2008, Pieck, A.C., Drescher, A., Wiesmann, K.G., Messerschmidt, J., Weber, G., Strumberg, D., Hilger, R.A., Scheulen, M.E., Jaehde, U.

In this study, we investigated the kinetics of oxaliplatin-DNA adduct formation in white blood cells of cancer patients in relation to efficacy as well as oxaliplatin-associated neurotoxicity. Thirty-seven patients with various solid tumours received 130 mg m−2 oxaliplatin as a 2-h infusion. Oxaliplatin-DNA adduct levels were measured in the first cycle using adsorptive stripping voltammetry. Platinum concentrations were measured in ultrafiltrate and plasma using a validated flameless atomic absorption spectrometry method. DNA adduct levels showed a characteristic time course, but were not correlated to platinum pharmacokinetics and varied considerably among individuals. In patients showing tumour response, adduct levels after 24 and 48 h were significantly higher than in nonresponders. Oxaliplatin-induced neurotoxicity was more pronounced but was not significantly different in patients with high adduct levels. The potential of oxaliplatin-DNA adduct measurements as pharmacodynamic end point should be further investigated in future trials.

2008, Veldhoen, Sandra, Laufer, Sandra D., Restle, Tobias

Despite the fact that non-viral nucleic acid delivery systems are generally considered to be less efficient than viral vectors, they have gained much interest in recent years due to their superior safety profile compared to their viral counterpart. Among these synthetic vectors are cationic polymers, branched dendrimers, cationic liposomes and cellpenetrating peptides (CPPs). The latter represent an assortment of fairly unrelated sequences essentially characterised by a high content of basic amino acids and a length of 10-30 residues. CPPs are capable of mediating the cellular uptake of hydrophilic macromolecules like peptides and nucleic acids (e.g. siRNAs, aptamers and antisenseoligonucleotides), which are internalised by cells at a very low rate when applied alone. Up to now, numerous sequences have been reported to show cell-penetrating properties and many of them have been used to successfully transport a variety of different cargos into mammalian cells. In recent years, it has become apparent that endocytosis is a major route of internalisation even though the mechanisms underlying the cellular translocation of CPPs are poorly understood and still subject to controversial discussions. In this review, we will summarise the latest developments in peptide-based cellular delivery of nucleic acid cargos. We will discuss different mechanisms of entry, the intracellular fate of the cargo, correlation studies of uptake versus biological activity of the cargo as well as technical problems and pitfalls.

2000, Yáñez, J., Berndt, H.

An integrated HPF-system using HPLC and HT-HHP-nebulizer is used for matrix separation by the determination of heavy metals in highly concentrated solutions with FAAS. The separation of the matrix (NaCl) is achieved in a HPLC RP-C18 column after heavy metal complexing with trans-1,2-diaminciclohexane-N,N,N ,N -tetraacetic acid (CDTA). Matrix separation and the metal determination can be realized in less than one minute, without any interference from the matrix. The detection limits of Cd(II), Co(II), Cr(VI), Cu(II), Mn(II) and Zn(II) by FAAS were improved in one order of magnitude in compare with the direct determination by pneumatic nebulization nebulizer.

2001, Kulmala, M., Hämeri, K., Aalto, P.P., Mäkelä, J.M., Pirjola, L., Nilsson, E. Douglas, Buzorius, G., Rannik, Ü., Dal Maso, M., Seidl, W., Hoffman, T., Janson, R., Hansson, H.-C., Viisanen, Y., Laaksonen, A., O’dowd, C.D.

Aerosol formation and subsequent particle growth in ambient air have been frequently observed at a boreal forest site (SMEAR II station) in Southern Finland. The EU funded project BIOFOR (Biogenic aerosol formation in the boreal forest) has focused on: (a) determination of formation mechanisms of aerosol particles in the boreal forest site; (b) verification of emissions of secondary organic aerosols from the boreal forest site; and (c) quantification of the amount of condensable vapours produced in photochemical reactions of biogenic volatile organic compounds (BVOC) leading to aerosol formation. The approach of the project was to combine the continuous measurements with a number of intensive field studies. These field studies were organised in three periods, two of which were during the most intense particle production season and one during a non-event season. Although the exact formation route for 3 nm particles remains unclear, the results can be summarised as follows: Nucleation was always connected to Arctic or Polar air advecting over the site, giving conditions for a stable nocturnal boundary layer followed by a rapid formation and growth of a turbulent convective mixed layer closely followed by formation of new particles. The nucleation seems to occur in the mixed layer or entrainment zone. However two more prerequisites seem to be necessary. A certain threshold of high enough sulphuric acid and ammonia concentrations is probably needed as the number of newly formed particles was correlated with the product of the sulphuric acid production and the ammonia concentrations. No such correlation was found with the oxidation products of terpenes. The condensation sink, i.e., effective particle area, is probably of importance as no nucleation was observed at high values of the condensation sink. From measurement of the hygroscopic properties of the nucleation particles it was found that inorganic compounds and hygroscopic organic compounds contributed both to the particle growth during daytime while at night time organic compounds dominated. Emissions rates for several gaseous compounds was determined. Using four independent ways to estimate the amount of the condensable vapour needed for observed growth of aerosol particles we get an estimate of 2–10×107 vapour molecules cm−3. The estimations for source rate give 7.5–11×104 cm−3 s−1. These results lead to the following conclusions: The most probable formation mechanism is ternary nucleation (water-sulphuric acid-ammonia). After nucleation, growth into observable sizes (~3 nm) is required before new particles appear. The major part of this growth is probably due to condensation of organic vapours. However, there is lack of direct proof of this phenomenon because the composition of 1–5 nm size particles is extremely difficult to determine using the present state-of-art instrumentation.

2007, Ayers, Duncan, Clements, Dylan N., Salway, Fiona, Day, Philip J.R.

Background: The quantification of gene expression in tissue samples requires the use of reference genes to normalise transcript numbers between different samples. Reference gene stability may vary between different tissues, and between the same tissue in different disease states. We evaluated the stability of 9 reference genes commonly used in human gene expression studies. Realtime reverse transcription PCR and a mathematical algorithm were used to establish which reference genes were most stably expressed in normal and diseased canine articular tissues and two canine cell lines stimulated with lipolysaccaride (LPS). Results: The optimal reference genes for comparing gene expression data between normal and diseased infrapatella fat pad were RPL13A and YWHAZ (M = 0.56). The ideal reference genes for comparing normal and osteoarthritic (OA) cartilage were RPL13A and SDHA (M = 0.57). The best reference genes for comparing normal and ruptured canine cranial cruciate ligament were B2M and TBP (M = 0.59). The best reference genes for normalising gene expression data from normal and LPS stimulated cell lines were SDHA and YWHAZ (K6) or SDHA and HMBS (DH82), which had expression stability (M) values of 0.05 (K6) and 0.07 (DH82) respectively. The number of reference genes required to reduce pairwise variation (V) to <0.20 was 4 for cell lines, 5 for cartilage, 7 for cranial cruciate ligament and 8 for fat tissue. Reference gene stability was not related to the level of gene expression. Conclusion: The reference genes demonstrating the most stable expression within each different canine articular tissue were identified, but no single reference gene was identified as having stable expression in all different tissue types. This study underlines the necessity to select reference genes on the basis of tissue and disease specific expression profile evaluation and highlights the requirement for the identification of new reference genes with greater expression stability for use in canine articular tissue gene expression studies.

2004, Kulmala, M., Suni, T., Lehtinen, K.E.J., Dal Maso, M., Boy, M., Reissell, A., Rannik, Ü., Aalto, P., Keronen, P., Hakola, H., Bäck, J., Hoffmann, T., Vesala, T., Hari, P.

The possible connections between the carbon balance of ecosystems and aerosol-cloud-climate interactions play a significant role in climate change studies. Carbon dioxide is a greenhouse gas, whereas the net effect of atmospheric aerosols is to cool the climate. Here, we investigated the connection between forest-atmosphere carbon exchange and aerosol dynamics in the continental boundary layer by means of multiannual data sets of particle formation and growth rates, of CO2 fluxes, and of monoterpene concentrations in a Scots pine forest in southern Finland. We suggest a new, interesting link and a potentially important feedback among forest ecosystem functioning, aerosols, and climate: Considering that globally increasing temperatures and CO2 fertilization are likely to lead to increased photosynthesis and forest growth, an increase in forest biomass would increase emissions of non-methane biogenic volatile organic compounds and thereby enhance organic aerosol production. This feedback mechanism couples the climate effect Of CO2 with that of aerosols in a novel way.

2007, Maccoux, Lindsey J., Clements, Dylan N., Salway, Fiona, Day, Philip J.R.

Background: Real-time reverse transcriptase quantitative polymerase chain reaction (real-time RTqPCR) is the most accurate measure of gene expression in biological systems. The comparison of different samples requires the transformation of data through a process called normalisation. Reference or housekeeping genes are candidate genes which are selected on the basis of constitutive expression across samples, and allow the quantification of changes in gene expression. At present, no reference gene has been identified for any organism which is universally optimal for use across different tissue types or disease situations. We used microarray data to identify new reference genes generated from total RNA isolated from normal and osteoarthritic canine articular tissues (bone, ligament, cartilage, synovium and fat). RTqPCR assays were designed and applied to each different articular tissue. Reference gene expression stability and ranking was compared using three different mathematical algorithms. Results: Twelve new potential reference genes were identified from microarray data. One gene (mitochondrial ribosomal protein S7 [MRPS7]) was stably expressed in all five of the articular tissues evaluated. One gene HIRA interacting protein 5 isoform 2 [HIRP5]) was stably expressed in four of the tissues evaluated. A commonly used reference gene glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was not stably expressed in any of the tissues evaluated. Most consistent agreement between rank ordering of reference genes was observed between Bestkeeper© and geNorm, although each method tended to agree on the identity of the most stably expressed genes and the least stably expressed genes for each tissue. New reference genes identified using microarray data normalised in a conventional manner were more stable than those identified by microarray data normalised by using a real-time RT-qPCR methodology. Conclusion: Microarray data normalised by a conventional manner can be filtered using a simple stepwise procedure to identify new reference genes, some of which will demonstrate good measures of stability. Mitochondrial ribosomal protein S7 is a new reference gene worthy of investigation in other canine tissues and diseases. Different methods of reference gene stability assessment will generally agree on the most and least stably expressed genes, when co-regulation is not present.

2007, Gaigalat, Lars, Schlüter, Jan-Philip, Hartmann, Michelle, Mormann, Sascha, Tauch, Andreas, Pühler, Alfred, Kalinowski, Jörn

Background: The major uptake system responsible for the transport of fructose, glucose, and sucrose in Corynebacterium glutamicum ATCC 13032 is the phosphoenolpyruvate:sugar phosphotransferase system (PTS). The genes encoding PTS components, namely ptsI, ptsH, and ptsF belong to the fructose-PTS gene cluster, whereas ptsG and ptsS are located in two separate regions of the C. glutamicum genome. Due to the localization within and adjacent to the fructose-PTS gene cluster, two genes coding for DeoR-type transcriptional regulators, cg2118 and sugR, are putative candidates involved in the transcriptional regulation of the fructose-PTS cluster genes. Results: Four transcripts of the extended fructose-PTS gene cluster that comprise the genes sugRcg2116, ptsI, cg2118-fruK-ptsF, and ptsH, respectively, were characterized. In addition, it was shown that transcription of the fructose-PTS gene cluster is enhanced during growth on glucose or fructose when compared to acetate. Subsequently, the two genes sugR and cg2118 encoding for DeoR-type regulators were mutated and PTS gene transcription was found to be strongly enhanced in the presence of acetate only in the sugR deletion mutant. The SugR regulon was further characterized by microarray hybridizations using the sugR mutant and its parental strain, revealing that also the PTS genes ptsG and ptsS belong to this regulon. Binding of purified SugR repressor protein to a 21 bp sequence identified the SugR binding site as an AC-rich motif. The two experimentally identified SugR binding sites in the fructose-PTS gene cluster are located within or downstream of the mapped promoters, typical for transcriptional repressors. Effector studies using electrophoretic mobility shift assays (EMSA) revealed the fructose PTS-specific metabolite fructose-1-phosphate (F-1-P) as a highly efficient, negative effector of the SugR repressor, acting in the micromolar range. Beside F-1-P, other sugar-phosphates like fructose-1,6-bisphosphate (F-1,6- P) and glucose-6-phosphate (G-6-P) also negatively affect SugR-binding, but in millimolar concentrations.

2005, Vaattovaara, P., Räsänen, M., Kühn, T., Joutsensaari, J., Laaksonen, A.

New particle formation and growth has a very important role in many climate processes. However, the overall knowlegde of the chemical composition of atmospheric nucleation mode (particle diameter, d<20 nm) and the lower end of Aitken mode particles (d≤50 nm) is still insufficient. In this work, we have applied the UFO-TDMA (ultrafine organic tandem differential mobility analyzer) method to shed light on the presence of an organic fraction in the nucleation mode size class in different atmospheric environments. The basic principle of the organic fraction detection is based on our laboratory UFO-TDMA measurements with organic and inorganic compounds. Our laboratory measurements indicate that the usefulness of the UFO-TDMA in the field experiments would arise especially from the fact that atmospherically the most relevant inorganic compounds do not grow in subsaturated ethanol vapor, when particle size is 10 nm in diameter and saturation ratio is about 86% or below it. Furthermore, internally mixed particles composed of ammonium bisulfate and sulfuric acid with sulfuric acid mass fraction ≤33% show no growth at 85% saturation ratio. In contrast, 10 nm particles composed of various oxidized organic compounds of atmospheric relevance are able to grow in those conditions. These discoveries indicate that it is possible to detect the presence of organics in atmospheric nucleation mode sized particles using the UFO-TDMA method. In the future, the UFO-TDMA is expected to be an important aid to describe the composition of atmospheric newly-formed particles.

2007, Carrol, Enitan D., Salway, Fiona, Pepper, Stuart D., Saunders, Emma, Mankhambo, Limangeni A., Ollier, William E., Hart, C. Anthony, Day, Phillip

Background: The challenge of gene expression studies is to reliably quantify levels of transcripts, but this is hindered by a number of factors including sample availability, handling and storage. The PAXgene™ Blood RNA System includes a stabilizing additive in a plastic evacuated tube, but requires 2.5 mL blood, which makes routine implementation impractical for paediatric use. The aim of this study was to modify the PAXgene™ Blood RNA System kit protocol for application to small, sick chidren, without compromising RNA integrity, and subsequently to perform quantitative analysis of ICAM and interleukin-6 gene expression. Aliquots of 0.86 mL PAXgene™ reagent were put into microtubes and 0.3 mL whole blood added to maintain the same recommended proportions as in the PAXgene™ evacuated tube system. RNA quality was assessed using the Agilent BioAnalyser 2100 and an in-house TaqMan™ assay which measures GAPDH transcript integrity by determining 3' to 5' ratios. qPCR analysis was performed on an additional panel of 7 housekeeping genes. Three reference genes (HPRT1, YWHAZ and GAPDH) were identified using the GeNORM algorithm, which were subsequently used to normalising target gene expression levels. ICAM-1 and IL-6 gene expression were measured in 87 Malawian children with invasive pneumococcal disease. Results: Total RNA yield was between 1,114 and 2,950 ng and the BioAnalyser 2100 demonstrated discernible 18s and 28s bands. The cycle threshold values obtained for the seven housekeeping genes were between 15 and 30 and showed good consistency. Median relative ICAM and IL-6 gene expression were significantly reduced in non-survivors compared to survivors (ICAM: 3.56 vs 4.41, p = 0.04, and IL-6: 2.16 vs 6.73, p = 0.02). Conclusion: We have successfully modified the PAXgene™ blood collection system for use in small children and demonstrated preservation of RNA integrity and successful quantitative real-time PCR analysis.