Assessment of Epigenetic and Phenotypic Variation in Populus nigra Regenerated via Sequential Regeneration

Somatic variation has been demonstrated in tissue culture regenerated plants of many species. In the genus Populus, phenotypic variation caused by changes in 5-methylcytosine within the plant genome have been reported. To date, the phenotypic and epigenetic stability of plants regenerated from sequential regeneration has not been tested in trees. In this study, we detected DNA methylation of CCGG sites in regenerated plants of five generations in Populus nigra using methylation-sensitive amplified polymorphisms, and evaluated their growth performance and physiological traits. About 10.86–26.80% of CCGG sites in the regenerated plant genome were demethylated and 5.50–8.45% were methylated, resulting in significantly lower DNA methylation levels among all regenerated plants than among donor plants. We detected a significant difference in methylation levels between first regeneration regenerated plants (G1) and those of the other four generations (G2–G5); there were no significant differences among the four later generations. Therefore, the dramatic decrease in DNA methylation levels occurred only in the first and second poplar regenerations; levels then stabilized later in the regeneration process, indicating that two regeneration events were sufficient to change the methylation statuses of almost all CCGG sites sensitive to regeneration. Differences in growth and physiological traits were observed between regenerated plants and donor plants, but were significant only among plants of certain generations. Significant correlations were detected between methylation level and transpiration rate, net photosynthetic rate, peroxidase activity, and instant water utilization efficiency, indicating the involvement of epigenetic regulation in this unpredictable phenotypic variation.

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DNA methylation in plants and its role in tissue culture

Genome ◽

10.1139/g89-130 ◽

1989 ◽

Vol 31 (2) ◽

pp. 717-729 ◽

Cited By ~ 78

Author(s):

P. T. H. Brown

Keyword(s):

Dna Methylation ◽

Tissue Culture ◽

Zea Mays ◽

Somaclonal Variation ◽

Inbred Line ◽

Phenotypic Variation ◽

Methylation Status ◽

Structural Genes ◽

Gene Methylation ◽

Regenerated Plants

Regeneration of plants via tissue culture often results in a number of plants subsequently showing phenotypic or genotypic deviations from the parental type. This variation has been called somaclonal variation. In an analysis of regenerated Zea mays plants of the inbred line A188, high levels of phenotypic variation were observed. Subsequent analysis of these regenerated plants shows that a high proportion of the regenerants demonstrate significant alterations in the methylation status of both housekeeping and structural genes. These results are described and the theory of gene methylation is reviewed with regard to the differences that exist between plant and animal systems.Key words: 5-methylcytosine, 5-azacytidine, tissue culture, cereals, somaclonal variation.

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MULTIPLE ALLELE APPROACH TO THE STUDY OF GENES IN DROSOPHILA MELANOGASTER THAT ARE INVOLVED IN IMAGINAL DISC DEVELOPMENT

Genetics ◽

10.1093/genetics/89.2.355 ◽

1978 ◽

Vol 89 (2) ◽

pp. 355-370 ◽

Cited By ~ 2

Author(s):

Allen Shearn ◽

Grafton Hersperger ◽

Evelyn Hersperger ◽

Ellen Steward Pentz ◽

Paul Denker

Keyword(s):

Drosophila Melanogaster ◽

Phenotypic Variation ◽

Mutant Allele ◽

Imaginal Disc ◽

Reference Allele ◽

Multiple Allele ◽

Significant Difference ◽

Chromosome Mutations ◽

Cold Sensitive

ABSTRACT The phenotypes of five different lethal mutants of Drosophila melanogaster that have small imaginal discs were analyzed in detail. From these results, we inferred whether or not the observed imaginal disc phenotype resulted exclusively from a primary imaginal disc defect in each mutant. To examine the validity of these inferences, we employed a multiple-allele method. Lethal alleles of the five third-chromosome mutations were identified by screening EMS-treated chromosomes for those which fail to complement with a chromosome containing all five reference mutations. Twenty-four mutants were isolated from 13,197 treated chromosomes. Each of the 24 was then tested for complementation with each of the five reference mutants. There was no significant difference in the mutation frequencies at these five loci. The stage of lethality and the imaginal disc morphology of each mutant allele were compared to those of its reference allele in order to examine the range of defects to be found among lethal alleles of each locus. In addition, hybrids of the alleles were examined for intracistronic complementation. For two of the five loci, we detected no significant phenotypic variation among lethal alleles. We infer that each of the mutant alleles at these two loci cause expression of the null activity phenotype. However, for the three other loci, we did detect significant phenotypic variation among lethal alleles. In fact, one of the mutant alleles at each of these three loci causes no detectable imaginal disc defect. This demonstrates that attempting to assess the developmental role of a gene by studying a single mutant allele may lead to erroneous conclusions. As a byproduct of the mutagenesis procedure, we have isolated two dominant, cold-sensitive mutants.

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Transformative Learning in Mastery-Oriented CS0 Course

Higher Education for the Future ◽

10.1177/23476311211007255 ◽

2021 ◽

pp. 234763112110072

Author(s):

Srinivasan Lakshminarayanan ◽

N. J. Rao ◽

G. K. Meghana

Keyword(s):

Transformative Learning ◽

First Year ◽

Guided Discovery ◽

Engineering Programs ◽

Transformative Experiences ◽

Significant Difference ◽

Cognitive Levels ◽

Almost All ◽

Core Course

The introductory programming course, commonly known as CS1 and offered as a core course in the first year in all engineering programs in India, is unique because it can address higher cognitive levels, metacognition and some aspects of the affective domain. It can provide much needed transformative experiences to students coming from a system of school education that is dominantly performance-driven. Unfortunately, the CS1 course, as practiced in almost all engineering programs, is also performance-driven because of a variety of compulsions. This paper suggests that the inclusion of a course CS0 can bring about transformative learning that can potentially make a significant difference in the quality of learning in all subsequent engineering courses. The suggested instruction design of this course takes the advantage of the unique features of a course in programming. The proposed CS0 course uses “extreme apprenticeship” and “guided discovery” methods of instruction. The effectiveness of these instruction methods was established through the use of the thematic analysis, a well-known qualitative research method, and the associated coding of transformative learning experiences and instruction components.

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Androgenic-Induced Transposable Elements Dependent Sequence Variation in Barley

International Journal of Molecular Sciences ◽

10.3390/ijms22136783 ◽

2021 ◽

Vol 22 (13) ◽

pp. 6783

Author(s):

Renata Orłowska ◽

Katarzyna A. Pachota ◽

Wioletta M. Dynkowska ◽

Agnieszka Niedziela ◽

Piotr T. Bednarek

Keyword(s):

Dna Methylation ◽

Transposable Elements ◽

Dna Sequence ◽

Sequence Variation ◽

Nuclear Dna ◽

Point Mutations ◽

Mobile Elements ◽

Dna Demethylation ◽

Plant Genome

A plant genome usually encompasses different families of transposable elements (TEs) that may constitute up to 85% of nuclear DNA. Under stressful conditions, some of them may activate, leading to sequence variation. In vitro plant regeneration may induce either phenotypic or genetic and epigenetic changes. While DNA methylation alternations might be related, i.e., to the Yang cycle problems, DNA pattern changes, especially DNA demethylation, may activate TEs that could result in point mutations in DNA sequence changes. Thus, TEs have the highest input into sequence variation (SV). A set of barley regenerants were derived via in vitro anther culture. High Performance Liquid Chromatography (RP-HPLC), used to study the global DNA methylation of donor plants and their regenerants, showed that the level of DNA methylation increased in regenerants by 1.45% compared to the donors. The Methyl-Sensitive Transposon Display (MSTD) based on methylation-sensitive Amplified Fragment Length Polymorphism (metAFLP) approach demonstrated that, depending on the selected elements belonging to the TEs family analyzed, varying levels of sequence variation were evaluated. DNA sequence contexts may have a different impact on SV generated by distinct mobile elements belonged to various TE families. Based on the presented study, some of the selected mobile elements contribute differently to TE-related SV. The surrounding context of the TEs DNA sequence is possibly important here, and the study explained some part of SV related to those contexts.

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Do Deeper Levels of Cervical Biopsies Preceded by a Pap Smear Diagnosis of LSIL, ASCUS, or NILM/HPV+ Increase the Yield of Identifying Clinically Significant Lesions?

American Journal of Clinical Pathology ◽

10.1093/ajcp/aqaa161.356 ◽

2020 ◽

Vol 154 (Supplement_1) ◽

pp. S163-S164

Author(s):

K G Manjee ◽

W G Watkin

Keyword(s):

Pap Smear ◽

Past History ◽

Prior History ◽

Cervical Biopsy ◽

P16 Immunohistochemistry ◽

Hpv Status ◽

Significant Difference ◽

History Of ◽

Clinically Significant ◽

Almost All

Abstract Introduction/Objective Cervical biopsy is performed following an abnormal pap smear or positive HPV testing in an attempt to uncover clinically significant lesions [HSIL/invasive carcinoma (HSIL+)]. An excisional procedure is considered if biopsy confirms HSIL+. When preceded by pap smear of LSIL, ASCUS, NILM/HPV+ or persistent HPV, continued surveillance is recommended for biopsies showing no SIL or LSIL. In our laboratory, cervical biopsies are routinely sectioned at 3 levels. Deeper levels are often ordered when initial sections are non-diagnostic. p16 immunohistochemistry, with or without deeper levels, is often ordered to confirm HSIL, or to differentiate HSIL from mimics. In this study, we examine whether and in what clinical situations does obtaining additional levels uncover clinically significant lesions. Methods 430 cervical biopsies between January-May 2018, with recent cytology of LSIL, ASCUS or NILM/HPV+ were identified in the pathology database. HPV status (if known), final biopsy diagnosis and past history of LSIL/HSIL were recorded. For each biopsy, orders for additional levels and/or p16 immunohistochemistry were recorded resulting in 4 categories: C1-no additional levels or p16, C2-deeper only, C3-deeper+p16 and C4-p16 only. Final diagnoses were divided into HSIL+, LSIL and no SIL. Results There was no significant difference in prior history of LSIL/HSIL and HPV status between all categories. Biopsy results were as follows: HSIL+: 11/222 (5%) C1; 1/78 (1%) C2; 7/43 (16%) C3; 15/87 (17%) C4 LSIL: 91/222 (41%) C1; 7/78 (9%) C2; 16/43 (37%) C3; 35/87 (40%) C4 No SIL: 120/222 (54%) C1; 70/78 (90%) C2; 20/43 (46%) C3; 37/87 (42%) C4 The average number of additional levels in C2 and C3 was 3.8 and 1.8, respectively. Conclusion Deeper levels alone did not enhance the detection of HSIL+. Almost all LSIL/HSIL were detected when initial levels were diagnostic or suspicious and supported by p16 immunohistochemistry. 3 levels are adequate to detect clinically significant lesions.

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RT-PCR analysis of Deformed wing virus in honeybees (Apis mellifera) and mites (Varroa destructor)

Journal of General Virology ◽

10.1099/vir.0.81401-0 ◽

2005 ◽

Vol 86 (12) ◽

pp. 3419-3424 ◽

Cited By ~ 210

Author(s):

Constanze Yue ◽

Elke Genersch

Keyword(s):

Varroa Destructor ◽

Pcr Analysis ◽

Body Parts ◽

Rt Pcr ◽

Larval Food ◽

Viral Pathogen ◽

Deformed Wing Virus ◽

Significant Difference ◽

Almost All ◽

Viral Sequences

Deformed wing virus (DWV) is a honeybee viral pathogen either persisting as an inapparent infection or resulting in wing deformity. The occurrence of deformity is associated with the transmission of DWV through Varroa destructor during pupal stages. Such infections with DWV add to the pathology of V. destructor and play a major role in colony collapse in the course of varroosis. Using a recently developed RT-PCR protocol for the detection of DWV, individual bees and mites originating from hives differing in Varroa infestation levels and the occurrence of crippled bees were analysed. It was found that 100 % of both crippled and asymptomatic bees were positive for DWV. However, a significant difference in the spatial distribution of DWV between asymptomatic and crippled bees could be demonstrated: when analysing head, thorax and abdomen of crippled bees, all body parts were always strongly positive for viral sequences. In contrast, for asymptomatic bees viral sequences could be detected in RNA extracted from the thorax and/or abdomen but never in RNA extracted from the head. DWV replication was demonstrated in almost all DWV-positive body parts of infected bees. Analysing individual mites for the presence of DWV revealed that the percentage of DWV-positive mites differed between mite populations. In addition, it was demonstrated that DWV was able to replicate in some but not all mites. Interestingly, virus replication in mites was correlated with wing deformity. DWV was also detected in the larval food, implicating that in addition to transmission by V. destructor DWV is also transmitted by feeding.

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DIFFERENT APPROACHES OF CLIENTS AND CONSULTANTS TO CONTRACTORS’ QUALIFICATION AND SELECTION

Journal of Civil Engineering and Management ◽

10.3846/13923730.2005.9636357 ◽

2005 ◽

Vol 11 (4) ◽

pp. 267-276 ◽

Cited By ~ 4

Author(s):

Mehmedali Egemen ◽

Abdulrezak N. Mohamed

Keyword(s):

Construction Industry ◽

Selection Processes ◽

Significant Difference ◽

Different Types ◽

Almost All ◽

High Willingness

Nowadays, clients are the dominant groups in almost all types of industries. However, the construction industry is unique and consultants, as representatives of clients, are very important figures in this industry as well. By presenting survey findings of 91 clients and 50 consultants, this study reveals clients’ and consultants’ differing expectations of contracting organisations during contractor qualification and selection. The study has clearly confirmed the fact that consultants’ perspectives are rather different and their contractors’ expectations of their clients vary very significantly from the clients themselves. Furthermore, significantly different results were found even among different types of consultants and different categories of clients. Moreover, this study showed that both clients and consultants had high willingness to continue working with the same contractor in possible future works assuming they are satisfied with the previous works. The criteria, which contribute to achieving full client and/or consultant satisfaction and hence lead to possible repetitive works are identified and the results showed the existence of significant difference between clients and consultants perspectives regarding this issue as well. The framework presented within this paper aims to help the contracting organisations to compare and recognise the different approaches and perceptions of both clients and consultants during contractor qualification and selection processes. The contracting organisations in the related sectors will be able to use the framework provided within this study to recognise the overall demand in a more complete and better manner and hence formulate or modify strategies accordingly.

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DNA methylation-based sex classifier to predict sex and identify sex chromosome aneuploidy

10.1101/2020.10.19.345090 ◽

2020 ◽

Author(s):

Yucheng Wang ◽

Eilis Hannon ◽

Olivia A Grant ◽

Tyler J Gorrie-Stone ◽

Meena Kumari ◽

...

Keyword(s):

Dna Methylation ◽

Sex Chromosome ◽

Klinefelter Syndrome ◽

Association Studies ◽

Gene Expression Omnibus ◽

Sex Chromosome Aneuploidy ◽

Chromosome Aneuploidy ◽

Wide Range ◽

Almost All ◽

Methylation Patterns

AbstractSex is an important covariate of epigenome-wide association studies due to its strong influence on DNA methylation patterns across numerous genomic positions. Nevertheless, many samples on the Gene Expression Omnibus (GEO) frequently lack a sex annotation or are incorrectly labelled. Considering the influence that sex imposes on DNA methylation patterns, it is necessary to ensure that methods for filtering poor samples and checking of sex assignment are accurate and widely applicable. In this paper, we presented a novel method to predict sex using only DNA methylation density signals, which can be readily applied to almost all DNA methylation datasets of different formats (raw IDATs or text files with only density signals) uploaded to GEO. We identified 4345 significantly (p < 0.01) sex-associated CpG sites present on both 450K and EPIC arrays, and constructed a sex classifier based on the two first components of PCAs from the two sex chromosomes. The proposed method is constructed using whole blood samples and exhibits good performance across a wide range of tissues. We further demonstrated that our method can be used to identify samples with sex chromosome aneuploidy, this function is validated by five Turner syndrome cases and one Klinefelter syndrome case. The proposed method has been integrated into the wateRmelon Bioconductor package.

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

Bullettin of the Gioenia Academy of Natural Sciences of Catania ◽

10.35352/gioenia.v53i383.90 ◽

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.

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Evaluation of the relationship between MIH severity and dental fear among the children

Medical Science and Discovery ◽

10.36472/msd.v6i10.318 ◽

2019 ◽

Vol 6 (10) ◽

pp. 284-287

Author(s):

Can Özükoç

Keyword(s):

Behavioral Problems ◽

Dental Anxiety ◽

Pediatric Dentistry ◽

Dental Fear ◽

Common Condition ◽

Molar Incisor Hypomineralization ◽

Significant Difference ◽

Fear Survey Schedule ◽

Almost All ◽

The Relationship

Objective: Molar incisor hypomineralization (MIH), a quite common condition in pediatric dentistry, whose treatment might seem complicated, manifests itself with severe dental anxiety and fear that can cause behavioral problems. Although dental fear is seen in almost all cases, it is believed that dental fear will increase as the severity of MIH increases. This study evaluates the relationship between MIH severity and dental fear. Material and Methods: Children Fear Survey Schedule-Dental Subscale (CFSS-DS) was used to measure dental fear in 58 (51.79%) children whose teeth suffered from mild, moderate or severe MIH and 54 (48.21%) children with healthy teeth. Scores between 1 (not afraid at all) and 5 (very afraid) were given according to the responses. Each question was evaluated separately in order to obtain the total score. Results: Children with severe MIH who participated in the study were proved to be more afraid of the dentists, drill sounds, injections, placement of instruments in the mouth, choking and going to the hospital; and there was a statistically significant difference (p<0.05). Conclusion: Although it was observed that the severity of MIH and dental fear are correlated and dental fear increases with the increase in the MIH severity, further studies in this subject are necessary.

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