Speeding Those Laboratory Checkout Lines
Small metal barcodes have been developed for labeling large sample arrays. Nicewarner-Peña et al. (p. 137) electrochemically synthesized metal rods a few tenths of a micrometer in diameter and several micrometers in length in which different metals are stacked sequentially. The different reflectivity of metals such as gold, silver, copper, and nickel allows numerous sequences to be read out with ordinary light microscopy (with three metals, about a quarter million different codes can be created). The noble metal surface can be readily derivatized for use with fluorescence bioassays.
Quasar Double Helix
Relativistic jets of collimated hot plasma from active galactic nuclei provide information about the physical and chemical properties that drive these energetic structures. Lobanov and Zensus (p. 128) used the HALCA radio telescope spacecraft and an array of ground-based radio telescopes to create a high-resolution image of the structure of the jet from quasar 3C273. The jet's exquisite double-helix structure, which results from different modes of a Kelvin-Helmholtz instability, should provide an important test for improving models of the difficult-to-observe active galactic nuclei.
Dial M for Spin Control
The ability to coherently control an ensemble of carriers in a semiconductor in response to an external magnetic field is a fundamental issue for spintronics, where not just the charge but the spin states of the carriers will be exploited for information processing. Kawakami et al. (p. 131) show that a ferromagnetic layer deposited on GaAs exerts an unexpectedly strong influence on the spin dynamics of excited carriers within the semiconductor. Interpreted as a feedback mechanism of dynamic nuclear polarization, the results indicate the adjacent ferromagnetic layer “imprints” a nuclear magnetic moment in the semiconductor that influences the spin dynamics of the photogenerated carriers.
Customized Chemical Patterns
Chemical waves, such as reaction fronts on metal surfaces or Ca waves in cells, can be modified in many ways, such as by pulsing reactants or introducing physical barriers. Wolff et al. (p. 134) show that localized surface heating can be used to control the evolution of chemical waves produced during the oxidation of CO on a Pt surface. Wave fronts can be launched and redirected, either under operator control or feedback optimized under computer control.
One Layer at a Time
Our understanding of how climate influenced culture in the southwestern United States during the latter half of the Holocene would be improved by a more complete record of regional precipitation, but for the period before written records, we must rely on proxies to determine moisture variations. Polyak and Asmerom (p. 148) analyzed data from five New Mexican stalagmites, covering the past 4000 years, to reconstruct precipitation changes, which they relate to records of cultural development in the region.
Evolving a Balancing Act
Elongation factor Tu (EF-Tu) is responsible for supplying amino acid-transfer RNA (aa-tRNA) conjugates to the ribosome, where they are used in protein synthesis. Because there is only one EF-Tu and there are at least 20 different varieties of aa-tRNA, it had been thought that this would be a relatively nonspecific interaction. LaRiviere et al. (p. 165; see the Perspective by Ibba) took a closer look and found that the binding affinities of EF-Tu for different aa-tRNAs do indeed fall within a narrow range. However, this uniformity results from the compensatory adjustment of pairing a stronger binding amino acid with a weaker binding tRNA, and vice versa. The authors suggest that EF-Tu may be a site for kinetic proofreading; incorrectly matched aa-tRNA conjugates either dissociate from EF-Tu before reaching the ribosome or bind so tightly as to be undeliverable.
Can Plants Keep Up with Climate?
How rapidly can organisms adapt to global climate change? From an experimental study on a native legume of the American Great Plains, Etterson and Shaw (p. 151) have calculated the number of generations needed for adaptive changes to take place, and compare this estimate with the trajectory of predicted climate change. Adaptive evolution in response to global change is constrained by antagonistic genetic correlations among traits within populations of the plant, which suggests that plants of this kind might not adapt sufficiently rapidly to projected climate changes.
How to Copy a Genome
Replication of genomic DNA occurs during the S or synthesis phase of the cell cycle. Although we have detailed knowledge of the dynamics of a few specific replication origins, little is known about how replication occurs for an entire genome. Raghuraman et al. (p. 115) developed a DNA microarray assay that allowed them to analyze the replication of the entire yeast genome. Replication of the ends of each chromosome is highly correlated, and, unlike mammalian cells, there is essentially no correlation between replication and transcription.
Finding the Heart of the Centromere
The high content of repetitive sequences in the centromere, which is vital for normal partitioning of chromosomes during cell division, has made it one of the most intractable regions of the human genome. Schueler et al. (p. 109; see the news story by Pennisi) developed a genomic map from the X chromosome arm to its centromeric satellite DNA. Human chromosome rearrangements were used to infer the region essential for centromere function, and that definition was tested in an artificial chromosome assay. Analysis of sequences in this region provided clues to the evolution of the centromere as well as the potential for a recent origin for the functional sequences.
Tracking Triglyceride Genes
The apolipoprotein gene cluster on human chromosome 11 has been extensively studied as a region known to exert effects on triglyceride levels and cardiovascular disease. Pennacchio et al. (p. 169; see the news story by Seydel) have used comparative genomics between mouse and human sequences to identify a new apolipoprotein gene, APOAV, located near the cluster. When the human gene was expressed as a transgene in mice, plasma triglyceride decreased. In contrast, knockout mice had increased plasma triglyceride levels compared to wild-type mice. Studies of single nucleotide polymorphisms (SNPs) in the APOAV region in two independent human populations also indicated that this gene may influence triglyceride levels in humans.
Regulating Cell Proliferation
Increased amounts of cyclin E and its protein kinase partner cyclin-dependent kinase 2 (CDK2) promote progression of cells from G1 to S phase of the cell cycle, and the abundance of cyclin E is regulated by proteolysis. Koepp et al. (p. 173; see the Perspective by Bartek and Lukas) have identified the human ubiquitin ligase subunit, named Fbw7, that binds phosphorylated cyclin E and targets it to the SCF complex, where it is ubiquitinated and later degraded. Thus, similar mechanisms are used in yeast, worms, flies, and mammals to regulate abundance of cyclin E. The functional characterization of Fbw7 suggests that it could function as a tumor suppressor.
A Beneficial Triplet Repeat
Triplet repeat expansions occur in several human genetic diseases and always result in a deleterious phenotype. Studying the bacterium Escherichia coli, Ritz et al. (p. 158) describe a triplet repeat expansion that is beneficial. An E. coli strain that grows poorly because of a defect in the reduction of protein disulfide bonds undergoes a phenotypic reversion at high frequency because of reversible expansion of a TCT repeat sequence in the ahpC gene. Remarkably, this genetic alteration restores normal cell growth because it introduces a single amino acid into the AhpC protein that converts it from a peroxidase to a disulfide reductase. The ready mutational interconversion of these two enzyme activities may allow the bacteria to survive conditions of oxidative or disulfide stress.
Evolution of Virulence in Toxoplasma
Toxoplasma, which undergoes sexual reproduction and might be expected to show a high degree of genetic mixing among strains, exists as only a few genetically distinct “clonal types.” Grigg et al. (p. 161) analyzed polymorphic loci and found that the three major types originated from rare crossing events between two ancestors. Such reassortment may have been crucial in the development of virulence, as a cross between two avirulent strains resulted in an organism that was highly virulent in mice. Virulence is likely to be attributable to a combination of factors rather than a single gene.
Protection from Prions
Prions are the likely causative agents in new variant Creutzfeldt-Jakob disease (vCJD) and bovine spongiform encephalopathy (BSE), as well as scrapie. Experimental vaccination against prion disease in mice has been impaired by poor immunogenicity of the prion protein (PrPSc) resulting from partial immune tolerance to the endogenous host form of the protein, PrPc. Heppner et al. (p. 178) generated transgenic mice in which the clonal antibody repertoire was skewed toward prion recognition. Immunization of these animals with PrPSc resulted in protection from neuropathic changes associated with scrapie, even when genes for endogenous PrPc were reintroduced.
Oxygen and Oil
Fossil fuels are created by the burial and compression of organic matter in sedimentary rocks over geologic time scales. Controversy has developed over the importance of exposure to oxygen to create nonprotein alkyl carbon, a precursor needed for oil generation. Gelinas et al. (p. 145) show that the time of exposure to oxygen is inversely correlated with the concentration of nonprotein alkyl carbon. The effects of sedimentary rock redox conditions on oil-generation potential can now be quantified.
Supercritical Route to Conformal Copper Films
Although there are many routes for depositing metal films on substrates, in electronic devices it is often necessary to deposit films conformally into a trench or over a ridge to make robust connections. Blackburn et al. (p. 141) describe a method in which organometallic copper and nickel compounds, solubilized in supercritical CO2, thermally decompose to deposit high-aspect-ratio metal lines with widths under 100 nanometers onto native silicon oxide or metal nitrides. This one-step approach may prove advantageous in fabricating copper interconnects.
Putting the Pieces Together
Plants respond to light with numerous changes in developmental and physiological processes. However, the exact process by which the light signal is transduced into developmental alterations has remained obscure. Using a variety of assays in Arabidopsis, Wang et al. (p. 154) demonstrate a physical interaction between the blue-light photoreceptors, cryptochromes, and COP1, a ubiquitin ligase that can promote degradation of proteins by the 26S proteasome. Among the proteins that can be targeted for destruction by the proteasome is HY5, which is a transcription factor that can bind to and regulate promoters of light-inducible genes. The demonstration of a physical connection between these components helps explain the signaling pathway by which blue light affects plant growth and development.
Archaeology and Australian Megafauna
In a study that dated megafaunal burial sites across Australia, Roberts et al (8 June 2001) concluded that all large animals on the continent were extinct by around 46,400 years ago, and suggested that remains at some sites have been disturbed and therefore must be dated with caution. A comment by Field and Fullagar disagrees with the “argument for disturbance made by Roberts et al.” for at least one site, Cuddie Springs, stating that “stratigraphic integrity of a site cannot be assessed by dating alone.” In response, Roberts et al. reaffirm their claim that “reliable ages … can only be determined by direct dating,” and offer a proposal to reconcile the discrepancy between the optical dates cited by Field and Fullagar and the ages reported in the Roberts et al. study. The full text of these comments can be seen at