Exploring TERRA (TElomeric Repeat-containing RNA) Expression and Regulation During Cell Growth in Saccharomyces cerevisiae

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High yield production of a soluble bifidobacterial β-galactosidase (BbgIV) inE. coliDH5α with improved catalytic efficiency for the synthesis of prebiotic galactooligosaccharides

The bifidobacterial β-galactosidase (BbgIV) was produced in E. coli DH5α at 37 and 30 °C in a 5 L bioreactor under varied conditions of dissolved oxygen (dO2) and pH. The yield of soluble BbgIV was significantly (P < 0.05) increased once the dO2 dropped to 0–2% and remained at such low values during the exponential phase. Limited dO2 significantly (P < 0.05) increased the plasmid copy number and decreased the cells growth rate. Consequently, the BbgIV yield increased to its maximum (71–75 mg per g dry cell weight), which represented 20–25% of the total soluble proteins in the cells. In addition, the specific activity and catalytic efficiency of BbgIV were significantly (P < 0.05) enhanced under limited dO2 conditions. This was concomitant with a change in the enzyme secondary structure, suggesting a link between the enzyme structure and function. The knowledge generated from this work is very important for producing BbgIV as a biocatalyst for the development of a cost-effective process for the synthesis of prebiotic galactooligosaccharides from lactose.

Nucleation and growth of carbon nanotubes in a mechano-thermal process

Separate nucleation and growth processes of carbon nanotubes were found in a mechano-thermal method in which carbon nanotubes are produced by first mechanical milling of graphite powder at room temperature and subsequent thermal annealing up to 1400 °C. The ball-milled graphite contains nucleation structures (nanosized metal particles and deformed (0 0 2) layers containing pentagons), and disordered carbon as a free carbon atom source. The subsequent annealing activates the growth of two types of multi-walled nanotubes in the absence of carbon vapor. Thin nanotubes (diameter <20 nm) are formed via crystallization of the disordered carbon with the preferred formation of the (0 0 2) basal planes. Thick nanotubes (diameter >20 nm) are formed through a metal catalytic solution–precipitation process (solid–liquid–solid). In both cases, carbon nanotubes grew out from disordered carbon particles with closed tips.

Growth and structure of prismatic boron nitride nanorods

Prismatic boron nitride nanorods have been grown on single crystal silicon substrates by mechanical ball-milling followed by annealing at 1300 °C. Growth takes place by rapid surface diffusion of BN molecules, and follows heterogeneous nucleation at catalytic particles of an Fe/Si alloy. Lattice imaging transmission electron microscopy studies reveal a central axial row of rather small truncated pyramidal nanovoids on each nanorod, surrounded by three basal planar BN domains which, with successive deposition of epitaxial layers adapt to the void geometry by crystallographic faceting. The bulk strain in the nanorods is taken up by the presence of what appear to be simple nanostacking faults in the external, near-surface domains which, like the nanovoids are regularly repetitive along the nanorod length. Growth terminates with a clear cuneiform tip for each nanorod. Lateral nanorod dimensions are essentially determined by the size of the catalytic particle, which remains as a foundation essentially responsible for base growth. Growth, structure, and dominating facets are shown to be consistent with a system which seeks lowest bulk and surface energies according to the well-known thermodynamics of the capillarity of solids.

Synthesis and growth of hematite nanodiscs through a facile hydrothermal approach

This study reports a facile hydrothermal method for the synthesis of monodispersed hematite (α-Fe2O3) nanodiscs under mild conditions. The method has features such as no use of surfactants, no toxic precursors, and no requirements of high-temperature decomposition of iron precursors in non-polar solvents. By this method, α-Fe2O3 nanodiscs were achieved with diameter of 50 ± 10 nm and thickness of ~6.5 nm by the hydrolysis of ferric chloride. The particle characteristics (e.g., shape, size, and distribution) and functional properties (e.g., magnetic and catalytic properties) were investigated by various advanced techniques, including TEM, AFM, XRD, BET, and SQUID. Such nanodiscs were proved to show unique magnetic properties, i.e., superparamagnetic property at a low temperature (e.g., 20 K) but ferromagnetic property at a room temperature (~300 K). They also exhibit low-temperature (<623 K) catalytic activity in CO oxidation because of extremely clean surfaces due to non-involvement of surfactants, compared with those spheres and ellipsoids capped by PVP molecules.

Growth mechanism and photocatalytic properties of SrWO4 microcrystals synthesized by injection of ions into a hot aqueous solution

This paper reports our initial research to obtain SrWO4 microcrystals by the injection of ions into a hot aqueous solution and their photocatalytic (PC) properties. These microcrystals were structurally characterized by X-ray diffraction (XRD), Rietveld refinements and Fourier transform (FT)-Raman spectroscopy. The shape and average size of these SrWO 4 microcrystals were observed by field emission scanning electron microscopy (FE-SEM) and transmission electron microscopy (TEM). In addition, we have investigated the PC activity of microcrystals for the degradation of rhodamine B (RhB) and rhodamine 6G (Rh6G) dyes. XRD patterns, Rietveld refinement data and FT-Raman spectroscopy confirmed that SrWO4 microcrystals have a scheelite-type tetragonal structure without deleterious phases. FT-Raman spectra exhibited 12 Raman-active modes in a range from 50 to 1000 cm-1. FE-SEM and TEM images suggested that the SrWO4 microcrystals (rice-like - 95%; star-, flower-, and urchin-like - 5%) were formed by means of primary/secondary nucleation events and self-assembly processes. Based on these FE-SEM/TEM images, a crystal growth mechanism was proposed and discussed in details in this work. Finally, a good PC activity was first discovered of the SrWO4 microcrystals for the degradation of RhB after 80 min and Rh6G after 50 min dyes under ultraviolet-light, respectively. © 2012 The Society of Powder Technology Japan. Published by Elsevier B.V. and The Society of Powder.

Bio-hydrogen production based on catalytic reforming of volatiles generated by cellulose pyrolysis: an integrated process for ZnO reduction and zinc nanostructures fabrication

The paper presents a process of cellulose thermal degradation with bio-hydrogen generation and zinc nanostructures synthesis. Production of zinc nanowires and zinc nanoflowers was performed by a novel processes based on cellulose pyrolysis, volatiles reforming and direct reduction of ZnO. The bio-hydrogen generated in situ promoted the ZnO reduction with Zn nanostructures formation by vapor–solid (VS) route. The cellulose and cellulose/ZnO samples were characterized by thermal analyses (TG/DTG/DTA) and the gases evolved were analyzed by FTIR spectroscopy (TG/FTIR). The hydrogen was detected by TPR (Temperature Programmed Reaction) tests. The results showed that in the presence of ZnO the cellulose thermal degradation produced larger amounts of H2 when compared to pure cellulose. The process was also carried out in a tubular furnace with N2 atmosphere, at temperatures up to 900 °C, and different heating rates. The nanostructures growth was catalyst-free, without pressure reduction, at temperatures lower than those required in the carbothermal reduction of ZnO with fossil carbon. The nanostructures were investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS) and transmission electron microscopy (TEM). The optical properties were investigated by photoluminescence (PL). One mechanism was presented in an attempt to explain the synthesis of zinc nanostructures that are crystalline, were obtained without significant re-oxidation and whose morphologies are dependent on the heating rates of the process. This route presents a potential use as an industrial process taking into account the simple operational conditions, the low costs of cellulose and the importance of bio-hydrogen and nanostructured zinc.

New catalytic processes for the upgrading of furfural and 5-hydroxymethylfurfural to chemicals and fuels

The demand of energy, fuels and chemicals is increasing due to the strong growth of some countries in the developing world and the development of the world economy. Unfortunately, the general picture derived sparked an exponential increase in crude oil prices with a consequent increase of the chemical, by-products and energy, depleting the global market. Nowadays biomass are the most promising alternative to fossil fuels for the production of chemicals and fuels. In this work, the development of three different catalytic processes for the valorization of biomass-derived has been investigated. 5-hydroxymethylfurfural oxidation was studied under mild reaction condition using gold and gold/copper based catalysts synthetized from pre-formed nanoparticles and supported onto TiO2 and CeO2. The analysis conducted on catalysts showed the formation of alloys gold/copper and a strong synergistic effect between the two metals. For this reason the bimetallic catalysts supported on titania showed a higher catalytic activity respect to the monometallic catalysts. The process for the production of 2,5-bishydroxymethyl furan (BHMF) was also optimized by means the 5-hydroxymethylfurfural hydrogenation using the Shvo complex. Complete conversion of HMF was achieved working at 90 °C and 10 bar of hydrogen. The complex was found to be re-usable for at least three catalytic cycles without suffering any type of deactivation. Finally, the hydrogenation of furfural and HMF was carried out, developing the process of hydrogen transfer by using MgO as a catalyst and methanol as a hydrogen donor. Quantitative yields to alcohols have been achieved in a few hours working in mild condition: 160 °C and at autogenous pressure. The only by-products formed were light products such as CO, CO2 and CH4 (products derived from methanol transformation), easily separable from the reaction solution depressurizing the reactor.

The catalytic class I(A) PI3K isoforms play divergent roles in breast cancer cell migration

Transforming growth factor-β (TGFβ) plays an important role in breast cancer metastasis. Here phosphoinositide 3-kinase (PI3K) signalling was found to play an essential role in the enhanced migration capability of fibroblastoid cells (FibRas) derived from normal mammary epithelial cells (EpH4) by transduction of oncogenic Ras (EpRas) and TGFβ1. While expression of the PI3K isoform p110δ was down-regulated in FibRas cells, there was an increase in the expression of p110α and p110β in the fibroblastoid cells. The PI3K isoform p110β was found to specifically contribute to cell migration in FibRas cells, while p110α contributed to the response in EpH4, EpRas and FibRas cells. Akt, a downstream targets of PI3K signalling, had an inhibitory role in the migration of transformed breast cancer cells, while Rac, Cdc42 and the ribosomal protein S6 kinase (S6K) were necessary for the response. Together our data reveal a novel specific function of the PI3K isoform p110β in the migration of cells transformed by oncogenic H-Ras and TGF-β1.

Targeting the phosphoinositide 3-kinase p110-α isoform impairs cell proliferation, survival, and tumor growth in small cell lung cancer

The phosphoinositide 3-kinase (PI3K) pathway is fundamental for cell proliferation and survival and is frequently altered and activated in neoplasia, including carcinomas of the lung. In this study, we investigated the potential of targeting the catalytic class I(A) PI3K isoforms in small cell lung cancer (SCLC), which is the most aggressive of all lung cancer types.

Nitric oxide down-regulates the expression of the catalytic NADPH oxidase subunit Nox1 in rat renal mesangial cells

Glomerular mesangial cells can produce high amounts of nitric oxide (NO) and reactive oxygen species (ROS). Here we analyzed the impact of NO on the ROS-generating system, particularly on the NADPH oxidase Nox1. Nox1 mRNA and protein levels were markedly decreased by treatment of mesangial cells with the NO-releasing compound DETA-NO in a concentration- and time-dependent fashion. By altering the cGMP signaling system with different inhibitors or activators, we revealed that the effect of NO on Nox1 expression is at least in part mediated by cGMP. Analysis of a reporter construct comprising the 2547 bp of the nox1 promoter region revealed that a stimulatory effect of IL-1beta on nox1 transcription is counteracted by an inhibitory effect of IL-1beta-evoked endogenous NO formation. Moreover, pretreatment of mesangial cells with DETA-NO attenuated platelet-derived growth factor (PDGF)-BB or serum stimulated production of superoxide as assessed by real-time EPR spectroscopy and dichlorofluorescein formation. Transfection of mesangial cells with siRNAs directed against Nox1 and Nox4 revealed that inhibition of Nox1, but not Nox4 expression, is responsible for the reduced ROS formation by NO. Obviously, there exists a fine-tuned crosstalk between NO and ROS generating systems in the course of inflammatory diseases.

Targeting class IA PI3K isoforms selectively impairs cell growth, survival, and migration in glioblastoma.

The phosphoinositide 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) pathway is frequently activated in human cancer and plays a crucial role in glioblastoma biology. We were interested in gaining further insight into the potential of targeting PI3K isoforms as a novel anti-tumor approach in glioblastoma. Consistent expression of the PI3K catalytic isoform PI3K p110α was detected in a panel of glioblastoma patient samples. In contrast, PI3K p110β expression was only rarely detected in glioblastoma patient samples. The expression of a module comprising the epidermal growth factor receptor (EGFR)/PI3K p110α/phosphorylated ribosomal S6 protein (p-S6) was correlated with shorter patient survival. Inhibition of PI3K p110α activity impaired the anchorage-dependent growth of glioblastoma cells and induced tumor regression in vivo. Inhibition of PI3K p110α or PI3K p110β also led to impaired anchorage-independent growth, a decreased migratory capacity of glioblastoma cells, and reduced the activation of the Akt/mTOR pathway. These effects were selective, because targeting of PI3K p110δ did not result in a comparable impairment of glioblastoma tumorigenic properties. Together, our data reveal that drugs targeting PI3K p110α can reduce growth in a subset of glioblastoma tumors characterized by the expression of EGFR/PI3K p110α/p-S6.

Molecular cloning and characterization of an amidase from Arabidopsis thaliana capable of converting indole-3-acetamide into the plant growth hormone, indole-3-acetic acid

Acylamidohydrolases from higher plants have not been characterized or cloned so far. AtAMI1 is the first member of this enzyme family from a higher plant and was identified in the genome of Arabidopsis thaliana based on sequence homology with the catalytic-domain sequence of bacterial acylamidohydrolases, particularly those that exhibit indole-3-acetamide amidohydrolase activity. AtAMI1 polypeptide and mRNA are present in leaf tissues, as shown by immunoblotting and RT-PCR, respectively. AtAMI1 was expressed from its cDNA in enzymatically active form and exhibits substrate specificity for indole-3-acetamide, but also some activity against l-asparagine. The recombinant enzyme was characterized further. The results show that higher plants have acylamidohydrolases with properties similar to the enzymes of certain plant-associated bacteria such as Agrobacterium-, Pseudomonas- and Rhodococcus-species, in which these enzymes serve to synthesize the plant growth hormone, indole-3-acetic acid, utilized by the bacteria to colonize their host plants. As indole-3-acetamide is a native metabolite in Arabidopsis thaliana, it can no longer be ruled out that one pathway for the biosynthesis of indole-3-acetic acid involves indole-3-acetamide-hydrolysis by AtAMI1.

Assembly of a catalytic unit for RNA microhelix aminoacylation using nonspecific RNA binding domains

An assembly of a catalytic unit for aminoacylation of an RNA microhelix is demonstrated here. This assembly may recapitulate a step in the historical development of tRNA synthetases. The class-defining domain of a tRNA synthetase is closely related to the primordial enzyme that catalyzed synthesis of aminoacyl adenylate. RNA binding elements are imagined to have been added so that early RNA substrates could be docked proximal to the activated amino acid. RNA microhelices that recapitulate the acceptor stem of modern tRNAs are potential examples of early substrates. In this work, we examined a fragment of Escherichia coli alanyl-tRNA synthetase, which catalyzes aminoacyl adenylate formation but is virtually inactive for catalysis of RNA microhelix aminoacylation. Fusion to the fragment of either of two unrelated nonspecific RNA binding domains activated microhelix aminoacylation. Although the fusion proteins lacked the RNA sequence specificity of the natural enzyme, their activity was within 1–2 kcal⋅mol−1 of a truncated alanyl-tRNA synthetase that has aminoacylation activity sufficient to sustain cell growth. These results show that, starting with an activity for adenylate synthesis, barriers are relatively low for building catalytic units for aminoacylation of RNA helices.

Identification of the yeast 20S proteasome catalytic centers and subunit interactions required for active-site formation

The proteasome is responsible for degradation of substrates of the ubiquitin pathway. 20S proteasomes are cylindrical particles with subunits arranged in a stack of four heptameric rings. The outer rings are composed of α subunits, and the inner rings are composed of β subunits. A well-characterized archaeal proteasome has a single type of each subunit, and the N-terminal threonine of the β subunit is the active-site nucleophile. Yeast proteasomes have seven different β subunits and exhibit several distinct peptidase activities, which were proposed to derive from disparate active sites. We show that mutating the N-terminal threonine in the yeast Pup1 β subunit eliminates cleavage after basic residues in peptide substrates, and mutating the corresponding threonine of Pre3 prevents cleavage after acidic residues. Surprisingly, neither mutation has a strong effect on cell growth, and they have at most minor effects on ubiquitin-dependent proteolysis. We show that Pup1 interacts with Pup3 in each β subunit ring. Our data reveal that different proteasome active sites contribute very differently to protein breakdown in vivo, that contacts between particular subunits in each β subunit ring are critical for active-site formation, and that active sites in archaea and different eukaryotes are highly similar.