Results 21 to 30 of about 287,665 (235)
Optimal localization patterns in bacterial protein synthesis [PDF]
Physical Review E 98(3), 032417 (2018), 2019 In $\textit{Escherichia coli}$ bacterium, the molecular compounds involved in protein synthesis, messenger RNAs (mRNAs) and ribosomes, show marked intracellular localization patterns. Yet a quantitative understanding of the physical principles which would allow one to control protein synthesis by designing, bioengineering, and optimizing these ...
arxiv +1 more source
PCR amplification of a long rDNA segment with one primer pair in agriculturally important nematodes
Journal of Nematology, 2019 Ribosomal DNA has been a reliable source of taxonomic and phylogenetic markers due to its high copy number in the genome and stable variation with few polymorphisms due to the homogenizing effect of concerted evolution.
Carta L. K., Li S.
doaj +1 more source
Treacle controls the nucleolar response to rDNA breaks via TOPBP1 recruitment and ATR activation
Nature Communications, 2020 DNA double-strand breaks in ribosomal DNA repeats is associated with repression of ribosomal RNA synthesis. Here the authors reveal a cooperation between TOPBP1 and Treacle in the signaling cascade that triggers transcriptional inhibition and nucleolar ...
Clémence Mooser +15 more
doaj +1 more source
Physical modeling of ribosomes along messenger RNA: estimating kinetic parameters from ribosome profiling experiments using a ballistic model [PDF]
arXiv, 2022 Gene expression consists in the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. Here, by taking into account mRNA degradation, we model the motion of ribosomes along mRNA with a ballistic model where particles ...
arxiv
Thermodynamic cost, speed, fluctuations, and error reduction of biological copy machines [PDF]
J. Phys. Chem. Lett. (2020) 11, 3136-3143, 2020 Due to large fluctuations in cellular environments, transfer of information in biological processes without regulation is inherently error-prone. The mechanistic details of error-reducing mechanisms in biological copying processes have been a subject of active research; however, how error reduction of a process is balanced with its thermodynamic cost ...
arxiv +1 more source
Segregative phase separation scenario of the formation of the bacterial nucleoid [PDF]
Soft Matter 14 (2018) 7368-7381, 2018 The mechanism responsible for the compaction of the genomic DNA of bacteria inside a structure called the nucleoid is a longstanding but still lively debated question. Most puzzling is the fact that the nucleoid occupies only a small fraction of the cell, although it is not separated from the rest of the cytoplasm by any membrane and would occupy a ...
arxiv +1 more source
Kinetic Proofreading and the Limits of Thermodynamic Uncertainty [PDF]
Phys. Rev. E 101, 022415 (2020), 2019 To mitigate errors induced by the cell's heterogeneous noisy environment, its main information channels and production networks utilize the kinetic proofreading (KPR) mechanism. Here, we examine two extensively-studied KPR circuits, DNA replication by the T7 DNA polymerase and translation by the E. coli ribosome. Using experimental data, we analyze the
arxiv +1 more source
Mediating Ribosomal Competition by Splitting Pools [PDF]
LCSS Vol 5 Issue 5 (Nov 2020), 2020 Synthetic biology constructs often rely upon the introduction of "circuit" genes into host cells, in order to express novel proteins and thus endow the host with a desired behavior. The expression of these new genes "consumes" existing resources in the cell, such as ATP, RNA polymerase, amino acids, and ribosomes. Ribosomal competition among strands of
arxiv +1 more source
Memorias do Instituto Oswaldo Cruz, 2004 A ribosome association factor (AF) was isolated from the yeast Sacchharomyces cerevisiae. Partial amino acid sequence of AF was determined from its fragment of 25 kDa isolated by treating AF with 2-(2-nitrophenylsulfenyl)-3-methyl-3'-Bromoindolenine ...
Heriberto Correia +5 more
doaj +1 more source
Coarse-Grained model of the demixing of DNA and non-binding globular macromolecules [PDF]
Journal of Physical Chemistry B 121 (2017) 6351-6358, 2017 The volume occupied by the unconstrained genomic DNA of prokaryotes in saline solutions is thousand times larger than the cell. Moreover, it is not separated from the rest of the cell by a membrane. Nevertheless, it occupies only a small fraction of the cell called the nucleoid.
arxiv +1 more source