Fasting status as a consideration for human serum collection and preparation prior to depletion and analysis

The use of comparative serum proteomic analysis has the potential to reveal protein expression changes present at different stages of disease progression. Depletion strategies allow for the enrichment of low-abundance proteins, which are more likely to be clinically significant biomarkers. We have observed that patient serum samples filtered through 0.22 microm cellulose acetate spin filters prior to depletion showed a variable level of retention of patient material on the upper part of the filter. This could potentially be related to the fasting status of the patient as a reduction in the lipid content of samples through the incorporation of a centrifugation step prior to filtration was found to reduce this effect. In order to determine if proteins were being selectively retained during filtration, a 2-D difference gel electrophoresis (2-D DIGE) experiment was performed. This demonstrated no significant selective retention of protein within crude serum samples. However, as this analysis was carried out on crude serum, it must be emphasised that protein loss could be manifest in the low-abundance proteins which would be masked in our analysis. Depletion of the retentate was not possible due to technical limitations, however based on our results a centrifugation step might act as an alternative to filtration in serum processing prior to depletion.     

Aqueous Ammonia Soaking of Switchgrass Followed by Simultaneous Saccharification and Fermentation

Simultaneous saccharification and fermentation (SSF) of switchgrass was performed following aqueous ammonia pretreatment. Switchgrass was soaked in aqueous ammonium hydroxide (30%) with different liquid–solid ratios (5 and 10 ml/g) for either 5 or 10 days. The pretreatment was carried out at atmospheric conditions without agitation. A 40–50% delignification (Klason lignin basis) was achieved, whereas cellulose content remained unchanged and hemicellulose content decreased by approximately 50%. The Sacccharomyces cerevisiae (D₅A)-mediated SSF of ammonia-treated switchgrass was investigated at two glucan loadings (3 and 6%) and three enzyme loadings (26, 38.5, and 77 FPU/g cellulose), using Spezyme CP. The percentage of maximum theoretical ethanol yield achieved was 72. Liquid–solid ratio and steeping time affected lignin removal slightly, but did not cause a significant change in overall ethanol conversion yields at sufficiently high enzyme loadings. These results suggest that ammonia steeping may be an effective method of pretreatment for lignocellulosic feedstocks.     

Novel cyclopropyl diketones and 14-membered macrolides from the soil fungus Hamigera avellanea BCC 17816

Two novel cyclopropyl diketones, hamavellone A (1) and B (2), and two new 14-membered nonaketide macrolactones, hamigeromycin A (3) and B (4), together with six known compounds, 89-250904-F1 (radicicol analogue A, 5), pseurotin A (6), emodin (7), ω-hydroxyemodin (8), and emodin bianthrones (9 and 10) were isolated from the soil fungus Hamigera avellanea BCC 17816. The structures of the new compounds were defined by analysis of NMR and MS data. The absolute stereochemistry of 3 was addressed by chemical correlation to 5. Hamavellone B (2) exhibited antimalarial activity with an IC₅₀ of 5.2 μg/mL, whereas it also showed comparable cytotoxicity.     

Structures of aza-macrocyclic ligands with polyphosphonated dangling groups

Two phosphonated hexaaza-macrocycles with 24- and 26-membered rings have been synthesized via a Mannich reaction and characterized. The novel crystal structures of the macrocyclic ligands show the extended 3-D hydrogen bonded structure in their solid states. These ligands have unusual ring conformations with two or four pendent arms wrapping around the macrocycle with alternating up and down orders. Strong hydrogen bonding between the protonated phosphonate groups and the deprotonated phosphonated groups was observed in those structures together with the complicated solvent hydrogen bonding networks.     

Conditional glycosylation in eukaryotic cells using a biocompatible chemical inducer of dimerization

Chemical inducers of dimerization (CIDs) are cell-permeable small molecules capable of dimerizing two protein targets. The most widely used CID, the natural product rapamycin and its relatives, is immunosuppressive due to interactions with endogenous targets and thus has limited utility in vivo. Here we report a new biocompatible CID, Tmp-SLF, which dimerizes E. coli DHFR and FKBP and has no endogenous mammalian targets that would lead to unwanted in vivo side effects. We employed Tmp-SLF to modulate gene expression in a yeast three-hybrid assay. Finally, we engineered the Golgi-resident glycosyltransferase FucT7 for tunable control by Tmp-SLF in mammalian cells.     

Photochemistry of adsorbed nitrate

In the atmosphere, gas-phase nitrogen oxides including nitric acid react with particle surfaces (e.g., mineral dust and sea salt aerosol) to yield adsorbed nitrate, yet little is known about the photochemistry of nitrate on the surface of these particles. In this study, nitrate adsorbed on alumina surfaces, a surrogate for mineral dust aerosol, is irradiated with broadband light (lambda > 300 nm) in the absence and presence of coadsorbed water, at <1% and 45 +/- 2% relative humidity (%RH), respectively, and molecular oxygen. Upon irradiation, the nitrate ion readily undergoes photolysis to yield nitrogen-containing gas-phase products, NO2, NO, and N2O. Although NO2, NO, and N2O form under the different conditions investigated, both coadsorbed water and molecular oxygen change the gas-phase product distribution, with NO being the major product under dry and humid conditions in the absence of molecular oxygen and NO2 the major product in the presence of molecular oxygen. To the best of our knowledge, this is the first study to investigate the role of solvation by coadsorbed water in the photochemistry of adsorbates at solid interfaces and the roles that molecular oxygen, adsorbed water, and relative humidity may have in photochemical processes on aerosol surfaces that have the potential to alter the chemical balance of the atmosphere.     

Mirror image forms of snow flea antifreeze protein prepared by total chemical synthesis have identical antifreeze activities

The recently discovered glycine-rich snow flea antifreeze protein (sfAFP) has no sequence homology with any known proteins. No experimental structure has been reported for this interesting protein molecule. Here we report the total chemical synthesis of the mirror image forms of sfAFP (i.e., L-sfAFP, the native protein, and D-sfAFP, the native protein's enantiomer). The predicted 81 amino acid residue polypeptide chain of sfAFP contains Cys residues at positions 1, 13, 28, and 43 and was prepared from four synthetic peptide segments by sequential native chemical ligation. After purification, the full-length synthetic polypeptide was folded at 4 degrees C to form the sfAFP protein containing two disulfides. Chemically synthesized sfAFP had the expected antifreeze activity in an ice recrystallization inhibition assay. Mirror image D-sfAFP protein was prepared by the same synthetic strategy, using peptide segments made from d-amino acids, and had an identical but opposite-sign CD spectrum. As expected, D-sfAFP displays the same antifreeze properties as L-sfAFP, because ice presents an achiral surface for sfAFP binding. Facile synthetic access to sfAFP will enable determination of its molecular structure and systematic elucidation of the molecular basis of the antifreeze properties of this unique protein.     

"Giant" multishell CdSe nanocrystal quantum dots with suppressed blinking

Semiconductor nanocrystal quantum dots (NQDs) comprise an important class of inorganic fluorophores for applications from optoelectronics to biology. Unfortunately, to date, NQD optical properties (e.g., their efficient and particle-size-tunable photoluminescence) have been susceptible to instabilities at the bulk and single-particle levels. Specifically, ensemble quantum yields (QYs) in emission are dependent upon NQD surface chemistry and chemical environment, while at the single-particle level, NQDs are characterized by significant fluorescence intermittency (blinking) that hinders applications as single-photon light sources for quantum informatics and biolabels for real-time monitoring of single biomolecules. Furthermore, while NQDs are significantly more photostable than their organic dye counterparts, traditional NQDs photobleach over periods of seconds to many minutes. Here, we demonstrate for the first time that by encapsulating the NQD core in a sufficiently thick inorganic shell, we are able to divorce NQD function from NQD surface chemistry and chemical environment. We show that our "giant" NQDs (g-NQDs) are functionally distinct from standard core-only, core/shell and even core/multishell NQDs. g-NQDs are substantially less sensitive to changes in surface chemistry. They do not photobleach under continuous laser excitation over periods of several hours repeated over several days, and they exhibit markedly different blinking behavior; >20% of the g-NQDs do not blink, while >40% have on-time fractions of >80%. All of these observations are in stark contrast with control samples comprising core-only and standard, thinner core/multishell NQDs.     

Probing the structure of CH5+ by dissociative charge exchange

Dissociative charge exchange of CH5+ with Cs, coupled with quasiclassical trajectory calculations on an ab initio PES for CH5, has been used to probe the structure of the CH5+ cation. Product kinetic energy release distributions and branching ratios for CH5 --> CH4 + H and CH5 --> CH3 + H2 have been compared. The agreement of the product branching ratios provides evidence for the fluxional nature of CH5+.