Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3

Both DNA methylation and post-translational histone modifications contribute to gene silencing, but the mechanistic relationship between these epigenetic marks is unclear. Mutations in two Arabidopsis genes, the KRYPTONITE (KYP) histone H3 lysine 9 (H3K9) methyltransferase and the CHROMOMETHYLASE3 (CMT3) DNA methyltransferase, cause a reduction of CNG DNA methylation, suggesting that H3K9 methylation controls CNG DNA methylation. Here we show that the chromodomain of CMT3 can directly interact with the N-terminal tail of histone H3, but only when it is simultaneously methylated at both the H3K9 and H3K27 positions. Furthermore, using chromatin immunoprecipitation analysis and immunohistolocalization experiments, we found that H3K27 methylation colocalizes with H3K9 methylation at CMT3-controlled loci. The H3K27 methylation present at heterochromatin was not affected by mutations in KYP or in several Arabidopsis PcG related genes including the Enhancer of Zeste homologs, suggesting that a novel pathway controls heterochromatic H3K27 methylation. Our results suggest a model in which H3K9 methylation by KYP, and H3K27 methylation by an unknown enzyme provide a combinatorial histone code for the recruitment of CMT3 to silent loci.     

Identification and Expression Analysis of Two Genes Involved in the Biosynthesis of t-Anethole in Fennel (Foeniculum vulgare Mill.) and Their Up-Regulation in Leaves in Response to Methyl Jasmonate Treatments

Journal of Plant Growth Regulation - Fennel (Foeniculum vulgare Mill.), a medicinal plant from the Apiaceae, is used in traditional medicine. For the first time in F. vulgare, partial cDNA of two...     

Tumor-derived exosomes: Implication in angiogenesis and antiangiogenesis cancer therapy

Tumor cells utilize different strategies to communicate with neighboring tissues for facilitating tumor progression and invasion, one of these strategies has been shown to be the release of exosomes. Exosomes are small nanovesicles secreted by all kind of cells in the body, especially cancer cells, and mediate cell to cell communications. Exosomes play an important role in cancer invasiveness by harboring various cargoes that could accelerate angiogenesis. Here first, we will present an overview of exosomes, their biology, and their function in the body. Then, we will focus on exosomes derived from tumor cells as tumor angiogenesis mediators with a particular emphasis on the underlying mechanisms in various cancer origins. Also, exosomes derived from stem cells and tumor-associated macrophages will be discussed in this regard. Finally, we will discuss the novel therapeutic strategies of exosomes as drug delivery vehicles against angiogenesis.     

Multi-template homology-based structural model of L-2-haloacid dehalogenase (DehL) from Rhizobium sp. RC1

Dehalogenases are of high interest due to their potential applications in bioremediation and in synthesis of various industrial products. DehL is an L-2-haloacid dehalogenase (EC 3.8.1.2) that catalyses the cleavage of halide ion from L-2-halocarboxylic acid to produce D-2-hydroxycarboxylic acid. Although DehL utilises the same substrates as the other L-2-haloacid dehalogenases, its deduced amino acid sequence is substantially different (<25%) from those of the rest L-2-haloacid dehalogenases. To date, the 3D structure of DehL is not available. This limits the detailed understanding of the enzyme’s reaction mechanism. The present work predicted the first homology-based model of DehL and defined its active site. The monomeric unit of the DehL constitutes α/β structure that is organised into two distinct structural domains: main and subdomains. Despite the sequence disparity between the DehL and other L-2-haloacid dehalogenases, its structural model share similar fold as the experimentally solved L-DEX and DehlB structures. The findings of the present work will play a crucial role in elucidating the molecular details of the DehL functional mechanism.     

Effect of pristine and functionalized single- and multi-walled carbon nanotubes on CO<Subscript>2</Subscript> separation of mixed matrix membranes based on polymers of intrinsic microporosity (PIM-1): a molecular dynamics simulation study

Molecular dynamics (MD) and grand canonical Monte Carlo (GCMC) simulations were conducted to investigate the transport properties of carbon dioxide, methane, nitrogen, and oxygen through pure and mixed matrix membranes (MMMs) based on polymers of intrinsic microporosity (PIM-1). For this purpose, first, 0.5 to 3 wt% of pristine single-walled carbon nanotube (p-SWCNT) and multi-walled carbon nanotube (p-MWCNT) were embedded into the pure PIM-1, and then for better dispersion of CNT particles into the polymer matrix and to improve the performance of the resulting MMMs, polyethylene glycol (PEG) functionalized SWCNT and MWCNT (f-SWCNT and f-MWCNT, respectively) were loaded. The characterization of the obtained MMMs was carried out by using density, glass transition temperature, X-ray pattern, and fractional free volume calculations. Comparing the obtained results with the available reported experimental data, indicate the authenticity of the applied simulation approach. The simulation results exhibit that the pristine and PEG-functionalized CNT particles improve the transport properties such as diffusivity, solubility, and permeability of the PIM-1 membranes, without sacrificing their selectivity. Also, the MMMs incorporated with 2 wt% of the functionalized CNT particles indicate better performance for the CO₂ separation from other gases. According to the calculated results, the highest permeability and diffusivity for CO₂ are observed in the [PIM-1/f-SWCNT] MMM among the other membranes which represent that the loading of the f-SWCNTs can enhance the CO₂ separation performance of PIM-1 more than other CNTs studied in this work.     

The natural mutation by deletion of Lys9 in the thrombin A-chain affects the pKa value of catalytic residues, the overall enzyme's stability and conformational transitions linked to Na+ binding

The catalytic competence of the natural thrombin mutant with deletion of the Lys9 residue in the A-chain (deltaK9) was found to be severely impaired, most likely due to modification of the 60-loop conformation and catalytic triad geometry, as supported by long molecular dynamics (MD) simulations in explicit water solvent. In this study, the pH dependence of the catalytic activity and binding of the low-molecular mass inhibitor N-alpha-(2-naphthylsulfonyl-glycyl)-4-amidinophenylalanine-piperidine (alpha-NAPAP) to the wild-type (WT) and deltaK9 thrombin forms were investigated, along with their overall structural stabilities and conformational properties. Two ionizable groups were found to similarly affect the activity of both thrombins. The pKa value of the first ionizable group, assigned to the catalytic His57 residue, was found to be 7.5 and 6.9 in ligand-free deltaK9 and WT thrombin, respectively. Urea-induced denaturation studies showed higher instability of the deltaK9 mutant compared with WT thrombin, and disulfide scrambling experiments proved weakening of the interchain interactions, causing faster release of the reduced A-chain in the mutant enzyme. The sodium ion binding affinity was not significantly perturbed by Lys9 deletion, although the linked increase in intrinsic fluorescence was lower in the mutant. Essential dynamics (ED) analysis highlighted different conformational properties of the two thrombins in agreement with the experimental conformational stability data. Globally, these findings enhanced our understanding of the perturbations triggered by Lys9 deletion, which reduces the overall stability of the molecule, weakens the A-B interchain interactions, and allosterically perturbs the geometry and protonation state of catalytic residues of the enzyme.     

Performance assessment of new-generation Fitbit technology in deriving sleep parameters and stages

ABSTRACT

We compared performance in deriving sleep variables by both Fitbit Charge 2?, which couples body movement (accelerometry) and heart rate variability (HRV) in combination with its proprietary interpretative algorithm (IA), and standard actigraphy (Motionlogger® Micro Watch Actigraph: MMWA), which relies solely on accelerometry in combination with its best performing ‘Sadeh’ IA, to electroencephalography (EEG: Zmachine® Insight+ and its proprietary IA) used as reference. We conducted home sleep studies on 35 healthy adults, 33 of whom provided complete datasets of the three simultaneously assessed technologies. Relative to the Zmachine EEG method, Fitbit showed an overall Kappa agreement of 54% in distinguishing wake/sleep epochs and sensitivity of 95% and specificity of 57% in detecting sleep epochs. Fitbit, relative to EEG, underestimated sleep onset latency (SOL) by ~11 min and overestimated sleep efficiency (SE) by ~4%. There was no statistically significant difference between Fitbit and EEG methods in measuring wake after sleep onset (WASO) and total sleep time (TST). Fitbit showed substantial agreement with EEG in detecting rapid eye movement and deep sleep, but only moderate agreement in detecting light sleep. The MMWA method showed 51% overall Kappa agreement with the EEG one in detecting wake/sleep epochs, with sensitivity of 94% and specificity of 53% in detecting sleep epochs. MMWA, relative to EEG, underestimated SOL by ~10 min. There was no significant difference between Fitbit and MMWA methods in amount of bias in estimating SOL, WASO, TST, and SE; however, the minimum detectable change (MDC) per sleep variable with Fitbit was better (smaller) than with MMWA, respectively, by ~10 min, ~16 min, ~22 min, and ~8%. Overall, performance of Fitbit accelerometry and HRV technology in conjunction with its proprietary IA to detect sleep vs. wake episodes is slightly better than wrist actigraphy that relies solely on accelerometry and best performing Sadeh IA. Moreover, the smaller MDC of Fitbit technology in deriving sleep parameters in comparison to wrist actigraphy makes it a suitable option for assessing changes in sleep quality over time, longitudinally, and/or in response to interventions.     

The Effect of Continued Training with Crocin on Apoptosis Markers in Liver Tissue of High Fat Diet Induced Diabetic Rats

Diabetes mellitus (DM) disease can affect process of apoptosis by increasing oxidative stress, nevertheless exercise and crocin can improve apoptosis; therefore present study aimed to investigate the effect of continued training with crocin on apoptosis markers in liver tissue of diabetic rats. In this experimental study 32 diabetic rats based on fasting glucose divided into four groups of eight rats including: 1) sham, 2) training, 3) crocin, and 4) training with crocin also for investigate the effect of DM induction on apoptosis markers, eight healthy rats assigned in healthy control group. During eight weeks groups 2 and 4 ran 60 minutes on treadmill with intensity of 50–55% maximum speed for three sessions per week and groups 3 and 4 received 25 mg/kg/day crocin peritoneally. Shapiro–Wilk, one-way ANOVA with Tukey’s post-hot tests were used for statistical analysis of data (P ≤ 0.05). DM induction significantly increased Bcl-2 as well as decreased Bax and P52 (P ≤ 0.05) nevertheless training and training with crocin significantly decreased Bcl-2 and increased Bax and P53 (P ≤ 0.05); crocin significantly decreased Bcl-2 and increased P53 (P ≤ 0.05) and training with crocin had higher effect on increase of Bax and P53 compare to training (P ≤ 0.05) also increase of Bax compare to crocin. Although training and crocin alone can improve apoptotic markers in diabetic rats, nevertheless training simultaneously with crocin have better effects than training alone.     

Distinct signature of altered homeostasis in aging rod photoreceptors: implications for retinal diseases

Background

Advanced age contributes to clinical manifestations of many retinopathies and represents a major risk factor for age-related macular degeneration, a leading cause of visual impairment and blindness in the elderly. Rod photoreceptors are especially vulnerable to genetic defects and changes in microenvironment, and are among the first neurons to die in normal aging and in many retinal degenerative diseases. The molecular mechanisms underlying rod photoreceptor vulnerability and potential biomarkers of the aging process in this highly specialized cell type are unknown.

Methodology/Principal Findings

To discover aging-associated adaptations that may influence rod function, we have generated gene expression profiles of purified rod photoreceptors from mouse retina at young adult to early stages of aging (1.5, 5, and 12 month old mice). We identified 375 genes that showed differential expression in rods from 5 and 12 month old mouse retina compared to that of 1.5 month old retina. Quantitative RT-PCR experiments validated expression change for a majority of the 25 genes that were examined. Macroanalysis of differentially expressed genes using gene class testing and protein interaction networks revealed overrepresentation of cellular pathways that are potentially photoreceptor-specific (angiogenesis and lipid/retinoid metabolism), in addition to age-related pathways previously described in several tissue types (oxidative phosphorylation, stress and immune response).

Conclusions/Significance

Our study suggests a progressive shift in cellular homeostasis that may underlie aging-associated functional decline in rod photoreceptors and contribute to a more permissive state for pathological processes involved in retinal diseases.