Results 21 to 30 of about 10,709 (124)
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
Phylogenetic analysis of Polystigma and its relationship to Phyllachorales
Phytopathologia Mediterranea, 2015 Polystigma amygdalinum, which causes red leaf blotch of almond, is one of the few fungal plant pathogens to remain a taxonomic enigma, primarily because it has resisted cultivation and causes almond leaf blotch only in restricted regions of the world. To
Azadeh HABIBI +2 more
doaj +1 more source
BMC Ecology and Evolution, 2021 Background Autotetraploid Carassius auratus (4n = 200, RRRR) (abbreviated as 4nRR) is derived from whole genome duplication of Carassius auratus red var. (2n = 100, RR) (abbreviated as RCC).
Chun Zhao +10 more
doaj +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
BMC Evolutionary Biology, 2009 Background Although DNA sequence analysis is becoming a powerful tool for identifying species, it is not easy to assess whether the observed genetic disparity corresponds to reproductive isolation.
Okuyama Yudai, Kato Makoto
doaj +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
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
Are there insertions in the ribosomal DNA of vertebrates?
Nucleic Acids Research, 1985 We have analysed the Eco RI restriction pattern of rDNA of the newt Triturus vulgaris and of some other amphibian species by Southern blotting and hybridization with nick-translated Xenopus rDNA prepared from the recombinant plasmids pXlr11 and pXlr12 (21).
Karin Kraus, Klaus Lohmann
openaire +4 more sources