Oxidation of p53 through DNA Charge Transport Involves a Network of Disulfides within the DNA-Binding Domain

Transcription factor p53 plays a critical role in the cellular response to stress stimuli. We have seen that p53 dissociates selectively from various promoter sites as a result of oxidation at long-range through DNA-mediated charge transport (CT). Here, we examine this chemical oxidation and determine the residues in p53 that are essential for oxidative dissociation, focusing on the network of cysteine residues adjacent to the DNA-binding site. Of the eight mutants studied, only the C275S mutation shows decreased affinity for the Gadd45 promoter site. However, both mutations C275S and C277S result in substantial attenuation of oxidative dissociation, with C275S causing the most severe attenuation. Differential thiol labeling was used to determine the oxidation states of cysteine residues within p53 after DNA-mediated oxidation. Reduced cysteines were iodoacetamide-labeled, whereas oxidized cysteines participating in disulfide bonds were ^(13)C_2D_2-iodoacetamide-labeled. Intensities of respective iodoacetamide-modified peptide fragments were analyzed by mass spectrometry. A distinct shift in peptide labeling toward ^(13)C_2D_2-iodoacetamide-labeled cysteines is observed in oxidized samples, confirming that chemical oxidation of p53 occurs at long range. All observable cysteine residues trend toward the heavy label under conditions of DNA CT, indicating the formation of multiple disulfide bonds among the cysteine network. On the basis of these data, it is proposed that disulfide formation involving C275 is critical for inducing oxidative dissociation of p53 from DNA

FXR1 Is an IL-19-Responsive RNA-Binding Protein that Destabilizes Pro-inflammatory Transcripts in Vascular Smooth Muscle Cells

This work identifies the fragile-X-related protein (FXR1) as a reciprocal regulator of HuR target transcripts in vascular smooth muscle cells (VSMCs). FXR1 was identified as an HuR-interacting protein by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The HuR-FXR1 interaction is abrogated in RNase-treated extracts, indicating that their association is tethered by mRNAs. FXR1 expression is induced in diseased but not normal arteries. siRNA knockdown of FXR1 increases the abundance and stability of inflammatory mRNAs, while overexpression of FXR1 reduces their abundance and stability. Conditioned media from FXR1 siRNA-treated VSMCs enhance activation of naive VSMCs. RNA EMSA and RIP demonstrate that FXR1 interacts with an ARE and an element in the 3′ UTR of TNFα. FXR1 expression is increased in VSMCs challenged with the anti-inflammatory cytokine IL-19, and FXR1 is required for IL-19 reduction of HuR. This suggests that FXR1 is an anti-inflammation responsive, HuR counter-regulatory protein that reduces abundance of pro-inflammatory transcripts

Investigation of the nonlocal coherent-potential approximation

Recently the nonlocal coherent-potential approximation (NLCPA) has been introduced by Jarrell and Krishnamurthy for describing the electronic structure of substitutionally disordered systems. The NLCPA provides systematic corrections to the widely used coherent-potential approximation (CPA) whilst preserving the full symmetry of the underlying lattice. Here an analytical and systematic numerical study of the NLCPA is presented for a one-dimensional tight-binding model Hamiltonian, and comparisons with the embedded cluster method (ECM) and molecular coherent potential approximation (MCPA) are made.Comment: 18 pages, 5 figure

Effects of dietary of Artemia urmiana nauplii enriched with fish and vegetable oil on body composition of Rainbow trout, Oncorhynchus mykiss

HUFA (highly unsaturated fatty acids) content is one of the most important indices for determination of food value in fish larvae feeding. The HUFA has also an important role in fish larvae health, growth and survival. Because of this, enrichment methods for increasing of HUFA content in Artemia nauplii was developed. The aim of this study was to determine the impacts of dietary of fish and vegetable oil on Rainbow trout, Oncorhynchs mykiss, body composition. The experiments were carried out in six different treatments with three replicates for 2 weeks. The feeding treatments during the first 10 days included: 1) Commercial diet, 2) A. Urmiana nauplii enriched with fish oil, 3) A. urmiana nauplii enriched with Sunflower oil, 4) A. urmiana nauplii enriched with Canola oil, 5) A. urmiana nauplii enriched with Soybean oil, 6) Newly hatched un-enriched A. urmiana nauplii. The highest concentrations of fatty acids in diet were oleic, palmitotic, linoleic, eicosapentaenoic acid (EPA) and stearic acid, while in larvae tissue of trout in all treatments were oleic, linolenic, linoleic, stearic and docosahexaenoic acid (DHA), respectively. The concentrations of eicosapentaenoic acid [20:5(n-3)] in contrast with docosahexaenoic acid [22:6(n-3)] in the Commercial diet were significantly reduced (P<0.05). The highest concentrations of EPA was observed in nauplii enriched with fish oil in which statistically significant in comparison with the other treatments (P<0.05). The DHA content in newly hatched non-enriched nauplii and nauplii enriched with vegetable oil were zero. The results showed that vegetable oil (Canola, Sunflower and Soybean) in comparison with fish oil give more suitable results and thus, the present study suggests that early life stage of larvae growth can be feed wih nauplii enriched with Canola oil

Modern Supercapacitors Technologies and Their Applicability in Mature Electrical Engineering Applications

Supercapacitors can store a million times more energy per unit mass or volume compared to electrolytic capacitors. Due to their low internal resistance, they are capable of driving or absorbing pulsative high currents. Over the last quarter, century supercapacitor (SC) manufacturers have developed several families of mass-scale devices with high-power density and a longer cycle life that helped the end-users to improve their energy storage systems and products. Today, there are three common device families, namely, (i) symmetrical double-layer capacitors (EDLCs), (ii) hybrid capacitors with a lithium electrode, and (iii) battery capacitors based on pseudo capacitance concepts. This review paper compares these families and provides an overview of several state-of-the-art applications in electric vehicles (EVs), microgrids, and consumer electronics

Single-cell analysis of attenuation-driven transcription reveals new principles of bacterial gene regulation

Transcription attenuation fine-tunes biosynthetic gene expression in bacteria via premature termination upon metabolic signals. In transcription initiation-controlled bacterial systems, promoter architecture and transcription factor binding sets the size of transcriptional bursts at σ70 promoters, while distal enhancer elements and associated transcriptional activators modulate burst frequency at σ 54 promoters. Using the tryptophan biosynthesis operon as a model, we show that transcription attenuation, acting post-initiation and alongside transcriptional repression, simultaneously modulates both burst size and frequency from a σ70 promoter. This challenges the view that frequency modulation requires distal enhancer input and reveals that post-initiation mechanisms can shape divergent transcriptional bursting. We also uncover that bacteria use cross-feeding as a previously unrecognised strategy for controlling cell-to-cell variation in gene expression, with implications for metabolic coordination among cells.These findings redefine transcription dynamics within cell populations and suggest new principles by which bacteria regulate gene expression to adapt to environmental change

Percutaneous balloon pulmonary valvuloplasty of critical pulmonary stenosis and severe pulmonary stenosis in neonates and early infancy: A challenge in the cyanotic

Introduction: Pulmonary stenosis with an intact ventricular septum (PS-IVS) is one of the common causes of cyanotic heart disease in neonates with diverse morphologies as well as management and treatment protocols. The aim of this study was to evaluate short and midterm results of balloon pulmonary valvuloplasty (BPV) for this disorder. Methods: Between 2012 and 2016, Totally 45 neonates and infants under 6 months old were evaluated. The patients had a minimum right-to-left ventricular pressure ratio of 1, right-to-left shunting at the patent foramen ovale or atrial septal defect level, and tricuspid valve Z-scores higher than -4. Results: Immediately after the procedure, the right ventricular pressure dropped to the normal values in 8 (20) patients. The immediate procedural success rate was seen in 42 (93.3) cases: the right-to-left ventricular pressure ratio dropped to below 50 or the level of O2 saturation rose above 75. Of three cases unresponsive to BPV, two of them underwent patent ductus arteriosus (PDA) stenting and one procedural death occurred. At 6 months' follow-up, of 42 patients, this pressure was still within the normal range in 36 (80) infants, while it had returned to high values in 9 (20) patients and necessitated repeat valvuloplasty. After BPV, severe pulmonary valve regurgitation was observed in 14.2 patients; the condition was more common when high-profile noncompliant balloons were used. Conclusion: Balloon pulmonary valvuloplasty in infants with PS-IVS confers acceptable results insofar as it improves echocardiographic parameters and hemodynamic changes at short- and midterm follow-ups. Balloon selection with sizes more than 1.2 of the diameter of the pulmonary valve annulus and the use of noncompliant high-pressure balloons results in higher degrees of pulmonary regurgitation. © 2021 The Author(s)

FXR1 Is an IL-19-Responsive RNA-Binding Protein that Destabilizes Pro-inflammatory Transcripts in Vascular Smooth Muscle Cells

This work identifies the fragile-X-related protein (FXR1) as a reciprocal regulator of HuR target transcripts in vascular smooth muscle cells (VSMCs). FXR1 was identified as an HuR-interacting protein by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The HuR-FXR1 interaction is abrogated in RNase-treated extracts, indicating that their association is tethered by mRNAs. FXR1 expression is induced in diseased but not normal arteries. siRNA knockdown of FXR1 increases the abundance and stability of inflammatory mRNAs, while overexpression of FXR1 reduces their abundance and stability. Conditioned media from FXR1 siRNA-treated VSMCs enhance activation of naive VSMCs. RNA EMSA and RIP demonstrate that FXR1 interacts with an ARE and an element in the 3′ UTR of TNFα. FXR1 expression is increased in VSMCs challenged with the anti-inflammatory cytokine IL-19, and FXR1 is required for IL-19 reduction of HuR. This suggests that FXR1 is an anti-inflammation responsive, HuR counter-regulatory protein that reduces abundance of pro-inflammatory transcripts

Novel non-coding FOXP3 transcript isoform associated to potential transcriptional interference in human regulatory T cells

CD4+ regulatory T cells (T(REGS)) are critical for immune tolerance and the transcription factor Forkhead Box P3 (FOXP3) plays a crucial role in their differentiation and function. Recently, an alternative promoter has been reported for FOXP3, which is active only in T(REGS) and could have profound implications for the output of the locus, and therefore, for the functionality of these cells. By direct RNA sequencing we identified multiple novel FOXP3 transcriptional products, including one relatively abundant isoform with an extended 5’ UTR that we named ‘longFOXP3’. Western blotting, analysis of public mass spectrometry data, and transfection of in vitro transcribed RNA suggested that longFOXP3 is not coding. Furthermore, we show using two distinct RNA single-molecule fluorescence in situ hybridization technologies that transcription from the upstream promoter correlates with decreased levels of FOXP3 at the mRNA and protein levels. Together, we provide compelling evidence that the transcriptional output of the human FOXP3 locus is far more complex than that of the current annotation and warrants a more detailed analysis to identify coding and non-coding transcript isoforms. Furthermore, the alternative promoter may interfere with the activity of the canonical promoter, evoking intragenic transcriptional interference, and in this way, fine-tune the levels of FOXP3 in human T(REGS)

The mitochondrial genome sequence of the ciliate Paramecium caudatum reveals a shift in nucleotide composition and codon usage within the genus Paramecium

<p>Abstract</p> <p>Background</p> <p>Despite the fact that the organization of the ciliate mitochondrial genome is exceptional, only few ciliate mitochondrial genomes have been sequenced until today. All ciliate mitochondrial genomes are linear. They are 40 kb to 47 kb long and contain some 50 tightly packed genes without introns. Earlier studies documented that the mitochondrial guanine + cytosine contents are very different between <it>Paramecium tetraurelia </it>and all studied <it>Tetrahymena </it>species. This raises the question of whether the high mitochondrial G+C content observed in <it>P. tetraurelia </it>is a characteristic property of <it>Paramecium </it>mtDNA, or whether it is an exception of the ciliate mitochondrial genomes known so far. To test this question, we determined the mitochondrial genome sequence of <it>Paramecium caudatum </it>and compared the gene content and sequence properties to the closely related <it>P. tetraurelia</it>.</p> <p>Results</p> <p>The guanine + cytosine content of the <it>P. caudatum </it>mitochondrial genome was significantly lower than that of <it>P. tetraurelia </it>(22.4% vs. 41.2%). This difference in the mitochondrial nucleotide composition was accompanied by significantly different codon usage patterns in both species, i.e. within <it>P. caudatum </it>clearly A/T ending codons dominated, whereas for <it>P. tetraurelia </it>the synonymous codons were more balanced with a higher number of G/C ending codons. Further analyses indicated that the nucleotide composition of most members of the genus <it>Paramecium </it>resembles that of <it>P. caudatum </it>and that the shift observed in <it>P. tetraurelia </it>is restricted to the <it>P. aurelia </it>species complex.</p> <p>Conclusions</p> <p>Surprisingly, the codon usage bias in the <it>P. caudatum </it>mitochondrial genome, exemplified by the effective number of codons, is more similar to the distantly related <it>T. pyriformis </it>and other single-celled eukaryotes such as <it>Chlamydomonas</it>, than to the closely related <it>P. tetraurelia</it>. These differences in base composition and codon usage bias were, however, not reflected in the amino acid composition. Most probably, the observed picture is best explained by a hitherto unknown (neutral or adaptive) mechanism that increased the guanine + cytosine content in <it>P. tetraurelia </it>mtDNA on the one hand, and strong purifying selection on the ancestral amino acid composition on the other hand. These contradicting forces are counterbalanced by a considerably altered codon usage pattern.</p