Unusual Substrates Research Articles

Salt‐adapted bacteria isolated from the Rouge River and potential for degradation of contaminants and biotechnological applications

The current work extends the phenotypic and molecular characterization of the bacterial culture collection from the Rouge River to gain an understanding of the physiology of the strains and their potential for biotechnological applications. Phenotypic and molecular analyses were performed on six unique strains. Most of the strains tested for hydrolytic activities were positive for the production of enzymes, in contrast to previously described species that showed very little hydrolase activities. Little antibiotic resistance was seen among the strains, although Halobacillus (strain 9‐gw1‐su5‐2) was found to be the most resistant to antibiotics. Results revealed the physiological diversity of the strains in terms of their ability to metabolize unusual and refractory substrates. Of the 31 toxic organic compounds, 2 to 18 were used by the strains. Clostridium (strain 9‐gw1‐su5‐2) exhibited the broadest utilization capability. The isolates were versatile in their nutrient abilities and represented a potential source of bacteria and/or genetic material for the degradation of contaminants and biotechnological applications.

Effects of a Flood on Foraging Ecology and Population Dynamics of Swainson's Warblers

Abstract Swainson's Warblers (Limnothlypis swainsonii) have been described as terrestrial leaf litter foraging specialists, and are thought to vacate flooded areas entirely. We report Swainson's Warblers occupying a flooded area in Arkansas and foraging on unusual substrates. We observed Swainson's Warblers feeding in novel ways in the tree canopy and on floating debris. This is the first report of Swainson's Warblers occupying and foraging in flooded habitat, and suggests this species may have more short-term flexibility in foraging substrate than previously thought. Return rates to flooded territories were reduced compared to years without floods and several marked individuals switched to an unflooded area protected by man-made levees. The altered hydrology of rivers constrained by levees may reduce habitat quality for this species.

Stress-Induced Changes of Phospholipids in Betaproteobacterium Aromatoleum aromaticum Strain EbN1 due to Alkylbenzene Growth Substrates

The denitrifying betaproteobacterium strain EbN1 degrades toluene and ethylbenzene under anoxic conditions. Alkylbenzenes are unusual substrates, since their extraordinary chemical stability necessitates complex reactions and their toxic properties as solvents challenge cellular viability. To study the solvent impact on membrane lipid composition, strain EbN1 was grown at low, standard and semi-inhibitory concentrations of toluene (70, 240, and 740 µM) and ethylbenzene (80, 210, and 315 µM). At semi-inhibitory concentrations, phosphatidylglycerol increased at the expense of phosphatidylethanolamine. Moreover, phosphatidylcholine proportions increased and tentatively identified N-hexanoyl-phosphatidylethanolamine was detected. All observed changes in membrane lipid composition are interpreted as the organism’s response to prevent the maceration of the cell membrane.

Structure of a Eukaryotic Nonribosomal Peptide Synthetase Adenylation Domain That Activates a Large Hydroxamate Amino Acid in Siderophore Biosynthesis

Nonribosomal peptide synthetases (NRPSs) are large, multidomain proteins that are involved in the biosynthesis of an array of secondary metabolites. We report the structure of the third adenylation domain from the siderophore-synthesizing NRPS, SidN, from the endophytic fungus Neotyphodium lolii. This is the first structure of a eukaryotic NRPS domain, and it reveals a large binding pocket required to accommodate the unusual amino acid substrate, N(delta)-cis-anhydromevalonyl-N(delta)-hydroxy-L-ornithine (cis-AMHO). The specific activation of cis-AMHO was confirmed biochemically, and an AMHO moiety was unambiguously identified as a component of the fungal siderophore using mass spectroscopy. The protein structure shows that the substrate binding pocket is defined by 17 amino acid residues, in contrast to both prokaryotic adenylation domains and to previous predictions based on modeling. Existing substrate prediction methods for NRPS adenylation domains fail for domains from eukaryotes due to the divergence of their signature sequences from those of prokaryotes. Thus, this new structure will provide a basis for improving prediction methods for eukaryotic NRPS enzymes that play important and diverse roles in the biology of fungi.

Simultaneous nutrients and carbon removal during pretreated swine slurry degradation in a tubular biofilm photobioreactor

The biodegradation potential of an innovative enclosed tubular biofilm photobioreactor inoculated with a Chlorella sorokiniana strain and an acclimated activated sludge consortium was evaluated under continuous illumination and increasing pretreated (centrifuged) swine slurry loading rates. This photobioreactor configuration provided simultaneous and efficient carbon, nitrogen, and phosphorous treatment in a single-stage process at sustained nitrogen and phosphorous removals efficiencies ranging from 94% to 100% and 70-90%, respectively. Maximum total organic carbon (TOC), NH(4) (+), and PO(4) (3-) removal rates of 80 +/- 5 g C m(r) (-3) day(-1), 89 +/- 5 g N m(r) (-3) day(-1), and 13 +/- 3 g P m(r) (-3) day(-1), respectively, were recorded at the highest swine slurry loadings (TOC of 1,247 +/- 62 mg L(-1), N-NH(4) (+) of 656 +/- 37 mg L(-1), P-PO(4) (3+) of 117 +/- 19 mg L(-1), and 7 days of hydraulic retention time). The unusual substrates diffusional pathways established within the phototrophic biofilm (photosynthetic O(2) and TOC/NH(4) (+) diffusing from opposite sides of the biofilm) allowed both the occurrence of a simultaneous denitrification/nitrification process at the highest swine slurry loading rate and the protection of microalgae from any potential inhibitory effect mediated by the combination of high pH and high NH(3) concentrations. In addition, this biofilm-based photobioreactor supported efficient biomass retention (>92% of the biomass generated during the pretreated swine slurry biodegradation).

Palladium‐Catalyzed Substitution of Allylic Fluorides

As unusual substrates for the Tsuji-Trost allylation reaction, allylic fluorides are responsive to palladium-catalyzed substitution. Their activity towards this reaction fits in the series OCO(2)Me>OBz>>F>>OAc. The classic stereoretention mechanism that involves sequential inversions does not operate in this case. Several distinct cases are considered.

Catalytic C-C Bond Formation in Natural Products Synthesis: Highlights From The Years 2000 – 2005

The development of new catalytic reactions for C-C bond formation has played a significant role in natural products synthesis. In this article we review catalytic C-C bond formation with respect to the carbon atoms hybridization and the products formed. The reactions of unusual substrates and the development of new reaction conditions and catalyst systems are included. This survey highlights the use of catalysts in natural products synthesis during the years 2000-2005.

Peptide Microarray Analysis of Substrate Specificity of the Transmembrane Ser/Thr Kinase KPI-2 Reveals Reactivity with Cystic Fibrosis Transmembrane Conductance Regulator and Phosphorylase

Human lemur (Lmr) kinases are predicted to be Tyr kinases based on sequences and are related to neurotrophin receptor Trk kinases. This study used homogeneous recombinant KPI-2 (Lmr2, LMTK2, Cprk, brain-enriched protein kinase) kinase domain and a library of 1,154 peptides on a microarray to analyze substrate specificity. We found that KPI-2 is strictly a Ser/Thr kinase that reacts with Ser either preceded by or followed by Pro residues but unlike other Pro-directed kinases does not strictly require an adjacent Pro residue. The most reactive peptide in the library corresponds to Ser-737 of cystic fibrosis transmembrane conductance regulator, and the recombinant R domain of cystic fibrosis transmembrane conductance regulator was a preferred substrate. Furthermore the KPI-2 kinase phosphorylated peptides corresponding to the single site in phosphorylase and purified phosphorylase b, making this only the second known phosphorylase b kinase. Phosphorylase was used as a specific substrate to show that KPI-2 is inhibited in living cells by addition of nerve growth factor or serum. The results demonstrate the utility of the peptide library to probe specificity and discover kinase substrates and offer a specific assay that reveals hormonal regulation of the activity of this unusual transmembrane kinase.

Role of eosinophil peroxidase in host defense and disease pathology

Three unusual substrates—bromide (Br −), nitrite (NO 2 −), and thiocyanate (SCN −)—compete for oxidation by eosinophil peroxidase (EPO) in physiologic fluids in the presence of H 2O 2 to yield, respectively, hypobromous acid (HOBr), nitrogen dioxide (NO 2 ), or hypothiocyanous acid (HOSCN). These oxidant products have strikingly different reactivities: HOBr and NO 2 are potent, widely reactive, membrane-lytic oxidants whereas HOSCN is a weak, SH-specific oxidant that penetrates into cells and imposes an intracellular oxidant stress that can activate kinase pathways and transcription factors that profoundly influence gene expression in host cells. All three oxidants are lethal for pathogens. SCN − is the strongly preferred substrate for the EPO/H 2O 2. Specific biomarkers document that EPO-dependent oxidants are generated at sites of inflammation, but direct evidence that these oxidants cause disease is confined to the observation that an EPO knockout mouse line has dramatically less pathologic damage than do wild type animals in a murine model of ulcerative colitis.

Bendable GaAs metal-semiconductor field-effect transistors formed with printed GaAs wire arrays on plastic substrates

Micro/nanowires of GaAs with integrated ohmic contacts have been prepared from bulk wafers by metal deposition and patterning, high-temperature annealing, and anisotropic chemical etching. These wires provide a unique type of material for high-performance devices that can be built directly on a wide range of unusual device substrates, such as plastic or paper. In particular, transfer printing organized arrays of these wires at low temperatures onto plastic substrates yield high-quality bendable metal-semiconductor field-effect transistors. Electrical and mechanical characterization of devices on poly(ethylene terephthalate) illustrates the level of performance that can be achieved. These results indicate promise for this approach to high-speed flexible circuits for emerging applications in consumer and military electronic systems.

Extreme bendability of single-walled carbon nanotube networks transferred from high-temperature growth substrates to plastic and their use in thin-film transistors

In this paper we describe printing methods for transferring single-walled carbon nanotubes (SWNTs) from high-temperature growth substrates to flexible, low-cost plastic supports. Thin-film transistors (TFTs) built with networks of transferred SWNTs grown by chemical vapor deposition show good performance—mobilities and on∕off current ratios similar to those of devices fabricated on the growth substrates for a wide range of channel lengths. Bending tests on these TFTs show that their output current varies only in a narrow (±5%) range, even for bend radii that induce surface strains larger than 1%. Similar structures evaluated under sharp folding, with strains larger than 20%, show that the SWNT networks are operational even under extreme bending conditions. This level of mechanical robustness, the good electrical performance, and optical transparency make transferred SWNT networks an attractive type of electronic material for applications in macroelectronics, sensors, and other systems that require wide area coverage and unusual substrates.

Dynamic Kinetic Resolution during a Cascade Reaction on Substrates with Chiral All‐Carbon Quaternary Centers

Unusual substrates for cascade reactions: Racemic β-ketoesters with all-carbon quaternary centers were used as starting materials in a dynamic kinetic resolution process to produce complex polycycles in high enantio- and diastereoselectivities (see scheme; TBS=tert-butyldimethylsilyl). The cascade reactions involved epimerization in the second step through the formation and cleavage of multiple CC bonds in a retro-aldol/aldol equilibrium.

31P NMR and Genetic Analysis Establish hinT as the Only Escherchia coli Purine Nucleoside Phosphoramidase and as Essential for Growth under High Salt Conditions

Eukaryotic cells encode AMP-lysine (AMP-N-epsilon-(N-alpha-acetyl lysine methyl ester) 5'-phosphoramidate) hydrolases related to the rabbit histidine triad nucleotide-binding protein 1 (Hint1) sequence. Bacterial and archaeal cells have Hint homologs annotated in a variety of ways, but the enzymes have not been characterized, nor have phenotypes been described due to loss of enzymatic activity. We developed a quantitative (31)P NMR assay to determine whether Escherichia coli possesses an adenosine phosphoramidase activity. Indeed, soluble lysates prepared from wild-type laboratory E. coli exhibited activity on the model substrate adenosine 5'-monophosphoramidate (AMP-NH(2)). The E. coli Hint homolog, which had been comprehensively designated ycfF and is here named hinT, was cloned, overexpressed, purified, and characterized with respect to purine nucleoside phosphoramidate substrates. Bacterial hinT was several times more active than human or rabbit Hint1 on five model substrates. In addition, bacterial and mammalian enzymes preferred guanosine versus adenosine phosphoramidates as substrates. Analysis of the lysates from a constructed hinT knock-out strain of E. coli demonstrated that all of the cellular purine nucleoside phosphoramidase activity is due to hinT. Physiological analysis of this mutant revealed that the loss of hinT results in failure to grow in media containing 0.75 m KCl, 0.9 m NaCl, 0.5 m NaOAc, or 10 mm MnCl(2). Thus, cation-resistant bacterial cell growth may be dependent on the hydrolysis of adenylylated and/or guanylylated phosphoramidate substrates by hinT.

Adsorption of Helium and Other Gases to Carbon Nanotubes and Nanotube Bundles

There is considerable interest in the adsorption of helium and other gases to unconventional substrates. Carbon nanotubes and bundles of such tubes provide a relatively unique and interesting substrate opportunity. We describe recent experimental and theoretical work from a number of groups that sheds light on the behavior of various gases adsorbed to these unusual substrates.

Cyclic Ketones and Substituted α‐Keto Acids as Alternative Substrates for Novel Biginelli‐Like Scaffold Syntheses.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Cyclic ketones and substituted α-keto acids as alternative substrates for novel Biginelli-like scaffold syntheses

The reactions of benzocyclic ketones and α-ketoacids as carbonyl components in the Biginelli reaction were investigated. These unusual Biginelli substrates furnished novel drug-like dihydropyrimidinone scaffolds suitable for further elaboration.

Magnetic properties of highly resistive BaFeO3 thin films epitaxially grown on SrTiO3 single-crystal substrates

We have synthesized single-crystalline films of BaFeO3 (BFO), which may contain unusual tetravalent Fe ions, on (100) and (111) SrTiO3 substrates by pulsed laser-beam deposition. The epitaxially grown BFO is considered to have a pseudocubic perovskite-type crystal structure with some oxygen vacancies. The films were found to be highly insulating, and showed a high value of dielectric constant of ε=59. The magnetization curve of the films exhibited hysteresis, as well as small remanent magnetization. The origin of the observed small magnetization can be ascribed to the mixed valence state of the Fe4+ and Fe3+ ions. The present epitaxially grown BFO apparently had some different magnetic and dielectric properties from those for bulk BFO as well as for the previously reported other Fe4+ oxides: coexisting high resistivity and spontaneous magnetization at room temperature.

An Organic FET structure for unconventional substrates

ABSTRACTA structure for organic TFTs suitable for being transferred on unusual substrates is described in each technological step. The proposed device consists in a “bottom-structure” assembled on a flexible and transparent insulating layer, without any substrate, with source and drain contacts on one side and the gate on the opposite side. The main advantage is to avoid the substrate because the insulator itself is able to support the whole structure. For this reason, application to any kind of substrates after the built-in process is possible.

An Organic FET structure for unconventional substrates

ABSTRACTA structure for organic TFTs suitable for being transferred on unusual substrates is described in each technological step. The proposed device consists in a “bottom-structure” assembled on a flexible and transparent insulating layer, without any substrate, with source and drain contacts on one side and the gate on the opposite side. The main advantage is to avoid the substrate because the insulator itself is able to support the whole structure. For this reason, application to any kind of substrates after the built-in process is possible.

Distinctive features of the two classes of eukaryotic peptide deformylases

Peptide deformylases (PDFs) are essential enzymes of the N-terminal protein processing pathway of eubacteria. The recent discovery of two types of PDFs in higher plants, PDF1A and PDF1B, and the detection of PDF1A in humans, have raised questions concerning the importance of deformylation in eukaryotes. Here, we have characterized fully in vitro and compared the properties of the two classes of eukaryotic PDFs, PDF1A and PDF1B, using the PDFs from Arabidopsis thaliana and Lycopersicon esculentum. We have shown that the PDFs of a given class (1A or 1B) all display similar features, independently of their origin. We also observed similar specificity of all plant PDFs for natural substrate peptides, but identified a number of biochemical differences between the two classes (1A or 1B). The main difference lies at the level of the bound cofactor, iron for PDF1B-like bacterial PDFs, and zinc for PDF1A. The nature of the metal cation has important consequences concerning the relative sensitivity to oxygen of the two plant PDFs. Investigation of the specificity of these enzymes with unusual substrates revealed additional differences between the two types of PDFs, enabling us to identify specific inhibitors with a lower affinity against PDF1As. However, the two plant PDFs were inhibited equally strongly in vitro by actinonin, an antibiotic that specifically acts on bacterial PDFs. Uptake of actinonin by A. thaliana seedlings was used to investigate the function of PDFs in the plant. Because it induces an albino phenotype, we conclude that deformylation is likely to play an essential role in the chloroplast.