Single-molecule DNA sequencing of a viral genome

The full promise of human genomics will be realized only when the genomes of thousands of individuals can be sequenced for comparative analysis. A reference sequence enables the use of short read length. We report an amplification-free method for determining the nucleotide sequence of more than 280,000 individual DNA molecules simultaneously. A DNA polymerase adds labeled nucleotides to surface-immobilized primer-template duplexes in stepwise fashion, and the asynchronous growth of individual DNA molecules was monitored by fluorescence imaging. Read lengths of >25 bases and equivalent phred software program quality scores approaching 30 were achieved. We used this method to sequence the M13 virus to an average depth of >150x and with 100% coverage; thus, we resequenced the M13 genome with high-sensitivity mutation detection. This demonstrates a strategy for high-throughput low-cost resequencing.     

An inhibitor of FtsZ with potent and selective anti-staphylococcal activity

FtsZ is an essential bacterial guanosine triphosphatase and homolog of mammalian beta-tubulin that polymerizes and assembles into a ring to initiate cell division. We have created a class of small synthetic antibacterials, exemplified by PC190723, which inhibits FtsZ and prevents cell division. PC190723 has potent and selective in vitro bactericidal activity against staphylococci, including methicillin- and multi-drug-resistant Staphylococcus aureus. The putative inhibitor-binding site of PC190723 was mapped to a region of FtsZ that is analogous to the Taxol-binding site of tubulin. PC190723 was efficacious in an in vivo model of infection, curing mice infected with a lethal dose of S. aureus. The data validate FtsZ as a target for antibacterial intervention and identify PC190723 as suitable for optimization into a new anti-staphylococcal therapy.     

Brood parasitic cowbird nestlings use host young to procure resources

Young brood parasites that tolerate the company of host offspring challenge the existing evolutionary view of family life. In theory, all parasitic nestlings should be ruthlessly self-interested and should kill host offspring soon after hatching. Yet many species allow host young to live, even though they are rivals for host resources. Here we show that the tolerance of host nestlings by the parasitic brown-headed cowbird Molothrus ater is adaptive. Host young procure the cowbird a higher provisioning rate, so it grows more rapidly. The cowbird's unexpected altruism toward host offspring simply promotes its selfish interests in exploiting host parents.     

Vibrationally quantum-state-specific reaction dynamics of H atom abstraction by CN radical in solution

Solvent collisions can often mask initial disposition of energy to the products of solution-phase chemical reactions. Here, we show with transient infrared absorption spectra obtained with picosecond time resolution that the nascent HCN products of reaction of CN radicals with cyclohexane in chlorinated organic solvents exhibit preferential excitation of one quantum of the C-H stretching mode and up to two quanta of the bending mode. On time scales of approximately 100 to 300 picoseconds, the HCN products undergo relaxation to the vibrational ground state by coupling to the solvent bath. Comparison with reactions of CN radicals with alkanes in the gas phase, known to produce HCN with greater C-H stretch and bending mode excitation (up to two and approximately six quanta, respectively), indicates partial damping of the nascent product vibrational motion by the solvent. The transient infrared spectra therefore probe solvent-induced modifications to the reaction free energy surface and chemical dynamics.     

Genetic dissection of transcriptional regulation in budding yeast

To begin to understand the genetic architecture of natural variation in gene expression, we carried out genetic linkage analysis of genomewide expression patterns in a cross between a laboratory strain and a wild strain of Saccharomyces cerevisiae. Over 1500 genes were differentially expressed between the parent strains. Expression levels of 570 genes were linked to one or more different loci, with most expression levels showing complex inheritance patterns. The loci detected by linkage fell largely into two categories: cis-acting modulators of single genes and trans-acting modulators of many genes. We found eight such trans-acting loci, each affecting the expression of a group of 7 to 94 genes of related function.