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Bacteria
Published in Julius P. Kreier, Infection, Resistance, and Immunity, 2022
DNA carries the genetic information to determine heritable properties of an organism (i.e., its phenotype). The DNA is initially transcribed into complementary polymers of ribonucleic acid (RNA) in the form called messenger RNA (mRNA). The mRNA subsequently serves as a template for synthesis of protein molecules; a process that is mediated by ribosomes. Ribosomes are microparticles composed of protein linked to another class of RNA called ribosomal RNA (rRNA). Ribosomes consist of smaller (30S) and larger (50S) subunits and tend to form aggregates or strands called polyribosomes.
The Injured Cell
Published in Jeremy R. Jass, Understanding Pathology, 2020
The nucleus is enclosed by a nuclear membrane and comprises chromosomes and a nucleolus. The material forming the chromosomes is called chromatin and consists of DNA and protein. The chromosomes only assume their characteristic condensed form during mitosis (cell division) (Fig. 5). During the remainder of the cell cycle (interphase), chromosomes are highly dispersed and cannot be seen individually. Chromatin exists either in a densely packed form (heterochromatin) or a more dispersed form (euchromatin). Euchromatin is the form that is being genetically expressed (transcribed). Chromatin has a very complicated structure. Short lengths of DNA (about 200 base pairs) are packaged up with proteins (histones) to form complexes known as nucleosomes. These are assembled as repeating units into higher order chromatin structures. The nucleolus is the site of ribosomal RNA synthesis and ribosome assembly.
rDNA: Evolution Over a Billion Years
Published in S. K. Dutta, DNA Systematics, 2019
Ribosomal RNA genes have been studied at the DNA level in 190 organisms ranging from bacteria to man. The details of these studies are summarized in Table 1 and those organisms in which the rDNA has been cloned and the spacer region analyzed are discussed in greater depth. The driving force for the evolving structure of the rDNA locus appears to be continually higher demands on the amount of rRNA required by organisms for their protein synthesizing machinery. Thus, in lower eukaryotes the rDNA is seen to be amplified in tandem arrays or as extrachromosomal copies while the 5S rDNA begins to be seen independently of the main rDNA unit. In higher eukaryotes the tandem arrays become longer, extrachromosomal copies of rDNA are confined to certain developmental stages, and the spacer regions (generated as a result of the tandem arrangement of the rDNA units) attain defined characteristics. The spacer regions house the transcription initiation signals and in both Drosophila sp. and Xenopus sp. the repeated sequences preceding transcription initiation contain extensive homology with the transcription initiation signal region. These regions appear to act as sites for sequestering RNA polymerase molecules to increase the efficiency of initiation and produce more rRNA per unit time. Other repeated sequences are also found in the spacer regions of mammals in particular.
Dysbiotic but nonpathogenic shift in the fecal mycobiota of patients with rheumatoid arthritis
Published in Gut Microbes, 2022
Eun Ha Lee, Hyun Kim, Jung Hee Koh, Kwang Hyun Cha, Kiseok Keith Lee, Wan-Uk Kim, Cheol-Ho Pan, Yong-Hwan Lee
The V3–V4 regions of 16S ribosomal RNA (rRNA) genes were amplified using the Illumina-adapted universal primers 314F/805R. Each PCR reaction contained 12.5 ng of genomic DNA, 2.5 μL of Ex Taq 10× PCR buffer (Takara, Japan), 2.5 μL of dNTP mixture (Takara), 0.125 μL of Takara Ex Taq (Takara), 5 μL of each primer (200 nM final concentration), and distilled water to a total volume of 25 μL. The following thermocycler protocol was used: initial denaturing at 95°C for 3 min; 25 cycles of denaturing at 95°C for 30s, primer annealing at 55°C for 30s, and extension at 72°C for 30s; and final extension at 72°C for 5 min. PCR products were purified using AMPure XP beads (Beckman Coulter, USA), then quantified using a KAPA Library Quantification kit (KAPA Biosystems, USA). Sequencing was conducted on the MiSeq platform using a paired-end 2 ×300 base pairs reagent kit (Illumina, USA).
Exploring the rationale for thermotherapy in COVID-19
Published in International Journal of Hyperthermia, 2021
Javier Mancilla-Galindo, Norma Galindo-Sevilla
Ribosomes are composed of ribosomal RNA (rRNA) and proteins. Cells exposed to 42 °C characteristically almost cease production of rRNA to only 3% after 1 h, through diverse mechanisms [26,27]. This significantly reduces translation of proteins to preserve energy. Other mechanisms being altered at 42 °C are the adequate processing of certain mRNAs [28] and the inhibition of polyadenylation (a process which adds a poly(A) tail to RNA, leading to more stable and efficient lecture of RNA) [29]. Polyadenylation of the coronavirus RNA genome is known to promote virus survival through enhanced translation and replication [30]. Taken together, inhibition of protein synthesis and polyadenylation of viral RNA could potentially and significantly dampen SARS-CoV-2 infectivity.
Two acute myeloid leukemia patient subsets are identified based on the constitutive PI3K-Akt-mTOR signaling of their leukemic cells; a functional, proteomic, and transcriptomic comparison
Published in Expert Opinion on Therapeutic Targets, 2018
Ina Nepstad, Kimberley J. Hatfield, Elise Aasebø, Maria Hernandez-Valladares, Annette K. Brenner, Sushma Bartaula-Brevik, Frode Berven, Frode Selheim, Jørn Skavland, Bjørn Tore Gjertsen, Håkon Reikvam, Øystein Bruserud
Two recent studies compared the translatome for non-hematopoietic cells cultured with and without an mTOR inhibitor, i.e. genes whose expression varies dependent on the strength of the PI3K-Akt-mTOR signaling, and the proteins encoded by most of these genes are involved in regulation of transcription or translation [29]. There was no overlap with the genes identified in the two ribosomal RNA profile studies and the proteins showing differential expression when comparing high and low signaling patients in our study. This observation suggests that the mTOR-dependent translatome differs among non-hematopoietic and hematopoietic/leukemic cells.