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1
Wilfinger, William W., Hamid R. Eghbalnia, Karol Mackey, Robert Miller, and Piotr Chomczynski. "Whole blood RNA extraction efficiency contributes to variability in RNA sequencing data sets." PLOS ONE 18, no. 11 (2023): e0291209. http://dx.doi.org/10.1371/journal.pone.0291209.
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Numerous methodologies are used for blood RNA extraction, and large quantitative differences in recovered RNA content are reported. We evaluated three archived data sets to determine how extraction methodologies might influence mRNA and lncRNA sequencing results. The total quantity of RNA recovered /ml of blood affects RNA sequencing by impacting the recovery of weakly expressed mRNA, and lncRNA transcripts. Transcript expression (TPM counts) plotted in relation to transcript size (base pairs, bp) revealed a 30% loss of short to midsized transcripts in some data sets. Quantitative recovery of RNA is of considerable importance, and it should be viewed more judiciously. Transcripts common to the three data sets were subsequently normalized and transcript mean TPM counts and TPM count coefficient of variation (CV) were plotted in relation to increasing transcript size. Regression analysis of mean TPM counts versus transcript size revealed negative slopes in two of the three data sets suggesting a reduction of TPM transcript counts with increasing transcript size. In the third data set, the regression slope line of mRNA transcript TPM counts approximates zero and TPM counts increased in proportion to transcript size over a range of 200 to 30,000 bp. Similarly, transcript TPM count CV values also were uniformly distributed over the range of transcript sizes. In the other data sets, the regression CV slopes increased in relation to transcript size. The recovery of weakly expressed and /or short to midsized mRNA and lncRNA transcripts varies with different RNA extraction methodologies thereby altering the fundamental sequencing relationship between transcript size and TPM counts. Our analysis identifies differences in RNA sequencing results that are dependent upon the quantity of total RNA recovery from whole blood. We propose that incomplete RNA extraction directly impacts the recovery of mRNA and lncRNA transcripts from human blood and speculate these differences contribute to the “batch” effects commonly identified between sequencing results from different archived data sets.
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Lee, Jeong Hyun, Na Young Park, Myung Hee Lee, and Sang Ho Choi. "Characterization of the VibriovulnificusputAP Operon, Encoding Proline Dehydrogenase and Proline Permease, and Its Differential Expression in Response to Osmotic Stress." Journal of Bacteriology 185, no. 13 (2003): 3842–52. http://dx.doi.org/10.1128/jb.185.13.3842-3852.2003.
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ABSTRACT The Vibrio vulnificus putAP genes encoding a proline dehydrogenase and a proline permease are transcribed in the same direction. Proline dehydrogenase activity and the level of putA transcript were determined to reach a maximum in exponential phase and were then repressed when growth slowed down. Northern blotting and primer extension analyses revealed that transcription of putAP genes results in two different transcripts, transcript A (putA transcript) and transcript AP (putAP transcript). Expression of putAP genes was directed by two promoters, promoter P putA and promoter P putAP . A crp null mutation decreased proline dehydrogenase activity and the level of the put transcripts, indicating that transcription of putAP is under the positive control of cyclic AMP receptor protein. Proline dehydrogenase and the level of both put transcripts were increased by proline but repressed by glutamate. In contrast, the level of transcript A, not transcript AP, increased when proline dehydrogenase was induced by NaCl. Since P putA activity, not P putAP activity, was increased by NaCl, it is apparent that transcript A and transcript AP are transcribed through P putA and P putAP , respectively. Cells challenged with NaCl and various hyperosmotic stresses accumulated higher levels of glutamate than control cells, indicating that glutamate is a compatible solute in V. vulnificus.
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Raff, J. W., W. G. Whitfield, and D. M. Glover. "Two distinct mechanisms localise cyclin B transcripts in syncytial Drosophila embryos." Development 110, no. 4 (1990): 1249–61. http://dx.doi.org/10.1242/dev.110.4.1249.
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We demonstrate that two independent mechanisms act on maternally derived cyclin B transcripts to concentrate the transcripts at the posterior pole of the Drosophila oocyte and at the cortex of the syncytial embryo. The cortical accumulation occurs because the cyclin B transcript is concentrated around nuclei and comigrates with them to the cortex. The perinuclear localisation of the transcript is blocked by inhibitors of microtubule polymerisation and the transcript colocalises with microtubular structures during the cell cycle, suggesting that the transcript is associated either directly or indirectly with microtubules. Neither microtubules nor actin filaments are required to maintain the posterior concentration of cyclin B transcripts. Instead, this seems to depend on the association of the transcripts with a component of the posterior cytoplasm. The distribution pattern of the transcript at the posterior pole throughout embryogenesis and in a variety of mutant embryos suggests that this component is associated with polar granules.
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Vo, Kevin, Yashica Sharma, Anohita Paul, et al. "Importance of Transcript Variants in Transcriptome Analyses." Cells 13, no. 17 (2024): 1502. http://dx.doi.org/10.3390/cells13171502.
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RNA sequencing (RNA-Seq) has become a widely adopted technique for studying gene expression. However, conventional RNA-Seq analyses rely on gene expression (GE) values that aggregate all the transcripts produced under a single gene identifier, overlooking the complexity of transcript variants arising from different transcription start sites or alternative splicing. Transcript variants may encode proteins with diverse functional domains, or noncoding RNAs. This study explored the implications of neglecting transcript variants in RNA-Seq analyses. Among the 1334 transcription factor (TF) genes expressed in mouse embryonic stem (ES) or trophoblast stem (TS) cells, 652 were differentially expressed in TS cells based on GE values (365 upregulated and 287 downregulated, ≥absolute 2-fold changes, false discovery rate (FDR) p-value ≤ 0.05). The 365 upregulated genes expressed 883 transcript variants. Further transcript expression (TE) based analyses identified only 174 (<20%) of the 883 transcripts to be upregulated. The remaining 709 transcripts were either downregulated or showed no significant changes. Meanwhile, the 287 downregulated genes expressed 856 transcript variants and only 153 (<20%) of the 856 transcripts were downregulated. The other 703 transcripts were either upregulated or showed no significant change. Additionally, the 682 insignificant TF genes (GE values < absolute 2-fold changes and/or FDR p-values > 0.05) between ES and TS cells expressed 2215 transcript variants. These included 477 (>21%) differentially expressed transcripts (276 upregulated and 201 downregulated, ≥absolute 2-fold changes, FDR p-value ≤ 0.05). Hence, GE based RNA-Seq analyses do not represent accurate expression levels due to divergent transcripts expression from the same gene. Our findings show that by including transcript variants in RNA-Seq analyses, we can generate a precise understanding of a gene’s functional and regulatory landscape; ignoring the variants may result in an erroneous interpretation.
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Harris, Rebecca Louise, Carmen Wilma van den Berg, and Derrick John Bowen. "ASGR1 and ASGR2, the Genes that Encode the Asialoglycoprotein Receptor (Ashwell Receptor), Are Expressed in Peripheral Blood Monocytes and Show Interindividual Differences in Transcript Profile." Molecular Biology International 2012 (August 2, 2012): 1–10. http://dx.doi.org/10.1155/2012/283974.
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Background. The asialoglycoprotein receptor (ASGPR) is a hepatic receptor that mediates removal of potentially hazardous glycoconjugates from blood in health and disease. The receptor comprises two proteins, asialoglycoprotein receptor 1 and 2 (ASGR1 and ASGR2), encoded by the genes ASGR1 and ASGR2. Design and Methods. Using reverse transcription amplification (RT-PCR), expression of ASGR1 and ASGR2 was investigated in human peripheral blood monocytes. Results. Monocytes were found to express ASGR1 and ASGR2 transcripts. Correctly spliced transcript variants encoding different isoforms of ASGR1 and ASGR2 were present in monocytes. The profile of transcript variants from both ASGR1 and ASGR2 differed among individuals. Transcript expression levels were compared with the hepatocyte cell line HepG2 which produces high levels of ASGPR. Monocyte transcripts were 4 to 6 orders of magnitude less than in HepG2 but nonetheless readily detectable using standard RT-PCR. The monocyte cell line THP1 gave similar results to monocytes harvested from peripheral blood, indicating it may provide a suitable model system for studying ASGPR function in this cell type. Conclusions. Monocytes transcribe and correctly process transcripts encoding the constituent proteins of the ASGPR. Monocytes may therefore represent a mobile pool of the receptor, capable of reaching sites remote from the liver.
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Dharmani, Prof Aarti, Jaya Yadav, Jiya Shukla, and Chinmai Rane. "YouTube Transcript Summarizer." International Journal of Research Publication and Reviews 5, no. 3 (2024): 7035–39. http://dx.doi.org/10.55248/gengpi.5.0324.0811.
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Jain Jahnavi Jain, Sarthak. "YouTube Transcript Summarizer." International Journal of Science and Research (IJSR) 12, no. 2 (2023): 1107–8. http://dx.doi.org/10.21275/sr23214121307.
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Baldwin, TJ, CM Yoshihara, K. Blackmer, CR Kintner, and SJ Burden. "Regulation of acetylcholine receptor transcript expression during development in Xenopus laevis." Journal of Cell Biology 106, no. 2 (1988): 469–78. http://dx.doi.org/10.1083/jcb.106.2.469.
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The level of transcripts encoding the skeletal muscle acetylcholine receptor (AChR) was determined during embryonic development in Xenopus laevis. cDNAs encoding the alpha, gamma, and delta subunits of the Xenopus AChR were isolated from Xenopus embryo cDNA libraries using Torpedo AChR cDNAs as probes. The Xenopus AChR cDNAs have greater than 60% amino acid sequence homology to their Torpedo homologues and hybridize to transcripts that are restricted to the somites of developing embryos. Northern blot analysis demonstrates that a 2.3-kb transcript hybridizes to the alpha subunit cDNA, a 2.4-kb transcript hybridizes to the gamma subunit cDNA, and that two transcripts, of 1.9 and 2.5 kb, hybridize to the delta subunit cDNA. RNase protection assays demonstrate that transcripts encoding alpha, gamma, and delta subunits are coordinately expressed at late gastrula and that the amount of each transcript increases in parallel with muscle-specific actin mRNA during the ensuing 12 h. After the onset of muscle activity the level of actin mRNA per somite remains relatively constant, whereas the level of alpha subunit and delta subunit transcripts decrease fourfold per somite and the level of gamma subunit transcript decreases greater than 50-fold per somite. The decrease in amount of AChR transcripts per somite, however, occurs when embryos are paralyzed with local anaesthetic during their development. These results demonstrate that AChR transcripts in Xenopus are initially expressed coordinately, but that gamma subunit transcript levels are regulated differently than alpha and delta at later stages. Moreover, these results demonstrate that AChR transcript levels in Xenopus myotomal muscle cells are not responsive to electrical activity and suggest that AChR transcript levels are influenced by other regulatory controls.
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Sarkar, Hirak, Avi Srivastava, Héctor Corrada Bravo, Michael I. Love, and Rob Patro. "Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data." Bioinformatics 36, Supplement_1 (2020): i102—i110. http://dx.doi.org/10.1093/bioinformatics/btaa448.
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Abstract Motivation Advances in sequencing technology, inference algorithms and differential testing methodology have enabled transcript-level analysis of RNA-seq data. Yet, the inherent inferential uncertainty in transcript-level abundance estimation, even among the most accurate approaches, means that robust transcript-level analysis often remains a challenge. Conversely, gene-level analysis remains a common and robust approach for understanding RNA-seq data, but it coarsens the resulting analysis to the level of genes, even if the data strongly support specific transcript-level effects. Results We introduce a new data-driven approach for grouping together transcripts in an experiment based on their inferential uncertainty. Transcripts that share large numbers of ambiguously-mapping fragments with other transcripts, in complex patterns, often cannot have their abundances confidently estimated. Yet, the total transcriptional output of that group of transcripts will have greatly reduced inferential uncertainty, thus allowing more robust and confident downstream analysis. Our approach, implemented in the tool terminus, groups together transcripts in a data-driven manner allowing transcript-level analysis where it can be confidently supported, and deriving transcriptional groups where the inferential uncertainty is too high to support a transcript-level result. Availability and implementation Terminus is implemented in Rust, and is freely available and open source. It can be obtained from https://github.com/COMBINE-lab/Terminus. Supplementary information Supplementary data are available at Bioinformatics online.
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Crouse, G. F., E. J. Leys, R. N. McEwan, E. G. Frayne, and R. E. Kellems. "Analysis of the mouse dhfr promoter region: existence of a divergently transcribed gene." Molecular and Cellular Biology 5, no. 8 (1985): 1847–58. http://dx.doi.org/10.1128/mcb.5.8.1847-1858.1985.
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The use of murine dihydrofolate reductase (dhfr) gene amplification mutants enabled us to identify important structural and functional features of the dhfr promoter region. We found another transcription unit, at least 14 kilobases in size, which initiates within 130 base pairs of the major dhfr transcript and is transcribed divergently. The 5' ends of both transcripts were analyzed and found to have multiple initiation sites. The major dhfr transcript and the divergent transcript appear to share the same promoter region; the longer transcripts of the dhfr gene overlap with the divergent transcripts and use a different promoter region. The divergent transcript appears to code for a protein; an homologous sequence to its first exon is found in the corresponding location near the human dhfr gene.
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Crouse, G. F., E. J. Leys, R. N. McEwan, E. G. Frayne, and R. E. Kellems. "Analysis of the mouse dhfr promoter region: existence of a divergently transcribed gene." Molecular and Cellular Biology 5, no. 8 (1985): 1847–58. http://dx.doi.org/10.1128/mcb.5.8.1847.
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The use of murine dihydrofolate reductase (dhfr) gene amplification mutants enabled us to identify important structural and functional features of the dhfr promoter region. We found another transcription unit, at least 14 kilobases in size, which initiates within 130 base pairs of the major dhfr transcript and is transcribed divergently. The 5' ends of both transcripts were analyzed and found to have multiple initiation sites. The major dhfr transcript and the divergent transcript appear to share the same promoter region; the longer transcripts of the dhfr gene overlap with the divergent transcripts and use a different promoter region. The divergent transcript appears to code for a protein; an homologous sequence to its first exon is found in the corresponding location near the human dhfr gene.
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Sage, Sophie Elena, Pamela Nicholson, Tosso Leeb, Vinzenz Gerber, and Vidhya Jagannathan. "Long-Read Transcriptome of Equine Bronchoalveolar Cells." Genes 13, no. 10 (2022): 1722. http://dx.doi.org/10.3390/genes13101722.
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We used Pacific Biosciences long-read isoform sequencing to generate full-length transcript sequences in equine bronchoalveolar lavage fluid (BALF) cells. Our dataset consisted of 313,563 HiFi reads comprising 805 Mb of polished sequence information. The resulting equine BALF transcriptome consisted of 14,234 full-length transcript isoforms originating from 7017 unique genes. These genes consisted of 6880 previously annotated genes and 137 novel genes. We identified 3428 novel transcripts in addition to 10,806 previously known transcripts. These included transcripts absent from existing genome annotations, transcripts mapping to putative novel (unannotated) genes and fusion transcripts incorporating exons from multiple genes. We provide transcript-level data for equine BALF cells as a resource to the scientific community.
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Romero-Morelos, Pablo, Ana Lilia González-Yebra, Daniela Muñoz-López, Elia Lara-Lona, and Beatriz González-Yebra. "Frequencies of BCR::ABL1 Transcripts in Patients with Chronic Myeloid Leukemia: A Meta-Analysis." Genes 15, no. 2 (2024): 232. http://dx.doi.org/10.3390/genes15020232.
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Chronic myeloid leukemia (CML) is associated with the Philadelphia chromosome and distinct BCR::ABL1 gene transcripts. We assessed the frequencies of these transcripts in Mexico, Latin America, and worldwide. We determined the prevalence of BCR::ABL1 transcripts in CML patients and intercontinental or regional variations using specialized databases and keywords. We analyzed 34 studies from 20 countries, encompassing 5795 patients. Keyword-based searches in specialized databases guided data collection. ANOVA was employed for transcript distribution analysis. The b3a2 transcript was most prevalent globally, followed by b2a2, with e1a2 being the least frequent. Interestingly, Mexico City exhibited a higher incidence of b2a2, while b3a2 predominated in the remaining country. Overall, no significant intercontinental or regional variations were observed. b3a2 was the most common BCR::ABL1 transcript worldwide, with b2a2 following closely; e1a2 was infrequent. Notably, this trend remained consistent in Mexico. Evaluating transcript frequencies holds clinical relevance for CML management. Understanding the frequency of transcript informs personalized CML treatments.
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Vallim, Marcelo A., Bernard J. H. Janse, Jill Gaskell, Aline A. Pizzirani-Kleiner, and Daniel Cullen. "Phanerochaete chrysosporiumCellobiohydrolase and Cellobiose Dehydrogenase Transcripts in Wood." Applied and Environmental Microbiology 64, no. 5 (1998): 1924–28. http://dx.doi.org/10.1128/aem.64.5.1924-1928.1998.
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ABSTRACT The transcripts of structurally related cellobiohydrolase genes inPhanerochaete chrysosporium-colonized wood chips were quantified. The transcript patterns obtained were dramatically different from the transcript patterns obtained previously in defined media. Cellobiose dehydrogenase transcripts were also detected, which is consistent with the hypothesis that such transcripts play an important role in cellulose degradation.
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Morales, Joannella, Shashikant Pujar, Jane E. Loveland, et al. "A joint NCBI and EMBL-EBI transcript set for clinical genomics and research." Nature 604, no. 7905 (2022): 310–15. http://dx.doi.org/10.1038/s41586-022-04558-8.
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AbstractComprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, the absence of a standard for clinical reporting and browser display complicates the process of consistent interpretation and reporting. To address these challenges, Ensembl/GENCODE1 and RefSeq2 launched a joint initiative, the Matched Annotation from NCBI and EMBL-EBI (MANE) collaboration, to converge on human gene and transcript annotation and to jointly define a high-value set of transcripts and corresponding proteins. Here, we describe the MANE transcript sets for use as universal standards for variant reporting and browser display. The MANE Select set identifies a representative transcript for each human protein-coding gene, whereas the MANE Plus Clinical set provides additional transcripts at loci where the Select transcripts alone are not sufficient to report all currently known clinical variants. Each MANE transcript represents an exact match between the exonic sequences of an Ensembl/GENCODE transcript and its counterpart in RefSeq such that the identifiers can be used synonymously. We have now released MANE Select transcripts for 97% of human protein-coding genes, including all American College of Medical Genetics and Genomics Secondary Findings list v3.0 (ref. 3) genes. MANE transcripts are accessible from major genome browsers and key resources. Widespread adoption of these transcript sets will increase the consistency of reporting, facilitate the exchange of data regardless of the annotation source and help to streamline clinical interpretation.
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Sawers, R. Gary. "Differential turnover of the multiple processed transcripts of the Escherichia coli focA-pflB operon." Microbiology 152, no. 8 (2006): 2197–205. http://dx.doi.org/10.1099/mic.0.28951-0.
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Expression of the anaerobically inducible focA-pflB operon of Escherichia coli is subject to complex transcriptional and post-transcriptional control, which generates eight transcripts whose 5′ ends span ∼1.2 kb. All eight transcripts have the same 3′ end. The 5′ ends of three of the transcripts, termed 6, 6a and 7, are located upstream of the operon. The promoters generating transcripts 6 and 7 are anaerobically regulated by FNR and ArcA∼P, while promoter 6a is constitutively active. The 5′ ends of the other five transcripts are all located within the operon. Most of the 5′ ends of these operon-internal transcripts result from RNA polymerase-dependent processing of the three longer primary transcripts, 6, 6a and 7. Here, it is demonstrated that subsequent to, and distinct from, these processing events, post-transcriptional modification of these transcripts also occurs through the action of the endoribonuclease RNase E. Transcripts 6 and 7 exhibit differential stability with half-lives of 1 and 5 min, respectively. Transcript 7, which has the longer half-life, is the longest transcript of the operon and has a ∼340 base untranslated leader. Two of the operon-internal transcripts, 4 and 5, also have comparatively short half-lives in the wild-type, which are significantly increased in a mutant with impaired RNase E activity. A precursor-product relationship is observed between the longer transcripts 3–7 and transcripts 1 and 2. The 5′ ends of transcripts 1 and 2 are closest to the pflB gene and have half-lives of approximately 7–8 min. The consequence of this regulation is an accumulation of full-length pflB transcript and comparably low levels of dicistronic transcript. This ensures different levels of synthesis of the formate transporter FocA and pyruvate formate-lyase during anaerobic growth, while maintaining coordinate regulation. Transcript analysis throughout the growth phase revealed that maximal anaerobic expression of the focA-pflB operon was restricted to exponentially growing cells. Expression of transcript 7 peaked in early to mid-exponential phase, while the levels of transcript 6 steadily accumulated toward the late-exponential phase of growth. Taken together, these findings indicate that although subject to common positive control by ArcA∼P and FNR, the transcripts generated by promoters 6 and 7 are subject to differential temporal and post-transcriptional regulation.
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Bulbarelli, Alessandra, Alessandra Valentini, Marcella DeSilvestris, M. Domenica Cappellini, and Nica Borgese. "An Erythroid-Specific Transcript Generates the Soluble Form of NADH-Cytochrome b5 Reductase in Humans." Blood 92, no. 1 (1998): 310–19. http://dx.doi.org/10.1182/blood.v92.1.310.413k24_310_319.
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Two forms of NADH-cytochrome b5 reductase (b5R), an erythrocyte-restricted soluble form, active in methemoglobin reduction, and a ubiquitous membrane-associated form involved in lipid metabolism, are produced from one gene. In the rat, the two forms are generated from alternative transcripts differing in the first exon, however, biogenesis of human b5R was less understood. Recently, two different transcripts (M and S), differing in the first exon were also described in humans. Here, we have investigated the tissue-specificity and the role of the S-transcript in the generation of soluble b5R. By RNase protection assays designed to simultaneously detect alternative b5R transcripts in the same sample, the S transcript was undetectable in nonerythroid and in erythroleukemic K562 cells induced to differentiate, but was present in terminal erythroblast cultures, and represented a major b5R transcript in reticulocytes. Analysis of the translation products of the M- and S-transcripts in HeLa cells transfected with the corresponding cDNAs demonstrated that the S-transcript generates soluble b5R, presumably from an internal initiation codon. Our results indicate that the S-transcript is expressed at late stages of erythroid maturation to generate soluble b5R.
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Ohmen, J. D., K. A. Burke, and J. E. McEwen. "Divergent overlapping transcripts at the PET122 locus in Saccharomyces cerevisiae." Molecular and Cellular Biology 10, no. 6 (1990): 3027–35. http://dx.doi.org/10.1128/mcb.10.6.3027-3035.1990.
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PET122 is one of three nuclear genes specifically required for translation of the mitochondrial mRNA for cytochrome c oxidase subunit III in Saccharomyces cerevisiae. The nucleotide sequence of 2,862 base pairs (bp) of yeast genomic DNA encompassing the PET122 locus shows very close spacing between the PET122 gene (254 codons) and two unidentified open reading frames, termed ORF2 and ORF3. ORF2 is encoded by the same strand of DNA as PET122 and is located 53 bp downstream of PET122, while ORF3 is encoded on the opposite strand and is located 215 bp upstream of PET122. Five transcripts, with sizes of 2.9, 2.3, 2.1, 1.5, and 1.4 kilobases (kb), are produced from this locus. The 2.1- and 1.4-kb transcripts encode ORF3, the 1.5-kb transcript encodes ORF2, and the 2.9- and 2.3-kb transcripts encode PET122. A particularly interesting feature of the ORF3-PET122-ORF2 transcription unit is a 535-base overlap between the 2.3-kb PET122 transcript produced from one strand and a 2.1-kb ORF3 transcript produced from the opposite strand. Similarly, the 2.9-kb PET122 transcript overlaps the 2.1-kb ORF3 transcript by more than 900 bases and the 1.5-kb ORF3 transcript by at least 200 bases. Hence, these pairs of transcripts are antisense to one another and have the potential to regulate, in an interdependent fashion, the posttranscriptional expression of ORF3 and PET122.
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Ohmen, J. D., K. A. Burke, and J. E. McEwen. "Divergent overlapping transcripts at the PET122 locus in Saccharomyces cerevisiae." Molecular and Cellular Biology 10, no. 6 (1990): 3027–35. http://dx.doi.org/10.1128/mcb.10.6.3027.
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PET122 is one of three nuclear genes specifically required for translation of the mitochondrial mRNA for cytochrome c oxidase subunit III in Saccharomyces cerevisiae. The nucleotide sequence of 2,862 base pairs (bp) of yeast genomic DNA encompassing the PET122 locus shows very close spacing between the PET122 gene (254 codons) and two unidentified open reading frames, termed ORF2 and ORF3. ORF2 is encoded by the same strand of DNA as PET122 and is located 53 bp downstream of PET122, while ORF3 is encoded on the opposite strand and is located 215 bp upstream of PET122. Five transcripts, with sizes of 2.9, 2.3, 2.1, 1.5, and 1.4 kilobases (kb), are produced from this locus. The 2.1- and 1.4-kb transcripts encode ORF3, the 1.5-kb transcript encodes ORF2, and the 2.9- and 2.3-kb transcripts encode PET122. A particularly interesting feature of the ORF3-PET122-ORF2 transcription unit is a 535-base overlap between the 2.3-kb PET122 transcript produced from one strand and a 2.1-kb ORF3 transcript produced from the opposite strand. Similarly, the 2.9-kb PET122 transcript overlaps the 2.1-kb ORF3 transcript by more than 900 bases and the 1.5-kb ORF3 transcript by at least 200 bases. Hence, these pairs of transcripts are antisense to one another and have the potential to regulate, in an interdependent fashion, the posttranscriptional expression of ORF3 and PET122.
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Muis, Muhammad Danil, Muhammad Rifki Fauzan, Parman Sukarno, and Aulia Arif Wardana. "Access Control and File Distribution Management for Electronic Diploma and Transcript using Ethereum Smart Contract and IPFS." Jurnal Sistem Informasi 17, no. 2 (2021): 48–61. http://dx.doi.org/10.21609/jsi.v17i2.1093.
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This reserach build access control and file distribution management system for electronic diploma and transcript using ethereum smart contract and InterPlanetary File System (IPFS). The falsification of diplomas/transcripts is one of the problems in education. In Indonesia, falsification of diplomas/transcripts is a form of criminal act of falsifying letters. In addition, diplomas/transcripts that have not been digitalized make them easily damaged, lost, and difficult to manage. Therefore, this research developed digital diploma/transcript as digital twin from the hardcopy of diploma/tramscript. This research used IPFS to store data in a distributed system and Smart Contracts Blockchain to store and protect the digital diploma/transcript. The system also comes with access control to create and give approval for diplomas or transcripts to be published and saved into the system. Access control settings will be saved using the blockchain. This research using Quality of Service test method for measurethroughput, packet loss, and delay. Beside that, tis research also analysis the usage of Central Processing Unit and Random Access Memory from the system. Based on the test that has been done, the fake diploma/transcript detection system can be run properly by using 1 node to 5 nodes. The best throughput value during the process of making and validating the diploma/transcript is to use 1 node. The value of packet loss in the process of making and validating the certificate/transcript has a very good category. The value of delay in the process of making and validating the diploma/transcript has a very good category.
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Krishna, Dr T. Bala Murali. "YOUTUBE TRANSCRIPT SUMMARIZER." INTERANTIONAL JOURNAL OF SCIENTIFIC RESEARCH IN ENGINEERING AND MANAGEMENT 08, no. 03 (2024): 1–13. http://dx.doi.org/10.55041/ijsrem29057.
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This paper presents the development of an innovative video summarization system utilizing Natural Language Processing (NLP) and Machine Learning techniques. The exponential growth of video content on platforms like YouTube has posed a significant challenge in efficient content consumption. To address this challenge, we propose a YouTube transcript summarizer that generates concise and informative summaries of video transcripts, enabling users to grasp key content material without the need for complete viewing. Unlike images, where data extraction is feasible from a single frame, understanding the context of a video typically requires viewing the entire content. Our study seeks to alleviate this issue by reducing the transcript length while preserving its comprehensiveness. Leveraging NLP and Machine Learning algorithms, such as Logistic Regression, we extract transcripts from user-provided video links and summarize the content into a precise representation using Word2Vec and Logistic Regression. By distilling the essence of YouTube video transcripts while retaining their pivotal elements, our system offers users a more streamlined and effective way to consume video content. Keywords: Transcript Summarizer, YouTube, NLP, Word2Vec, Logistic Regression, Summary.
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Sridhar, Srinivasan, Nazmul Kazi, Indika Kahanda, and Bernadette McCrory. "Psychiatry Transcript Annotation: Process Study and Improvements." Proceedings of the International Symposium on Human Factors and Ergonomics in Health Care 10, no. 1 (2021): 71–75. http://dx.doi.org/10.1177/2327857921101030.
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Background: The demand for psychiatry is increasing each year. Limited research has been performed to improve psychiatrist work experience and reduce daily workload using computational methods. There is currently no validated tool or procedure for the mental health transcript annotation process for generating “gold-standard” data. The purpose of this paper was to determine the annotation process for mental health transcripts and how it can be improved to acquire more reliable results considering human factors elements. Method: Three expert clinicians were recruited in this study to evaluate the transcripts. The clinicians were asked to fully annotate two transcripts. An additional five subjects were recruited randomly (aged between 20-40) for this pilot study, which was divided into two phases, phase 1 (annotation without training) and phase 2 (annotation with training) of five transcripts. Kappa statistics were used to measure the inter-rater reliability and accuracy between subjects. Results: The inter-rater reliability between expert clinicians for two transcripts were 0.26 (CI 0.19 to 0.33) and 0.49 (CI 0.42 to 0.57), respectively. In the pilot testing phases, the mean inter-rater reliability between subjects was higher in phase 2 with training transcript (k= 0.35 (CI 0.052 to 0.625)) than in phase 1 without training transcript (k= 0.29 (CI 0.128 to 0.451)). After training, the accuracy percentage among subjects was significantly higher in transcript A (p=0.04) than transcript B (p=0.10). Conclusion: This study focused on understanding the annotation process for mental health transcripts, which will be applied in training machine learning models. Through this exploratory study, the research found appropriate categorical labels that should be included for transcripts annotation, and the importance of training the subjects. Contributions of this case study will help the psychiatric clinicians and researchers in implementing the recommended data collection process to develop a more accurate artificial intelligence model for fully- or semi-automated transcript annotation.
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Frojmark, Anne-Sophie, Jitendra Badhai, Edward J. Davey, and Niklas Dahl. "Diamond Blackfan Anemia: An RPS19 Transcript Variant Specifically Interacts with Nuclear Proteins." Blood 106, no. 11 (2005): 1032. http://dx.doi.org/10.1182/blood.v106.11.1032.1032.
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Abstract Diamond Blackfan Anemia (DBA) is a rare congenic anemia characterized by reduced erythrocyte precursors. Mutations in the ribosomal protein S19 (RPS19) gene are found in about 20% of patients, although it is unclear how this relates to the pathophysiology of the disease. Two transcripts have been reported for human RPS19 in the NCBI database (BC000023 and BC018616), which only differ in the length of the 5′UTR. Both transcripts predict translation to the same protein product and we therefore speculate that the extended 5′UTR may be of importance. While the short (569bp) transcript is well studied, the long (873bp) transcript has not been investigated. We determined the size and tissue distribution as a basic characterization of the long RPS19 transcript. Furthermore, we examined proteins interacting with the different RPS19 transcript variants. Two methods were used determine the size of long RPS19 transcript. Ribonuclease protection assays and 5′-RACE indicate a transcript length consistent with the reported sequence with a 5′UTR of 372bp. Interestingly the 5′UTR predicted in the long transcript contains sequence for a previously reported promoter, suggesting a second novel promoter. Tissue distribution was determined using reverse transcriptase PCR on isolated RNA from a panel of tissues including heart, bone marrow, fetal liver, liver, brain, fetal brain, muscle, kidney, uterus, adrenal gland, lungs, placenta, prostate testes, ovary, thymus, colon, lymphocytes and from K562 and HeLa cell lines. Analysis indicated a ubiquitously expression of the long RPS19 transcript. In order to investigate interactions between the RPS19 transcripts and regulatory proteins, a UV cross-linking assay was performed using in vitro transcribed RNA representing both short and long transcripts. A protein of 55 kDa from nuclear fractions prepared from the erythroid cell lines K562, UT-7 and Cos-1 cells was found to bind to the long RPS19 transcript but not to the short RPS19 transcript. Our results provide evidence for an additional long, RPS19 transcript containing an extended 5′UTR that is ubiquitously transcribed and indicates the existence of a second promoter for RPS19. We further show that a nuclear protein, present in two different erythroid cell lines, interacts with the long RPS19 transcript indicating a function for the extended 5′UTR. This data suggests additional regulatory pathways involving RPS19 mRNA which may be of relevance to the understanding of the molecular mechanisms behind DBA.
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Yu, Jinyi, Shuting Li, Simin Shen, et al. "The transcript NR 134251.1 of lncRNA APTR with an opposite function to all transcripts inhibits proliferation and induces apoptosis by regulating proliferation and apoptosis-related genes." Human & Experimental Toxicology 42 (January 3, 2023): 096032712211502. http://dx.doi.org/10.1177/09603271221150247.
Full textAbstract:
Arsenic (As) exposure has been a global public health concern for hundreds of millions worldwide. LncRNA APTR (Alu-mediated p21 transcriptional regulator) plays an essential role in tumor growth and development. However, its function in arsenic-induced toxicological responses is still unknown. In this study, we found that the expressions of all transcripts and the transcript NR 134251.1 of APTR were increased in a dose-dependent manner in 16HBE cells treated with sodium arsenite (NaAsO2). Silencing the transcript NR 134251.1 of APTR inhibited cell proliferation and induced apoptosis. However, silencing all transcripts of APTR had the opposite function to the transcript NR 134251.1. Then we examined the protein level of the proliferation and apoptosis-related genes after silencing the transcript NR 134251.1 of APTR. The results showed that silencing the transcript NR 134251.1 of APTR up-regulated the expression of transcription factor E2F1 and regulated its downstream genes involved in proliferation and apoptosis, including p53, phospho-p53-S392, phospho-p53-T55, p21, Cyclin D1, PUMA, Fas, Bim, BIK, Caspase-3, Caspase-7, and Cyt-c. In conclusion, arsenic induced APTR expression and the transcript NR 134251.1 of APTR have an opposite function to all transcripts, providing a theoretical basis for the prevention and treatment of arsenic exposure.
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Erho, Nicholas, Christine Buerki, Timothy J. Triche, Elai Davicioni, and Ismael A. Vergara. "Transcriptome-Wide Detection of Differentially Expressed Coding and Non-Coding Transcripts and Their Clinical Significance in Prostate Cancer." Journal of Oncology 2012 (2012): 1–11. http://dx.doi.org/10.1155/2012/541353.
Full textAbstract:
Prostate cancer is a clinically and biologically heterogeneous disease. Deregulation of splice variants has been shown to contribute significantly to this complexity. High-throughput technologies such as oligonucleotide microarrays allow for the detection of transcripts that play a role in disease progression in a transcriptome-wide level. In this study, we use a publicly available dataset of normal adjacent, primary tumor, and metastatic prostate cancer samples (GSE21034) to detect differentially expressed coding and non-coding transcripts between these disease states. To achieve this, we focus on transcript-specific probe selection regions, that is, those probe sets that correspond unambiguously to a single transcript. Based on this, we are able to pinpoint at the transcript-specific level transcripts that are differentially expressed throughout prostate cancer progression. We confirm previously reported cases and find novel transcripts for which no prior implication in prostate cancer progression has been made. Furthermore, we show that transcript-specific differential expression has unique prognostic potential and provides a clinically significant source of biomarker signatures for prostate cancer risk stratification. The results presented here serve as a catalog of differentially expressed transcript-specific markers throughout prostate cancer progression that can be used as basis for further development and translation into the clinic.
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Kowara, Renata, Filip Gołebiowski, Paweł Chrzan, Jaroslaw Skokowski, Andrzej Karmolinski, and Tadeusz Pawełczyk. "Abnormal FHIT gene transcript and c-myc and c-erbB2 amplification in breast cancer." Acta Biochimica Polonica 49, no. 2 (2002): 341–50. http://dx.doi.org/10.18388/abp.2002_3792.
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Searching for ways to improve the characterization of breast cancer we examined the relationship between the status of the FHIT gene transcript and amplification of c-myc and the c-erbB2 oncogene. Abnormal FHIT transcript was detected in 32 of 79 cancers examined. The presence of Fhit protein estimated by Western blots was evident only in cancers exhibiting a normal-sized FHIT transcript. This indicates that abnormal FHIT transcripts observed in our study did not encode any Fhit protein or the amount of such protein was very low. There was no association between the presence of aberrant FHIT gene transcript with age, tumor size, estrogen and progesterone receptor status, local metastases and histological grading. However, the abnormalities in FHIT gene transcripts were observed with different frequency depending on the histopathological type of the tumor. The aberrant FHIT transcript was detected in 60% of lobular cancers and only in 28% of ductal cancers. Analyzing the occurrence of c-myc and c-erbB2 amplification and the presence of aberrant FHIT gene transcripts we found that the aberrant FHIT transcript more frequently occurred in tissues with c-myc amplification. There was a significant (P < 0.05) correlation between the occurrence of the aberrant FHIT gene transcript with accompanying c-myc amplification and positive lymph node status. However, in order to evaluate the predictive value of these findings in breast cancer, an extended clinical follow up will be necessary.
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Shirtavde, Hiteshri, Ayushmati Swain, Simmi Singh, and Tushar Singh. "YouTube Transcript Summarizer." International Journal of Recent Advances in Multidisciplinary Topics 5, no. 5 (2024): 102–6. https://doi.org/10.5281/zenodo.11221964.
Full textAbstract:
The "YouTube Transcript Summarizer" is a pioneering Chrome extension project designed to enhance the user experience by providing concise and insightful summaries of YouTube video transcripts. Leveraging Natural Language Processing (NLP) techniques, the extension aims to empower users by offering a convenient and time-efficient way to comprehend video content without the need for full viewing. The extension integrates seamlessly into the YouTube interface, allowing users to generate accurate text summaries from video transcripts at their discretion. This innovative tool utilizes advanced algorithms to process the transcript data, extracting key themes, concepts, and relevant information from lengthy video content. Through a user-friendly interface, it presents condensed summaries, enabling users to grasp the essential points, main arguments, and crucial details of the video without watching the entire content. The extension prioritizes accuracy and efficiency, ensuring that the generated summaries are comprehensive and informative. Its development involves the application of machine learning models and text analysis techniques to accurately condense the content into a coherent and understandable summary. Ultimately, the "YouTube Transcript Summarizer" project aims to revolutionize how users engage with video content on YouTube, offering a time-saving and insightful solution for obtaining quick, meaningful insights from video transcripts.
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Wan, Xiao, Long-Hai Zou, Bao-Qiang Zheng, and Yan Wang. "Circadian Regulation of Alternative Splicing of Drought-Associated CIPK Genes in Dendrobium catenatum (Orchidaceae)." International Journal of Molecular Sciences 20, no. 3 (2019): 688. http://dx.doi.org/10.3390/ijms20030688.
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Dendrobium catenatum, an epiphytic and lithophytic species, suffers frequently from perennial shortage of water in the wild. The molecular mechanisms of this orchid’s tolerance to abiotic stress, especially drought, remain largely unknown. It is well-known that CBL-interacting protein kinase (CIPKs) proteins play important roles in plant developmental processes, signal transduction, and responses to abiotic stress. To study the CIPKs’ functions for D. catenatum, we first identified 24 CIPK genes from it. We divided them into three subgroups, with varying intron numbers and protein motifs, based on phylogeny analysis. Expression patterns of CIPK family genes in different tissues and in response to either drought or cold stresses suggested DcaCIPK11 may be associated with signal transduction and energy metabolism. DcaCIPK9, -14, and -16 are predicted to play critical roles during drought treatment specifically. Furthermore, transcript expression abundances of DcaCIPK16 showed polar opposites during day and night. Whether under drought treatment or not, DcaCIPK16 tended to emphatically express transcript1 during the day and transcript3 at night. This implied that expression of the transcripts might be regulated by circadian rhythm. qRT-PCR analysis also indicated that DcaCIPK3, -8, and -20 were strongly influenced by circadian rhythmicity. In contrast with previous studies, for the first time to our knowledge, our study revealed that the major CIPK gene transcript expressed was not always the same and was affected by the biological clock, providing a different perspective on alternative splicing preference.
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Oliveira, Marcelo Braga de, Carolina de Alcântara Maneschy, Jairo Augusto Américo de Castro, Katarine Antonia dos Santos Barile, Maurício Koury Palmeira, and Carlos Eduardo de Melo Amaral. "Association between the BCR-ABL gene transcripts and the laboratory hematological profile." REVISTA CIÊNCIAS EM SAÚDE 12, no. 3 (2022): 61–66. http://dx.doi.org/10.21876/rcshci.v12i3.1281.
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Objective: This study describes the hematological parameters associated with the BCR-ABL gene transcripts in patients with chronic myeloid leukemia (CML). Methods: We reviewed the results of 100 detectable patients for one of the BCR-ABL gene transcripts. The eligibility criteria were based on the presence of one of the leukemic transcripts (b2a2, b3a2, and b2a2/b3a2) and complete epidemiological and hematological data. The data were obtained from the LabMaster computerized system. The Kruskal-Wallis test was used to compare the medians of the quantitative variables between the transcripts of the BCR-ABL gene and the chi-square test to compare the qualitative ones, adopting the p-value with a level of significance less than or equal to 0.05. Results: Forty-five patients (45%) presented the b2a2 transcript, 24 (24%) the b3a2 transcript and 31 (31%) a b2a2/b3a2 coexpression. Individuals who expressed the b3a2 transcript had higher leukocyte counts and platelet levels, but we found no differences compared with individuals who expressed the other transcript. Conclusion: In this study, the BCR-ABL gene transcripts did not influence the hematological parameters of patients with CML.
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Chatterjee, Sumana, Emily Cottrell, Stephen J. Rose та ін. "GHR gene transcript heterogeneity may explain phenotypic variability in GHR pseudoexon (6Ψ) patients". Endocrine Connections 9, № 3 (2020): 211–22. http://dx.doi.org/10.1530/ec-20-0026.
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Objectives The homozygous GH receptor (GHR) pseudoexon (6Ψ) mutation leads to growth hormone insensitivity (GHI) with clinical and biochemical heterogeneity. We investigated whether transcript heterogeneity (6Ψ-GHR to WT-GHR transcript ratio) and/or concurrent defects in other short stature (SS) genes contribute to this. Methods 6Ψ-GHR and WT-GHR mRNA transcripts of four 6Ψ patients (height SDS −4.2 to −3.1) and one control fibroblast were investigated by RT-PCR. Transcripts were quantified by qRT-PCR and delta delta CT analysis and compared using ANOVA with Bonferroni correction. In eleven 6Ψ patients, 40 genes known to cause GHI/SS were analysed by targeted next generation sequencing. Results RT-PCR confirmed 6Ψ-GHR transcript in the 6Ψ patients but not in the control. 6Ψ-GHR transcript levels were comparable in patients 1 and 3 but significantly different among all other patients. The mean 6Ψ:WT transcript ratios ranged from 29–71:1 for patients 1–4 and correlated negatively with height SDS (R = −0.85; P < 0.001). Eight deleterious variants in six genes were detected, but the number of gene hits did not correlate with the degree of SS in individual 6Ψ patients. Conclusion Variable amounts of 6Ψ- and WT-GHR transcripts were identified in 6Ψ patients but no 6Ψ transcript was present in the control. Higher 6Ψ:WT-GHR transcript ratio correlated with SS severity and may explain the phenotypic variability. Analysis of known SS genes suggested that phenotypic variation is independent of the genetic background. This is the first report of transcript heterogeneity producing a spectrum of clinical phenotypes in different individuals harbouring an identical homozygous genetic mutation.
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Ku, Yee-Shan, Xiao Lin, Kejing Fan, et al. "The Identification of MATE Antisense Transcripts in Soybean Using Strand-Specific RNA-Seq Datasets." Genes 13, no. 2 (2022): 228. http://dx.doi.org/10.3390/genes13020228.
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Natural antisense transcripts (NATs) have been generally reported as negative regulators of their sense counterparts. Multidrug and toxic compound extrusion (MATE) proteins mediate the transport of various substrates. Although MATEs have been identified genome-wide in various plant species, their transcript regulators remain unclear. Here, using the publicly available strand-specific RNA-seq datasets of Glycine soja (wild soybean) which have the data from various tissues including developing pods, developing seeds, embryos, cotyledons and hypocotyls, roots, apical buds, stems, and flowers, we identified 35 antisense transcripts of MATEs from 28 gene loci after transcriptome assembly. Spearman correlation coefficients suggested the positive expression correlations of eight MATE antisense and sense transcript pairs. By aligning the identified transcripts with the reference genome of Glycine max (cultivated soybean), the MATE antisense and sense transcript pairs were identified. Using soybean C08 (Glycine max), in developing pods and seeds, the positive correlations between MATE antisense and sense transcript pairs were shown by RT-qPCR. These findings suggest that soybean antisense transcripts are not necessarily negative transcription regulators of their sense counterparts. This study enhances the existing knowledge on the transcription regulation of MATE transporters by uncovering the previously unknown MATE antisense transcripts and their potential synergetic effects on sense transcripts.
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Al-Amri, Majid N. "Listening to foreign language student teachers: The use of transcripts to study classroom interactions." South African Journal of Education 44, no. 1 (2024): 1–13. http://dx.doi.org/10.15700/saje.v44n1a2317.
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Although many issues about the use of transcripts for studying classroom interactions have been addressed in other studies, little attention has been given to the use of transcripts to study student teachers’ classroom interactions. To achieve a deeper understanding of student teachers’ perspectives and permit the formulation of a more appropriate framework, it is crucial to hear from student teachers and investigate their experiences about the use of transcripts. Therefore, in the study reported on here we used 7 focus-group interviews of approximately 6 Saudi EFL (English as a foreign language) student teachers in each group to investigate their perceptions on the use of transcripts for studying their classroom interactions. The data were thematically analysed. Three themes that represented the participants’ experiences of using transcripts to study their classroom interactions emerged: using the transcript analysis, learning from the transcript analysis, and committing to using the transcript analysis. The findings reveal that most participants felt they had autonomy in using transcripts to study their classroom interactions, but experienced some challenges. Most students were determined to change their classroom interaction based on their analyses of classroom interactions but only a few demonstrated the determination to continue using the transcript analysis approach.
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Anderson, Warren D., Fabiana M. Duarte, Mete Civelek, and Michael J. Guertin. "Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R." Bioinformatics 36, no. 9 (2020): 2926–28. http://dx.doi.org/10.1093/bioinformatics/btaa011.
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Abstract Summary Nascent transcript measurements derived from run-on sequencing experiments are critical for the investigation of transcriptional mechanisms and regulatory networks. However, conventional mRNA gene annotations significantly differ from the boundaries of primary transcripts. New primary transcript annotations are needed to accurately interpret run-on data. We developed the primaryTranscriptAnnotation R package to infer the transcriptional start and termination sites of primary transcripts from genomic run-on data. We then used these inferred coordinates to annotate transcriptional units identified de novo. This package provides the novel utility to integrate data-driven primary transcript annotations with transcriptional unit coordinates identified in an unbiased manner. Highlighting the importance of using accurate primary transcript coordinates, we demonstrate that this new methodology increases the detection of differentially expressed transcripts and provides more accurate quantification of RNA polymerase pause indices. Availability and implementation https://github.com/WarrenDavidAnderson/genomicsRpackage/tree/master/primaryTranscriptAnnotation. Supplementary information Supplementary data are available at Bioinformatics online.
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Chan, R. Y. Y., H. M. Schulman, and P. Ponka. "Expression of ferrochelatase mRNA in erythroid and non-erythroid cells." Biochemical Journal 292, no. 2 (1993): 343–49. http://dx.doi.org/10.1042/bj2920343.
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Ferrochelatase, which catalyses the last step in haem biosynthesis, i.e. the insertion of Fe(II) into protophorphyrin IX, is present in all cells, but is particularly abundant in erythroid cells during haemoglobinization. Using mouse ferrochelatase cDNA as a probe two ferrochelatase transcripts, having lengths of 2.9 kb and 2.2 kb, were found in extracts of mouse liver, kidney, brain, muscle and spleen, the 2.9 kb transcript being more abundant in the non-erythroid tissues and the 2.2 kb transcript more predominant in spleen. In mouse erythroleukemia cells the 2.9 kb ferrochelatase transcript is also more abundant; however, following induction of erythroid differentiation by dimethyl sulphoxide there is a preferential increase in the 2.2 kb transcript, which eventually predominates. With mouse reticulocytes, the purest immature erythroid cell population available, over 90% of the total ferrochelatase mRNA is present as the 2.2 kb transcript. Since there is probably only one mouse ferrochelatase gene, the occurrence of two ferrochelatase transcripts could arise from the use of two putative polyadenylation signals in the 3′ region of ferrochelatase DNA. This possibility was explored by using a 389 bp DNA fragment produced by PCR with synthetic oligoprimers having sequence similarity with a region between the polyadenylation sites. This fragment hybridized only to the 2.9 kb ferrochelatase transcript, indicating that the two transcripts differ at their 3′ ends and suggesting that the 2.2 kb transcript results from the utilization of the upstream polyadenylation signal. The preferential utilization of the upstream polyadenylation signal may be an erythroid-specific characteristic of ferrochelatase gene expression.
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Singh, Prashant, Diogo Troggian Veiga, Robert Rossi, et al. "Systemic Lupus Erythematosus (SLE) patients’ Peripheral Blood Mononuclear Cells (PBMCs) display an altered transcript isoform repertoire." Journal of Immunology 202, no. 1_Supplement (2019): 117.19. http://dx.doi.org/10.4049/jimmunol.202.supp.117.19.
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Abstract Alternative splicing (AS) is a key mechanism of biological diversity in eukaryotes allowing a single gene to generate multiple mRNA transcript isoforms, yielding unique proteins that may have distinct or opposing functions. Alterations in AS have been associated with numerous diseases. SLE patients display autoantibodies to components of the spliceosome, chiefly anti-Sm/RNP, anti-Ro/La, and anti-dsDNA. We performed Long-Read sequencing using Pacific Biosciences equipment (LR-Seq), as well as short read RNA-Seq, from adolescent SLE patients’ and healthy controls’ PBMCs, to discover and quantitate splice junctions. A computational pipeline was built to differentially quantify splice junctions in the LR-Seq sequenced isoforms, both known and novel using rMATS (Multivariate Analysis of Transcript Splicing). Compared to Gencode, LR-Seq revealed ~9000 novel transcript isoforms. 55% of all transcripts were expressed in 2 or more samples. A majority of these transcripts belonged to genes associated with cell cycle, metabolism, and inflammation. Additionally, we interrogated our SLE LR-Seq generated transcriptome with publicly available RNA-Seq data from adult SLE and healthy donors. We observed 250 differential expression of exon skipping (ES) splice junctions in transcript isoforms of genes, a majority of which did not exhibit any significant change in gene expression. Of the 250 ES transcript isoforms, 160 exon inclusion events were observed in SLE PBMCs. Fifty percent of the exon inclusion events were found to be in novel transcript isoforms. Thus LR-Seq, besides revealing novel transcripts, allows us to study changes in transcript isoform expression.
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Hann, Louane E., W. James Cook, Susan L. Uprichard, David M. Knipe, and Donald M. Coen. "The Role of Herpes Simplex Virus ICP27 in the Regulation of UL24 Gene Expression by Differential Polyadenylation." Journal of Virology 72, no. 10 (1998): 7709–14. http://dx.doi.org/10.1128/jvi.72.10.7709-7714.1998.
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ABSTRACT Herpes simplex virus specifies two sets of transcripts from theUL24 gene, short transcripts (e.g., 1.4 kb), processed at the UL24 poly(A) site, and long transcripts (e.g., 5.6 kb), processed at the UL26 poly(A) site. The 1.4- and 5.6-kb transcripts initiate from the same promoter but are expressed with early and late kinetics, respectively. Measurements of transcript levels following actinomycin D treatment of infected cells revealed that the 1.4- and 5.6-kb UL24 transcripts have similar stabilities, consistent with UL24 transcript kinetics being regulated by differential polyadenylation rather than by differential stabilities. Although the UL24 poly(A) site, which gives rise to short transcripts, is encountered first during processing, long transcripts processed at the UL26 site are equally or more abundant; thus, operationally, the UL24site is weak. Using a series of viral ICP27 mutants, we investigated whether ICP27, which has been suggested to stimulate the usage of weak poly(A) sites, stimulates 1.4-kb transcript accumulation. We found that accumulation of 1.4-kb transcripts did not require ICP27 during viral infection. Rather, ICP27 was required for full expression of 5.6-kb transcripts, and the decrease in 5.6-kb transcripts relative to 1.4-kb transcripts was not due solely to reduced DNA synthesis. Our results indicate that temporal expression of UL24transcripts can be regulated by differential polyadenylation and that although ICP27 is not required for processing at the operationally weakUL24 poly(A) site, it does modulate 5.6-kb transcript levels at a step subsequent to transcriptional initiation.
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Phelps, Dawn E., Kuang-Ming Hsiao, Yan Li, et al. "Coupled Transcriptional and Translational Control of Cyclin-Dependent Kinase Inhibitor p18INK4cExpression during Myogenesis." Molecular and Cellular Biology 18, no. 4 (1998): 2334–43. http://dx.doi.org/10.1128/mcb.18.4.2334.
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ABSTRACT Terminal differentiation of many cell types involves permanent withdrawal from the cell division cycle. The p18 INK4c protein, a member of the p16/INK4 cyclin-dependent kinase (CDK) inhibitor family, is induced more than 50-fold during myogenic differentiation of mouse C2C12 myoblasts to become the predominant CDK inhibitor complexed with CDK4 and CDK6 in terminally differentiated myotubes. We have found that the p18 INK4c gene expresses two mRNA transcripts—a 2.4-kb transcript, p18(L), and a 1.2-kb transcript, p18(S). In proliferating C2C12 myoblasts, only the larger p18(L) transcript is expressed from an upstream promoter. As C2C12 cells are induced to differentiate into permanently arrested myotubes, the abundance of the p18(L) transcript decreases. The smaller p18(S) transcript expressed from a downstream promoter becomes detectable by 12 h postinduction and is the predominant transcript expressed in terminally differentiated myotubes. Both transcripts contain coding exons 2 and 3, but p18(L) uniquely contains an additional noncoding 1.2-kb exon, exon 1, corresponding exclusively to the 5′ untranslated region (5′ UTR). The expression pattern of the shorter p18(S) transcript, but not that of the longer p18(L) transcript, correlates with terminal differentiation of muscle, lung, liver, thymus, and eye lens cells during mouse embryo development. The presence of the long 5′ UTR in exon 1 attenuated the translation of p18(L) transcript, while its absence from the shorter p18(S) transcript resulted in significantly more efficient translation of the p18 protein. Our results demonstrate that during terminal muscle cell differentiation, induction of the p18 protein is regulated by promoter switching coupled with translational control.
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Kovesdi, I., and M. J. Smith. "Quantitative assessment of actin transcript number in eggs, embryos, and tube feet of the sea star Pisaster ochraceus." Molecular and Cellular Biology 5, no. 11 (1985): 3001–8. http://dx.doi.org/10.1128/mcb.5.11.3001-3008.1985.
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Actin coding sequence cDNA probes were used to quantitate the number of transcripts in RNA from eggs, embryos, and tube feet of the sea star Pisaster ochraceus. Transcript concentrations were measured in both total RNA and in poly(A)+ RNA by titration and hybridization kinetic methods. Surprisingly, the actin transcript number in sea star eggs is two orders of magnitude greater than in sea urchin eggs. There are at least 2.9 X 10(5) actin transcripts per sea star egg, 1.2 X 10(5) per 48-h gastrula and 1.9 X 10(5) per 72-h gastrula. The number of actin transcripts per unit mass of extracted tube foot RNA is lower than in developmental stages. The relative abundance and size of actin transcripts was determined by Northern and dot blot analyses using probes containing actin coding DNA or 3'-untranslated-region sequences. The actin transcript in eggs and embryos is 2,300 nucleotides (nt) long and originates from the Cy (cytoplasmic) gene class. In tube feet, the most abundant actin transcript is 2,200 nt long and originates from the M (muscle) gene class. Tube feet also contain, at lower abundance, 2,300-nt transcripts of the Cy gene type expressed in eggs and embryos.
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Kovesdi, I., and M. J. Smith. "Quantitative assessment of actin transcript number in eggs, embryos, and tube feet of the sea star Pisaster ochraceus." Molecular and Cellular Biology 5, no. 11 (1985): 3001–8. http://dx.doi.org/10.1128/mcb.5.11.3001.
Full textAbstract:
Actin coding sequence cDNA probes were used to quantitate the number of transcripts in RNA from eggs, embryos, and tube feet of the sea star Pisaster ochraceus. Transcript concentrations were measured in both total RNA and in poly(A)+ RNA by titration and hybridization kinetic methods. Surprisingly, the actin transcript number in sea star eggs is two orders of magnitude greater than in sea urchin eggs. There are at least 2.9 X 10(5) actin transcripts per sea star egg, 1.2 X 10(5) per 48-h gastrula and 1.9 X 10(5) per 72-h gastrula. The number of actin transcripts per unit mass of extracted tube foot RNA is lower than in developmental stages. The relative abundance and size of actin transcripts was determined by Northern and dot blot analyses using probes containing actin coding DNA or 3'-untranslated-region sequences. The actin transcript in eggs and embryos is 2,300 nucleotides (nt) long and originates from the Cy (cytoplasmic) gene class. In tube feet, the most abundant actin transcript is 2,200 nt long and originates from the M (muscle) gene class. Tube feet also contain, at lower abundance, 2,300-nt transcripts of the Cy gene type expressed in eggs and embryos.
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Rosa, Villegas-Ruíz, Caballero-Palacios, et al. "Expression of ZNF695 Transcript Variants in Childhood B-Cell Acute Lymphoblastic Leukemia." Genes 10, no. 9 (2019): 716. http://dx.doi.org/10.3390/genes10090716.
Full textAbstract:
B-cell acute lymphoblastic leukemia is the most commonly diagnosed childhood malignancy worldwide; more than 50% of these cases are diagnosed in Mexico. Although the five-year survival rate is >80%, 30% of patients experience relapse with poor prognosis. Cancer-associated gene expression profiles have been identified in several malignancies, and some transcripts have been used to predict disease prognosis. The human transcriptome is incompletely elucidated; moreover, more than 80% of transcripts can be processed via alternative splicing (AS), which increases transcript and protein diversity. The human transcriptome is divided; coding RNA accounts for 2%, and the remaining 98% is noncoding RNA. Noncoding RNA can undergo AS, promoting the diversity of noncoding transcripts. We designed specific primers to amplify previously reported alternative transcript variants of ZNF695 and showed that six ZNF695 transcript variants are co-expressed in cancer cell lines. The amplicons were sequenced and identified. Additionally, we analyzed the expression of these six transcript variants in bone marrow from B-cell acute lymphoblastic leukemia patients and observed that ZNF695 transcript variants one and three were the predominant variants expressed in leukemia. Moreover, our results showed the co-expression of coding and long noncoding RNA. Finally, we observed that long noncoding RNA ZNF695 expression predicted survival rates.
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Ahmed Elnour, Abdalla Abdelrahman, and Mahdi H. A. Abdalla. "P210 and P190 BCR-ABL fusion transcripts variants frequencies among Philadelphia chromosome-positive chronic myeloid leukemia in Sudan." International Journal of Biomedical Research 9, no. 5 (2018): 172. http://dx.doi.org/10.7439/ijbr.v9i5.4736.
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Breakpoint cluster region-abelson (BCR-ABL) leukemic fusion gene types in chronic myeloid leukemia (CML) correlate with the disease clinical course and outcome. There are variations in the reports of previous studies about the frequencies and distribution of BCR-ABL transcripts in chronic myelogenous leukaemia among Sudanese patients. This research aims to determine the frequencies of BCR-ABL fusion transcript variants in Sudan. One hundred (informed consent) Philadelphia positive chronic myeloid leukaemia patients, in chronic phase, were enrolled in this study. EDTA anticoagulated peripheral blood samples were collected from each participant, RNA was extracted from mononuclear cells by (TRIzol) reagent. BCR-ABL transcripts were detected by qRT-PCR technique with specific primers forP190 and P210 BCR-ABL transcript variants. The typical p210 BCR-ABL transcripts (b3a2 or b2a2) were detected in all patients (100%) the b3a2 transcript was detected in 96/100 (96%) and the b2a2 transcript was detected in 4/100 (4%).co-expression of p210/p190 (b2a3/e1a2) was detected in 6/100 (6%). p190 variant was not detected independently.
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Sakkas, Lazaros I., Charles Tourtellotte, Steve Berney, Allen R. Myers та Chris D. Platsoucas. "Increased Levels of Alternatively Spliced Interleukin 4 (IL-4δ2) Transcripts in Peripheral Blood Mononuclear Cells from Patients with Systemic Sclerosis". Clinical Diagnostic Laboratory Immunology 6, № 5 (1999): 660–64. http://dx.doi.org/10.1128/cdli.6.5.660-664.1999.
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ABSTRACT Recent in vitro studies have shown that interleukin 4 (IL-4) induces and gamma interferon (IFN-γ) inhibits collagen production. To define the TH1(IFN-γ) and TH2(IL-4) cytokine profiles in systemic sclerosis (Sscl), a disease characterized by widespread fibrosis, we investigated IL-4 and IFN-γ transcripts in peripheral blood mononuclear cells and plasma protein levels in 13 patients with Sscl. Two previously identified IL-4 transcripts, a full-length transcript and an alternatively spliced (truncated) transcript (designated IL-4δ2), were identified in patients and normal controls. Significantly increased levels of total IL-4 transcripts (full-length plus IL-4δ2 transcripts) were found in patients with Sscl in comparison to those found in healthy controls (P = 0.003), and this increase was primarily due to an increase in the level of the alternatively spliced IL-4δ2 form. The IL-4δ2/full-length-IL-4 transcript ratio was significantly increased in Sscl patients (P < 0.0001, versus healthy controls). Sequencing analysis revealed that the frequency of IL-4 clones carrying the IL-4δ2 transcript was also substantially increased in patients with Sscl. Plasma IL-4 protein levels were increased in Sscl patients compared to those in healthy controls (P = 0.001) and correlated with total IL-4 transcript levels. The up-regulation of the fibrogenic IL-4 (a TH2 cytokine) in Sscl suggests a pathogenic role for IL-4 in this disease.
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PLANT, Matthew H., and Odette LANEUVILLE. "Characterization of a novel transcript of prostaglandin endoperoxide H synthase 1 with a tissue-specific profile of expression." Biochemical Journal 344, no. 3 (1999): 677–85. http://dx.doi.org/10.1042/bj3440677.
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The enzyme prostaglandin endoperoxide H synthase (PGHS) has a pivotal role in the prostanoid biosynthetic pathway because it catalyses the formation of prostaglandin H2 (PGH2), the common precursor of prostanoids. Two PGHS isoforms have been reported, PGHS-1 and PGHS-2, which have 61% identity (at the amino acid level) and 73% similarity (at the nucleotide level) between the two human enzymes. Transcription of the PGHS-1 gene leads to the formation of two transcripts (2.8 and 5.1 kb); two transcripts of 2.8 and 4.5 kb are produced from the PGHS-2 gene. By Northern blot analysis with the entire coding region of human PGHS-1, 2.8 and 5.1 kb transcripts as well as a novel 4.5 kb transcript were detected in the human megakaryoblastic cell line MEG-01. We designed a strategy to characterize the 4.5 kb PGHS transcript. Probes specific for each PGHS-1 and PGHS-2 were designed on the basis of the 3ʹ untranslated region (3ʹ UTR), where no similarity is present. The 4.5 kb transcript was detected only with the PGHS-1-specific 3ʹ UTR probes and not with the PGHS-2-specific 3ʹ UTR probe. To investigate the origin of the 4.5 kb PGHS-1 transcript, the remaining 947 bp of the 5.1 kb PGHS-1 transcript was generated by 3ʹ rapid amplification of cDNA ends (3ʹ RACE) and sequenced. A non-canonical polyadenylation signal (AAGAAA) located upstream of a potential cleavage site (CA) was found and could generate the 4.5 kb PGHS-1 transcript. Analysis of the sequence also produced several possible G/U-rich elements downstream of the potential cleavage site. An RNA dot-blot with 50 different human tissues was probed with the 4.5 and 5.1 kb PGHS-1-specific probes. A signal for the 4.5 kb PGHS-1 transcript was detected in the bladder and appendix. Signals of lower intensity were detected in the colon, bone marrow, small intestine, uterus, prostate, peripheral leucocyte, lymph node and stomach. In conclusion, our results suggest that the cell line MEG-01, the bladder and the appendix contain a new PGHS-1 transcript of 4.5 kb that can be produced from the PGHS-1 gene and we provide a better strategy for distinguishing PGHS-1 transcripts from PGHS-2.
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Frisch, M. "Transcript." Oral History Review 15, no. 2 (1987): 7–37. http://dx.doi.org/10.1093/ohr/15.2.7.
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Symposium. "Transcript." Indiana International & Comparative Law Review 33, no. 2 (2023): 373–422. http://dx.doi.org/10.18060/27376.
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Biancardi, M. N., L. Magnani, C. M. Johnson, and R. A. Cabot. "178 TRANSCRIPT ABUNDANCE OF METHYLTRANSFERASES SPECIFIC FOR H3K9 DIFFER AT DISCRETE STAGES OF PORCINE OOCYTE AND CLEAVAGE STAGE EMBRYO DEVELOPMENT." Reproduction, Fertility and Development 21, no. 1 (2009): 188. http://dx.doi.org/10.1071/rdv21n1ab178.
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Covalent modification of histone proteins plays a key role in transcriptional regulation. Methylation of the lysine residue 9 of histone protein 3 (H3K9) is globally remodeled during cleavage development. The aim of this study was to determine the relative transcript abundance of the 5 histone methyltransferases (HMTases) that have been shown to methylate H3K9, in porcine oocytes and cleavage stage embryos. We hypothesized that transcript levels for each of these HMTases (Suv39h1, Suv39h2, ESET, GLP, and G9a) would differ in their respective abundance at each developmental stage and that some would undergo dramatic changes in transcript abundance during development. To test this hypothesis, quantitative RT-PCR was performed on mRNA isolated from pools of 78–457 germinal vesicle (GV) and metaphase II (MII)-stage oocytes and 4-cell (4C) and blastocyst (BL)-stage embryos produced by either parthenogenetic activation (PA) or in vitro fertilization (IVF); each pool constituted an experimental replicate, and a minimum of 3 replicates were performed for each stage. Along with the 5 HMTases, transcripts for YWHAG were assayed and used as a normalizer. PCR data were quantified using Δ CT and 2ΔΔ CT methods; in the latter case, Δ CT values from the GV stage were used as the calibrator. All data were analyzed by ANOVA and Tukey’s multiple-comparison test. In GV oocytes, Suv39h2 transcripts were in the highest abundance, while ESET transcripts were in the lowest abundance, ESET transcripts being 1450-fold less abundant than Suv39h2 (P < 0.05). In MII oocytes, Suv39h2, GLP, and G9a transcripts were present in highest abundance and were not significantly different from each other; Suv39h1 transcripts were 18-fold less abundant, and ESET transcripts were 6650-fold less abundant than GLP transcripts (P < 0.05). ESET transcripts were present in the least abundance in 4C-PA embryos, 84-fold less than GLP (P < 0.05); no difference in transcript levels for Suv39h1, Suv39h2, GLP, and G9a were detected. ESET transcripts were not detectable 4C-IVF embryos. ESET transcripts were present in the least abundance in BL-PA embryos, 39-fold less abundant than GLP; there was no difference in transcript abundance between Suv39h1, Suv39h2, and G9a. In BL-IVF-stage embryos, ESET transcripts were in the lowest abundance, 97-fold less abundant than GLP (P < 0.05). Analysis of how transcripts for each individual HMTase change from the GV oocyte to the BL embryo revealed no significant change in G9a transcript abundance. GLP transcripts decrease 7-fold at the 4C stage (GV v. 4C, P < 0.05). No difference in relative abundance of ESET transcripts was detectable at GV, MII, or BL-IVF stages; ESET was not detectable in 4C-IVF embryos. SuvH1 transcripts decreased 9-fold in BL-IVF (GV v. BL, P < 0.05); SuvH2 transcripts decreased 21-fold at the 4C-IVF and BL-IVF stages (GV v. 4C, BL, P < 0.05). The differences in transcript abundance of these genes indicate that their expression may change in order to regulate the transcription of genes important in early development.
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Wu, Zhanhe, Boban Markovic, Colin N. Chesterman та Beng H. Chong. "Characterization of Fcγ Receptors on Human Megakaryocytes". Thrombosis and Haemostasis 75, № 04 (1996): 661–67. http://dx.doi.org/10.1055/s-0038-1650339.
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SummaryMegakaryocyte and platelet Fcγ receptors (FcR) are of importance in the pathophysiology of immune complex-mediated thrombocytopenias such as heparin-induced thrombocytopenia. In this study, FcγR proteins and mRNAs in normal human megakaryocytes were examined. FcγR proteins were studied with immunocytochemical staining, dual colour flow cytometry and immunoprecipitation using monoclonal antibodies against FcγR I, FcγR II and FcγR III. FcγR mRNAs were measured with biotinylated cDNA or oligonucleotide probes using a novel quantitative in situ hybridization technique. Using these techniques, FcγR II protein and mRNA, but not FcγR I and FcγR III proteins and transcripts were detected in megakaryocytes. Further, transcript analysis showed that megakaryocytes contain only the transcript of FcγR IIA gene but no transcripts of FcγR IIB nor FcγR IIC genes; FcγR IIA transcripts with and without the transmembrane (TM) exon are present in approximately equal proportions. In contrast, neutrophils and macrophages also contain FcγR IIA transcript but FcγR IIA transcript with the TM exon predominates suggesting cell lineage-specific FcγR IIA expression. FcγR IIA transcript lacking the TM exon predicts the presence of a potential soluble form of FcγR in platelets and megakaryocytes which may have a physiological role as it can compete with the membrane-bound FcγR IIA for binding of IgG-containing immune complexes and thus protect these cells from excessive binding and injurious effects of immune complexes.
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Iswarya, M., P. Sai Krishna, K. Naveen, M. Ganesh, and M. Yasin. "Video Transcript Summarization Using Bert." International Journal of Research Publication and Reviews 4, no. 3 (2023): 1837–41. http://dx.doi.org/10.55248/gengpi.2023.4.32991.
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Farhat-Maghribi, Sulaf, Wafa Habbal, and Fawza Monem. "Frequency ofBCR-ABLTranscript Types in Syrian CML Patients." Journal of Oncology 2016 (2016): 1–5. http://dx.doi.org/10.1155/2016/8420853.
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Background. In Syria, CML patients are started on tyrosine kinase inhibitors (TKIs) and monitored until complete molecular response is achieved.BCR-ABLmRNA transcript type is not routinely identified, contrary to the recommendations. In this study we aimed to identify the frequency of differentBCR-ABLtranscripts in Syrian CML patients and highlight their significance on monitoring and treatment protocols.Methods. CML patients positive forBCR-ABLtranscripts by quantitative RT-PCR were enrolled.BCR-ABLtranscript types were investigated using a home-made PCR method that was adapted from published protocols and optimized. The transcript types were then confirmed using a commercially available research kit.Results. Twenty-four transcripts were found in 21 patients. The most common was b2a2, followed by b3a2, b3a3, and e1a3 present solely in 12 (57.1%), 3 (14.3%), 2 (9.5%), and 1 (4.8%), respectively. Three samples (14.3%) contained dual transcripts. While b3a2 transcript was apparently associated with warning molecular response to imatinib treatment, b2a2, b3a3, and e1a3 transcripts collectively proved otherwise (P=0.047).Conclusion. It might be advisable to identify theBCR-ABLtranscript type in CML patients at diagnosis, using an empirically verified method, in order to link the detected transcript with the clinical findings, possible resistance to treatment, and appropriate monitoring methods.
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Kleidon, Jill, Nora Plesofsky, and Robert Brambl. "Transcripts and transcript-binding proteins in mitochondria of Neurospora crassa." Mitochondrion 2, no. 5 (2003): 345–60. http://dx.doi.org/10.1016/s1567-7249(03)00002-3.
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