Reducing spatial flaws in oligonucleotide arrays by using neighborhood information

We address the problem of detection and correction of spatial flaws in oligonucleotide microarrays. We present two similar procedures, of which one is intended solely for use with replicates and the other has wider applicability. By constructing a set of replicates, with one realistically flawed, we are able to examine the extent to which our procedures are capable of repairing the flaw. We find that, for this purpose, our procedures are superior to the existing 'Harshlight' procedure.     

Review: nuclear structure and DNA replication

DNA replication is a highly conserved process among eukaryotes where it occurs within a unique organelle-the nucleus. The importance of this structure is indicated by the fact that assembly of prereplication complexes on cellular chromatin is delayed until mitosis is completed and a nuclear structure has formed. Although nuclear structure is dispensable for DNA replication in vitro, it does appear to play a role in vivo by regulating the concentration of proteins required to initiate DNA replication, by facilitating the assembly or activity of DNA replication forks, and by determining where in the genome initiation of DNA replication occurs.     

Brain mechanisms for extracting spatial information from smell

Forty years ago, von Békésy demonstrated that the spatial source of an odorant is determined by comparing input across nostrils, but it is unknown how this comparison is effected in the brain. To address this, we delivered odorants to the left or right of the nose, and contrasted olfactory left versus right localization with olfactory identification during brain imaging. We found nostril-specific responses in primary olfactory cortex that were predictive of the accuracy of left versus right localization, thus providing a neural substrate for the behavior described by von Békésy. Additionally, left versus right localization preferentially engaged a portion of the superior temporal gyrus previously implicated in visual and auditory localization, suggesting that localization information extracted from smell was then processed in a convergent brain system for spatial representation of multisensory inputs.     

Signal transduction: receptor clusters as information processing arrays

The organization of transmembrane receptors into higher-order arrays occurs in cells as different as bacteria, lymphocytes and neurons. What are the implications of receptor clustering for short-term and long-term signaling processes that occur in response to ligand binding?     

Oligonucleotide structure influences the interactions between cationic polymers and oligonucleotides

We examined the effect of oligodeoxynucleotide (ODN) structure on the interactions between cationic polymers and ODNs. Unstructured and hairpin structured ODNs were used to form complexes with the model cationic polymer, poly-L-lysine (pLL), and the characteristics of these polymer-ODN interactions were subsequently examined. We found that hairpin structured ODNs formed complexes with pLL at slightly lower pLL:ODN charge ratios as compared to unstructured ODNs and that, at high charge ratios, greater fractions of the hairpin ODNs were complexed, as measured by dye exclusion. The dissociation of pLL-ODN interactions was tested further by challenge with heparin, which induced complex disruption. Both the kinetics and heparin dose response of ODN release were determined. The absolute amount and the kinetic rate of ODN release from the complexes of pLL and unstructured ODN were greater, as compared to hairpin ODNs. Our results therefore highlight the role of ODN structure on the association-dissociation behavior of polymer-ODN complexes. These findings have implications for the selection of ODN sequences and design of polymeric carriers used for cellular delivery of ODNs.     

P1 plasmid replication: replicon structure

Bacteriophage P1 lysogenizes Escherichia coli as a unit-copy plasmid. We have undertaken to define the plasmid-encoded elements implicated in P1 plasmid maintenance. We show that a 2081 base-pair fragment of the 90,000 base P1 plasmid confers the capacity for controlled plasmid replication. DNA sequence analysis reveals several open reading frames in this fragment. The largest is shown to encode a 32,000 Mr protein required for plasmid replication. The corresponding gene, repA, has been identified genetically. A set of five 19 base-pair repeats is located upstream from repA; a set of nine similar repeats is located immediately downstream from repA. Each set of repeats, when cloned into pBR322, exerts incompatibility towards a P1 replicon. The upstream set, designated incC, consists of direct repeats that are spaced about two turns of the DNA helix apart; the downstream set, designated incA, consists of nine repeats arranged three in one orientation and six in the other. Spacing between incA repeats were three or four turns of the helix apart. The organization of the plasmid maintenance regions of P1 and the unit-copy sex factor plasmid, F, is strikingly similar. Although the DNA sequences of this region in the two plasmids exhibit little homology, a 9 base-pair sequence that appears four times in the origin region of members of the Enterobacteriaceae also occurs twice as direct repeats in similar positions in P1 and F. This sequence, where it occurs in E. coli, has been postulated to be the binding site for the essential replication protein determined by dnaA. The dnaA protein appears not to be essential for the replication of either plasmid; therefore, the function of the sequence in P1 and F may be regulatory.     

Extracting biological information from DNA arrays: an unexpected link between arginine and methionine metabolism in Bacillus subtilis

Background  

In global gene expression profiling experiments, variation in the expression of genes of interest can often be hidden by general noise. To determine how biologically significant variation can be distinguished under such conditions we have analyzed the differences in gene expression when Bacillus subtilis is grown either on methionine or on methylthioribose as sulfur source.     

Calculating three-dimensional molecular structure from atom-atom distance information: cyclosporin A

In recent years methods for deriving spatial molecular structure from atom-atom distance information have gained in importance due to the emergence of two-dimensional nuclear magnetic resonance (n.m.r) techniques, which make it possible to obtain such distance information for polypeptides, small proteins, sugars, and DNA fragments in solution. Distance geometry (DG) and restrained molecular dynamics (MD) refinement are applied to a cyclic polypeptide, the immunosuppressive drug cyclosporin A, and the results are compared. Two different procedures, DG followed by restrained MD, and straightforward restrained MD starting from the X-ray structure, both lead to a unique conformation that satisfies the 58 experimentally determined distance constraints. The results nicely show the relative merits of DG and restrained MD techniques for determining spatial molecular structure from distance information.     

Mining functional information associated with expression arrays

Deciphering the networks of interactions between molecules in biological systems has gained momentum with the monitoring of gene expression patterns at the genomic scale. Expression array experiments provide vast amounts of experimental data about these networks, the analysis of which requires new computational methods. In particular, issues related to the extraction of biological information are key for the end users. We propose here a strategy, implemented in a system called GEISHA (gene expression information system for human analysis) and able to detect biological terms significantly associated to different gene expression clusters by mining collections of Medline abstracts. GEISHA is based on a comparison of the frequency of abstracts linked to different gene clusters and containing a given term. Interpretation by the end user of the biological meaning of the terms is facilitated by embedding them in the corresponding significant sentences and abstracts and by establishing relations with other, equally significant terms. The information provided by GEISHA for the available yeast expression data compares favorably with the functional annotations provided by human experts, demonstrating the potential value of GEISHA as an assistant for the analysis of expression array experiments. Electronic Publication     

Printing protein arrays from DNA arrays

We describe a method, DNA array to protein array (DAPA), which allows the 'printing' of replicate protein arrays directly from a DNA array template using cell-free protein synthesis. At least 20 copies of a protein array can be obtained from a single DNA array. DAPA eliminates the need for separate protein expression, purification and spotting, and also overcomes the problem of long-term functional storage of surface-bound proteins.     

Shaping time: chromatin structure and the DNA replication programme

DNA is replicated according to a precise and reproducible temporal pattern. The S-phase programme has previously been analyzed in metazoan and yeast cells using different methods: cytological chromosome banding in human cells and DNA isotopic-labeling techniques in yeast. Microarray-based approaches for the analysis of the replication programme and chromatin structure are bringing us closer to a molecular understanding of the factors that determine replication time. In this article, I assess the impact of recent investigations and compare our knowledge of DNA replication-timing controls in yeast with those of metazoans.     

Wild cherries invading natural grasslands: unraveling colonization history from population structure and spatial patterns

Invasive success of many fleshy-fruited plants has been linked to opportunistic interactions with generalist frugivores. Prunus mahaleb is a small tree, producing large quantities of little, bright black, sugary drupes that are consumed by vertebrates. It is native to the Mediterranean region but has become invasive in several countries. This study was carried out at a nature reserve including remnant mountain grasslands of high conservation value in the southern Argentine Pampas. Our aim is to reconstruct the colonization history of invading populations proposing a generalized model to describe the invasion process: colonization events result in the establishment of a founder tree followed by a lag phase until it reaches massive seed production and enables an increase in local recruitment and plant density. To test this hypothesis, we analyzed population age structures and contrasted them with those predicted using a Leslie matrix growth model. We found that matrix model predictions fit well to actual age structures. Our results reveal the existence of an 8–18-year lag period between the establishment of the founder tree and local effective recruitment. The end of this lag coincides with an abrupt increase in individual fruit production that may have a strong effect on bird attraction and successful seed dispersal. This lag phase represents an opportunity for preventing further spread of P. mahaleb. Early detection and rapid eradication of new invasion focuses should be targeted as a principal aim of an effective control strategy.