Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays

Motivation: High-density DNA microarrays provide us with usefultools for analyzing DNA and RNA comprehensively. However, thebackground signal caused by the non-specific binding (NSB) betweenprobe and target makes it difficult to obtain accurate measurements.To remove the background signal, there is a set of backgroundprobes on Affymetrix Exon arrays to represent the amount ofnon-specific signals, and an accurate estimation of non-specificsignals using these background probes is desirable for improvementof microarray analyses. Results: We developed a thermodynamic model of NSB on shortnucleotide microarrays in which the NSBs are modeled by duplexformation of probes and multiple hypothetical targets. We fittedthe observed signal intensities of the background probes withthose expected by the model to obtain the model parameters.As a result, we found that the presented model can improve theaccuracy of prediction of non-specific signals in comparisonwith previously proposed methods. This result will provide auseful method to correct for the background signal in oligonucleotidemicroarray analysis. Availability: The software is implemented in the R languageand can be downloaded from our website (http://www-shimizu.ist.osaka-u.ac.jp/shimizu_lab/MSNS/). Contact: furusawa{at}ist.osaka-u.ac.jp Supplementary information: Supplementary data are availableat Bioinformatics online. The authors wish it to be known that, in their opinion, thefirst two authors should be regarded as joint First Authors. Associate Editor: Trey Ideker     

Large-scale phosphosite quantification in tissues by a spike-in SILAC method

Despite progress in mass spectrometry (MS)-based phosphoproteomics, large-scale in vivo analyses remain challenging. Here we report a 'spike-in' stable-isotope labeling with amino acids in cell culture (SILAC) methodology using standards derived from labeled mouse liver cell lines, using which we analyzed insulin signaling. With this approach we identified 15,000 phosphosites and quantitatively compared 10,000 sites in response to insulin treatment, creating a very large, accurately quantified in vivo phosphoproteome dataset.     

Benthivorous fish reduce stream invertebrate drift in a large-scale field experiment

Drift as a low-energy cost means of migration may enable stream invertebrates to leave risky habitats or to escape after encountering a predator. While the control of the diurnal patterns of invertebrate drift activity by fish predators has received considerable interest, it remains unclear whether benthivorous fish reduce or increase drift activity. We performed a large-scale field experiment in a second-order stream to test if invertebrate drift was controlled by two benthivorous fish species (gudgeon Gobio gobio and stone loach Barbatula barbatula). An almost fishless reference reach was compared with a reach stocked with gudgeon and loach, and density and structure of the invertebrate communities in the benthos and in the drift were quantified in both reaches. The presence of gudgeon and stone loach reduced the nocturnal drift of larvae of the mayfly Baetis rhodani significantly, in contrast to the findings of most previous studies that fish predators induced higher night-time drift. Both drift density and relative drift activity of B. rhodani were lower at the fish reach during the study period that spanned 3 years. Total invertebrate drift was not reduced, by contrast, possibly due to differences in vulnerability to predation or mobility between the common invertebrate taxa. For instance, Chironomidae only showed a slight reduction in drift activity at the fish reach, and Oligochaeta showed no reduction at all. Although benthic community composition was similar at both reaches, drift composition differed significantly between reaches, implying that these differences were caused by behavioural changes of the invertebrates rather than by preferential fish consumption. The direction and intensity of changes in the drift activity of stream invertebrates in response to the presence of benthivorous fish may depend on the extent to which invertebrate taxa can control their drifting behaviour (i.e. active versus passive drift). We conclude that invertebrate drift is not always a mechanism of active escape from fish predators in natural streams, especially when benthos-feeding fish are present.     

Cooperative, non-specific binding of a zinc finger peptide to DNA.

The DNA binding and structural properties of Xfin-31 (Lee, M.S., Gippert, G.P., Soman, K.V., Case, D.A. and Wright, P.E., 1989, Science 245, 635-637), a twenty five amino acid zinc finger peptide, in the reduced, oxidized and zinc complex forms, as well as the fourteen residue helical segment of the zinc finger (residues 12-25) have been compared using affinity coelectrophoresis (ACE) and circular dichroism (CD) spectroscopy. The zinc complex and oxidized peptides bind cooperatively to DNA although the cooperativity factor, omega, is more than 15-fold greater for the zinc complex. The reduced peptide in the absence of zinc and the helical segment do not bind cooperatively (omega = 1). Hence, the binding constant for singly contiguous sites (K omega) ranges over 100-fold for the various peptides even though the intrinsic binding constants (K) are similar. An increase in binding order and affinity for the other forms of Xfin-31 is correlated with an increasing similarity of the CD spectrum to that of the Xfin-31 zinc complex. The surprising DNA binding activity of the oxidized peptide may result from hydrophobic interactions between the amino-terminal loop formed by the Cys3-Cys6 disulfide bond and conserved hydrophobic residues in the carboxyl-terminal segment. Xfin-31 may be a particularly useful model for studying several poorly understood aspects of cooperative, non-specific DNA binding since it is small, has a stable, well-defined structure, and structures of zinc fingers bound to DNA have been determined.     

Elimination of non-specific binding in western blots from non-reducing gels

The reaction of some antibodies with Western blots of protein shows strong non-specific binding especially at a region that corresponds to about 70-90 kDa. This binding is independent of protein concentration. Further analysis indicated that the factor responsible for the non-specific binding is 2-mercaptoethanol in the gel sample buffer. Gel electrophoresis of total tissue homogenates in the absence of this reducing agent resulted in dramatic elimination of the non-specific background binding without affecting the mobility of the two proteins we studied.     

Hemi-methylated oriC DNA binding activity found in non-specific acid phosphatase

The lacZ – hobH fusion clone, containing an Escherichia coli DNA segment located at 92 min on the chromosomal map, was screened as a producer of E. coli oriC hemi-methylated binding activity. We have purified the protein encoded by this locus to near homogeneity. The protein corresponds to the monomeric form of a non-specific acid phosphatase (NAP) whose gene has been designated aphA. oriC DNA footprinting experiments showed protection of hemi-methylated probe by partially purified NAP, but not by purified preparations. Yet, gel retardation experiments with an oriC oligonucleotide demonstrated DNA binding activity of purified NAP in the presence of Mg²⁺. This experiment also showed an increased affinity of the protein for the hemi-methylated probe compared with the fully or unmethylated form. Indirect immunofluorescence microscopy revealed the existence of discrete NAP foci at mid-cell in cells with two nucleoids, but at cell poles in those with one nucleoid.     

Predator-induced changes in population structure and individual quality of Microtus voles: a large-scale field experiment

In small mammal populations with multiannual oscillations in density, observational data have revealed cyclic changes in population structure, reproduction, and individual quality, but mechanisms inducing these changes have remained an open question. We analysed data collected during a 3-year predator reduction experiment to find out the effects of predators on population structure, reproductive parameters, and individual quality of Microtus voles (the field vole M. agrestis and the sibling vole M. rossiaemeridionalis ) in western Finland. Voles were collected by snap trapping in April, June, August, and October during 1997–1999. The yearly reduction of predators from April to October had a clear positive effect on the abundance of sibling voles but did not significantly affect the densities of field voles. Predator reduction apparently also affected the age ratio and mean body size in late summer, as well as pancreatic weights of voles. However, all observed differences between predator reduction and control areas, except those in abundance, were small and may mainly reflect a generally higher survival leading to higher densities of voles in predator reduction areas. Our results also indicated a relative lack of high quality food at population peaks but not because of reduced foraging activity in the presence of predators. We conclude that the indirect effects of vole-eating predators on the population growth of main prey are small compared to the detrimental direct effects on prey survival. In the case of less preferred prey, indirect effects of predation through reduced interspecific competition may play a role at high densities.     

Alleviation of restriction by DNA condensation and non-specific DNA binding ligands

During conditions of cell stress, the type I restriction and modification enzymes of bacteria show reduced, but not zero, levels of restriction of unmethylated foreign DNA. In such conditions, chemically identical unmethylated recognition sequences also occur on the chromosome of the host but restriction alleviation prevents the enzymes from destroying the host DNA. How is this distinction between chemically identical DNA molecules achieved? For some, but not all, type I restriction enzymes, alleviation is partially due to proteolytic degradation of a subunit of the enzyme. We identify that the additional alleviation factor is attributable to the structural difference between foreign DNA entering the cell as a random coil and host DNA, which exists in a condensed nucleoid structure coated with many non-specific ligands. The type I restriction enzyme is able to destroy the ‘naked’ DNA using a complex reaction linked to DNA translocation, but this essential translocation process is inhibited by DNA condensation and the presence of non-specific ligands bound along the DNA.     

Response of double-crested cormorants to a large-scale egg oiling experiment on Lake Huron

We report on a management experiment examining the effects of large-scale egg oiling on double-crested cormorant nest abundance and measures of seasonal cormorant density (bird-days/km²) from 2000 to 2005. We employed the staircase design to distinguish transient responses to management treatments from site and year effects that generally contribute to variation in populations. The response to egg oiling in Georgian Bay was as expected with a decline in nest abundance attributable to egg oiling. In the North Channel, nest abundance did not decline because of egg oiling but increased, reflecting either retention of nesting adults or recruitment to colonies. This surprising outcome may stem from fish escapement from pen rearing facilities in the vicinity of the oiling experiment in the North Channel. We observed no effect of egg oiling on the July–August seasonal density of cormorants. The strongest effect size was associated with site effects followed by year effects for nest abundance and seasonal density. The effect size of egg oiling on variation in nest abundance did not exceed 5% for any year in both the North Channel and Georgian Bay. Fish pen culture appears to affect coastal distribution of cormorants. © 2011 The Wildlife Society.     

Elimination of the non-specific binding of avidin to tissue sections

Summary A simple procedure is described for eliminating non-specific staining with avidin—peroxidase conjugates. Murine ovaries were embedded in either paraffin wax or epoxy resin and, after blocking endogenous peroxidase activity, were treated with 10 µg/ml biotinylatedPisum sativum agglutinin. Avidin—peroxidase conjugates (5 µg/ml), diluted in standard 0.05m tris-buffered saline, pH 7.6, containing 0.139m NaCl, produced considerable background coloration and intense mast cell staining in controls without the lectin. This background diminished as the ionic strength of the buffer was raised. At 0.125m Tris-buffered saline (containing 0.347m NaCl) the background was completely unstained, with elimination of all binding to mast cells and only minimal loss of specific lectin binding.     

Porphyrin intercalation and non-specific 'edge on' outside binding to natural DNA

A theoretical two-mode binding model for porphyrin binding to natural DNA is presented. One of the binding modes is assumed to be base sequence specific with binding sites n base-pairs long. The other binding mode has binding sites which consist of only one base-pair and can involve cooperativity. The model fits satisfactorily to data for H2TMPyP-4, Cu(II)TMPyP-3 and Cu(II)TMPyP-4 binding to calf thymus DNA in both a high (mu congruent to 1.0 M) and a low (mu congruent to 0.2 M) ionic strength buffer. The results show that the fraction of porphyrin bound in the non-specific mode reaches a maximum at certain input DNA to porphyrin concentrations ratios. The value of this maximum decreased, and its position shifted to higher DNA to porphyrin concentration ratios for binding in the high ionic strength buffer. The value of the cooperativity parameter obtained through the fitting process suggests that the non-specific binding is positively cooperative. The results are compared with the data analysed using other techniques.     

Thioaptamer interactions with prion proteins: sequence-specific and non-specific binding sites

Binding of nucleic acids to the prion protein (PrP) created a conundrum that required distinguishing between non-specific interactions and biologically important polynucleotides. In the process of developing selective ligands for PrP, we found using a single-stranded DNA thioaptamer library that the binding of thioaptamers to PrP occurs on at least two different sites on the protein. Selection against recombinant (rec) PrP of Syrian hamster (SHa) sequence 90-231 folded into an alpha-helical-rich conformation identified a 12-base consensus sequence within a series of 20 thioaptamers, all of which consist of 40 bases. Each thioaptamer was comprised of both normal and thio-dA modified bases. One thioaptamer designated 97 bound to recSHaPrP with affinity of 0.58(+/-0.1) nM; lower affinities for bovine (Bo), and human (Hu) were found, establishing that binding is dependent on the primary structure of PrP. High affinity binding of thioaptamer 97 to PrP was found to be mediated through the dodecyl sequence GACACAAGCCGA within the consensus region with five critical backbone modifications 5' to each dA residue. A control oligonucleotide with an equivalent number of phosphorothioates to thioaptamer 97 and a scrambled consensus sequence could not distinguish among the three PrP sequences. Control oligonucleotides bearing non-selected sequences bound to PrP at a sequence-independent DNA-binding site. In contrast, the high-affinity binding of thioaptamer 97 to PrP depends on (1) backbone modifications, (2) oligonucleotide sequence, and (3) PrP sequence.     

In vivo non-specific binding of lambda CI and Cro repressors is significant

We propose a thermodynamic model that includes the non-specific binding of the lambda phage regulatory proteins CI and Cro. By fitting the model to experimental in vivo data on activities of the two promoters P(RM) and P(R) versus concentration, we estimate the free energy upon non-specific binding to be -4.1+/-0.9 kcal/mol for CI and -4.2+/-0.8 kcal/mol for Cro. For concentrations >100 nM of CI or Cro, we find that >50% of these proteins are non-specifically bound. In particular, in a lysogen (approximately 250 CI monomeric equivalents per cell) nearly 90% of CI is non-specifically bound.