scholarly journals DNA Methylation Changes Induced by Cold in Psychrophilic and Psychrotolerant Naganishia Yeast Species

2020 ◽  
Vol 8 (2) ◽  
pp. 296
Author(s):  
Benedetta Turchetti ◽  
Gianpiero Marconi ◽  
Ciro Sannino ◽  
Pietro Buzzini ◽  
Emidio Albertini
Keyword(s):  
Dna Methylation ◽  
Cold Stress ◽  
Yeast Species ◽  
Elongation Factor ◽  
Chitin Synthase ◽  
Nonsignificant Increase ◽  
Significant Difference ◽  
Genes Encoding ◽  
Different Response ◽  
Psychrotolerant Yeast

The involvement of DNA methylation in the response to cold stress of two different yeast species (Naganishia antarctica, psychrophilic, and Naganishia albida, psychrotolerant), exhibiting different temperature aptitudes, has been studied. Consecutive incubations at respective optimum temperatures, at 4 °C (cold stress) and at optimum temperatures again, were performed. After Methylation Sensitive Amplified Polymorphism (MSAP) fingerprints a total of 550 and 423 clear and reproducible fragments were amplified from N. antarctica and N. albida strains, respectively. The two Naganishia strains showed a different response in terms of level of DNA methylation during cold stress and recovery from cold stress. The percentage of total methylated fragments in psychrophilic N. antarctica did not show any significant change. On the contrary, the methylation of psychrotolerant N. albida exhibited a nonsignificant increase during the incubation at 4 °C and continued during the recovery step, showing a significant difference if compared with control condition, resembling an uncontrolled response to cold stress. A total of 12 polymorphic fragments were selected, cloned, and sequenced. Four fragments were associated to genes encoding for elongation factor G and for chitin synthase export chaperon. To the best of our knowledge, this is the first study on DNA methylation in the response to cold stress carried out by comparing a psychrophilic and a psychrotolerant yeast species.

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

scholarly journals Association of expression of epigenetic molecular factors with DNA methylation and sensitivity to chemotherapeutic agents in cancer cell lines

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Suleyman Vural ◽  
Alida Palmisano ◽  
William C. Reinhold ◽  
Yves Pommier ◽  
Beverly A. Teicher ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Antitumor Agents ◽  
Cancer Cell Lines ◽  
Chemotherapeutic Agents ◽  
Epigenetic Factors ◽  
Expression Of Genes ◽  
Genes Encoding

Abstract Background Altered DNA methylation patterns play important roles in cancer development and progression. We examined whether expression levels of genes directly or indirectly involved in DNA methylation and demethylation may be associated with response of cancer cell lines to chemotherapy treatment with a variety of antitumor agents. Results We analyzed 72 genes encoding epigenetic factors directly or indirectly involved in DNA methylation and demethylation processes. We examined association of their pretreatment expression levels with methylation beta-values of individual DNA methylation probes, DNA methylation averaged within gene regions, and average epigenome-wide methylation levels. We analyzed data from 645 cancer cell lines and 23 cancer types from the Cancer Cell Line Encyclopedia and Genomics of Drug Sensitivity in Cancer datasets. We observed numerous correlations between expression of genes encoding epigenetic factors and response to chemotherapeutic agents. Expression of genes encoding a variety of epigenetic factors, including KDM2B, DNMT1, EHMT2, SETDB1, EZH2, APOBEC3G, and other genes, was correlated with response to multiple agents. DNA methylation of numerous target probes and gene regions was associated with expression of multiple genes encoding epigenetic factors, underscoring complex regulation of epigenome methylation by multiple intersecting molecular pathways. The genes whose expression was associated with methylation of multiple epigenome targets encode DNA methyltransferases, TET DNA methylcytosine dioxygenases, the methylated DNA-binding protein ZBTB38, KDM2B, SETDB1, and other molecular factors which are involved in diverse epigenetic processes affecting DNA methylation. While baseline DNA methylation of numerous epigenome targets was correlated with cell line response to antitumor agents, the complex relationships between the overlapping effects of each epigenetic factor on methylation of specific targets and the importance of such influences in tumor response to individual agents require further investigation. Conclusions Expression of multiple genes encoding epigenetic factors is associated with drug response and with DNA methylation of numerous epigenome targets that may affect response to therapeutic agents. Our findings suggest complex and interconnected pathways regulating DNA methylation in the epigenome, which may both directly and indirectly affect response to chemotherapy.

Elongation factor EF-1 alpha gene dosage alters translational fidelity in Saccharomyces cerevisiae

1989 ◽  
Vol 9 (10) ◽  
pp. 4571-4575
Author(s):  
J M Song ◽  
S Picologlou ◽  
C M Grant ◽  
M Firoozan ◽  
M F Tuite ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Gene Dosage ◽  
Elongation Factor ◽  
Nonsense Suppression ◽  
Translational Fidelity ◽  
Genes Encoding ◽  
Alpha Gene ◽  
Nonsense Codons

Changes in the dosage of genes encoding elongation factor EF-1 alpha were shown to cause parallel changes in the misreading of nonsense codons. Higher amounts of EF-1 alpha were correlated with increased nonsense suppression, suggesting that the level of EF-1 alpha is critically involved in translational fidelity.

scholarly journals Analysis of Symptom Development in Relation to Quantity of Rice stripe virus in Rice (Oryza sativa) to Simplify Evaluation of Resistance

2019 ◽  
Vol 109 (4) ◽  
pp. 701-707 ◽  
Author(s):  
Mitsuru Okuda ◽  
Takuya Shiba ◽  
Masahiro Hirae ◽  
Akira Masunaka ◽  
Minoru Takeshita
Keyword(s):  
Oryza Sativa ◽  
Quantitative Polymerase Chain Reaction ◽  
Relative Concentration ◽  
Elongation Factor ◽  
Experimental System ◽  
Rice Stripe Virus ◽  
Strong Positive Correlation ◽  
Significant Difference ◽  
Grade Scale ◽  
New Formula

Rice stripe virus (RSV) is one of the most devastating pathogens of rice (Oryza sativa) in rice-growing regions of East Asia. We analyzed the increase in RSV accumulation in infected rice plants over time and evaluated the association between disease severity and RSV accumulation with the aim of establishing an experimental system for accurate and efficient evaluation of RSV resistance in rice. As an index of RSV accumulation in plants, relative concentration of RNA corresponding to the coat protein gene region was measured using reverse-transcription quantitative polymerase chain reaction. Actin and elongation factor 1a were used as the host reference genes. RSV concentrations tended to increase with time from 7 to 28 days after inoculation, and a strong positive correlation was observed between the log RSV concentrations in the midsections of the uppermost leaves and in the stems at the first leaf sheath position. We analyzed RSV concentrations at these two locations 21 days after inoculation with RSV and assessed severity of disease symptoms based on a commonly used scale (Washio’s six-grade scale) rated as A (most severe), B, Bt, C, Cr, or D (mild symptoms). RSV concentrations at both locations were high in plants graded A, B, or Bt, with no significant difference in concentration of RSV among the three grades, but concentrations were significantly higher in the three grades compared with that in the plants in grade D. RSV concentrations were highly variable among plants in grades C and Cr. On the basis of these data, we propose a new formula to estimate the range of disease severities with greater ease and practical value. The values calculated by the new formula corresponded well to those based on Washio’s six-grade scale.

scholarly journals DNA methylation and retinal degenerative diseases: at the crossroad between genes and diet

2020 ◽  
Vol 53 (383) ◽  
pp. MISC1-MISC3
Author(s):  
Andrea Maugeri
Keyword(s):  
Dna Methylation ◽  
Methylation Level ◽  
Integrated Approach ◽  
Dietary Factors ◽  
Epigenetic Mechanisms ◽  
Degenerative Diseases ◽  
Retinal Cells ◽  
Significant Difference ◽  
Retinal Degenerative Diseases ◽  
The Impact

Retinal degenerative diseases are the leading causes of blindness and low vision among working-age and older adults worldwide, with 170 and 130 million individuals suffering from age-related macular degeneration (AMD) and diabetic retinopathy, respectively. Although several studies began to show benefits from dietary interventions against retinal degenerative disease, an integrated approach is needed to understand molecular mechanisms underpinning the protective or risky effect of dietary factors. A specific area of research that elucidates mechanisms involved in gene-diet interaction is the Nutri-epigenomics, the study of the impact of diet on gene expression by modulating epigenetic mechanisms. The present research investigated the role of DNA methylation – one of the most commonly analysed epigenetic mechanisms - in the pathophysiology of retinal degenerative diseases, by exploiting a multiple integrated approach. In vitro studies initially helped us to understand how pathological features of retinal degeneration (e.g. oxidative stress, inflammation and hyperglycaemia) modulated functions of enzymes involved in the methylation of Long Interspersed Nuclear Element 1 (LINE-1) sequences in retinal cells. We also proved that some nutrients (e.g. resveratrol and curcumin) might counteract these effects and restore DNA methylation level in retinal cells under oxidative, inflammatory and high glucose conditions. We further analysed whether LINE-1 methylation level differed between patients with AMD and controls without posterior segment eye diseases. Interestingly, we noted a significant difference between the two groups, with higher LINE-1 methylation level in blood samples from AMD patients. This evidence -albeit promising for biomarker discovery- requires confirmation by further large-size prospective studies taking into account different factors. Our research, in fact, also suggested that the risk of retinal degenerative diseases derives from the combination of genetic risk variants, clinical characteristics, environmental exposures and unhealthy lifestyles, which in turn are interrelated. Thus, it would be interesting to study how the exposome -the totality of exposures individuals experience over the course of life- might induce epigenetic mechanisms able to reduce or increase the risk for retinal degenerative diseases.

NIMG-13. RESPONSE ASSESSMENT IN GLIOBLASTOMA PATIENTS TREATED WITH DENDRITIC CELL-BASED IMMUNOTHERAPY: A COMPARATIVE ANALYSIS OF MACDONALD, RANO, MRANO, IRANO AND VOLUMETRIC MEASUREMENTS

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi130-vi130
Author(s):  
Johanna Heugenhauser ◽  
Malik Galijasevic ◽  
Stephanie Mangesius ◽  
Johanna Buchroithner ◽  
Friedrich Erhart ◽  
...  
Keyword(s):  
Dendritic Cell ◽  
Progression Free Survival ◽  
Response Assessment ◽  
Assessment Tools ◽  
Assessment Criteria ◽  
Newly Diagnosed ◽  
Significant Difference ◽  
Different Response ◽  
The Impact ◽  
Spearman Test

Abstract INTRODUCTION Response assessment in the treatment of glioblastoma (GB) based on MR-imaging is still challenging, in particular for immunotherapeutic strategies. Several assessment tools have been proposed. In this post-hoc analysis we compared response assessment criteria (MacDonald, RANO, mRANO, Vol.-mRANO, iRANO) in newly diagnosed GB patients treated with tumor lysate-charged autologous dendritic cells (Audencel) and determined the differences in prediction of progression free survival (PFS) and overall survival (OS). METHODS 76 patients with newly diagnosed GB enrolled in a multicenter randomized phase II trial receiving standard of care (SOC, n= 40) or SOC + Audencel vaccine (n= 36) were included. Tumor volumes were calculated by semiautomatic segmentation. To detect differences in PFS among the assessment criteria Kruskal-Wallis-test, for correlation analysis Spearman test was used. RESULTS There was a significant difference in median PFS based on the different assessments (mRANO 8.55 months [9.10-14.03], Vol.-mRANO 8.61 months [9.72-14.92] compared to MacDonald 4.04 months [5.21-8.75] and RANO 4.16 months [5.28-8.61]. For the vaccination arm only, median PFS by iRANO was 5.95 months [5.70-11.54]). There was no difference in PFS between SOC and SOC + Audencel using the different response criteria. The best correlation between PFS and OS was detected for mRANO (r= 0.65, p< 0.001) and Vol.-mRANO (r= 0.69, p< 0.001). At an 8-month landmark, the impact of progressive disease on median OS was best shown for mRANO (13.70 months [13.13-18.98], and Vol.-mRANO 12.03 months [12.51-17.94]) compared to MacDonald 17.97 months [15.45-20.92], RANO 17.97 months [15.92-20.95] and iRANO 17.34 months [14.99-22.73]. CONCLUSION When comparing different response assessments in GB patients treated with dendritic cell-based immunotherapy the best correlation between PFS and OS was observed for mRANO and Vol.-mRANO. Overall, no difference in PFS and OS was seen between the two treatment arms. iRANO was not superior for predicting OS in patients treated with Audencel.

Pseudopestalotiopsis gilvanii sp. nov. and Neopestalotiopsis formicarum leaves spot pathogens from guarana plant: a new threat to global tropical hosts

Phytotaxa ◽  
2021 ◽  
Vol 489 (2) ◽  
pp. 121-139
Author(s):  
GILVANA F. GUALBERTO ◽  
ARICLÉIA DE M. CATARINO ◽  
THIAGO F. SOUSA ◽  
JEFERSON C. CRUZ ◽  
ROGÉRIO E. HANADA ◽  
...  
Keyword(s):  
Plant Pathogen ◽  
Elaeis Guineensis ◽  
Elongation Factor ◽  
Leaf Tissue ◽  
Euterpe Oleracea ◽  
Internal Transcribed Spacer Region ◽  
Tropical Regions ◽  
Tropical Plants ◽  
Wide Range ◽  
Genes Encoding

Pestalotioid species (Pestalotiopsis, Pseudopestalotiopsis and Neopestalotiopsis) cause extremely damaging diseases in a wide range of hosts across the word. Recently, pestalotioid strains isolated from damaged guarana leaf tissue were subject to morphological and molecular characterization. Six monosporic isolates were obtained and analysed based on the following conidial characters: length, width, septation, absence or presence of basal appendage, number and length of apical appendages. For phylogenetic inference, sequences of the Internal Transcribed Spacer region (ITS), partial sequences of the genes encoding the translation elongation factor 1-α (tef1-α) and β-tubulin (tub2) were used. Three out of six strains analysed were identified as Neopestalotiopsis formicarum, while the three other isolates are described here as a new species of Pseudopestalotiopsis, named Ps. gilvanii sp. nov.. The pathogenicity of N. formicarum and Ps. gilvanii were confirmed following Koch’s postulate. Besides guarana, the potential of N. formicaram and Ps. gilvanii to cause diseases in other economically important tropical plants were investigated. Ps. gilvanii was pathogenic to açaí palms (Euterpe oleracea, E. precatoria), and oil palm (Elaeis guineensis), but not to banana (Musa paradisiaca var. pacovan) and rubber trees (Hevea brasiliensis). N. formicarum was not pathogenic to rubber trees but was pathogenic to other species tested. To our knowledge this is the first report of N. formicarum as a plant pathogen in the guarana plant, and Ps. gilvanii as novel plant pathogen capable of causing disease in important plant crops from tropical regions.

scholarly journals DNA Methylation of Steroidogenic Enzymes in Benign Adrenocortical Tumors: New Insights in Aldosterone-Producing Adenomas

2020 ◽  
Vol 105 (12) ◽  
pp. e4605-e4615
Author(s):  
Guido Di Dalmazi ◽  
Luca Morandi ◽  
Beatrice Rubin ◽  
Catia Pilon ◽  
Sofia Asioli ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Outcome Measure ◽  
Cushing Syndrome ◽  
Steroidogenic Enzymes ◽  
Gene Expressions ◽  
Main Outcome Measure ◽  
Adrenocortical Tumors ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Fresh Frozen

Abstract Context DNA methylation has been identified among putative regulatory mechanisms for CYP11B2 expression in primary aldosteronism. Objective The objective of this work is to investigate DNA methylation and expression of genes encoding steroidogenic enzymes in benign adrenocortical tumors. Design and Setting This cross-sectional study took place at university hospitals. Patients We collected fresh-frozen tissues from patients with benign adrenocortical adenomas (n = 48) (nonfunctioning n = 9, autonomous cortisol secretion n = 9, Cushing syndrome n = 17, aldosterone-producing [APA] n = 13) and adrenal cortex adjacent to APA (n = 12). We collected formalin-fixed, paraffin-embedded (FFPE) specimens of paired APA and concurrent aldosterone-producing cell clusters (APCCs) (n = 6). Intervention DNA methylation levels were evaluated by quantitative bisulfite next-generation sequencing in fresh-frozen tissues (CYP11A1, CYP11B1, CYP11B2, CYP17A1, CYP21A2, HSD3B1, HSD3B2, NR5A1, STAR, and TSPO) and FFPE APA/APCC paired samples (CYP11B2). CYP11B1, CYP11B2, CYP17, CYP21, and STAR gene expressions were examined by quantitative real-time polymerase chain reaction. Main Outcome Measure The main outcome measure was DNA methylation. Results CYP11B2 methylation levels were significantly lower in APA than in other adrenal tissues (P < .001). Methylation levels of the remaining genes were comparable among groups. Overall, CYP11B2 expression and DNA methylation were negatively correlated (ρ = –0.379; P = .003). In FFPE-paired APA/APCC samples, CYP11B2 methylation level was significantly lower in APA than in concurrent APCCs (P = .028). Conclusions DNA methylation plays a regulatory role for CYP11B2 expression and may contribute to aldosterone hypersecretion in APA. Lower CYP11B2 methylation levels in APA than in APCCs may suggest an APCC-to-APA switch via progressive CYP11B2 demethylation. Conversely, DNA methylation seems not to be relevant in regulating the expression of genes encoding steroidogenic enzymes other than CYP11B2.

scholarly journals Integrated Genome-Wide Analysis of an Isogenic Pair of Pseudomonas aeruginosa Clinical Isolates with Differential Antimicrobial Resistance to Ceftolozane/Tazobactam, Ceftazidime/Avibactam, and Piperacillin/Tazobactam

2020 ◽  
Vol 21 (3) ◽  
pp. 1026 ◽  
Author(s):  
Weihua Huang ◽  
Joelle El Hamouche ◽  
Guiqing Wang ◽  
Melissa Smith ◽  
Changhong Yin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Pseudomonas Aeruginosa ◽  
Antimicrobial Resistance ◽  
Multidrug Resistant ◽  
Clinical Isolates ◽  
Epigenetic Mechanism ◽  
Phenotypic Change ◽  
Genome Wide ◽  
Family Protein ◽  
Significant Difference

Multidrug-resistant (MDR) Pseudomonas aeruginosa is one of the main causes of morbidity and mortality in hospitalized patients and the leading cause of nosocomial infections. We investigated, here, two MDR P. aeruginosa clinical isolates from a hospitalized patient with differential antimicrobial resistance to ceftazidime/avibactam (CZA), ceftolozane/tazobactam (C/T), and piperacillin/tazobactam (P/T). Their assembled complete genomes revealed they belonged to ST235, a widespread MDR clone; and were isogenic with only a single nucleotide variant, causing G183D mutation in AmpC β-lactamase, responsible for a phenotypic change from susceptible to resistant to CZA and C/T. Further epigenomic profiling uncovered two conserved DNA methylation motifs targeted by two distinct putative methyltransferase-containing restriction-modification systems, respectively; more intriguingly, there was a significant difference between the paired isolates in the pattern of genomic DNA methylation and modifications. Moreover, genome-wide gene expression profiling demonstrated the inheritable genomic methylation and modification induced 14 genes being differentially regulated, of which only toxR (downregulated), a regulatory transcription factor, had its promoter region differentially methylate and modified. Since highly expressed opdQ encodes an OprD porin family protein, therefore, we proposed an epigenetic regulation of opdQ expression pertinent to the phenotypic change of P. aeruginosa from resistant to susceptible to P/T. The disclosed epigenetic mechanism controlling phenotypic antimicrobial resistance deserves further experimental investigation.

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