Deciphering Histone Modifications in Rice by Chromatin Immunoprecipitation (ChIP): Applications to Study the Impact of Stress Imposition

The spatial organization of chromatin, the methylome, and histone modifications represents epigenetic layers that greatly intersect each other, influencing genome regulation and allowing high flexibility in stress response. Although changes in specific histone modification marks could be extensively associated with transcriptional regulation of stress-responsive genes, a link between specific epigenetic signatures and plant stress tolerance has not yet been established. This chapter includes some examples of the associations found between fluctuations in these marks and regulation of plant stress-responsive genes. Chromatin immunoprecipitation (ChIP) has been widely used to uncover the landscape of histone modifications. However, ChIP involves multiple steps and requires optimizations targeting the tissue and the plant species. Here, we detail the ChIP procedure currently used in our laboratory, for leaf tissues of young rice seedlings, to decipher the dynamic feature of specific chemical modifications of histones that may influence the expression of stress-responsive genes. We show the success achieved after introducing specific optimizations and highlight the key critical steps and trouble shootings that may occur. A thorough understanding of stress-induced fluctuations of specific histone modifications may unveil new strategies to improve plant adaptation and performance in suboptimal conditions

A modular reactor to simulate biofilm development in orthopedic materials

Surfaces of medical implants are generally designed to encourage soft- and/or hard-tissue adherence, eventually leading to tissue- or osseo-integration. Unfortunately, this feature may also encourage bacterial adhesion and biofilm formation. To understand the mechanisms of bone tissue infection associated with contaminated biomaterials, a detailed understanding of bacterial adhesion and subsequent biofilm formation on biomaterial surfaces is needed. In this study, a continuous-flow modular reactor composed of several modular units placed in parallel was designed to evaluate the activity of circulating bacterial suspensions and thus their predilection for biofilm formation during 72 h of incubation. Hydroxyapatite discs were placed in each modular unit and then removed at fixed times to quantify biofilm accumulation. Biofilm formation on each replicate of material, unchanged in structure, morphology, or cell density, was reproducibly observed. The modular reactor therefore proved to be a useful tool for following mature biofilm formation on different surfaces and under conditions similar to those prevailing near human-bone implants. [Int Microbiol 2013; 16(3):191-198]Keywords: orthopedic materials · orthopedic conditions · modular reactors · continuous flow · biomaterials · biofilm formatio

Abiotic stress and induced DNA hypomethylation cause interphase chromatin structural changes in rice rDNA loci

Global climate change, i.e. higher and more variable temperatures, and a gain in soil salinity are increasing plant stress with direct consequences on crop yield and quality levels. Rice productivity is strongly affected by abiotic stress conditions. The regulation of chromatin structure in response to environmental stress is poorly understood. We investigated the interphase chromatin organization from rice plants in non-stress versus stress conditions. We have used a cytogenetic approach, based on fluorescence in situ hybridization (FISH) with 45S, 5S rDNA and centromeric probes on rice tissue sections. The abiotic stress conditions included cold, heat and mild salinity and were applied during seed germination. In contrast to cold, saline and heat stresses caused extensive decondensation of 45S rDNA chromatin and also an increase in the distance between the 2 homologous 5S rDNA loci. 5-Azacytidine (5-AC), a DNA hypomethylating drug, greatly increased 45S rDNA chromatin decondensation and interestingly was able to induce polarization of centromeres in rice interphase nuclei. The abiotic stresses tested did not perturb the spatial position of centromeres, typically with circular arrangement around the nucleolus. The results suggest a role for chromatin plasticity in a world of climate changes

The assessment of bacterial nanocellulose functionalized with metal nanoparticles

[Excerpt] Introduction Biocompatibility is one of the mandatory requirements of indwelling medical devices to avoid foreign body reactions and consequential surgical removal.This research was funded by FEDER funds through the Operational Competitiveness Program–COMPETE, under the project POCI-01-0247-FEDER-068924 and by National Funds through Fundação para a Ciência e Tecnologia (FCT), under the project UID/CTM/00264/2020. Cátia Alves, Liliana Melro, Behnaz Mehravani, and Ana Isabel Ribeiro acknowledge FCT, MCTES, FSE, and UE PhD grants 2022.10454.BD, 2020.04919.BD, 2022.13094.BD, and SFRH/BD/137668/2018

Salt tolerant and sensitive rice varieties display differential methylome flexibility under salt stress

DNA methylation has been referred as an important player in plant genomic responses to environmental stresses but correlations between the methylome plasticity and specific traits of interest are still far from being understood. In this study, we inspected global DNA methylation levels in salt tolerant and sensitive rice varieties upon salt stress imposition. Global DNA methylation was quantified using the 5-methylcytosine (5mC) antibody and an ELISAbased technique, which is an affordable and quite pioneer assay in plants, and in situ imaging of methylation sites in interphase nuclei of tissue sections. Variations of global DNA methylation levels in response to salt stress were tissue- and genotype-dependent. We show a connection between a higher ability of DNA methylation adjustment levels and salt stress tolerance. The salt-tolerant rice variety Pokkali was remarkable in its ability to quickly relax DNA methylation in response to salt stress. In spite of the same tendency for reduction of global methylation under salinity, in the salt-sensitive rice variety IR29 such reduction was not statistically supported. In ‘Pokkali’, the salt stress-induced demethylation may be linked to active demethylation due to increased expression of DNA demethylases under salt stress. In ‘IR29’, the induction of both DNA demethylases and methyltransferases may explain the lower plasticity of DNA methylation. We further show that mutations for epigenetic regulators affected specific phenotypic parameters related to salinity tolerance, such as the root length and biomass. This work emphasizes the role of differential methylome flexibility between salt tolerant and salt sensitive rice varieties as an important player in salt stress tolerance, reinforcing the need to better understand the connection between epigenetic networks and plant responses to environmental stresses.Fundação para a Ciência e Tecnologia (FCT

Effects of a psychoeducational intervention for direct care workers caring for people with dementia: results from a 6-month follow-up study

YesThis study aimed to assess the effects of a psycho-educational intervention, designed to improve direct care workers’ stress, burnout and job satisfaction and person-centered communicative behavior with people with dementia. A pretest-posttest control group design was conducted in four aged-care facilities. Two experimental facilities received a psycho-educational intervention; two control facilities received an education-only. Data were gathered from fifty three care workers at baseline, immediately and six months after the intervention, through self-administrated instruments and video-recorded morning care sessions. The experimental group showed a significant decrease in care workers’ burnout and a significant improvement in several communicative behaviors (e.g., involvement). Stress levels deteriorated at six months and no intervention effects were found for job satisfaction. The findings highlight the importance of providing care workers with both technical competences and tools for stress management as this might be associated with a reduction of their levels of exhaustion and improved communicative behaviors.Foundation for Science and Technolog

Methamphetamine mimics the neurochemical profile of aging in rats and impairs recognition memory

Brain neurochemistry and cognition performance are thought to decline with age. Accumulating data indicate that similar events occur after prolonged methamphetamine (MA) exposure. Using the rat as a model, the present study was designed to uncover common alteration patterns in brain neurochemistry and memory performance between aging and prolonged MA exposure. To this end, animals were treated with a chronic binge MA administration paradigm (20 mg/kg/day from postnatal day 91 to 100). Three-age control groups received isovolumetric saline treatment and were tested at the MA age-matched period, and at 12 and 20 months. We observed that both MA and aged animals presented a long, but not short, time impairment in novelty preference and an increased anxiety-like behavior. Neurochemical analysis indicated similar MA- and age-related impairments in dopamine, serotonin and metabolites in the striatum, prefrontal cortex and hippocampus. Thus, the present data illustrate that MA may be used to mimic age-related effects on neurotransmitter systems and advocate MA treatment as a feasible animal model to study neuronal processes associated with aging.info:eu-repo/semantics/publishedVersio

Human-umbilical cord matrix mesenchymal cells improved left ventricular contractility independently of infarct size in swine myocardial infarction with reperfusion

Funding Information: This work was funded by: i) national funds through FCT - Portuguese Foundation for Science and Technology, under the scope of the Cardiovascular R&D Center - UnIC (UIDB/00051/2020 and UIDP/00051/2020); ii) “la Caixa” Banking Foundation and FCT under the project code LCF/PR/HP17/52190002”; iii) the QREN project 2013/30196; and iv) the European Structural and Investment Funds (ESIF), under the Lisbon Portugal Regional Operational Program and National Funds through FCT [POCI-01-0145-FEDER-030985]. RNG and TLL were funded by the FCT individual fellowships [SFRH/BD/144490/2019] and [PD/BD/127997/2016], respectively. Funding sources had no interference in the design of the study, study governance, data collection and analysis, nor in manuscript writing or its scientific and intellectual content. Publisher Copyright: 2023 Raposo, Cerqueira, Leite, Moreira-Costa, Laundos, Miranda, Mendes-Ferreira, Coelho, Gomes, Pinto-do-Ó, Nascimento, Lourenço, Cardim and Leite-Moreira.Background: Human umbilical cord matrix-mesenchymal stromal cells (hUCM-MSC) have demonstrated beneficial effects in experimental acute myocardial infarction (AMI). Reperfusion injury hampers myocardial recovery in a clinical setting and its management is an unmet need. We investigated the efficacy of intracoronary (IC) delivery of xenogeneic hUCM-MSC as reperfusion-adjuvant therapy in a translational model of AMI in swine. Methods: In a placebo-controlled trial, pot-belied pigs were randomly assigned to a sham-control group (vehicle-injection; n = 8), AMI + vehicle (n = 12) or AMI + IC-injection (n = 11) of 5 × 105 hUCM-MSC/Kg, within 30 min of reperfusion. AMI was created percutaneously by balloon occlusion of the mid-LAD. Left-ventricular function was blindly evaluated at 8-weeks by invasive pressure-volume loop analysis (primary endpoint). Mechanistic readouts included histology, strength-length relationship in skinned cardiomyocytes and gene expression analysis by RNA-sequencing. Results: As compared to vehicle, hUCM-MSC enhanced systolic function as shown by higher ejection fraction (65 ± 6% vs. 43 ± 4%; p = 0.0048), cardiac index (4.1 ± 0.4 vs. 3.1 ± 0.2 L/min/m2; p = 0.0378), preload recruitable stroke work (75 ± 13 vs. 36 ± 4 mmHg; p = 0.0256) and end-systolic elastance (2.8 ± 0.7 vs. 2.1 ± 0.4 mmHg*m2/ml; p = 0.0663). Infarct size was non-significantly lower in cell-treated animals (13.7 ± 2.2% vs. 15.9 ± 2.7%; Δ = −2.2%; p = 0.23), as was interstitial fibrosis and cardiomyocyte hypertrophy in the remote myocardium. Sarcomere active tension improved, and genes related to extracellular matrix remodelling (including MMP9, TIMP1 and PAI1), collagen fibril organization and glycosaminoglycan biosynthesis were downregulated in animals treated with hUCM-MSC. Conclusion: Intracoronary transfer of xenogeneic hUCM-MSC shortly after reperfusion improved left-ventricular systolic function, which could not be explained by the observed extent of infarct size reduction alone. Combined contributions of favourable modification of myocardial interstitial fibrosis, matrix remodelling and enhanced cardiomyocyte contractility in the remote myocardium may provide mechanistic insight for the biological effect.publishersversionpublishe

Study of 16 Portuguese activated sludge systems based on filamentous bacteria populations and their relationships with environmental parameters

A survey in 16 activated sludge waste water treatment plants (WWTP) was conducted to contribute to the knowledge of the environmental parameters that determine the composition of the filamentous community. A total of 128 samples of mixed liquor from municipal WWTP were collected during 2 years, and 22 filamentous morphotypes were identified. The most frequent and abundant filamentous bacteria were, in both cases and by this order, type 0041/0675, type 0092, Microthrix parvicella and 1851, nocardioforms and Haliscomenobacter hydrossis. Concerning dominance, type 1851 was the most frequently dominant morphotype, followed by M. parvicella and types 0092 and 0041/0675. These were also, and by this order, the dominant morphotypes during bulking occurrences. Significant correlations were obtained between the abundance of filamentous bacteria and environmental parameters, but multivariate statistical analysis only confirmed the correlation between type 0092 and Sludge Volume Index (SVI), emphasizing the association of this filament with bulking. The discussion of the results in light of published works was complicated by the random use of terms such as frequency, abundance, and dominance with different and often unclear meanings. This reinforces the need of clarifying these terms when discussing the causes of filamentous overgrowth in WWTP.Portuguese Foundation for Science and Technology (FCT) and the European Community fund FEDER, through Program COMPETE, in the ambit of the Projects FCOMP-01-0124-FEDER-007025 (PTDC/AMB/68393/2006), PEst-OE/EQB/LA0023/2013, RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462), and the Project BBioEnv - Biotechnology and Bioengineering for a sustainable world,REF. NORTE-07-0124- FEDER-000048, co-funded by the Programa Operacional Regional do Norte (ON.2 – O Novo Norte), QREN, FEDER. PhD grant SFRH/BD/64848/200