in multiunit housing, suggesting that Pb and Cd are constituents of thirdhand smoke that lingers long after smoking has ended.     

Identification of differentially expressed proteins in blood plasma of control and cigarette smoke-exposed mice by 2-D DIGE/MS

Cigarette smoke exposure is known to induce obstructive lung disease and several cardiovascular disease states in humans and also in animal models. Smoking leads to oxidative stress and inflammation that are important in triggering pulmonary and cardiovascular disease. The objective of the current study was to quantify differences in expression levels of plasma proteins of cigarette smoke -exposed and control mice, at the time of disease onset, and identify these proteins for use as potential biomarkers of the onset of smoking-induced disease. We utilized 2-D DIGE/MS to characterize these proteomic changes. 2-D DIGE of plasma samples identified 11 differentially expressed proteins in cigarette smoke -exposed mice. From these 11 proteins, 9 were downregulated and 2 were upregulated. The proteins identified are involved in vascular function, coagulation, metabolism and immune function. Among these, the alterations in fibrinogen (2.2-fold decrease), α-1-antitrypsin (1.8-fold increase) and arginase (4.5-fold decrease) are of particular interest since these have been directly linked to cardiovascular and lung pathology. Differences in expression levels of these proteins were also confirmed by immunoblotting. Thus, we observe that chronic cigarette smoke exposure in mice leads to prominent changes in the protein expression profile of blood plasma and these changes in turn can potentially serve as markers predictive of the onset and progression of cardiovascular and pulmonary disease.     

Seed germination of the carnivorous plant Byblis gigantea (Byblidaceae) is cued by warm stratification and karrikinolide

Byblidaceae is one of the most poorly studied carnivorous plant families, with seed dormancy and germination biology remaining unresolved. This knowledge deficit has significant conservation and management implications, particularly as the most southerly distributed species, the south‐west Western Australian endemic Byblis gigantea, is listed as critically endangered. This study examined the ecophysiology of seed dormancy and germination in B. gigantea in concert with a study of the population dynamics of a single plant community. Mass seedling emergence and plant establishment were observed after a wildfire in 2007 in the natural population, followed by a rapid decline in mature individuals (91%) over a 4‐year monitoring period, with almost no inter‐fire recruitment (1.4% of all emergence) observed. Seeds possessed a fully developed embryo, and the germination characteristics of fresh seeds classified them as showing physiological dormancy. Seed dormancy was partially alleviated by warm stratification (30 °C) for 8 weeks prior to incubation at 15 °C, with c. 40% germination observed. With the additional exposure of seeds to the germination‐active chemical in smoke, karrikinolide, the germination of warm‐stratified seeds increased to 89%. Seeds also displayed orthodox storage behaviour and appeared to be amenable to long‐term seed banking for conservation. These results present the first observation of the stimulation of the germination of a carnivorous plant by a smoke‐derived compound. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 143–152.