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Article ; Online: Alterations in gene expression and microbiome composition upon calcium-sensing receptor deletion in the mouse esophagus.

Abdulnour-Nakhoul, Solange M / Kolls, Jay K / Flemington, Erik K / Ungerleider, Nathan A / Nakhoul, Hani N / Song, Kejing / Nakhoul, Nazih L

American journal of physiology. Gastrointestinal and liver physiology

2024 Volume 326, Issue 4, Page(s) G438–G459

Abstract: The calcium-sensing receptor (CaSR), a G protein-coupled receptor, regulates ... ...

Abstract	The calcium-sensing receptor (CaSR), a G protein-coupled receptor, regulates Ca
MeSH term(s)	Animals ; Mice ; Calcium/metabolism ; Receptors, Calcium-Sensing/genetics ; Receptors, Calcium-Sensing/metabolism ; Esophagus/metabolism ; Microbiota ; Inflammation ; Gene Expression
Chemical Substances	Calcium (SY7Q814VUP) ; Receptors, Calcium-Sensing
Language	English
Publishing date	2024-01-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	603840-2
ISSN	1522-1547 ; 0193-1857
ISSN (online)	1522-1547
ISSN	0193-1857
DOI	10.1152/ajpgi.00066.2023
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Article ; Online: SpliceTools, a suite of downstream RNA splicing analysis tools to investigate mechanisms and impact of alternative splicing.

Flemington, Erik K / Flemington, Samuel A / O'Grady, Tina M / Baddoo, Melody / Nguyen, Trang / Dong, Yan / Ungerleider, Nathan A

Nucleic acids research

2023 Volume 51, Issue 7, Page(s) e42

Abstract: As a fundamental aspect of normal cell signaling and disease states, there is great interest in determining alternative splicing (AS) changes in physiologic, pathologic, and pharmacologic settings. High throughput RNA sequencing and specialized software ... ...

Abstract	As a fundamental aspect of normal cell signaling and disease states, there is great interest in determining alternative splicing (AS) changes in physiologic, pathologic, and pharmacologic settings. High throughput RNA sequencing and specialized software to detect AS has greatly enhanced our ability to determine transcriptome-wide splicing changes. Despite the richness of this data, deriving meaning from sometimes thousands of AS events is a substantial bottleneck for most investigators. We present SpliceTools, a suite of data processing modules that arms investigators with the ability to quickly produce summary statistics, mechanistic insights, and functional significance of AS changes through command line or through an online user interface. Utilizing RNA-seq datasets for 186 RNA binding protein knockdowns, nonsense mediated RNA decay inhibition, and pharmacologic splicing inhibition, we illustrate the utility of SpliceTools to distinguish splicing disruption from regulated transcript isoform changes, we show the broad transcriptome footprint of the pharmacologic splicing inhibitor, indisulam, we illustrate the utility in uncovering mechanistic underpinnings of splicing inhibition, we identify predicted neo-epitopes in pharmacologic splicing inhibition, and we show the impact of splicing alterations induced by indisulam on cell cycle progression. Together, SpliceTools puts rapid and easy downstream analysis at the fingertips of any investigator studying AS.
MeSH term(s)	Alternative Splicing/genetics ; RNA Splicing ; Sulfonamides ; Transcriptome/genetics ; Sequence Analysis, RNA/methods
Chemical Substances	N-(3-chloro-7-indolyl)-1,4-benzenedisulphonamide ; Sulfonamides
Language	English
Publishing date	2023-03-01
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad111
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Article: Transcriptomic analysis identifies B-lymphocyte kinase as a therapeutic target for desmoplastic small round cell tumor cancer stem cell-like cells.

Magrath, Justin W / Flinchum, Dane A / Hartono, Alifiani B / Sampath, Shruthi Sanjitha / O'Grady, Tina M / Baddoo, Melody / Haoyang, Liang / Xu, Xiaojiang / Flemington, Erik K / Lee, Sean B

Oncogenesis

2024 Volume 13, Issue 1, Page(s) 2

Abstract: Desmoplastic small round cell tumor (DSRCT) is an aggressive pediatric cancer caused by the EWSR1-WT1 fusion oncoprotein. The tumor is refractory to treatment with a 5-year survival rate of only 15-25%, necessitating the development of novel therapeutics, ...

Abstract	Desmoplastic small round cell tumor (DSRCT) is an aggressive pediatric cancer caused by the EWSR1-WT1 fusion oncoprotein. The tumor is refractory to treatment with a 5-year survival rate of only 15-25%, necessitating the development of novel therapeutics, especially those able to target chemoresistant subpopulations. Novel in vitro cancer stem cell-like (CSC-like) culture conditions increase the expression of stemness markers (SOX2, NANOG) and reduce DSRCT cell line susceptibility to chemotherapy while maintaining the ability of DSRCT cells to form xenografts. To gain insights into this chemoresistant model, RNA-seq was performed to elucidate transcriptional alterations between DSRCT cells grown in CSC-like spheres and normal 2-dimensional adherent state. Commonly upregulated and downregulated genes were identified and utilized in pathway analysis revealing upregulation of pathways related to chromatin assembly and disassembly and downregulation of pathways including cell junction assembly and extracellular matrix organization. Alterations in chromatin assembly suggest a role for epigenetics in the DSRCT CSC-like state, which was further investigated with ATAC-seq, identifying over 10,000 differentially accessible peaks, including 4444 sphere accessible peaks and 6,120 adherent accessible peaks. Accessible regions were associated with higher gene expression, including increased accessibility of the CSC marker SOX2 in CSC-like culture conditions. These analyses were further utilized to identify potential CSC therapeutic targets, leading to the identification of B-lymphocyte kinase (BLK) as a CSC-enriched, EWSR1-WT1-regulated, druggable target. BLK inhibition and knockdown reduced CSC-like properties, including abrogation of tumorsphere formation and stemness marker expression. Importantly, BLK knockdown reduced DSRCT CSC-like cell chemoresistance, making its inhibition a promising target for future combination therapy.
Language	English
Publishing date	2024-01-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2674437-5
ISSN	2157-9024
ISSN	2157-9024
DOI	10.1038/s41389-023-00504-z
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Article ; Online: Profiling the activity of the para-caspase MALT1 in B-cell acute lymphoblastic leukemia for potential targeted therapeutic application.

Safa, Firas M / Rasmussen, Terri / Fontan, Lorena / Xia, Min / Melnick, Ari / Wiestner, Adrian / Lobelle-Rich, Patricia / Burger, Jan A / Mouawad, Yara / Safah, Hana / Flemington, Erik K / Saba, Nakhle S

Haematologica

2024 Volume 109, Issue 5, Page(s) 1348–1358

Abstract: B-cell acute lymphoblastic leukemia (B-ALL) remains a hard-to-treat disease with a poor prognosis in adults. Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is a para-caspase required for B-cell receptor (BCR)-mediated NF-κB ... ...

Abstract	B-cell acute lymphoblastic leukemia (B-ALL) remains a hard-to-treat disease with a poor prognosis in adults. Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is a para-caspase required for B-cell receptor (BCR)-mediated NF-κB activation. Inhibition of MALT1 in preclinical models has proven efficacious in many B-cell malignancies including chronic lymphocytic leukemia, mantle cell lymphoma and diffuse large B-cell lymphoma. We sought to examine the role of MALT1 in B-ALL and determine the biological consequences of its inhibition. Targeting MALT1 with both Z-VRPR-fmk and MI-2 efficiently kills B-ALL cells independent of the cell-of-origin (pro, pre, mature) or the presence of the Philadelphia chromosome, and spares normal B cells. The mechanism of cell death was through apoptotic induction, mostly in cycling cells. The proteolytic activity of MALT1 can be studied by measuring its ability to cleave its substrates. Surprisingly, with the exception of mature B-ALL, we did not detect cleavage of MALT1 substrates at baseline, nor after proteasomal inhibition or following activation of pre-BCR. To explore the possibility of a distinct role for MALT1 in B-ALL, independent of signaling through BCR, we studied the changes in gene expression profiling following a 24-hour treatment with MI-2 in 12 B-ALL cell lines. Our transcriptome analysis revealed a strong inhibitory effect on MYC-regulated gene signatures, further confirmed by Myc protein downregulation, concomitant with an increase in the Myc degrader FBXW7. In conclusion, our evidence suggests a novel role for MALT1 in B-ALL through Myc regulation and provides support for clinical testing of MALT1 inhibitors in B-ALL.
MeSH term(s)	Mucosa-Associated Lymphoid Tissue Lymphoma Translocation 1 Protein/metabolism ; Mucosa-Associated Lymphoid Tissue Lymphoma Translocation 1 Protein/antagonists & inhibitors ; Mucosa-Associated Lymphoid Tissue Lymphoma Translocation 1 Protein/genetics ; Humans ; Caspases/metabolism ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; Neoplasm Proteins/antagonists & inhibitors ; Apoptosis ; Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/metabolism ; Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/drug therapy ; Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics ; Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/pathology ; Cell Line, Tumor ; Molecular Targeted Therapy ; Gene Expression Profiling
Chemical Substances	Mucosa-Associated Lymphoid Tissue Lymphoma Translocation 1 Protein (EC 3.4.22.-) ; MALT1 protein, human (EC 3.4.22.-) ; Caspases (EC 3.4.22.-) ; Neoplasm Proteins
Language	English
Publishing date	2024-05-01
Publishing country	Italy
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2333-4
ISSN	1592-8721 ; 0017-6567 ; 0390-6078
ISSN (online)	1592-8721
ISSN	0017-6567 ; 0390-6078
DOI	10.3324/haematol.2023.283178
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Article: Data of relative mRNA and protein abundances of androgen receptor splice variants in castration-resistant prostate cancer

Ma, Tianfang / Ungerleider, Nathan / Zhang, Derek Y. / Corey, Eva / Flemington, Erik K. / Dong, Yan

Data in Brief. 2021 Feb., v. 34

2021

Abstract: These data include secondary analysis of publicly available RNA-seq data from castration-resistant prostate cancer (CRPC) patients as well as RT-qPCR and Western blotting analyses of patient-derived xenograft models and a CRPC cell line. We applied ... ...

Abstract	These data include secondary analysis of publicly available RNA-seq data from castration-resistant prostate cancer (CRPC) patients as well as RT-qPCR and Western blotting analyses of patient-derived xenograft models and a CRPC cell line. We applied Spearman correlation analysis to assess the relationship between canonical androgen receptor (AR) splicing and alternative AR splicing. We also assessed the ratio of AR splice variants (AR-Vs) to the full-length AR (AR-FL) at the RNA and protein levels by absolute RT-qPCR and Western blotting, respectively. These data are critical for studying the mechanisms underlying upregulated expression of AR-Vs after AR-directed therapies and the importance of AR-Vs to castration-resistant progression of prostate cancer. Data presented here are related to the research article by Ma et al., “Increased transcription and high translation efficiency lead to accumulation of androgen receptor splice variant after androgen deprivation therapy”, Cancer Lett. In Press [1].
Keywords	androgen receptors ; androgens ; cell lines ; prostatic neoplasms ; sequence analysis ; xenotransplantation
Language	English
Dates of publication	2021-02
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2021.106774
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Article ; Online: Data of relative mRNA and protein abundances of androgen receptor splice variants in castration-resistant prostate cancer.

Ma, Tianfang / Ungerleider, Nathan / Zhang, Derek Y / Corey, Eva / Flemington, Erik K / Dong, Yan

Data in brief

2021 Volume 34, Page(s) 106774

Abstract	These data include secondary analysis of publicly available RNA-seq data from castration-resistant prostate cancer (CRPC) patients as well as RT-qPCR and Western blotting analyses of patient-derived xenograft models and a CRPC cell line. We applied Spearman correlation analysis to assess the relationship between canonical androgen receptor (AR) splicing and alternative AR splicing. We also assessed the ratio of AR splice variants (AR-Vs) to the full-length AR (AR-FL) at the RNA and protein levels by absolute RT-qPCR and Western blotting, respectively. These data are critical for studying the mechanisms underlying upregulated expression of AR-Vs after AR-directed therapies and the importance of AR-Vs to castration-resistant progression of prostate cancer. Data presented here are related to the research article by Ma et al., "Increased transcription and high translation efficiency lead to accumulation of androgen receptor splice variant after androgen deprivation therapy", Cancer Lett. In Press [1].
Language	English
Publishing date	2021-01-18
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409 ; 2352-3409
ISSN (online)	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2021.106774
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Article ; Online: Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis.

Mei, Suyu / Flemington, Erik K / Zhang, Kun

BMC genomics

2018 Volume 19, Issue 1, Page(s) 505

Abstract: Background: Bacterial invasive infection and host immune response is fundamental to the understanding of pathogen pathogenesis and the discovery of effective therapeutic drugs. However, there are very few experimental studies on the signaling cross- ... ...

Abstract	Background: Bacterial invasive infection and host immune response is fundamental to the understanding of pathogen pathogenesis and the discovery of effective therapeutic drugs. However, there are very few experimental studies on the signaling cross-talks between bacteria and human host to date. Methods: In this work, taking M. tuberculosis H37Rv (MTB) that is co-evolving with its human host as an example, we propose a general computational framework that exploits the known bacterial pathogen protein interaction networks in STRING database to predict pathogen-host protein interactions and their signaling cross-talks. In this framework, significant interlogs are derived from the known pathogen protein interaction networks to train a predictive l Results: The computational results show that the proposed method achieves excellent performance of cross validation as well as low predicted positive rates on the less significant interlogs and non-interlogs, indicating a low risk of false discovery. We further conduct gene ontology (GO) and pathway enrichment analyses of the predicted pathogen-host protein interaction networks, which potentially provides insights into the machinery that M. tuberculosis H37Rv targets human genes and signaling pathways. In addition, we analyse the pathogen-host protein interactions related to drug resistance, inhibition of which potentially provides an alternative solution to M. tuberculosis H37Rv drug resistance. Conclusions: The proposed machine learning framework has been verified effective for predicting bacteria-host protein interactions via known bacterial protein interaction networks. For a vast majority of bacterial pathogens that lacks experimental studies of bacteria-host protein interactions, this framework is supposed to achieve a general-purpose applicability. The predicted protein interaction networks between M. tuberculosis H37Rv and Homo sapiens, provided in the Additional files, promise to gain applications in the two fields: (1) providing an alternative solution to drug resistance; (2) revealing the patterns that M. tuberculosis H37Rv genes target human immune signaling pathways.
MeSH term(s)	Area Under Curve ; Bacterial Proteins/metabolism ; Databases, Genetic ; Drug Resistance, Bacterial/genetics ; Gene Ontology ; Host-Pathogen Interactions/genetics ; Humans ; Immune System/metabolism ; Immune System/microbiology ; Logistic Models ; Mycobacterium tuberculosis/metabolism ; Protein Interaction Maps/genetics ; ROC Curve ; Signal Transduction/genetics ; Tuberculosis/genetics ; Tuberculosis/immunology ; Tuberculosis/microbiology ; Tuberculosis/pathology
Chemical Substances	Bacterial Proteins
Language	English
Publishing date	2018-06-28
Publishing country	England
Document type	Journal Article
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-018-4873-9
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Article ; Online: Driver gene mutations based clustering of tumors: methods and applications.

Zhang, Wensheng / Flemington, Erik K / Zhang, Kun

Bioinformatics (Oxford, England)

2018 Volume 34, Issue 13, Page(s) i404–i411

Abstract: Motivation: Somatic mutations in proto-oncogenes and tumor suppressor genes constitute a major category of causal genetic abnormalities in tumor cells. The mutation spectra of thousands of tumors have been generated by The Cancer Genome Atlas (TCGA) and ...

Abstract	Motivation: Somatic mutations in proto-oncogenes and tumor suppressor genes constitute a major category of causal genetic abnormalities in tumor cells. The mutation spectra of thousands of tumors have been generated by The Cancer Genome Atlas (TCGA) and other whole genome (exome) sequencing projects. A promising approach to utilizing these resources for precision medicine is to identify genetic similarity-based sub-types within a cancer type and relate the pinpointed sub-types to the clinical outcomes and pathologic characteristics of patients. Results: We propose two novel methods, ccpwModel and xGeneModel, for mutation-based clustering of tumors. In the former, binary variables indicating the status of cancer driver genes in tumors and the genes' involvement in the core cancer pathways are treated as the features in the clustering process. In the latter, the functional similarities of putative cancer driver genes and their confidence scores as the 'true' driver genes are integrated with the mutation spectra to calculate the genetic distances between tumors. We apply both methods to the TCGA data of 16 cancer types. Promising results are obtained when these methods are compared to state-of-the-art approaches as to the associations between the determined tumor clusters and patient race (or survival time). We further extend the analysis to detect mutation-characterized transcriptomic prognostic signatures, which are directly relevant to the etiology of carcinogenesis. Availability and implementation: R codes and example data for ccpwModel and xGeneModel can be obtained from http://webusers.xula.edu/kzhang/ISMB2018/ccpw_xGene_software.zip. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Cluster Analysis ; DNA Mutational Analysis/methods ; Genes, Neoplasm ; Genomics/methods ; Humans ; Models, Genetic ; Mutation ; Neoplasms/genetics ; Prognosis ; Software
Language	English
Publishing date	2018-06-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/bty232
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Article ; Online: Reversal of splicing infidelity is a pre-activation step in B cell differentiation.

O'Grady, Tina M / Baddoo, Melody / Flemington, Samuel A / Ishaq, Eman Y / Ungerleider, Nathan A / Flemington, Erik K

Frontiers in immunology

2022 Volume 13, Page(s) 1060114

Abstract: Introduction: B cell activation and differentiation is central to the adaptive immune response. Changes in exon usage can have major impacts on cellular signaling and differentiation but have not been systematically explored in differentiating B cells.!# ...

Abstract	Introduction: B cell activation and differentiation is central to the adaptive immune response. Changes in exon usage can have major impacts on cellular signaling and differentiation but have not been systematically explored in differentiating B cells. Methods: We analyzed exon usage and intron retention in RNA-Seq data from subsets of human B cells at various stages of differentiation, and in an in vitro laboratory model of B cell activation and differentiation (Epstein Barr virus infection). Results: Blood naïve B cells were found to have an unusual splicing profile, with unannotated splicing events in over 30% of expressed genes. Splicing changed substantially upon naïve B cell entry into secondary lymphoid tissue and before activation, involving significant increases in exon commitment and reductions in intron retention. These changes preferentially involved short introns with weak splice sites and were likely mediated by an overall increase in splicing efficiency induced by the lymphoid environment. The majority of transcripts affected by splicing changes showed restoration of encoded conserved protein domains and/or reduced targeting to the nonsense-mediated decay pathway. Affected genes were enriched in functionally important immune cell activation pathways such as antigen-mediated signaling, cell cycle control and mRNA processing and splicing. Discussion: Functional observations from donor B cell subsets in progressive states of differentiation and from timecourse experiments using the in vitro model suggest that these widespread changes in mRNA splicing play a role in preparing naïve B cells for the decisive step of antigen-mediated activation and differentiation.
MeSH term(s)	Humans ; Alternative Splicing ; Epstein-Barr Virus Infections ; Herpesvirus 4, Human/genetics ; RNA, Messenger/genetics ; Cell Differentiation/genetics
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2022-12-19
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2022.1060114
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Article ; Online: A Polymorphism in the Epstein-Barr Virus EBER2 Noncoding RNA Drives

Wang, Yiping / Ungerleider, Nathan / Hoffman, Brett A / Kara, Mehmet / Farrell, Paul J / Flemington, Erik K / Lee, Nara / Tibbetts, Scott A

mBio

2022 Volume 13, Issue 3, Page(s) e0083622

Abstract: The oncogenic gammaherpesviruses, including human Epstein-Barr virus (EBV), human Kaposi's sarcoma-associated herpesvirus (KSHV), and murine gammaherpesvirus 68 (MHV68, γHV68, MuHV-4), are associated with numerous malignancies, including B cell lymphomas ...

Abstract	The oncogenic gammaherpesviruses, including human Epstein-Barr virus (EBV), human Kaposi's sarcoma-associated herpesvirus (KSHV), and murine gammaherpesvirus 68 (MHV68, γHV68, MuHV-4), are associated with numerous malignancies, including B cell lymphomas and nasopharyngeal carcinoma. These viruses employ numerous molecular strategies to colonize the host, including the expression of noncoding RNAs (ncRNAs). As the first viral ncRNAs identified, EBV-encoded RNA 1 and 2 (EBER1 and EBER2, respectively) have been investigated extensively for decades; however, their specific
MeSH term(s)	Animals ; Epstein-Barr Virus Infections/genetics ; Gammaherpesvirinae/genetics ; Herpesvirus 4, Human/physiology ; Herpesvirus 8, Human/genetics ; Humans ; Mice ; Nucleotides ; Polymorphism, Genetic ; RNA, Untranslated/genetics ; RNA, Untranslated/metabolism ; RNA, Viral ; Rhadinovirus/genetics ; Virus Latency/genetics
Chemical Substances	Epstein-Barr virus encoded RNA 2 ; Nucleotides ; RNA, Untranslated ; RNA, Viral
Language	English
Publishing date	2022-06-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.00836-22
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