+publisher:"Rutgers University" +contributor:("Belden, William J")

Rutgers University

1. Yildirim, Evrim, 1981-. Studies aimed at understanding how phosphorylation and miRNAs contribute to the circadian clock mechanism in drosophila.

Degree: PhD, Biochemistry, 2014, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/45581/

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Circadian (≈24 hr) rhythms in physiology and behavior are driven by endogenous cellular clocks that can be synchronized (entrained) by environmental cues, most notably the… (more)

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Circadian (≈24 hr) rhythms in physiology and behavior are driven by endogenous cellular clocks that can be synchronized (entrained) by environmental cues, most notably the daily light-dark and temperature cycles. Circadian timing mechanisms in a wide variety of organisms are based on a small set of species-specific clock genes that participate in negative transcriptional feedback loops intertwined with post-transcriptional and post- translational regulatory schemes that ultimately drive cyclical gene expression. Phosphorylation is the most pervasive post-translational modification of clock proteins and is central to setting the pace of the clock. PERIOD (PER), the main repressor in animal clocks, is progressively phosphorylated during its life cycle, which has potent effects on its stability and nuclear localization. In this thesis I used D. melanogaster as an animal model system and identified a new role for PER phosphorylation in entraining to light-dark and temperature cycles. Prior work showed that the light-mediated degradation of TIMELESS (TIM), a key partner of PER, is critical for photic entrainment. My studies have significantly revised this model with the demonstration that the light-mediated degradation of TIM leads to an increase in the phosphorylation of two nearby sites on PER (S826/828), and that blocking phosphorylation at these sites causes altered entrainment, revealing a surprising new role for PER in circadian responses to environmental cues. In related work I contributed to studies that identified phosphorylation sites on the central circadian transcription factor termed CLOCK (CLK), and showed that these modifications are also involved in entrainment. Together, these studies reveal that phosphorylation of PER and CLK is not only critical for setting the pace of the clock but also its ability to interpret external time cues. In another study I found that the miRNA bantam (ban) regulates Clk through three target sites on its 3’ UTR. Flies harboring mutations in ban target sites on Clk show weaker circadian rhythms and less CLK protein staining specifically in the s-LNvs, the key circadian pacemaker cells. These findings show that ban imparts robustness to circadian rhythms by adjusting CLK levels in master pacemaker neurons, and suggest a non- conventional mode-of-operation for ban on Clk expression.

Advisors/Committee Members: GUNDERSON, SAMUEL I (chair), Edery, Isaac (co-chair), Padgett, Richard W (internal member), Belden, William J (outside member).

Subjects/Keywords: Circadian rhythms; Phosphorylation

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APA (6^th Edition):

Yildirim, Evrim, 1. (2014). Studies aimed at understanding how phosphorylation and miRNAs contribute to the circadian clock mechanism in drosophila. (Doctoral Dissertation). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/45581/

Chicago Manual of Style (16^th Edition):

Yildirim, Evrim, 1981-. “Studies aimed at understanding how phosphorylation and miRNAs contribute to the circadian clock mechanism in drosophila.” 2014. Doctoral Dissertation, Rutgers University. Accessed January 18, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/45581/.

MLA Handbook (7^th Edition):

Yildirim, Evrim, 1981-. “Studies aimed at understanding how phosphorylation and miRNAs contribute to the circadian clock mechanism in drosophila.” 2014. Web. 18 Jan 2021.

Vancouver:

Yildirim, Evrim 1. Studies aimed at understanding how phosphorylation and miRNAs contribute to the circadian clock mechanism in drosophila. [Internet] [Doctoral dissertation]. Rutgers University; 2014. [cited 2021 Jan 18]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/45581/.

Council of Science Editors:

Yildirim, Evrim 1. Studies aimed at understanding how phosphorylation and miRNAs contribute to the circadian clock mechanism in drosophila. [Doctoral Dissertation]. Rutgers University; 2014. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/45581/

Rutgers University

2. Skorupa, Jennifer A., 1990-. IGFBP-3 induced by ribotoxic stress is not secreted prior to nuclear localization in mammary epithelial cells.

Degree: MS, Endocrinology and Animal Biosciences, 2018, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/56124/

► Ribotoxic stressors such as anisomycin (ANS) and deoxynivalenol (DON) induce apoptosis in MAC-T cells. These agents also increase IGFBP-3 expression and knockdown of IGFBP-3 mitigates… (more)

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APA (6^th Edition):

Skorupa, Jennifer A., 1. (2018). IGFBP-3 induced by ribotoxic stress is not secreted prior to nuclear localization in mammary epithelial cells. (Masters Thesis). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/56124/

Chicago Manual of Style (16^th Edition):

Skorupa, Jennifer A., 1990-. “IGFBP-3 induced by ribotoxic stress is not secreted prior to nuclear localization in mammary epithelial cells.” 2018. Masters Thesis, Rutgers University. Accessed January 18, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/56124/.

MLA Handbook (7^th Edition):

Skorupa, Jennifer A., 1990-. “IGFBP-3 induced by ribotoxic stress is not secreted prior to nuclear localization in mammary epithelial cells.” 2018. Web. 18 Jan 2021.

Vancouver:

Skorupa, Jennifer A. 1. IGFBP-3 induced by ribotoxic stress is not secreted prior to nuclear localization in mammary epithelial cells. [Internet] [Masters thesis]. Rutgers University; 2018. [cited 2021 Jan 18]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/56124/.

Council of Science Editors:

Skorupa, Jennifer A. 1. IGFBP-3 induced by ribotoxic stress is not secreted prior to nuclear localization in mammary epithelial cells. [Masters Thesis]. Rutgers University; 2018. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/56124/

3. Bekdash, Rola Aldana, 1971-. Epigenetic effects of fetal alcohol exposure on hypothalamic proopiomelanocortin gene.

Degree: Neuroscience, 2012, Rutgers University

URL: http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000063984

Subjects/Keywords: Fetal alcohol syndrome; Fetus—Development; Gene expression

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APA (6^th Edition):

Bekdash, Rola Aldana, 1. (2012). Epigenetic effects of fetal alcohol exposure on hypothalamic proopiomelanocortin gene. (Thesis). Rutgers University. Retrieved from http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000063984

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):

Bekdash, Rola Aldana, 1971-. “Epigenetic effects of fetal alcohol exposure on hypothalamic proopiomelanocortin gene.” 2012. Thesis, Rutgers University. Accessed January 18, 2021. http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000063984.

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

MLA Handbook (7^th Edition):

Bekdash, Rola Aldana, 1971-. “Epigenetic effects of fetal alcohol exposure on hypothalamic proopiomelanocortin gene.” 2012. Web. 18 Jan 2021.

Vancouver:

Bekdash, Rola Aldana 1. Epigenetic effects of fetal alcohol exposure on hypothalamic proopiomelanocortin gene. [Internet] [Thesis]. Rutgers University; 2012. [cited 2021 Jan 18]. Available from: http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000063984.

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

Council of Science Editors:

Bekdash, Rola Aldana 1. Epigenetic effects of fetal alcohol exposure on hypothalamic proopiomelanocortin gene. [Thesis]. Rutgers University; 2012. Available from: http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000063984

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

4. Mashruwala, Ameya Ashutosh, 1983-. The influence of oxygen upon the lifestyle choices of Staphylococcus aureus.

Degree: PhD, Microbial Biology, 2017, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/53737/

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Biofilms are communities of microorganisms attached to a surface or each other. Biofilm associated cells are the etiologic agents of recurrent Staphylococcus aureus infections. Oxygen… (more)

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Biofilms are communities of microorganisms attached to a surface or each other. Biofilm associated cells are the etiologic agents of recurrent Staphylococcus aureus infections. Oxygen is utilized by S. aureus as a terminal electron acceptor (TEA). Infected human tissues are hypoxic or anoxic. S. aureus increases biofilm formation in response to hypoxia, but how this occurs is unknown. This thesis reports that oxygen influences biofilm formation in its capacity as a TEA for cellular respiration. Genetic, physiological, or chemical inhibition of respiratory processes elicited increased biofilm formation. Impaired respiration led to increased cell lysis via divergent regulation of two processes: increased expression of the AtlA murein hydrolase and decreased expression of the AtlA-inhibitory glycopolymers, WTA. The AltA-dependent release of cytosolic DNA contributed to increased biofilm formation. The fibronectin binding protein A, which is known to interact with AtlA, was also found to be involved in fermentative biofilm formation. Further, cell lysis and biofilm formation were governed by the SrrAB and the SaeRS two-component regulatory systems (TCRS). Genetic evidence suggests that SrrAB-dependent biofilm formation occurs in response to the accumulation of reduced menaquinone. SaeRS-dependent biofilm formation also occurred in response to changes in the respiratory status of the cell, via an as yet undefined signal molecule(s). Further, a high cellular titer of phosphorylated SaeR is required for biofilm formation. Epistasis analyses found that SaeRS and SrrAB influence biofilm formation independent of one another, in vitro. SrrAB and SaeRS governed host colonization in vivo, in the context of a mouse model of orthopedic implant-associated biofilm formation. Of these two TCRS, SrrAB is the dominant system driving biofilm formation in vivo. Biofilms impart protection from innate immunity as well as therapeutic agents. Data presented suggest that pre-formed biofilms, established by fermenting S. aureus, can be prompted to detach and disperse upon exposure to a TEA (oxygen or nitrate). Exposure to oxygen (reaeration) results in increased growth but decreased transcription of atlA and decreased release of DNA. Reaeration is also accompanied by increased transcription of sspA which encodes for a protease capable of cleaving AtlA. Biofilm dispersal was blocked in a strain that is incapable of respiration, suggesting changes in cellular respiratory status are being sensed to trigger dispersal. The transcription of atlA and sspA upon reaeration was modulated in a divergent manner by SrrAB. Data presented suggest that SrrAB achieves divergent regulation of atlA, in two separate growth conditions, via the small RNA, rsaE, as an intermediary. In summation, the results presented define the bases for how oxygen dictates the lifestyle choices of S. aureus. The studies also establish the mechanistic and regulatory bases underlying the formation of anaerobic and fermentative biofilms by S. aureus.

Advisors/Committee Members: Boyd, Jeffrey M (chair), Belden, William J (internal member), Bhattacharya, Debashish (internal member), Stock, Ann M (outside member).

Subjects/Keywords: Staphylococcus aureus infections; Biofilms

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

APA (6^th Edition):

Mashruwala, Ameya Ashutosh, 1. (2017). The influence of oxygen upon the lifestyle choices of Staphylococcus aureus. (Doctoral Dissertation). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/53737/

Chicago Manual of Style (16^th Edition):

Mashruwala, Ameya Ashutosh, 1983-. “The influence of oxygen upon the lifestyle choices of Staphylococcus aureus.” 2017. Doctoral Dissertation, Rutgers University. Accessed January 18, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/53737/.

MLA Handbook (7^th Edition):

Mashruwala, Ameya Ashutosh, 1983-. “The influence of oxygen upon the lifestyle choices of Staphylococcus aureus.” 2017. Web. 18 Jan 2021.

Vancouver:

Mashruwala, Ameya Ashutosh 1. The influence of oxygen upon the lifestyle choices of Staphylococcus aureus. [Internet] [Doctoral dissertation]. Rutgers University; 2017. [cited 2021 Jan 18]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/53737/.

Council of Science Editors:

Mashruwala, Ameya Ashutosh 1. The influence of oxygen upon the lifestyle choices of Staphylococcus aureus. [Doctoral Dissertation]. Rutgers University; 2017. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/53737/

Rutgers University

5. Datar, Ketaki Rajendra, 1994-. The effect of alcohol consumption on mammary epithelial cell composition and mammary tumorigenesis.

Degree: MS, Microbiology and Molecular Genetics, 2019, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/61726/

► Breast cancer is the most common cancer in women worldwide and in 2019 it is estimated that approximately 41,000 women will die from the disease.… (more)

▼ Breast cancer is the most common cancer in women worldwide and in 2019 it is estimated that approximately 41,000 women will die from the disease. There are a variety of factors that increase risk for breast cancer one of which is alcohol consumption. However, the mechanism that underlies this increased risk is unknown. The mammary gland is a dynamic organ composed of a multiple cell types including adipose cells, fibroblasts, immune cells, and epithelial cells. The epithelial cells can be categorized into luminal and basal epithelial cells, whose composition is maintained and controlled by a pool of mammary stem cells. Mammary stem cells are quiescent and long lived, and therefore have the potential to accumulate mutations and transform into breast cancer stem cells. Breast cancer stem cells have the potential to maintain a tumor and may not be irradiated by conventional therapies, leading to relapse. Therefore, understanding what regulates the overall mammary epithelial cell hierarchy is key to improving breast cancer treatments. The goal of this project was to determine whether alcohol consumption alters the mammary epithelial cell composition to favor a tumorigenic state, whether alcohol consumption affects tumor latency, and whether alcohol alters the mammary tumor epithelial cell composition. The MMTV-Wnt1 mouse model is a useful model for studying the role of mammary stem cells in breast cancer, as the tumors that develop in this model arise from a stem or stem-like cell, and downstream targets of the Wnt signaling cascade have been found to be upregulated in breast cancer. To investigate the effect of alcohol on mammary epithelial cell composition and tumorigenesis, 7- week old MMTV-Wnt1 female mice were given a 20% alcohol solution in place of drinking water sweetened with 0.2% saccharin. Control animals were given a 0.12% saccharin solution for the entire duration of the study. Animals were weighed once per week and were sacrificed after either 8 weeks to analyze the preneoplastic mammary gland or after the first tumor had reached 1.5cm in diameter. Animals in the alcohol group gained more weight compared to the controls, and this difference in weight gain was due to an increase in overall caloric intake due to alcohol consumption. Mammary epithelial cells were isolated and analyzed by flow cytometry and plated for mammosphere/tumorsphere assays. Mammary glands from the alcohol group exhibited an increase in the luminal progenitor population, but a decrease in mammosphere forming efficiency. Alcohol consumption decreased tumor latency in animals that presented with tumors by 43 weeks of age, however, alcohol consumption did not effect on the tumor epithelial cell composition nor the tumorsphere forming efficiency. Alcohol consumption decreased the expression of the epithelial-mesenchymal transition (EMT) factors Snail and Twist in the mammary gland mRNA, and the proliferation marker Ki67. It also decreased expression of Snail in mRNA from the mammary tumor. Alcohol did not affect estrogen… Advisors/Committee Members: Cohick, Wendie S (chair), Belden, William J (internal member), Suh, Nanjoo (internal member), School of Graduate Studies.

Subjects/Keywords: Mammary; Breast – Cancer; Alcohol – Physiological effect

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

APA (6^th Edition):

Datar, Ketaki Rajendra, 1. (2019). The effect of alcohol consumption on mammary epithelial cell composition and mammary tumorigenesis. (Masters Thesis). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/61726/

Chicago Manual of Style (16^th Edition):

Datar, Ketaki Rajendra, 1994-. “The effect of alcohol consumption on mammary epithelial cell composition and mammary tumorigenesis.” 2019. Masters Thesis, Rutgers University. Accessed January 18, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/61726/.

MLA Handbook (7^th Edition):

Datar, Ketaki Rajendra, 1994-. “The effect of alcohol consumption on mammary epithelial cell composition and mammary tumorigenesis.” 2019. Web. 18 Jan 2021.

Vancouver:

Datar, Ketaki Rajendra 1. The effect of alcohol consumption on mammary epithelial cell composition and mammary tumorigenesis. [Internet] [Masters thesis]. Rutgers University; 2019. [cited 2021 Jan 18]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/61726/.

Council of Science Editors:

Datar, Ketaki Rajendra 1. The effect of alcohol consumption on mammary epithelial cell composition and mammary tumorigenesis. [Masters Thesis]. Rutgers University; 2019. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/61726/

Rutgers University

6. Zhu, Qiaoqiao, 1991-. Crosstalk between long non-coding RNAs and circadian chromatin.

Degree: PhD, Circadian rhythms, 2020, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/64311/

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The circadian rhythm is governed by transcriptional negative feedback facilitated by oscillating histone modifications and chromatin remodeling. The circadian rhythm is entrained by external zeitgebers… (more)

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The circadian rhythm is governed by transcriptional negative feedback facilitated by oscillating histone modifications and chromatin remodeling. The circadian rhythm is entrained by external zeitgebers (light and temperature) and are conserved in Neurospora, Drosophila, zebrafish, and mammals. The clock gene frequency in Neurospora and Period2 in vertebrates have natural antisense transcripts (NATs) whose function is not understood. In this dissertation I examined the connection among the circadian clock, non-coding RNAs and heterochromatin formation on both on the genome-wide and locus-specific level using a multi-organism approach. I performed a genome-wide study, using RNA-seq and ChIP-seq to understand the role of H3 lysine 4 methyltransferase (KMT2/SET-1) and histone H3 lysine 9 methyltransferase (KMT1/DIM-5) in Neurospora to understand the role of 2 seemingly opposing modifications. Integrated analysis of RNA-seq and ChIP-seq showed crosstalk and redistributions between histone H3 lysine 4 tri-methylation (H3K4me3) and histone H3 lysine 9 tri-methylation (H3K9me3). I also examined how perturbing the expression of a diurnal lncRNA affected downstream heterochromatin formation at the telomeres. The core circadian clock controls rhythms in TERRA, a long noncoding RNA that originates from telomeres and my research shows alcohol disrupts the diurnal rhythm in TERRA and heterochromatin at the telomere, which in theory makes telomeres more susceptible to DNA damage. I also examined the Per2 NAT, Per2AS and found the diurnal rhythm in Per2AS is dependent on BMAL1. Using the ChIRP-MS, I identified Per2AS-interacting proteins. Specifically, I found hnRNP M interacts with Per2AS and hnRNP M is required to maintain the normal amplitude and period of Per2. Furthermore, I demonstrate that hnRNP M is necessary for H3K9me3 and H3K27me3 at Per2. These findings support a model where Per2AS may serve as scaffold for hnRNP M and other associated proteins that assist in heterochromatin formation at Per2. Collectively, this dissertation furthers our understanding of the circadian clock, non-coding RNAs, and circadian regulated facultative heterochromatin formation.

Advisors/Committee Members: Belden, William J. (chair), Anthony, Tracy G (internal member), Sarkar, Dipak (internal member), Lee, KiBum (outside member), School of Graduate Studies.

Subjects/Keywords: Ribonucleases; Endocrinology and Animal Biosciences

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

APA (6^th Edition):

Zhu, Qiaoqiao, 1. (2020). Crosstalk between long non-coding RNAs and circadian chromatin. (Doctoral Dissertation). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/64311/

Chicago Manual of Style (16^th Edition):

Zhu, Qiaoqiao, 1991-. “Crosstalk between long non-coding RNAs and circadian chromatin.” 2020. Doctoral Dissertation, Rutgers University. Accessed January 18, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/64311/.

MLA Handbook (7^th Edition):

Zhu, Qiaoqiao, 1991-. “Crosstalk between long non-coding RNAs and circadian chromatin.” 2020. Web. 18 Jan 2021.

Vancouver:

Zhu, Qiaoqiao 1. Crosstalk between long non-coding RNAs and circadian chromatin. [Internet] [Doctoral dissertation]. Rutgers University; 2020. [cited 2021 Jan 18]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/64311/.

Council of Science Editors:

Zhu, Qiaoqiao 1. Crosstalk between long non-coding RNAs and circadian chromatin. [Doctoral Dissertation]. Rutgers University; 2020. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/64311/

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