In Silico Insight into Nucleosome Repositioning Via Oxygen Delivery and Extracellular Movement

2021 ◽  
Author(s):  
Jacob Duane Madison
Keyword(s):  
In Silico ◽  
Binding Motif ◽  
Oxygen Intake ◽  
Ph Domain ◽  
Nutrient Delivery ◽  
Histone Octamer ◽  
Partial Pressures ◽  
Energy Dependent ◽  
Insight Into ◽  
Biomechanical Strain

Abstract OBJECTIVEHistones and resulting nucleosomes occur within DNA regulating gene expression by slowing, pausing, or halting transcriptional machinery. Positions within the genome have been found with higher affinity for the histone octamer than others. Histone/nucleosome repositioning is adjusted via energy dependent remodeling complexes, and a harmonizing array of constellation proteins and molecules. The energy required to create transcriptional environments is created through oxygen intake, nutrient presence, and extracellular movement. In this paper we aim to help facilitate an in silico framework for further experimentation into how partial pressures of oxygen and other gases impact genetic transcription along with extracellular movement and nutrient delivery.RESULTSCell and tissue culture experimentation with biomechanical strain and variable partial pressures of oxygen and other gases can be made into the expression levels of genes such as PH domain leucine-rich repeat-containing protein phosphatase 1 (PHLPP1), and Neuroligin 1 (NLGN1). These genes show in silico to have a higher affinity for a histone octamer binding motif, needing adequate cellular energy to be expressed. Extracellular movement and adequate cellular oxygenation are required to properly reposition nucleosome sequences for transcription.

Insight into the impact of EGFR L792Y/F/H mutations on sensitivity to osimertinib: an in silico study

2021 ◽  
Vol 45 (10) ◽  
pp. 4756-4765
Author(s):  
Daoxing Chen ◽  
Liting Zhang ◽  
Yanan Liu ◽  
Jiali Song ◽  
Jingwen Guo ◽  
...  
Keyword(s):  
In Silico ◽  
In Silico Study ◽  
The Impact ◽  
Insight Into

EGFR L792Y/F/H mutation makes it difficult for Osimertinib to recognize ATP pockets.

In vivo/in silico insight into the effect of titanium dioxide nanoparticle on serum paraoxonase 1 activity in rat

2021 ◽  
pp. 1-11
Author(s):  
Hessameddin Mortazavi ◽  
Hossein Omidi-Ardali ◽  
Seyed Asadollah Amini ◽  
Javad Saffari-Chaleshtori ◽  
Keihan Ghatreh Samani
Keyword(s):  
Titanium Dioxide ◽  
In Silico ◽  
Paraoxonase 1 ◽  
Titanium Dioxide Nanoparticle ◽  
Serum Paraoxonase ◽  
Insight Into

scholarly journals A strategy to suppress STAT1 signalling conserved in pathogenic poxviruses and paramyxoviruses

2021 ◽  
Author(s):  
Callum Talbot-Cooper ◽  
Teodors Pantelejevs ◽  
John P. Shannon ◽  
Christian R. Cherry ◽  
Marcus T. Au ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Nipah Virus ◽  
Sh2 Domain ◽  
Binding Motif ◽  
Virus Infections ◽  
Stat Proteins ◽  
Interferon Stimulated Genes ◽  
Independent Mode ◽  
Insight Into ◽  
Diverse Virus

The induction of interferon-stimulated genes by signal transducer and activator of transcription (STAT) proteins, is a critical host defence to fight virus infections. Here, a highly expressed poxvirus protein 018 is shown to inhibit IFN-induced signalling by binding the SH2 domain of STAT1 to prevent STAT1 association with an activated IFN receptor. Despite the presence of additional inhibitors of IFN-induced signalling, a poxvirus lacking 018 was attenuated in mice. The 2.0-angstrom crystal structure of the 018:STAT1 complex reveals a mechanism for a high-affinity, pTyr-independent mode of binding to an SH2 domain. Furthermore, the STAT1 binding motif of 018 shows sequence similarity to the STAT1-binding proteins from Nipah virus, which like 018, block the association of STAT1 with an IFN receptor. Taken together, these results provide detailed mechanistic insight into a potent mode of STAT1 antagonism, found to exist in genetically diverse virus families.

How atmospheric escape sculped the evolution of the Martian CO2 atmosphere over time

2021 ◽  
Author(s):  
Manuel Scherf ◽  
Herbert Lichtenegger ◽  
Sergey Dyadechkin ◽  
Helmut Lammer ◽  
Raven Adam ◽  
...  
Keyword(s):  
Numerical Models ◽  
Atmospheric Escape ◽  
Ion Escape ◽  
Thermal Escape ◽  
Partial Pressures ◽  
Argon Isotopes ◽  
Atmospheric Loss ◽  
4.1 Ga ◽  
Insight Into ◽  
Volcanic Outgassing

<p>Mars likely had a denser atmosphere during the Noachian eon about 3.6 to 4.0 billion years ago (Ga). How dense this atmosphere might have been, and which escape mechanisms dominated its loss are yet not entirely clear. However, non-thermal escape processes and potential sequestration into the ground are believed to be the main drivers for atmospheric loss from the present to about 4.1 Ga.</p> <p>To evaluate non-thermal escape over the last ~4.1 billion years, we simulated the ion escape of Mars' CO<sub>2</sub> atmosphere caused by its dissociation products C and O atoms with numerical models of the upper atmosphere and its interaction with the solar wind (see Lichtenegger et al. 2021; https://arxiv.org/abs/2105.09789). We use the planetward-scattered pick-up ions for sputtering estimates of exospheric particles including <sup>36</sup>Ar and <sup>38</sup>Ar isotopes, and compare ion escape, with sputtering and photochemical escape rates. For solar EUV fluxes ≥3 times the present-day Sun (earlier than ~2.6 Ga) ion escape becomes the dominant atmospheric non-thermal loss process until thermal escape takes over during the pre-Noachian eon (earlier than ~4.0 - 4.1 Ga). If we extrapolate the total escape of CO<sub>2</sub>-related dissociation products back in time until ~4.1 Ga, we obtain a theoretical equivalent to CO<sub>2</sub> partial pressure of more than ~3 bar, but this amount did not necessarily have to be present and represents a maximum that could have been lost to space within the last ~4.1 Ga.</p> <p>Argon isotopes can give an additional insight into the evolution of the Martian atmosphere. The fractionation of <sup>36</sup>Ar/<sup>38</sup>Ar isotopes through sputtering and volcanic outgassing from its initial chondritic value of 5.3, as measured in the 4.1 billion years old Mars meteorite ALH 84001, until the present day can be reproduced for assumed CO<sub>2</sub> partial pressures between ~0.2-3.0 bar, depending on the cessation time of the Martian dynamo (assumed between 3.6-4.0 Ga) - if atmospheric sputtering of Ar started afterwards. The later the dynamo ceased away, the lower the pressure could have been to reproduce <sup>36</sup>Ar/<sup>38</sup>Ar.</p> <p>Prior to ~4.1 Ga (i.e., during the pre-Noachian eon), thermal escape should have been the most important driver of atmospheric escape at Mars, and together with non-thermal losses, might have prevented a stable and dense CO<sub>2</sub> atmosphere during the first ~400 million years. Our results indicate that, while Mars could have been warm and wet at least sporadically between ~3.6-4.1 Ga, it likely has been cold and dry during the pre-Noachian eon (see also Scherf and Lammer 2021; https://arxiv.org/abs/2102.05976).</p>

Biosynthesis of the uridine-derived nucleoside antibiotic A-94964: identification and characterization of the biosynthetic gene cluster provide insight into the biosynthetic pathway

2019 ◽  
Vol 17 (3) ◽  
pp. 461-466 ◽  
Author(s):  
Taro Shiraishi ◽  
Makoto Nishiyama ◽  
Tomohisa Kuzuyama
Keyword(s):  
Gene Cluster ◽  
In Silico ◽  
Biosynthetic Pathway ◽  
Gene Deletion ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Identification And Characterization ◽  
Insight Into

The biosynthetic pathway of the uridine-derived nucleoside antibiotic A-94964 was proposed via in silico analysis coupled with gene deletion experiments.

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