Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize

Helitrons are a family of mobile elements that were discovered in 2001 and are now known to exist in the entire eukaryotic kingdom. Helitrons, particularly those of maize, exhibit an intriguing property of capturing gene fragments and placing them into the mobile element. Helitron-captured genes are sometimes transcribed, giving birth to chimeric transcripts that intertwine coding regions of different captured genes. Here, we perused the B73 maize genome for high-quality, putative Helitrons that exhibit plus/minus polymorphisms and contain pieces of more than one captured gene. Selected Helitrons were monitored for expression via in silico EST analysis. Intriguingly, expression validation of selected elements by RT–PCR analysis revealed multiple transcripts not seen in the EST databases. The differing transcripts were generated by alternative selection of splice sites during pre-mRNA processing. Selection of splice sites was not random since different patterns of splicing were observed in the root and shoot tissues. In one case, an exon residing in close proximity but outside of the Helitron was found conjoined with Helitron-derived exons in the mature transcript. Hence, Helitrons have the ability to synthesize new genes not only by placing unrelated exons into common transcripts, but also by transcription readthrough and capture of nearby exons. Thus, Helitrons have a phenomenal ability to “display” new coding regions for possible selection in nature. A highly conservative, minimum estimate of the number of new transcripts expressed by Helitrons is ∼11,000 or ∼25% of the total number of genes in the maize genome

Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing

Meiotic recombination rates can vary widely across genomes, with hotspots ofintense activity interspersed among cold regions. In yeast, hotspots tend to occur inpromoter regions of genes, whereas in humans and mice hotspots are largely definedby binding sites of the PRDM9 protein. To investigate the detailed recombinationpattern in a flowering plant we use shotgun resequencing of a wild population of themonkeyflower Mimulus guttatus to precisely locate over 400,000 boundaries ofhistoric crossovers or gene conversion tracts. Their distribution defines some 13,000hotspots of varying strengths, interspersed with cold regions of undetectably lowrecombination. Average recombination rates peak near starts of genes and fall offsharply, exhibiting polarity. Within genes, recombination tracts are more likely toterminate in exons than in introns. The general pattern is similar to that observed inyeast, as well as in PRDM9-knockout mice, suggesting that recombination initiationdescribed here in Mimulus may reflect ancient and conserved eukaryoticmechanism

The Intelligent Room Project

At the MIT Artificial Intelligence Laboratory we have been working on technologies for an Intelligent Room. Rather than pull people into the virtual world of the computer we are trying to pull the computer out into the real world of people. To do this we are combining robotics and vision technology with speech understanding systems, and agent based architectures to provide ready at hand computation and information services for people engaged in day to day activities, both on their own and in conjunction with others. We have built a layered architecture where at the bottom level vision systems track people and identify their activities and gestures, and through word spotting decide whether people in the room are talking to each other or to the room itself. At the next level an agent architecture provides a uniform interface to such specially built systems, and to other off the shelf software, such as web browsers, etc. At the highest level we are able to build application systems that p..

Integration of Cot Analysis, DNA Cloning, and High-Throughput Sequencing Facilitates Genome Characterization and Gene Discovery

Cot-based sequence discovery represents a powerful means by which both low-copy and repetitive sequences can be selectively and efficiently fractionated, cloned, and characterized. Based upon the results of a Cot analysis, hydroxyapatite chromatography was used to fractionate sorghum (Sorghum bicolor) genomic DNA into highly repetitive (HR), moderately repetitive (MR), and single/low-copy (SL) sequence components that were consequently cloned to produce HRCot, MRCot, and SLCot genomic libraries. Filter hybridization (blotting) and sequence analysis both show that the HRCot library is enriched in sequences traditionally found in high-copy number (e.g., retroelements, rDNA, centromeric repeats), the SLCot library is enriched in low-copy sequences (e.g., genes and “nonrepetitive ESTs”), and the MRCot library contains sequences of moderate redundancy. The Cot analysis suggests that the sorghum genome is approximately 700 Mb (in agreement with previous estimates) and that HR, MR, and SL components comprise 15%, 41%, and 24% of sorghum DNA, respectively. Unlike previously described techniques to sequence the low-copy components of genomes, sequencing of Cot components is independent of expression and methylation patterns that vary widely among DNA elements, developmental stages, and taxa. High-throughput sequencing of Cot clones may be a means of “capturing” the sequence complexity of eukaryotic genomes at unprecedented efficiency. [Online supplementary material is available at www.genome.org. The sequence data described in this paper have been submitted to the GenBank under accession nos. AZ921847-AZ923007. Reagents, samples, and unpublished information freely provided by H. Ma and J. Messing.

Hexamethonium- and methyllycaconitine-induced changes in acetylcholine release from rat motor nerve terminals

1. The neuronal nicotinic receptor antagonists hexamethonium and methyllycaconitine (MLA) have been used to study the putative prejunctional nicotinic ACh receptors (AChRs) mediating a negative-feedback control of ACh release from motor nerve terminals in voltage-clamped rat phrenic nerve/hemidiaphragm preparations. 2. Hexamethonium (200 μM), but not MLA (0.4–2.0 μM), decreased the time constant of decay of both endplate currents (e.p.cs) and miniature endplate currents (m.e.p.cs), indicating endplate ion channel block with hexamethonium. However, driving function analysis and reconvolution of e.p.cs and m.e.p.cs indicated that this ion channel block did not compromise the analysis of e.p.c. quantal content. 3. At low frequencies of stimulation (0.5–2 Hz), hexamethonium (200 μM) and MLA (2.0 μM) increased e.p.c. quantal content by 30–40%. At high frequencies (50–150 Hz) neither compound affected e.p.c. quantal content. All effects on quantal content were paralleled by changes in the size of the pool of quanta available for release. 4. The low frequency augmentation of e.p.c. quantal content by hexamethonium was absent when extracellular [Ca(2+)] was lowered from 2.0 to 0.5 mM. 5. At the concentrations studied, MLA and hexamethonium produced a small (10–20%) decrease in the peak amplitude of m.e.p.cs. 6. Neither apamin (100 nM) nor charybdotoxin (80 nM) had effects on spontaneous or nerve evoked current amplitudes at any frequency of stimulation. Thus the ability of nicotinic antagonists to augment e.p.c. quantal content is not due to inhibition of Ca(2+)-activated K(+)-channels. 7. We suggest that hexamethonium and MLA increase evoked ACh release by blocking prejunctional nicotinic AChRs. These receptors exert a negative feedback control over evoked ACh release and are probably of the α-bungarotoxin-insensitive neuronal type