subject:(RNA Messenger mesh )

University of Florida

1. Zambetti, Gerard Paul, 1958-. The role of subcellular compartments and structures in eukaryotic gene expression.

Degree: 1989, University of Florida

Subjects/Keywords: Cells; Cytochalasins; Cytoskeleton; DNA; Hela cells; Histones; Messenger RNA; Polyribosomes; RNA; Signals; Gene Expression Regulation ( mesh ); RNA, Messenger ( mesh ); Transcription, Genetic ( mesh )

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APA (6^th Edition):

Zambetti, Gerard Paul, 1. (1989). The role of subcellular compartments and structures in eukaryotic gene expression. (Thesis). University of Florida. Retrieved from https://ufdc.ufl.edu/AA00012891

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Zambetti, Gerard Paul, 1958-. “The role of subcellular compartments and structures in eukaryotic gene expression.” 1989. Thesis, University of Florida. Accessed March 07, 2021. https://ufdc.ufl.edu/AA00012891.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Zambetti, Gerard Paul, 1958-. “The role of subcellular compartments and structures in eukaryotic gene expression.” 1989. Web. 07 Mar 2021.

Vancouver:

Zambetti, Gerard Paul 1. The role of subcellular compartments and structures in eukaryotic gene expression. [Internet] [Thesis]. University of Florida; 1989. [cited 2021 Mar 07]. Available from: https://ufdc.ufl.edu/AA00012891.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Zambetti, Gerard Paul 1. The role of subcellular compartments and structures in eukaryotic gene expression. [Thesis]. University of Florida; 1989. Available from: https://ufdc.ufl.edu/AA00012891

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Hong Kong University of Science and Technology

2. Sun, Xin LIFS. Identification of LDB3 as a PICK1 binding partner.

Degree: 2017, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-103556 ; https://doi.org/10.14711/thesis-991012564268803412 ; http://repository.ust.hk/ir/bitstream/1783.1-103556/1/th_redirect.html

► Delivery of different proteins to proper locations is important for them to exert specific function. Thereby, protein trafficking plays a critical role in maintaining the… (more)

Subjects/Keywords: Proteins ; Messenger RNA ; Membrane proteins

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APA (6^th Edition):

Sun, X. L. (2017). Identification of LDB3 as a PICK1 binding partner. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-103556 ; https://doi.org/10.14711/thesis-991012564268803412 ; http://repository.ust.hk/ir/bitstream/1783.1-103556/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Sun, Xin LIFS. “Identification of LDB3 as a PICK1 binding partner.” 2017. Thesis, Hong Kong University of Science and Technology. Accessed March 07, 2021. http://repository.ust.hk/ir/Record/1783.1-103556 ; https://doi.org/10.14711/thesis-991012564268803412 ; http://repository.ust.hk/ir/bitstream/1783.1-103556/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Sun, Xin LIFS. “Identification of LDB3 as a PICK1 binding partner.” 2017. Web. 07 Mar 2021.

Vancouver:

Sun XL. Identification of LDB3 as a PICK1 binding partner. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2017. [cited 2021 Mar 07]. Available from: http://repository.ust.hk/ir/Record/1783.1-103556 ; https://doi.org/10.14711/thesis-991012564268803412 ; http://repository.ust.hk/ir/bitstream/1783.1-103556/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Sun XL. Identification of LDB3 as a PICK1 binding partner. [Thesis]. Hong Kong University of Science and Technology; 2017. Available from: http://repository.ust.hk/ir/Record/1783.1-103556 ; https://doi.org/10.14711/thesis-991012564268803412 ; http://repository.ust.hk/ir/bitstream/1783.1-103556/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Lethbridge

3. University of Lethbridge. Faculty of Arts and Science. Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation .

Degree: 2019, University of Lethbridge

URL: http://hdl.handle.net/10133/5666

► Cap-dependent translation drives the global synthesis of proteins. Under stress conditions global protein production is attenuated, yet the translation of ATF4 is upregulated through uORF-… (more)

Subjects/Keywords: Messenger RNA; Proteins – Synthesis; Ribosomes

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APA (6^th Edition):

Science, U. o. L. F. o. A. a. (2019). Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation . (Thesis). University of Lethbridge. Retrieved from http://hdl.handle.net/10133/5666

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Science, University of Lethbridge. Faculty of Arts and. “Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation .” 2019. Thesis, University of Lethbridge. Accessed March 07, 2021. http://hdl.handle.net/10133/5666.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Science, University of Lethbridge. Faculty of Arts and. “Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation .” 2019. Web. 07 Mar 2021.

Vancouver:

Science UoLFoAa. Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation . [Internet] [Thesis]. University of Lethbridge; 2019. [cited 2021 Mar 07]. Available from: http://hdl.handle.net/10133/5666.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Science UoLFoAa. Elucidating the role of eukaryotic initiation factor 5B (eIF5B) in non-canonical translation initiation . [Thesis]. University of Lethbridge; 2019. Available from: http://hdl.handle.net/10133/5666

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Hong Kong

4. Lui, Wan, Thomas. An analysis of the functional significance of the 3'-untranslated region of CHOP/Gadd153 messenger RNA.

Degree: 2013, University of Hong Kong

URL: http://hdl.handle.net/10722/192840

► CHOP, or Gadd153, is a 29 kDa protein that plays a pivotal role in the mediation of cellular stress-induced cell death. The expression of the… (more)

▼ CHOP, or Gadd153, is a 29 kDa protein that plays a pivotal role in the mediation of cellular stress-induced cell death. The expression of the gene encoding CHOP/Gadd153 is regulated at both the transcriptional and post-transcriptional levels. Compared to transcription, the regulation of Chop gene expression at the post-transcriptional level is much less understood. In this study, the role played by the 3’-untranslated region of CHOP mRNA (3UTRChop) in mediating mRNA stability was examined. A reporter plasmid was constructed so that the mRNA expressed has 3UTRChop as its 3’-untranslated region. Partial 5’ deletions, or deletion of short internal (~30 nucleotides) sequences, or the deletion of a putative AU-rich element (ARE) within 3UTRChop, all resulted in the elevation of the steady state levels of mRNA and the encoded reporter protein, EGFP. Deletion of the ARE or sequences remote from ARE resulted in the reduced rate of mRNA degradation. Such data suggested that 3UTRChop is closely related to mRNA stability. The effect of cellular stress on the functioning of 3UTRChop was studied by examining the change in mRNA level in cells treated with arsenic trioxide (ATO). The presence of arsenic stress stimulated a marked increase in the steady state level of not only the reporter mRNA, but also control mRNAs that did not have 3UTRChop as the 3’-untranslated region. A non-specific effect of arsenic stress on mRNA levels was therefore suggested. Consistent with the increase in the level of reporter mRNA, the expression of EGFP protein was also increased. Arsenic stress and partial deletion of 3UTRChop produce additive increase in mRNA level and EGFP protein level implying that the mRNA destabilizing function of 3UTRChop is unlikely to be stress-regulated. The contribution of 3UTRChop in mRNA translation was then examined using reporter constructs that expressed EGFP mRNA having its original 5’ and 3’-untranslated regions replaced with 5UTRChop and 3UTRChop respectively. In the presence of wild-type 3UTRChop, the abolition of the translation repressor functions of 5UTRChop produced only mild increase in EGFP expression. However, the additional partial deletion of 3UTRChop resulted in massive increase in EGFP expression. In the presence of wild-type 5UTRChop, the partial deletion of 3UTRChop resulted in only a small increase in EGFP expression. Such data demonstrated a complementary relationship between 5UTRChop and 3UTRChop in the regulation of Chop expression in unstressed cells. EGFP mRNA having 5UTRChop and 3UTRChop as the 5’ and 3’-untranslated region respectively expressed significant EGFP protein only in the presence of ATO. The expression of EGFP was not significantly affected with swopping of 3UTRChop with another 3UTR. 3UTRChop is therefore not essential for the mediation of ATO-stimulated expression of EGFP. The present study demonstrated that full length 3UTRChop may have constitutive mRNA destabilizing effect that is not alleviated by cellular stress. The evaluation of the relative contributions of… Advisors/Committee Members: Wong, NS (advisor).

Subjects/Keywords: Messenger RNA.

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APA (6^th Edition):

Lui, Wan, T. (2013). An analysis of the functional significance of the 3'-untranslated region of CHOP/Gadd153 messenger RNA. (Thesis). University of Hong Kong. Retrieved from http://hdl.handle.net/10722/192840

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Lui, Wan, Thomas. “An analysis of the functional significance of the 3'-untranslated region of CHOP/Gadd153 messenger RNA.” 2013. Thesis, University of Hong Kong. Accessed March 07, 2021. http://hdl.handle.net/10722/192840.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Lui, Wan, Thomas. “An analysis of the functional significance of the 3'-untranslated region of CHOP/Gadd153 messenger RNA.” 2013. Web. 07 Mar 2021.

Vancouver:

Lui, Wan T. An analysis of the functional significance of the 3'-untranslated region of CHOP/Gadd153 messenger RNA. [Internet] [Thesis]. University of Hong Kong; 2013. [cited 2021 Mar 07]. Available from: http://hdl.handle.net/10722/192840.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Lui, Wan T. An analysis of the functional significance of the 3'-untranslated region of CHOP/Gadd153 messenger RNA. [Thesis]. University of Hong Kong; 2013. Available from: http://hdl.handle.net/10722/192840

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Missouri – Columbia

5. Shebl, Bassem. The influence of mRNA secondary structures on ribosome conformational dynamics.

Degree: 2016, University of Missouri – Columbia

URL: http://hdl.handle.net/10355/62520

► [ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Synthesizing proteins in the cell is a critical aspect of life. Protein synthesis is a… (more)

▼ [ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Synthesizing proteins in the cell is a critical aspect of life. Protein synthesis is a complicated process and involve highly functional machines at a molecular level. The ribosome is the molecular machine that translate coded sequences of nucleic acids into functional proteins. Understanding how ribosomes function is key to understanding protein synthesis / translation. We focus our work on ribosomes from bacterial cells. This allows us to study much simpler systems and extrapolate our knowledge to higher levels. One key challenge in the field is to be able to isolate a high quantity of good and active ribosomes out of the cell to study it in a controlled environment. Classically known methods involve extensive resources, high technical expertise, and a week of preparation. We developed a one-step protocol to purify ribosomes that are more active than the ones purified from classical methods. This developed technique saves time and money and results in much higher amounts of product. This approach also makes the technique approachable to a wider community of scientists and researchers. The same methodology could be applied towards purifying other molecular machines in the cells. Using these ribosomes, we wanted to investigate how the ribosomes function in cells when faced with specific signals. These signals are utilized by the cells to control protein synthesis. However, in dome diseased cells and for some viruses, normal protein synthesis is overridden by the invaders to produce faulty proteins that could result in a wide range of diseases such as Alzheimer and others. In this study, we investigated how the ribosome functions in the presence of such signals and how close do they need to be to the ribosome to affect protein synthesis. This allows us to design drugs to mimic or inhibit such changes thus fixing faulty protein production or sometimes induce it to inhibit protein synthesis in bacterial cells and as such designing and producing novel drugs. Advisors/Committee Members: Cornish, Peter V. (advisor).

Subjects/Keywords: Proteins – Synthesis; Messenger RNA; Ribosomes

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APA (6^th Edition):

Shebl, B. (2016). The influence of mRNA secondary structures on ribosome conformational dynamics. (Thesis). University of Missouri – Columbia. Retrieved from http://hdl.handle.net/10355/62520

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Shebl, Bassem. “The influence of mRNA secondary structures on ribosome conformational dynamics.” 2016. Thesis, University of Missouri – Columbia. Accessed March 07, 2021. http://hdl.handle.net/10355/62520.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Shebl, Bassem. “The influence of mRNA secondary structures on ribosome conformational dynamics.” 2016. Web. 07 Mar 2021.

Vancouver:

Shebl B. The influence of mRNA secondary structures on ribosome conformational dynamics. [Internet] [Thesis]. University of Missouri – Columbia; 2016. [cited 2021 Mar 07]. Available from: http://hdl.handle.net/10355/62520.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Shebl B. The influence of mRNA secondary structures on ribosome conformational dynamics. [Thesis]. University of Missouri – Columbia; 2016. Available from: http://hdl.handle.net/10355/62520

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Rutgers University

6. Zhou, Mi, 1987-. Role of DcpS in mammalian RNA regulation and human diseases.

Degree: PhD, Cell and Developmental Biology, 2015, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/48745/

►

In eukaryotic cells, mRNA degradation plays an important role in the control of gene expression and is therefore highly regulated. The scavenger decapping enzyme DcpS… (more)

▼

In eukaryotic cells, mRNA degradation plays an important role in the control of gene expression and is therefore highly regulated. The scavenger decapping enzyme DcpS is a multifunctional protein that plays a critical role in mRNA degradation. We first sought to identify DcpS target genes in mammalian cells using a cell permeable DcpS inhibitor compound, RG3039, which was initially developed for therapeutic treatment of Spinal Muscular Atrophy (SMA). Microarray analysis following DcpS decapping inhibition by RG3039 revealed the steady state levels of 222 RNAs were altered. Of a subset selected for validation by qRT-PCR, two non-coding transcripts dependent on DcpS decapping activity, were identified and referred to as DcpS Responsive Noncoding Transcript (DRNT) 1 and 2 respectively. Only the increase in DRNT1 transcript was accompanied with an increase of its RNA stability and this increase was dependent on both DcpS and Xrn1. Our data indicate that DcpS is a transcript-restricted modulator of RNA stability in mammalian cells and the RG3039 quinazoline compound is pleotropic, influence gene expression in both an apparent DcpS dependent and independent manner. A surprising development was uncovered in a collaborative study where two distinct mutations in the DcpS gene (c.636+1G>A, DcpSIns15 and c.947C>T, DcpST316M) were identified as the underlying cause of autosomal recessive intellectual disability within a consanguineous family. Both of the mutations were confirmed to disrupt DcpS decapping activity in vitro and/or in vivo, indicating that the decapping activity of DcpS is critical for normal neurological development. Consistent with a role for DcpS in neuronal cells, our studies with the DcpSIns15 variant uncovered a link between this variant DcpS and Spinal Muscular Atrophy (SMA). Exogenous expression of DcpSIns15 in SMA patient fibroblast cells increased SMN2 mRNA and corresponding SMN protein levels. Our findings suggest that strategies to shift wild type DcpS splicing patterns to partially yield the variant DcpS Ins15 splicing pattern may be beneficial for SMA therapeutics.

Advisors/Committee Members: Kiledjian, Megerditch (chair), Covey, Lori (internal member), Gunderson, Samuel (internal member), Copeland, Paul (outside member).

Subjects/Keywords: Messenger RNA; Gene expression

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APA (6^th Edition):

Zhou, Mi, 1. (2015). Role of DcpS in mammalian RNA regulation and human diseases. (Doctoral Dissertation). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/48745/

Chicago Manual of Style (16^th Edition):

Zhou, Mi, 1987-. “Role of DcpS in mammalian RNA regulation and human diseases.” 2015. Doctoral Dissertation, Rutgers University. Accessed March 07, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/48745/.

MLA Handbook (7^th Edition):

Zhou, Mi, 1987-. “Role of DcpS in mammalian RNA regulation and human diseases.” 2015. Web. 07 Mar 2021.

Vancouver:

Zhou, Mi 1. Role of DcpS in mammalian RNA regulation and human diseases. [Internet] [Doctoral dissertation]. Rutgers University; 2015. [cited 2021 Mar 07]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/48745/.

Council of Science Editors:

Zhou, Mi 1. Role of DcpS in mammalian RNA regulation and human diseases. [Doctoral Dissertation]. Rutgers University; 2015. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/48745/

University of Florida

7. Campa, Michael Joseph, 1955-. Endogenous amino acid transport and translation of rat liver mRNA in Xenopus laevis oocytes.

Degree: 1989, University of Florida

URL: https://ufdc.ufl.edu/AA00006101

Subjects/Keywords: Amino acids; Diabetes; Gels; Incubation; Liver; Messenger RNA; Microinjections; Oocytes; Rats; RNA; Amino Acids ( mesh ); Biochemistry and Molecular Biology thesis Ph.D ( mesh ); Biological Transport ( mesh ); Oocytes ( mesh ); RNA, Messenger ( mesh ); Xenopus Laevis ( mesh )

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APA (6^th Edition):

Campa, Michael Joseph, 1. (1989). Endogenous amino acid transport and translation of rat liver mRNA in Xenopus laevis oocytes. (Thesis). University of Florida. Retrieved from https://ufdc.ufl.edu/AA00006101

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Campa, Michael Joseph, 1955-. “Endogenous amino acid transport and translation of rat liver mRNA in Xenopus laevis oocytes.” 1989. Thesis, University of Florida. Accessed March 07, 2021. https://ufdc.ufl.edu/AA00006101.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Campa, Michael Joseph, 1955-. “Endogenous amino acid transport and translation of rat liver mRNA in Xenopus laevis oocytes.” 1989. Web. 07 Mar 2021.

Vancouver:

Campa, Michael Joseph 1. Endogenous amino acid transport and translation of rat liver mRNA in Xenopus laevis oocytes. [Internet] [Thesis]. University of Florida; 1989. [cited 2021 Mar 07]. Available from: https://ufdc.ufl.edu/AA00006101.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Campa, Michael Joseph 1. Endogenous amino acid transport and translation of rat liver mRNA in Xenopus laevis oocytes. [Thesis]. University of Florida; 1989. Available from: https://ufdc.ufl.edu/AA00006101

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Florida

8. Hector, Ronald Earl, 1972-. Posttranscriptional regulation of gene expression by a nuclear polyadenylated RNA binding protein.

Degree: 2000, University of Florida

URL: https://ufdc.ufl.edu/AA00038398

Subjects/Keywords: Heterogeneous nuclear ribonucleoproteins; In vitro fertilization; Introns; Messenger RNA; Nucleotides; Polyadenylation; RNA; Small nucleolar RNA; Splicing; Yeasts; Department of Molecular Genetics and Microbiology thesis Ph.D ( mesh ); Gene Expression Regulation ( mesh ); Genetic Techniques ( mesh ); Nuclear Proteins ( mesh ); RNA Precursors ( mesh ); RNA, Messenger ( mesh ); RNA-Binding Proteins ( mesh ); Research ( mesh ); City of Gainesville ( local )

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APA (6^th Edition):

Hector, Ronald Earl, 1. (2000). Posttranscriptional regulation of gene expression by a nuclear polyadenylated RNA binding protein. (Thesis). University of Florida. Retrieved from https://ufdc.ufl.edu/AA00038398

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Hector, Ronald Earl, 1972-. “Posttranscriptional regulation of gene expression by a nuclear polyadenylated RNA binding protein.” 2000. Thesis, University of Florida. Accessed March 07, 2021. https://ufdc.ufl.edu/AA00038398.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Hector, Ronald Earl, 1972-. “Posttranscriptional regulation of gene expression by a nuclear polyadenylated RNA binding protein.” 2000. Web. 07 Mar 2021.

Vancouver:

Hector, Ronald Earl 1. Posttranscriptional regulation of gene expression by a nuclear polyadenylated RNA binding protein. [Internet] [Thesis]. University of Florida; 2000. [cited 2021 Mar 07]. Available from: https://ufdc.ufl.edu/AA00038398.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Hector, Ronald Earl 1. Posttranscriptional regulation of gene expression by a nuclear polyadenylated RNA binding protein. [Thesis]. University of Florida; 2000. Available from: https://ufdc.ufl.edu/AA00038398

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Florida

9. Davis, Christopher Alan, 1971-. Manganese superoxide dismutase post-transcriptional regulation and cytoprotective potential.

Degree: 2001, University of Florida

URL: https://ufdc.ufl.edu/AA00067613

Subjects/Keywords: Research ( mesh ); Superoxide Dismutase ( mesh ); Gene Expression Regulation ( mesh ); Cytoprotection ( mesh ); RNA, Messenger ( mesh ); Binding Sites ( mesh ); Apoptosis ( mesh ); Cisplatin ( mesh ); Antioxidants ( mesh ); Mutagenesis, Site-Directed ( mesh ); Department of Biochemistry and Molecular Biology thesis Ph.D ( mesh )

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APA (6^th Edition):

Davis, Christopher Alan, 1. (2001). Manganese superoxide dismutase post-transcriptional regulation and cytoprotective potential. (Thesis). University of Florida. Retrieved from https://ufdc.ufl.edu/AA00067613

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Davis, Christopher Alan, 1971-. “Manganese superoxide dismutase post-transcriptional regulation and cytoprotective potential.” 2001. Thesis, University of Florida. Accessed March 07, 2021. https://ufdc.ufl.edu/AA00067613.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Davis, Christopher Alan, 1971-. “Manganese superoxide dismutase post-transcriptional regulation and cytoprotective potential.” 2001. Web. 07 Mar 2021.

Vancouver:

Davis, Christopher Alan 1. Manganese superoxide dismutase post-transcriptional regulation and cytoprotective potential. [Internet] [Thesis]. University of Florida; 2001. [cited 2021 Mar 07]. Available from: https://ufdc.ufl.edu/AA00067613.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Davis, Christopher Alan 1. Manganese superoxide dismutase post-transcriptional regulation and cytoprotective potential. [Thesis]. University of Florida; 2001. Available from: https://ufdc.ufl.edu/AA00067613

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Florida

10. Nykamp, Keith Robert, 1974-. Coordination of MRNA 3' end formation and nuclear export by a nuclear poly(A)-Binding protein.

Degree: 2003, University of Florida

URL: https://ufdc.ufl.edu/AA00025840

Subjects/Keywords: DNA; Exons; Heterogeneous nuclear ribonucleoproteins; In vitro fertilization; Messenger RNA; Polyadenylation; Proteins; RNA; Splicing; Yeasts; Department of Molecular Genetics and Microbiology thesis Ph.D ( mesh ); Heterogeneous-Nuclear Ribonucleoproteins – genetics ( mesh ); Polyadenylation – genetics ( mesh ); RNA Polymerase II – genetics ( mesh ); RNA, Messenger – genetics ( mesh ); RNA-Binding Proteins – genetics ( mesh ); Research ( mesh ); Yeasts ( mesh )

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APA (6^th Edition):

Nykamp, Keith Robert, 1. (2003). Coordination of MRNA 3' end formation and nuclear export by a nuclear poly(A)-Binding protein. (Thesis). University of Florida. Retrieved from https://ufdc.ufl.edu/AA00025840

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Nykamp, Keith Robert, 1974-. “Coordination of MRNA 3' end formation and nuclear export by a nuclear poly(A)-Binding protein.” 2003. Thesis, University of Florida. Accessed March 07, 2021. https://ufdc.ufl.edu/AA00025840.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Nykamp, Keith Robert, 1974-. “Coordination of MRNA 3' end formation and nuclear export by a nuclear poly(A)-Binding protein.” 2003. Web. 07 Mar 2021.

Vancouver:

Nykamp, Keith Robert 1. Coordination of MRNA 3' end formation and nuclear export by a nuclear poly(A)-Binding protein. [Internet] [Thesis]. University of Florida; 2003. [cited 2021 Mar 07]. Available from: https://ufdc.ufl.edu/AA00025840.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Nykamp, Keith Robert 1. Coordination of MRNA 3' end formation and nuclear export by a nuclear poly(A)-Binding protein. [Thesis]. University of Florida; 2003. Available from: https://ufdc.ufl.edu/AA00025840

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Minnesota

11. Nair, Asha. A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs.

Degree: PhD, Biomedical Informatics and Computational Biology, 2018, University of Minnesota

URL: http://hdl.handle.net/11299/199034

► High-throughput Next Generation RNA sequencing (RNA-Seq) technology is affluent with information about the transcriptome, which includes both protein-coding and multiple non-coding regions. In a diseased… (more)

▼ High-throughput Next Generation RNA sequencing (RNA-Seq) technology is affluent with information about the transcriptome, which includes both protein-coding and multiple non-coding regions. In a diseased state, complex interactions between these regions can go awry. Identification of such interactions is critical to translate the underlying biology of the transcriptome, especially for lethal diseases such as cancer. The field of bioinformatics is currently deficient in workflows that can analyze both coding and non-coding regions together efficiently, to identify disease-specific interactions. In this dissertation, I developed three coherent bioinformatics solutions that aim to address these shortcomings in RNA-Seq. First, a comprehensive workflow called MAPR-Seq was developed to analyze and report various features of protein-coding messenger RNAs. Second, a workflow for non-coding circular RNAs, called Circ-Seq, was developed to identify, quantify and annotate expressed circular RNAs. Third, an integration workflow called ReMIx was developed to identify microRNA response elements (MREs) and integrate them with the different types of RNAs (messenger RNAs, circular RNAs, and microRNAs). Collectively, the three workflows were applied to the largest cohort of breast cancer samples (n=885) from The Cancer Genome Atlas (TCGA). Based on the results obtained from these workflows, I present several key findings that are pertinent to breast cancer. I show that circular RNAs may be a marker for tumor proliferation in estrogen response positive (ER+) breast cancer subtype. I also show how triple negative (TN) breast cancer subtype-specific MRE signatures of messenger RNA – microRNA interactions can be obtained using RNA-Seq data, which has not been explored to date and thus, is a novel undertaking. In the end, my results highlight candidate messenger RNAs, circular RNAs and microRNAs that are found to be associated with MAPK and PI3K/AKT signaling cascades in TN breast cancer subtype. In general, the developed bioinformatics solutions can also be applied to RNA-Seq data of other cancer subtypes and diseases to identify unique messenger RNA – microRNA – circular RNA candidates that could be promising diagnostic targets towards improving treatment options for complex diseases.

Subjects/Keywords: circular RNA; integration; messenger RNA; micro RNA; MRE; RNA-Seq

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APA (6^th Edition):

Nair, A. (2018). A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs. (Doctoral Dissertation). University of Minnesota. Retrieved from http://hdl.handle.net/11299/199034

Chicago Manual of Style (16^th Edition):

Nair, Asha. “A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs.” 2018. Doctoral Dissertation, University of Minnesota. Accessed March 07, 2021. http://hdl.handle.net/11299/199034.

MLA Handbook (7^th Edition):

Nair, Asha. “A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs.” 2018. Web. 07 Mar 2021.

Vancouver:

Nair A. A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs. [Internet] [Doctoral dissertation]. University of Minnesota; 2018. [cited 2021 Mar 07]. Available from: http://hdl.handle.net/11299/199034.

Council of Science Editors:

Nair A. A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs. [Doctoral Dissertation]. University of Minnesota; 2018. Available from: http://hdl.handle.net/11299/199034

University of Florida

12. Eller, Mark Steven, 1954-. The isolation and characterization of a protein synthesis inhibitor from human placenta.

Degree: 1984, University of Florida

URL: https://ufdc.ufl.edu/AA00054617

Subjects/Keywords: Gels; In vitro fertilization; Incubation; Messenger RNA; Molecular weight; Polyribosomes; Protein synthesis; Reticulocytes; Ribosomes; RNA; Biochemistry and Molecular Biology thesis Ph.D ( mesh ); Placenta ( mesh ); RNA – biosynthesis ( mesh )

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APA (6^th Edition):

Eller, Mark Steven, 1. (1984). The isolation and characterization of a protein synthesis inhibitor from human placenta. (Thesis). University of Florida. Retrieved from https://ufdc.ufl.edu/AA00054617

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Eller, Mark Steven, 1954-. “The isolation and characterization of a protein synthesis inhibitor from human placenta.” 1984. Thesis, University of Florida. Accessed March 07, 2021. https://ufdc.ufl.edu/AA00054617.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Eller, Mark Steven, 1954-. “The isolation and characterization of a protein synthesis inhibitor from human placenta.” 1984. Web. 07 Mar 2021.

Vancouver:

Eller, Mark Steven 1. The isolation and characterization of a protein synthesis inhibitor from human placenta. [Internet] [Thesis]. University of Florida; 1984. [cited 2021 Mar 07]. Available from: https://ufdc.ufl.edu/AA00054617.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Eller, Mark Steven 1. The isolation and characterization of a protein synthesis inhibitor from human placenta. [Thesis]. University of Florida; 1984. Available from: https://ufdc.ufl.edu/AA00054617

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Florida

13. Whalen, Patrick. Analysis of the ribozyme mediated cleavage of the RNA associated with retinal disease.

Degree: 2000, University of Florida

URL: https://ufdc.ufl.edu/AA00054909

Subjects/Keywords: Diseases; Gene therapy; Genetic mutation; Introns; Magnesium; Messenger RNA; Nucleotides; Oligonucleotides; RNA; Transgenes; Department of Molecular Genetics and Microbiology thesis Ph.D ( mesh ); Night Blindness – genetics ( mesh ); Night Blindness – therapy ( mesh ); RNA, Catalytic ( mesh ); RNA, Messenger ( mesh ); Retinitis Pigmentosa – genetics ( mesh ); Retinitis Pigmentosa – therapy ( mesh )

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APA (6^th Edition):

Whalen, P. (2000). Analysis of the ribozyme mediated cleavage of the RNA associated with retinal disease. (Thesis). University of Florida. Retrieved from https://ufdc.ufl.edu/AA00054909

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Whalen, Patrick. “Analysis of the ribozyme mediated cleavage of the RNA associated with retinal disease.” 2000. Thesis, University of Florida. Accessed March 07, 2021. https://ufdc.ufl.edu/AA00054909.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Whalen, Patrick. “Analysis of the ribozyme mediated cleavage of the RNA associated with retinal disease.” 2000. Web. 07 Mar 2021.

Vancouver:

Whalen P. Analysis of the ribozyme mediated cleavage of the RNA associated with retinal disease. [Internet] [Thesis]. University of Florida; 2000. [cited 2021 Mar 07]. Available from: https://ufdc.ufl.edu/AA00054909.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Whalen P. Analysis of the ribozyme mediated cleavage of the RNA associated with retinal disease. [Thesis]. University of Florida; 2000. Available from: https://ufdc.ufl.edu/AA00054909

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Florida

14. Bowman, Mary Catherine, 1969-. Structural and functional characterization of the phosphoprotein subunit of the Sendai virus RNA-dependent RNA polymerase.

Degree: 1997, University of Florida

URL: https://ufdc.ufl.edu/AA00031500

Subjects/Keywords: Amino acids; In vitro fertilization; Messenger RNA; Nucleocapsid; Phosphorylation; Plasmids; Proteins; RNA; Sendai virus; Virology; Department of Molecular Genetics and Microbiology thesis Ph.D ( mesh ); Mutagenesis, Site-Directed ( mesh ); Phosphoproteins ( mesh ); Phosphorylation ( mesh ); RNA Replicase ( mesh ); RNA, Viral ( mesh ); Research ( mesh ); Respirovirus ( mesh ); Structure-Activity Relationship ( mesh ); Transcription, Genetic ( mesh ); City of Winter Park ( local )

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APA (6^th Edition):

Bowman, Mary Catherine, 1. (1997). Structural and functional characterization of the phosphoprotein subunit of the Sendai virus RNA-dependent RNA polymerase. (Thesis). University of Florida. Retrieved from https://ufdc.ufl.edu/AA00031500

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Bowman, Mary Catherine, 1969-. “Structural and functional characterization of the phosphoprotein subunit of the Sendai virus RNA-dependent RNA polymerase.” 1997. Thesis, University of Florida. Accessed March 07, 2021. https://ufdc.ufl.edu/AA00031500.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Bowman, Mary Catherine, 1969-. “Structural and functional characterization of the phosphoprotein subunit of the Sendai virus RNA-dependent RNA polymerase.” 1997. Web. 07 Mar 2021.

Vancouver:

Bowman, Mary Catherine 1. Structural and functional characterization of the phosphoprotein subunit of the Sendai virus RNA-dependent RNA polymerase. [Internet] [Thesis]. University of Florida; 1997. [cited 2021 Mar 07]. Available from: https://ufdc.ufl.edu/AA00031500.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Bowman, Mary Catherine 1. Structural and functional characterization of the phosphoprotein subunit of the Sendai virus RNA-dependent RNA polymerase. [Thesis]. University of Florida; 1997. Available from: https://ufdc.ufl.edu/AA00031500

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Florida

15. Krecic, Annette Marie, 1968-. Nuclear and cytoplasmic functions of a yeast heterogeneous nuclear ribonucleoprotein.

Degree: 1998, University of Florida

URL: https://ufdc.ufl.edu/AA00047751

Subjects/Keywords: Cytoplasm; Heterogeneous nuclear ribonucleoproteins; In vitro fertilization; Messenger RNA; Polyadenylation; Proteins; RNA; Signals; Splicing; Yeasts; Amino Acid Sequence ( mesh ); Base Sequence ( mesh ); Cell Nucleus ( mesh ); Cytoplasm ( mesh ); Department of Molecular Genetics and Microbiology thesis Ph.D ( mesh ); Endonucleases – physiology ( mesh ); Molecular Sequence Data ( mesh ); RNA Precursors ( mesh ); RNA Processing, Post-Transcriptional – physiology ( mesh ); RNA Splicing – physiology ( mesh ); RNA, Messenger ( mesh ); Research ( mesh ); Ribonucleoproteins – genetics ( mesh ); Ribonucleoproteins – physiology ( mesh )

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APA (6^th Edition):

Krecic, Annette Marie, 1. (1998). Nuclear and cytoplasmic functions of a yeast heterogeneous nuclear ribonucleoprotein. (Thesis). University of Florida. Retrieved from https://ufdc.ufl.edu/AA00047751

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Krecic, Annette Marie, 1968-. “Nuclear and cytoplasmic functions of a yeast heterogeneous nuclear ribonucleoprotein.” 1998. Thesis, University of Florida. Accessed March 07, 2021. https://ufdc.ufl.edu/AA00047751.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Krecic, Annette Marie, 1968-. “Nuclear and cytoplasmic functions of a yeast heterogeneous nuclear ribonucleoprotein.” 1998. Web. 07 Mar 2021.

Vancouver:

Krecic, Annette Marie 1. Nuclear and cytoplasmic functions of a yeast heterogeneous nuclear ribonucleoprotein. [Internet] [Thesis]. University of Florida; 1998. [cited 2021 Mar 07]. Available from: https://ufdc.ufl.edu/AA00047751.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Krecic, Annette Marie 1. Nuclear and cytoplasmic functions of a yeast heterogeneous nuclear ribonucleoprotein. [Thesis]. University of Florida; 1998. Available from: https://ufdc.ufl.edu/AA00047751

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Florida

16. Latner, Donald Ray. Characterization of the vaccinia virus J3 protein as a positive transcription elongation factor.

Degree: 2001, University of Florida

URL: https://ufdc.ufl.edu/AA00011180

Subjects/Keywords: Genes; Genetic mutation; In vitro fertilization; Infections; Messenger RNA; Nucleotides; Peptide elongation factors; RNA; Vaccinia virus; Viruses; Gene Expression ( mesh ); Gene Expression Regulation ( mesh ); Transcription Factors ( mesh ); Transcription, Genetic ( mesh ); Vaccinia virus ( mesh ); Viral Proteins ( mesh )

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APA (6^th Edition):

Latner, D. R. (2001). Characterization of the vaccinia virus J3 protein as a positive transcription elongation factor. (Thesis). University of Florida. Retrieved from https://ufdc.ufl.edu/AA00011180

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Latner, Donald Ray. “Characterization of the vaccinia virus J3 protein as a positive transcription elongation factor.” 2001. Thesis, University of Florida. Accessed March 07, 2021. https://ufdc.ufl.edu/AA00011180.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Latner, Donald Ray. “Characterization of the vaccinia virus J3 protein as a positive transcription elongation factor.” 2001. Web. 07 Mar 2021.

Vancouver:

Latner DR. Characterization of the vaccinia virus J3 protein as a positive transcription elongation factor. [Internet] [Thesis]. University of Florida; 2001. [cited 2021 Mar 07]. Available from: https://ufdc.ufl.edu/AA00011180.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Latner DR. Characterization of the vaccinia virus J3 protein as a positive transcription elongation factor. [Thesis]. University of Florida; 2001. Available from: https://ufdc.ufl.edu/AA00011180

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Florida

17. Ing, Nancy Hughes, 1957-. Ovine uterine milk proteins structure, biosynthesis, and function.

Degree: 1988, University of Florida

URL: https://ufdc.ufl.edu/AA00022379

Subjects/Keywords: Amino acids; Endometrium; Ewes; Messenger RNA; Pregnancy; Proteins; RNA; Secretion; Sheep; Uterus; Biochemistry and Molecular Biology thesis Ph.D ( mesh ); Milk Proteins ( mesh ); Sheep ( mesh )

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APA (6^th Edition):

Ing, Nancy Hughes, 1. (1988). Ovine uterine milk proteins structure, biosynthesis, and function. (Thesis). University of Florida. Retrieved from https://ufdc.ufl.edu/AA00022379

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Ing, Nancy Hughes, 1957-. “Ovine uterine milk proteins structure, biosynthesis, and function.” 1988. Thesis, University of Florida. Accessed March 07, 2021. https://ufdc.ufl.edu/AA00022379.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Ing, Nancy Hughes, 1957-. “Ovine uterine milk proteins structure, biosynthesis, and function.” 1988. Web. 07 Mar 2021.

Vancouver:

Ing, Nancy Hughes 1. Ovine uterine milk proteins structure, biosynthesis, and function. [Internet] [Thesis]. University of Florida; 1988. [cited 2021 Mar 07]. Available from: https://ufdc.ufl.edu/AA00022379.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Ing, Nancy Hughes 1. Ovine uterine milk proteins structure, biosynthesis, and function. [Thesis]. University of Florida; 1988. Available from: https://ufdc.ufl.edu/AA00022379

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Utah

18. Ball, Jennifer R. RNA recognition by the nucleoporin Nup153;.

Degree: PhD, Oncological Sciences;, 2004, University of Utah

URL: http://content.lib.utah.edu/cdm/singleitem/collection/etd1/id/11/rec/1150

► Trafficking events across the nuclear envelope (NE) require specific interactions between cargo-receptor complexes and proteins of the nuclear pore complex (NPC). Although great strides have… (more)

▼ Trafficking events across the nuclear envelope (NE) require specific interactions between cargo-receptor complexes and proteins of the nuclear pore complex (NPC). Although great strides have been made to elucidate protein and RNA transport pathways, many aspects of nuclear transport, particularly how cargo interacts with components of the NPC, remain undefined. In order to better understand the interactions that drive RNA export, I have focused on further defining the association between RNA cargo and the nucleoporin Nup153, a central regulator of nuclear transport. Overexpression of a C-terminal fragment of Nup153 in somatic cells inhibited poly(A)+ RNA export suggesting that Nup153 contributes to mRNA export. Further, perturbation of Nup153 function in Xenopus oocytes demonstrated Nup153 is important for mRNA, U snRNA and 5S rRNA export. Moreover, an RNA binding domain was mapped within the N-terminus of Nup 153 and was shown to bind RNA directly. The property of RNA association is conserved in Drosophila, Xenopus and human, underscoring the importance of this domain in higher eukaryotes. Although it is clear that Nup153 function is important for RNA export, exactly how this nuclear pore protein contributes to RNA export is unknown. One way to elucidate how Nup153 interfaces with RNA in the cell is to dissect the interactions mediated by this nucleoporin. Towards this end, the goal of this dissertation is to define the molecular targets of Nup153 in order to better understand the mechanisms by which Nup153, and the pore itself, functions. Initially, I found that the RNA binding domain (RBD) of Nup153 associates with cellular RNA and further characterization of this domain revealed that Nup153 preferentially associates with single-stranded RNA in a manner that distinctly mirrors properties that relay the identity of mRNA to the nuclear export machinery. I have also defined minimal length and base composition requirements for RNA association with Nup153. In collaboration with others, I have correlated Nup153-RNA association with functional RNA export in vivo. These collaborative studies indicate that direct contact between mRNA and Nup153 may occur cooperatively with protein contacts and that this interface between Nup153, mRNA and protein is critical to mRNA export and potentially concurrent mRNP remodeling and quality control.

Subjects/Keywords: Physiology; RNA Messenger

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APA (6^th Edition):

Ball, J. R. (2004). RNA recognition by the nucleoporin Nup153;. (Doctoral Dissertation). University of Utah. Retrieved from http://content.lib.utah.edu/cdm/singleitem/collection/etd1/id/11/rec/1150

Chicago Manual of Style (16^th Edition):

Ball, Jennifer R. “RNA recognition by the nucleoporin Nup153;.” 2004. Doctoral Dissertation, University of Utah. Accessed March 07, 2021. http://content.lib.utah.edu/cdm/singleitem/collection/etd1/id/11/rec/1150.

MLA Handbook (7^th Edition):

Ball, Jennifer R. “RNA recognition by the nucleoporin Nup153;.” 2004. Web. 07 Mar 2021.

Vancouver:

Ball JR. RNA recognition by the nucleoporin Nup153;. [Internet] [Doctoral dissertation]. University of Utah; 2004. [cited 2021 Mar 07]. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd1/id/11/rec/1150.

Council of Science Editors:

Ball JR. RNA recognition by the nucleoporin Nup153;. [Doctoral Dissertation]. University of Utah; 2004. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd1/id/11/rec/1150

University of Texas Southwestern Medical Center

19. Tsai, Pei-Ling. The Role of NS1-BP in Influenza Virus Replication.

Degree: 2012, University of Texas Southwestern Medical Center

URL: http://hdl.handle.net/2152.5/1100

► Influenza A viruses are negative-sense, segmented RNA viruses which cause about 500,000 deaths worldwide per year. Genomic studies have shown that the non-structural protein (NS1)… (more)

Subjects/Keywords: Nuclear Pore; Influenza A Virus; RNA, Messenger

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APA (6^th Edition):

Tsai, P. (2012). The Role of NS1-BP in Influenza Virus Replication. (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/1100

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Tsai, Pei-Ling. “The Role of NS1-BP in Influenza Virus Replication.” 2012. Thesis, University of Texas Southwestern Medical Center. Accessed March 07, 2021. http://hdl.handle.net/2152.5/1100.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Tsai, Pei-Ling. “The Role of NS1-BP in Influenza Virus Replication.” 2012. Web. 07 Mar 2021.

Vancouver:

Tsai P. The Role of NS1-BP in Influenza Virus Replication. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2012. [cited 2021 Mar 07]. Available from: http://hdl.handle.net/2152.5/1100.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Tsai P. The Role of NS1-BP in Influenza Virus Replication. [Thesis]. University of Texas Southwestern Medical Center; 2012. Available from: http://hdl.handle.net/2152.5/1100

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Texas Southwestern Medical Center

20. Tuckerman, Jason Robert. Heme-Based Oxygen Sensors of Commensal, Symbiotic, and Pathogenic Bacteria.

Degree: 2012, University of Texas Southwestern Medical Center

URL: http://hdl.handle.net/2152.5/1115

► Direct oxygen sensors are proteins that serve as "on-off switches" to cause reversible and adaptive changes in the activities of other proteins or genes, with… (more)

▼ Direct oxygen sensors are proteins that serve as "on-off switches" to cause reversible and adaptive changes in the activities of other proteins or genes, with great specificity in response to fluctuations in oxygen concentration. The heme-based oxygen sensors are a large class of direct oxygen sensors that feature direct binding of oxygen to a sensory heme-containing domain. This heme-binding region couples to a regulatory domain within the same polypeptide. The types of functionalities controlled by these oxygen-specific switches are diverse, and include the regulation of protein activities, gene expression, and second messenger elaboration. A primary focus of this work was the biochemical characterization of a pair of heme-based oxygen sensors involved in the control of the bacterial second messenger cyclic diguanylic acid (c-di-GMP) in Escherichia coli. We discovered that these enzymes, designated DosC and DosP, serve as a diguanylate cyclase and c-di-GMP phosphodiesterase pair that associate with components of the E. coli RNA degradosome in vivo. Importantly, one member of these degradosomes, PNPase, is a direct, high-affinity target of c-di-GMP. These findings imply that specialized oxygen-sensing degradosomes exist in E. coli. In these oxygen-sensing degradosomes cellular oxygen levels regulate PNPase processing of specific RNA transcripts via c-di-GMP. A secondary focus of this work was the characterization of a novel two-component system in M. tuberculosis involved in the non-replicating persistent phase of this bacterium in a typical TB infection. Here, the activities of two heme-containing histidine kinases, DosT and DevS, were discovered to be inhibited specifically by oxygen. As DosT and DevS are the primary regulators of the dormancy survival regulator (DosR/DevR) transcription factor, these results contributed a molecular explanation for the numerous observations linking oxygen and DevR to the dormancy phenotype of M. tuberculosis seen both in vitro and in vivo. Advisors/Committee Members: Gilles-Gonzalez, Marie-Alda.

Subjects/Keywords: Cyclic GMP; RNA; Second Messenger Systems

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APA (6^th Edition):

Tuckerman, J. R. (2012). Heme-Based Oxygen Sensors of Commensal, Symbiotic, and Pathogenic Bacteria. (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/1115

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Tuckerman, Jason Robert. “Heme-Based Oxygen Sensors of Commensal, Symbiotic, and Pathogenic Bacteria.” 2012. Thesis, University of Texas Southwestern Medical Center. Accessed March 07, 2021. http://hdl.handle.net/2152.5/1115.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Tuckerman, Jason Robert. “Heme-Based Oxygen Sensors of Commensal, Symbiotic, and Pathogenic Bacteria.” 2012. Web. 07 Mar 2021.

Vancouver:

Tuckerman JR. Heme-Based Oxygen Sensors of Commensal, Symbiotic, and Pathogenic Bacteria. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2012. [cited 2021 Mar 07]. Available from: http://hdl.handle.net/2152.5/1115.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Tuckerman JR. Heme-Based Oxygen Sensors of Commensal, Symbiotic, and Pathogenic Bacteria. [Thesis]. University of Texas Southwestern Medical Center; 2012. Available from: http://hdl.handle.net/2152.5/1115

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Columbia University

21. Martinez, Jose Carlos. Regulation of Neuronal mRNA Localization by Exclusion.

Degree: 2018, Columbia University

URL: https://doi.org/10.7916/D8F49125

► Intra-axonal protein synthesis is important for the proper wiring of the nervous system and can have restorative or pathogenic effects in response to nerve injury… (more)

Subjects/Keywords: Neurosciences; Cytology; Messenger RNA; Nervous system

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APA (6^th Edition):

Martinez, J. C. (2018). Regulation of Neuronal mRNA Localization by Exclusion. (Doctoral Dissertation). Columbia University. Retrieved from https://doi.org/10.7916/D8F49125

Chicago Manual of Style (16^th Edition):

Martinez, Jose Carlos. “Regulation of Neuronal mRNA Localization by Exclusion.” 2018. Doctoral Dissertation, Columbia University. Accessed March 07, 2021. https://doi.org/10.7916/D8F49125.

MLA Handbook (7^th Edition):

Martinez, Jose Carlos. “Regulation of Neuronal mRNA Localization by Exclusion.” 2018. Web. 07 Mar 2021.

Vancouver:

Martinez JC. Regulation of Neuronal mRNA Localization by Exclusion. [Internet] [Doctoral dissertation]. Columbia University; 2018. [cited 2021 Mar 07]. Available from: https://doi.org/10.7916/D8F49125.

Council of Science Editors:

Martinez JC. Regulation of Neuronal mRNA Localization by Exclusion. [Doctoral Dissertation]. Columbia University; 2018. Available from: https://doi.org/10.7916/D8F49125

22. Roalofs, Scott F. Gene activity analysis of Saccharomyces cerevisiae metallo-aminopeptidase gene deletion strains using DNA microarrays and verification with quantitative RT-PCR.

Degree: MS(M.S.), Applied Natural Science, 2018, Colorado State University – Pueblo

URL: http://hdl.handle.net/10217/187682

► Metallo-Aminopeptidase gene family 1 (M1AP) encode enzymes that cleave 1-3 amino acids from the N-terminus of a peptide. Previous studies involving M1AP inhibitors indicate that… (more)

Subjects/Keywords: Saccharomyces cerevisiae; Aminopeptidases; DNA microarrays; Messenger RNA

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APA (6^th Edition):

Roalofs, S. F. (2018). Gene activity analysis of Saccharomyces cerevisiae metallo-aminopeptidase gene deletion strains using DNA microarrays and verification with quantitative RT-PCR. (Masters Thesis). Colorado State University – Pueblo. Retrieved from http://hdl.handle.net/10217/187682

Chicago Manual of Style (16^th Edition):

Roalofs, Scott F. “Gene activity analysis of Saccharomyces cerevisiae metallo-aminopeptidase gene deletion strains using DNA microarrays and verification with quantitative RT-PCR.” 2018. Masters Thesis, Colorado State University – Pueblo. Accessed March 07, 2021. http://hdl.handle.net/10217/187682.

MLA Handbook (7^th Edition):

Roalofs, Scott F. “Gene activity analysis of Saccharomyces cerevisiae metallo-aminopeptidase gene deletion strains using DNA microarrays and verification with quantitative RT-PCR.” 2018. Web. 07 Mar 2021.

Vancouver:

Roalofs SF. Gene activity analysis of Saccharomyces cerevisiae metallo-aminopeptidase gene deletion strains using DNA microarrays and verification with quantitative RT-PCR. [Internet] [Masters thesis]. Colorado State University – Pueblo; 2018. [cited 2021 Mar 07]. Available from: http://hdl.handle.net/10217/187682.

Council of Science Editors:

Roalofs SF. Gene activity analysis of Saccharomyces cerevisiae metallo-aminopeptidase gene deletion strains using DNA microarrays and verification with quantitative RT-PCR. [Masters Thesis]. Colorado State University – Pueblo; 2018. Available from: http://hdl.handle.net/10217/187682

Hong Kong University of Science and Technology

23. Lam, Sheung Wai LIFS. Elucidating the role of Pabpn1 in mRNA alternative polyadenylation during satellite cell activation.

Degree: 2016, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-100400 ; https://doi.org/10.14711/thesis-b1626258 ; http://repository.ust.hk/ir/bitstream/1783.1-100400/1/th_redirect.html

► Satellite cells are muscle stem cells that are primarily quiescent in resting muscle. Upon injury, satellite cells will activate, proliferate, and differentiate to repair the… (more)

Subjects/Keywords: Satellite cells ; Messenger RNA ; Gene expression

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APA (6^th Edition):

Lam, S. W. L. (2016). Elucidating the role of Pabpn1 in mRNA alternative polyadenylation during satellite cell activation. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-100400 ; https://doi.org/10.14711/thesis-b1626258 ; http://repository.ust.hk/ir/bitstream/1783.1-100400/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Lam, Sheung Wai LIFS. “Elucidating the role of Pabpn1 in mRNA alternative polyadenylation during satellite cell activation.” 2016. Thesis, Hong Kong University of Science and Technology. Accessed March 07, 2021. http://repository.ust.hk/ir/Record/1783.1-100400 ; https://doi.org/10.14711/thesis-b1626258 ; http://repository.ust.hk/ir/bitstream/1783.1-100400/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Lam, Sheung Wai LIFS. “Elucidating the role of Pabpn1 in mRNA alternative polyadenylation during satellite cell activation.” 2016. Web. 07 Mar 2021.

Vancouver:

Lam SWL. Elucidating the role of Pabpn1 in mRNA alternative polyadenylation during satellite cell activation. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2016. [cited 2021 Mar 07]. Available from: http://repository.ust.hk/ir/Record/1783.1-100400 ; https://doi.org/10.14711/thesis-b1626258 ; http://repository.ust.hk/ir/bitstream/1783.1-100400/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Lam SWL. Elucidating the role of Pabpn1 in mRNA alternative polyadenylation during satellite cell activation. [Thesis]. Hong Kong University of Science and Technology; 2016. Available from: http://repository.ust.hk/ir/Record/1783.1-100400 ; https://doi.org/10.14711/thesis-b1626258 ; http://repository.ust.hk/ir/bitstream/1783.1-100400/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Hong Kong University of Science and Technology

24. Wong, Julie Hiu Tung. Defining the role of ncbp-1 and ncbp-2 to regulate sensory ray identity in C. elegans.

Degree: 2012, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-7527 ; https://doi.org/10.14711/thesis-b1176678 ; http://repository.ust.hk/ir/bitstream/1783.1-7527/1/th_redirect.html

► Gene modulations in eukaryotes are very important for guiding the differentiation of cell types that are specialized to serve a particular function. Pre-messenger ribonucleic acid… (more)

Subjects/Keywords: Caenorhabditis elegans – Genetics ; Messenger RNA ; Protein binding

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APA (6^th Edition):

Wong, J. H. T. (2012). Defining the role of ncbp-1 and ncbp-2 to regulate sensory ray identity in C. elegans. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-7527 ; https://doi.org/10.14711/thesis-b1176678 ; http://repository.ust.hk/ir/bitstream/1783.1-7527/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Wong, Julie Hiu Tung. “Defining the role of ncbp-1 and ncbp-2 to regulate sensory ray identity in C. elegans.” 2012. Thesis, Hong Kong University of Science and Technology. Accessed March 07, 2021. http://repository.ust.hk/ir/Record/1783.1-7527 ; https://doi.org/10.14711/thesis-b1176678 ; http://repository.ust.hk/ir/bitstream/1783.1-7527/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Wong, Julie Hiu Tung. “Defining the role of ncbp-1 and ncbp-2 to regulate sensory ray identity in C. elegans.” 2012. Web. 07 Mar 2021.

Vancouver:

Wong JHT. Defining the role of ncbp-1 and ncbp-2 to regulate sensory ray identity in C. elegans. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2012. [cited 2021 Mar 07]. Available from: http://repository.ust.hk/ir/Record/1783.1-7527 ; https://doi.org/10.14711/thesis-b1176678 ; http://repository.ust.hk/ir/bitstream/1783.1-7527/1/th_redirect.html.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Wong JHT. Defining the role of ncbp-1 and ncbp-2 to regulate sensory ray identity in C. elegans. [Thesis]. Hong Kong University of Science and Technology; 2012. Available from: http://repository.ust.hk/ir/Record/1783.1-7527 ; https://doi.org/10.14711/thesis-b1176678 ; http://repository.ust.hk/ir/bitstream/1783.1-7527/1/th_redirect.html

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

New Jersey Institute of Technology

25. Nambiar, Ram Mohan. PolyA DB3: a database cataloging polyadenation sites(pas) across different species and their conservation.

Degree: MSin Bioinformatics - (M.S.), Computer Science, 2018, New Jersey Institute of Technology

URL: https://digitalcommons.njit.edu/theses/1636

► Polyadenation is an important process occurring in the messenger RNA that involves cleavage of 3 end nascent mRNAs and addition of poly(A) tails. For… (more)

Subjects/Keywords: Polyadenation; Messenger RNA; Bioinformatics; Computer Sciences

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APA (6^th Edition):

Nambiar, R. M. (2018). PolyA DB3: a database cataloging polyadenation sites(pas) across different species and their conservation. (Thesis). New Jersey Institute of Technology. Retrieved from https://digitalcommons.njit.edu/theses/1636

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Nambiar, Ram Mohan. “PolyA DB3: a database cataloging polyadenation sites(pas) across different species and their conservation.” 2018. Thesis, New Jersey Institute of Technology. Accessed March 07, 2021. https://digitalcommons.njit.edu/theses/1636.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Nambiar, Ram Mohan. “PolyA DB3: a database cataloging polyadenation sites(pas) across different species and their conservation.” 2018. Web. 07 Mar 2021.

Vancouver:

Nambiar RM. PolyA DB3: a database cataloging polyadenation sites(pas) across different species and their conservation. [Internet] [Thesis]. New Jersey Institute of Technology; 2018. [cited 2021 Mar 07]. Available from: https://digitalcommons.njit.edu/theses/1636.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Nambiar RM. PolyA DB3: a database cataloging polyadenation sites(pas) across different species and their conservation. [Thesis]. New Jersey Institute of Technology; 2018. Available from: https://digitalcommons.njit.edu/theses/1636

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Hong Kong

26. Wong, Po-yu. The 3'-untranslated region of CHOP mRNA encodes information that determines the expression level of the CHOP gene.

Degree: 2015, University of Hong Kong

URL: http://hdl.handle.net/10722/223569

► CHOP is a stress-inducible protein that acts as a transcription co-regulatory factor for genes that are involved in cellular responses to stress. Previous studies demonstrated… (more)

▼ CHOP is a stress-inducible protein that acts as a transcription co-regulatory factor for genes that are involved in cellular responses to stress. Previous studies demonstrated that the activation of promoter activity of the CHOP gene is a major mechanism underlying the increase in the mRNA level of the CHOP gene in stressed cells. It is however not certain if the cellular mRNA degradation mechanism for CHOP mRNA might also be stress-sensitive so that together with stress-stimulated transcription a highly precise control of CHOP mRNA level can be achieved. To examine such a possibility, a series of CHOP-expressing plasmids were constructed and used to express the full length CHOP mRNA with or without deletion mutations in its 3’untranslated region in cultured cells. Realtime PCR quantitation demonstrated that the level of the expressed full length CHOP mRNA was the same in unstressed and stressed cells. Deletion mutations of the 3UTR of CHOP mRNA resulted in changes of CHOP-mRNA levels relative to the wild type mRNA but otherwise such changes were not affected by cellular stress. To ascertain if deletion mutations of the 3’UTR of CHOP mRNA alone were sufficient to cause changes in mRNA levels without requiring the participation of the rest of the CHOP mRNA sequence, another series of expression plasmids were constructed that will express EGFP mRNA having its original 3’UTR replaced with either the 3’UTR of CHOP mRNA, or 3’UTR of CHOP mRNA with deletions mutations the same as those of the pCHOP series of plasmids. Analysis of real-time PCR data obtained for the quantitation of mRNA levels expressed from the E3 series of plasmids showed the same changes of the expressed mRNA levels caused by the deletion mutations in the 3’UTR. The changes in mRNA levels were again independent of cellular stress. To examine if the change in mRNA levels would result in proportionate changes of translation, the abundance of the reporter protein (GFP) expressed from plasmids of the E3-series was quantitated directly by Western blot and indirectly by measurement of FITC fluorescence by FACS analysis. The decrease in mRNA expression due to the deletion of the first 30 ribonucleotides in the 3’UTR CHOP is always met with more of less proportionate decrease in the reporter protein expressed from this mutant mRNA. However, the change in mRNA level expressed from other pCHOP and E3 deletion mutants may not always cause a corresponding change in level of translational product. Results of this study suggest that unlike transcriptional synthesis of CHOP mRNA that is tightly stress-regulated, the degradation mechanism of CHOP mRNA is stress-insensitive and it may only be passively involved in preventing excessive synthesis of the CHOP mRNA. The degradation of the CHOP is closely related to the nucleotide sequence of its 3’UTR. Additional function of the nucleotide sequence of the 3’UTR of CHOP mRNA is also suggested by results of the present study.

Subjects/Keywords: Messenger RNA; Cytogenetics

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APA (6^th Edition):

Wong, P. (2015). The 3'-untranslated region of CHOP mRNA encodes information that determines the expression level of the CHOP gene. (Thesis). University of Hong Kong. Retrieved from http://hdl.handle.net/10722/223569

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Wong, Po-yu. “The 3'-untranslated region of CHOP mRNA encodes information that determines the expression level of the CHOP gene.” 2015. Thesis, University of Hong Kong. Accessed March 07, 2021. http://hdl.handle.net/10722/223569.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Wong, Po-yu. “The 3'-untranslated region of CHOP mRNA encodes information that determines the expression level of the CHOP gene.” 2015. Web. 07 Mar 2021.

Vancouver:

Wong P. The 3'-untranslated region of CHOP mRNA encodes information that determines the expression level of the CHOP gene. [Internet] [Thesis]. University of Hong Kong; 2015. [cited 2021 Mar 07]. Available from: http://hdl.handle.net/10722/223569.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Wong P. The 3'-untranslated region of CHOP mRNA encodes information that determines the expression level of the CHOP gene. [Thesis]. University of Hong Kong; 2015. Available from: http://hdl.handle.net/10722/223569

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Texas – Austin

27. Zicker, Alicia A. Distinct roles for the 5' and 3' untranslated regions in the degradation and stability of chloroplast tufA mRNA.

Degree: PhD, Ecology, Evolution, and Behavior, 2005, University of Texas – Austin

URL: http://hdl.handle.net/2152/1765

► The tufA gene encodes the chloroplast elongation factor Tu and is found in the chloroplast genome in Chlamydomonas reinhardtii, whereas it is in the nucleus… (more)

▼ The tufA gene encodes the chloroplast elongation factor Tu and is found in the chloroplast genome in Chlamydomonas reinhardtii, whereas it is in the nucleus in land plants. When C. reinhardtii is treated with chloramphenicol (CAP), an inhibitor of ribosome elongation, the stability of the 1.7-kb tufA mRNA is increased, and a RNA of ~1.5 kb over-accumulates. When CAP and the transcription inhibitor rifampicin are added together, tufA mRNA can be chased into the 1.5-kb RNA (which is subsequently degraded), suggesting that it is an intermediate in the degradation pathway. Mapping of the 5' and 3' ends of the 1.5-kb RNA showed that it is truncated at the 5' end, and is missing 177-181 nucleotides; there was no evidence of truncation at the 3' end. The 5' end of this intermediate lies 76-80 nucleotides upstream of the tufA start codon, and within a vii small ORF that has predicted secondary structure. Interestingly, the degradation intermediate did not over-accumulate in a chloroplast ribosome-deficient mutant, suggesting that its stabilization requires elongation-arrested ribosomes. Finally, evidence was obtained that the intermediate accumulates in the absence of CAP, especially in older cultures. These results indicate that a major pathway for degradation of tufA mRNA in vivo begins at the 5' end of the RNA, probably with an endonucleolytic cleavage, but 5' to 3' exonuclease activity cannot be ruled out. To determine whether the 5' or 3' UTR of tufA is destabilizing, the corresponding regions of an atpA-aadA-rbcL gene (which gives high mRNA levels) were replaced with one or both tufA UTRs, and transformed into the chloroplast. Northern blot analysis of the transformants indicated, quite surprisingly, that the 3' UTR of tufA is strongly destabilizing. The results suggest that the UTRs of tufA have distinct, but also interacting roles in mediating decay of tufA mRNA. To determine if the 3' UTR of tufA can regulate protein expression, constructs were made using Renilla luciferase as reporter, and transformed into chloroplasts. Luminescence measurements of the transformants indicated that the 3' UTR of tufA can regulate expression at the protein level, but no more so than the 5' UTR Advisors/Committee Members: Herrin, David L. (advisor).

Subjects/Keywords: Chloroplasts; Messenger RNA

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Zicker, A. A. (2005). Distinct roles for the 5' and 3' untranslated regions in the degradation and stability of chloroplast tufA mRNA. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/1765

Chicago Manual of Style (16^th Edition):

Zicker, Alicia A. “Distinct roles for the 5' and 3' untranslated regions in the degradation and stability of chloroplast tufA mRNA.” 2005. Doctoral Dissertation, University of Texas – Austin. Accessed March 07, 2021. http://hdl.handle.net/2152/1765.

MLA Handbook (7^th Edition):

Zicker, Alicia A. “Distinct roles for the 5' and 3' untranslated regions in the degradation and stability of chloroplast tufA mRNA.” 2005. Web. 07 Mar 2021.

Vancouver:

Zicker AA. Distinct roles for the 5' and 3' untranslated regions in the degradation and stability of chloroplast tufA mRNA. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2005. [cited 2021 Mar 07]. Available from: http://hdl.handle.net/2152/1765.

Council of Science Editors:

Zicker AA. Distinct roles for the 5' and 3' untranslated regions in the degradation and stability of chloroplast tufA mRNA. [Doctoral Dissertation]. University of Texas – Austin; 2005. Available from: http://hdl.handle.net/2152/1765

Columbia University

28. Hamilton, Keith. Structural and Biochemical Studies of the Human pre-mRNA 3’-end Processing Complex.

Degree: 2021, Columbia University

URL: https://doi.org/10.7916/d8-6xaw-xv26

► Most eukaryotic pre-mRNAs undergo 3′-end cleavage and polyadenylation prior to their export from the nucleus. A large number of proteins in several complexes participate in… (more)

▼ Most eukaryotic pre-mRNAs undergo 3′-end cleavage and polyadenylation prior to their export from the nucleus. A large number of proteins in several complexes participate in this 3′-end processing, including cleavage and polyadenylation specificity factor (CPSF) in mammals. The CPSF can be further divided into two sub-complexes: mPSF (mammalian polyadenylation specificity factor) which recognizes the AAUAAA polyadenylation signal (PAS) in the pre- mRNA, and mCF (mammalian cleavage factor) which cleaves the RNA. mPSF consists of CPSF160, CPSF30, WDR33, and hFip1. This thesis shows that AAUAAA PAS is recognized with ∼3 nM affinity by the CPSF160–WDR33–CPSF30 ternary complex, while the proteins alone or the binary complexes do not bind the PAS with high affinity. Furthermore, it is shown that mutations of residues in CPSF30 that have van der Waals interactions with the bases of the PAS lead to a sharp reduction in the affinity. Finally, variations of the AAUAAA or removing the bases downstream also reduce the binding significantly. This thesis goes on to characterize the structure of the CPSF30—hFip1 complex, which was not observed in the previous EM structures of the mPSF. It was known that CPSF30 ZF4–ZF5 recruits the hFip1 subunit of CPSF, although the details of this interaction have not been characterized. Here we report the crystal structure of human CPSF30 ZF4–ZF5 in complex with residues 161–200 of hFip1 at 1.9 Å. Unexpectedly, the structure reveals one hFip1 molecule binding to each ZF4 and ZF5, with a conserved mode of interaction. Mutagenesis studies confirm that the CPSF30–hFip1 complex has 1:2 stoichiometry in vitro. Mutation of each binding site in CPSF30 still allows one copy of hFip1 to bind, while mutation of both sites abrogates binding. Our fluorescence polarization binding assays show that ZF4 has higher affinity for hFip1, with a Kd of 1.8 nM. We also demonstrate that two copies of the catalytic module of poly(A) polymerase (PAP) are recruited by the CPSF30–hFip1 complex in vitro, and both hFip1 binding sites in CPSF30 can support polyadenylation.

Subjects/Keywords: Biochemistry; Biophysics; Messenger RNA – Analysis; Mutagenesis

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Hamilton, K. (2021). Structural and Biochemical Studies of the Human pre-mRNA 3’-end Processing Complex. (Doctoral Dissertation). Columbia University. Retrieved from https://doi.org/10.7916/d8-6xaw-xv26

Chicago Manual of Style (16^th Edition):

Hamilton, Keith. “Structural and Biochemical Studies of the Human pre-mRNA 3’-end Processing Complex.” 2021. Doctoral Dissertation, Columbia University. Accessed March 07, 2021. https://doi.org/10.7916/d8-6xaw-xv26.

MLA Handbook (7^th Edition):

Hamilton, Keith. “Structural and Biochemical Studies of the Human pre-mRNA 3’-end Processing Complex.” 2021. Web. 07 Mar 2021.

Vancouver:

Hamilton K. Structural and Biochemical Studies of the Human pre-mRNA 3’-end Processing Complex. [Internet] [Doctoral dissertation]. Columbia University; 2021. [cited 2021 Mar 07]. Available from: https://doi.org/10.7916/d8-6xaw-xv26.

Council of Science Editors:

Hamilton K. Structural and Biochemical Studies of the Human pre-mRNA 3’-end Processing Complex. [Doctoral Dissertation]. Columbia University; 2021. Available from: https://doi.org/10.7916/d8-6xaw-xv26

29. Michaels, Mary Jessamine. Identification of body fluids by mRNA analysis with minion nanopore sequencing.

Degree: 2018, NC Docks

URL: http://libres.uncg.edu/ir/wcu/f/Michaels2018.pdf

► The identification of body fluids present on evidence items in a criminal investigation can be vital to understanding the nature of a crime, particularly in… (more)

▼ The identification of body fluids present on evidence items in a criminal investigation can be vital to understanding the nature of a crime, particularly in cases of sexual assault. Although crime labs can confirm the presence of body fluids like semen and blood on a piece of evidence using traditional serological techniques, they cannot confirm the presence of saliva or vaginal fluid or differentiate peripheral blood from menstrual blood. Due to the unique patterns of gene expression in different cell types, different body fluids contain distinct messenger RNA (mRNA) molecules, which can be analyzed to generate mRNA profiles for confirmatory identification of body fluids. High throughput sequencing methods present the opportunity to generate large amounts of data from low level forensic samples that is not achievable with more traditional techniques. In this study, the MinION sequencer by Oxford Nanopore Technologies (ONT), which is a small and affordable high throughput sequencer that generates data rapidly and in real time, was assessed to determine its ability to generate high quality data from forensic type samples. Semen, saliva, blood, vaginal fluid, and menstrual blood from eight different donors were collected on sterile swabs. Additionally, a tenfold dilution series was performed on semen, blood, and saliva samples from three donors each and decreasing volumes of semen were pipetted onto vaginal swabs from three sets of donors. DNA and RNA were co-extracted from half swabs. DNA fractions were taken forward for short tandem repeat (STR) analysis. For RNA fractions, cDNA was generated, and a multiplex PCR targeting two genes per body fluid was performed. Amplicons were sequenced on the MinION with the 1D Ligation Sequencing Kit by ONT. Full DNA profiles were obtained for all semen, blood, and menstrual blood samples, and most of the saliva and vaginal fluid samples. Profiles were obtained for diluted semen, saliva, and blood samples, and mixed profiles were obtained for the semen/vaginal fluid mixture samples. The multiplex PCR was highly specific for each body fluid, with little to no cross reactivity. The MinION was able to obtain at least 1,000X coverage of target genes and little to no off target reads, even for some diluted samples. Both vaginal fluid and semen genes were detected in mixture samples. Optimization of the MinION sequencing workflow to maximize read counts and minimize costs should be explored. Despite the high input requirements stated by ONT for sequencing, the MinION appears to be able to generate high quality data with lower DNA/RNA input.

Subjects/Keywords: Body fluids – Analysis; Messenger RNA – Analysis; Messenger RNA – Biotechnology; DNA fingerprinting; Forensic genetics – Technique

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APA (6^th Edition):

Michaels, M. J. (2018). Identification of body fluids by mRNA analysis with minion nanopore sequencing. (Thesis). NC Docks. Retrieved from http://libres.uncg.edu/ir/wcu/f/Michaels2018.pdf

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Michaels, Mary Jessamine. “Identification of body fluids by mRNA analysis with minion nanopore sequencing.” 2018. Thesis, NC Docks. Accessed March 07, 2021. http://libres.uncg.edu/ir/wcu/f/Michaels2018.pdf.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Michaels, Mary Jessamine. “Identification of body fluids by mRNA analysis with minion nanopore sequencing.” 2018. Web. 07 Mar 2021.

Vancouver:

Michaels MJ. Identification of body fluids by mRNA analysis with minion nanopore sequencing. [Internet] [Thesis]. NC Docks; 2018. [cited 2021 Mar 07]. Available from: http://libres.uncg.edu/ir/wcu/f/Michaels2018.pdf.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Michaels MJ. Identification of body fluids by mRNA analysis with minion nanopore sequencing. [Thesis]. NC Docks; 2018. Available from: http://libres.uncg.edu/ir/wcu/f/Michaels2018.pdf

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Florida

30. Pietromonaco, Salvatore F., 1954-. The evolution and biosynthesis of the proteins of animal mitochondrial ribosomes.

Degree: 1986, University of Florida

URL: https://ufdc.ufl.edu/AA00053674

Subjects/Keywords: Amino acids; Antibodies; Cattle; Complementary DNA; Gels; Messenger RNA; Mitochondria; Rats; Ribosomes; RNA; Biochemistry and Molecular Biology thesis Ph.D ( mesh ); Mitochondria ( mesh ); RNA, Ribosomal ( mesh ); Ribosomal Proteins – biosynthesis ( mesh )

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APA (6^th Edition):

Pietromonaco, Salvatore F., 1. (1986). The evolution and biosynthesis of the proteins of animal mitochondrial ribosomes. (Thesis). University of Florida. Retrieved from https://ufdc.ufl.edu/AA00053674

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Pietromonaco, Salvatore F., 1954-. “The evolution and biosynthesis of the proteins of animal mitochondrial ribosomes.” 1986. Thesis, University of Florida. Accessed March 07, 2021. https://ufdc.ufl.edu/AA00053674.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Pietromonaco, Salvatore F., 1954-. “The evolution and biosynthesis of the proteins of animal mitochondrial ribosomes.” 1986. Web. 07 Mar 2021.

Vancouver:

Pietromonaco, Salvatore F. 1. The evolution and biosynthesis of the proteins of animal mitochondrial ribosomes. [Internet] [Thesis]. University of Florida; 1986. [cited 2021 Mar 07]. Available from: https://ufdc.ufl.edu/AA00053674.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Pietromonaco, Salvatore F. 1. The evolution and biosynthesis of the proteins of animal mitochondrial ribosomes. [Thesis]. University of Florida; 1986. Available from: https://ufdc.ufl.edu/AA00053674

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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Open Access Theses and Dissertations