Molecular adaptation to resistance exercise
Adam P. Sharples, James P. Morton, Henning Wackerhage in Molecular Exercise Physiology, 2022
Beyond the acute regulation of the activity of the ribosome (the amount of protein synthesized per mRNA), mTORC1 can also regulate the number of ribosomes, or the translational capacity of the cell. mTORC1 regulates ribosome mass through the phosphorylation of a key ribosomal RNA transcription factor (upstream binding factor; UBF) and the preferential translation of ribosomal proteins. The transcription of ribosomal DNA is so essential to the function of cells that it has a specialized RNA polymerase (POL I) whose only role is to translate rDNA into the 47S pre-ribosomal RNA. The polycistronic 47S rRNA is then cleaved into the mature 5, 5.8, 18 and 28S rRNAs that make up ~80% of all the RNA in a mammalian cell (53). The transcription of rDNA is thought to be the first step in ribosome biogenesis (the production of new ribosomes) and this process is regulated by the protooncogene myc, and the transcription factors SL1 and UBF. Important for the regulation of ribosome biogenesis in response to resistance exercise, myc transcription increases, and the transcriptional activity of UBF is increased in response to phosphorylation by S6K1. In fact, activation of S6K1 is enough to drive ribosome biogenesis (54). So, following resistance exercise, UBF phosphorylation increases in relation to increased ribosomal RNA synthesis (52).
Nonhistone Nuclear Phosphoproteins
Lubomir S. Hnilica in Chromosomal Nonhistone Proteins, 2018
Atmar et al.130 found somewhat analagous phosphoproteins in the lower eukaryote Physarum polycephalum. Nucleoli of this slime mold contain two polypeptides of 52,000 and 70,000 mol wt which are the predominant phosphorylated proteins of the organelle. Their in vitro phosphorylation is stimulated by the presence of polyamines. The 70,000 mol wt polypeptide exists as a dimer of 139,000 and is part of the nucleolar ribosomal deoxyri-bonucleoprotein complex.69 This protein also binds with high affinity and specificity to the palindromic ribosomal DNA. Furthermore, the protein stimulates rRNA synthesis as much as fivefold when added to the purified rDNP complex which contains RNA polymerase I. Dephosphorylation of the protein by alkaline phosphatase treatment abolished the specific DNA binding ability as well as the stimulatory effects on transcription. Thus, this protein may be a specific regulator of transcription of ribosomal DNA and phosphorylation of the protein may regulate its activity.
DNA TECHNIQUES FOR THE AUTHENTICATION OF CHINESE MEDICINAL MATERIALS
Kevin Chan, Henry Lee in The Way Forward for Chinese Medicine, 2001
Traditional RFLP analysis is not suitable for Chinese medicinal materials as it demands large amount of intact DNA. Therefore, PCR-RFLP, a method requiring small amount of DNA for analysis is used. In this method, a defined DNA fragment is first amplified by PCR and then digested with a restriction endonuclease to generate restriction polymorphic profiles unique to the concerned species. It is desirable that the region for PCR-RFLP analysis is flanked by sequence conserved across species so that it can be readily amplified by using "universal" primers. Two of the suitable candidates for such regions are ribosomal DNA (rDNA) and large subunit of ribulose-1,5-bisphosphate carboxylase L (rbcL) gene. The PCR-RFLP of rDNA has been carried out on Glehnia and Atractylodes (Mizukami et al. 1993; 1996; Cheng et al. 1997) and we have also successfully used this approach to discriminate Panax species from their adulterants (Figure 9.3) (Ngan et al. 1998) and?
Identification of gut microbiome and transcriptome changes in ulcerative colitis and pouchitis
Published in Scandinavian Journal of Gastroenterology, 2022
Xin Gao, Di Huang, Li-Sheng Yang, An-Qi He, Kai-Yu Li, Tong Liu, Gang Liu
According to the OMEGA Stool DNA Kit instructions (D4015, Omega, Inc., Norwalk, CT), genomic DNA extraction from Stool samples was performed. The concentration and purity of DNA samples were determined by NanoDrop2000 spectrophotometer and unqualified DNA samples will be discarded. Primers for the 16S ribosomal DNA V3–V4 regions of the bacterial genome were designed in the experiment. The primer sequence of 336F was 5′-GTACTCCTACGGGAGGCAGCA-3′, and the primer sequence of 806R was 5′-GTGGACTACHVGGGTWTCTAAT-3′. A PCR system was established to specifically amplify the V3–V4 region of the 16S ribosomal DNA of the sample genome. Qualified agarose gels were sent to LC-Bio Technology (Hangzhou, China) for Miseq library construction then performed sequencing on Illumina Miseq PE300 platform.
Use of argyrophilic nucleolar–organizer region-associated protein synthesis in skeletal muscle cells for prediction of chronic carbon monoxide exposure
Published in Toxin Reviews, 2020
Harun Gunes, Ayhan Saritas, Recep Eroz, Serdar Colakoglu
Nucleolar–organizer regions (NORs) are genetic loci located on the secondary constriction of acrocentric chromosomes (chromosomes 13, 14, 15, 21, and 22) in humans. NORs are formed by ribosomal DNA (rDNA) and proteins (Trere 2000). They are transcribed into ribosomal RNAs (rRNA) which are converted to pre-ribosomes in the nucleolus and join mature ribosomes in the cytoplasm (Hernandez-Verdun 2006). Active NORs can be stained with Silver nitrate (AgNO3) via the precipitation of metallic silver granules in the interphase. Activity status of NORs closely correlates with the amount of these granules (Jimenez et al.1988). Silver binds with non-histone-associated proteins which are transcriptionally active or transcribed and still having residual rRNA. Those proteins are called argyrophilic NOR (AgNOR)-associated proteins due to their silver affinity (Trere 2000).
Diagnostic Utility of Quantitative Polymerase Chain Reaction versus Culture in Endophthalmitis and Uveitis
Published in Ocular Immunology and Inflammation, 2019
Harpal Singh Sandhu, Amir Hajrasouliha, Henry J. Kaplan, Wei Wang
For genetic assays, samples were tested for DNA of bacteria, fungi, and viruses by comprehensive polymerase chain reaction. DNA isolation and PCR were performed in our on-site microbiology lab within 36 h, as described previously.1 DNA was isolated by DNeasy Blood & Tissue Kit (Qiagen, Washington DC, USA). Real-time PCR was performed using the Stratigen MX3005P system (Agilent Technologies, Santa Clara, CA, USA). Our viral panel included primers for HSV-1, HSV2, CMV, VZV, EBV, and HHV-6 (Table 6). All samples were also tested for bacterial 16S and fungal 18S/28S ribosomal DNA. There is no universal primer for parasites, but all samples were tested for toxoplasmosis and toxocariasis. Ecoli DNA served as a positive control for all tests, and no DNA or sample DNA without a primer was also run as a negative control. Those performing PCR on-site did have access to clinical information. A cycle threshold value of 30 was set as the cut-off for a positive test. If positive for bacterial, fungal, or parasitic DNA, the PCR product was sent to the CGeMM DNA core facility at the University of Louisville for sequencing using the ABI 3130XL Genetic Analyzer with a 36 cm array and POP7 polymer (Appliebiosystem, Foster city, CA, USA), where those performing the test had no access to clinical information, and the resulting sequence was compared to known microbial sequences in the National Center for Biotechnology Information databases in order to identify the organism. The material cost of performing PCR was approximately $25 USD per case, not including labor costs.
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- DNA
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- Ribosomal Rna
- Transcription
- Spacer DNA
- Rnr1
- Rnr2
- Rnr3
- Rnr4
- Rnr5