Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing.

Transcription factor-DNA interactions are some of the most important processes in biology because they directly control hereditary information. The targets of most transcription factor are unknown. In this report, we introduce Bind-n-Seq, a new high-throughput method for analyzing protein-DNA interactions in vitro, with several advantages over current methods. The procedure has three steps (i) binding proteins to randomized oligonucleotide DNA targets, (ii) sequencing the bound oligonucleotide with massively parallel technology and (iii) finding motifs among the sequences. De novo binding motifs determined by this method for the DNA-binding domains of two well-characterized zinc-finger proteins were similar to those described previously. Furthermore, calculations of the relative affinity of the proteins for specific DNA sequences correlated significantly with previous studies (R(2 )= 0.9). These results present Bind-n-Seq as a highly rapid and parallel method for determining in vitro binding sites and relative affinities

Lateral flow (immuno)assay: its strengths, weaknesses, opportunities and threats. A literature survey

Lateral flow (immuno)assays are currently used for qualitative, semiquantitative and to some extent quantitative monitoring in resource-poor or non-laboratory environments. Applications include tests on pathogens, drugs, hormones and metabolites in biomedical, phytosanitary, veterinary, feed/food and environmental settings. We describe principles of current formats, applications, limitations and perspectives for quantitative monitoring. We illustrate the potentials and limitations of analysis with lateral flow (immuno)assays using a literature survey and a SWOT analysis (acronym for 'strengths, weaknesses, opportunities, threats'). Articles referred to in this survey were searched for on MEDLINE, Scopus and in references of reviewed papers. Search terms included 'immunochromatography', 'sol particle immunoassay', 'lateral flow immunoassay' and 'dipstick assay'

Planning When Goals Change: A Moving Target Search Approach

International audienceDevising intelligent robots or agents that interact with humans is a major challenge for artificial intelligence. In such contexts, agents must constantly adapt their decisions according to human activities and modify their goals. In this paper, we tackle this problem by introducing a novel planning approach, called Moving Goal Planning (MGP), to adapt plans to goal evolutions. This planning algorithm draws inspiration from Moving Target Search (MTS) algorithms. In order to limit the number of search iterations and to improve its efficiency, MGP delays as much as possible triggering new searches when the goal changes over time. To this purpose, MGP uses two strategies: Open Check (OC) that checks if the new goal is still in the current search tree and Plan Follow (PF) that estimates whether executing actions of the current plan brings MGP closer to the new goal. Moreover, MGP uses a parsimonious strategy to update incrementally the search tree at each new search that reduces the number of calls to the heuristic function and speeds up the search. Finally, we show evaluation results that demonstrate the effectiveness of our approach

Random Costs in Combinatorial Optimization

The random cost problem is the problem of finding the minimum in an exponentially long list of random numbers. By definition, this problem cannot be solved faster than by exhaustive search. It is shown that a classical NP-hard optimization problem, number partitioning, is essentially equivalent to the random cost problem. This explains the bad performance of heuristic approaches to the number partitioning problem and allows us to calculate the probability distributions of the optimum and sub-optimum costs.Comment: 4 pages, Revtex, 2 figures (eps), submitted to PR

Phase Transition in the Number Partitioning Problem

Number partitioning is an NP-complete problem of combinatorial optimization. A statistical mechanics analysis reveals the existence of a phase transition that separates the easy from the hard to solve instances and that reflects the pseudo-polynomiality of number partitioning. The phase diagram and the value of the typical ground state energy are calculated.Comment: minor changes (references, typos and discussion of results

Survival of phyllosticta citricarpa, anamorph of the citrus black spot pathogen

Please read the abstract in the section 06resume of this documentDissertation (MSc)--University of Pretoria, 2008.Microbiology and Plant Pathologyunrestricte

Manganese-induced hydroxyl radical formation in rat striatum is not attenuated by dopamine depletion or iron chelation in vivo

The present studies were aimed at investigating the possible roles of dopamine (DA) and iron in production of hydroxyl radicals (.OH) in rat striatum after Mn2+ intoxication. For this purpose, DA depletions were assessed concomitant with in vivo 2,3- and 2,5-dihydroxybenzoic acid (DHBA) formation from the reaction of salicylate with .OH, of which 2,3-DHBA is a nonenzymatic adduct. Following intrastriatal Mn2+ injection, marked 2,3-DHBA increases were observed in a time- and dose-dependent fashion reaching maximum levels at 6-18 h and a plateau beyond 0.4 μmol (fourfold increase). The delayed increase of 2,3-DHBA levels suggests that Mn2+ induces OH formation in the living brain by an indirect process. The early DA depletion (2 h) and relatively late .OH formation (6 h) indicate independent processes by Mn2+. In addition, depletion of DA (about 90%) by reserpine pretreatment did not significantly alter Mn2+-induced 2,3-DHBA formation or the extent of DA depletion, suggesting that DA or DA autoxidation are not participating in Mn2+-induced .OH formation in vivo. Furthermore, Mn2+ injection did not significantly alter the low molecular weight iron pool in striatum, and co-injections of the iron-chelator deferoxamine with Mn2+ into striatum did not significantly attenuate Mn2+-induced 2,3-DHBA formation. These findings suggest no role of chelatable iron in generation of Mn2+-induced .OH, but do not exclude a role for mitochondrial heme-iron or peroxynitrite (Fe-independent) in Mn2+-induced .OH formation

Selective decline of 5-HT1A receptor binding sites in rat cortex, hippocampus and cholinergic basal forebrain nuclei during aging

The effect of aging on 5-HT1A receptor binding in several forebrain areas associated with the basal forebrain cholinergic system was investigated in rats of 3-, 24- and 30-months-old by receptor autoradiography and biochemical binding assay using [H-3]8-OH-DPAT as a ligand. Autoradiographic measurements demonstrated a marked region-specific decline of ligand binding in: (i) regions of the basal forebrain cholinergic cell groups, i.e. the medial septum, diagonal band nuclei and magnocellular nucleus basalis, (ii) the frontal and parietal neocortex and (iii) the dentate gyrus of the hippocampus. No change or- only a slight decrease of the 5-HT1A receptor density was found in other areas investigated: the CA1 and CA3 sectors of hippocampus, the cingular and perirhinal cerebral cortex and the lateral septum. The autoradiographic findings were substantiated by the biochemical binding assay, which revealed a comparable loss of 5-HT1A receptor in the hippocampus and neocortex at the age of 30 months. The results clearly show that with increasing age the decrement of 5-HT1A receptor binding in the rat forebrain is remarkably region-selective and particularly affects the cholinergic cell groups that innervate cortex and hippocampus. This phenomenon appears to be especially significant in relation to the neuronal substrates underlying the age-related alterations of mood and cognition. (C) 1997 Elsevier Science B.V