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rDNA: Evolution Over a Billion Years
Published in S. K. Dutta, DNA Systematics, 2019
The overall structure of the rDNA is described by a spacer region and a region giving rise to a primary precursor transcript. The precursor rRNA consists of an external transcribed spacer (ETS) preceding the 18S rRNA gene at the 5′ end of the transcript, a 5.8S rRNA gene separated from both the 18S and 28S rRNA by internal transcribed spacers (ITS 1 and ITS 2), and the 28S rRNA gene at the 3′ end of the transcript.174 The structure of the rDNA has been determined at the nucleotide sequence level. The two major EcoRI fragments of the rDNA were first cloned in the bacterial plasmid pSC1013 to produce CD18, containing mainly the 28S gene and CD30 containing the rest of the rDNA unit. The large EcoRI fragment in CD30 was transferred to the colicinegenic plasmid El (ColE1176) and renamed pXlr12.175 Another spacer region EcoRI fragment (pX1r4) was cloned by Wellauer et al.,167 transferred to the Col El plasmid, and renamed pXlr14.177 These two clones, pXlr12 and pXlr14, provided the basis for most of the early work on the structural mapping of X. laevis rDNA (Figure 9).
Phylogeny of Syzygium
Published in K. N. Nair, The Genus Syzygium, 2017
Harrington and Gadek (2004) examined phylogeny of the Syzygium group (66 species comprising Acmena, Acmenosperma, Anetholea, Cleistocalyx, Syzygium, and Waterhousea plus 6 unnamed species) by analyzing sequence variations in internal transcribed spacer (ITS) and external transcribed spacer (ETS) regions of the nuclear ribosomal DNA. The above study did not support segregation of the above Old World syzygioid genera, because all of these Syzygium suballiances were found nested within Syzygium. In another study with an expanded taxon coverage, Biffin et al. (2006) inferred phylogeny in as many as 87 species of the syzygioid genera using sequence analyses of the chloroplast DNA genes matK, ndhF, and the rpl16 intron. The results of this study supported Harrington and Gadek (2004) in recognizing all the conventional Syzygium suballiances in one single genus, Syzygium, but with a few major cryptic clades. Using the RNA secondary structure partitioning and RNA-specific evolutionary models (paired sites) of the nrDNA ITS sequences from 76 taxon Syzygium and 45 taxon Myrtaceae data sets, Biffin et al. (2007) demonstrated that the phylogeny of Syzygium was found to be consistent with the topologies drawn from the standard four-state models of ITS analysis by Harrington and Gadek (2004) and the cpDNA analysis by Biffin et al. (2006). However, the RNA-specific approach of Biffin et al. (2007) showed several topological differences in the phylogeny of the Myrtaceae from the conventional tribal classifications of Wilson et al. (2005). This indicates that RNA-specific models, which account for the mutational dynamics of ITS, may have an impact on the accuracy of phylogenies estimated from these regions compared with the standard four-state models.
Validation of PRKCB Immunohistochemistry as a Biomarker for the Diagnosis of Ewing Sarcoma
Published in Fetal and Pediatric Pathology, 2023
Victor Zota, Gene P. Siegal, David Kelly, Julia A. Bridge, Anders Berglund, Katherine Bui, Farah Khalil, Damon R. Reed, Soner Altiok, Anthony Magliocco, Marilyn M. Bui
Several variant translocations have been described as well, most of which result in fusions between EWSR1 and other members of the ETS family of transcriptional regulators, such as ERG on 21q22, ETV1 on 7p21.2, ETV4 on 17q21, and FEV on 2q35 [9]. Because EWSR1-FLI1 is the most common oncogenic event in ES, seen in 85% of ES, previous studies have focused on identifying genes modulated by this chimeric transcript that act as master transcriptional regulators. Inhibition of EWSR1-FLI1 in ES cells led to the identification of a large number of target genes dysregulated by EWSR1-FLI1 [10–13]. Among genes upregulated by EWR1-FLI1 are NR0B1, NKX2.2, and GLI1, which have been shown to be critical in the process of oncogenic transformation [10, 12, 14]. Among downregulated genes are those involved in evasion of apoptosis, cell cycle arrest, drug resistance, growth inhibition, and immortalization; these genes include CCND1, IGFBP3, GSTM4, CDKN1A, TGFBR2, TERT, VEGFA, CAV1, and EZH2 [11, 15–21].
Determinants of environmental tobacco smoke at work and at home: analysis of baseline data from the Kong Cohort Study, Southern Iran
Published in Journal of Substance Use, 2022
Sakineh Dadipoor, Abdul Azim Nejatizade, Hossein Farshidi, Abdullah Gharibzade, Teamur Aghamolaei, Amin Ghanbarnejad
As the data were largely collected through self-reports, the validity of the data is to a great extent a function of the participants’ responses. However, the interviewers did their best to assure respondents of the confidentiality of the information they provided to lower this bias to some extent. This research was conducted among Kong residents and the generalizability of findings is, thus, limited. The present research only included participants above 40 years of age. Other age groups were excluded, and this can be another limitation. Another limitation concerns the information provided on exposure to ETS. Recalling this information might have been difficult for some. Some others might have been unwilling to share this information or might have felt ashamed to do so. They might have negatively evaluated or underestimated ETS too. Furthermore, reporting the rate of exposure to ETS among nonsmokers with a large sample in a particular geographical context with local idiosyncrasies can pave the way for planning preventive programs and guiding them in the target area. Prospective researchers are advised to look into the moderating factors involved in each determinant and extract them from qualitative and observational research so that purposeful and effective interventions can be developed to reduce ETS significantly.
ETV6-related thrombocytopenia and platelet dysfunction
Published in Platelets, 2021
Jorge Di Paola, Marlie H. Fisher
Thrombopoiesis involves a sequence of complex cellular events in mature bone marrow megakaryocytes, culminating in the generation of proplatelet extensions that release platelets into circulation [1]. ETV6 is a member of the ETS family of transcription factors, indispensable for bone marrow hematopoiesis and required for normal megakaryopoiesis. ETV6 encodes the E26 Transformation-Specific (Ets) family transcription repressor and tumor suppressor variant 6. There are 27 members of the Ets family of transcription factors, representing a vast network of inter and intra-molecular interactions to achieve combinatorial regulation of gene expression [2]. ETV6 is a canonical member of the Ets family, containing an 85 amino acid ETS DNA binding domain at the C terminal end of the protein, an N terminal PNT (pointed) dimerization domain, and a central linker domain [3]. ETV6 maps to chromosome 12p13 and transcribes a 57-kDa protein with these three functional domains. All Ets transcription factors bind to the highly conserved 5ʹGGA(A/T)3ʹ motif in the promoter region of target genes [4]. While monomeric ETV6 is sterically hindered from the DNA-binding interface, dimerization through the PNT domain facilitates cooperative DNA binding and transcriptional regulatory activity [5]. ETV6 has been reported to bind to co-repressors such as HDAC3, NCOR, and Sin3A, forming a multi-protein transcriptional complex that regulates histone acetylation and chromatin condensation at target promoters, thereby influencing gene expression [6,7].