Electrophoretic mobility of semi-flexible double-stranded DNA in defect-controlled polymer networks: Mechanism investigation and role of structural parameters

2015 ◽  
Vol 142 (23) ◽  
pp. 234904 ◽  
Author(s):  
Kateryna Khairulina ◽  
Xiang Li ◽  
Kengo Nishi ◽  
Mitsuhiro Shibayama ◽  
Ung-il Chung ◽  
...  
Keyword(s):  
Electrophoretic Mobility ◽  
Structural Parameters ◽  
Polymer Networks ◽  
Double Stranded Dna

scholarly journals A Guide through the Dental Dimethacrylate Polymer Network Structural Characterization and Interpretation of Physico-Mechanical Properties

Materials ◽  
2019 ◽  
Vol 12 (24) ◽  
pp. 4057 ◽  
Author(s):  
Izabela Maria Barszczewska-Rybarek
Keyword(s):  
Mechanical Properties ◽  
Chemical Structure ◽  
Structural Parameters ◽  
Polymer Network ◽  
Polymer Networks ◽  
Impact Resistance ◽  
Organic Matrices ◽  
Dental Restorative

Material characterization by the determination of relationships between structure and properties at different scales is essential for contemporary material engineering. This review article provides a summary of such studies on dimethacrylate polymer networks. These polymers serve as photocuring organic matrices in the composite dental restorative materials. The polymer network structure was discussed from the perspective of the following three aspects: the chemical structure, molecular structure (characterized by the degree of conversion and crosslink density (chemical as well as physical)), and supramolecular structure (characterized by the microgel agglomerate dimensions). Instrumental techniques and methodologies currently used for the determination of particular structural parameters were summarized. The influence of those parameters as well as the role of hydrogen bonding on basic mechanical properties of dimethacrylate polymer networks were finally demonstrated. Mechanical strength, modulus of elasticity, hardness, and impact resistance were discussed. The issue of the relationship between chemical structure and water sorption was also addressed.

Exploring secondary interactions and the role of temperature in moisture-contaminated polymer networks through molecular simulations

Soft Matter ◽  
2021 ◽  
Vol 17 (10) ◽  
pp. 2942-2956
Author(s):  
Rishabh D. Guha ◽  
Ogheneovo Idolor ◽  
Katherine Berkowitz ◽  
Melissa Pasquinelli ◽  
Landon R. Grace
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Temperature Variation ◽  
Polymer Networks ◽  
Molecular Simulations ◽  
Effect Of Temperature ◽  
Secondary Interactions ◽  
Dynamics Simulations ◽  
Secondary Bonding

We investigated the effect of temperature variation on the secondary bonding interactions between absorbed moisture and epoxies with different morphologies using molecular dynamics simulations.

scholarly journals Cytosolic Ribosomal Mutations That Abolish Accumulation of Circular Intron in the Mitochondria Without Preventing Senescence of Podospora anserina

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 697-705 ◽  
Author(s):  
Philippe Silar ◽  
France Koll ◽  
Michèle Rossignol
Keyword(s):  
Mitochondrial Dna ◽  
Ribosomal Proteins ◽  
Podospora Anserina ◽  
Cox1 Gene ◽  
Accuracy Control ◽  
Additional Function ◽  
Mutant Proteins ◽  
Double Stranded Dna ◽  
Dna Modifications

The filamentous fungus Podospora anserina presents a degeneration syndrome called Senescence associated with mitochondrial DNA modifications. We show that mutations affecting the two different and interacting cytosolic ribosomal proteins (S7 and S19) systematically and specifically prevent the accumulation of senDNAα (a circular double-stranded DNA plasmid derived from the first intron of the mitochondrial cox1 gene or intron α) without abolishing Senescence nor affecting the accumulation of other usually observed mitochondrial DNA rearrangements. One of the mutant proteins is homologous to the Escherichia coli S4 and Saccharomyces cerevisiae S13 ribosomal proteins, known to be involved in accuracy control of cytosolic translation. The lack of accumulation of senDNAα seems to result from a nontrivial ribosomal alteration unrelated to accuracy control, indicating that S7 and S19 proteins have an additional function. The results strongly suggest that modified expression of nucleus-encoded proteins contributes to Senescence in P. anserina. These data do not fit well with some current models, which propose that intron α plays the role of the cytoplasmic and infectious Determinant of Senescence that was defined in early studies.

scholarly journals Structural studies on M. tuberculosis O6-methylguanine methyltransferase

2014 ◽  
Vol 70 (a1) ◽  
pp. C832-C832
Author(s):  
Menico Rizzi ◽  
Riccardo Miggiano ◽  
Samarpita Lahiri ◽  
Giuseppe Perugino ◽  
Maria Ciaramella ◽  
...  
Keyword(s):  
Excision Repair ◽  
Single Step ◽  
Double Stranded Dna ◽  
Nucleotide Excision ◽  
Enzymatic Systems ◽  
Methylguanine Methyltransferase ◽  
Mutagenic Effects ◽  
Wild Type Form

Mycobacterium tuberculosis (MTB) is an extremely well adapted human pathogen capable to survive for decades inside the hostile environment represented by the host's infected macrophages despite exposure to multiple potential DNA-damaging stresses. In order to maintain a remarkable low level of genetic diversity, MTB deploys different strategies of DNA repair, including multi-enzymatic systems, such as Nucleotide Excision Repair, and single-step repair. In particular, to counteract the mutagenic effects of DNA alkylation, MTB performs the direct alkylated-base reversal by sacrificing one molecule of a DNA-protein alkyltransferase, such as O6-methylguanine methyltransferase (OGT; orf: Rv1316c). We present here the biochemical and structural characterization of recombinant mycobacterial OGT (MtOGT) in its wild-type form along with its mutated variants mimicking the ones occurring in relevant clinical strains (i.e. MtOGT-T15S and MtOGT-R37L). Our studies reveal that MtOGT-R37L is severely impaired in its activity as consequence of its ten-fold lower affinity for modified double-stranded DNA (dsDNA) (1). Further investigations on a new structure-based panel of OGT versions, designed to explore different molecular environment at position 37, allowed us a better understanding of the functional role of the MtOGT Arg37-bearing loop during catalysis. Moreover, we solved the crystal structure of MtOGT in covalent complex with modified dsDNA that reveals an unprecedented MtOGT::DNA architecture, suggesting that the MtOGT monomer performing the catalysis needs assisting unreacted subunits during cooperative DNA binding. This work is supported by European Community FP7 program SYSTEMTB (Health-F4-2010-241587)

scholarly journals CRISPR enriches for cells with mutations in a p53-related interactome, and this can be inhibited

2021 ◽  
Author(s):  
Long Jiang ◽  
Katrine Ingelshed ◽  
Yunbing Shen ◽  
Sanjaykumar V. Boddul ◽  
Vaishnavi Srinivasan Iyer ◽  
...  
Keyword(s):  
Cellular Response ◽  
Human Cancer ◽  
Genetic Alterations ◽  
Dna Breaks ◽  
Data Set ◽  
Human Cancer Cell Lines ◽  
Cycle Arrest ◽  
Double Stranded Dna ◽  
A Cell

CRISPR/Cas9 can be used to inactivate or modify genes by inducing double-stranded DNA breaks1–3. As a protective cellular response, DNA breaks result in p53-mediated cell cycle arrest and activation of cell death programs4,5. Inactivating p53 mutations are the most commonly found genetic alterations in cancer, highlighting the important role of the gene6–8. Here, we show that cells deficient in p53, as well as in genes of a core CRISPR-p53 tumor suppressor interactome, are enriched in a cell population when CRISPR is applied. Such enrichment could pose a challenge for clinical CRISPR use. Importantly, we identify that transient p53 inhibition suppresses the enrichment of cells with these mutations. Furthermore, in a data set of >800 human cancer cell lines, we identify parameters influencing the enrichment of p53 mutated cells, including strong baseline CDKN1A expression as a predictor for an active CRISPR-p53 axis. Taken together, our data identify strategies enabling safe CRISPR use.

scholarly journals Structure and Strength of Artificial Soils Containing Monomineral Clay Fractions

Materials ◽  
2021 ◽  
Vol 14 (16) ◽  
pp. 4688
Author(s):  
Grzegorz Jozefaciuk ◽  
Kamil Skic ◽  
Agnieszka Adamczuk ◽  
Patrycja Boguta ◽  
Krzysztof Lamorski
Keyword(s):  
Fine Particles ◽  
Structural Parameters ◽  
Fractal Dimensions ◽  
Soil Strength ◽  
Uniaxial Compression Test ◽  
Mineral Particle ◽  
Type Curve ◽  
Surface Fractal ◽  
First Time

Structure and strength are responsible for soil physical properties. This paper determines in a uniaxial compression test the strength of artificial soils containing different proportions of various clay-size minerals (cementing agents) and silt-size feldspar/quartz (skeletal particles). A novel empirical model relating the maximum stress and the Young’s modulus to the mineral content basing on the Langmuir-type curve was proposed. By using mercury intrusion porosimetry (MIP), bulk density (BD), and scanning electron microscopy (SEM), structural parameters influencing the strength of the soils were estimated and related to mechanical parameters. Size and shape of particles are considered as primary factors responsible for soil strength. In our experiments, the soil strength depended primarily on the location of fine particles in respect to silt grains and then, on a mineral particle size. The surface fractal dimension of mineral particles played a role of a shape parameter governing soil strength. Soils containing minerals of higher surface fractal dimensions (rougher surfaces) were more mechanically resistant. The two latter findings appear to be recognized herein for the first time.

scholarly journals PARN-like Proteins Regulate Gene Expression in Land Plant Mitochondria by Modulating mRNA Polyadenylation

2021 ◽  
Vol 22 (19) ◽  
pp. 10776
Author(s):  
Takashi Hirayama
Keyword(s):  
Mitochondrial Gene ◽  
Plant Mitochondria ◽  
Short Review ◽  
Land Plant ◽  
Mrna Processing ◽  
Regulate Gene Expression ◽  
Double Stranded Dna ◽  
Regulatory Systems ◽  
Mrna Polyadenylation

Mitochondria have their own double-stranded DNA genomes and systems to regulate transcription, mRNA processing, and translation. These systems differ from those operating in the host cell, and among eukaryotes. In recent decades, studies have revealed several plant-specific features of mitochondrial gene regulation. The polyadenylation status of mRNA is critical for its stability and translation in mitochondria. In this short review, I focus on recent advances in understanding the mechanisms regulating mRNA polyadenylation in plant mitochondria, including the role of poly(A)-specific ribonuclease-like proteins (PARNs). Accumulating evidence suggests that plant mitochondria have unique regulatory systems for mRNA poly(A) status and that PARNs play pivotal roles in these systems.

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