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Articles 1 - 7 of 7
Full-Text Articles in Molecular Biology
Identification Of Novel Δnp63Α-Regulated Mirnas Using An Optimized Small Rna-Seq Analysis Pipeline, Suraj Sakaram, Michael P. Craig, Natasha T. Hill, Amjad Aljiagthmi, Christian Garrido, Oleg Paliy, Michael Bottomley, Michael L. Raymer, Madhavi Kadakia
Identification Of Novel Δnp63Α-Regulated Mirnas Using An Optimized Small Rna-Seq Analysis Pipeline, Suraj Sakaram, Michael P. Craig, Natasha T. Hill, Amjad Aljiagthmi, Christian Garrido, Oleg Paliy, Michael Bottomley, Michael L. Raymer, Madhavi Kadakia
Biochemistry and Molecular Biology Faculty Publications
Advances in high-throughput sequencing have enabled profiling of microRNAs (miRNAs), however, a consensus pipeline for sequencing of small RNAs has not been established. We built and optimized an analysis pipeline using Partek Flow, circumventing the need for analyzing data via scripting languages. Our analysis assessed the effect of alignment reference, normalization method, and statistical model choice on biological data. The pipeline was evaluated using sequencing data from HaCaT cells transfected with either a non-silencing control or siRNA against ΔNp63α, a p53 family member protein which is highly expressed in non-melanoma skin cancer and shown to regulate a number of miRNAs. …
Microrna Involvement In The Onset And Progression Of Barrett’S Esophagus: A Systematic Review, Reilly J. Clark, Michael P. Craig, Sangeeta Agrawal, Madhavi Kadakia
Microrna Involvement In The Onset And Progression Of Barrett’S Esophagus: A Systematic Review, Reilly J. Clark, Michael P. Craig, Sangeeta Agrawal, Madhavi Kadakia
Biochemistry and Molecular Biology Faculty Publications
Esophageal adenocarcinoma (EAC) is a highly aggressive malignancy that develops from Barrett's esophagus (BE), an intestinal metaplasia of the distal esophagus. microRNAs (miRNAs), short non-coding regulatory RNAs, are frequently dysregulated in BE and are thought to play key roles in the onset of BE and its progression to EAC. miRNAs thus have potential diagnostic and prognostic value and are increasingly being used as cancer biomarkers. This review summarizes the current literature related to miRNAs that are dysregulated in BE within the context of Hedgehog, Notch, MAPK, NF kappa-B, Wnt and epithelial-mesenchymal transition (EMT) signaling which are thought to drive BE …
Lipin1 Regulates Skeletal Muscle Differentiation Through The Pkc/Hdac5/Mef2c:Myod -Mediated Pathway, Abdulrahman M. Jama
Lipin1 Regulates Skeletal Muscle Differentiation Through The Pkc/Hdac5/Mef2c:Myod -Mediated Pathway, Abdulrahman M. Jama
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Our previous characterization of global lipin1-deficient (fld) mice demonstrated that lipin1 played a novel role in skeletal muscle (SM) regeneration. The clinical relevance of lipin1 has been observed in patients with lipin1 null mutations where they exhibited severe rhabdomyolysis with aggregated and dysfunctional mitochondria. Lipin1 is a key gene that plays an important role in lipid biosynthesis and metabolism. It has dual functions as it contains a phosphatase activity that converts phosphatidic acid (PA) to diacylglycerol (DAG), the penultimate step in triglycerides (TAG) biosynthesis as well as transcriptional co-activator function. In the cytosol and ER, lipin1 carries out its lipid …
A Novel Method To Analyze Dna Breaks And Repair In Human Cells, Caitlin Elizabeth Goodman
A Novel Method To Analyze Dna Breaks And Repair In Human Cells, Caitlin Elizabeth Goodman
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Microsatellites repeat sequences are prone to forming non-canonical DNA structures and mutations. These areas of the genome can undergo expansions and contractions and are responsible for a variety of inherited neurological and neuromuscular disorders. Hairpin structures formed by trinucleotide repeats can lead to replication fork stalling, and fork collapse causing DNA double strand breaks. Various mechanisms are involved in processing microsatellites including mismatch repair, base excision repair, and crossover junction endonuclease cleavage. These processes, which are supposed to protect the genome, could also be the culprits which are causing mutations. In order to test and study this hypothesis, the use …
Discovery Of Small Molecules Blocking Oncogenic K-Ras Activity, Sarah E. Kovar
Discovery Of Small Molecules Blocking Oncogenic K-Ras Activity, Sarah E. Kovar
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Ras proteins were the first human oncogenes discovered. Although Ras has been found to be the most frequently mutated oncogene, there are currently no anti-Ras-specific drugs available in the clinic. Ras is responsible for initiating cellular pathways that include proliferation, survival, and apoptosis. There are three ubiquitously expressed Ras isoforms in mammalian cells: H-, N-, and K-Ras. Interaction with the plasma membrane is required for Ras biological activity. When Ras interaction with the plasma membrane is blocked, Ras activity is inhibited. Two compounds (from Dr. Ketcha, WSU Chemistry Department) were tested and shown to dissociate K-Ras, but not H-Ras from …
Availability Of Fermentable Nutrients Affect Gut Microbiota Composition, Trupthi Mehta
Availability Of Fermentable Nutrients Affect Gut Microbiota Composition, Trupthi Mehta
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Recent studies have increasingly established the role of gut microbiota in human health and disease. Diseases such as inflammatory bowel disease, colon cancer, cardiovascular disease and many neurological disorders have been linked to specific gut microbiota composition and disturbances. There have also been attempts in recent years to modulate gut microbial composition with the use of prebiotics and probiotics to promote healthy gut and prevent diseases. This thesis investigates whether the availability of fermentable nutrients high in fiber and antioxidants such as found in green coffee, roasted coffee, and salami infused with various prebiotics altered the composition and abundance of …
Avicin Is A Potent Sphingomyelinase Inhibitor That Blocks K-Ras Plasma Membrane Interaction And Its Oncogenic Activity, Christian M. Garrido
Avicin Is A Potent Sphingomyelinase Inhibitor That Blocks K-Ras Plasma Membrane Interaction And Its Oncogenic Activity, Christian M. Garrido
Browse all Theses and Dissertations
Ras proteins are small GTPases that regulate cell growth, differentiation and apoptosis. There are three main isoforms: H-, N-, and K-Ras in mammalian cells, and they cycle between an active GTP- and inactive GDP-bound states. Constitutively active Ras mutations are found in ~15% of all human cancers. Of those, oncogenic K-Ras is found in ~98% of pancreatic, ~52% colorectal, and ~32% of lung cancers. In nearly 30 years since its discovery, there are no anti-K-Ras drugs currently available for clinical use. Since K-Ras must be localized to the plasma membrane (PM) for its full biological activity, targeting K-Ras PM interaction …