Use of chromatin immunoprecipitation (ChIP) to detect transcription factor binding to highly homologous promoters in chromatin isolated from unstimulated and activated primary human B cells

The Chromatin Immunoprecipiation (ChIP) provides a powerful technique for identifying the in vivo association of transcription factors with regulatory elements. However, obtaining meaningful information for promoter interactions is extremely challenging when the promoter is a member of a class of highly homologous elements. Use of PCR primers with small numbers of mutations can limit cross-hybridization with non-targeted sequences and distinguish a pattern of binding for factors with the regulatory element of interest. In this report, we demonstrate the selective in vivo association of NF-κB, p300 and CREB with the human Iγ1 promoter located in the intronic region upstream of the Cγ1 exons in the immunoglobulin heavy chain locus. These methods have the ability to extend ChIP analysis to promoters with a high degree of homology

A Functional Phylogenomic View of the Seed Plants

A novel result of the current research is the development and implementation of a unique functional phylogenomic approach that explores the genomic origins of seed plant diversification. We first use 22,833 sets of orthologs from the nuclear genomes of 101 genera across land plants to reconstruct their phylogenetic relationships. One of the more salient results is the resolution of some enigmatic relationships in seed plant phylogeny, such as the placement of Gnetales as sister to the rest of the gymnosperms. In using this novel phylogenomic approach, we were also able to identify overrepresented functional gene ontology categories in genes that provide positive branch support for major nodes prompting new hypotheses for genes associated with the diversification of angiosperms. For example, RNA interference (RNAi) has played a significant role in the divergence of monocots from other angiosperms, which has experimental support in Arabidopsis and rice. This analysis also implied that the second largest subunit of RNA polymerase IV and V (NRPD2) played a prominent role in the divergence of gymnosperms. This hypothesis is supported by the lack of 24nt siRNA in conifers, the maternal control of small RNA in the seeds of flowering plants, and the emergence of double fertilization in angiosperms. Our approach takes advantage of genomic data to define orthologs, reconstruct relationships, and narrow down candidate genes involved in plant evolution within a phylogenomic view of species' diversification

Do children with falling blood lead levels have improved cognition? Pediatrics 110:787–791

ABSTRACT. Objective. Exposure to lead at levels encountered by urban children impairs cognitive development. An observational study suggested improvement in IQ when blood lead level fell, but the only randomized trial of chelation showed no benefit in IQ. Methods. We did a new analysis of the data from the clinical trial using change in blood lead level as the independent variable. The 741 children began with blood lead levels between 20 and 44 g/dL, and were 13 to 33 months old at randomization to chelation or placebo. Blood lead levels were measured repeatedly, and cognitive tests were given at baseline, 6 months, and 36 months follow-up. Results. By 6 months after randomization, blood lead levels had fallen by similar amounts in both chelated and placebo children, despite the immediate drops in the chelated group; there was no association between change in blood lead level and change in cognitive test score. Blood lead levels continued to fall. At 36 months followup, in the placebo group only, cognitive test scores had increased 4.0 points per 10 g/dL fall in blood lead level from baseline to 36 months follow-up and 5.1 points from 6 to 36 months. Conclusions. The improvement in scores in the placebo group only implies that factors other than declining blood lead levels per se are responsible for cognitive improvement; it is possible but less likely that succimer, the active drug, impairs cognition. Pediatrics 2002;110: 787-791; child, preschool; environmental exposure; lead poisoning/blood/etiology; cognition/physiology; chelation therapy. ABBREVIATIONS. TLC, Treatment of Lead-Exposed Children; MDI, Mental Development Index; SD, standard deviation. P rospective data from multiple studies in several countries show that lead exposure insufficient to produce symptoms still results in cognitive deficits in young children. Peak blood lead level, which is usually achieved around 2 years of age, is associated with lower scores on IQ tests administered at 4 years old and later. 1 It is not known whether such effects can be reduced or prevented once exposure has taken place. In an observational study, New York children 13 to 87 months old with blood lead levels between 25 and 55 g/dL were given chelation with EDTA and therapeutic iron when clinically indicated, then followed for 6 months. Those whose blood lead levels fell the most had improved cognitive test scores, independent of whether they had been given iron or chelation therapy. The New York study, conducted by Ruff and colleagues, 2 was not a formal trial. Children could not be randomized to a greater drop in blood lead level and their cognitive test scores compared. Rather, the differences in children's cognitive test scores between baseline and 6-month follow-up were compared with the differences in their blood lead levels, adjusting statistically for other differences. This kind of study and analysis does not permit experimental inference the way a trial does. If replicated, however