Point mutation of the autophosphorylation site or in the nuclear location signal causes protein kinase A RII beta regulatory subunit to lose its ability to revert transformed fibroblasts.

The RII beta regulatory subunit of cAMP-dependent protein kinase (PKA) contains an autophosphorylation site and a nuclear location signal, KKRK. We approached the structure-function analysis of RII beta by using site-directed mutagenesis. Ser114 (the autophosphorylation site) of human RII beta was replaced with Ala (RII beta-P) or Arg264 of KKRK was replaced with Met (RII beta-K). ras-transformed NIH 3T3 (DT) cells were transfected with expression vectors for RII beta, RII beta-P, and RII beta-K, and the effects on PKA isozyme distribution and transformation properties were analyzed. DT cells contained PKA-I and PKA-II isozymes in a 1:2 ratio. Over-expression of wild-type or mutant RII beta resulted in an increase in PKA-II and the elimination of PKA-I. Only wild-type RII beta cells demonstrated inhibition of both anchorage-dependent and -independent growth and phenotypic change. The growth inhibitory effect of RII beta overexpression was not due to suppression of ras expression but was correlated with nuclear accumulation of RII beta. DT cells demonstrated growth inhibition and phenotypic change upon treatment with 8-Cl-cAMP. RII beta-P or RII beta-K cells failed to respond to 8-Cl-cAMP. These data suggest that autophosphorylation and nuclear location signal sequences are integral parts of the growth regulatory mechanism of RII beta.

A genetic screen identifies cellular factors involved in retroviral -1 frameshifting.

To identify cellular factors that function in -1 ribosomal frameshifting, we have developed assays in the yeast Saccharomyces cerevisiae to screen for host mutants in which frameshifting is specifically affected. Expression vectors have been constructed in which the mouse mammary tumor virus gag-pro frameshift region is placed upstream of the lacZ gene or the CUP1 gene so that the reporters are in the -1 frame relative to the initiation codon. These vectors have been used to demonstrate that -1 frameshifting is recapitulated in yeast in response to retroviral mRNA signals. Using these reporters, we have isolated spontaneous host mutants in two complementation groups, ifs1 and ifs2, in which frameshifting is increased 2-fold. These mutants are also hypersensitive to antibiotics that target the 40S ribosomal subunit. We have cloned the IFS1 gene and shown that it encodes a previously undescribed protein of 1091 aa with clusters of acidic residues in the carboxyl-terminal region. Haploid cells lacking 82% of the IFS1 open reading frame are viable and phenotypically identical to ifs1-1 mutants. This approach could help identify potential targets for antiretroviral agents.

Identification of receptor-binding domains on human interleukin 5 and design of an interleukin 5-derived receptor antagonist.

A detailed structure-function analysis of human interleukin 5 (hIL5) has been performed. The hIL5 receptor is composed of two different polypeptide chains, the alpha and beta subunits. The alpha subunit alone is sufficient for ligand binding, but association with the beta subunit leads to a 2- to 3-fold increase in binding affinity. The beta chain is shared with the receptors for IL3 and granulocyte/macrophage-colony-stimulating factor--hence the descriptor beta C (C for common). All hIL5 mutants were analyzed in a solid-phase binding assay for hIL5R alpha interaction and in a proliferation assay using IL5-dependent cell lines for receptor-complex activation. Most residues affecting binding to the receptor alpha subunit were clustered in a loop connecting beta-strand 1 and helix B (mutants H38A, K39A, and H41A), in beta-strand 2 (E89A and R91A; weaker effect for E90A) and close to the C terminus (T109A, E110A, W111S, and I112A). Mutations at one position, E13 (Glu13), caused a reduced activation of the hIL5 receptor complex. In the case of E13Q, only 0.05% bioactivity was detected on a hIL5-responsive subclone of the mouse promyelocytic cell line FDC-P1. Moreover, on hIL5-responsive TF1 cells, the same mutant was completely inactive and proved to have antagonistic properties. Interactions of this mutant with both receptor subunits were nevertheless indistinguishable from those of nonmutated hIL5 by crosslinking and Scatchard plot analysis of transfected COS-1 cells.

Dense carbon monoliths for supercapacitors with outstanding volumetric capacitances

A commercially available dense carbon monolith (CM) and four carbon monoliths obtained from it have been studied as electrochemical capacitor electrodes in a two-electrode cell. CM has: (i) very high density (1.17 g cm−3), (ii) high electrical conductivity (9.3 S cm−1), (iii) well-compacted and interconnected carbon spheres, (iv) homogeneous microporous structure and (v) apparent BET surface area of 957 m2g−1. It presents interesting electrochemical behaviors (e.g., excellent gravimetric capacitance and outstanding volumetric capacitance). The textural characteristics of CM (porosity and surface chemistry) have been modified by means of different treatments. The electrochemical performances of the starting and treated monoliths have been analyzed as a function of their porous textures and surface chemistry, both on gravimetric and volumetric basis. The monoliths present high specific and volumetric capacitances (292 F g−1 and 342 F cm−3), high energy densities (38 Wh kg−1 and 44 Wh L−1), and high power densities (176 W kg−1 and 183 W L−1). The specific and volumetric capacitances, especially the volumetric capacitance, are the highest ever reported for carbon monoliths. The high values are achieved due to a suitable combination of density, electrical conductivity, porosity and oxygen surface content.

Hemorheological alterations in sickle cell anemia and their clinical consequences: the role of genetic modulators

Sickle cell anemia (SCA) is an autosomal recessive chronic hemolytic anemia, caused by homozygosity for the HBB:c.20A>T mutation. The disease presents with high clinical heterogeneity, stroke being the most devastating manifestation. This study aimed to identify genetic modulators of severe hemolysis and stroke risk in children with SCA, as well as understand their consequences at the hemorheological level. Sixty-six children with SCA were categorised according to their degree of cerebral vasculopathy (Stroke/Risk/Control). Relevant data were collected from patients’ medical records. Several polymorphic regions in genes related to vascular cell adhesion and tonus were characterized by molecular methodologies. Data analyses were performed using R software. Several in silico tools (e.g. TFBind, MatInspector) were applied to investigate the main variant consequences. Some genetic variants in vascular adhesion molecule-1 gene promoter and endothelial nitric oxide synthase gene were associated with higher levels of hemolysis and stroke events. They modify important transcription factor binding sites or disturb the corresponding protein structure/function. Our findings emphasize the relevance of the genetic variants in modulating the degree of hemolysis and development of cerebral vasculopathy due to their effect on gene expression, modification of protein biological activities related with erythrocyte/endothelial interactions and consequent hemorheological abnormalities in SCA.

(Table 1) Some structural characteristics of communities and detritus flux through the lower boundary of a given water column in different regions of the Kara Sea

Vertical fluxes of autochtonous detritus at different levels were estimated using the algorithm of structure-function analysis. The calculations are based on pelagic ecosystem parameters in the Kara Sea observed in September 1993 (temperature, primary production, biomass of phytoplankton, bacteria, protozoa, and zooplankton, trophic and size composition, etc.). At eight stations in different parts of the sea where sedimentation traps were set, the range of calculated fluxes of autochtonous detritus through the lower boundary of the water column was 13-90 mgC/m**2/day. The flux was much higher in the estuary of the Yenisey River (55-90 mgC/m**2/day) than in the northeastern regions (I8-50 mgC/m**2/day) and, especially, in the relatively deep southwestern part of the sea (13-35 mgC/m**2/day). The calculated fluxes of autochtonous detritus in shallow water regions (where conditions are variable and poorly known hydrologically and where outflow of allochtonous detritus is substantial) cannot be compared to data from sedimentation traps.

Functional characterisation of an engineered multidomain human P450 E1 by molecular Lego

The human cytochrome P450s constitute an important family of monooxygenase enzymes that carry out essential roles in the metabolism of endogenous compounds and foreign chemicals. We present here results of a fusion between a human P450 enzyme and a bacterial reductase that for the first time is shown does not require the addition of lipids or detergents to achieve wild-type-like activities. The fusion enzyme, P450 2E1-BMR, contains the N-terminally modified residues 22-493 of the human P450 2E1 fused at the C-terminus to residues 473-1049 of the P450 BM3 reductase (BMR). The P450 2E1-BMR enzyme is active, self-sufficient and presents the typical marker activities of the native human P450 2E1: the hydroxylation of p-nitrophenol (K (M)=1.84 +/- 0.09 mM and k (cat) of 2.98 +/- 0.04 nmol of p-nitrocatechol formed per minute per nanomole of P450) and chlorzoxazone (K (M)=0.65 +/- 0.08 mM and k (cat) of 0.95 +/- 0.10 nmol of 6-hydroxychlorzoxazone formed per minute per nanomole of P450). A 3D model of human P450 2E1 was generated to rationalise the functional data and to allow an analysis of the surface potentials. The distribution of charges on the model of P450 2E1 compared with that of the FMN domain of BMR provides the ground for the understanding of the interaction between the fused domains. The results point the way to successfully engineer a variety of catalytically self-sufficient human P450 enzymes for drug metabolism studies in solution.

Inhibition of S/G(2) phase CDK4 reduces mitotic fidelity

Cyclin-dependent kinase 4 (CDK4)/cyclin D has a key role in regulating progression through late G(1) into S phase of the cell cycle. CDK4-cyclin D complexes then persist through the latter phases of the cell cycle, although little is known about their potential roles. We have developed small molecule inhibitors that are highly selective for CDK4 and have used these to define a role for CDK4-cyclin D in G(2) phase. The addition of the CDK4 inhibitor or small interfering RNA knockdown of cyclin D3, the cyclin D partner, delayed progression through G(2) phase and mitosis. The G(2) phase delay was independent of ATM/ATR and p38 MAPK but associated with elevated Wee1. The mitotic delay was because of failure of chromosomes to migrate to the metaphase plate. However, cells eventually exited mitosis, with a resultant increase in cells with multiple or micronuclei. Inhibiting CDK4 delayed the expression of the chromosomal passenger proteins survivin and borealin, although this was unlikely to account for the mitotic phenotype. These data provide evidence for a novel function for CDK4-cyclin D3 activity in S and G(2) phase that is critical for G(2)/M progression and the fidelity of mitosis.

Characterization of tissue transglutaminase 2 in macrophage function

Apoptosis is a highly regulated process that removes damaged or unwanted cells in vivo and defective clearance of apoptotic cells by macrophages has significant immunological implications. Tissue transglutaminase 2 (TG2) is a Ca2+-dependent protein cross linking enzyme known to play an important role in cell proliferation, differentiation, carcinogenesis, programmed death, and aging. TG2 as a guanosine triphosphate (GTP)-binding or GTP- hydrolyzing protein for mediating signal transduction and as a cell cycle regulator emphasized the importance of this enzyme in aging process. The ubiquitous presence of TG2 compared to the other organ-specific TGases has attracted special attention as a cellular aging device. TG2 activity and expression are known to increase in aging humans suggesting possible involvement in several age-related processes such as decrease in vascular compliance and increased stiffening of conduit arteries, cataract formation, Alzheimer's disease and senescent epidermal keratinocytes. Our work aims to characterize the role of TG2 and its partners (e.g. syndecan-4 and ß3 integrin) in macrophage function. THP-1 cell derived macrophage-like cells and primary human macrophages were analyzed for the expression and function of TG2. Macrophage-apoptotic cell interaction studies in the presence of TG2 inhibitors resulted in significant inhibition of interaction. Macrophage cell surface TG2 and, in particular, its cell surface cross linking activity was found to be crucial in apoptotic cell clearance. Syndecan-4 association with TG2 implies possible cooperation of these proteins and knockdown studies of syndecan-4 reveal its importance in apoptotic cell clearance. Our current findings suggest that TG2 has a crucial but yet to be fully defined role in apoptotic cell clearance.

Identifying a novel functional domain within the p115 tethering factor required for Golgi ribbon assembly and membrane trafficking

The tethering factor p115 has been shown to facilitate Golgi biogenesis and membrane traffic in cells in culture. However, the role of p115 within an intact animal is largely unknown. Here, we document that RNAi-mediated depletion of p115 in C. elegans causes accumulation of the yolk protein (YP170) in body cavity and the retention of the yolk receptor RME-2 in the ER and the Golgi within oocytes.Structure-function analyses of p115 have identified two homology (H1-2) regions within the N-terminal globular head and the coiled-coil 1 (CC1) domain as essential for p115 function. We identify a novel C-terminal domain of p115 as necessary for Golgi ribbon formation and cargo trafficking. We show that p115 mutants lacking the fourth CC domain (CC4) act in a dominant negative manner to disrupt Golgi and prevent cargo trafficking in cells containing endogenous p115. Furthermore, using RNAi-mediated "replacement" strategy we show that CC4 is necessary for Golgi ribbon formation and membrane trafficking in cells depleted of endogenous p115.p115 has been shown to bind a subset of ER-Golgi SNAREs through CC1 and CC4 domains (Shorter et al., 2002). Our findings show that CC4 is required for p115 function and suggest that both the CC1 and the CC4 SNARE-binding motifs may participate in p115-mediated membrane tethering.

Structure-activity relations in Cs-doped heteropolyacid catalysts for biodiesel production

A series of insoluble heteropolytungstate (H3PW12O40 HPW) salts, CsxH3−xPW12O40 (x=0.9–3x=0.9–3), were synthesized and characterized using a range of bulk and surface sensitive probes including N2 porosimetry, powder XRD, FTIR, XPS, 31P MAS NMR, and NH3 calorimetry. Materials with Cs content in the range x=2.0–2.7x=2.0–2.7 were composed of dispersed crystallites with surface areas ∼100 m2 g−1 and high Brönsted acid strengths [ΔH0ads(NH3)=−150 kJmol−1], similar to the parent heteropolyacid. The number of accessible surface acid sites probed by α -pinene isomerization correlated well with those determined by NH3 adsorption calorimetry and surface area measurements. CsxH3−xPW12O40 were active toward the esterification of palmitic acid and transesterification of tributyrin, important steps in fatty acid and ester processing for biodiesel synthesis. Optimum performance occurs for Cs loadings of x=2.0–2.3x=2.0–2.3, correlating with the accessible surface acid site density. These catalysts were recoverable with no leaching of soluble HPW.

Comparative study of periphyton community structure in long and short-hydroperiod Everglades marshes

The Florida Everglades is a mosaic of short and long-hydroperiod marshes that differ in the depth, duration, and timing of inundation. Algae are important primary producers in widespread Everglades’ periphyton mats, but relationships of algal production and community structure to hydrologic variability are poorly understood. We quantified differences in algal biomass and community structure between periphyton mats in 5 short and 6 long-hydroperiod marshes in Everglades National Park (ENP) in October 2000. We related differences to water depth and total phosphorus (TP) concentration in the water, periphyton and soils. Long and short-hydroperiod marshes differed in water depth (73 cm vs. 13 cm), periphyton TP concentrations (172μg g−1 vs. 107 μg g−1, respectively) and soil TP (284 μg g−1 vs. 145 μg g−1). Periphyton was abundant in both marshes, with short-hydroperiod sites having greater biomass than long-hydroperiod sites (2936 vs. 575 grams ash-free dry mass m−2). A total of 156 algal taxa were identified and separated into diatom (68 species from 21 genera) and “soft algae” (88 non-diatom species from 47 genera) categories for further analyses. Although diatom total abundance was greater in long-hydroperiod mats, diatom species richness was significantly greater in short- hydroperiod periphyton mats (62 vs. 47 diatom taxa). Soft algal species richness was greater in long-hydroperiod sites (81 vs. 67 soft algae taxa). Relative abundances of individual taxa were significantly different among the two site types, with soft algal distributions being driven by water depth, and diatom distributions by water depth and TP concentration in the water and periphyton. Periphyton communities differ between short and long-hydroperiod marshes, but because they share many taxa, alterations in hydroperiod could rapidly

Noise in gallium nitride-based quantum well structures used for nanometer devices in the frequency range 1 Hz--3 Mhz and temperature range 77K--324K

Electronic noise has been investigated in AlxGa1−x N/GaN Modulation-Doped Field Effect Transistors (MODFETs) of submicron dimensions, grown for us by MBE (Molecular Beam Epitaxy) techniques at Virginia Commonwealth University by Dr. H. Morkoç and coworkers. Some 20 devices were grown on a GaN substrate, four of which have leads bonded to source (S), drain (D), and gate (G) pads, respectively. Conduction takes place in the quasi-2D layer of the junction (xy plane) which is perpendicular to the quantum well (z-direction) of average triangular width ∼3 nm. A non-doped intrinsic buffer layer of ∼5 nm separates the Si-doped donors in the AlxGa1−xN layer from the 2D-transistor plane, which affords a very high electron mobility, thus enabling high-speed devices. Since all contacts (S, D, and G) must reach through the AlxGa1−xN layer to connect internally to the 2D plane, parallel conduction through this layer is a feature of all modulation-doped devices. While the shunting effect may account for no more than a few percent of the current IDS, it is responsible for most excess noise, over and above thermal noise of the device. ^ The excess noise has been analyzed as a sum of Lorentzian spectra and 1/f noise. The Lorentzian noise has been ascribed to trapping of the carriers in the AlxGa1−xN layer. A detailed, multitrapping generation-recombination noise theory is presented, which shows that an exponential relationship exists for the time constants obtained from the spectral components as a function of 1/kT. The trap depths have been obtained from Arrhenius plots of log (τT2) vs. 1000/T. Comparison with previous noise results for GaAs devices shows that: (a) many more trapping levels are present in these nitride-based devices; (b) the traps are deeper (farther below the conduction band) than for GaAs. Furthermore, the magnitude of the noise is strongly dependent on the level of depletion of the AlxGa1−xN donor layer, which can be altered by a negative or positive gate bias VGS. ^ Altogether, these frontier nitride-based devices are promising for bluish light optoelectronic devices and lasers; however, the noise, though well understood, indicates that the purity of the constituent layers should be greatly improved for future technological applications. ^

Droplet etching of deep nanoholes for filling with self-aligned complex quantum structures

Strain-free epitaxial quantum dots (QDs) are fabricated by a combination of Al local droplet etching (LDE) of nanoholes in AlGaAs surfaces and subsequent hole filling with GaAs. The whole process is performed in a conventional molecular beam epitaxy (MBE) chamber. Autocorrelation measurements establish single-photon emission from LDE QDs with a very small correlation function g (2)(0)≃ 0.01 of the exciton emission. Here, we focus on the influence of the initial hole depth on the QD optical properties with the goal to create deep holes suited for filling with more complex nanostructures like quantum dot molecules (QDM). The depth of droplet etched nanoholes is controlled by the droplet material coverage and the process temperature, where a higher coverage or temperature yields deeper holes. The requirements of high quantum dot uniformity and narrow luminescence linewidth, which are often found in applications, set limits to the process temperature. At high temperatures, the hole depths become inhomogeneous and the linewidth rapidly increases beyond 640 °C. With the present process technique, we identify an upper limit of 40-nm hole depth if the linewidth has to remain below 100 μeV. Furthermore, we study the exciton fine-structure splitting which is increased from 4.6 μeV in 15-nm-deep to 7.9 μeV in 35-nm-deep holes. As an example for the functionalization of deep nanoholes, self-aligned vertically stacked GaAs QD pairs are fabricated by filling of holes with 35 nm depth. Exciton peaks from stacked dots show linewidths below 100 μeV which is close to that from single QDs.

(Table 1) Stable isotope records of clathrite and water

Aragonitic clathrites are methane-derived precipitates that are found at sites of massive near-seafloor gas hydrate (clathrate) accumulations at the summit of southern Hydrate Ridge, Cascadia margin. These platy carbonate precipitates form inside or in proximity to gas hydrate, which in our study site currently coexists with a fluid that is highly enriched in dissolved ions as salts are excluded during gas hydrate formation. The clathrites record the preferential incorporation of 18O into the hydrate structure and hence the enrichment of 16O in the surrounding brine. We measured d18O values as high as 2.27 per mil relative to Peedee belemnite that correspond to a fluid composition of -1.18 per mil relative to standard mean ocean water. The same trend can be observed in Ca isotopes. Ongoing clathrite precipitation causes enrichment of the 44Ca in the fluid and hence in the carbonates. Carbon isotopes confirm a methane source for the carbonates. Our triple stable isotope approach that uses the three main components of carbonates (Ca, C, O) provides insight into multiple parameters influencing the isotopic composition of the pore water and hence the isotopic composition of the clathrites. This approach provides a tool to monitor the geochemical processes during clathrate and clathrite formation, thus recording the evolution of the geochemical environment of gas hydrate systems.