Texas Digital Library
UT Southwestern Medical Center Institutional Repository (University of Texas)Not a member yet
10274 research outputs found
Sort by
Commando
Get PDFSometimes, my brain seems to do its own thing; revealing thoughts or feelings that I would have preferred to keep to myself
The Roles of Codon Usage in Translation and Transcription
No full textCodon usage biases are found in all eukaryotic and prokaryotic genomes that can regulate gene expression. Although codon usage has been previously shown to regulate translation elongation speed in fungal systems, its effect in animal systems is not clear. In our first study, using a Drosophila cell-free translation system to directly compare the velocity of translation elongation, we demonstrated that optimal codons speed up translation elongation while non-optimal codons slow it down. In addition, codon usage regulates ribosome movement and stalling on mRNA during translation. Finally, we showed that codon usage affects protein structure and function both in vitro and in Drosophila cells, potentially by regulating co-translational protein folding process. This study indicates that the effects of codon usage on translation elongation speed is a conserved mechanism from fungi to animals and there is a codon usage "code" fine tuning translation elongation speed to achieve optimal co-translational folding.
In addition to the role of codon usage in translation, it has also been shown to play a role in regulating gene transcription of reporter genes and there is a global correlation between codon usage and mRNA levels. To further characterize the role of codon usage in gene transcription, we performed nuclear RNA-seq in Neurospora and found that there is a genome-wide strong correlation between gene codon usage bias and nuclear RNA levels, suggesting that codon usage has a global role in impacting transcription in a translation-independent manner. To uncover the underlying mechanism, we performed a genetic screening by performing RNA-seq in over 250 Neurospora single gene knockout strains and identified 18 mutants with significantly reduced correlation between codon usage and mRNA levels. In addition, the deletion of these 18 genes resulted in mRNA level changes in a codon usage-dependent manner. Interestingly, most of these identified genes, such as set-2, are predicted to play a role in regulating transcription or chromatin structures. Together, these results further established the role of synonymous codon sequences in regulating gene transcription and identified potential factors contributing to gene transcription level in a codon dependent manner
When a beautiful woman wakes up
Get PDFThis piece was written about a choice made at a crossroads, and the darker truth that might have continued if a different choice had been made. It examines the reality of perpetuating trauma, prior to a point an individual realizes the deserving of something more. This piece shows the secret darkness that might exist in any of us if we choose not to exalt our being to be something more beautiful
Medical therapies to improve CV and renal outcomes in patients with T2D and ASCVD: state of the art in 2022
Get PDFDetailed formal protocol with illustrations and extensive bibliography.A recording of the protocol presentation is available on UT Southwestern's Mediasite. Note: Access to the video is restricted to authorized UT Southwestern users only.UT Southwestern--Internal Medicin
Hypertrophic cardiomyopathy update: 2022
Get PDFDetailed formal protocol with illustrations and extensive bibliography.A recording of the protocol presentation is available on UT Southwestern's Mediasite. Note: Access to the video is restricted to authorized UT Southwestern users only.UT Southwestern--Internal Medicin
The Visit
No full textAmy Richards works in the Molecular Diagnostics lab, Infectious Disease section. She enjoys writing whether it's complete paragraphs in emails to her colleagues or one of over ten journals she simultaneously maintains. She is not allowed into an office supply store unsupervised.
About the work: In my normal life, I'm ridiculously verbose. Therefore a 10-word story was a challenge for me. The subject matter is really painful in this story, so I figured a quick snapshot would do nicely
Arthur
Get PDFAmy Richards works in the Molecular Diagnostics lab, Infectious Disease section. Creative endeavors in her personal life allow her to balance her logical, rational work life.
About the work: This is a work of non-fiction in that the events and people portrayed actually happened and actually exist, respectively. Creativity was then employed to give the illusion that Robert (my partner) & I on vacation could be entertaining
Variations in Mevalonate Pathway Flux in Human Cells with Familial Hypercholesterolemia
No full textThe general metadata -- e.g., title, author, abstract, subject headings, etc. -- is publicly available, but access to the submitted files is restricted to UT Southwestern campus access and/or authorized UT Southwestern users.BACKGROUND: HMG-CoA reductase (HMGCR) is a membrane protein of the endoplasmic reticulum (ER) that catalyzes the reduction of HMG-CoA to mevalonate, a rate-limiting step in the synthesis of cholesterol and nonsterol isoprenoids. Sterol and nonsterol isoprenoids exert stringent feedback control on HMGCR through multiple mechanisms. This ensures constant synthesis of essential nonsterol isoprenoids, while avoiding toxic overaccumulation of cholesterol. One regulator of HMGCR is UBIAD-1, a vitamin K2 biosynthetic enzyme. Individuals with familial hypercholesterolemia (FH) suffer from cholesterol excess due to the inability of cells to take up cholesterol from the environment, leading to a cholesterol depleted cellular state and an increase in cholesterol production.
OBJECTIVE: In this study, we examine the effect of sterol and nonsterol isoprenoid depletion via statins followed by mevalonate treatment on the expression of genes and proteins in the mevalonate pathway and localization of UBIAD-1 in human fibroblasts.
METHODS: Cells expressing FH mutations and control cells were grown on culture plates or coverslips and fed media containing FCS, or FCS plus compactin and 0.05 mM, 0.2 mM, 1 mM, 3 mM, or 10 mM mevalonate. After overnight feeding, cells were harvested for immunofluorescence visualization, and qRT-PCR and immunoblot analysis of genes and proteins related to cholesterol and nonsterol isoprenoid synthesis.
RESULTS: Immunoblot analysis indicates that FH cells generally express higher amounts of sterol biosynthetic enzymes but lower amounts of CoQ10 biosynthetic enzymes than control cells. qRT-PCR showed that genes of the CoQ10 pathway in FH cells are expressed to a significantly less extent than in control cells, and that sterol synthetic genes are relatively unaffected in FH cells but upregulated in control cells fed compactin and mevalonate. Immunofluorescence and quantitation of UBIAD-1 Golgi localization indicate that compactin causes UBIAD-1 to migrate to the ER in both cells, and that FH cells require a greater concentration of mevalonate following the addition of compactin to restore Golgi localization.
CONCLUSION: The FH phenotype causes a cellular deficiency of sterols, leading cells to upregulate mechanisms toward sterol synthesis at the expense of CoQ10 synthesis, which results in a relative CoQ10 deficiency in FH cells
Butyrate Sensing by Campylobacter jejuni Impacts Bacterial-Host Interactions
Get PDFThe intestinal microbial ecosystem aids the host in digestion and nutrition by breaking down goods and providing beneficial vitamins and metabolites, including short-chain fatty acids (SCFAs) and lactate. Due to the abundance and intestinal distribution of these metabolites, bacterial pathogens can use them as biogeographical cues to discriminate among different regions of the host intestines. Indeed, Campylobacter jejuni, a commensal bacterium of the lower intestinal tract of avian species and a leading cause of bacterial diarrheal disease in humans, recognizes intestinal niches that support growth by sensing molecular cues produced by the microbiota. How C. jejuni senses and responds to microbiota-generated SCFAs and organic acids is not understood. Herein, I identified and characterized the C. jejuni BumSR two-component signal transduction system (TCS) that specifically directs a response to butyrate.
Deletion of either C. jejuni bumS or bumR abolishes butyrate-modulated transcriptional changes in gene expression. Analysis of ΔbumS and ΔbumR mutants in a chick model of commensalism indicated that bumR is important for early colonization. This contrasts with a human volunteer infection study that demonstrated bumR is essential for infection of humans. Mutational analyses of genes within the BumSR regulon in the natural avian host revealed additional colonization factors including peb3, a putative glycoprotein adhesin/substrate binding protein, and Cjj0580, a putative d- and tri-carboxylate transporter.
Through multiple biochemical assays, I discovered that BumS lacks kinase activity in vitro but possesses specific phosphatase activity towards BumR. These activities are not directly influenced by butyrate, suggesting that other metabolites, perhaps resulting from butyrate catabolism, are the direct cues sensed by BumS to modulate butyrate-dependent responses. By site-directed mutagenesis, I identified residues in the conserved H box that are required for BumS phosphatase activity. Consistent with previous work, phospho-BumR exhibits enhanced binding of target promoters in electrophoretic mobility shift assays, indicating that phosphorylated BumR likely has higher affinity to bind DNA at target promoters in vivo to either enhance or repress gene expression. Overall, this highlights BumSR as a non-canonical and first-identified TCS that directs a response to butyrate to modulate colonization gene expression through a phosphatase-dependent mechanism
The Art of Viral Oncogenesis: Lessons from Human Papillomavirus and Polyomavirus Transformed Cancers
No full textThe general metadata -- e.g., title, author, abstract, subject headings, etc. -- is publicly available, but access to the submitted files is restricted to UT Southwestern campus access and/or authorized UT Southwestern users.Viruses account for about 15% of all human cancer. Understanding viral oncogenesis can substantially broaden our general knowledge on the molecular mechanisms of carcinogenesis. In this dissertation, I focused on two types of DNA oncoviruses, human papillomavirus (HPV) and polyomavirus (HPyV), and identified novel mechanisms by which these two types of viruses cause human cancers. In HPV transformed cancer cells, I identified a novel circular RNA species, circE7, that spans and encodes the HPV E7 oncoprotein. I later demonstrated that circE7 translated E7 protein accounts for a substantial proportion of the E7 protein in a HPV transformed cancer cell line, and whose absence significantly impacts cancer cell proliferation in vitro and in vivo. In Merkel Cell Polyomavirus (MCPyV) transformed MCC cancer cells, I identified the activation of non-canonical NF-κB pathway activation by the MCPyV small T (ST) oncoprotein. I further demonstrated that the ectopically activated non-canonical NF-κB pathway is required for cell growth in low serum. The inhibition of non-canonical NF-κB signaling by a small peptide inhibitor also resulted in impaired cell growth in vitro and in vivo due to ER stress mediated apoptosis, suggesting a novel therapeutic intervention strategy for viral positive MCC (VP-CC) patients