bluuebunny/crossref_metadata_2025 huggingface dataset:
An arms race: innate antiviral responses and counteracting viral strategies
Authors: Schröder M. , Bowie A.G.
Published: January 2008

Viral recognition is mediated by different classes of PRRs (pattern-recognition receptors) among which the TLRs (Toll-like receptors) and the RLHs [RIG (retinoic-acid-inducible)-like helicases] play major roles. The detection of PAMPs (pathogen-associated molecular patterns) by these PRRs leads to the initiation of signalling pathways that ultimately result in the activation of transcription factors such as NF-κB (nuclear factor κB) and IRF-3 [IFN (interferon) regulatory factor-3] and IRF-7 and the induction of pro-inflammatory cytokines and type I IFNs. Viruses have evolved a fine-tuned mechanism to evade detection by the immune system or to interfere with the resulting signalling pathways. Here, we discuss viral evasion proteins that specifically interfere with TLR and/or RLH signalling.
The contribution of the budding yeast histone H2A C-terminal tail to DNA-damage responses
Authors: Chambers A.L. , Downs J.A.
Published: January 2008

The cellular response to DNA damage involves extensive interaction with and manipulation of chromatin. This includes the detection and repair of the DNA lesion, but there are also transcriptional responses to DNA damage, involving the up- or down-regulation of numerous genes. Therefore changes to chromatin structure, including covalent modification of histone proteins, are known to occur during DNA-damage responses. One of the most well characterized DNA-damage-responsive chromatin modification events is the phosphorylation of the SQ motif found in the C-terminal tail of histone H2A or the H2AX variant in higher eukaryotes. In the budding yeast, a number of additional residues in this region of histone H2A that contribute to the cellular response to DNA damage have been identified, providing an insight into the nature and complexity of the DNA-damage histone code.
Biological consequences of statins in Candida species and possible implications for human health
Authors: Wikhe K. , Westermeyer C. , Macreadie I.G.
Published: January 2008

The statins, simvastatin and atorvastatin are the most widely prescribed drugs. Statins lower cholesterol levels through their action on HMG-CoA (3-hydroxy-3-methylglutaryl-CoA) reductase, an essential enzyme for the biosynthesis of cholesterol. Fungal HMG-CoA reductases are also inhibited by statins, resulting in reduced levels of ergosterol (the fungal equivalent of cholesterol) and concomitant growth inhibition. This effect occurs in a range of fungal species and possibly affects fungal colonization of people on statin therapy. Furthermore, it may suggest that statins could have a role in new antifungal therapies. Possibly associated with the reduction in ergosterol levels, statins also inhibit respiratory growth. In the yeast, Candida glabrata, passage with statins dramatically increased the frequencies of petite mutants that were devoid of mitochondrial DNA, suggesting that statins caused a defect in the maintenance of mitochondrial DNA. These observations in C. glabrata may provide further insights into side effects of statins in humans undergoing treatment for hypercholesterolaemia. In addition, C. glabrata may be highly useful for the preliminary screening of agents to reduce statin side effects.
Identifying in vivo pathways using genome-wide genetic networks
Authors: Gray J.V. , Krause S.A.
Published: January 2008

Synthetic genetic interactions occur between two genes when the double mutant displays a phenotype much more severe than does either single mutant alone. Global networks of such interactions are now being systematically determined, spearheaded by the budding yeast genome. Genetic interactions reflect in vivo relationships between gene products. Extracting that functional information from such genetic networks is now possible by exploiting and modifying the key concept of congruence. Here, we focus on synthetic genetic interactions between pairs of null mutations in non-essential yeast genes. We summarize how to identify biological pathways from these emerging networks, using illustrative examples.
Single-mutation-induced stability loss in protein lysozyme
Authors: Ye L. , Wu Z. , Eleftheriou M. , Zhou R.
Published: January 2008

Recent NMR experiments have revealed that a single residue mutation W62G on protein hen's-egg white lysozyme can cause a dramatic loss of long-range interactions and protein stability; however, the molecular mechanism for this surprising phenomenon is not completely clear. In this mini-review, we have summarized some of our recent work on the molecular mechanism with large-scale molecular modelling, and also utilized a new wavelet method to analyse the local structural clusters present in both the wild-type and mutant folding trajectories. These extensive MD (Molecular Dynamics) simulations (10+ μs) were performed in 8 M urea, mimicking the experimental condition. Detailed analyses revealed that the Trp62 residue is the key to a co-operative long-range interaction within the wild-type protein: it acts as a bridge between neighbouring basic residues, mainly arginine residues, through π-type hydrogen bonds or π-cation interactions to form an Arg-Trp-Arg ‘sandwich-like’ local structure. The local cluster near Trp62 further extends its interaction to other clusters, such as the one near Trp111, through Arg112, which is involved in such an Arg-Trp-Arg bridging structure, thus achieving the long-range interactions for the wild-type. On the other hand, the mutant does not have this bridging effect and forms much less local clusters or contacts, and therefore results in a much less stable structure. Overall, these findings not only support the general conclusions of the experiment, but also provide a detailed but somewhat different molecular picture of the disruption of the long-range interactions.
Natural methods of protein stabilization: thermostable biocatalysts
Authors: Littlechild J.A. , Guy J. , Connelly S. , Mallett L. , Waddell S. , Rye C.A. , Line K. , Isupov M.
Published: January 2008

Enzymes that are naturally found in thermophilic and hyperthermophilic organisms are being used as robust biocatalysts in the fine chemical and pharmaceutical industries. They have important use in these industries due to their increased stability which is often required during commercial reaction conditions. The approach used in these studies is to learn how nature has managed to stabilize these proteins using a detailed knowledge of their biochemical properties and three-dimensional structures. This is illustrated with several different classes of enzyme that have been studied at Exeter. These include alcohol dehydrogenase, aminoacylase, pyroglutamyl carboxypeptidase, γ-lactamase, dehalogenase and lysophospholipase.
Stability and stabilization ofD-amino acid oxidase from the yeastTrigonopsis variabilis
Authors: Nidetzky B.
Published: January 2008

The use of DAO (D-amino acid oxidase) for the conversion of cephalosporin C has provided a significant case for the successful implementation of an O2-dependent biocatalyst on an industrial scale. Improvement of the operational stability of the immobilized oxidase is, however, an important goal of ongoing process optimization. We have examined DAO from the yeast Trigonopsis variabilis with the aim of developing a rational basis for the stabilization of the enzyme activity at elevated temperature and under conditions of substrate turnover. Loss of activity in the resting enzyme can occur via different paths of denaturation. Partial thermal unfolding and release of the FAD cofactor, kinetically coupled with aggregation, contribute to the overall inactivation rate of the oxidase at 50°C. Oxidation of Cys108 into a stable cysteine sulfinic acid causes both decreased activity and stability of the enzyme. Strategies to counteract each of the denaturation steps in DAO are discussed. Fusion to a pull-down domain is a novel approach to produce DAO as protein-based insoluble particles that display high enzymatic activity per unit mass of catalyst.
Protein engineering applications of industrially exploitable enzymes: Geobacillus stearothermophilus LDH and Candida methylica FDH
Authors: Karagüler N.G. , Sessions R.B. , Binay B. , Ordu E.B. , Clarke A.R.
Published: January 2008

Enzymes have become important tools in several industries due to their ability to produce chirally pure and complex molecules with interesting biological properties. The NAD+-dependent LDH (lactate dehydrogenase) [bsLDH [Geobacillus stearothermophilus (formerly Bacillus stearothermophilus) LDH] from G. stearothermophilus and the NAD+-dependent FDH (formate dehydrogenase) [cmFDH (Candida methylica FDH)] enzyme from C. methylica are particularly crucial enzymes in the pharmaceutical industry and are related to each other in terms of NADH use and regeneration. LDH catalyses the interconversion of pyruvate (oxo acid) and lactate (α-hydroxy acid) using the NADH/NAD+ pair as a redox cofactor. Employing LDH to reduce other oxo acids can generate chirally pure α-hydroxy acids of use in the production of pharmaceuticals. One important use of FDH is to regenerate the relatively expensive NADH cofactor that is used by NAD+-dependent oxidoreductases such as LDH. Both LDH and FDH from organisms of interest were previously cloned and overproduced. Therefore they are available at a low cost. However, both of these enzymes show disadvantages in the large-scale production of chirally pure compounds. We have applied two routes of protein engineering studies to improve the properties of these two enzymes, namely DNA shuffling and site-directed mutagenesis. Altering the substrate specificity of bsLDH by DNA shuffling and changing the coenzyme specificity of cmFDH by site-directed mutagenesis are the most successful examples of our studies. The present paper will also include the details of these examples together with some other applications of protein engineering regarding these enzymes.
Precarious Changes: Gender and Generational Politics in Contemporary Italy
Authors: Fantone Laura
Published: January 2008

The issue of a generational exchange in Italian feminism has been crucial over the last decade. Current struggles over precariousness have revived issues previously raised by feminists of the 1970s, recalling how old forms of instability and precarious employment are still present in Italy. This essay starts from the assumption that precariousness is a constitutive aspect of many young Italian women's lives, young Italian feminist scholars have been discussing the effects of such precarity on their generation. This article analyses the literature produced by political groups of young scholars interested in gender and feminism connected to debates on labour and power in contemporary Italy. One of the most successful strategies that younger feminists have used to gain visibility has involved entering current debates on precariousness, thus forcing a connection with the larger Italian labour movement. In doing so, this new wave of feminism has destabilized the universalism assumed by the 1970s generation. By pointing to a necessary generational change, younger feminists have been able to mark their own specificity and point to exploitative power dynamics within feminist groups, as well as in the family and in the workplace without being dismissed. In such a layered context, many young feminists argue that precariousness is a life condition, not just the effect of job market flexibility and not solely negative. The literature produced by young feminists addresses the current strategies engineered to make ‘their’ precarious life more sustainable. This essay analyses such strategies in the light of contemporary Italian politics. The main conclusion is that younger Italian women's experience requires new strategies and tools for struggle, considering that the visibility of women as political subjects is still quite minimal. Female precariousness can be seen as a fruitful starting point for a dialogue across differences, addressing gender and reproduction, immigration, work and social welfare at the same time.
The Feminization of Labour in Cognitive Capitalism
Authors: Morini Cristina
Published: January 2008

The article starts with a definition of the concept feminization of labour. It aims to signal how, at both the Italian and the global level, precarity, together with certain qualitative characteristics historically present in female work, have become decisive factors for current productive processes, to the point of progressively transforming women into a strategic pool of labour. Since the early 1990s, Italy has seen a massive increase in the employment of women, within the wave of legislation that has introduced various flexible contracts – so-called atypical work. I show how cognitive capitalism tends to prioritize extracting value from relational and emotional elements, which are more likely to be part of women's experiential baggage. The results of a study conducted in November 2006 among freelance workers of the Rizzoli Corriere della sera group, the largest publishing group in Italy, will be used to show how women are able to move more easily on the shifting sands of precarity, within the context of cognitive work.
‘Precari su Marte’: An Experiment in Activism against Precarity
Authors: De Sario Beppe
Published: January 2008

This article discusses how the issue of precarity has developed into a new catalyst for activism in Italy and demonstrates how this activism is linked to changes in the employment and capitalist manufacturing environment of the 1980s and 1990s. It links events in Italy to the activism of the global anti-neoliberal movement and discusses how various activist movements (the independent Marxist tradition, creative activism, social activism, Lesbian, Gay, Bisexual and Transgender (LGBT), radical feminist activism) are mobilizing around the issue of precarity. This article focuses specifically on the activist network ‘Precari su Marte’ (Precarious on Mars) which has been active in Turin since 2005. It demonstrates how the theoretical and practical evolution of this network has led to various outcomes, including experimenting with creative forms of political practice at MayDay demonstrations and questioning the boundaries of gender.
Searching for Gravity Waves with Interferometers
Authors: Schechter Bruce
Published: January 2008

A collaboration of physicists from Caltech and MIT has recently produced detailed plans for a pair of large detectors, based on laser interferometry, that they believe should be sensitive enough to detect gravity waves from several types of astrophysical sources. The detectors, which will each consist of an L-shaped vacuum chamber 4 kilometers long through which laser-interferometer beams will travel, are tentatively to be located in Columbia, Maine, and at Edwards Air Force Base, California. The projected cost is between $50 and $60 million. If this sum is forthcoming from NSF the detectors could be on the air as early as 1991. According to Ronald Drever (Caltech), who, along with Rainer Weiss (MIT), heads the collaboration, the leap in sensitivity from existing detectors to their planned interferometer is like “going from the human eye to the Mount Palomar telescope.” Successful detection would not only help sort out competing theories of gravity, but open up a new window on violent processes throughout the universe.
Squeezing the Quantum Noise Limits
Authors: Levi Barbara G.
Published: January 2008

While it is true that quantum mechanics imposes strict limits on the precision of measurements, we can sometimes improve measurement precision without violating the uncertainty principle. The rub is that this improvement may be formidable to achieve in practice—and always comes at the expense of a loss in the precision of a complementary measurement. Last October a team at AT&T Bell Labs succeeded in reducing the noise observed from an optical cavity below the “shot noise”—the level of fluctuations associated with variations in the vacuum fields, which is the ultimate limit to accuracy that would be predicted by semiclassical models. Although the Bell Labs experiment reduced the noise below this level by only 7 to 10%, it bolstered hopes that continued progress might eventually yield reductions in noise by factors of ten. Manipulation of the quantum noise limitations might be absolutely critical to such precision measurements as detection of gravity waves, whose faint signals are likely to be near the measurement limit of laser interferometers or mechanical oscillators. The phenomenon might possibly find applications in optical communication or optical memory systems.
Aladdin, Fighting Back, Surpasses Performance Goals
Authors: Schwarzschild Bertram
Published: January 2008

Since the first of the year, the circulating electron beam of the Aladdin synchrotron light source at the University of Wisconsin has been surpassing 100 milliamps—its “nominal commissioning level”—and it's still getting better. This happy news must be understood in the less happy context of recent years (PHYSICS TODAY, August, page 45, and November, page 58). When construction of this roughly square electron storage ring—27 meters on a side—was begun in 1977, the goal was to achieve a stored electron beam current of at least 100 milliamps with a maximum electron energy of 1 GeV. The purpose was to provide experimenters with synchrotron light beams of adequate intensity in the spectral range from the vacuum ultraviolet up to about 4 keV in the soft-x-ray regime. This synchrotron radiation, generated as the electron beam negotiates the rounded corners of the Aladdin square, was intended eventually to be augmented by the outputs of wigglers and undulators inserted in the long straight sections of the ring.
Cause and Impact of Chernobyl Accident Still Hazy
Authors: Levi Barbara Goss
Published: January 2008

At the Soviet Union's Chernobyl nuclear power plant, the plume of smoke is gone, but a cloud of uncertainty still obscures the cause of the severe accident there. That accident, which began early on Saturday, 26 April, caused an intense fire that lasted many days, melted unknown quantities of reactor fuel and released into the environment a large fraction of the reactor's inventory of volatile radioactive fission products (including perhaps a million times more iodine-131 than came from Three Mile Island). On 11 May Soviet officials reported that they had stabilized the reactor and had successfully prevented the core from melting through the bottom of the containment building. Although the crisis is past, formidable tasks lie ahead. These chores include entombing the severely damaged core; isolating or decontaminating an area more than 30 km in radius around the plant, from which about 100 000 people have been evacuated; monitoring radiation levels over far more extensive areas; and determining the cause of the accident to prevent repetitions elsewhere.
Panel Reaffirms High-Field Magnet Choice for Supercollider
Authors: Schwarzschild Bertram
Published: January 2008

The Superconducting Super Collider, if it is built before the end of the century, will certainly be the largest scientific instrument in the world. But whether its circumference should be 100 miles, or a mere 50 miles, has been a bone of some contention. The design energy is not at issue: SSC is to be an ultra-highenergy proton-proton storage-ring collider with countercirculating beams of 20-TeV protons providing p–p collisions at 40 TeV in the center of mass. The radius of the gargantuan storage ring required to keep these protons going round in circles varies inversely as the strength of the superconducting bending magnets one chooses to make up the ring.
Princeton Tokamak Reaches Record Plasma Ion Temperature
Authors: Schwarzschild Bertram
Published: January 2008

The large Tokamak Fusion Test Reactor at the Princeton Plasma Physics Laboratory has entered a new regime of “enhanced confinement” operation. The first spectacular consequence of this new regime is the attainment of a record ion temperature of 20 keV—more than 200 million kelvin. For the first time, a tokamak is creating plasmas with ion temperatures hot enough for ignition and fusion-reactor operation.
Plastic Ball Flies to CERN—And Higher Energies
Authors: Schwarzschild Bertram
Published: January 2008

At the Lawrence Berkeley Lab's Bevalac in February, the Plastic Ball nuclear particle detector was being carefully crated for its jumbo-jet flight to CERN—and higher heavy-ion energies. For the past four years, this hollow, faceted ball of 814 plastic/CaF2 scintillation modules has been monitoring the fragments coming off high-energy heavy-ion collisions at the Bevalac, which can accelerate heavy-ion beams to 2 GeV/nucleon. From the outside, we see mostly the cabled ends of photomultiplier tubes. The Plastic Ball, built at LBL in collaboration with the Gesellschaft fur Schwerionenforschung (GSI) in Darmstadt, was the first nuclear-physics detector capable of simultaneously identifying and measuring essentially all of the charged particles produced in a high-energy heavy-ion collision. Among the Plastic Ball's successes has been the first observation of “collective flow” in compressed nuclear matter.
Reports on Subfields of Physics: Plasmas and Fluids
Authors: Schechter Bruce
Published: January 2008

Plasma physics and fluid physics are large fields that are themselves divided into subdisciplines: Plasma physics is practiced by fusion and space researchers and applied to the development of novel particle accelerators and coherent-light sources, to isotope separation and to astrophysics; fluid physics is important to geophysics, biology, medicine, meteorology, combustion research and pollution control—as well as to plasma physics. The panel devotes one chapter each to fluid physics; general plasma physics, fusion plasmas, confinement and heating; and space and astrophysical plasmas. The highlights and recommendations of the panel report are numerous; space limitations permit only a relatively small number of these to be described below.
Reports on Subfields of Physics: Scientific Interfaces and Technological Applications
Authors: Schechter Bruce
Published: January 2008

Six of the Brinkman volumes are devoted to the major subfields of physics. However, even the casual reader of those volumes will quickly see that the division of physics into subfields is a somewhat arbitrary exercise: Particle physicists do cosmology, cosmologists do nuclear physics, nuclear physicists do atomic physics and so on. Even more striking is the degree to which physics contributes to and benefits from other sciences. Whole industries also trace their roots to recent research in physics. Modern technologies such as microelectronics and optical communication would be impossible without the aid of modern physics. Physics has also played a pivotal role in the development of national defense systems and in arms control. The physics survey volume entitled Physics Through the 1990s: Scientific Interfaces and Technological Applications explores the profound impact physics has had on society and the economy through its interfaces with other natural sciences and its applications to technology, medicine and national defense.
Superconductivity and Magnetism in Organic Metals
Authors: Chaikin Paul M. , Greene Richard L.
Published: January 2008

Seven years ago Klaus Bechgaard of the University of Copenhagen synthesized a family of selenium-based organic compounds now known as Bechgaard salts (see figure 1). A few months later his collaborators at the University of Paris, Orsay, found these materials to be superconducting below about 1.5 K, culminating the search for organic superconductivity that began in the early 1960s. (See PHYSICS TODAY, February 1981, page 17.)
Pioneer Scientists in Pre-Independance India
Authors: Blanpied William A.
Published: January 2008

The conviction that scientific rationality can lead to intellectual liberation and thus convey benefits to a society that are at least as important as the material benefits derived from research has been central to Western thinking since the 17th century. That conviction is evident, for example, in the career of Benjamin Franklin, and is reflected in most of the official documents associated with the establishment of the American Republic. Studies by several scholars—most notably Joseph Needham in his Science and Civilization in China—indicate that the development of science in other societies has also been deeply rooted in a cultural tradition of tolerance. If so, then it can be argued that neither modern science nor the conditions required to capture its tangible benefits can thrive in any society unless science can be harmonized with the cultural traditions of that society.
Physics of Electrophotography
Authors: Burland Donald M. , Schein Lawrence B.
Published: January 2008

Electrophotographic printing and copying systems are based on two wellknown but not well-understood physical phenomena: electrostatic charging and photoconductivity. That some materials can acquire an electric charge by contact or rubbing has been known at least since the time of Thales of Miletus, around 600 B.C., and much work has been done on understanding the phenomenology of the effect, particularly in the 18th and 19th centuries; nevertheless the underlying physics of electrostatic charging of insulators remains unclear. Photoconductivity is a considerably more recent discovery, dating back only to 1873, when Willoughby Smith discovered the effect in selenium. Early work concentrated on crystalline covalent solids; only recently has the photoconductivity of highly insulating amorphous materials been studied. In fact the invention of electrophotography was a major catalyst to research in both electrostatic charging and photoconductivity.
Special Issue: The Education of the Professional Physicist
Authors: Kelly William C.
Published: January 2008

What kind of education do colleges and universities in the United States now give students who want to become physicists? Are we educating enough of them, and are we educating them well enough to meet national needs in the next decade? Do institutions of higher education have the resources they need for this task? Are employers satisfied with the results? These are some of the questions addressed in this special issue of PHYSICS TODAY.
Physics in the Colleges
Authors: Gollub Jerry P. , Abraham Neal B.
Published: January 2008

Institutions that focus primarily on undergraduate education produce a surprisingly large fraction of the bachelor's degrees awarded annually in physics in the United States. More than half of the students majoring in physics in 1984–85 were at the 577 institutions that do not award doctoral degrees, which we will refer to as “colleges.” About 40% of US citizens starting graduate study in physics in 1985–86 came from US colleges.
Education for Research
Authors: Beasley Malcolm R. , Jones Lawrence W.
Published: January 2008

Physics research may be represented as striving toward two objectives: to improve our understanding of the nature of matter and energy and to develop inputs to tomorrow's technology and engineering. The first corresponds to basic research, the second to applied research. How do we train future researchers to carry out such work? In the United States, it is primarily through graduate education, specifically for the PhD; most professional physicists earn a master's degree only incidentally—as a stepping stone toward the PhD, not as a terminal degree. In many other countries this is not the case. In Japan, for example, a large fraction of industrial researchers have only master's degrees. By contrast, in Germany more PhDs are produced but a PhD does not qualify one for a university professorship.
Becoming a Professional Physicist: A Statistical Overview
Authors: Porter Beverly Fearn , Czujko Roman
Published: January 2008

In the past decade and a half, major changes have taken place in patterns of physics-degree production and employment of physicists, and new changes are on the horizon. Industrial opportunities continue to expand and positions in academe are on the verge of reopening as the bulk of physics professors hired in the early 1960s move toward retirement. The number of US citizens completing degrees with the aim of pursuing a professional career in physics, however, remains limited. Our major focus in this article will be on graduate training, a requisite for most professional work in physics, but we will also pay attention to the important role that undergraduate and secondary-school preparation plays and to the varied career options available to individuals with a solid physics background.
The Shifting Balance of Power in Experimental Particle Physics
Authors: Irvine John , Martin Ben R. , Skea James E. F. , Peacock Tim , Minchin Nigel , Crouch David
Published: January 2008

For 30 years after the second world war, the United States dominated experimental particle physics. This dominance was particularly pronounced during the 1950s, when the leading US machines dwarfed those in Western Europe, while ostensibly equivalent facilities in the Soviet Union posed little threat. The 1960s witnessed the beginning of a European challenge from the new Proton Synchrotron at the joint European laboratory CERN near Geneva and from various smaller machines in national laboratories such as DESY at Hamburg. Yet despite a broad similarity in the research facilities available on either side of the Atlantic, the major discoveries of the 1960s—the Ω−, the two types of neutrino, CP violation and deep inelastic electron scattering—all came from the US.
The Cost of Physics Journals
Authors: Barschall Henry H.
Published: January 2008

Science libraries all over the United States face serious financial problems associated with the increased costs of journals.
Newton and the Infinite Universe
Authors: Harrison Edward
Published: January 2008

Isaac Newton formulated his ideas on space and the universe during his early years at Cambridge in response to René Descartes's 1644 publication Principles of Philosophy. Sometime between 1666 and 1668, in an unpublished manuscript that we refer to by its opening words, De gravitatione, Newton wrote that an “infinite and eternal” divine power coexists with space, which “extends infinitely in all directions” and “is eternal in duration.” Descartes claimed that where there is no matter there can be no space; on the contrary, argued Newton, space, by virtue of omnipresent spirit, exists where there is no matter. Descartes claimed that matter extends indefinitely; on the contrary, argued Newton, God has created in infinite space a material system of finite extent.
Einstein and Germany
Authors: Stern Fritz
Published: January 2008

There was nothing simple about Albert Einstein, ever. His apparent simplicity concealed an impenetrable complexity. Even the links to his native Germany were prematurely ambiguous. At a time when most Germans thought their country a hospitable home, a perfect training ground for their talents, Einstein was repelled: In 1894, as a 15-year-old, he left Germany and became a Swiss citizen. Twenty years later, a few weeks before the outbreak of the Great War, he returned to Germany and remained for 18 years of troubled renown, years in which he appreciated what was congenial and opposed what was antipathetic in Germany. Long before Hitler's rise, he felt unease.
Special Issue: Superconductivity
Authors: Tinkham Michael
Published: January 2008

On countless occasions, I have begun a talk on some aspect of superconductivity by intoning the time-honored sentence “Superconductivity was discovered in 1911 by Heike Kamerlingh Onnes in Leiden, just three years after he had first succeeded in liquefying helium.” Accordingly, I could hardly resist the invitation to serve as guest editor of this issue of PHYSICS TODAY, which celebrates the 75th anniversary of that historic event by highlighting some current examples of the broad impact of his discovery.
Analog Superconducting Electronics
Authors: Richards Paul L.
Published: January 2008

Because of inherent advantages in dynamic range and noise rejection, digital signal processing is used whenever possible in modern systems. Critical applications remain for analog components, however, where the signal frequency, signal level, or the data rate is not compatible with digital processing.
Reports on Subfields of Physics: Elementary-Particle Physics
Authors: Schechter Bruce
Published: January 2008

In the past 20 years the subnuclear world—which, due to a seemingly endless supply of “elementary” particles, was once likened to a zoo—has become a gratifyingly orderly place. The Elementary-Particle Physics Panel of the physics survey committee begins its report with a summary of the astounding progress of the last two decades: the emergence of a standard model of the universe as being made of quarks and leptons bound together by photons, gluons and W and Z particles; the unification of the weak and electromagnetic forces in a single gauge-field theory; the understanding of baryon and meson structure in terms of quantum chromodynamics; the theory of interacting quarks and gluons; the possibility of a grand unification of all of the forces of nature; and the convergence of elementary-particle physics and cosmology, each helping to elucidate the other. So much, the panel report explains, has been achieved. But many questions remain:

▸ What is the origin of mass, and what sets the masses of the different elementary particles? Is the Higgs hypothesis—which seeks to explain the breaking of symmetry—correct, and can the Higgs particles be found? If the Higgs hypothesis is wrong, what will replace it?

▸ Are there quark and lepton generations beyond the three already known? Why do these particles form generations?

▸ Are the quarks and leptons truly elementary, or does matter have a still deeper level of structure?

▸ Are new theoretical ideas like technicolor and supersymmetry correct? Can the strong and electroweak interactions be unified?

▸ Are there as yet undiscovered fundamental forces?
Reports on Subfields of Physics: Condensed-Matter Physics
Authors: Schechter Bruce
Published: January 2008

Such extraordinary technological innovations as the transistor, superconducting magnets, solid-state lasers, liquidcrystal displays and highly sensitive detectors of radiant energy come under the umbrella of condensed-matter physics. The basic contributions of condensed-matter physics to the study of critical phenomena, broken symmetry and defects have had a major impact on nuclear physics, elementaryparticle physics, astrophysics, molecular physics and chemistry. The panel report on condensed-matter physics is a fascinating tour of this diverse yet unified field. Some of the stops include:
The Growth of Novel Silicon Materials
Authors: Bean John C.
Published: January 2008

In the industrialized world, we are seldom more than a few meters from a crystal of silicon. One crystal may be strapped to our wrist, in an electronic watch; others may be buried within a nearby calculator, video recorder or auto ignition system—indeed, one may even be lurking in the quartz movement of a new “antique” clock. These crystals are extraordinarily perfect: No more than than one atom in 1013 is out of a proper lattice site, and the total impurity concentration may be less than 0.1 parts per billion. Yet a microprocessor or a megabit memory can be fabricated in a crystal of silicon costing only 15–20 cents
Anomalous dynamics of cell migration
Authors: Dieterich Peter , Klages Rainer , Preuss Roland , Schwab Albrecht
Published: January 2008

Cell movement—for example, during embryogenesis or tumor metastasis—is a complex dynamical process resulting from an intricate interplay of multiple components of the cellular migration machinery. At first sight, the paths of migrating cells resemble those of thermally driven Brownian particles. However, cell migration is an active biological process putting a characterization in terms of normal Brownian motion into question. By analyzing the trajectories of wild-type and mutated epithelial (transformed Madin–Darby canine kidney) cells, we show experimentally that anomalous dynamics characterizes cell migration. A superdiffusive increase of the mean squared displacement, non-Gaussian spatial probability distributions, and power-law decays of the velocity autocorrelations is the basis for this interpretation. Almost all results can be explained with a fractional Klein–Kramers equation allowing the quantitative classification of cell migration by a few parameters. Thereby, it discloses the influence and relative importance of individual components of the cellular migration apparatus to the behavior of the cell as a whole.
Domain requirement of moenomycin binding to bifunctional transglycosylases and development of high-throughput discovery of antibiotics
Authors: Cheng Ting-Jen Rachel , Sung Ming-Ta , Liao Hsin-Yu , Chang Yi-Fan , Chen Chia-Wei , Huang Chia-Ying , Chou Lien-Yang , Wu Yen-Da , Chen Yin-Hsuan , Cheng Yih-Shyun E. , Wong Chi-Huey , Ma Che , Cheng Wei-Chieh
Published: January 2008

Moenomycin inhibits bacterial growth by blocking the transglycosylase activity of class A penicillin-binding proteins (PBPs), which are key enzymes in bacterial cell wall synthesis. We compared the binding affinities of moenomycin A with various truncated PBPs by using surface plasmon resonance analysis and found that the transmembrane domain is important for moenomycin binding. Full-length class A PBPs from 16 bacterial species were produced, and their binding activities showed a correlation with the antimicrobial activity of moenomycin against
Enterococcus faecalis
and
Staphylococcus aureus
. On the basis of these findings, a fluorescence anisotropy-based high-throughput assay was developed and used successfully for identification of transglycosylase inhibitors.
Simultaneous Interaction of Arabidopsis thaliana with Bradyrhizobium Sp. Strain ORS278 and Pseudomonas syringae pv. tomato DC3000 Leads to Complex Transcriptome Changes
Authors: Cartieaux Fabienne , Contesto Céline , Gallou Adrien , Desbrosses Guilhem , Kopka Joachim , Taconnat Ludivine , Renou Jean-Pierre , Touraine Bruno
Published: January 2008

Induced systemic resistance (ISR) is a process elicited by telluric microbes, referred to as plant growth-promoting rhizobacteria (PGPR), that protect the host plant against pathogen attacks. ISR has been defined from studies using Pseudomonas strains as the biocontrol agent. Here, we show for the first time that a photosynthetic Bradyrhizobium sp. strain, ORS278, also exhibits the ability to promote ISR in Arabidopsis thaliana, indicating that the ISR effect may be a widespread ability. To investigate the molecular bases of this response, we performed a transcriptome analysis designed to reveal the changes in gene expression induced by the PGPR, the pathogen alone, or by both. The results confirm the priming pattern of ISR described previously, meaning that a set of genes, of which the majority was predicted to be influenced by jasmonic acid or ethylene, was induced upon pathogen attack when plants were previously colonized by PGPR. The analysis and interpretation of transcriptome data revealed that 12-oxo-phytodienoic acid, an intermediate of the jasmonic acid biosynthesis pathway, is likely to be an actor in the signaling cascade involved in ISR. In addition, we show that the PGPR counterbalanced the pathogen-induced changes in expression of a series of genes.
First Report of Phytophthora spp. as Pathogens of Pandorea jasminoides in Italy
Authors: Pane A. , Cacciola S. O. , Chimento A. , Allatta C. , Scibetta S. , di San Lio G. Magnano
Published: January 2008

In the summer of 2005, approximately 5% of a nursery stock of 12-month-old potted plants of bower vine (Pandorea jasminoides (Lindl.) K. Schum.) in Sicily (Italy) showed wilt, leaf chlorosis, defoliation, root rot, and collapse of the entire plant. Three Phytophthora spp. (20, 50, and 30% of the isolations of the first, second, and third species, respectively) were isolated from rotted roots on BNPRAH selective medium (2). Single-hypha isolates of the first species formed petaloid colonies on potato dextrose agar (PDA) and had an optimum growth temperature of 25°C (9.3 mm/day); on V8 juice agar, they produced uni- and bipapillate, ovoid to limoniform sporangia with mean dimensions of 45 × 30 μm and a mean length/width (l/w) ratio of 1.4:1. They did not produce gametangia when paired with A1 and A2 isolates of Phytophthora nicotianae. The second species formed arachnoides colonies on PDA, had an optimum growth temperature of 30°C (6.9 mm/day) and produced sporangia that were uni- and bipapillate, ellipsoid, ovoid, or pyriform to spherical (dimensions 44 × 34 μm; l/w ratio 1.3:1). All isolates were A2 mating type and produced amphyginous antheridia and spherical oogonia with smooth walls. The third species formed rosaceous colonies on PDA, had an optimum growth temperature of 28 to 30°C (11.9 mm/day), and produced uni- and bipapillate, ellipsoid or limoniform, caducous sporangia (dimensions 52 × 26 μm; l/w ratio 2.1:1) with a tapered base and a long pedicel (as much as 150 μm). All isolates were A1 type and produced amphigynous antheridia and spherical oogonia with smooth walls. The three species were identified as P. citrophthora, P. nicotianae, and P. tropicalis, respectively. The electrophoretic analysis of the mycelial proteins and four isozymes (1) confirmed the identification. Blast analysis of the sequence of the internal transcribed spacer region of the rDNA of a P. tropicalis isolate from bower vine (GenBank Accession No. EU076731) showed 99% similarity with the sequence of a P. tropicalis isolate from Cuphea ignea (GenBank Accession No. DQ118649). The pathogenicity of three isolates from bower vine, IMI 395552 (P. citrophthora), IMI 395553 (P. nicotianae), and IMI 395346 (P. tropicalis), was tested on 3-month-old potted bower vine plants (10 plants for each isolate) by applying 10 ml of a suspension (2 × 104 zoospores/ml) to the root crown. The plants were maintained at 24°C and 95 to 100% relative humidity. All inoculated plants wilted after 4 weeks. Noninoculated control plants remained healthy. The three Phytophthora spp. were reisolated from symptomatic plants. To our knowledge, this is the first report of Phytophthora root rot of bower vine in Italy.

References: (1) S. O. Cacciola et al. Plant Dis. 90:680, 2006. (2) D. C. Erwin and O. K. Ribeiro. Phytophthora Diseases Worldwide. The American Phytopathological Society, St. Paul, MN, 1996.
First Report of the European Lineage of Phytophthora ramorum on Viburnum and Osmanthus spp. in a California Nursery
Authors: Grünwald N. J. , Goss E. M. , Larsen M. M. , Press C. M. , McDonald V. T. , Blomquist C. L. , Thomas S. L.
Published: January 2008

Phytophthora ramorum S. Werres & A.W.A.M. de Cock is the causal agent of sudden oak death in California and Oregon forests and ramorum blight on a broad range of host species in wildlands and nurseries. It is thought to be an introduced pathogen and only three clonal lineages are known (3). The North American lineage (lineage NA1, mating type A2) is responsible for infections in California and Oregon forests. The European lineage (lineage EU1, predominantly A1) is responsible for infections in Europe, but has also been found in nurseries in Oregon and Washington. A third lineage (NA2) has only been isolated in a few instances from nurseries in Washington and California. In June 2006, P. ramorum was isolated from diseased Viburnum tinus, Osmanthus heterophyllus, and O. fragrans cultivars from a Humboldt County retail nursery in northern California. We genotyped isolates and placed them into clonal lineages using microsatellite markers developed for P. ramorum (3,4). Genomic DNA was extracted from mycelia with the FastDNA SPIN kit (Q-Biogene, Morgan, Irvine, CA). Primers used were PrMS6, Pr9C3, PrMS39, PrMS43a, PrMS43b, and PrMS45 (3) and 18, 64, and 82 (4). We sized fluorescently labeled amplicons using capillary electrophoresis (3100 Avant Genetic Analyzer, Applied Biosystems, Foster City, CA). Isolate genotypes were compared with control isolates of known clonal lineage, including BBA9/95 (EU1), Pr102 (NA1), and WSDA3765 (NA2). Three of four isolates belonged to genotype EU1. The fourth isolate, obtained from O. fragrans, belonged to genotype NA1. We repeated genotyping on independent genomic DNA extractions and obtained identical results. Two EU1 isolates and the single NA1 isolate were tested for mating type (1) and found to be of A1, A1, and A2 mating type, respectively. The coexistence of A1 and A2 mating types in the same retail nursery suggests the potential for sexual reproduction, as is the case in P. infestans where clonal and sexual populations exist (2), although to date, sexual reproduction in nature has not been documented in P. ramorum. The California retail nursery infestation highlights the risks associated with the unintentional transport of host nursery stock infested with P. ramorum.

References: (1) C. M. Brasier and S. Kirk. Mycol. Res. 108:823, 2004. (2) N. J. Grünwald and W. G. Flier. Ann. Rev. Phytopathol. 43:171, 2005. (3) K. Ivors et al. Mol. Ecol. 15:1493, 2006. (4) S. Prospero et al. Mol. Ecol. 16:2958, 2007.
First Report of Rice yellow mottle virus in Rice in The Gambia
Authors: Sere Y. , Sorho F. , Onasanya A. , Jobe L. , Darboe S. , Bojang Y. , Touray M. L. , Pinel-Galzi A. , Fargette D.
Published: January 2008

Rice yellow mottle virus (RYMV) of the genus Sobemovirus is a major biotic constraint to rice (Oryza sativa) production in Africa. First reported in Kenya during 1966, RYMV was later found in most countries in Africa where rice is grown (1). In countries in westernmost Africa (The Gambia, Guinea-Bissau, Mauritania, and Senegal), plants with leaf yellowing and mottling symptoms were observed, but RYMV was never isolated. Rice is the staple food in The Gambia. In 2006, four samples were collected from local rice varieties in the Kuntaur Region in the center of The Gambia. Mechanical inoculation with leaf extracts from all samples caused typical yellow mottle symptoms on the susceptible rice varieties BG90-2, Bouaké 189, and IR64. RYMV was detected in the four samples collected by ELISA with polyclonal antisera (2). The 720-nt coat protein gene was amplified for each isolate by reverse-transcriptase-PCR with primers 5′-CAAAGATGGCCAGGAA-3′ (sense) and 5′-CTCCCCCACCCATCCCGAGAATT-3′ (antisense) (2). The RT-PCR products were directly sequenced (EMBL Accession Nos. AM765810, AM765811, AM765812, and AM765813) and then aligned using ClustalW with a pool of RYMV coat protein sequences from West African isolates (EMBL Accession Nos. AJ279905, AJ279901, AJ885137, AJ885124, and AJ279935). Phylogenetic reconstruction by maximum-likelihood with PAUP indicated that the isolates from The Gambia formed a monophyletic group with over 97% nucleotide identity and are closely related to isolates of other countries in West Africa (Burkina Faso, Côte d'Ivoire, Guinea, Mali, and Sierra-Leone) with 91 to 94% identity. Detection of RYMV in The Gambia indicates that RYMV is present in westernmost Africa, which is referred to as the ‘rice belt’ of Africa, and shows that RYMV is widely distributed from eastern Africa (Tanzania) to the western part of the continent.

References: (1) N. K. Kouassi et al. Plant Dis. 89:124, 2005. (2) A. Pinel et al. Arch. Virol. 145:1621, 2000.