Matrix-assisted laser desorption/ionization mass spectrometry of DNA using photocleavable biotin

Oligonucleotides containing a photocleavable biotin (5'-PC-biotin) were analyzed by matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) with wavelengths in the ultraviolet (UV) and infrared (IR) from solution and after capture on streptavidin-coated agarose or magnetic beads. The analysis was used to monitor the release of the oligonucleotides as a result of photochemical cleavage of the biotinylated linker. Near-UV pulses (UV-MALDI) led to predominant release of the photocleaved product. In contrast, only the uncleaved analyte was detected using IR pulses (IR-MALDI). Results from MALDI analysis are also presented for DNA containing a photocleavable 5'-amino group which can be covalently linked to a variety of activated surfaces and marker molecules. In a demonstration of this approach, a 5'-PC-biotinylated 49 nt RNA oligonucleotide was enzymatically synthesized using a PC-biotin-r(AG) dinucleotide primer, captured on streptavidin coated magnetic beads and analyzed by UV-MALDI. Potential applications of photocleavable linkers combined with MALDI for the analysis of nucleic acids are discussed.     

Chelating ability of proctolin tetrazole analogue

The aim of the investigation was to establish the chelating ability of a new proctolin analogue of the sequence Arg-Tyr-LeuPsi[CN(4)]Ala-Thr towards copper(II) ions. The insertion of the tetrazole moiety into the peptide sequence has considerably changed the coordination ability of the ligand. Potentiometric and spectroscopic (UV-Vis, CD, EPR) results indicate that the incorporation of 1,5-disubstituted tetrazole ring favours the formation of a stable complex form of CuH(-1)L. This 4N coordination type complex is the dominant species in the physiological pH range. The tetrazole moiety provides one of these nitrogens. The data indicate that Cu(II) ions are strongly trapped inside the peptide backbone. These findings suggest that Cu(II) can hold peptide chains in a bent conformation. This bent conformation may be essential for bioactivity of the tetrazole peptides.     

Mechanisms of resistance to BCR-ABL and other kinase inhibitors

In this article, we are reviewing the molecular mechanisms that lead to kinase inhibitor resistance. As the oncogenic BCR-ABL kinase is the target of the first approved small-molecule kinase inhibitor imatinib, we will first focus on the structural and mechanistic basis for imatinib resistance. We will then show ways how next generations of BCR-ABL inhibitors and alternative targeting strategies have helped to offer effective treatment options for imatinib-resistant patients. Based on these insights, we discuss commonalities and further mechanisms that lead to resistance to other kinase inhibitors in solid tumors. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).     

Ecosystem respiration in a heterogeneous temperate peatland and its sensitivity to peat temperature and water table depth

Background and aims

Ecosystem respiration (R _eco ) is controlled by thermal and hydrologic regimes, but their relative importance in defining the CO₂ emissions in peatlands seems to be site specific. The aim of the paper is to investigate the sensitivity of R _eco to variations in temperature and water table depth (WTD) in a wet, geogenous temperate peatland with a wide variety of vegetation community groups.

Methods

The CO₂ fluxes were measured using chambers. Measurements were made at four microsites with different vegetation communities and peat moisture and temperature conditions every 3 to 4 weeks during the period 2008–2009, 2 years with contrasting WTD patterns. Models were used to examine the relative response of each microsite to variations in peat temperature and WTD and used to estimate annual total R _eco .

Results

Temporal variations in R _eco were strongly related to peat temperature at the 5 cm depth. However, two of the microsites did not show any significant change in this relationship while two others showed contrasting responses including an increase and decrease in temperature sensitivity with deeper WTD. Average R _eco varied among the microsites and tended to be greatest for those with greatest leaf area which also positively correlated with deeper WTD, ash content and degree of peat decomposition at 20 cm. A combined temperature and WTD model explained up to 94 % of the temporal variation in daily average R _eco and was used to show that on an annual basis, R _eco was between 5 and 18 % greater in the warmer year with deeper WTD.

Conclusion

Microsite-specific responses were related to differences in vegetation and peat characteristics among microsites. R _eco may have remained insensitive to WTD variations at one microsite due to the dominance of autotrophic respiration from abundant sedge biomass. At a Sphagnum-dominated microsite, a lack of response may have been due to relatively small variations in WTD that did not greatly influence microbial respiration or due to offsets between decreasing and increasing respiration rates in near-surface and deeper peat. The microsite with the most recalcitrant peat had reduced R _eco sensitivity to temperature under more aerobic conditions while another microsite showed the opposite response, perhaps due to less nutrient availability during the wet year. Ultimately, micro-site specific models with both soil temperature and WTD as explanatory variables described temporal variations in R _eco and highlighted the significant spatial variations in respiration rates that may occur within a single wetland.     

A Comparison of the Effects of Ocular Preservatives on Mammalian and Microbial ATP and Glutathione Levels

The aim of this study was to investigate the mechanism of action of the preservative sodium chlorite (NaClO²), and the relationship with intracellular glutathione depletion. A detailed comparison of the dose responses of two cultured ocular epithelial cell types and four species of microorganism was carried out, and comparisons were also made with the quaternary ammonium compound benzalkonium chloride (BAK), and the oxidant hydrogen peroxide (H²O²). The viability of mammalian and microbial cells was assessed in the same way, by the measurement of intracellular ATP using a bioluminescence method. Intracellular total glutathione was measured by reaction with 5,5′-dithiobis-2-nitrobenzoic acid in a glutathione reductase-dependent recycling assay. BAK and H²O² caused complete toxicity to conjunctival and corneal epithelial cells at ～25?ppm, in contrast to NaClO², where >100?ppm was required. The fungi Candida albicans and Alternaria alternata had a higher resistance to NaClO² than the bacteria Staphyloccus aureus and Pseudomonas aeruginosa, but the bacteria were extremely resistant to H²O². NaClO² caused substantial depletion of intracellular glutathione in all cell types, at concentrations ranging from <10?ppm in Pseudomonas, 25–100?ppm in epithelial cells, to >500?ppm in fungal cells. The mechanisms of cytotoxicity of NaClO², H²O² and BAK all appeared to differ. NaClO² was found to have the best balance of high antibacterial toxicity with low ocular toxicity. The lower toxicity of NaClO² to the ocular cells, compared with BAK and H²O², is in agreement with fewer reported adverse effects of application in the eye.     

Recombinant Lloviu virus as a tool to study viral replication and host responses

Next generation sequencing has revealed the presence of numerous RNA viruses in animal reservoir hosts, including many closely related to known human pathogens. Despite their zoonotic potential, most of these viruses remain understudied due to not yet being cultured. While reverse genetic systems can facilitate virus rescue, this is often hindered by missing viral genome ends. A prime example is Lloviu virus (LLOV), an uncultured filovirus that is closely related to the highly pathogenic Ebola virus. Using minigenome systems, we complemented the missing LLOV genomic ends and identified cis-acting elements required for LLOV replication that were lacking in the published sequence. We leveraged these data to generate recombinant full-length LLOV clones and rescue infectious virus. Similar to other filoviruses, recombinant LLOV (rLLOV) forms filamentous virions and induces the formation of characteristic inclusions in the cytoplasm of the infected cells, as shown by electron microscopy. Known target cells of Ebola virus, including macrophages and hepatocytes, are permissive to rLLOV infection, suggesting that humans could be potential hosts. However, inflammatory responses in human macrophages, a hallmark of Ebola virus disease, are not induced by rLLOV. Additional tropism testing identified pneumocytes as capable of robust rLLOV and Ebola virus infection. We also used rLLOV to test antivirals targeting multiple facets of the replication cycle. Rescue of uncultured viruses of pathogenic concern represents a valuable tool in our arsenal for pandemic preparedness.     

Effect of hyperosmolarity on recombinant protein productivity in baculovirus expression system

A lot of strategies were applied to improve recombinant protein productivity in the baculovirus expression system. In this study we propose for foreign protein production fed-batch cultivation method at hyperosmotic environment induced by increased NaCl content. Obtained results suggested relatively high tolerance and adaptation abilities of Tn-5 insect cells exposed to hyperosmotic stress. The cells under hyperosmotic conditions increased the specific rate of glucose consumption and lactate production. The release of additional energy and precursors as a result of increased metabolism by osmotically stressed culture was involved in recombinant protein synthesis. Recombinant nucleoprotein productivity in nutritional feeding cultures exposed to hyperosmolarity was about 72% higher than that obtained in batch culture at physiological osmolarity, but 31% was a result of feeding and the rest 41% was a result of hyperosmolarity and increasing Na(+) concentration.     

Production of human papillomavirus type 16 early proteins in Bac-To-Bac Expression System (GibcoBRL)

Human papillomavirus type 16 (HPV16) is a major agent in cervical cancer etiology. Its early proteins are responsible for virus persistence, replication and initiation of neoplastic disease. In the present study we describe a use of baculovirus-insect cell expression system for production and study of HPV16 E2 and E4 proteins. The E2 protein binds specifically to viral DNA and E4 protein shows characteristic cytopathic effects on cells.     

The Role of Propagating and Localized Surface Plasmons for SERS Enhancement in Periodic Nanostructures

Periodic arrays of plasmonic nanopillars have been shown to provide large, uniform surface-enhanced Raman scattering (SERS) enhancements. We show that these enhancements are the result of the combined impact of localized and propagating surface plasmon modes within the plasmonic architecture. Here, arrays of periodically arranged silicon nanopillars of varying sizes and interpillar gaps were fabricated to enable the exploration of the SERS response from two different structures; one featuring only localized surface plasmon (LSP) modes and the other featuring LSP and propagating (PSP) modes. It is shown that the LSP modes determine the optimal architecture, and thereby determine the optimum diameter for the structures at a given incident. However, the increase in the SERS enhancement factor for a system in which LSP and PSP cooperatively interact was measured to be over an order of magnitude higher and the peak in the diameter dependence was significantly broadened, thus, such structures not only provide larger enhancement factors but are also more forgiving of lithographic variations.