Broad and thematic remodeling of the surfaceome and glycoproteome on isogenic cells transformed with driving proliferative oncogenes.

The cell surface proteome, the surfaceome, is the interface for engaging the extracellular space in normal and cancer cells. Here we apply quantitative proteomics of N-linked glycoproteins to reveal how a collection of some 700 surface proteins is dramatically remodeled in an isogenic breast epithelial cell line stably expressing any of six of the most prominent proliferative oncogenes, including the receptor tyrosine kinases, EGFR and HER2, and downstream signaling partners such as KRAS, BRAF, MEK, and AKT. We find that each oncogene has somewhat different surfaceomes, but the functions of these proteins are harmonized by common biological themes including up-regulation of nutrient transporters, down-regulation of adhesion molecules and tumor suppressing phosphatases, and alteration in immune modulators. Addition of a potent MEK inhibitor that blocks MAPK signaling brings each oncogene-induced surfaceome back to a common state reflecting the strong dependence of the oncogene on the MAPK pathway to propagate signaling. Cell surface protein capture is mediated by covalent tagging of surface glycans, yet current methods do not afford sequencing of intact glycopeptides. Thus, we complement the surfaceome data with whole cell glycoproteomics enabled by a recently developed technique called activated ion electron transfer dissociation (AI-ETD). We found massive oncogene-induced changes to the glycoproteome and differential increases in complex hybrid glycans, especially for KRAS and HER2 oncogenes. Overall, these studies provide a broad systems-level view of how specific driver oncogenes remodel the surfaceome and the glycoproteome in a cell autologous fashion, and suggest possible surface targets, and combinations thereof, for drug and biomarker discovery

Doctor of Philosophy

dissertationMagnetic Resonance guided High Intensity Focused Ultrasound (MRgHIFU) treatments are a promising modality for cancer treatments in which a focused beam of ultrasound energy is used to kill tumor tissue. However, obstacles still exist to its widespread clinical implementation, including long treatment times. This research demonstrates reductions in treatment times through intelligent selection of the usercontrollable parameters, including: the focal zone treatment path, focal zone size, focal zone spacing, and whether to treat one or several focal zone locations at any given time. Several treatments using various combinations of these parameters were simulated using a finite difference method to solve the Pennes bio-heat transfer equation for an ultrasonically heated tissue region with a wide range of acoustic, thermal, geometric, and tumor properties. The total treatment time was iteratively optimized using either a heuristic method or routines included in the Matlab software package, with constraints imposed for patient safety and treatment efficacy. The results demonstrate that large reductions in treatment time are possible through the intelligent selection of user-controllable treatment parameters. For the treatment path, treatment times are reduced by as much as an order of magnitude if the focal zones are arranged into stacks along the axial direction and a middle-front-back ordering is followed. For situations where normal tissue heating constraints are less stringent, these focal zones should have high levels of adjacency to further decrease treatment times; however, adjacency should be reduced in some cases where normal tissue constraints are more stringent. Also, the use of smaller, more concentrated focal zones produces shorter treatment times than larger, more diluted focal zones, a result verified in an agar phantom model. Further, focal zones should be packed using only a small amount of overlap in the axial direction and with a small gap in the transverse direction. These studies suggest that all treatment time reductions occur due to selection of parameters that advantageously use mechanisms of decreasing the focal zone size to concentrate the power density, increasing thermal superposition in the tumor, decreasing thermal superposition in the normal tissue, and advantageously using nonlinear rates of thermal dose deposition with increasing temperature

The Civil War Brought to Life: Civil War re-enactments and their use in the classroom

Link to an accompanying website on http://re-enactments.weebly.comThe purpose of this thesis paper was to examine re-enactments and how they could be used as educational tools in the classroom. The paper starts with explaining re-enacting and what has been written about it. The research discusses how in the realm of re-enacting there is a major focus on authenticity. Authenticity is never completely defined as it is different for each individual re-enactor. The research also talks about the two main reasons why people choose to re-enact. Though every re-enactors decision to join a group is different, the two main reasons seem to be to educate the public or to entertain. The paper then takes the discussion of authenticity and why people re-enact and apply them to a local re-enactment group. There is a brief history of the 1st NY Light Artillery and their fight in the Civil War, followed by a look at the re-enactment group. The paper is concluded by looking at how re-enactments could be used in a classroom. It is suggested that re-enactments be used as a supplemental tool to teach the Civil War. It is shown that the sights and smells and other senses allow the students to remember and store information that will help solidify what they have learned.SUNY BrockportEducation and Human DevelopmentMaster of Science in Education (MSEd)Education and Human Development Master's These

Mechanism of imidazolium ionic liquids toxicity in Saccharomyces cerevisiae and rational engineering of a tolerant, xylose-fermenting strain

Additional file 3. Fermentation profiles of Y133 and Y133-IIL in the presence of 1 % [BMIM]Cl at pH 6.5 and pH 5.0, and either aerobic or anaerobic conditions (n = 3, Mean ± S.E, except n = 2 for Y133 pH 6.5 anaerobic 72 h)

Maximal Oxidative Capacity during Exercise Is Associated with Skeletal Muscle Fuel Selection and Dynamic Changes in Mitochondrial Protein Acetylation

SummaryMaximal exercise-associated oxidative capacity is strongly correlated with health and longevity in humans. Rats selectively bred for high running capacity (HCR) have improved metabolic health and are longer-lived than their low-capacity counterparts (LCR). Using metabolomic and proteomic profiling, we show that HCR efficiently oxidize fatty acids (FAs) and branched-chain amino acids (BCAAs), sparing glycogen and reducing accumulation of short- and medium-chain acylcarnitines. HCR mitochondria have reduced acetylation of mitochondrial proteins within oxidative pathways at rest, and there is rapid protein deacetylation with exercise, which is greater in HCR than LCR. Fluxomic analysis of valine degradation with exercise demonstrates a functional role of differential protein acetylation in HCR and LCR. Our data suggest that efficient FA and BCAA utilization contribute to high intrinsic exercise capacity and the health and longevity benefits associated with enhanced fitness

Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics

The addition of the monosaccharide beta-N-acetyl-D-glucosamine to proteins (O-GlcNAc glycosylation) is an intracellular, post-translational modification that shares features with phosphorylation. Understanding the cellular mechanisms and signaling pathways that regulate O-GlcNAc glycosylation has been challenging because of the difficulty of detecting and quantifying the modification. Here, we describe a new strategy for monitoring the dynamics of O-GlcNAc glycosylation using quantitative mass spectrometry-based proteomics. Our method, which we have termed quantitative isotopic and chemoenzymatic tagging (QUIC-Tag), combines selective, chemoenzymatic tagging of O-GlcNAc proteins with an efficient isotopic labeling strategy. Using the method, we detect changes in O-GlcNAc glycosylation on several proteins involved in the regulation of transcription and mRNA translocation. We also provide the first evidence that O-GlcNAc glycosylation is dynamically modulated by excitatory stimulation of the brain in vivo. Finally, we use electron-transfer dissociation mass spectrometry to identify exact sites of O-GlcNAc modification. Together, our studies suggest that O-GlcNAc glycosylation occurs reversibly in neurons and, akin to phosphorylation, may have important roles in mediating the communication between neurons

Inhibition of microbial biofuel production in drought-stressed switchgrass hydrolysate

Additional file 2. Maps of significant gene ontology terms for chemical genomics data. Untreated biomass composition. Detailed hydrolysate composition

Medicago PhosphoProtein Database: a repository for Medicago truncatula phosphoprotein data

The ability of legume crops to fix atmospheric nitrogen via a symbiotic association with soil rhizobia makes them an essential component of many agricultural systems. Initiation of this symbiosis requires protein phosphorylation-mediated signaling in response to rhizobial signals named Nod factors. Medicago truncatula (Medicago) is the model system for studying legume biology, making the study of its phosphoproteome essential. Here, we describe the Medicago PhosphoProtein Database (MPPD; http://phospho.medicago.wisc.edu), a repository built to house phosphoprotein, phosphopeptide, and phosphosite data specific to Medicago. Currently, the MPPD holds 3,457 unique phosphopeptides that contain 3,404 non-redundant sites of phosphorylation on 829 proteins. Through the web-based interface, users are allowed to browse identified proteins or search for proteins of interest. Furthermore, we allow users to conduct BLAST searches of the database using both peptide sequences and phosphorylation motifs as queries. The data contained within the database are available for download to be investigated at the user’s discretion. The MPPD will be updated continually with novel phosphoprotein and phosphopeptide identifications, with the intent of constructing an unparalleled compendium of large-scale Medicago phosphorylation data

Attempted forced copulation by an immature Red-winged Blackbird male: Video evidence from the Grand River Grasslands of Iowa and potential explanations

Forced copulations are a type of sexual coercion that typically occurs when the fitness interests of males and females are in conflict. Forced copulations are rare in most species of birds, and there are only a few reports in passerine species. Here we report the first published observation of an immature Red-winged Blackbird Agelaius phoeniceus male attempting a forced copulation on a nesting Red-winged Blackbird female. We describe the behaviour and discuss potential explanations and implications for our observations