Relevant bibliographies by topics / Transcript variants

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Academic literature on the topic 'Transcript variants'

Author: Grafiati
Published: 14 March 2023

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Journal articles on the topic "Transcript variants"

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Ouyang, Hongjia, Jiao Yu, Xiaolan Chen, Zhijun Wang, and Qinghua Nie. "A novel transcript of MEF2D promotes myoblast differentiation and its variations associated with growth traits in chicken." PeerJ 8 (February 4, 2020): e8351. http://dx.doi.org/10.7717/peerj.8351.

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Background Development of skeletal muscle is closely related to broiler production traits. The myocyte-specific enhancer binding factor (MEF) 2D gene (MEF2D) and its variant transcripts play important parts in myogenesis. Methods To identify the transcript variants of chicken MEF2D gene and their function, this study cloned chicken MEF2D gene and identified its transcript variants from different tissue samples. The expression levels of different transcripts of MEF2D gene in different tissues and different periods were measured, and their effects on myoblast proliferation and differentiation were investigated. Variations in MEF2D were identified and association analysis with chicken production traits carried out. Results Four novel transcript variants of MEF2D were obtained, all of which contained highly conserved sequences, including MADS-Box and MEF2-Domain functional regions. Transcript MEF2D-V4 was expressed specifically in muscle, and its expression was increased during embryonic muscle development. The MEF2D-V4 could promote differentiation of chicken myoblasts and its expression was regulated by RBFOX2. The single nucleotide polymorphism g.36186C > T generated a TAG stop codon, caused MEF2D-V4 to terminate translation early, and was associated with several growth traits, especially on early body weight. Conclusion We cloned the muscle-specific transcript of MEF2D and preliminarily revealed its role in embryonic muscle development.
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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 (May 29, 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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Morales, Joannella, Shashikant Pujar, Jane E. Loveland, Alex Astashyn, Ruth Bennett, Andrew Berry, Eric Cox, et al. "A joint NCBI and EMBL-EBI transcript set for clinical genomics and research." Nature 604, no. 7905 (April 6, 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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Cook, Taylor W., Amy M. Wilstermann, Jackson T. Mitchell, Nicholas E. Arnold, Surender Rajasekaran, Caleb P. Bupp, and Jeremy W. Prokop. "Understanding Insulin in the Age of Precision Medicine and Big Data: Under-Explored Nature of Genomics." Biomolecules 13, no. 2 (January 30, 2023): 257. http://dx.doi.org/10.3390/biom13020257.

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Insulin is amongst the human genome’s most well-studied genes/proteins due to its connection to metabolic health. Within this article, we review literature and data to build a knowledge base of Insulin (INS) genetics that influence transcription, transcript processing, translation, hormone maturation, secretion, receptor binding, and metabolism while highlighting the future needs of insulin research. The INS gene region has 2076 unique variants from population genetics. Several variants are found near the transcriptional start site, enhancers, and following the INS transcripts that might influence the readthrough fusion transcript INS–IGF2. This INS–IGF2 transcript splice site was confirmed within hundreds of pancreatic RNAseq samples, lacks drift based on human genome sequencing, and has possible elevated expression due to viral regulation within the liver. Moreover, a rare, poorly characterized African population-enriched variant of INS–IGF2 results in a loss of the stop codon. INS transcript UTR variants rs689 and rs3842753, associated with type 1 diabetes, are found in many pancreatic RNAseq datasets with an elevation of the 3′UTR alternatively spliced INS transcript. Finally, by combining literature, evolutionary profiling, and structural biology, we map rare missense variants that influence preproinsulin translation, proinsulin processing, dimer/hexamer secretory storage, receptor activation, and C-peptide detection for quasi-insulin blood measurements.
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Rosa, Villegas-Ruíz, Caballero-Palacios, Pérez-López, Murata, Zapata-Tarres, Cárdenas-Cardos, Paredes-Aguilera, Rivera-Luna, and Juárez-Méndez. "Expression of ZNF695 Transcript Variants in Childhood B-Cell Acute Lymphoblastic Leukemia." Genes 10, no. 9 (September 16, 2019): 716. http://dx.doi.org/10.3390/genes10090716.

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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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Valenzuela-Palomo, Alberto, Lara Sanoguera-Miralles, Elena Bueno-Martínez, Ada Esteban-Sánchez, Inés Llinares-Burguet, Alicia García-Álvarez, Pedro Pérez-Segura, Susana Gómez-Barrero, Miguel de la Hoya, and Eladio A. Velasco-Sampedro. "Splicing Analysis of 16 PALB2 ClinVar Variants by Minigene Assays: Identification of Six Likely Pathogenic Variants." Cancers 14, no. 18 (September 19, 2022): 4541. http://dx.doi.org/10.3390/cancers14184541.

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PALB2 loss-of-function variants are associated with significant increased risk of breast cancer as well as other types of tumors. Likewise, splicing disruptions are a common mechanism of disease susceptibility. Indeed, we previously showed, by minigene assays, that 35 out of 42 PALB2 variants impaired splicing. Taking advantage of one of these constructs (mgPALB2_ex1-3), we proceeded to analyze other variants at exons 1 to 3 reported at the ClinVar database. Thirty-one variants were bioinformatically analyzed with MaxEntScan and SpliceAI. Then, 16 variants were selected for subsequent RNA assays. We identified a total of 12 spliceogenic variants, 11 of which did not produce any trace of the expected minigene full-length transcript. Interestingly, variant c.49-1G > A mimicked previous outcomes in patient RNA (transcript ∆(E2p6)), supporting the reproducibility of the minigene approach. A total of eight variant-induced transcripts were characterized, three of which (∆(E1q17), ∆(E3p11), and ∆(E3)) were predicted to introduce a premature termination codon and to undergo nonsense-mediated decay, and five (▼(E1q9), ∆(E2p6), ∆(E2), ▼(E3q48)-a, and ▼(E3q48)-b) maintained the reading frame. According to an ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme, which integrates mgPALB2 data, six PALB2 variants were classified as pathogenic/likely pathogenic, five as VUS, and five as likely benign. Furthermore, five ±1,2 variants were catalogued as VUS because they produced significant proportions of in-frame transcripts of unknown impact on protein function.
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John, Miya, and Caroline E. Ford. "Pan-Tissue and -Cancer Analysis of ROR1 and ROR2 Transcript Variants Identify Novel Functional Significance for an Alternative Splice Variant of ROR1." Biomedicines 10, no. 10 (October 13, 2022): 2559. http://dx.doi.org/10.3390/biomedicines10102559.

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ROR1/2 are putative druggable targets increasing in significance in translational oncology. Expression of ROR1/2 mRNA and transcript variants has not been systematically examined thus far. ROR1/2 transcript variant sequences, signal peptides for cell surface localisation, and mRNA and transcript variant expression were examined in 34 transcriptomic datasets including 33 cancer types and 54 non-diseased human tissues. ROR1/2 have four and eight transcript variants, respectively. ROR1/2 mRNA and transcript variant expression was detected in various non-diseased tissues. Our analysis identifies predominant expression of ROR1 transcript variant ENST00000545203, which lacks a signal peptide for cell surface localisation, rather than the predicted principal variant ENST00000371079. ENST00000375708 is the predominantly expressed transcript variant of ROR2. ROR1/2 expression in healthy human tissues should be carefully considered for safety assessment of targeted therapy. Studies exploring the function and significance of the predominantly expressed ROR1 transcript variant ENST00000545203 are warranted.
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Germeshausen, Manuela, Magda Grudzien, Cornelia Zeidler, Hengameh Abdollahpour, Sevgi Yetgin, Nima Rezaei, Matthias Ballmaier, Bodo Grimbacher, Karl Welte, and Christoph Klein. "Novel HAX1 mutations in patients with severe congenital neutropenia reveal isoform-dependent genotype-phenotype associations." Blood 111, no. 10 (May 15, 2008): 4954–57. http://dx.doi.org/10.1182/blood-2007-11-120667.

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Abstract Homozygous mutations in HAX1 cause an autosomal recessive form of severe congenital neutropenia (CN). By screening 88 patients with CN, we identified 6 additional patients with HAX1 mutations carrying 4 novel mutations. Of these, 2 affect both published transcript variants of HAX1; the other 2 mutations affect only transcript variant 1. Analysis of the patients' genotypes and phenotypes revealed a striking correlation: Mutations affecting transcript variant 1 only were associated with CN (23 of 23 patients), whereas mutations affecting both transcript variants caused CN and neurologic symptoms, including epilepsy and neurodevelopmental delay (6 of 6 patients). In contrast to peripheral blood, transcript variant 2 was markedly expressed in human brain tissue. The clinical phenotype of HAX1 deficiency appears to depend on the localization of the mutation and their influence on the transcript variants. Therefore, our findings suggest that HAX1 isoforms may play a distinctive role in the neuronal system.
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Bueno-Martínez, Elena, Lara Sanoguera-Miralles, Alberto Valenzuela-Palomo, Víctor Lorca, Alicia Gómez-Sanz, Sara Carvalho, Jamie Allen, et al. "RAD51D Aberrant Splicing in Breast Cancer: Identification of Splicing Regulatory Elements and Minigene-Based Evaluation of 53 DNA Variants." Cancers 13, no. 11 (June 7, 2021): 2845. http://dx.doi.org/10.3390/cancers13112845.

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RAD51D loss-of-function variants increase lifetime risk of breast and ovarian cancer. Splicing disruption is a frequent pathogenic mechanism associated with variants in susceptibility genes. Herein, we have assessed the splicing and clinical impact of splice-site and exonic splicing enhancer (ESE) variants identified through the study of ~113,000 women of the BRIDGES cohort. A RAD51D minigene with exons 2–9 was constructed in splicing vector pSAD. Eleven BRIDGES splice-site variants (selected by MaxEntScan) were introduced into the minigene by site-directed mutagenesis and tested in MCF-7 cells. The 11 variants disrupted splicing, collectively generating 25 different aberrant transcripts. All variants but one produced negligible levels (<3.4%) of the full-length (FL) transcript. In addition, ESE elements of the alternative exon 3 were mapped by testing four overlapping exonic microdeletions (≥30-bp), revealing an ESE-rich interval (c.202_235del) with critical sequences for exon 3 recognition that might have been affected by germline variants. Next, 26 BRIDGES variants and 16 artificial exon 3 single-nucleotide substitutions were also assayed. Thirty variants impaired splicing with variable amounts (0–65.1%) of the FL transcript, although only c.202G>A demonstrated a complete aberrant splicing pattern without the FL transcript. On the other hand, c.214T>C increased efficiency of exon 3 recognition, so only the FL transcript was detected (100%). In conclusion, 41 RAD51D spliceogenic variants (28 of which were from the BRIDGES cohort) were identified by minigene assays. We show that minigene-based mapping of ESEs is a powerful approach for identifying ESE hotspots and ESE-disrupting variants. Finally, we have classified nine variants as likely pathogenic according to ACMG/AMP-based guidelines, highlighting the complex relationship between splicing alterations and variant interpretation.
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De la Cruz-Hernández, Erick, Alejandro García-Carrancá, Alejandro Mohar-Betancourt, Alfonso Dueñas-González, Adriana Contreras-Paredes, Enrique Pérez-Cardenas, Roberto Herrera-Goepfert, and Marcela Lizano-Soberón. "Differential splicing of E6 within human papillomavirus type 18 variants and functional consequences." Journal of General Virology 86, no. 9 (September 1, 2005): 2459–68. http://dx.doi.org/10.1099/vir.0.80945-0.

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Persistent infections of the uterine cervix with ‘high-risk’ human papillomavirus (HPV) are now recognized as necessary for the development of cervical cancer. Among them, HPV types 16 and 18 exhibit numerous variants associated with different risks for cervical cancer development. In this study, the questions of whether different HPV type 18 variants exhibit changes in early gene transcription and the molecular mechanisms underlying these differences were investigated. It was shown that, indeed, type 18 variants exhibited singular differences in E6 transcripts in vivo. Higher levels of the E6*I transcript were detected regularly in clones harbouring the African variant, as opposed to low levels of this transcript detected in clones containing the reference clone (Asian–Amerindian), where significantly higher levels of full-length E6 transcript were usually observed. As a direct consequence, higher levels of p53 protein were found in the presence of African E6, as opposed to the low levels of p53 observed with the Asian–Amerindian E6. These variations in consequence affected the levels of cellular proteins regulated by p53, such as Bax. Similar changes in the relative levels of E6 transcripts were observed when tumours containing type 18 E6 variants were analysed. The different ability of cells containing variant E6 genes to form tumours in nude mice was suggested by the fact that tumour volumes were considerably higher when cells expressed the Asian–Amerindian E6. Mutagenesis analysis of the reference clone showed that a C491A change reverts the phenotype. These results suggest that different splicing patterns of E6 within HPV type 18 variants may possibly have biological implications in viral tumorigenesis.
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Dissertations / Theses on the topic "Transcript variants"

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Chandra, Shubhra. "Delineating the role of Hepatocyte nuclear factor 1 beta (HNF1B) transcript variants in prostate cancer." Thesis, Queensland University of Technology, 2020. https://eprints.qut.edu.au/135713/1/Shubhra_Chandra_Thesis.pdf.

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Genome Wide Association Studies (GWAS) has identified HNF1B located at chromosome 17q12 as foremost risk gene for prostate cancer susceptibility in multi-ethnic populations. This thesis characterises the HNF1B transcript variants along with defining their expression pattern and functional attributes in prostate cancer. Future research will enable the discovery of the molecular mechanism of their actions and whether targeting these HNF1B transcript variants in cancer may prove a useful therapeutic strategy.
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MARRANCI, ANDREA. "Analysis of the expression of all BRAF transcript variants and of their implication in post-transcriptional regulation mediated by miRNAs in melanoma." Doctoral thesis, Università di Siena, 2017. http://hdl.handle.net/11365/1005876.

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BRAF is a widely studied oncogene and its functions are well characterized in several cellular contests and diseases. However the regulation of the expression of BRAF is mostly unknown. With the aim to understand the post-transcriptional regulation of BRAF, we performed 3’RACE in A375 melanoma cells and we found 2 different 3’UTRs: the one commonly reported in many data bases (Reference) and a new one that is only predicted (X1). The two 3’UTRs are completely different in sequence and length (120nt vs 1350nt). Furthermore, they are transcribed from exon 18 or thanks to an alternative splicing event occurring between exon 18 and a newly discovered exon 19 (X1). By using Real Time PCR, we confirmed the expression of both transcripts in melanoma and non-melanoma cell lines. Moreover, using RNA-SEQ data available at TCGA, we showed the co-expression of Reference and X1 BRAF transcripts also in human biopsies. Due to our discovery that BRAF exists in at least 2 different transcript variants, we decided to investigate further the expression of all the BRAF isoforms reported in NCBI and Ensembl. To do so, we took advantage of the RNA-seq data of more than 4,800 patients belonging to 9 different cancer types. We show that BRAF mRNA exists as a pool of 3 isoforms (reference BRAF, BRAF-X1 and BRAF-X2) that differ in the last part of their open reading frames, as well as in the length (BRAF-ref: 76nt; BRAF-X1 and X2: up to 7kb) and in the sequence of their 3’UTRs. In melanoma cells, the X1 isoform is expressed at the highest level, while the most prevalent among the three isoforms varies from one cancer type to another. Moreover, the relative abundance among the three BRAF isoforms is maintained in melanoma cells with acquired resistance to BRAF and MEK inhibitors driven by BRAF gene amplification or expression of the Δ[3-10] splicing variant. Besides their 3’UTRs, also the very last part of the coding sequences differ among the three isoforms. By immunoprecipitation of BRAF in A375 cells and subsequently Mass-SPEC analysis, we revealed the existence of Reference and X1 proteins which are expressed at similar levels, while X2 is not detectable because quicky degraded by the proteasome. Furthermore functional studies show that the two proteins account together for BRAF activities both in vitro and in vivo. Given the differences in length and sequence between the reference and the X1 3’UTR, we hypothesized that the two isoforms undergo different regulation mediated by RNA-binding proteins or non-coding RNAs. We focused on post-transcriptional regulation by microRNAs. MicroRNAs (miRNAs) are small non-coding RNAs that negatively regulate the expression of target messenger RNAs (mRNAs) and for this reason play a key role in virtually all cellular processes. In spite of the availability of several prediction algorithms, the identification of specific miRNA-target interactions remains a challenge. In order to overcome this problem we developed an innovative method, called miR-CATCH v2.0, for the high-throughput identification of microRNAs that bind a target transcript. The protocol is based on the affinity purification of the target mRNA and bound miRNAs by using two different pools of 3’biotinylated anti-sense DNA probes (ODD and EVEN). We designed 12 probes (6 ODD probes and 6 EVEN probes) for the purification of X1-3’UTR-miRNAs complexes and we performed three separate and independent captures in A375 metastatic melanoma cells. MicroRNAs were identified through small RNA-sequencing and the top-scoring miRNAs that resulted consistently enriched in all the captures will be validated in vitro and in vivo experiments.
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Heller, Susanne. "Molecular mechanisms involved in glioma cell interactions in vitro and studies of PDGF B transcript variants." Doctoral thesis, Uppsala University, Department of Genetics and Pathology, 2000. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-1252.

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Glioblastoma multiforme is a malignant brain tumor characterized by heterogeneity.Interactions between heterogeneous tumor cells are supposed to affect the behavior of awhole tumor cell population. In this thesis an in vitro model system of clonal glioma celllines originating from one glioblastoma tumor was used, and the behavior of cells incocultures was studied and compared the behavior of cells grown separately. The resultsindicate the presence of two types of interactions. In one, paracrine signals acted via extra-cellular media. This was associated with increased growth of the whole co-culture followedby a selective force driving one clone to dominance. In the other type, the cell clones grewside by side without signs of paracrine signalling, in a balance resulting in an increasedterminal cell density. Further investigations focused on mechanisms of interactions in thiscombination.

Two cell clones were chosen, a GFAP+ and a GFAP-, for further experiments. Withdifferential display PCR it was possible to investigate their specific gene expressionpatterns. Seventeen cDNA fragments were differentially expressed, among them twocorresponded to known transcription factors, ATF3 and prox-1, one to a cytoskeletal protein,α-tropomyosin. The collection also contained eight ESTs (Expressed Sequence Tags) wherethe corresponding genes are unknown at present. Expression of the isolated sequences werealso analyzed in a panel of 12 different glioma cell lines and the results illustrate thecomplexity of gene expression and of tumor heterogeneity. Genes, the expression levels ofwhich were modulated in co-cultures and/or were cell density dependent, were alsoidentified.

PDGF B is suggested to play a role in sarcomas. The gene codes for an mRNA transcriptwith long UTRs, parts of which are deleted in the homologous oncogene v-sis. The UTRs ofPDGF B mRNAs in human sarcomas were investigated for deletions similar to v-sis thatmight result in increased protein levels. A new transcript variant was identified, lacking a149 base region in the 3'UTR, but its presence was not associated with increased levels ofprotein. Alterations in the 5'UTR were found more likely to be associated with increasedprotein levels.

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CAPUA, G. DI. "CHARACTERIZATION OF HUMAN TENEURIN-4 TRANSCRIPT IN OVARIAN CANCER DERIVED CELL LINES." Doctoral thesis, Università degli Studi di Milano, 2012. http://hdl.handle.net/2434/171959.

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Teneurins are transmembrane glycoproteins encoded by ODZ genes. Teneurins are a unique protein family conserved from flies and worms to human and are mainly expressed in the developing and adult nervous system where they are thought to be crucial for neurogenesis and axon-guidance. Teneurins are also expressed outside CNS where they have been proposed to play a role in morphogenesis and cell migration. Vertebrate teneurin expression pattern has been studied most extensively in mice and chicken, however still very little is known about their biological function and mechanism of action in humans. Moreover, experimental data concerning the molecular structure of vertebrate teneurins transcripts is scarce, and human ODZ4 messenger has not been subject to a detailed characterization before. Furthermore, recent studies have evidenced that some ODZs, specifically ODZ2 and 4, could be involved in tumor development in a still unclear mode. To this respect, in our preliminary study we demonstrated the expression of ODZ2 in human ovarian and breast cancer-derived cell lines by RT-PCR. Therefore, in this thesis work we have evaluated the expression of ODZ4 in human ovarian and breast cancer-derived cell lines by RT-PCR. As a result, we have characterized two partial ODZ4 full-length messengers expressed by these cell types. The exon-expression pattern analysis indicates that these ODZ4 transcripts can be differentiated by the presence of an insert region corresponding to a non-adjacent genomic sequence that lies between exons 6 and 7. Additionally, the number of exons expressed differs depending on the type of cell line analyzed, even though they may derive from the same tissue type. Further, exonic deletions were not detected along these ODZ4 transcripts but many other truncated splice variants were observed. This study intends to generate new molecular information necessary for the elucidation of the functional role of ODZ4 in human cancer.
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Haghighat, Roya. "Identification of unique CD44 variant transcripts in human colon cancer." Thesis, McGill University, 1996. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=23892.

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In the past decade, new concepts have emerged on the role of adhesion molecules in the communication, motility, differentiation, and survival of cells in the body. The traditional view on the role of cell adhesion molecules in cell differentiation and tissue architecture has changed following the discovery that some adhesion proteins, including CD44, are involved in tumor progression in both animal and human tissues. CD44 is a glycoprotein which has differently spliced isoforms with various combinations of up to 9 variant exons numbered v2 to v10. The aim of this study was to characterize CD44 transcripts associated with colorectal neoplasia. The hypothesis is that discrete transcripts of CD44 are generated during the progression from normal to carcinomatous colonic epithelium, contributing to determinant changes in cell adhesion. Our results showed: (i) a high level of expression of CD44 v8-v10 transcripts in all tumor cells by in situ hybridization technique, (ii) 4 transcripts of CD44v7 with 650, 740, 1000, and 1150 bases in RNA extracted from tumor cases and studied by RT-PCR followed by Southern blotting, and (iii) the 1150 transcript was the only one found in both carcinoma and polyps. This transcript has therefore the potential to be used as an early marker of progression in colorectal neoplasia. It is reasonable to suggest that these new transcript species generate protein isoforms with different adhesion properties, as compared to standard CD44.
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Martin, Juliette. "Le Gene Agouti Bovin : Organisation Structurale et expression tissulaire : Production par génie génétique de trois variants protéiques." Limoges, 2001. http://www.theses.fr/2001LIMO0048.

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La pigmentation chez les mammifères est définie par la distribution ainsi que par les quantités relatives de deux pigments, la phaléomélanine et l'eumélanine qui produisent respectivement des colorations rouge/jaune et marron/noir. Aujourd'hui, plus de 150 mutations différentes affectant plus de 60 loci distincts modifiant la coloration du pelage ont été identifiées chez la souris. Deux principaux loci, agouti (a) et extension (E) contrôlent les quantités relatives des pigments. Le gène extension code le récepteur (MClr) de l'hormone hypophysaire α-MSH. Cette dernière stimule la production d'eumélanine en se fixant sur le récepteur ancré dans la menbrane des mélanocytes. Par sa liaison à MClr, la protéine Agouti favorise la synthèse de la phaléomélanine. Le travail présenté dans ce mémoire a été entrepris dans le cadre d'un programme de recherche de marqueurs génétiques des races bovines françaises en collaboration avec les centres de recherche de l'INRA et les UPRA. L'étude des exons codants du gène agouti bovin n'a pas permis de mettre en évidence l'existence de différents allèles associés aux races bovines étudiées. Aussi, avons nous orientés nos travaux de recherche vers lé́tude des transcrits du gène agouti afin d'expliquer les variations de pigmentation de la robe des races bovines étudiées. Ces recherches nous ont conduit à identifier, en plus du transcrit bovin de référence, deux transcrits spécifiques de la peau. Ces transcrits diffèrent dans leurs structures et leur séquence, et définissent deux groupes de races bovines: le premier comprend les races Prim'Holstein noire, Limousine X prim'Holstein, Montbéliarde et Limousine et le deuxième les races Prim'holstein blanche, charolaise X Prim'Holstein, Blonde d'Aquitaine, Charolaise et Salers. La prodution par génie génétique des pépdides deduits des transcrits bovins permettra d'obtenir des anticorps spécifiques. Ces derniers seront utilisés dans des études d'immunodetection. La mise en évidence de sites d'épissage alternatifs au sein des transcrits spécifiques de la peau et l'obtention des séquences 5' non-codantes ont également conduit à établir la première structure partielle du gène Agouti bovin
The work presented in this report was begun within the framework of a research program for genetic markers of the French bovine species in association with INRA and UPRA. .
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Ross, Heather Hamilton. "Characterization and Functional Analysis of a Newly Identified Human MT5-MMP Transcript Variant Isolated from Multipotent NT2 Cells." VCU Scholars Compass, 2006. http://hdl.handle.net/10156/1498.

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Griffith, Malachi. "Methods for transcript variant discovery and alternative expression analysis : application to the study of fluorouracil resistance in colorectal cancer." Thesis, University of British Columbia, 2010. http://hdl.handle.net/2429/18621.

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RNA transcripts are expressed from tens of thousands of loci across the human genome. Several studies have suggested that many genes are alternatively expressed to produced multiple mRNA isoforms and many of these remain undiscovered. Identifying specific isoforms associated with human diseases such as cancer has potential to lead to improved treatments. The scale and complexity of the transcriptome present significant barriers to (1) identifying isoforms and (2) applying knowledge to human disease research. Recent advances in genome-wide microarray and sequencing platforms have begun to provide the capacity and resolution to address these challenges. The goal of this thesis was to develop novel methods that allow genome-wide identification and quantification of mRNA isoforms. I first approached this problem by creating a microarray design platform for alternative expression analysis called 'ALEXA-array' (www.AlexaPlatform.org). To evaluate the ALEXA-array approach I used it to generate a microarray design that I then used to measure differential expression of mRNA isoforms in 5-fluorouracil (5-FU) sensitive and resistant colorectal cancer cell lines. This approach identified several isoforms potentially involved in 5-FU resistance. While the ALEXA-array approach was successful, I identified several limitations of the method. For example, the approach was insensitive to isoforms with small differences in sequence content and limited by both the transcriptome annotations and the number of microarray features available at design time. I developed a second method, ‘ALEXA-seq’, to take advantage of advances in massively parallel sequencing. Applying this method to the same cell lines I showed that the approach was able to overcome many limitations of the microarray approach. Several additional candidate 5-FU resistance isoforms were identified. Both the ALEXA-array and ALEXA-seq approaches identified expression of an aberrant isoform of the uridine monophosphate synthetase as a top candidate. Interestingly, this gene was suspected to function in the conversion of 5-FU to active anti-cancer metabolites. Additional characterization was performed to elucidate the expression pattern, transcript diversity and sequence variation of this gene in a panel of cell lines and tumours. The methods presented here should help to identify mRNA isoforms with potential utility as therapeutic targets or as prognostic or diagnostic markers.
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Young, Kyle E. "Alternative splicing of the zebrafish myosin phosphatase targeting subunit, MYPT1, produces a novel isoform." Scholarly Commons, 2016. https://scholarlycommons.pacific.edu/uop_etds/173.

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Alternative splicing of the zebrafish Myosin Phosphatase Targeting Subunit, MYPT1, produces a novel isoform (TV202). TV202 and the truncated TV202Δ ere shown to form an active complex with Protein Phosphatase 1 β (PP1β) via stress fiber assay. TV202 was also shown to be localized in the cytoplasm, enriched in a paranuclear manner. TV202Δ was found the be localized inside the nucleus. It was also found that TV202 was zygotically, but not maternally, expressed during early zebrafish development via RT-PCR.
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Iwai, Akio. "Siah-1L, a novel transcript variant belonging to the human Siah family of proteins, regulates β-catenin activity in a p53-dependent manner." Kyoto University, 2005. http://hdl.handle.net/2433/144711.

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Books on the topic "Transcript variants"

1

Ginsberg, Allen. Howl: Original draft facsimile, transcript & variant versions, fully annotated by author, with contemporaneous correspondence, account of first public reading, legal skirmishes, precursor texts & bibliography. New York: Harper & Row, 1986.

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1943-, Miles Barry, ed. Howl: Original draft facsimile, transcript & variant versions, fully annotated by author, with contemporaneous correspondence, account of first public reading, legal skirmishes, percusor texts & bibliography. (Harmondsworth): Viking, 1987.

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Allen, Ginsberg. Howl: Original draft facsimile, transcript & variant versions, fully annotated by author, with contemporaneous correspondence, account of first public reading, legal skirmishes, precursor texts & bibliography. New York: Harper & Row, 1986.

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Allen, Ginsberg. Howl: Original draft facsimile, transcript and variant versions, fully annotated by author, with contemporaneous correspondence, account of first public reading, legal skirmishes, precursor texts and bibliography. New York, NY: Harper Perennial Modern Classics, 2006.

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Allen, Ginsberg. Howl: Original Draft Facsimile, Transcript and Variant Versions. HarperCollins, 1988.

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Allen, Ginsberg. Howl: Original Draft Facsimile, Transcript and Variant Versions. HarperCollins, 1988.

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Sieburg, Heinz, ed. Vielfalt der Sprachen - Varianz der Perspektiven. transcript Verlag, 2013. http://dx.doi.org/10.1515/transcript.9783839420300.

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Sieburg, Heinz, ed. Vielfalt der Sprachen - Varianz der Perspektiven. transcript-Verlag, 2013. http://dx.doi.org/10.14361/transcript.9783839420300.

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Allen, Ginsberg. Howl: Original draft facsimile, transcript & variant versions, fully annotated by author, with contemporaneous correspondence, account of first public ... skirmishes, precursor texts & bibliography. Harper & Row, 1986.

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Allen, Ginsberg. Howl: Original draft facsimile, transcript & variant versions, fully annotated by author, with contemporaneous correspondence, account of first public ... skirmishes, precursor texts & bibliography. Harper & Row, 1986.

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Book chapters on the topic "Transcript variants"

1

Freeman, Lita A. "Cloning Full-Length Transcripts and Transcript Variants Using 5′ and 3′ RACE." In Methods in Molecular Biology, 3–17. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-60327-369-5_1.

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Sun, Cong, Qiang Wu, Ye-chao Han, Ting-ting Tang, and Li-li Wang. "Prediction of Three-Dimensional Structure of PPARγ Transcript Variant 1 Protein." In Lecture Notes in Electrical Engineering, 2813–19. Dordrecht: Springer Netherlands, 2013. http://dx.doi.org/10.1007/978-94-007-7618-0_355.

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Villa, E., A. Dugani, L. Cammellini, P. Buttafuoco, A. Grottola, I. Ferretti, A. Ferrari, and F. Manenti. "Prevalence of Wild-Type and Variant Transcripts of Liver Estrogen Receptors in Chronic Liver Disease." In New Trends in Hepatology, 197–203. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-0357-9_22.

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Mottaz, Anaïs, Emilie Pasche, Pierre-André Michel, Luc Mottin, Douglas Teodoro, and Patrick Ruch. "Designing an Optimal Expansion Method to Improve the Recall of a Genomic Variant Curation-Support Service." In Studies in Health Technology and Informatics. IOS Press, 2022. http://dx.doi.org/10.3233/shti220603.

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The importance of genomic data for health is rapidly growing but accessing and gathering information about variants from different sources is hindered by highly heterogeneous representations of variants, as outlined by clinical associations (AMP/ASCO/CAP) in their recommendations. To enable a smooth and effective retrieval of variant-containing documents from different resources, we developed a tool (https://goldorak.hesge.ch/synvar/) that generates for any given SNP – including variant not present in existing databases – its corresponding description at the genome, transcript and protein levels. It provides variant descriptions in the HGVS format as well as in many non-standard formats found in the literature along with database identifiers. We present the SynVar service and evaluate its impact on the recall of a genomic variant curation-support service. Using SynVar to search variants in the literature enables to increase the recall by +133.8% without a strong impact on precision (i.e. 93%).
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Soileau, Jeanne Pitre. "Running and Imaginative Games." In What the Children Said, 214–47. University Press of Mississippi, 2021. http://dx.doi.org/10.14325/mississippi/9781496835734.003.0007.

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This chapter begins with a transcript of a recorded session held at Gates of Prayer Hebrew School. The words of the children demonstrate that children, whatever denomination they belong to, participate in the schooyard games they encounter in their daily life. The chapter also contains children’s accounts of running games. Tag is by far the most varied and popular running game recorded, with a seemingly limitless set of variants. Running games introduced to students as part of their physical education are often adapted to schoolyard play. “Dodge ball,” “Basketball,” and “Football” have street versions enthusiastically played. Dramatic running games having a story line includes such imaginative play as “Prisoner’s Base,” “Monsters,” “Colored Eggs,” as well as reenactments of Television shows like Batman and “Charlie’s Angels.”
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Endo, Shiho, Kenta Motomura, Masakazu Tsuhako, Yuki Kakazu, Morikazu Nakamura, and Joji M. Otaki. "Search for Human-Specific Proteins Based on Availability Scores of Short Constituent Sequences: Identification of a WRWSH Protein in Human Testis." In Computational Biology and Chemistry. IntechOpen, 2020. http://dx.doi.org/10.5772/intechopen.89653.

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Little is known about protein sequences unique in humans. Here, we performed alignment-free sequence comparisons based on the availability (frequency bias) of short constituent amino acid (aa) sequences (SCSs) in proteins to search for human-specific proteins. Focusing on 5-aa SCSs (pentats), exhaustive comparisons of availability scores among the human proteome and other nine mammalian proteomes in the nonredundant (nr) database identified a candidate protein containing WRWSH, here called FAM75, as human-specific. Examination of various human genome sequences revealed that FAM75 had genomic DNA sequences for either WRWSH or WRWSR due to a single nucleotide polymorphism (SNP). FAM75 and its related protein FAM205A were found to be produced through alternative splicing. The FAM75 transcript was found only in humans, but the FAM205A transcript was also present in other mammals. In humans, both FAM75 and FAM205A were expressed specifically in testis at the mRNA level, and they were immunohistochemically located in cells in seminiferous ducts and in acrosomes in spermatids at the protein level, suggesting their possible function in sperm development and fertilization. This study highlights a practical application of SCS-based methods for protein searches and suggests possible contributions of SNP variants and alternative splicing of FAM75 to human evolution.
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Colombo, Mara, Paolo Radice, and Miguel de la Hoya. "Functional evidence (I) transcripts and RNA-splicing outline." In Clinical DNA Variant Interpretation, 121–44. Elsevier, 2021. http://dx.doi.org/10.1016/b978-0-12-820519-8.00004-1.

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Lucchesi, John C. "Epigenetic chromatin changes and the transcription cycle." In Epigenetics, Nuclear Organization & Gene Function, 57–68. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198831204.003.0005.

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In order to allow transcription to occur, the association of DNA with histone octamers and the compacted physical state of the chromatin fiber must be modified by the opportunistic binding of pioneer transcription factors to their cognate DNA binding sites. Once bound, pioneer factors recruit chromatin remodelers and histone-modifying enzymes for the purpose of repositioning nucleosomes and exposing regulatory regions (enhancers and gene promoters) to the components necessary for the initiation of transcription. Histone modifications, such as acetylation, methylation and ubiquitination, and the dynamic phosphorylation of specific amino acids on the major RNA polymerase II subunit activate transcription and attract the factors necessary to eliminate the pausing that normally occurs soon after initiation. Further histone modifications and the replacement of certain core histones by histone variants facilitate transcript elongation and termination. Two additional major epigenetic modifications that impact the process of transcription consist of the action of non-coding RNAs and DNA methylation.
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"Le multilinguisme comme caractéristique et défi de la littérature au Luxembourg." In Vielfalt der Sprachen - Varianz der Perspektiven, 107–42. transcript-Verlag, 2013. http://dx.doi.org/10.14361/transcript.9783839420300.107.

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"Schreiben in mehr als einer Sprache." In Vielfalt der Sprachen - Varianz der Perspektiven, 143–66. transcript-Verlag, 2013. http://dx.doi.org/10.14361/transcript.9783839420300.143.

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Conference papers on the topic "Transcript variants"

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Hoff, Andreas M., Sen Zhao, Bjarne Johannessen, and Rolf I. Skotheim. "Abstract 2700: Transcriptome analyses reveal fusion transcripts and transcript variants that are recurrent across sample series of testicular germ cell tumors." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-2700.

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Azmi, Muhammad Bilal. "In Silico Basis to Understand the Molecular Interaction of Human NNATGene With Therapeutic Compounds of Anorexia Nervosa." In INTERNATIONAL CONFERENCE ON BIOLOGICAL RESEARCH AND APPLIED SCIENCE. Jinnah University for Women, Karachi,Pakistan, 2022. http://dx.doi.org/10.37962/ibras/2022/1-2.

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Introduction: Anorexia nervosa (AN)– a perplexing heritable, psychiatric eating disorder condition characterized by low body weight. The prevalence of AN is found to be high in younger age adults with a raised mortality rate. Genetic studies have been insufficient in identifying the role of specific genes that predispose an individual to AN. Objectives: The objective was to explore the role of NNAT (neuronatin) gene variants and its structure based molecular interactions with therapeutic compounds of AN. To investigate the role of structural missense pathogenic variants (SNPs: single nucleotide polymorphism) or change in the expression of NNAT with possibility of AN. Methodology: NNAT gene protein coding sequence, SNPs were extracted and validated from public databases. Gene to gene interactions, protein localization and human tissue-specific expression analysis of NNAT gene showed highest tissue-specific expression in the brain. Estimates of functional impact of SNPs using transcript sequence and machine learning based approaches (in silico algorithms) were computed to investigate the pathogenicity and protein stability of NNAT variants. Sequence alignment, ab initio 3D structure-modeling of wild-type, validation and recognition of binding cavities of NNAT through in silico web based tools were performed. Alternate model prediction for NNAT variants through residue specific mutation approach and structural validation were also done through Chimera tool. The 3D compounds involved in the management of AN were extracted from the Drug Bank database, afterwards energy minimization and rule of drug-likeness were performed. The eligible 3D compounds were docked with identified variants, to evaluate the drugs binding molecular mechanics. Results & Conclusion: Overall, 10 NNAT missense variants were extracted on the basis of minor allele frequency (MAF < 0.001) and other consequence types. Further three variants were selected among ten according to the transcript sequence, which includesrs542858994 (F26L), rs539681368 (C30Y) and rs542858994 (F53L). Structures for these variants’ protein were generated, validated and docked with AN drugs. The functional impact analyses of selected missense SNPs of NNAT showed high risk pathogenicity and can cause changes in the physical and chemical properties of amino acids, thus affecting the function of protein. The computation of binding energies of variants of NNAT with AN compounds strengthen the hypothesis that these variants strongly interact with the AN drugs, hence reducing the level of free NNAT as well as target drugs, for neuronal functioning. Therefore, constitutionally reduced level of NNAT and binding of NNAT variants with AN drugs may serve as the basis to increases the susceptibility towards AN.
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Caswell, Jennifer L., Scott Huntsman, Donglei Hu, and Elad Ziv. "Abstract P2-03-13: Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors." In Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium; December 9-13, 2014; San Antonio, TX. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.sabcs14-p2-03-13.

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Shurr, AYL, C. Maurer, IG Turbin, M. Bernabeu-Herrero, M. Aldred, D. Patel, and CL Shovlin. "P112 Addressing the problem of variants of uncertain significance in genetic diagnosis of vascular pulmonary disease: a role for transcript expression in blood monocytes?" In British Thoracic Society Winter Meeting 2019, QEII Centre, Broad Sanctuary, Westminster, London SW1P 3EE, 4 to 6 December 2019, Programme and Abstracts. BMJ Publishing Group Ltd and British Thoracic Society, 2019. http://dx.doi.org/10.1136/thorax-2019-btsabstracts2019.255.

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Stanoszek, Lauren, Thomas Blomquist, Erin L. Crawford, Bradly Austermiller, Casey Spitzer, Paige FS Willey, and James C. Willey. "Abstract 2232: Effectiveness evaluation of an in vitro nucleic acid amplification test for quantification of BCR-ABL fusion transcript variants in human whole blood." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-2232.

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Blanchard, Anne AA, Xiuli Ma, Teresa Zelinski, Jiuyong Xie, Steven Cooper, and Yvonne Myal. "Abstract 751: Identification of variant claudin 1 transcripts in human breast tumors." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-751.

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Seidel, MF, MP Junier, and H. Vetter. "THU0028 Different variants of tnf-alpha mrna transcripts are expressed in rats with collagen-induced arthritis." In Annual European Congress of Rheumatology, Annals of the rheumatic diseases ARD July 2001. BMJ Publishing Group Ltd and European League Against Rheumatism, 2001. http://dx.doi.org/10.1136/annrheumdis-2001.825.

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Fagan-Solis, Katerina D., David A. McDonald, Lynnelle W. Thorpe, and Jodie M. Fleming. "Abstract 1193: LSR transcript variant iota drives nuclear localization and altered transcriptome regulation in breast cancer." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-1193.

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Sarver, Nava, and George A. Ricca. "SUSTAINED EXPRESSION OF FULL LENGTH AND VARIANT RECOMBINANT FACTOR VIII IN GENETICALLY ENGINEERED CELLS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643875.

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A major effort is presently underway to provide factor VIII (FVIII) in a form free of viral pathogens via a recombinant DNA approach. We have constructed two chimeric FVIII cDNA vectors based on the bovine papillomavirus mammalian expression system. The first vector (FVIII) contained a full length FVIII cDNA; the second vector (AFVIII) contained a cDNA insert with an extensive deletion, corresponding to amino acid residues 747 to 1560 in the region encoding the "B" domain. This internal region is removed during activation of the parental FVIII molecule and is believed not to be required for coagulant activity. We have found that recombinant FVIII produced by stable cell lines harboring either the full length or the variant FVIII was capable of restoring coagulant activity to FVIII deficient plasma in. vitro. This expressed activity was neutralized by anti-FVIII antibodies. Similar to observations with FVIII derived from human plasma, the two recombinant FVIII forms were (i) inactivated by the chelating agent EDTA, (ii) demonstrated a biphasic response of an initial activation followed by a decay in activity when treated with thrombin, and (iii) presented the expected peptide banding pattern by western blot analyses. A higher percentage of ΔFVIII transformants were isolated expressing coagulant activity compared to transformants harboring the complete FVIII cDNA. Among the positive transformants isolated, those harboring ΔFVIII produced higher levels of coagulant activity than their full length counterparts. Comparable steady state levels of FVIII specific transcripts were detected in FVIII and ΔFVIII transformants indicating that the difference in expression levels is due to a post transcriptional event(s). Our study demonstrates the efficacy of a full length and an abridged recombinant FVIII produced by stably transformed cells in correcting coagulation deficiency in. vitro. It further suggests the potential usefulness of other molecular variants for efficient expression in genetically engineered cells.
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Hoff, Andreas M., Torfinn Nome, Anne Cathrine Bakken, Torleiv O. Rognum, Arild Nesbakken, and Rolf I. Skotheim. "Abstract 2235: High frequency of fusion transcripts involving TCF7L2 in colorectal cancer: Novel fusion partner and splice variants." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-2235.

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Reports on the topic "Transcript variants"

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Dubcovsky, Jorge, Tzion Fahima, and Ann Blechl. Molecular characterization and deployment of the high-temperature adult plant stripe rust resistance gene Yr36 from wheat. United States Department of Agriculture, November 2013. http://dx.doi.org/10.32747/2013.7699860.bard.

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Stripe rust, caused by Puccinia striiformis f. sp. tritici is one of the most destructive fungal diseases of wheat. Virulent races that appeared within the last decade caused drastic cuts in yields. The incorporation of genetic resistance against this pathogen is the most cost-effective and environmentally friendly solution to this problem. However, race specific seedling resistance genes provide only a temporary solution because fungal populations rapidly evolve to overcome this type of resistance. In contrast, high temperature adult plant (HTAP) resistance genes provide a broad spectrum resistance that is partial and more durable. The cloning of the first wheat HTAP stripe rust resistance gene Yr36 (Science 2009, 323:1357), funded by our previous (2007-2010) BARD grant, provided us for the first time with an entry point for understanding the mechanism of broad spectrum resistance. Two paralogous copies of this gene are tightly linked at the Yr36 locus (WKS1 and WKS2). The main objectives of the current study were to characterize the Yr36 (WKS) resistance mechanism and to identify and characterize alternative WKSgenes in wheat and wild relatives. We report here that the protein coded by Yr36, designated WKS1, that has a novel architecture with a functional kinase and a lipid binding START domain, is localized to chloroplast. Our results suggest that the presence of the START domain may affect the kinase activity. We have found that the WKS1 was over-expressed on leaf necrosis in wheat transgenic plants. When the isolated WKS1.1 splice variant transcript was transformed into susceptible wheat it conferred resistance to stripe rust, but the truncated variant WKS1.2 did not confer resistance. WKS1.1 and WKS1.2 showed different lipid binding profiling. WKS1.1 enters the chloroplast membrane, while WKS1.2 is only attached outside of the chloroplast membrane. The ascorbate peroxidase (APX) activity of the recombinant protein of TmtAPXwas found to be reduced by WKS1.1 protein in vitro. The WKS1.1 mature protein in the chloroplast is able to phosphorylate TmtAPXprotein in vivo. WKS1.1 induced cell death by suppressing APX activity and reducing the ability of the cell to detoxify reactive oxygen. The decrease of APX activity reduces the ability of the plant to detoxify the reactive H2O2 and is the possible mechanism underlying the accelerated cell death observed in the transgenic plants overexpressing WKS1.1 and in the regions surrounding a stripe rust infection in the wheat plants carrying the natural WKS1.1 gene. WKS2 is a nonfunctional paralog of WKS1 in wild emmer wheat, probably due to a retrotransposon insertion close to the alternative splicing site. In some other wild relatives of wheat, such as Aegilops comosa, there is only one copy of this gene, highly similar to WKS2, which is lucking the retrotransposon insertion. WKS2 gene present in wheat and WKS2-Ae from A. showed a different pattern of alternative splice variants, regardless of the presence of the retrotransposon insertion. Susceptible Bobwhite transformed with WKS2-Ae (without retrotansposon insertion in intron10), which derived from Aegilops comosaconferred resistance to stripe rust in wheat. The expression of WKS2-Ae in transgenic plants is up-regulated by temperature and pathogen infection. Combination of WKS1 and WKS2-Ae shows improved stripe rust resistance in WKS1×WKS2-Ae F1 hybrid plants. The obtained results show that WKS1 protein is accelerating programmed cell death observed in the regions surrounding a stripe rust infection in the wheat plants carrying the natural or transgenic WKS1 gene. Furthermore, characterization of the epistatic interactions of Yr36 and Yr18 demonstrated that these two genes have additive effects and can therefore be combined to increase partial resistance to this devastating pathogen of wheat. These achievements may have a broad impact on wheat breeding efforts attempting to protect wheat yields against one of the most devastating wheat pathogen.
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Rafaeli, Ada, and Russell Jurenka. Molecular Characterization of PBAN G-protein Coupled Receptors in Moth Pest Species: Design of Antagonists. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7593390.bard.

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The proposed research was directed at determining the activation/binding domains and gene regulation of the PBAN-R’s thereby providing information for the design and screening of potential PBAN-R-blockers and to indicate possible ways of preventing the process from proceeding to its completion. Our specific aims included: (1) The identification of the PBAN-R binding domain by a combination of: (a) in silico modeling studies for identifying specific amino-acid side chains that are likely to be involved in binding PBAN with the receptor and; (b) bioassays to verify the modeling studies using mutant receptors, cell lines and pheromone glands (at tissue and organism levels) against selected, designed compounds to confirm if compounds are agonists or antagonists. (2) The elucidation ofthemolecular regulationmechanisms of PBAN-R by:(a) age-dependence of gene expression; (b) the effect of hormones and; (c) PBAN-R characterization in male hair-pencil complexes. Background to the topic Insects have several closely related G protein-coupled receptors (GPCRs) belonging to the pyrokinin/PBAN family, one with the ligand pheromone biosynthesis activating neuropeptide or pyrokinin-2 and another with diapause hormone or pyrokinin-1 as a ligand. We were unable to identify the diapause hormone receptor from Helicoverpa zea despite considerable effort. A third, related receptor is activated by a product of the capa gene, periviscerokinins. The pyrokinin/PBAN family of GPCRs and their ligands has been identified in various insects, such as Drosophila, several moth species, mosquitoes, Triboliumcastaneum, Apis mellifera, Nasoniavitripennis, and Acyrthosiphon pisum. Physiological functions of pyrokinin peptides include muscle contraction, whereas PBAN regulates pheromone production in moths plus other functions indicating the pleiotropic nature of these ligands. Based on the alignment of annotated genomic sequences, the primary and secondary structures of the pyrokinin/PBAN family of receptors have similarity with the corresponding structures of the capa or periviscerokinin receptors of insects and the neuromedin U receptors found in vertebrates. Major conclusions, solutions, achievements Evolutionary trace analysisof receptor extracellular domains exhibited several class-specific amino acid residues, which could indicate putative domains for activation of these receptors by ligand recognition and binding. Through site-directed point mutations, the 3rd extracellular domain of PBAN-R was shown to be critical for ligand selection. We identified three receptors that belong to the PBAN family of GPCRs and a partial sequence for the periviscerokinin receptor from the European corn borer, Ostrinianubilalis. Functional expression studies confirmed that only the C-variant of the PBAN-R is active. We identified a non-peptide agonist that will activate the PBAN-receptor from H. zea. We determined that there is transcriptional control of the PBAN-R in two moth species during the development of the pupa to adult, and we demonstrated that this transcriptional regulation is independent of juvenile hormone biosynthesis. This transcriptional control also occurs in male hair-pencil gland complexes of both moth species indicating a regulatory role for PBAN in males. Ultimate confirmation for PBAN's function in the male tissue was revealed through knockdown of the PBAN-R using RNAi-mediated gene-silencing. Implications, both scientific and agricultural The identification of a non-peptide agonist can be exploited in the future for the design of additional compounds that will activate the receptor and to elucidate the binding properties of this receptor. The increase in expression levels of the PBAN-R transcript was delineated to occur at a critical period of 5 hours post-eclosion and its regulation can now be studied. The mysterious role of PBAN in the males was elucidated by using a combination of physiological, biochemical and molecular genetics techniques.
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