An autonomous molecular computer for logical control of gene expression

Early biomolecular computer research focused on laboratory-scale, human-operated computers for complex computational problems. Recently, simple molecular-scale autonomous programmable computers were demonstrated allowing both input and output information to be in molecular form. Such computers, using biological molecules as input data and biologically active molecules as outputs, could produce a system for 'logical' control of biological processes. Here we describe an autonomous biomolecular computer that, at least in vitro, logically analyses the levels of messenger RNA species, and in response produces a molecule capable of affecting levels of gene expression. The computer operates at a concentration of close to a trillion computers per microlitre and consists of three programmable modules: a computation module, that is, a stochastic molecular automaton; an input module, by which specific mRNA levels or point mutations regulate software molecule concentrations, and hence automaton transition probabilities; and an output module, capable of controlled release of a short single-stranded DNA molecule. This approach might be applied in vivo to biochemical sensing, genetic engineering and even medical diagnosis and treatment. As a proof of principle we programmed the computer to identify and analyse mRNA of disease-related genes associated with models of small-cell lung cancer and prostate cancer, and to produce a single-stranded DNA molecule modelled after an anticancer drug.     

Competition and mutualism among the gut helminths of a mammalian host

Most animal species are infected with multiple parasite species; however, the role of interspecific parasite interactions in influencing parasite dynamics and shaping parasite communities has been unclear. Although laboratory studies have found evidence of cross-immunity, immunosuppression and competition, analyses of hosts in the field have generally concluded that parasite communities are little more than random assemblages. Here we present evidence of consistent interspecific interactions in a natural mammalian system, revealed through the analysis of parasite intensity data collected from a free-ranging rabbit (Oryctolagus cuniculus) population, sampled monthly for a period of 23 yr. The wild rabbit plays host to a diverse gut helminth community that reflects the communities seen in other economically important domestic herbivores. These findings suggest that parasite interactions could have profound implications for the dynamics of parasite communities. The efficacy of parasite control programmes could be jeopardized if such interactions are not taken into account. In contrast, a clear understanding of such interactions may provide the basis for the development of more environmentally acceptable methods of parasite control.     

Historical phenology: grape ripening as a past climate indicator

French records of grape-harvest dates in Burgundy were used to reconstruct spring-summer temperatures from 1370 to 2003 using a process-based phenology model developed for the Pinot Noir grape. Our results reveal that temperatures as high as those reached in the 1990s have occurred several times in Burgundy since 1370. However, the summer of 2003 appears to have been extraordinary, with temperatures that were probably higher than in any other year since 1370.     

Room-temperature ferroelectricity in strained SrTiO3

Systems with a ferroelectric to paraelectric transition in the vicinity of room temperature are useful for devices. Adjusting the ferroelectric transition temperature (T(c)) is traditionally accomplished by chemical substitution-as in Ba(x)Sr(1-x)TiO(3), the material widely investigated for microwave devices in which the dielectric constant (epsilon(r)) at GHz frequencies is tuned by applying a quasi-static electric field. Heterogeneity associated with chemical substitution in such films, however, can broaden this phase transition by hundreds of degrees, which is detrimental to tunability and microwave device performance. An alternative way to adjust T(c) in ferroelectric films is strain. Here we show that epitaxial strain from a newly developed substrate can be harnessed to increase T(c) by hundreds of degrees and produce room-temperature ferroelectricity in strontium titanate, a material that is not normally ferroelectric at any temperature. This strain-induced enhancement in T(c) is the largest ever reported. Spatially resolved images of the local polarization state reveal a uniformity that far exceeds films tailored by chemical substitution. The high epsilon(r) at room temperature in these films (nearly 7,000 at 10 GHz) and its sharp dependence on electric field are promising for device applications.     

Sequential proteome alterations during genesis and progression of colon cancer

Changes in the proteome of colon mucosal cells accompany the transition from normal mucosa via adenoma and invasive cancer to metastatic disease. Samples from 15 patients with sporadic sigmoid cancers were analyzed. Proteins were separated by two-dimensional gel electrophoresis. Relative differences in expression levels between normal tissue, adenoma, carcinoma and metastasis were evaluated in both intra- and inter-patient comparisons. Up- and down-regulated proteins (<twofold) during development to cancer or metastasis were excised and submitted to peptide mass fingerprinting and MS/MS sequence analysis, facilitated by the use of a compact disc workstation. In total, 112 protein spots were found to be differentially regulated, of which 72 were determined as to protein identity, 46 being up-regulated toward the progression of cancer, and 26 down-regulated. Several of the identifications correlate with proteins of the cell cycle, cytoskeleton or metabolic pathways. The pattern changes now identified have the potential for design of marker panels for assistance in diagnostics and therapeutic strategies in colorectal cancer.Received 2 February 2004; received after revision 16 March 2004; accepted 18 March 2004     

Tonks-Girardeau gas of ultracold atoms in an optical lattice

Strongly correlated quantum systems are among the most intriguing and fundamental systems in physics. One such example is the Tonks-Girardeau gas, proposed about 40 years ago, but until now lacking experimental realization; in such a gas, the repulsive interactions between bosonic particles confined to one dimension dominate the physics of the system. In order to minimize their mutual repulsion, the bosons are prevented from occupying the same position in space. This mimics the Pauli exclusion principle for fermions, causing the bosonic particles to exhibit fermionic properties. However, such bosons do not exhibit completely ideal fermionic (or bosonic) quantum behaviour; for example, this is reflected in their characteristic momentum distribution. Here we report the preparation of a Tonks-Girardeau gas of ultracold rubidium atoms held in a two-dimensional optical lattice formed by two orthogonal standing waves. The addition of a third, shallower lattice potential along the long axis of the quantum gases allows us to enter the Tonks-Girardeau regime by increasing the atoms' effective mass and thereby enhancing the role of interactions. We make a theoretical prediction of the momentum distribution based on an approach in which trapped bosons acquire fermionic properties, finding that it agrees closely with the measured distribution.     

Two-dimensional geometry of spin excitations in the high-transition-temperature superconductor YBa2Cu3O6+x

The fundamental building block of the copper oxide superconductors is a Cu4O4 square plaquette. The plaquettes in most of these materials are slightly distorted to form a rectangular lattice, for which an influential theory predicts that high-transition-temperature (high-T(c)) superconductivity is nucleated in 'stripes' aligned along one of the axes. This theory received strong support from experiments that indicated a one-dimensional character for the magnetic excitations in the high-T(c) material YBa2Cu3O6.6 (ref. 4). Here we report neutron scattering data on 'untwinned' YBa2Cu3O6+x crystals, in which the orientation of the rectangular lattice is maintained throughout the entire volume. Contrary to the earlier claim, we demonstrate that the geometry of the magnetic fluctuations is two-dimensional. Rigid stripe arrays therefore appear to be ruled out over a wide range of doping levels in YBa2Cu3O6+x, but the data may be consistent with liquid-crystalline stripe order. The debate about stripes has therefore been reopened.     

Continuous generation of single photons with controlled waveform in an ion-trap cavity system

The controlled production of single photons is of fundamental and practical interest; they represent the lowest excited quantum states of the radiation field, and have applications in quantum cryptography and quantum information processing. Common approaches use the fluorescence of single ions, single molecules, colour centres and semiconductor quantum dots. However, the lack of control over such irreversible emission processes precludes the use of these sources in applications (such as quantum networks) that require coherent exchange of quantum states between atoms and photons. The necessary control may be achieved in principle in cavity quantum electrodynamics. Although this approach has been used for the production of single photons from atoms, such experiments are compromised by limited trapping times, fluctuating atom-field coupling and multi-atom effects. Here we demonstrate a single-photon source based on a strongly localized single ion in an optical cavity. The ion is optimally coupled to a well-defined field mode, resulting in the generation of single-photon pulses with precisely defined shape and timing. We have confirmed the suppression of two-photon events up to the limit imposed by fluctuations in the rate of detector dark counts. The stream of emitted photons is uninterrupted over the storage time of the ion, as demonstrated by a measurement of photon correlations over 90 min.     

Evidence of power-law flow in the Mojave desert mantle

Studies of the Earth's response to large earthquakes can be viewed as large rock deformation experiments in which sudden stress changes induce viscous flow in the lower crust and upper mantle that lead to observable postseismic surface deformation. Laboratory experiments suggest that viscous flow of deforming hot lithospheric rocks is characterized by a power law in which strain rate is proportional to stress raised to a power, n (refs 2, 3). Most geodynamic models of flow in the lower crust and upper mantle, however, resort to newtonian (linear) stress-strain rate relations. Here we show that a power-law model of viscous flow in the mantle with n = 3.5 successfully explains the spatial and temporal evolution of transient surface deformation following the 1992 Landers and 1999 Hector Mine earthquakes in southern California. A power-law rheology implies that viscosity varies spatially with stress causing localization of strain, and varies temporally as stress evolves, rendering newtonian models untenable. Our findings are consistent with laboratory-derived flow law parameters for hot and wet olivine--the most abundant mineral in the upper mantle--and support the contention that, at least beneath the Mojave desert, the upper mantle is weaker than the lower crust.