bluuebunny/crossref_metadata_2025 huggingface dataset:
Special Issue: Optoelectronics
Authors: Kogelnik Herwig
Published: January 2008

This issue is devoted to what is variously called optoelectronics or photonics, and I have been privileged to assist PHYSICS TODAY as a guest editor in the coverage of this sparkling field. Photonics and microelectronics are the two key technologies of the rapidly growing information industry, and their advances are complementing each other in the tasks of the acquisition, transmission, storage and processing of increasing amounts of information. The principal technical elements of photonics are the photonic semiconductor devices, such as the junction laser, and the optical fibers made of fused silica. Advances in photonics are already making significant contributions to the transmission of information via optical fibers, to the high-capacity mass storage of information in laser disks, and to the acquisition of information with the help of optical fiber sensors. The first article, by Tingye Li (on page 24), presents a review and perspective of the lightwave transmission technology via optical fibers. Yasuharu Suematsu (on page 32) presents an overview of semiconductor junction lasers, which represent a central building block of photonics; progress in this field has allowed a shift of operation to the optimal wavelengths for fiberoptics and has led to significant improvements of laser reliability and spectral purity. Aram Mooradian (on page 42) deals with the ultimate limitations to the spectral purity or coherence of lasers, which are determined by the interplay of such fundamental processes as the spontaneous and stimulated emission of radiation. The fourth and final article, by Daniel S. Chemla (on page 56), describes new vistas opened up for photonic devices by the new physics and materials science of quantum wells in semiconductors, and sketches some potential applications. Fascinating as they are, these four reviews of selected areas of progress in photonics represent only an incomplete illustration of the whole field, which is advancing on a broad front. PHYSICS TODAY hopes to cover related topics in future issues.
Atomic Beams Stopped by Laser Light, and Trapped
Authors: Schwarzschild Bertram
Published: January 2008

The trapping of charged elementary particles and ions by various electromagnetic field configurations is a well established art. Last month (page 17) we told of a lone electron that was confined for almost a year in the vacuum of a Penning trap, yielding a superbly delicate observation of lowenergy relativistic hysteresis. But the trapping of electrically neutral particles—atoms in particular—is quite another matter. In the absence of the simple Lorentz force acting on a charged particle, one has to reach for a much weaker, second-order handle—the atom's magnetic or induced electric dipole moment. A variety of ingenious magnetic and laser traps have been proposed for atoms, but they all suffer a severe limitation: The weak dipole interaction with the trapping field yields only very shallow trapping potential wells, generally incapable of holding an atom moving much faster than a man can run—about 10 meters/second.
Storage Ring Intensifies Los Alamos Neutron Source
Authors: Schwarzschild Bertram
Published: January 2008

The new Proton Storage Ring built to enhance the neutron-beam generating capability of the LAMPF (LOS Alamos Meson Physics Facility) proton linac has received its first beam. When the $22-million ring is fully commissioned by the end of next year, the Los Alamos Neutron Scattering Center will become the country's most intense spallation source of neutrons, comparable to the new SNS spallation source at Britain's Rutherford Laboratory. Construction of the Los Alamos storage ring began in 1982.
Polarized Scattering Data Challenge Quantum Chromodynamics
Authors: Schwarzschild Bertram
Published: January 2008

It is a truism of elementary-particle theory that spin effects become negligible at high energy and large momentum transfer in collisions between protons—or any other spinning hadrons. But it doesn't appear to be true. For almost a decade now, Alan Krisch (University of Michigan) and his coworkers have been accumulating experimental evidence that spin-spin and spin-orbit interactions are far from negligible in large-angle proton-proton elastic scattering at high energies. Their most recent data with an unpolarized 28-GeV proton beam hitting a polarized target at the Brookhaven Alternating Gradient Synchrotron indicate a quite spectacular and unanticipated growth of left-right asymmetry (a spin-orbit effect) as one looks at ever larger scattering angles. Two months ago this Mighigan, Brookhaven, Notre Dame, Rice, Texas A&M, Zurich collaboration reported its first data taken with a polarized proton beam at the AGS—the first time a polarized beam has been achieved in a high-energy, strong-focusing proton synchrotron.
Chaotic Orbits and Spins in the Solar System
Authors: Schwarzchild Bertram
Published: January 2008

It was surely the intricate clockwork regularity of the solar system, as our ancestors observed and pondered it over millenia, that inspired the quest that culminated in the differential equations of Isaac Newton. It is somewhat ironic, therefore, that these same differential equations—usually regarded as epitomizing order and predictabilty—also appear to be generating chaos in the solar system. Nowadays, when one speaks of chaos, especially in an essentially conservative, Hamiltonian system like the solar system, one does not mean the unpredictability inherent in intrinsically disorderly phenomena such as thermal noise or innumerable random collisions. The modern study of chaos (PHYSICS TODAY, December 1983, page 46) deals with the onset of wild and unpredictable fluctuations in systems governed by simple, deterministic equations from which one would naively expect nothing but good behavior.
Cornell Electron-Positron Ring to be Upgraded
Authors: Schwarzchild Bertram
Published: January 2008

In June, NSF approved a three-year, $36-million project to upgrade Cornell's CESR electron-position storage ring. The approval came as good news for Karl Berkelman, who was to become director of the Cornell Newman Laboratory a few weeks later, succeeding Boyce McDaniel, who retires from the directorship he has held since he succeeded Robert Wilson in 1967.
Electron field emission from nanostructured cubic boron nitride islands
Authors: Teii Kungen , Matsumoto Seiichiro , Robertson John
Published: January 2008

Nanocrystal-assembled cubic boron nitride (cBN) islands are formed by using low-energy (∼20eV) ion irradiation in an inductively coupled fluorine-containing plasma. The temporal evolution of surface morphology and roughness reveals three-dimensional island growth for initial sp2-bonded BN and subsequent cBN, accompanied by a high frequency of renucleation. The formation of cBN islands enhances the field emission and reduces the turn-on field down to around 9V∕μm due to an increase in the island-related field. The results demonstrate the high potential of cBN for field emitters, comparable to other wide band gap semiconductors.
Nonlinear photoresists for maskless photolithography on the basis of Ag-doped As2S3 glassy films
Authors: Lyubin V. , Arsh A. , Klebanov M. , Dror R. , Sfez B.
Published: January 2008

Inorganic chalcogenide photoresists are widely used in microelectronics and optoelectronics. Here, we describe strongly nonlinear chalcogenide photoresists fabricated on the basis of Ag-doped As2S3 glassy films. Photoresists are prepared by vacuum coevaporation of As2S3 bulk glass and Ag. Superlinear dissolution characteristics of Ag-doped photoresists are explained in the framework of the so-called “percolation approach.” The advantages of superlinear photoresists for maskless photolithography are briefly discussed.
Lightwave Telecommunication
Authors: Li Tingye
Published: January 2008

In less than 20 years, the transmission of information by optical fibers has advanced from a mere theoretical proposal to a pervasive commercial reality. The rapid progress that has led to important applications (figure 1) has been marked by innovative breakthroughs as well as steady advances in all areas of lightwave technology. The demonstration of the laser in 1960 sparked intense interest in light as a medium for transmitting information. At that time, scientists began extensive research on optical devices, techniques and subsystems for processing signals, and on a variety of transmission media such as line-of-sight atmospheric paths and beam waveguides with periodic focusing elements. During the early 1960s, work on optical fibers as waveguides was mainly theoretical, as the available glass fibers exhibited transmission losses around 1000 decibels per kilometer—about two orders of magnitude too large for use in telecommunications.
Advances in Semiconductor Lasers
Authors: Suematsu Yasuharu
Published: January 2008

In the past decade the semiconductor laser—also known as the diode or junction laser—has become a key device in optical electronics because of its pure output spectrum and high quantum efficiency. Not coincidentally, its output can be modulated at very high speeds; this property and its compact size make it useful in a vast range of applications, from fiber-optic communications to optical radar.
Laser Linewidth
Authors: Mooradian Aram
Published: January 2008

One of the most important properties of laser light is its spectral purity and coherence. This unique quality has been important for the study of many new physical phenomena using laser sources that operate from the vacuum ultraviolet to the far infrared. An understanding of the mechanisms responsible for the broadening of the linewidth is necessary for the development of laser sources with sufficient spectral purity for various applications.
Quantum Wells for Photonics
Authors: Chemla Daniel S.
Published: January 2008

The crystalline and electronic structures of semiconductors reflect a delicate balance of very large electromagnetic forces, and consequently minute compositional variations or small perturbations can induce large changes in the properties of these materials. for several decades now, research scientists and device designers have exploited his exceptional flexibility to tailor the electronic and optical properties of semiconductors for a variety of fundamental studies and applications. Semiconductor technology has made its most apparent impact, of course, in solid-state electronics.
The Strategic Defense Initiative: Perception vs Reality
Authors: Panofsky Wolfgang K. H.
Published: January 2008

We have witnessed over the last year or so an enormous growth in the political impact, if not the technical impact, of the President's Strategic Defense Initiative, popularly called “Star Wars.” Some argue that without this initiative the Soviets would not have “returned to the bargaining table” to resume talks on strategic and intermediaterange weapons. Others argue that with SDI the United States cannot possibly reach an arms-control agreement with the Soviet Union. The true believers assert that SDI points the way to a future free of nuclear weapons, while opponents claim that it is a sure-fire prescription for a major escalation in the arms race, the militarization of space and a collapse of the current, albeit limited, arms-control regime. (See Gerold Yonas's article on page 24.)
The Differences Between One-Dimensional and Three-Dimensional Semiconductors
Authors: Conwell Esther M.
Published: January 2008

The semiconductors with which we are most familiar, such as germanium and silicon, behave similarly in all three dimensions: Under most circumstances, electrons, for example, move equally well along the three crystal axes. There are, however, materials whose structure is so anisotropic that their properties as measured along one axis differ drastically from those measured in the other directions. In such materials the electrons may behave as if they were confined to move in only one or two dimensions. In particular, the quasi-one-dimensional materials have aroused a great deal of interest over the past decade. Thus, for example, a recent international conference on low-dimensional conductors at Abano Terme, Italy, in June 1984, had about 500 participants and almost as many papers discussing quasi-one-dimensional metallic, semiconducting, and superconducting materials. (As we shall see, these are for the most part the same materials under different conditions of temperature, doping or pressure.)
Soft-X-Ray Microscopes
Authors: Howells Malcolm , Kirz Janos , Sayre David , Schmahl Günter
Published: January 2008

Biologists have long dreamed of a microscope capable of imaging specimens in their natural state, at molecular or near-molecular resolution. Physicists have for some years known that the soft-x-ray photon has properties that suit it for use as a probe in such microscopy. With the advent of synchrotron radiation sources, and with other technical advances, the difficulties that impeded the development of soft-x-ray microscopy have begun to give way, and in 1983 the technique produced the first images ever obtained of a living cell at a near-molecular resolution of 75 Å.
Acoustic Microscopy
Authors: Quate Calvin F.
Published: January 2008

The acoustic microscope is a new entry in the field of microscopic imaging. It comes after a delay of many years, but now appears to be well established. At last year's conference of the Royal Microscopical Society in London, for example, the booth traditionally reserved for new instruments was used to introduce commercial versions of acoustic instruments. Visitors to the exhibit learned that one can focus acoustic waves in water to a diffractionlimited waist and use them as a probe for microscopic examination. They found in examining their own samples that they could observe new detail with a resolution comparable to that achieved by optical microscopes. (See figures 1 and 2.)
Natural Engines
Authors: Wheatley John , Cox Arthur
Published: January 2008

Under certain circumstances, a flow of heat through a system can give rise to acoustic oscillations, converting some of the heat to work. Natural vibrators maintained by heat flows have been studied since the 1770s. Some of the best-known examples come from acoustics: the “singing flames” first investigated by Byron Higgins in 1777, the Sondhauss tube and the Rijke tube. Most experimenters in cryogenics have observed the “Taconis oscillations” that occur when a tube, closed at the top, is inserted into a liquid-helium dewar. A group at Tsukuba has studied such oscillations quantitatively. Oscillations driven by heat also occur on a very large scale, in certain classes of variable stars.
The American Connection to Soviet Microelectronics
Authors: Kuchment Mark
Published: January 2008

Ever since the cold war of the late 1940s, the US, joined at times by Europe, Canada and Japan, has sought to restrict sophisticated technology with military potential from reaching the Soviet Union and its Warsaw Pact allies. Despite such efforts, the US has not been completely successful in achieving the goal of limiting or eliminating the flow of militarily valuable data and products from West to East. The Soviet bloc has been able to acquire advanced technologies from the West in various ways—by espionage and entrepreneurship, as exemplified in Pentagon accounts of Vax 11/782 mini-computers and an array of microelectronics, seismographs and lasers shipped illegally to Warsaw Pact countries through a variety of real and phony companies in Europe and elsewhere. For all the horror stories of spying and smuggling, there have been virtually no instances of scientists and engineers defecting or emigrating to contribute to Soviet military R&D. That is why a case involving two American electrical engineers is so interesting. It is a conspicuous example of technology transfer that, as it happened, lifted a corner of the shroud of secrecy that long concealed military research in the Soviet Union.
Nuclear Winter: A Matter of Degrees
Authors: Levi Barbara G. , Rothman Tony
Published: January 2008

Although climatic impacts have long been on the list of potential consequences of nuclear war, two years ago they were predicted to be so devastating as to earn the label, “nuclear winter.” That term describes a world that is plunged into cold and darkness because the sunlight is blocked by smoke from fires ignited by nuclear explosions and by the dust from nuclear groundbursts. This vision is considerably more severe than any painted earlier because the calculations for the first time included massive injections of soot, the carbonaceous component of smoke. The soot strongly absorbs the incoming sunlight but transmits most of the outgoing infrared radiation, creating an inverse greenhouse effect.
The Surface Muon Beam
Authors: Bowen Theodore
Published: January 2008

Long ago, shortly before World War II, when I was but 13 years of age, I was excited by an article in Popular Mechanics magazine that described Ernest O. Lawrence's project to construct the world's greatest atom smasher, a 184-inch cyclotron, on a hill overlooking the Berkeley campus of the University of California. From that point on, my career goal was to become a physicist. While the 184-inch-cyclotron project has always symbolized to me the beauty and excitement of unlocking the mysteries of nature, I never suspected, even for many years into my career as a high-energy and cosmic-ray physicist, that I would have a rendezvous with destiny involving the 184-inch cyclotron: using it in its waning years to make my most significant contribution to the progress of science.
IL-1β is an essential mediator of the antineurogenic and anhedonic effects of stress
Authors: Koo Ja Wook , Duman Ronald S.
Published: January 2008

Stress decreases neurogenesis in the adult hippocampus, and blockade of this effect is required for the actions of antidepressants in behavioral models of depression. However, the mechanisms underlying these effects of stress have not been identified. Here, we demonstrate an essential role for the proinflammatory cytokine IL-1β. Administration of IL-1β or acute stress suppressed hippocampal cell proliferation. Blockade of the IL-1β receptor, IL-1RI, by using either an inhibitor or IL-1RI null mice blocks the antineurogenic effect of stress and blocks the anhedonic behavior caused by chronic stress exposure.In vivoandin vitrostudies demonstrate that hippocampal neural progenitor cells express IL-1RI and that activation of this receptor decreases cell proliferation via the nuclear factor-κB signaling pathway. These findings demonstrate that IL-1β is a critical mediator of the antineurogenic and depressive-like behavior caused by acute and chronic stress.
Histone arginine methylation is required for vernalization-induced epigenetic silencing of
FLC
in winter-annual
Arabidopsis thaliana
Authors: Schmitz Robert J. , Sung Sibum , Amasino Richard M.
Published: January 2008

Certain plant varieties typically require prolonged exposure to the cold of winter to become competent to flower rapidly in the spring. This process is known as vernalization. In
Arabidopsis thaliana
, vernalization renders plants competent to flower by epigenetically silencing the strong floral repressor
FLOWERING LOCUS C
(
FLC
). As a result of vernalization, levels of lysine-9 and lysine-27 trimethylation on histone 3, modifications that are characteristic of facultative heterochromatin in plants, increase at
FLC
chromatin. We have identified a mutant,
protein arginine methyltransferase 5
(
atprmt5
), that fails to flower rapidly after vernalization treatment.
AtPRMT5
encodes a type II protein arginine methyltransferase (PRMT) that, in winter-annual strains, is required for epigenetic silencing of
FLC
and for the vernalization-mediated histone modifications characteristic of the vernalized state. Furthermore, the levels of arginine methylation of
FLC
chromatin increase after vernalization. Therefore, arginine methylation of
FLC
chromatin is part of the histone code that is required for mitotic stability of the vernalized state.
ICA512 signaling enhances pancreatic β-cell proliferation by regulating cyclins D through STATs
Authors: Mziaut Hassan , Kersting Stephan , Knoch Klaus-Peter , Fan Wan-Hung , Trajkovski Mirko , Erdmann Katja , Bergert Hendrik , Ehehalt Florian , Saeger Hans-Detlev , Solimena Michele
Published: January 2008

Changes in metabolic demands dynamically regulate the total mass of adult pancreatic β-cells to adjust insulin secretion and preserve glucose homeostasis. Glucose itself is a major regulator of β-cell proliferation by inducing insulin secretion and activating β-cell insulin receptors. Here, we show that islet cell autoantigen 512 (ICA512)/IA-2, an intrinsic tyrosine phosphatase-like protein of the secretory granules, activates a complementary pathway for β-cell proliferation. On granule exocytosis, the ICA512 cytoplasmic domain is cleaved and the resulting
c
ytosolic fragment (ICA512-CCF) moves into the nucleus where it enhances the levels of phosphorylated STAT5 and STAT3, thereby inducing insulin gene transcription and granule biogenesis. We now show that knockdown of ICA512 decreases cyclin D1 levels and proliferation of insulinoma INS-1 cells, whereas β-cell regeneration is reduced in partially pancreatectomized
ICA512
−/−
mice. Conversely, overexpression of ICA512-CCF increases both cyclin D1 and D2 levels and INS-1 cell proliferation. Up-regulation of cyclin D1 and D2 by ICA512-CCF is affected by knockdown of STAT3 and STAT5, respectively, whereas it does not require insulin signaling. These results identify ICA512 as a regulator of cyclins D and β-cell proliferation through STATs and may have implication for diabetes therapy.
The phosphorylation state of Ser-129 in human α-synuclein determines neurodegeneration in a rat model of Parkinson disease
Authors: Gorbatyuk Oleg S. , Li Shoudong , Sullivan Layla F. , Chen Weijun , Kondrikova Galina , Manfredsson Fredric P. , Mandel Ronald J. , Muzyczka Nicholas
Published: January 2008

Studies have shown that α-synuclein (α-syn) deposited in Lewy bodies in brain tissue from patients with Parkinson disease (PD) is extensively phosphorylated at Ser-129. We used recombinant Adeno-associated virus (rAAV) to overexpress human wild-type (wt) α-syn and two human α-syn mutants with site-directed replacement of Ser-129 to alanine (S129A) or to aspartate (S129D) in the nigrostriatal tract of the rat to investigate the effect of Ser-129 phosphorylation state on dopaminergic neuron pathology. Rats were injected with rAAV2/5 vectors in the substantia nigra pars compacta (SNc) on one side of the brain; the other side remained as a nontransduced control. The level of human wt or mutant α-syn expressed on the injected side was about four times the endogenous rat α-syn. There was a significant reduction of dopaminergic neurons in the SNc and dopamine (DA) and tyrosine hydroxylase (TH) levels in the striatum of all S129A-treated rats as early as 4 wk postinjection. Nigral DA pathology occurred more slowly in the wt-injected animals, but by 26 wk the wt α-syn group lost nigral TH neurons equivalent to the mutated S129A group at 8 wk. In stark contrast, we did not observe any pathological changes in S129D-treated animals. Therefore, the nonphosphorylated form of S129 exacerbates α-syn-induced nigral pathology, whereas Ser-129 phosphorylation eliminates α-syn-induced nigrostriatal degeneration. This suggests possible new therapeutic targets for Parkinson Disease.
Nanoelectrochemistry of mammalian cells
Authors: Sun Peng , Laforge François O. , Abeyweera Thushara P. , Rotenberg Susan A. , Carpino James , Mirkin Michael V.
Published: January 2008

There is a significant current interest in development of new techniques for direct characterization of the intracellular redox state and high-resolution imaging of living cells. We used nanometer-sized amperometric probes in combination with the scanning electrochemical microscope (SECM) to carry out spatially resolved electrochemical experiments in cultured human breast cells. With the tip radius ≈1,000 times smaller than that of a cell, an electrochemical probe can penetrate a cell and travel inside it without apparent damage to the membrane. The data demonstrate the possibility of measuring the rate of transmembrane charge transport and membrane potential and probing redox properties at the subcellular level. The same experimental setup was used for nanoscale electrochemical imaging of the cell surface.
Structural basis for ligand-mediated mouse GITR activation
Authors: Zhou Zhaocai , Tone Yukiko , Song Xiaomin , Furuuchi Keiji , Lear James D. , Waldmann Herman , Tone Masahide , Greene Mark I. , Murali Ramachandran
Published: January 2008

Glucocorticoid-induced TNF receptor ligand (GITRL) is a member of the TNF super family (TNFSF). GITRL plays an important role in controlling regulatory T cells. The crystal structure of the mouse GITRL (mGITRL) was determined to 1.8-Å resolution. Contrary to the current paradigm that all ligands in the TNFSF are trimeric, mGITRL associates as dimer through a unique C terminus tethering arm. Analytical ultracentrifuge studies revealed that in solution, the recombinant mGITRL exists as monomers at low concentrations and as dimers at high concentrations. Biochemical studies confirmed that the mGITRL dimer is biologically active. Removal of the three terminal residues in the C terminus resulted in enhanced receptor-mediated NF-κB activation than by the wild-type receptor complex. However, deletion of the tethering C-terminus arm led to reduced activity. Our studies suggest that the mGITRL may undergo a dynamic population shift among different oligomeric forms via C terminus-mediated conformational changes. We hypothesize that specific oligomeric forms of GITRL may be used as a means to differentially control GITR receptor signaling in diverse cells.
[Retracted] Ginseng on Hyperglycemia: Effects and Mechanisms
Authors: Luo John Zeqi , Luo Luguang
Published: January 2008

It has been reported that American ginseng attenuates hyperglycemia and may present itself as a supplement to diabetes therapy. However, the lack of standardization in the usage of ginseng root leads to inconclusive results when applied to diabetes treatment. The mechanisms of American ginseng root in the treatment of diabetes remains a mystery. This greatly limits the effective utilization of American ginseng in facilitating diabetic therapy. Initiating studies have shown that American ginseng increases insulin production and reduces cell death in pancreatic β‐cells. Also, studies have revealed American ginseng′s ability to decrease blood glucose in type II diabetes patients as well as in streptozotocin‐induced diabetic animals (STZ‐diabetic mice). These data suggest that effects of ginseng in improving hyperglycemia may alter mitochondrial function as well as apoptosis cascades to ensure cell viability in pancreatic islet cells. This review briefly summarizes current knowledge of ginseng components and clinical studies related to diabetes. Further research will be needed to explore and identify the component(s) of ginseng, which may be responsible for the beneficial effects observed in animal studies which could then be extrapolated to human islets.
Assessment of seawater pollution by heavy metals in the neighbourhood of Algiers: use of the sea urchin, Paracentrotus lividus, as a bioindicator
Authors: Soualili Dina , Dubois Philippe , Gosselin Pol , Pernet Philippe , Guillou Monique
Published: January 2008

Soualili, D., Dubois, P., Gosselin, P., Pernet, P., and Guillou, M. 2008 Assessment of seawater pollution by heavy metals in the neighbourhood of Algiers: use of the sea urchin, Paracentrotus lividus, as a bioindicator. – ICES Journal of Marine Science, 65: 132–139. The objective of the study was to assess the levels of contamination by heavy metals near the Algiers metropolis, using a combination of chemical and toxicological data gained from analyses of sediments and biological parameters characteristic of the sea urchin, Paracentrotus lividus. Zinc, lead, cadmium, copper, and iron concentrations were determined in sediments and in sea urchin gonads. Sediment toxicity was assessed by bioassay based on the larval development of sea urchins. The most numerous larval abnormalities were found in a site near Algiers identified as highly polluted by lead. The levels of the other metals across the study area fell within the background concentrations reported in the literature for the Mediterranean Sea, with the exception of zinc, which showed high values in female gonads.
Cooperative Ethylene and Jasmonic Acid Signaling Regulates Selenite Resistance in Arabidopsis
Authors: Tamaoki Masanori , Freeman John L. , Pilon-Smits Elizabeth A.H.
Published: January 2008

Selenium (Se) is an essential element for many organisms, but excess Se is toxic. To better understand plant Se toxicity and resistance mechanisms, we compared the physiological and molecular responses of two Arabidopsis (Arabidopsis thaliana) accessions, Columbia (Col)-0 and Wassilewskija (Ws)-2, to selenite treatment. Measurement of root length Se tolerance index demonstrated a clear difference between selenite-resistant Col-0 and selenite-sensitive Ws-2. Macroarray analysis showed more pronounced selenite-induced increases in mRNA levels of ethylene- or jasmonic acid (JA)-biosynthesis and -inducible genes in Col-0 than in Ws-2. Indeed, Col-0 exhibited higher levels of ethylene and JA. The selenite-sensitive phenotype of Ws-2 was attenuated by treatment with ethylene precursor or methyl jasmonate (MeJA). Conversely, the selenite resistance of Col-0 was reduced in mutants impaired in ethylene or JA biosynthesis or signaling. Genes encoding sulfur (S) transporters and S assimilation enzymes were up-regulated by selenite in Col-0 but not Ws-2. Accordingly, Col-0 contained higher levels of total S and Se and of nonprotein thiols than Ws-2. Glutathione redox status was reduced by selenite in Ws-2 but not in Col-0. Furthermore, the generation of reactive oxygen species by selenite was higher in Col-0 than in Ws-2. Together, these results indicate that JA and ethylene play important roles in Se resistance in Arabidopsis. Reactive oxygen species may also have a signaling role, and the resistance mechanism appears to involve enhanced S uptake and reduction.
Myosin XI-K Is Required for Rapid Trafficking of Golgi Stacks, Peroxisomes, and Mitochondria in Leaf Cells of Nicotiana benthamiana
Authors: Avisar Dror , Prokhnevsky Alexey I. , Makarova Kira S. , Koonin Eugene V. , Dolja Valerian V.
Published: January 2008

A prominent feature of plant cells is the rapid, incessant movement of the organelles traditionally defined as cytoplasmic streaming and attributed to actomyosin motility. We sequenced six complete Nicotiana benthamiana cDNAs that encode class XI and class VIII myosins. Phylogenetic analysis indicates that these two classes of myosins diverged prior to the radiation of green algae and land plants from a common ancestor and that the common ancestor of land plants likely possessed at least seven myosins. We further report here that movement of Golgi stacks, mitochondria, and peroxisomes in the leaf cells of N. benthamiana is mediated mainly by myosin XI-K. Suppression of myosin XI-K function using dominant negative inhibition or RNA interference dramatically reduced movement of each of these organelles. When similar approaches were used to inhibit functions of myosin XI-2 or XI-F, only moderate to marginal effects were observed. Organelle trafficking was virtually unaffected in response to inhibition of each of the three class VIII myosins. Interestingly, none of the tested six myosins appears to be involved in light-induced movements of chloroplasts. Taken together, these data strongly suggest that myosin XI-K has a major role in trafficking of Golgi stacks, mitochondria, and peroxisomes, whereas myosins XI-2 and XI-F might perform accessory functions in this process. In addition, our analysis of thousands of individual organelles revealed independent movement patterns for Golgi stacks, mitochondria, and peroxisomes, indicating that the notion of coordinated cytoplasmic streaming is not generally applicable to higher plants.
Arabidopsis UEV1DPromotes Lysine-63–Linked Polyubiquitination and Is Involved in DNA Damage Response
Authors: Wen Rui , Torres-Acosta J. Antonio , Pastushok Landon , Lai Xiaoqin , Pelzer Lindsay , Wang Hong , Xiao Wei
Published: January 2008

DNA damage tolerance (DDT) in budding yeast requires Lys-63–linked polyubiquitination of the proliferating cell nuclear antigen. The ubiquitin-conjugating enzyme Ubc13 and the Ubc enzyme variant (Uev) methyl methanesulfonate2 (Mms2) are required for this process. Mms2 homologs have been found in all eukaryotic genomes examined; however, their roles in multicellular eukaryotes have not been elucidated. We report the isolation and characterization of four UEV1 genes from Arabidopsis thaliana. All four Uev1 proteins can form a stable complex with At Ubc13 or with Ubc13 from yeast or human and can promote Ubc13-mediated Lys-63 polyubiquitination. All four Uev1 proteins can replace yeast MMS2 DDT functions in vivo. Although these genes are ubiquitously expressed in most tissues, UEV1D appears to express at a much higher level in germinating seeds and in pollen. We obtained and characterized two uev1d null mutant T-DNA insertion lines. Compared with wild-type plants, seeds from uev1d null plants germinated poorly when treated with a DNA-damaging agent. Those that germinated grew slower, and the majority ceased growth within 2 weeks. Pollen from uev1d plants also displayed a moderate but significant decrease in germination in the presence of DNA damage. This report links Ubc13-Uev with functions in DNA damage response in Arabidopsis.
The Arabidopsis Small G Protein ROP2 Is Activated by Light in Guard Cells and Inhibits Light-Induced Stomatal Opening
Authors: Jeon Byeong Wook , Hwang Jae-Ung , Hwang Youngkyu , Song Won-Yong , Fu Ying , Gu Ying , Bao Fang , Cho Daeshik , Kwak June M. , Yang Zhenbiao , Lee Youngsook
Published: January 2008

ROP small G proteins function as molecular switches in diverse signaling processes. Here, we investigated signals that activate ROP2 in guard cells. In guard cells of Vicia faba expressing Arabidopsis thaliana constitutively active (CA) ROP2 fused to red fluorescent protein (RFP-CA-ROP2), fluorescence localized exclusively at the plasma membrane, whereas a dominant negative version of RFP-ROP2 (DN-ROP2) localized in the cytoplasm. In guard cells expressing green fluorescent protein–ROP2, the relative fluorescence intensity at the plasma membrane increased upon illumination, suggesting that light activates ROP2. Unlike previously reported light-activated factors, light-activated ROP2 inhibits rather than accelerates light-induced stomatal opening; stomata bordered by guard cells transformed with CA-rop2 opened less than controls upon light irradiation. When introduced into guard cells together with CA-ROP2, At RhoGDI1, which encodes a guanine nucleotide dissociation inhibitor, inhibited plasma membrane localization of CA-ROP2 and abolished the inhibitory effect of CA-ROP2 on light-induced stomatal opening, supporting the negative effect of active ROP2 on stomatal opening. Mutant rop2 Arabidopsis guard cells showed phenotypes similar to those of transformed V. faba guard cells; CA-rop2 stomata opened more slowly and to a lesser extent, and DN-rop2 stomata opened faster than wild-type stomata in response to light. Moreover, in rop2 knockout plants, stomata opened faster and to a greater extent than wild-type stomata in response to light. Thus, ROP2 is a light-activated negative factor that attenuates the extent of light-induced changes in stomatal aperture. The inhibition of light-induced stomatal opening by light-activated ROP2 suggests the existence of feedback regulatory mechanisms through which stomatal apertures may be finely controlled.
Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution
Authors: Salse Jérôme , Bolot Stéphanie , Throude Michaël , Jouffe Vincent , Piegu Benoît , Quraishi Umar Masood , Calcagno Thomas , Cooke Richard , Delseny Michel , Feuillet Catherine
Published: January 2008

The grass family comprises the most important cereal crops and is a good system for studying, with comparative genomics, mechanisms of evolution, speciation, and domestication. Here, we identified and characterized the evolution of shared duplications in the rice (Oryza sativa) and wheat (Triticum aestivum) genomes by comparing 42,654 rice gene sequences with 6426 mapped wheat ESTs using improved sequence alignment criteria and statistical analysis. Intraspecific comparisons identified 29 interchromosomal duplications covering 72% of the rice genome and 10 duplication blocks covering 67.5% of the wheat genome. Using the same methodology, we assessed orthologous relationships between the two genomes and detected 13 blocks of colinearity that represent 83.1 and 90.4% of the rice and wheat genomes, respectively. Integration of the intraspecific duplications data with colinearity relationships revealed seven duplicated segments conserved at orthologous positions. A detailed analysis of the length, composition, and divergence time of these duplications and comparisons with sorghum (Sorghum bicolor) and maize (Zea mays) indicated common and lineage-specific patterns of conservation between the different genomes. This allowed us to propose a model in which the grass genomes have evolved from a common ancestor with a basic number of five chromosomes through a series of whole genome and segmental duplications, chromosome fusions, and translocations.
A Genomic Map of Viroid RNA Motifs Critical for Replication and Systemic Trafficking
Authors: Zhong Xuehua , Archual Anthony J. , Amin Amy A. , Ding Biao
Published: January 2008

RNA replication and systemic trafficking play significant roles in developmental regulation and host–pathogen interactions. Viroids are the simplest noncoding eukaryotic RNA pathogens and genetic units that are capable of autonomous replication and systemic trafficking and offer excellent models to investigate the role of RNA structures in these processes. Like other RNAs, the predicted secondary structure of a viroid RNA contains many loops and bulges flanked by double-stranded helices, the biological functions of which are mostly unknown. Using Potato spindle tuber viroid infection of Nicotiana benthamiana as the experimental system, we tested the hypothesis that these loops/bulges are functional motifs that regulate replication in single cells or trafficking in a plant. Through a genome-wide mutational analysis, we identified multiple loops/bulges essential or important for each of these biological processes. Our results led to a genomic map of viroid RNA motifs that mediate single-cell replication and systemic trafficking, respectively. This map provides a framework to enable high-throughput studies on the tertiary structures and functional mechanisms of RNA motifs that regulate viroid replication and trafficking. Our model and approach should also be valuable for comprehensive investigations of the replication and trafficking motifs in other RNAs.
Requirement for the Budding Yeast Polo Kinase Cdc5 in Proper Microtubule Growth and Dynamics
Authors: Park Chong J. , Park Jung-Eun , Karpova Tatiana S. , Soung Nak-Kyun , Yu Li-Rong , Song Sukgil , Lee Kyung H. , Xia Xue , Kang Eugene , Dabanoglu Ilknur , Oh Doo-Yi , Zhang James Y. , Kang Young Hwi , Wincovitch Stephen , Huffaker Tim C. , Veenstra Timothy D. , McNally James G. , Lee Kyung S.
Published: January 2008

In many organisms, polo kinases appear to play multiple roles during M-phase progression. To provide new insights into the function of the budding yeast polo kinase Cdc5, we generated novel temperature-sensitive
cdc5
mutants by mutagenizing the C-terminal noncatalytic polo box domain, a region that is critical for proper subcellular localization. One of these mutants,
cdc5-11
, exhibited a temperature-sensitive growth defect with an abnormal spindle morphology. Strikingly, provision of a moderate level of benomyl, a microtubule-depolymerizing drug, permitted
cdc5-11
cells to grow significantly better than the isogenic
CDC5
wild type in a FEAR (cdc Fourteen Early Anaphase Release)-independent manner. In addition,
cdc5-11
required
MAD2
for both cell growth and the benomyl-remedial phenotype. These results suggest that
cdc5-11
is defective in proper spindle function. Consistent with this view,
cdc5-11
exhibited abnormal spindle morphology, shorter spindle length, and delayed microtubule regrowth at the nonpermissive temperature. Overexpression of
CDC5
moderately rescued the
spc98-2
growth defect. Interestingly, both Cdc28 and Cdc5 were required for the proper modification of the spindle pole body components Nud1, Slk19, and Stu2 in vivo. They also phosphorylated these three proteins in vitro. Taken together, these observations suggest that concerted action of Cdc28 and Cdc5 on Nud1, Slk19, and Stu2 is important for proper spindle functions.
Evolutionary Dynamics of Light-Independent Protochlorophyllide Oxidoreductase Genes in the Secondary Plastids of Cryptophyte Algae
Authors: Fong Anna , Archibald John M.
Published: January 2008

Plastid genes encoding light-independent protochlorophyllide oxidoreductase (LIPOR) subunits were isolated from cryptophyte algae, the first example of such genes in plastids of secondary endosymbiotic origin. The presence of functional and nonfunctional copies of LIPOR genes in cryptophytes suggests that light-independent chlorophyll biosynthesis is a nonessential pathway in these organisms.
Gene Overexpression/Suppression Analysis of Candidate Virulence Factors of
Candida albicans
Authors: Fu Yue , Luo Guanpingsheng , Spellberg Brad J. , Edwards John E. , Ibrahim Ashraf S.
Published: January 2008

We developed a conditional overexpression/suppression genetic strategy in
Candida albicans
to enable simultaneous testing of gain or loss of function in order to identify new virulence factors. The strategy involved insertion of a strong, tetracycline-regulated promoter in front of the gene of interest. To validate the strategy, a library of genes encoding glycosylphosphatidylinositol (GPI)-anchored surface proteins was screened for virulence phenotypes in vitro. During the screening, overexpression of
IFF4
was found to increase the adherence of
C. albicans
to plastic and to human epithelial cells, but not endothelial cells. Consistent with the in vitro results,
IFF4
overexpression modestly increased the tissue fungal burden during murine vaginal candidiasis. In addition to the in vitro screening tests,
IFF4
overexpression was found to increase
C. albicans
susceptibility to neutrophil-mediated killing. Furthermore,
IFF4
overexpression decreased the severity of hematogenously disseminated candidiasis in normal mice, but not in neutropenic mice, again consistent with the in vitro phenotype. Overexpression of 12 other GPI proteins did not affect normal GPI protein cell surface accumulation, demonstrating that the overexpression strategy did not affect the cell capacity for making such proteins. These data indicate that the same gene can increase or decrease candidal virulence in distinct models of infection, emphasizing the importance of studying virulence genes in different anatomical contexts. Finally, these data validate the use of a conditional overexpression/suppression genetic strategy to identify candidal virulence factors.
Toxoplasma gondii
and
Cryptosporidium parvum
Lack Detectable DNA Cytosine Methylation
Authors: Gissot Mathieu , Choi Sang-Woon , Thompson Reid F. , Greally John M. , Kim Kami
Published: January 2008

Epigenetic factors play a role in the expression of virulence traits in Apicomplexa. Apicomplexan genomes encode putative DNA cytosine methylation enzymes. To assess the presence of cytosine methylation of
Toxoplasma gondii
and
Cryptosporidium parvum
DNA, we used mass spectrometry analysis and confirmed that these organisms lack detectable methylcytosine in their DNA.
The Min System as a General Cell Geometry Detection Mechanism: Branch Lengths in Y-ShapedEscherichia coliCells Affect Min Oscillation Patterns and Division Dynamics
Authors: Varma Archana , Huang Kerwyn Casey , Young Kevin D.
Published: January 2008

InEscherichia coli, division site placement is regulated by the dynamic behavior of the MinCDE proteins, which oscillate from pole to pole and confine septation to the centers of normal rod-shaped cells. Some current mathematical models explain these oscillations by considering interactions among the Min proteins without recourse to additional localization signals. So far, such models have been applied only to regularly shaped bacteria, but here we test these models further by employing aberrantly shapedE. colicells as miniature reactors. The locations of MinCDE proteins fused to derivatives of green fluorescent protein were monitored in branched cells with at least three conspicuous poles. MinCDE most often moved from one branch to another in an invariant order, following a nonreversing clockwise or counterclockwise direction over the time periods observed. In cells with two short branches or nubs, the proteins oscillated symmetrically from one end to the other. The locations of FtsZ rings were consistent with a broad MinC-free zone near the branch junctions, and Min rings exhibited the surprising behavior of moving quickly from one possible position to another. Using a reaction-diffusion model that reproduces the observed MinCD oscillations in rod-shaped and roundE. coli, we predict that the oscillation patterns in branched cells are a natural response of Min behavior in cellular geometries having different relative branch lengths. The results provide further evidence that Min protein oscillations act as a general cell geometry detection mechanism that can locate poles even in branched cells.
Protein Subassemblies of theHelicobacter pyloriCag Type IV Secretion System Revealed by Localization and Interaction Studies
Authors: Kutter Stefan , Buhrdorf Renate , Haas Jürgen , Schneider-Brachert Wulf , Haas Rainer , Fischer Wolfgang
Published: January 2008

Type IV secretion systems are possibly the most versatile protein transport systems in gram-negative bacteria, with substrates ranging from small proteins to large nucleoprotein complexes. In many cases, such as thecagpathogenicity island ofHelicobacter pylori, genes encoding components of a type IV secretion system have been identified due to their sequence similarities to prototypical systems such as the VirB system ofAgrobacterium tumefaciens. The Cag type IV secretion system contains at least 14 essential apparatus components and several substrate translocation and auxiliary factors, but the functions of most components cannot be inferred from their sequences due to the lack of similarities. In this study, we have performed a comprehensive sequence analysis of all essential or auxiliary Cag components, and we have used antisera raised against a subset of components to determine their subcellular localization. The results suggest that the Cag system contains functional analogues to all VirB components except VirB5. Moreover, we have characterized mutual stabilization effects and performed a comprehensive yeast two-hybrid screening for potential protein-protein interactions. Immunoprecipitation studies resulted in identification of a secretion apparatus subassembly at the outer membrane. Combining these data, we provide a first low-resolution model of the Cag type IV secretion apparatus.