SPIDIA-RNA: first external quality assessment for the pre-analytical phase of blood samples used for RNA based analyses.

The diagnostic use of in vitro molecular assays can be limited by the lack of guidelines for collection, handling, stabilization and storage of patient specimens. One of the major goals of the EC funded project SPIDIA (www.spidia.eu) is to develop evidence-based quality guidelines for the pre-analytical phase of blood samples used for molecular testing which requires intracellular RNA analytes. To this end, a survey and a pan-European external quality assessment (EQA) were implemented. This report is the summary of the results of that trial. With the European Federation of Laboratory Medicine (EFLM) support, 124 applications for participation in the trial were received from 27 different European countries, and 102 laboratories actually participated in the trial. Each participating laboratory described their respective laboratory policies and practices as well as blood collection tubes typically used in performing this type of testing. The participating laboratories received two identical blood specimens: in an EDTA tubes (unstabilized blood; n=67) or in tubes designed specifically for the stabilization of intracellular RNA in blood (PAXgene® Blood RNA tubes; n=35). Laboratories were requested to perform RNA extraction according to the laboratory's own procedure as soon as possible upon receipt of the tubes for one tube and 24h after the first extraction for the second tube. Participants (n=93) returned the two extracted RNAs to SPIDIA facility for analysis, and provided details about the reagents and protocols they used for the extraction. At the SPIDIA facility responsible for coordinating the study, the survey data were classified, and the extracted RNA samples were evaluated for purity, yield, integrity, stability, and the presence of interfering substances affecting RT-qPCR assays. All participants received a report comparing the performance of the RNA they submitted to that of the other participants. All the results obtained by participants for each RNA quality parameter were classified as "in control", "warning", "out of control" and "missing" by consensus mean analysis. From the survey data, the most variable parameters were the volume of blood collected and the time and storage temperature between blood collection and RNA extraction. Analyzing the results of quality testing of submitted RNA samples we observed a data distribution of purity, yield, and presence of assay interference in agreement with expected values. The RNA Integrity Number (RIN) values distribution was, on the other hand, much wider than the optimal expected value, which led to an "in control" classification, even for partly degraded RNA samples. On the other hand, RIN values below 5 significantly correlated with a reduction of GAPDH expression levels. Furthermore, the distribution of the values of the four transcripts investigated (c-fos, IL-1ß, IL-8, and GAPDH) was wide and the RNA instability between samples separated by 24h were similar. Assuming the presence of at least two quality parameters "out of control" as an indication of a critical performance of the laboratory, 33% of the laboratories were included in this group. The results of this study will be the basis for implementing a second pan-European EQA and the results of both EQAs will be pooled and will provide the basis for the implementation of evidence-based guidelines for the pre-analytical phase of RNA analysis of blood samples.

Gene expression responses in larvae of the fleshfly Sarcophaga bullata after immune stimulation.

Insect larvae develop in decaying organic matter and their defence against various microorganisms must therefore be highly efficient. In the present study, we explored the transcriptional kinetics and induction levels of eight genes in Sarcophaga bullata larvae after infection or aseptic injury. Using real-time PCR, we studied the time-dependent immune response of larvae of the fleshfly S. bullata. We compared the mRNA levels of eight selected genes in induced and non-induced larvae. The third-instar larvae of S. bullata were induced by injecting a bacterial suspension of Escherichia coli, Staphylococcus aureus or Pseudomonas aeruginosa, or by simple aseptic injury with an entomological pin. We used intact larvae as a control for basal mRNA expression. Total RNA was isolated from the whole body, fat body and haemocytes. We determined the mRNA levels of genes encoding sapecin, transferrin, prophenoloxidase 1 and 2, storage-binding protein, cathe psin L, sarcocystatin, and 26/29 kDa protease. We found that there was massive up-regulation of genes encoding the fleshfly peptide sapecin, as well as the protein transferrin. We also detected down-regulation of, or no change in, the expression of genes that encode prophenoloxidase 1 and 2, storage-binding protein, cathepsin L, sarcocystatin, and 26/29 kDa protease.

Differential amplicons (ΔAmp)-a new molecular method to assess RNA integrity.

Integrity of the mRNA in clinical samples has major impact on the quality of measured expression levels. This is independent of the measurement technique being next generation sequencing (NGS), Quantitative real-time PCR (qPCR) or microarray profiling. If mRNA is highly degraded or damaged, measured data will be very unreliable and the whole study is likely a waste of time and money. It is therefore common strategy to test the quality of RNA in samples before conducting large and costly studies. Most methods today to assess the quality of RNA are ignorant to the nature of the RNA and, therefore, reflect the integrity of ribosomal RNA, which is the dominant species, rather than of mRNAs, microRNAs and long non-coding RNAs, which usually are the species of interest. Here, we present a novel molecular approach to assess the quality of the targeted RNA species by measuring the differential amplification (ΔAmp) of an Endogenous RNase Resistant (ERR) marker relative to a reference gene, optionally combined with the measurement of two amplicons of different lengths. The combination reveals any mRNA degradation caused by ribonucleases as well as physical, chemical or UV damage. ΔAmp has superior sensitivity to common microfluidic electrophoretic methods, senses the integrity of the actual targeted RNA species, and allows for a smoother and more cost efficient workflow.

Tuberous sclerosis causing mutants of the TSC2 gene product affect proliferation and p27 expression.

The autosomal dominant disease tuberous sclerosis (TSC) is caused by mutations in either TSC1 on chromosome 9q34, encoding hamartin, or TSC2 on chromosome 16p13.3, encoding tuberin. TSC is characterized by hamartomas that occur in many organs of affected patients and these have been considered to likely result from defects in proliferation control. Although the true biochemical functions of the two TSC proteins have not been clarified, a series of independent investigations demonstrated that modulated hamartin or tuberin expression cause deregulation of proliferation/cell cycle in human, rodent and Drosophila cells. In support of tuberin acting as a tumor suppressor, ectopic overexpression of TSC2 has been shown to decrease proliferation rates of mammalian cells. Furthermore, overexpression of TSC2 has been demonstrated to trigger upregulation of the cyclin-dependent kinase inhibitor p27. We report that three different naturally occurring and TSC causing mutations within the TSC2 gene eliminate neither the anti-proliferative capacity of tuberin nor tuberin's effects on p27 expression. For the first time these data provide strong evidence that deregulation of proliferation and/or upregulation of p27 are not likely to be the primary/only mechanisms of hamartoma development in TSC. These results demand reassessment of previous hypotheses of the pathogenesis of TSC.

Binding stoichiometry and structure of RecA-DNA complexes studied by flow linear dichroism and fluorescence spectroscopy. Evidence for multiple heterogeneous DNA co-ordination.

The interaction between RecA and DNA (in the form of unmodified single-stranded DNA, fluorescent single-stranded DNA and double-stranded DNA) is studied with linear dichroism and fluorescence spectroscopy. RecA is found to form a complex with single-stranded DNA with a binding stoichiometry of about four nucleotides per RecA monomer, in which the DNA bases appear to have a random orientation. Addition of ATP gamma S (a non-hydrolyzable analog of ATP) reduces the stoichiometry to about three nucleotides per RecA and causes the DNA bases to adopt an orientation preferentially perpendicular to the fiber axis. This complex can incorporate an additional strand of single-stranded DNA or double-stranded DNA, yielding a total stoichiometry of six nucleotides or three nucleotides and three base-pairs, respectively, per RecA. RecA, in the presence of ATP gamma S, is also found to interact with double-stranded DNA, with a stoichiometry of about three base-pairs per RecA. In all studied complexes, the tryptophan residues in the RecA protein are oriented with their planes preferentially parallel to the fiber axis, whereas in complexes involving ATP gamma S the planes of the DNA bases are oriented preferentially perpendicular to the fiber. This virtually excludes the possibility that the tryptophan residues are intercalated in the DNA helix. On the basis of these results, a model for the research of homology in the RecA-mediated, strand-exchange reaction in the genetic recombination process is proposed.

TGGA repeats impair nucleosome formation.

Nucleosomes, the building blocks of chromatin, are responsible for DNA packaging in eukaryotic cell nuclei. They play a structural role in genome condensation, and influence transcription and replication. Properties of the DNA sequence, such as curvature and flexibility, direct the location of nucleosomes. DNA sequences that position nucleosomes have been identified and rules that govern their properties have been formulated. However, DNA sequences that are refractory to nucleosome formation have been less well characterised and it is possible that they may perturb or alter chromatin structure. Here we identify such sequences by selecting those that refrain from nucleosome formation from a large pool of synthetic DNA fragments with a central region of 146 random base-pairs fitted with adapters for PCR amplification. These were used for in vitro salt-induced reconstitution of nucleosomes under thermodynamic equilibrium conditions. Fragments that did not form nucleosomes were purified, amplified by PCR, and the reconstitution was repeated. After 17 rounds of negative selection, the material was highly enriched in sequences reluctant to form nucleosomes. Cloning and sequencing revealed that 35% of the molecules had long repeats of TGGA, and their affinity for histone octamers was about half that of average DNA.

Structure of RecA-DNA complexes studied by combination of linear dichroism and small-angle neutron scattering measurements on flow-oriented samples.

By combining anisotropy of small-angle neutron scattering (SANS) and optical anisotropy (linear dichroism, l.d.) on flow-oriented RecA-DNA complexes, the average DNA-base orientation has been determined in RecA complexes with double-stranded (ds) as well as single-stranded (ss) DNA. From the anisotropy of the two-dimensional SANS intensity representation, the second moment orientation function S is obtained. Knowledge of S is crucial for the interpretation of l.d. spectra in terms of orientation of the DNA bases and the aromatic amino acid residues. The DNA-base planes are essentially perpendicular to the fibre axis of the complex between RecA and dsDNA in the presence of cofactor ATP gamma S. A somewhat tilted base geometry is found for the RecA-ATP gamma S complexes with single-stranded poly(dT) and poly(d epsilon A). This behaviour contrasts the RecA-ssDNA complex formed without cofactor which displays a poor orientation of the bases. Well-ordered bases in the ssDNA-RecA complex is possibly reflecting the role of RecA in preparing a nucleotide strand for base-pairing in the search-for-homology process. While the central SANS intensity is essentially independent of the pitch of the helical complex, a secondary intensity maximum, which becomes focused upon flow orientation, is found to be a sensitive measure of the pitch. The pitch values for the complexes compare well with cryo-electron microscopy results but are slightly larger than those seen for uranyl-stained samples.

Structure of a RecA-DNA complex from linear dichroism and small-angle neutron-scattering in flow-oriented solution.

Small-angle neutron-scattering (SANS) and ultraviolet linear dichroism (l.d.) were measured on identical samples of a RecA-double-stranded (ds) DNA complex, including cofactor adenosine 5'-O-thiotriphosphate, which were aligned by flow in two equivalent Couette devices made of niobium and silica, transparent to neutrons and to ultraviolet light, respectively. The SANS anisotropy indicates a modest orientation of the RecA-dsDNA fiber with the helix axis parallel to the flow field. By correlation with the corresponding l.d. of the DNA at the same orientation conditions, it is inferred that the DNA bases have a local orientation that is approximately perpendicular to the helix axis. By comparison with the worse orientation in single-stranded DNA-RecA, this conclusion suggests that the dsDNA in its complex with RecA is not strand separated, and may be accommodated as an essentially unperturbed, straight double helix running along the RecA polymer fiber. The SANS anisotropy is also found to support the assignment of a subsidiary intensity maximum as originating from the pitch of a helical fiber.

Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences.

Our laboratories recently completed SELEX experiments to isolate DNA sequences that most-strongly favor or disfavor nucleosome formation and positioning, from the entire mouse genome or from even more diverse pools of chemically synthetic random sequence DNA. Here we directly compare these selected natural and non-natural sequences. We find that the strongest natural positioning sequences have affinities for histone binding and nucleosome formation that are sixfold or more lower than those possessed by many of the selected non-natural sequences. We conclude that even the highest-affinity sequence regions of eukaryotic genomes are not evolved for the highest affinity or nucleosome positioning power. Fourier transform calculations on the selected natural sequences reveal a special significance for nucleosome positioning of a motif consisting of approximately 10 bp periodic placement of TA dinucleotide steps. Contributions to histone binding and nucleosome formation from periodic TA steps are more significant than those from other periodic steps such as AA (=TT), CC (=GG) and more important than those from the other YR steps (CA (=TG) and CG), which are reported to have greater conformational flexibility in protein-DNA complexes even than TA. We report the development of improved procedures for measuring the free energies of even stronger positioning sequences that may be isolated in the future, and show that when the favorable free energy of histone-DNA interactions becomes sufficiently large, measurements based on the widely used exchange method become unreliable.

Identification and characterization of genomic nucleosome-positioning sequences.

Positioned nucleosomes are believed to play important roles in transcriptional regulation and for the organization of chromatin in cell nuclei. Here, we have isolated the DNA segments in the mouse genome that form the most stable nucleosomes yet characterized. In separate molecules we find phased runs of three to four adenine nucleotides, extensive CA repeats, and in a few cases phased TATA tetranucleotides. The latter forms the most stable nucleosome yet characterized. One sequence with CAG repeats was also found. By fluorescence in situ hydridization the selected sequences are shown to be localized at the centromeric regions of mouse metaphase chromosomes.

Absorption flattening in the optical spectra of liposome-entrapped substances.

Measuring optical spectra of chromophore molecules entrapped in liposomes can lead to considerable distortion because of absorption flattening. This phenomenon is analyzed theoretically, and it is shown that the deviation from the Beer-Lambert law becomes larger as the molar absorptivity of the chromophore increases and as the number of entrapped molecules becomes larger. The theoretical equations are tested experimentally with intermediate-sized phospholipid vesicles containing entrapped cytochrome c. It is shown that considerable absorption flattening is observed with vesicles containing about 50 chromophore molecules. The equation given can be used to correct the spectrum.

Co-ordination of multiple DNA molecules in RecA fiber evidenced by linear dichroism spectroscopy.

Polarized light spectroscopy has been used to study the interaction of RecA protein with DNA. Several different DNA complexes have been identified and characterized with respect to stoichiometries, base orientation and nuclease accessibility. By using spectroscopically distinguishable DNAs, we determined the number of DNA molecules co-ordinated by the RecA fiber in each of these complexes, and established their base pairing abilities. Based on these observations, we discuss the molecular mechanism of the RecA-mediated strand exchange reaction.

Flow linear dichroism supports an accordion model for the salt-induced condensation of chromatin.

The salt-induced condensation of chromatin has been studied with flow-linear dichroism technique using an intercalative dye (methylene blue) to selectively monitor the linker orientation. At low ionic strength both linkers and chromatosomes (with their flat faces) are oriented preferentially parallel to the chromatin fibre axis. With increasing ionic strength both linkers and chromatosomes tilt successively towards a perpendicular orientation. Based on these results and structural considerations, an 'Accordion model' with a pentagonal nucleosomal arrangement is proposed for the salt-induced condensation of chromatin.

Conformational differences between latent and active plasminogen activator inhibitor, PAI-1: a spectroscopic study.

The protein conformation of latent and active PAI-1 has been studied with circular dichroism, absorbance and fluorescence spectroscopy. The far ultraviolet circular dichroism spectrum of latent PAI-1 displays a more negative band at 220 nm than active PAI-1, crossing the baseline at a lower wavelength. Active PAI-1 shows an absorption maximum at lower wavelength (269 nm) than present in latent PAI-1 (278 nm). In consistency, slow denaturation of active PAI-1 by incubation for two hours at 37 degrees C induces a shift in the absorption maximum from 268 nm to 274 nm. The fluorescence emission maximum of latent PAI-1 is at lower wavelength (335 nm) than that of active PAI-1 (340 nm). These spectroscopic differences are interpreted as reflecting a more tight conformation, with the tryptophan residues in a more apolar environment, in latent PAI-1 compared to active PAI-1.

A circular dichroism study of mitochondrial transhydrogenase from beef heart.

This paper describes a circular dichroism (CD) spectroscopy study of purified proton-pumping nicotinamide nucleotide transhydrogenase from beef heart. The CD spectrum obtained was used to estimate the content of secondary structures of the purified enzyme and suggests the presence of 40-45% alpha-helical structure and long, possibly membrane-spanning alpha-helices. The spectrum was essentially unaffected by the absence or presence of transhydrogenase substrates, suggesting that the catalytic and proton-translocating activities of the enzyme occur without major rearrangements at the level of secondary structures.

Ionic strength dependence of the binding of methylene blue to chromatin and calf thymus DNA.

The binding of the intercalating dye methylene blue (MB) to chromatin and to free DNA has been studied as a function of ionic strength at very low binding ratios (1 MB/400 DNA bases) using absorption spectroscopy. With increasing salt concentration MB is displaced from chromatin to a higher extent than from DNA. The free energy change for MB binding to chromatin is found to be approximately 5 kJ/mole lower than for binding to DNA. This difference can be explained by the reduced number of high affinity binding sites in chromatin due to the presence of histone proteins. The difference in binding energy is virtually independent of the degree of chromatin condensation and also of the valence of counter ions, suggesting that neither the affinity for, nor the number of intercalation sites in the linker DNA is markedly changed upon the salt-induced condensation. The unaffected thermodynamics of the linker binding suggests that factors such as DNA superhelicity and the electrostatic influence from the chromatosomes remain unchanged during chromatin condensation.

Reinterpretation of linear dichroism of chromatin supports a perpendicular linker orientation in the folded state.

We present a reinterpretation of linear dichroism data for the salt induced condensation of chromatin. A conflict between electric and flow linear dichroism data for identical chromatin samples, studied at varying degrees of Mg2+ induced folding, can be solved if the orientation in electric fields is mainly determined through the polarization of counter ions along the linker parts, whereas the orientation in flow is governed by the hydrodynamical response of the entire chromatin fiber. The orientation of a chromatin fiber in an electric field would then depend on the linker tilt angle so that at an angle larger than 55 degrees the fiber would tend to orient perpendicular to the applied field. The different orientation distributions obtained with the two methods of alignment may in this way provide extra information about the structure and folding of chromatin.

Electric and flow linear dichroism of unfolded and condensed chromatin: a comparative study at low and intermediate ionic strength.

Identical samples containing polynucleosomal chains of chicken erythrocyte (CE) and Ehrlich ascites tumour (EA) chromatin were studied under various ionic conditions with regard to electric linear dichroism (ELD) and flow linear dichroism (FLD). Both orientation techniques consistently confirmed that, in the limit of very low ionic strength and in the absence of multivalent cations, the reduced linear dichroism of chromatin is negative in the DNA-base absorption band, as expected for an extended zig-zag polynucleosomal conformation. With increasing electrolyte content, both ELD and FLD decreased drastically in amplitude, but in contrast to the ELD which remains negative in an intermediate range of low ionic strength (0.1-0.5 mM Mg2+) the FLD changes sign and becomes positive. The ELD and FLD amplitudes decrease with higher Mg2+ concentrations and FLD even vanishes in the region of 0.2-0.4 mM; both signals are positive above 0.4-0.5 mM Mg2+. The origin of the dissimilarities between ELD and FLD observations is still not fully understood. Several possibilities are considered: ELD signals are more influenced than FLD by the presence of short chromatin chains, nucleosomes and small pieces of naked DNA, while FLD is more susceptible to the presence of large, easily orientable, scattering aggregates. Different preferred orientation directions of the chromatin fibre with respect to electric and hydrodynamic fields may also be involved. Finally, FLD and ELD probably "see" different features of the chromatin structure.

Tuberous sclerosis gene products in proliferation control.

Two genes, TSC1 and TSC2, have been shown to be responsible for tuberous sclerosis (TSC). The detection of loss of heterozygosity of TSC1 or TSC2 in hamartomas, the growths characteristically occurring in TSC patients, suggested a tumor suppressor function for their gene products hamartin and tuberin. Studies analyzing ectopically modulated expression of TSC2 in human and rodent cells together with the finding that a homolog of TSC2 regulates the Drosophila cell cycle suggest that TSC is a disease of proliferation/cell cycle control. We discuss this question including very recent data obtained from analyzing mice expressing a modulated TSC2 transgene, and from studying the effects of deregulated TSC1 expression. Elucidation of the cellular functions of these proteins will form the basis of a better understanding of how mutations in these genes cause the disease and for the development of new therapeutic strategies.

UV-Vis spectroscopic and chemometric study on the aggregation of ionic dyes in water.

The monomer-dimer equilibrium in several ionic dyes (Methylene Blue, Acridine Orange, Nile Blue A, Neutral Red, Rhodamine 6G and Safranine O) has been investigated by means of UV-Vis spectroscopy. The data have been processed by a recently developed method for quantitative analysis of undefined mixtures, based on simultaneous resolution of the overlapping bands in the whole set of absorption spectra. In the cases of Acridine Orange a second chemometric approach has been used as a reference. It is based on a decomposition of the recorded spectra into a product of target and projection matrices using non iterative partial least squares (NIPALS). The matrices are then rotated to give the correct concentrations, spectral profiles of the components and the equilibrium constant. The dimeric constants determined by the two methods were in excellent agreement, evidencing the accuracy of the analysis. From the calculated dimeric constant and monomer and dimer spectra, the structures of the dimeric forms of the studied dyes are estimated.