Proteomic analysis of the Cdc48/Ubx network identifies a role for Ubx2 in the regulation of lipid biosynthesis

Cdc48/p97 is an essential, highly abundant hexameric member of the AAA (ATPase associated with various cellular activities) family. It has been linked to a variety of processes throughout the cell but it is best known for its role in the ubiquitin proteasome pathway. In this system it is believed that Cdc48 behaves as a segregase, transducing the chemical energy of ATP hydrolysis into mechanical force to separate ubiquitin-conjugated proteins from their tightly-bound partners.

Current models posit that Cdc48 is linked to its substrates through a variety of adaptor proteins, including a family of seven proteins (13 in humans) that contain a Cdc48-binding UBX domain. As such, due to the complexity of the network of adaptor proteins for which it serves as the hub, Cdc48/p97 has the potential to exert a profound influence on the ubiquitin proteasome pathway. However, the number of known substrates of Cdc48/p97 remains relatively small, and smaller still is the number of substrates that have been linked to a specific UBX domain protein. As such, the goal of this dissertation research has been to discover new substrates and better understand the functions of the Cdc48 network. With this objective in mind, we established a proteomic screen to assemble a catalog of candidate substrate/targets of the Ubx adaptor system.

Here we describe the implementation and optimization of a cutting-edge quantitative mass spectrometry method to measure relative changes in the Saccharomyces cerevisiae proteome. Utilizing this technology, and in order to better understand the breadth of function of Cdc48 and its adaptors, we then performed a global screen to identify accumulating ubiquitin conjugates in cdc48-3 and ubxΔ mutants. In this screen different ubx mutants exhibited reproducible patterns of conjugate accumulation that differed greatly from each other, pointing to various unexpected functional specializations of the individual Ubx proteins.

As validation of our mass spectrometry findings, we then examined in detail the endoplasmic-reticulum bound transcription factor Spt23, which we identified as a putative Ubx2 substrate. In these studies ubx2Δ cells were deficient in processing of Spt23 to its active p90 form, and in localizing p90 to the nucleus. Additionally, consistent with reduced processing of Spt23, ubx2Δ cells demonstrated a defect in expression of their target gene OLE1, a fatty acid desaturase. Overall, this work demonstrates the power of proteomics as a tool to identify new targets of various pathways and reveals Ubx2 as a key regulator lipid membrane biosynthesis.

Selective hydroxylation of small alkanes by the particulate methane monooxygenase

The particulate methane monooxygenase (pMMO) catalyzes the oxidation of methane to methanol under ambient temperatures and pressures. Other small alkanes and alkenes are also substrates of this enzyme. We measured and compared the initial rate constants of oxidation of small alkanes (C1 to C5) catalyzed by pMMO. Both primary and secondary alcohols were formed from oxidation of n-butane and n-pentane. The alcohols produced from alkane oxidation can be further oxidized, probably by pMMO, to aldehydes and ketones. The apparent regioselectivity for n-butane and n-pentane is 100% 2-alcohols because the formation of primary alcohols is slower than further oxidation of these alcohols. The hydroxylation at the secondary carbons is highly stereoselective: (R)-alcohols are preferentially formed. The enantiomeric excess increases slightly with decreasing reaction temperature. The steric course of hydroxylation on primary carbons was also studied by using isotopically substituted ethane: (S)- or (R)-CH_3-CHDT, and (S)- or (R)-CD_3- CHDT and the reactions were found to proceed with 100% retention of configuration. A primary isotopic effect of k_H/k_D=5.0 was observed in these experiments.

Negative regulation of transcription factors by Srb10 cyclin-dependent kinase

The ubiquitin-dependent proteolytic pathway plays an important role in a broad array of cellular processes, inducting cell cycle control and transcription. Biochemical analysis of the ubiquitination of Sic1, the B-type cyclin-dependent kinase (CDK) inhibitor in budding yeast helped to define a ubiquitin ligase complex named SCF^cdc4 (for Skp1, Cdc53/cullin, F-box protein). We found that besides Sic1, the CDK inhibitor Far1 and the replication initiation protein Cdc6 are also substrates of SCF^cdc4 in vitro. A common feature in the ubiquitination of the cell cycle SCF^cdc4 substrates is that they must be phosphorylated by the major cell cycle CDK, Cdc28. Gcn4, a transcription activator involved in the general control of amino acid biosynthesis, is rapidly degraded in an SCF^cdc4-dependent manner in vivo. We have focused on this substrate to investigate the generality of the SCF^cdc4 pathway. Through biochemical fractionations, we found that the Srb10 CDK phosphorylates Gcn4 and thereby marks it for recognition by SCF^cdc4 ubiquitin ligase. Srb10 is a physiological regulator of Gcn4 stability because both phosphorylation and turnover of Gcn4 are diminished in srb10 mutants. Furthermore, we found that at least two different CDKs, Pho85 and Srb10, conspire to promote the rapid degradation of Gcn4 in vivo. The multistress response transcriptional regulator Msn2 is also a substrate for Srb10 and is hyperphosphorylated in an Srb10-dependent manner upon heat stress-induced translocation into the nucleus. Whereas Msn2 is cytoplasmic in resting wild type cells, its nuclear exclusion is partially compromised in srb10 mutant cells. Srb10 has been shown to repress a subset of genes in vivo, and has been proposed to inhibit transcription via phosphorylation of the C-terminal domain of RNA polymerase II. Our results suggest a general theme that Srb10 represses the transcription of specific genes by directly antagonizing the transcriptional activators.

Hydrogen-Atom Transfer Photochemistry of Tetrakis(µ-pyrophosphito)diplatinate(II)

In many senses, the hydrogen-atom transfer reactions observed with the triplet excited state of pyrophosphito-bridged platinum(II) dimers resemble the reactions of organic ketone nπ* states. The first two chapters describe our attempts to understand the reactivity differences between these two chromophores. Reactivity of the metal dimers is strongly regulated by the detailed nature of the ligands that ring the axial site, the hydrogen-abstraction center. A hydrogen-bonded network linking the ligands facilitates H-atom transfer quenching with alcohols through the formation of a hydrogen-bonded complex between the alcohol and a dimer. For substrates of equal C-H bond strength that lack a hydroxyl group (e.g., benzyl hydrocarbons), the quenching rate is several orders of magnitude slower.

The shape and size of the axial site, as determined by the ligands, also discriminate among quenchers by their steric characteristics. Very small quenchers quench slowly because of high entropies of activation, while very large ones have large enthalpic barriers. The two effects find a balance with quenchers of "just the right size."

The third chapter discusses the design of a mass spectrometer that uses positron annihilation to ionize neutral molecules. The mass spectrometer creates positron-molecule adducts whose annihilation produces fragmentation products that may yield information on the bonding of positrons in such complexes.

Structural, morphological and optical properties of ZnO thin films grown on gamma-LiAlO2 substrate by pulsed laser deposition

ZnO thin films were deposited on the substrates of (100) gamma-LiAlO2 at 400, 550 and 700 degrees C using pulsed laser deposition (PLD) with the fixed oxygen pressure of 20 Pa, respectively. When the substrate temperature is 400 degrees C, the grain size of the film is less than 1 mu m observed by Leitz microscope and measured by X-ray diffraction (XRD). As the substrate temperature increases to 550 degrees C, highly-preferred c-orientation and high-quality ZnO film can be attained. While the substrate temperature rises to 700 degrees C, more defects appears on the surface of film and the ZnO films become polycrystalline again possibly because more Li of the substrate diffused into the ZnO film at high substrate temperature. The photoluminescence (PL) spectra of ZnO films at room temperature show the blue emission peaks centered at 430 nm. We suggest that the blue emission corresponds to the electron transition from the level of interstitial Zn to the valence band. Meanwhile, the films grown on gamma-LiAlO2 (LAO) exhibit green emission centered at 540 nm, which seemed to be ascribed to excess zinc and/or oxygen vacancy in the ZnO films caused by diffusion of Li. from the substrates into the films during the deposition.

Microstructure and laser-induced damage threshold of ZrO2 coatings dependence on annealing temperature

ZrO2 coatings were deposited on different substrates of Yb:YAG and fused silica by electron beam evaporation. After annealed for 12 h at 673 and 1073 K, respectively, weak absorption of coatings was measured by surface thermal lensing (STL) technique, and then laser-induced damage threshold (LIDT) was determined also. The crystalline phase of ZrO2 coatings and the size of the crystal grain were investigated by X-ray diffraction. It was found that microstructure of ZrO2 coatings was dependent on both annealing temperature and substrate structure, and coatings containing monoclinic phases had higher damage threshold than others. Due to the strong absorption of Yb:YAG, damage threshold of coatings on Yb:YAG was much less than that on fused silica. (C) 2004 Elsevier B.V. All rights reserved.

Biological Characteristics and Fishery Assessment of Alaska Plaice, Pleuronectes quadrituberculatus, in the Eastern Bering Sea

Alaska plaice, Pleuronectes quadrituberculatus, is one of the major flatfishes in the eastern Bering Sea ecosystem and is most highly concentrated in the shallow continental shelf of the eastern Bering Sea. Annual commercial catches have ranged from less than 1,000 metric tons (t) in 1963 to 62,000 t in 1988. Alaska plaice is a relatively large flatfish averaging about 32 cm in length and 390 g in weight in commercial catches. They are distributed from nearshore waters to a depth of about 100 m in the eastern Bering Sea during summer, but move to deeper continental shelf waters in winter to escape sea ice and cold water temperatures. Being a long-lived species (>30 years), they have a relatively low natural mortality rate estimated at 0.20. Maturing at about age 7, Alaska plaice spawn from April through June on hard sandy substrates of the shelf region, primarily around the 100 m isobath. Prey items primarily include polychaetes and other marine worms. In comparison with other flatfish, Alaska plaice and rock sole, Pleuronectes bilineatus, have similar diets but different habitat preferences with separate areas of peak population density which may minimize interspecific competition. Yellowfin sole, Pleuronectes asper, while sharing similar habitat, differs from these two species because of the variety of prey items in its diet. Competition for food resources among the three species appears to be low. The resource has experienced light exploitation since 1963 and is currently in good condition. Based on the results of demersal trawl surveys and age-structured analyses, the exploitable biomass increased from 1971 through the mid-1980’s before decreasing to the 1997 level of 500,000 t. The recommended 1998 harvest level, Allowable Biological Catch, was calculated from the Baranov catch equation based on the FMSY harvest level and the projected 1997 biomass, resulting in a commercial harvest of 69,000 t, or about 16% of the estimated exploitable biomass.

The temporal and spatial distribution, composition and abundance of Protozoa in Chaohu Lake, China: Relationship with eutrophication

Systematic investigations into the temporal and spatial distribution, composition and abundance of protozoa in two regions with different trophic levels in Chaohu Lake, a large, shallow and highly eutrophic freshwater lake in China, were conducted during 2002-2003. A total of 114 species of protozoa, including phytomastigophorans, zoomastigophorans, amoebae and ciliates, were identified from 120 polyurethane foam unit (PFU) samples exposed at four stations and from various types of natural substrates. Of the 114 taxa, 36 core species were found on PFU substrates and 23 of these were found on natural ones. Protozoan abundance and chemical physical parameters at nine sampling stations, four in the western lake and five in the eastern part, indicate trophic gradient changes along the lake. Seasonal variations in the species composition of major groups at littoral PFU sampling stations illustrate the effect of a severe algal bloom on the protozoan community structure. Temporal and spatial distributions of individual abundance as functions of water temperature and trophic status were revealed. This study demonstrates again that the PFU artificial substrate method samples protozoan communities more effectively than routine natural substrate methods. (c) 2005 Elsevier GmbH. All rights reserved.

Preparation and characterization of Si sheets by renewed SSP technique

Silicon sheets from powder (SSP) ribbons have been prepared by modified SSP technique using electronic-grade (9N purity) silicon powder. The surface morphology, crystallographic quality, composition and electric properties of the SSP ribbons were investigated by surface profiler, X-ray diffraction (XRD), scanning electron microscopy (SEM), metallurgical microscope, Auger electron spectroscopy (AES) and four-point probe apparatus, respectively. The results show that the SSP ribbon made from electronic-grade silicon powder is a suitable candidate for the substrates of crystalline silicon thin film (CSiTF) solar cells, which could meet the primary requirements of CSiTF solar cell process on the substrates, including surface smoothness, crystallographic quality, purity and electric conductivity, etc. (C) 2004 Elsevier B.V. All rights reserved.

Fast plasma sintering deposition of nano-structured silicon carbide coatings

Fast plasma sintering deposition of SiC nano-structured coatings was achieved using a specially designed non-transferred dc plasma torch operated at reduced pressure. Employing the Taguchi method, the deposition parameters were optimized and verified. With the optimized combination of deposition parameters, homogeneous SiC coatings were deposited on relatively large area substrates of Φ50 mm and 50×50 mm with a deposition rate as high as 20 μm/min. Ablation test showed that such coatings can be used as oxidation resistance coatings in high temperature oxidizing environment.

Nanocomposite multilayer film of preyssler-type polyoxometalates with fine tunable electrocatalytic activities

Through layer-by-layer (LBL) assembly technique, iron oxide (Fe3O4) nanoparticles coated by poly (diallyldimethylammonium chloride) (PDDA) and Preyssler-type polyoxometalates (NH4)(14)NaP5W30O110.31H(2)O (P5W30) were alternately deposited on quartz and ITO substrates, and 4-aminobenzoic acid modified glassy carbon electrodes. Thus-prepared multilayer films were characterized by UV-visible spectroscopy, X-ray photoelectron spectroscopy, and cyclic voltammetry. It was proved that the multilayer films are uniform and stable. And the electrocatalytic activities of the multilayer films can be fine-tuned by adjusting the assembly conditions in the LBL assembly process, such as the pH of the assembly solution. The multilayer films fabricated from P5W30 solutions dissolved in 0.1 M H2SO4 exhibit high electrocatalytic response and sensitivity toward the reduction of two substrates of important analytical interests, HNO2 and IO3- whereas the films assembled with P5W30 solutions dissolved in 1.0 M H2SO4 show remarkable electrocatalytic activity for the hydrogen evolution reaction (HER). Furthermore, the electrocatalytic properties of the HER of the latter film can be obtained from the former film upon exposure to 1.0 M H2SO4 for several hours.

Synthesis of tetra-iron substituted sandwich-type pentadecatungstodiarsenate and its multilayers on glassy carbon electrode by self-assembly with electrocatalytic properties

A novel sandwich-type compound, Na-12 [Fe-4 (H2O)(2) (As2W15O56)(2)] . 38H(2)O (denoted as Fe(4)AS(4)W(30)) was synthesized. The compound was well characterized by means of IR, UV-Vis, W-138 NMR and elemental analyses. Redox electrochemistry of the compound has been studied in acid buffer solutions using cyclic voltammetry(CV). The compound containing multilayer films has been fabricated on the 4-aminobenzoic acid(4-ABA) modified glassy carbon electrode(GCE) surface by alternate deposition with a quaternized poly (4-vinylpyridine) partially completed with [Os(bpy)(2)Cl](2+/-) (denoted as QPVP-Os). CV, X-ray photoelectron spectroscopy (XPS) and UV-Vis spectroscopy were used to characterize the asprepared multilayer films. It is proved that the multilayer films are uniform and stable. The electrocatalytic activities of the multilayer films were investigated on the reduction of two substrates of important analytical interest, NO2- and H2O2.

Layer-by-layer assembly of multilayer films consisting of silicotungstate and a cationic redox polymer on 4-aminobenzoic acid modified glassy carbon electrode and their electrocatalytic effects

A novel 4-aminobenzoic acid (4-ABA) monolayer film is formed on glassy carbon electrode (GCE) by amino cation radical method. Silicotungstic heteropolyanion (SiW12O404-, denoted as SiW12)-containing multilayer films have been fabricated on the 4-ABA modified GCE surface by alternate deposition with a quaternized poly(4-vinylpyridine) partially complexed with [Os(bpy)(2)Cl](2+/+) (denoted as QPVP-Os). Cyclic voltammetry (CV), X-ray photoelectron spectroscopy (XPS) and X-ray reflectivity (XR) have been used to characterise the as-prepared multilayer films. It is proved that the multilayer films are uniform and stable. The average thickness for a bilayer of QPVP-Os/SiW12 in the multilayer film is 30.2 Angstrom. The electrocatalytic activities of the multilayer films have been investigated on the reduction of three substrates of important analytical interests, HNO2, BrO3- and H2O2. Especially, the influence of layer number of the multilayer films on the electrocatalytic reduction of HNO2 has been investigated in detail. (C) 2000 Elsevier Science B.V. All rights reserved.

"It is Quietly Chaotic. It Confuses Time"*: Final Report of Excavations at the Bordley-Randall Site in Annapolis, Maryland, 1993-1995 (18AP50)

*This extract is from Gay P. Crowther's description of the Randall Court pathway (Cowther 1985).

Expression of liver-specific member of the 3β-hydroxysteroid dehydrogenase family, an isoform possessing an almost exclusive 3-ketosteroid reductase activity

We have recently characterized two types of rat 3β-hydroxysteroid dehydrogenase/Δ5-Δ4 isomerase (3β-HSD) isoenzymes expressed in adrenals and gonads. In addition, we have cloned a third type of cDNA encoding a predicted type III 3β-HSD protein specifically expressed in the male rat liver which shares 80% similarity with the two other isoenzymes. Transient expression in human HeLa cells of the cDNAs reveals that the type III 3β-HSD protein does not display oxidative activity for the classical substrates of 3β-HSD, in contrast to the type I 3β-HSD isoenzyme. However, in the presence of NADH, type III isoenzyme, in common with the type I isoform, converts 5α-androstane-3,17-dione (A-dione) and 5α-dihydrotestosterone (DHT) to the corresponding 3β-hydroxysteroids. In fact, the type I and the type III isoenzymes have the same affinity for DHT with K(m) values of 5.05 and 6.16 μM, respectively. When NADPH is used as cofactor, the affinity for DHT of the type III isoform becomes higher than that of the type I isoform with K(m) values of 0.12 and 1.18 μM, respectively. The type III isoform is thus a 3-ketoreductase using NADPH as preferred cofactor which is responsible for the conversion of 3-keto-saturated steroids such as DHT and A-dione into less active steroids.