Theses and Dissertations from UMD

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New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a give thesis/dissertation in DRUM

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2011 - 20123

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    Protein permeability pathways in the mitochondrial outer membrane during apoptosis
    (2012) Vidyaramanan, Ganesan; Colombini, Marco; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Apoptosis, a form of programmed cell death is a physiological, homeostatic process that guides the systematic removal of unwanted, dying or damaged cells from the body. A key step in apoptosis is the irreversible release of mitochondrial intermembrane space (IMS) proteins into the cytosol by a process called Mitochondrial Outer Membrane Permeabilization (MOMP). MOMP is regulated by a special class of proteins called Bcl-2 family proteins and a sphingolipid called ceramide. The pro-apoptotic Bcl-2 proteins, especially Bax and Bak can cooperate with ceramide to form channels in mitochondria that cause protein efflux during MOMP. The ability of ceramide to form protein-permeable channels in MOM is established. Bax and ceramide enhanced MOMP synergistically. The ability of Bax to stimulate ceramide channels was investigated. It was found that the apparent affinity of Bax for a ceramide channel increases with the ceramide channel size. The results indicate that Bax binds a small ceramide channel and drives its growth until the Bax molecule finds the best fit to the channel. This interaction between Bax and a ceramide channel does not require of the presence of other Bcl-2 proteins or mitochondrion-specific factors. The critical structural features of ceramide were investigated for their role in ceramide channel formation. Analogs of ceramide bearing modifications in the functional groups were analyzed for their ability to form channels to assess stability and also to interact with native ceramide to form channels to assess compatibility between interacting groups. The C1-hydroxyl was found to be indispensable for channel formation while the C3-hydroxyl was inconsequential to channel formation. The amide nitrogen with its ability to donate hydrogen was important for stability as methylating the nitrogen diminished the channel forming ability. Similarly, converting the carbonyl oxygen to a urea group, now more polar and a stronger hydrogen bond former resulted in more stable permeabilization. Changes to the hydrocarbon tails did not affect the ability to form channels. Phytoceramide, which has a C4 hydroxyl instead of the C4-C5 trans double bond formed stable channels but phytoceramide inhibited channel formation by ceramide suggesting incompatibility in structure. Bax activation involves translocation of Bax from the cytosol to the MOM, conformational changes and subsequent channel formation. All steps involved in Bax activation are not well-understood. We have used ionic strength as a modulating tool to dissect the different steps in Bax mediated MOMP. Increasing the ionic strength was found to delay formation of real-time permeability by Bax. Increasing the ionic strength resulted in smaller channels that grew in size slowly. The high permeability induced by low ionic strength was not reversed by raising the ionic strength suggesting that Bax channels are not in dynamic equilibrium with Bax monomers. Ionic strength also altered the sensitivity of Bax mediated MOMP to inhibition by Bcl-xL. Ionic strength, however did not affect Bax insertion into membranes. Thus, ionic strength presents a good diagnostic tool to modulate Bax mediated channel formation downstream of Bax insertion into membranes.
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    VISUALIZATION OF CERAMIDE CHANNELS BY TRANSMISSION ELECTRON MICROSCOPY
    (2011) SAMANTA, SOUMYA; COLOMBINI, MARCO; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Functional studies have shown that the sphingolipid ceramide, self-assembles in phospholipid membranes to form large channels capable of allowing proteins to cross the membrane. Here these channels are visualized by negative stain transmission electron microscopy. The images contain features consistent with stain-filled pores having a roughly circular profile. There is no indication of tilt, and the results are consistent with the formation of right cylinders. The sizes of the pores range from 5 to 40 nm in diameter with an asymmetric distribution indicating no apparent upper size limit. The size distribution matches well with the distribution of sizes calculated from electrophysiological measurements.
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    Bioorganic Chemistry of Sphingolipids: Pore Formation and Anion Transport
    (2011) Harrell, Jr., William A.; Davis, Jeffery T.; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Ceramide is an amphiphilic natural product that plays important roles in multiple cellular processes. Ceramide also is known to self-assemble into transmembrane pores under physiologically relevant concentrations. In order to study the role of ceramide's 1,3-diol functionality in the stabilization of transmembrane pores, ceramide analogs were prepared using protecting groups to block the 1,3-diol unit. Blocking the 1,3-diol with an acetal protecting group led to a drastic decrease in membrane-activity. Surprisingly, blocking the -OH groups of C2-ceramide 2 with simple esters yielded a C2-diacetate 16 analog with increased pore-forming activity. Additionally, a new function of C2-ceramide 2 has been discovered that has important biological implications. Working below concentrations in which it self-assembles into transmembrane pores, C2-ceramide 2 facilitated the transmembrane transport of biologically relevant anions such as Cl- and HCO3- via an anion exchange mechanism. The 1,3-diol functionality of the C2-ceramide 2 headgroup was found to play an integral role in the binding and transport of anions, as the isopropylidene C2-ceramide 18 analog was unable to facilitate transmembrane anion transport. D-erythro-Sphingosine 3, produced naturally by the metabolism of ceramide, lacks the amide functionality in its hydrophilic head-group. Unlike C2-ceramide 2, sphingosine 3 does not facilitate transmembrane Cl-/HCO3- exchange. Possible reasons for this failure to facilitate the transmembrane transport of anions are discussed, namely that sphingosine 3 does not bind HCO3- in a non-covalent manner. Instead, sphingosine 3 forms carbamates in the presence of HCO3- and CO2 in a solvent dependent manner.