This Week in SCIENCE, Volume 300, Issue 5625, Building Signaling
Connections
dated June 6 2003, is now available at:

http://www.sciencemag.org/content/vol300/issue5625/twis.shtml


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This Week in SCIENCE
June 6 2003, 300 (5625)

THIS WEEK IN SCIENCE
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Separate and Entangled
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Superconducting quantum bits (qubits) are currently being developed as
promising candidates for implementations in quantum computers. Although the
quality of single qubits has been improving with coherence times
sufficiently long to allow manipulation of the states of the qubit, the
ability to couple, or entangle, qubits together will be required for
quantum computing to be realized. Taking initial steps along this route,
Berkley et al. (p. 1548) entangled two macroscopic quantum systems,
current-biased Josephson junctions, that were separated by 0.7 millimeters
but coupled via capacitors. Spectroscopic studies show that the electronic
energy levels correspond to those expected for entanglement of the two
qubits.


CREDIT: BERKLEY ET AL.

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Tracking Carbon Sinks
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The sequestering of atmospheric CO2 by ecosystems is the focus of two
studies. European terrestrial ecosystems may comprise a net carbon sink
analogous to that seen for North America. Net uptake has been inferred from
inverse atmospheric models that are based on CO2 fluxes. Janssens et al.
(p. 1538) compare estimates derived from both atmospheric reconstructions
and ecosystem inventory approaches to quantify the carbon balance of
Europe's four dominant ecosystem types: forests, grasslands, croplands, and
peatlands. They find that European terrestrial ecosystems sequester only 7
to 13% of European fossil emissions and that this is only about one-third
that of the previous estimates. Although the uncertainties within both
estimates remain large, the differences are likely the result of how
non-CO2 compounds such as methane are treated. The effect of climate on
plant growth in general has been assessed by Nemani et al. (p. 1560), who
constructed a global record for the period from 1982 to 1999. They compared
the data with relevant information on precipitation and temperature to
infer where major changes have occurred. Most of the increase in plant
growth that they documented occurred in the tropics, particularly in South
America, where decreases in cloud cover increased primary production.

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Optical Analogs of Two-Dimensional NMR
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A key development in nuclear magnetic resonance (NMR) was the introduction
of multidimensional spectroscopy, in which one NMR spectrum evolves under
the influence of subsequent magnetization pulses of defined phase and
duration. In optical spectroscopy, analogous experiments can be performed
with phase matching, in which short pulses create a coherent excited state
that can then be perturbed with additional pulses that come in along
different directions. Tian et al. (p. 1553; see the Perspective by Jonas)
now show that shaped ultrafast optical pulses in a collinear geometry can
be used to select particular nonlinear polarizations that can enhance or
suppress particular coherences. In a model system (a rubidium vapor), the
effect of such "phase cycling" on cross peaks provided information on how
different excited states observed in fluorescence were coupled or
interacted anharmonically.

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How Does Your Comet Glow?
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About 8 years ago, x-ray satellites showed that comets emit x-rays, but the
underlying mechanism that produces the emission has proven elusive.
Beiersdorfer et al. (p. 1558) have obtained high- resolution spectra of
ions trapped in gases using the spare x-ray microcalorimeter spectrometer
from the ASTRO-E mission. The laboratory spectra can be explained by
double-capture of electrons in a charge-exchange process. These lab
measurements were used in an emission model that was able to fit the
spectrum of comet Linear C/1999 S4 taken by the Chandra X-ray Observatory.
Charge- exchange between solar wind ions and neutral gases in the coma is
sufficient to explain the x-ray emissions.

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>From Hotspots to Melting Pots
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During the glacial periods of the Pleistocene, the ranges of many organisms
contracted into isolated pockets or "refugia." One popular hypothesis has
been that diversity within a species will decline away from refugia because
of successive founder events during postglacial colonization. Petit et al.
(p. 1563) performed a meta-analysis of data from a large number of European
plant species and found that the overall pattern of diversity is in
conflict with this hypothesis. Although most species had the most
genetically divergent populations in the southern refugial areas (the
"hotspots"), the most diverse populations were typically located at more
distant northerly latitudes. The authors argue that this pattern most
likely is caused by admixture of divergent lineages coming out of different
refugia ("melting pots").

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Seeking Out Single-Stranded DNA
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The checkpoint signals that cells generate in response to DNA damage are
mediated by the ATR protein kinase, which functions in a complex with the
ATRIP protein. Zou and Elledge (p. 1542; see the Perspective by Carr) found
that the ATR-ATRIP complex was not recruited to sites of DNA damage in
cells that lacked replication protein A (RPA). Although RPA functions in
processes such as replication and recombination, it also appears to
initiate the checkpoint signal by binding to single-stranded DNA and then
interacting with the ATR-ATRIP complex, which phosphorylates substrate
proteins at the damage site.

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Wet Mantle Below the Mediterranean
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Water can be carried into the mantle by subduction, but it is unclear how
much of this water remains in the subducted slab when it enters the mantle
transition zone [depths of 410 to 660 kilometers (km)]. Van der Meijde et
al.(p. 1556) examined the frequency dependence of seismic waves at the
410-km velocity discontinuity and found evidence for greater-than-expected
water content in the transition zone below the Mediterranean. Several
subduction zones may transport water into the region. The phase transition
of olivine to wadsleyite at the 410-km discontinuity would enhance the
water content because the latter mineral retains more water in its
structure.


CREDIT: VAN DER MEIJDE ET AL.

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Cutting Down the Middle
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During cell division, two daughter cells are physically separated when an
actin ring forms in between the two new daughter nuclei and constricts.
Pardo and Nurse (p. 1569) describe a novel and unexpected role for the
equatorial microtubular structures in the control of the actin ring
localization during cytokinesis in fission yeast. In the absence of these
structures, the actin ring migrated dramatically to one end of the cell
while the two nuclei frequently collapsed together in the middle of the
cell. The equatorial microtubular structures are thus likely to be
essential for maintaining accurate positioning of the division plane should
cytokinesis be delayed.


CREDIT: PARDO AND NURSE

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A Disrupter of Insulin Signaling
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The protein kinase Akt is a key component in insulin signaling. Du et al.
(p. 1574) searched for proteins that directly interacted with Akt and found
a protein they call TRB3, a mammalian homolog of the Drosophila tribbles
protein, that functions as an inhibitor of the kinase. The amount of TRB3
RNA in livers from diabetic mice was increased compared to that in the wild
type. Infection of mice or of rat FAO hepatoma cells with adenovirus
expressing TRB3 caused hyperglycemia and reduced responses to insulin,
respectively. The results establish TRB3 as component in metabolic control
by insulin and as a potential therapeutic target for treatment of type II
diabetes.

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Spikes, Learning, and Hippocampal Neurons
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What are the patterns of neuronal activity by which memories are
established in the brain? An important step in this direction would be the
identification of neuronal firing that occurs specifically during encoding
and consolidation of memory.Wirth et al.(p. 1578) recorded from individual
neurons in the monkey hippocampus and found that the activity of cells
changed in parallel with the animals' learning of a location-scene
association task. In a significant proportion of the cells, changes in
activity were sustained after the animal had learned an association,
whereas in others the changes were more temporary. These findings show that
new associative learning is signaled by changes in a hippocampal neuron's
stimulus-selective response properties.

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No More DNA, We're Full
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Tetrahymena, a single-celled eukaryote, organizes its genome into a
germline micronucleus and a somatic macronucleus. The DNA in the
macronucleus is substantially rearranged, with up to ~15% being deleted.
This deletion is programmed by the micronucleus and is thought to involve
the RNA interference (RNAi) machinery. Yao et al. (p. 1581; see the
Perspective by Selker) show that direct injection of double-stranded RNA,
the substrate for RNAi, results in the specific and efficient deletion of
homologous genomic regions. Foreign DNA sequences introduced into the
micronucleus are efficiently deleted from daughter somatic macronuclei.
This process prevents their expression in vegetative cells and suggests
that this RNA-directed DNA deletion system operates to disable invading
DNA.

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Polishing the Number of Rice Genes
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The rice genome is useful not only for understanding rice, but other cereal
crops as well. The Rice Chromosome 10 Sequencing Consortium (p. 1566; see
the Perspective by Bevan) now offers a closer-to-finished sequence of
chromosome 10, the smallest of the 12 rice chromosomes. Compared with
previous draft sequences of the rice genome, this more polished sequence
analysis finds, among other various statistics, that the median predicted
size of genes is roughly 40% greater and the total predicted number of
genes is roughly doubled in comparison to previous predictions.

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Stressing Out the Neighbors
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Several experimental studies have shown that nanocrystalline metals deform
by a different mechanism in comparison to coarser grained materials and can
resist plastic deformation at high stress. They also tend to exhibit a
brittleness that leads to a "dimpling" of fracture surfaces on the larger
size scale of several grains. Hasnaoui et al. (p. 1550) used large-scale
simulations to show that these small grains tend to move in a cooperative
fashion. However, if a special grain boundary is present that does not
typically move under stress, such as that at a twin boundary, it can pin
its neighboring grains and prevent plastic deformation from occurring.

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The Ins and Outs on Pathogen Screening
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All multicellular organisms have common families of mechanisms that operate
during early stages of responses to pathogen attack. Studies in insects and
mammals have revealed the role of the Toll family and of the pattern
recognition molecules Nod 1 and 2 in activating similar, but not identical,
signal-transduction pathways. Lipopolysaccharide is not the sole pattern
recognized by the innate immune system, Girardin et al. (p. 1584) show that
intracellular Nod1 specifically detects a tripeptide bearing an exposed
diaminopimelate amino acid derived from the peptidoglycan of Gram-negative
bacteria. In contrast, Nod2, which is present on monocytes, macrophages,
and dendritic cells, senses a peptidoglycan dipeptide motif common to all
bacteria (unresponsive mutants of Nod2 have been implicated in Crohn's
disease). Thus, Nod1 allows discrimination between intracellular
Gram-positive and Gram-negative microorganisms and helps to shape
subsequent adaptive immune responses.