bluuebunny/crossref_metadata_2025 huggingface dataset:
A two-stream gyrotron traveling wave tube amplifier
Authors: Yang Yunyuan , Ding Wu
Published: July 2002

A new idea of using two electron beams to widen the bandwidth of a Gyrotron Traveling Wave Tube Amplifier is put forward. Theoretical and numerical investigation show that the new model can produce wideband and high power output and its gain is much higher compared to the existing wideband model. When the current of the two beams is 10 A, their voltages are, respectively, 90 and 153 kV, the velocity ratios are 1.0 and 0.62, and their axial momentum spreads are 5.5% and 1.2%, the output saturated bandwidth can reach at least 22%, the peak power, efficiency and gain are 395 kW, 16% and 62 dB, respectively. If the axial guiding magnetic field is tapered near the end of the interaction region, a constant bandwidth of 23% with a peak output power 280 kW can be achieved.
Paths to ignition by radio frequency heating during the B-field ramp
Authors: Myra J. R. , Aamodt R. E. , D’Ippolito D. A.
Published: July 2002

To conserve transformer volt-seconds, power to toroidal magnetic field coils, and to trigger an early transition into high confinement (H) mode, where the requirements on auxiliary power are lower, rf heating during the B-field ramp phase of ignition-class tokamaks is considered. The scheme is analyzed by modifying the usual plasma operating condition diagrams to apply to the ramp phase where the magnetic field, plasma current, and density are changing. It is shown that ion cyclotron range-of-frequencies direct electron heating during the ramp phase of IGNITOR [B. Coppi, M. Nassi, and L. E. Sugiyama, Phys. Scr. 45, 112 (1992)], as proposed by Majeski [R. Majeski, in AIP Conference Proceedings 485—Radio Frequency Power in Plasmas, Annapolis, MD (AIP, New York, 1999), p. 353], may be useful in optimizing the operating condition path to ignition.
Toroidal field effects on dipole equilibrium and stability at finite plasma pressure
Authors: Catto Peter J. , Krasheninnikov S. I.
Published: July 2002

The influence of a toroidal magnetic field on the equilibrium and stability of a plasma confined by the magnetic field of a point dipole is considered, since it may be necessary to introduce a toroidal magnetic field to smooth electron heating or other asymmetries in the toroidal direction that can lead to toroidal electric fields and a loss of confinement due to radial E×B drift. To begin, a toriodal magnetic field is shown to restore confinement by reducing electron heating departures from axisymmetry. Then the Grad–Shafranov equation for a point dipole in the presence of a toroidal field is solved to explicitly demonstrate that an equilibrium exists. Finally, it is shown that a toroidal magnetic field destabilizes the otherwise stable point dipole ballooning modes at high plasma pressure. Consequently, if a toroidal magnetic field is necessary to remove toroidal heating asymmetries in a dipole equilibrium, the heating may have to be performed transiently or at lower plasma pressures.
Interaction of an ultra-intense laser pulse with a nonuniform preformed plasma
Authors: Faure J. , Malka V. , Marquès J.-R. , Amiranoff F. , Courtois C. , Najmudin Z. , Krushelnick K. , Salvati M. , Dangor A. E. , Solodov A. , Mora P. , Adam J.-C. , Héron A.
Published: July 2002

The propagation of an ultra-intense laser pulse in a preformed plasma channel was investigated experimentally. Different regimes of propagation were observed when the pulse duration was varied. For a long pulse and powers lower than the critical power for self-focusing, PL/PC<1 (I0=2×1017 W/cm2), the laser pulse was guided by the preformed plasma channel over three Rayleigh lengths (4 mm) and a longitudinal plasma wave was generated by envelope self-modulation of the pulse. For a short pulse and PL/PC≫1, the interaction was dominated by self-focusing and Raman instabilities. Numerical simulations were run for the latter case, giving results comparable to the experiment. The simulations were also used to investigate the dynamics of the instabilities at high power. They showed that strong Raman side scattering first occurs at the beginning of the interaction and is then followed by self-focusing and envelope self-modulation.
How big is a small Langmuir probe?
Authors: Sheridan T. E.
Published: July 2002

The area of the sheath around a thin, disk-shaped electrode that is biased below the plasma potential has been computed using a hybrid simulation with cold, collisionless ions and Boltzmann electrons. That is, the “collecting area” of a double-sided, planar Langmuir probe has been determined for the ion saturation current regime. Sheath areas are calculated for probe radii from 10 to 45 electron Debye lengths and for probe biases from −5 to −30 times the electron temperature. The dependence of the sheath area on probe radius and bias is parameterized using simple empirical formulas.
The electrostatic sheath in a dusty plasma
Authors: Wang Xiaogang , Bhattacharjee A.
Published: July 2002

The electrostatic sheath in a conventional dc discharge involving dusty plasmas is revisited. Assuming Boltzmann responses for electrons and dust particles and taking into account the effect of ion flows, it is shown that the sheath around an electrically floated cylindrical wire contains electrons and ions but no dust particles. The dust particle density rises sharply at the plasma-sheath interface, as seen in a recent experiment [C. O. Thompson, N. D’Angelo, and R. L. Merlino, Phys. Plasmas 6, 1421 (1999)].
Drift wave simulations in stellarator geometry
Authors: Lewandowski J. L. V.
Published: July 2002

A model, based on gyro-kinetic ions and fluid electrons, to study drift waves in low-β [β=(kinetic pressure)/(magnetic pressure)] stellarator plasmas is presented. The model equations are written in straight-field-line coordinates and are valid for arbitrary, fully three-dimensional configurations with closed, nested magnetic surfaces. An implicit method, coupled with a subcycling technique for the electrons, is used to solve the time-dependent, along-the-field-line equations. Numerical calculations are carried out for a three-field-period toroidal heliac. The geometrical effects that enter the model equations are calculated and displayed in physical space using advanced visualization techniques.
Self-generated magnetic field by transverse plasmons in laser-produced plasma
Authors: Liu S. Q. , Li X. Q.
Published: July 2002

Quasisteady magnetic fields could be generated in laser-produced plasmas with high-frequency electromagnetic radiation through wave–wave and wave–particle interactions in the vicinity of the critical point. The behavior of self-generated magnetic fields can be described by nonlinear coupling equations. It is analytically indicated that self-generated magnetic fields are modulationally unstable with respect to the uniform state of a plasma; such an instability would localize the magnetic fields within narrow regions near the critical surface. The theory is supported by a detailed comparison with experiments in laser-produced plasmas.
Effect of convection on multifaceted asymmetric radiation from edge density limits
Authors: Stacey W. M.
Published: July 2002

A previous theory for the MARFE (multifaceted asymmetric radiation from edge) edge density limit has been extended to explicitly account in the linear stability analysis for the convective radial heat flux through the plasma edge. All other edge parameters being equal and the temperature dependence of the particle and heat diffusivities being the same, the MARFE density limit increases significantly and almost linearly with the convective fraction of the radial heat flux through the plasma edge. Calculations for parameters typical of present experiments indicate that it is important to explicitly represent heat convection, as well as conduction, in MARFE density limit predictions.
Picosecond optical mixing in fast photodetectors
Authors: Carruthers T. F. , Weller J. F.
Published: July 2002

We report a simple optical correlation technique which is capable of measuring the intrinsic response speeds of fast photosensitive electronic devices. The appeal of the method is that neither high-speed electrical connections to a device nor cross-correlation measurements between two devices are required. An example is given of measurements of the response speed of a GaAs Schottky barrier photodiode. Under appropriate illumination conditions the detector is found to be sufficiently fast to be capable of replacing optical second harmonic generation techniques for monitoring the quality of a beam of 1.5 ps pulses.
Quadratic electro-optic light modulation in a GaAs/AlGaAs multiquantum well heterostructure near the excitonic gap
Authors: Glick M. , Reinhart F. K. , Weimann G. , Schlapp W.
Published: July 2002

The electro-optic effect has been investigated in a GaAs/AlGaAs multiquantum well waveguide structure 50 meV from the excitonic transition. We extract r41=−1.6×10−10 cm/V and (R11−R12)=6×10−16 cm2/V2, nonlinear optical characteristics that differ from homogeneous GaAs layers. This (R11−R12) value is similar in magnitude but opposite in sign to that found in InGaAsP 130 meV from the band gap.
Electrical behavior of fast neutron irradiated semi-insulating GaAs during thermal recovery
Authors: Goltzené A. , Schwab C. , David J. P. , Roizes A.
Published: July 2002

Electrical measurements during the thermal recovery of fast neutron irradiated GaAs confirm the main steps around 400 and 600 °C, corresponding to the decay of electron paramagnetic resonance identified V2−Ga and As4+Ga centers.
High-speed, hybrid InGaAs p-i-n/photoconductor circuit
Authors: Downey P. M. , Bowers J. E. , Burrus C. A. , Mitschke F. , Mollenauer L. F.
Published: July 2002

A miniature coax circuit incorporating a sensitive InGaAs p-i-n and a picosecond photoconductor is described. This circuit is capable of detecting 0.1 fJ infrared pulses with a time resolution of 12 ps.
Ultrathin gate oxides formed by catalytic oxidation of silicon
Authors: Oellig Eva M. , Michel E. G. , Asensio M. C. , Miranda R.
Published: July 2002

A recipe to produce ultrathin gate oxides by K-promoted catalytic oxidation of Si is described. The thickness of the final oxide depends linearly on the amount of K predeposited. The resulting oxide is chemically homogeneous. The process takes place at temperatures much lower than those used in thermal oxidation. The maximum temperature required to desorb the catalyst is 600 °C.
Activation ratio of Fe in Fe-doped semi-insulating InP epitaxial layers grown by liquid phase epitaxy and metalorganic chemical vapor deposition
Authors: Sugawara M. , Kondo M. , Nakai K. , Yamaguchi A. , Nakajima K.
Published: July 2002

The activation ratio of Fe atoms introduced in semi-insulating (SI) InP layers grown by liquid phase epitaxy (LPE) and metalorganic chemical vapor deposition (MOCVD) has been investigated, employing the current-voltage characteristics of n+-SI-n+ InP diodes and secondary ion mass spectroscopy analysis. The result indicates that most Fe atoms in LPE-grown SI layers are electrically active as deep acceptors; however, a large amount of unactivated Fe atoms are present in MOCVD-grown SI layers. This difference between the two kinds of Fe-doped SI layers can be attributed to the difference in the growth mechanisms of LPE and MOCVD.
Abrupt p-type doping profile of carbon atomic layer doped GaAs grown by flow-rate modulation epitaxy
Authors: Kobayashi Naoki , Makimoto Toshiki , Horikoshi Yoshiji
Published: July 2002

Atomic layer doping of p-type carbon impurity in GaAs was demonstrated using flow-rate modulation epitaxy. An extremely narrow capacitance-voltage profile with 5.8 nm full width at half-maximum is observed in the wafer with a sheet hole density of 9.5×1011 cm−2. Atomic layer doping of carbon was performed by supplying trimethylgallium or trimethylaluminium instead of triethylgallium. It was found that the sheet hole density does not change before and after annealing for 1 h at 800 °C indicating that the carbon is a very stable impurity in GaAs. The diffusion coefficient of carbon is estimated to be 2×10−16 cm−2/s at 800 °C. This is the lowest value ever reported for p-type impurities.
Scanning tunneling microscopy on photoconductive semi-insulating GaAs
Authors: van de Walle G. F. A. , van Kempen H. , Wyder P. , Davidsson P.
Published: July 2002

The increase in surface conductivity upon illumination of semi-insulating GaAs was used to enable surface-topography measurements with a scanning tunneling microscope (STM). Images were recorded in ultrahigh vacuum and in air using a HeNe laser and a halogen lamp for the generation of a photoconductive top layer. From the current-voltage characteristics of the tip-sample contact the maximum feedback-controlled tunnel current at a given voltage can be deduced. A calculation of the increase in carrier density and conductance upon illumination is given, which confirms the possibility of using STM on highly resistive photoconductive materials. Further implications and applications are discussed.
X-ray characterization of surface and bulk structures of sputtered iron oxide thin film
Authors: Huang T. C. , York B. R.
Published: July 2002

The crystalline structures of a sputtered Co-doped iron oxide thin film have been successfully identified and correlated with magnetic properties. X-ray diffraction analysis showed that the bulk of the sputtered film has been properly converted to ferromagnetic γ-Fe2O3. However, the surface of the film was found to be solely hexagonal α-Fe2O3. The formation of an antiferromagnetic α-Fe2O3 surface on a ferromagnetic α-Fe2O3 film caused the magnetically dead layer previously observed by polarized neutron reflection and Kerr rotation measurements.
Silicon diffusion into AlxGa1−xAs (x=0–0.4) from a sputtered silicon film
Authors: Omura E. , Wu X. S. , Vawter G. A. , Hu E. L. , Coldren L. A. , Merz J. L.
Published: July 2002

Silicon diffusion into AlxGa1−xAs (x=0–0.4) from a sputtered Si film is described. It is shown that both the diffusion rate and the surface concentration of Si decrease with increasing Al mole fraction. The diffusion behavior of Si in AlxGa1−xAs is discussed in terms of the binding energy of the Al–As bond and mixed crystal disorder.
Propagation characteristics of picosecond electrical transients on coplanar striplines
Authors: Hsiang Thomas Y. , Whitaker John F. , Sobolewski Roman , Dykaar Douglas R. , Mourou Gerard A.
Published: July 2002

Using a cryogenic electro-optic sampling technique, we have studied the transient propagation characteristics of superconducting and normal indium lines in the picosecond regime. Transient dispersion effects, including increased rise time and increased pulse width, the introduction of ringing on the waveform, and a novel ‘‘pulse sharpening’’ were observed. A model that takes into consideration the effects of modal dispersion and superconducting complex conductivity was established, and an algorithm was developed that accurately describes all of the experimental findings.
Critical layer thickness in In0.2Ga0.8As/GaAs single strained quantum well structures
Authors: Fritz I. J. , Gourley P. L. , Dawson L. R.
Published: July 2002

We report accurate determination of the critical layer thickness (CLT) for single strained-layer epitaxy in the InGaAs/GaAs system. Our samples were molecular beam epitaxially grown, selectively doped, single quantum well structures comprising a strained In0.2Ga0.8As layer imbedded in GaAs. We determined the CLT by two sensitive techniques: Hall-effect measurements at 77 K and photoluminescence microscopy. Both techniques indicate a CLT of about 20 nm. This value is close to that determined previously (∼15 nm) for comparable strained-layer superlattices, but considerably less than the value of ∼45 nm suggested by recent x-ray rocking-curve measurements. We show by a simple calculation that photoluminescence microscopy is more than two orders of magnitude more sensitive to dislocations than x-ray diffraction. Our results re-emphasize the necessity of using high-sensitivity techniques for accurate determination of critical layer thicknesses.
Mass-spectrometer-controlled fabrication of Si/Ge superlattices
Authors: van de Leur R. H. M. , Schellingerhout A. J. G. , Mooij J. E. , Tuinstra F.
Published: July 2002

We have used a quadrupole mass spectrometer to control deposition rates during fabrication of compositionally modulated Si/Ge superlattices. Its performance has been evaluated by an x-ray diffraction study of a superlattice. The variation of the Si deposition rate was less than 3% during the whole deposition time of 30 min. This proves that a mass spectrometer can be successfully employed as rate monitor in Si molecular beam epitaxy systems.
Double heterostructure optoelectronic switch as a dynamic memory with low-power consumption
Authors: Kasahara K. , Tashiro Y. , Hamao N. , Sugimoto M. , Yanase T.
Published: July 2002

A pnn double heterostructure optoelectronic switch with dual extractor electrodes was dynamically operated as an optical memory with the resulting achievement of 20 μW holding power. This value represents a reduction in holding power of about three orders of magnitude as compared to that of conventional light-emitting optical bistable devices. Complete operation, involving optical writing, regeneration, and high-speed erasing of written data through a dual extractor-electrodes configuration, was carried out with a simple driving scheme.
Elastic constants of, and Stonely waves in, molybdenum films measured by Brillouin scattering
Authors: Bell J. A. , Zanoni R. , Seaton C. T. , Stegeman G. I. , Makous J. , Falco C. M.
Published: July 2002

The dispersion of Rayleigh, Stonely, and Sezawa acoustic waves guided by deposited thin molybdenum films has been used to evaluate selected elastic constants and film homogeneity. This work includes the first experimental observation of Stonely waves by Brillouin scattering.
Carbon-doped AlxGa1−xAs-GaAs quantum well lasers
Authors: Guido L. J. , Jackson G. S. , Hall D. C. , Plano W. E. , Holonyak N.
Published: July 2002

Data are presented demonstrating that carbon (C) can be used as the active p-type dopant in high-quality AlxGa1−xAs-GaAs quantum well laser crystals. We show, by fabricating three different types of stripe geometry laser diodes (oxide stripe, hydrogenated stripe, and impurity-induced layer-disordered stripe), that C is a stable dopant and compatible in behavior with typical integrated-circuit style of device processing. The data suggest that more complicated laser geometries are possible on C-doped material because of minimal pattern ‘‘undercutting’’ after processing by, for example, hydrogenation or impurity-induced layer disordering.
Ion-induced C segregation on Fe films on pyrolytic graphite under high-fluence D bombardment
Authors: Santaniello A. , Bohdansky J. , Roth J.
Published: July 2002

Fe films of 700–1700 Å were evaporated on pyrolytic graphite surfaces with both edge and base orientations, and bombarded with D ions at energies from 2 to 13 keV at fluences of 1019 D/cm2. The different ion energies and Fe film thicknesses allow different defect distributions in the graphite substrate of the samples. The Fe sputtering yield of the samples was measured directly by means of laser-induced fluorescence at temperatures ranging from room temperature to 900 K. The depth distribution of the components during mixing is obtained by means of Rutherford backscattering spectroscopy. At 800 K, a drastic reduction of the Fe sputtering yield is observed if energetic ions can reach the graphite substrate. C segregates on top of the Fe layers for D ion ranges larger than the Fe layer thickness. The thickness of the segregated C layers depends on the graphite orientation. For 13 keV D bombardment of 700 Å Fe samples, for example, it is about 100 Å for base graphite and about 1000 Å for edge graphite.
Anti-inflammatory role in septic shock of pituitary adenylate cyclase-activating polypeptide receptor
Authors: Martinez Carmen , Abad Catalina , Delgado Mario , Arranz Alicia , Juarranz Maria G. , Rodriguez-Henche Nieves , Brabet Philippe , Leceta Javier , Gomariz Rosa P.
Published: July 2002

Vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase-activating polypeptide (PACAP) are two mediators synthesized by immune cells, specially under inflammatory and antigen stimulation conditions. Reports have shown that neuropeptides attenuate the deleterious consequences of septic shock both by down-regulating the production of proinflammatory mediators and by stimulating the production of anti-inflammatory cytokines by activated macrophages. In this study, we used a knockout for the PACAP receptor (PAC1−/−) to demonstrate an important protective role for PAC1 receptor in endotoxic shock. Moreover, our results indicate that PAC1 receptor actsin vivoas an anti-inflammatory receptor, at least in part, by attenuating lipopolysaccharide (LPS)-induced production of proinflammatory IL-6, which appears to be the main cytokine regulating the expression of the majority of the acute phase protein genes, which are an important deleterious component of septic shock. Besides, our findings point to endogenously produced VIP and PACAP as participants of the natural anti-inflammatory machinery. Because VIP and PACAP are two attractive candidates for the development of therapies against acute and chronic inflammatory diseases, septic shock, and autoimmune diseases, this paper represents a contribution to the understanding of the mechanism of action of these anti-inflammatory agents.
Suppressors of transcriptional transgenic silencing in
Chlamydomonas
are sensitive to DNA-damaging agents and reactivate transposable elements
Authors: Jeong Byeong-ryool , Wu-Scharf Dancia , Zhang Chaomei , Cerutti Heriberto
Published: July 2002

In the unicellular green alga
Chlamydomonas reinhardtii
, the epigenetic silencing of transgenes occurs, as in land plants, at both the transcriptional and posttranscriptional levels. In the case of single-copy transgenes, transcriptional silencing takes place without detectable cytosine methylation of the introduced DNA. We have isolated two mutant strains, Mut-9 and Mut-11, that reactivate expression of a transcriptionally silenced single-copy transgene. These suppressors are deficient in the repression of a DNA transposon and a retrotransposon-like element. In addition, the mutants show enhanced sensitivity to DNA-damaging agents, particularly radiomimetic chemicals inducing DNA double-strand breaks. All of these phenotypes are much more prominent in a double mutant strain. These observations suggest that multiple partly redundant epigenetic mechanisms are involved in the repression of transgenes and transposons in eukaryotes, presumably as components of a system that evolved to preserve genomic stability. Our results also raise the possibility of mechanistic connections between epigenetic transcriptional silencing and DNA double-strand break repair.
Microbat paraphyly and the convergent evolution of a key innovation in Old World rhinolophoid microbats
Authors: Teeling Emma C. , Madsen Ole , Van Den Bussche Ronald A. , de Jong Wilfried W. , Stanhope Michael J. , Springer Mark S.
Published: July 2002

Molecular phylogenies challenge the view that bats belong to the superordinal group Archonta, which also includes primates, tree shrews, and flying lemurs. Some molecular studies also challenge microbat monophyly and instead support an alliance between megabats and representative rhinolophoid microbats from the families Rhinolophidae (horseshoe bats, Old World leaf-nosed bats) and Megadermatidae (false vampire bats). Another molecular study ostensibly contradicts these results and supports traditional microbat monophyly, inclusive of representative rhinolophoids from the family Nycteridae (slit-faced bats). Resolution of the microbat paraphyly/monophyly issue is essential for reconstructing the temporal sequence and deployment of morphological character state changes associated with flight and echolocation in bats. If microbats are paraphyletic, then laryngeal echolocation either evolved more than once in different microbats or was lost in megabats after evolving in the ancestor of all living bats. To examine these issues, we used a 7.1-kb nuclear data set for nine outgroups and twenty bats, including representatives of all rhinolophoid families. Phylogenetic analyses and statistical tests rejected both Archonta and microbat monophyly. Instead, bats are in the superorder Laurasiatheria and microbats are paraphyletic. Further, the superfamily Rhinolophoidea is polyphyletic. The rhinolophoid families Rhinolophidae and Megadermatidae belong to the suborder Yinpterochiroptera along with rhinopomatids and megabats. The rhinolophoid family Nycteridae belongs to the suborder Yangochiroptera along with vespertilionoids, noctilionoids, and emballonuroids. These results resolve the apparent conflict between previous molecular studies that sampled different rhinolophoid families. An important implication of rhinolophoid polyphyly is independent evolution of key anatomical innovations associated with the nasal-emission of echolocation pulses.
Hox cluster genomics in the horn shark,
Heterodontus
francisci
Authors: Kim Chang-Bae , Amemiya Chris , Bailey Wendy , Kawasaki Kazuhiko , Mezey Jason , Miller Webb , Minoshima Shinsei , Shimizu Nobuyoshi , Wagner Günter , Ruddle Frank
Published: July 2002

Reconstructing the evolutionary history of Hox cluster origins will lead to insights into the developmental and evolutionary significance of Hox gene clusters in vertebrate phylogeny and to their role in the origins of various vertebrate body plans. We have isolated two Hox clusters from the horn shark,
Heterodontus francisci
. These have been sequenced and compared with one another and with other chordate Hox clusters. The results show that one of the horn shark clusters (HoxM) is orthologous to the mammalian HoxA cluster and shows a structural similarity to the amphioxus cluster, whereas the other shark cluster (HoxN) is orthologous to the mammalian HoxD cluster based on cluster organization and a comparison with noncoding and Hox gene-coding sequences. The persistence of an identifiable HoxA cluster over an 800-million-year divergence time demonstrates that the Hox gene clusters are highly integrated and structured genetic entities. The data presented herein identify many noncoding sequence motifs conserved over 800 million years that may function as genetic control motifs essential to the developmental process.
Supramolecular organic photochemistry: Control of covalent bond formation through noncovalent supramolecular interactions and magnetic effects
Authors: Turro Nicholas J.
Published: July 2002

Supramolecular organic photochemistry, a field concerned with the interaction of light with supramolecular assemblies of organic molecules, has been inspired by the remarkable structural and dynamic features of guest@host chemistry, particularly as exemplified by enzymes. Exemplars of supramolecular organic photochemistry from soft-matter hosts (micelles) and hard-matter hosts (porous solids) are discussed with an emphasis on how noncovalent interactions, which are at the heart of supramolecular chemistry, can be systematically exploited to control the catalytic and magnetic effects on the formation of covalent bonds from photochemically produced pairs of radicals.
On the sequencing of the human genome
Authors: Waterston Robert H. , Lander Eric S. , Sulston John E.
Published: July 2002

Two recent papers using different approaches reported draft sequences of the human genome. The international Human Genome Project (HGP) used the hierarchical shotgun approach, whereas Celera Genomics adopted the whole-genome shotgun (WGS) approach. Here, we analyze whether the latter paper provides a meaningful test of the WGS approach on a mammalian genome. In the Celera paper, the authors did not analyze their own WGS data. Instead, they decomposed the HGP's assembled sequence into a “perfect tiling path”, combined it with their WGS data, and assembled the merged data set. To study the implications of this approach, we perform computational analysis and find that a perfect tiling path with 2-fold coverage is sufficient to recover virtually the entirety of a genome assembly. We also examine the manner in which the assembly was anchored to the human genome and conclude that the process primarily depended on the HGP's sequence-tagged site maps, BAC maps, and clone-based sequences. Our analysis indicates that the Celera paper provides neither a meaningful test of the WGS approach nor an independent sequence of the human genome. Our analysis does not imply that a WGS approach could not be successfully applied to assemble a draft sequence of a large mammalian genome, but merely that the Celera paper does not provide such evidence.
Structure of the full-length HPr kinase/phosphatase from
Staphylococcus xylosus
at 1.95 Å resolution: Mimicking the product/substrate of the phospho transfer reactions
Authors: Márquez José Antonio , Hasenbein Sonja , Koch Brigitte , Fieulaine Sonia , Nessler Sylvie , Russell Robert B. , Hengstenberg Wolfgang , Scheffzek Klaus
Published: July 2002

The histidine containing phospho carrier protein (HPr) kinase/phosphatase is involved in carbon catabolite repression, mainly in Gram-positive bacteria. It is a bifunctional enzyme that phosphorylates Ser-46-HPr in an ATP-dependent reaction and dephosphorylates P-Ser-46-HPr. X-ray analysis of the full-length crystalline enzyme from
Staphylococcus
xylosus
at a resolution of 1.95 Å shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. The N-terminal domain has a βαβ fold similar to a segment from enzyme I of the sugar phosphotransferase system and to the uridyl-binding portion of MurF; it is structurally organized in three dimeric modules exposed to form the propeller blades. Two unexpected phosphate ions associated with highly conserved residues were found in the N-terminal dimeric interface. The C-terminal kinase domain is similar to that of the
Lactobacillus casei
enzyme and is assembled in six copies to form the compact central hub of the propeller. Beyond previously reported similarity with adenylate kinase, we suggest evolutionary relationship with phosphoenolpyruvate carboxykinase. In addition to a phosphate ion in the phosphate-binding loop of the kinase domain, we have identified a second phosphate-binding site that, by comparison with adenylate kinases, we believe accommodates a product/substrate phosphate, normally covalently linked to Ser-46 of HPr. Thus, we propose that our structure represents a product/substrate mimic of the kinase/phosphatase reaction.
DNA-dependent protein kinase suppresses double-strand break-induced and spontaneous homologous recombination
Authors: Allen Chris , Kurimasa Akihiro , Brenneman Mark A. , Chen David J. , Nickoloff Jac A.
Published: July 2002

DNA-dependent protein kinase (DNA-PK), composed of Ku70, Ku80, and the catalytic subunit (DNA-PKcs), is involved in repairing double-strand breaks (DSBs) by nonhomologous end-joining (NHEJ). Certain proteins involved in NHEJ are also involved in DSB repair by homologous recombination (HR). To test the effects of DNA-PKcs on DSB-induced HR, we integrated
neo
direct repeat HR substrates carrying the I
-Sce
I recognition sequence into DNA-PKcs-defective Chinese hamster ovary (V3) cells. The DNA-PKcs defect was complemented with a human DNA-PKcs cDNA. DSB-induced HR frequencies were 1.5- to 3-fold lower with DNA-PKcs complementation. In complemented and uncomplemented strains, all products arose by gene conversion without associated crossover, and average conversion tract lengths were similar. Suppression of DSB-induced HR in complemented cells probably reflects restoration of NHEJ, consistent with competition between HR and NHEJ during DSB repair. Interestingly, spontaneous HR rates were 1.6- to >3.5-fold lower with DNA-PKcs complementation. DNA-PKcs may suppress spontaneous HR through NHEJ of spontaneous DSBs, perhaps at stalled or blocked replication forks. Because replication protein A (RPA) is involved in both replication and HR, and is phosphorylated by DNA-PKcs, it is possible that the suppression of spontaneous HR by DNA-PKcs reflects regulation of replication-dependent HR by DNA-PKcs, perhaps by means of phosphorylation of RPA.
Preferential maintenance of critically short telomeres in mammalian cells heterozygous for
mTert
Authors: Liu Yie , Kha Hue , Ungrin Mark , Robinson Murray O. , Harrington Lea
Published: July 2002

Prolonged growth of murine embryonic stem (ES) cells lacking the telomerase reverse transcriptase,
mTert
, results in a loss of telomere DNA and an increased incidence of end-to-end fusions and aneuploidy. Furthermore, loss of only one copy of
mTert
also results in telomere shortening intermediate between wild-type (wt) and
mTert
-null ES cells [Liu, Y., Snow, B. E., Hande, M. P., Yeung, D., Erdmann, N. J., Wakeham, A., Itie, A., Siderovski, D. P., Lansdorp, P. M., Robinson, M. O. & Harrington, L. (2000)
Curr. Biol.
10, 1459–1462]. Unexpectedly, although average telomere length in
mTert
+/−
ES cells declined to a similar level as
mTert
-null ES cells,
mTert
+/−
ES cell lines retained a minimal telomeric DNA signal at all chromosome ends. Consequently, no end-to-end fusions and genome instability were observed in the latest passages of
mTert
+/−
ES cell lines. These data uncover a functional distinction between the dosage-dependent function of telomerase in average telomere-length maintenance and the selective maintenance of critically short telomeres in cells heterozygous for
mTert
. In normal and tumor cells, we suggest that telomerase activity insufficient to maintain a given average telomere length may, nonetheless, provide a protective advantage from end-to-end fusion and genome instability.
Rapid prehistoric extinction of iguanas and birds in Polynesia
Authors: Steadman David W. , Pregill Gregory K. , Burley David V.
Published: July 2002

The Tongoleleka archaeological site on Lifuka Island, Kingdom of Tonga, is a rich accumulation of pottery, marine mollusks, and nonhuman bones that represents first human contact on a small island in Remote Oceania ≈2,850 years ago. The lower strata contain decorated Lapita-style pottery and bones of an extinct iguana (
Brachylophus
undescribed sp.) and numerous species of extinct birds. The upper strata instead feature Polynesian Plainware pottery and bones of extant species of vertebrates. A stratigraphic series of 20 accelerator-mass spectrometer radiocarbon dates on individual bones of the iguana, an extinct megapode (
Megapodius alimentum
), and the non-native chicken (
Gallus gallus
) suggests that anthropogenic loss of the first two species and introduction of the latter occurred on Lifuka within a time interval too short (a century or less) to be resolved by radiometric dating. The geologically instantaneous prehistoric collapse of Lifuka's vertebrate community contrasts with the much longer periods of faunal depletion on some other islands, thus showing that the elapse time between human arrival and major extinction events was highly variable on oceanic islands as well as on continents.
The procaspase-8 isoform, procaspase-8L, recruited to the BAP31 complex at the endoplasmic reticulum
Authors: Breckenridge David G. , Nguyen Mai , Kuppig Stephan , Reth Michael , Shore Gordon C.
Published: July 2002

BAP31 is an integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Here, we describe the procaspase-8 isoform, procaspase-8L, which is ubiquitously expressed and selectively recruited to the BAP31 complex in response to apoptotic signaling by E1A. Procaspase-8L is characterized by the
N
-terminal
ex
tension (Nex) domain, which extends procaspase-8/a at the N terminus and is required for selective association of procaspase-8L with the BAP31 complex. Gene deletion identified BAP31 and related BAP29 as required for processing of procaspase-8L in response to E1A, by a FADD-independent mechanism that was blocked by BCL-2. Further, Bap29,31 deletion, as well as a Nex-domain dominant-negative mutant, curtailed the activation of downstream caspases (IETDase and DEVDase) and cell death in response to E1A. Preferential recruitment of procaspase-8L by the BAP31 complex at the endoplasmic reticulum suggests an additional pathway for regulating initiator caspase-8 during apoptosis.
Somatosensory cortex dominated by the representation of teeth in the naked mole-rat brain
Authors: Catania Kenneth C. , Remple Michael S.
Published: July 2002

We investigated naked mole-rat somatosensory cortex to determine how brain areas are modified in mammals with unusual and extreme sensory specializations. Naked mole-rats (
Heterocephalus glaber
) have numerous anatomical specializations for a subterranean existence, including rows of sensory hairs along the body and tail, reduced eyes, and ears sensitive to low frequencies. However, chief among their adaptations are behaviorally important, enlarged incisors permanently exterior to the oral cavity that are used for digging, object manipulation, social interactions, and feeding. Here we report an extraordinary brain organization where nearly one-third (31%) of primary somatosensory cortex is devoted to the representations of the upper and lower incisors. In addition, somatosensory cortex is greatly enlarged (as a proportion of total neocortical area) compared with closely related laboratory rats. Finally, somatosensory cortex in naked mole-rats encompasses virtually all of the neocortex normally devoted to vision. These findings indicate that major cortical remodeling has occurred in naked mole-rats, paralleling the anatomical and behavioral specializations related to fossorial life.
The LEF1/β-catenin complex activates
movo
1, a mouse homolog of
Drosophila ovo
required for epidermal appendage differentiation
Authors: Li Baoan , Mackay Douglas R. , Dai Qian , Li Tony W. H. , Nair Mahalakshmi , Fallahi Magid , Schonbaum Christopher P. , Fantes Judith , Mahowald Anthony P. , Waterman Marian L. , Fuchs Elaine , Dai Xing
Published: July 2002

Drosophila ovo
/
svb
(
dovo
) is required for epidermal cuticle/denticle differentiation and is genetically downstream of the
wg
signaling pathway. Similarly, a mouse homolog of
dovo
,
movo
1, is required for the proper formation of hair, a mammalian epidermal appendage. Here, we provide biochemical evidence that
movo
1 encodes a nuclear DNA binding protein (mOvo1a) that binds to DNA sequences similar to those that dOvo binds to, further supporting the notion that mOvo1a and dOvo are genetically and biochemically homologous proteins. Additionally, we show that the
movo
1 promoter is activated by the lymphoid enhancer factor 1 (LEF1)/β-catenin complex, a transducer of
wnt
signaling. Collectively, our findings suggest that
movo
1 is a developmental target of
wnt
signaling during hair morphogenesis in mice, and that the
wg
/
wnt-ovo
link in epidermal appendage regulatory pathways has been conserved between mice and flies.
Growth factors regulate phototransduction in retinal rods by modulating cyclic nucleotide-gated channels through dephosphorylation of a specific tyrosine residue
Authors: Savchenko Alexei , Kraft Timothy W. , Molokanova Elena , Kramer Richard H.
Published: July 2002

Illumination of vertebrate rod photoreceptors leads to a decrease
in the cytoplasmic cGMP concentration and closure of cyclic
nucleotide-gated (CNG) channels. Except for Ca
2+
, which
plays a negative feedback role in adaptation, and
11-
cis
-retinal, supplied by the retinal pigment
epithelium, all of the biochemical machinery of phototransduction is
thought to be contained within rod outer segments without involvement
of extrinsic regulatory molecules. Here we show that insulin-like
growth factor-I (IGF-I), a paracrine factor released from the retinal
pigment epithelium, alters phototransduction by rapidly increasing the
cGMP sensitivity of CNG channels. The IGF-I-signaling pathway
ultimately involves a protein tyrosine phosphatase that catalyzes
dephosphorylation of a specific residue in the α-subunit of the rod
CNG channel protein. IGF-I conjointly accelerates the kinetics and
increases the amplitude of the light response, distinct from events
that accompany adaptation. These effects of IGF-I could result from the
enhancement of the cGMP sensitivity of CNG channels. Hence, in addition
to long-term control of development and survival of rods, growth
factors regulate phototransduction in the short term by modulating CNG
channels.
Complexation of peptidoglycan intermediates by the lipoglycodepsipeptide antibiotic ramoplanin: Minimal structural requirements for intermolecular complexation and fibril formation
Authors: Cudic Predrag , Kranz James K. , Behenna Douglas C. , Kruger Ryan G. , Tadesse Hellina , Wand A. Joshua , Veklich Yuri I. , Weisel John W. , McCafferty Dewey G.
Published: July 2002

The peptide antibiotic ramoplanin inhibits bacterial peptidoglycan (PG) biosynthesis by interrupting late-stage membrane-associated glycosyltransferase reactions catalyzed by the transglycosylase and MurG enzymes. The mechanism of ramoplanin involves sequestration of lipid-anchored PG biosynthesis intermediates, physically occluding these substrates from proper utilization by these enzymes. In this report, we describe the first molecular-level details of the interaction of ramoplanin with PG biosynthesis intermediates. NMR analysis in conjunction with chemical dissection of the PG monomer revealed that the ramoplanin octapeptide
d
-Hpg-
d
-Orn-
d
-
allo
Thr-Hpg-
d
-Hpg-
allo
Thr-Phe-
d
-Orn recognizes MurNAc-Ala-γ-
d
-Glu pyrophosphate, the minimum component of PG capable of high-affinity complexation and fibril formation. Ramoplanin therefore recognizes a PG binding locus different from the
N
-acyl-
d
-Ala-
d
-Ala moiety targeted by vancomycin. Because ramoplanin is structurally less complex than glycopeptide antibiotics such as vancomycin, peptidomimetic chemotherapeutics derived from this recognition sequence may find future use as antibiotics against vancomycin-resistant
Enterococcus faecium
, methicillin-resistant
Staphylococcus aureus
, and related pathogens.
Positive selection of self-MHC-reactive T cells by individual peptide–MHC class II complexes
Authors: Barton Gregory M. , Beers Courtney , deRoos Paul , Eastman Susan R. , Gomez Marcela E. , Forbush Katherine A. , Rudensky Alexander Y.
Published: July 2002

If T cells require specific interactions with MHC-bound peptides during positive selection, then the specificities of T cells selected by one peptide should be distinct from those selected by another. We have examined positive selection of CD4 T cells in four strains of mice, each overexpressing a different peptide–1-A
b
(A
b
) complex. We show that a subset of CD4 T cells is selected by the overexpressed peptide and that the specificities of the CD4 T cells, as measured by reactivity to wild-type antigen-presenting cells, vary greatly depending on which peptide is overexpressed. These differences in specificity are mediated through positive selection not negative selection. Each of the four peptide–A
b
complexes appears to adopt a different conformation, and these differences correlate with the differences in reactivity. Our results suggest that individual peptide–MHC complexes positively select different subsets of self-MHC-reactive T cells and that the conformation of the peptide–MHC complex may contribute to this process.
The RecA proteins of
Deinococcus radiodurans
and
Escherichia coli
promote DNA strand exchange via inverse pathways
Authors: Kim Jong-Il , Cox Michael M.
Published: July 2002

The RecA protein of
Escherichia coli
, and all filament-forming homologues identified to date, promote DNA strand exchange by a common, ordered pathway. A filament is first formed on single-stranded DNA, followed by uptake of the duplex substrate. These proteins are thereby targeted to single-strand gaps and tails where recombinational DNA repair is required. The observed course of DNA strand exchange promoted by the RecA protein from the extremely radioresistant bacterium
Deinococcus radiodurans
is the exact inverse of this established pathway. This reaction lies at the heart of a remarkably efficient system for the repair of DNA damage.
pRB binds to and modulates the transrepressing activity of the E1A-regulated transcription factor p120

E4F
Authors: Fajas Lluis , Paul Conception , Zugasti Olivier , Le Cam Laurent , Polanowska Jolanta , Fabbrizio Eric , Medema René , Vignais Marie-Luce , Sardet Claude
Published: July 2002

The retinoblastoma protein pRB is involved in the transcriptional control of genes essential for cell cycle progression and differentiation. pRB interacts with different transcription factors and thereby modulates their activity by sequestration, corepression, or activation. We report that pRB, but not p107 and p130, binds to and facilitates repression by p120

E4F

, a ubiquitously expressed GLI-Kruppel-related protein identified as a cellular target of E1A. The interaction involves two distinct regions of p120

E4F

and the C-terminal part of pRB.
In vivo
pRB–p120

E4F

complexes can only be detected in growth-arrested cells, and accordingly contain the hypophosphorylated form of pRB. Repression of an E4F-responsive promoter is strongly increased by combined expression of p120

E4F

and pRB, which correlates with pRB-dependent enhancement of p120

E4F

binding activity. Elevated levels of p120

E4F

have been shown to block growth of mouse fibroblasts in G
1
. We find this requires pRB, because
RB
−/−
fibroblasts are significantly less sensitive to excess p120

E4F

.
Nuclear hormone receptor CHR3 is a critical regulator of all four larval molts of the nematodeCaenorhabditis elegans
Authors: Kostrouchova Marta , Krause Michael , Kostrouch Zdenek , Rall Joseph Edward
Published: July 2002

CHR3 (nhr-23, NF1F4), the homologue ofDrosophilaDHR3 and mammalian ROR/RZR/RevErbA nuclear hormone receptors, is important for proper epidermal development and molting in the nematodeCaenorhabditis elegans. Disruption of CHR3 (nhr-23) function leads to developmental changes, including incomplete molting and a short, fat (dumpy) phenotype. Here, we studied the role of CHR3 during larval development by using expression assays and RNA-mediated interference. We show that the levels of expression of CHR3 (nhr-23) cycle during larval development and reduction of CHR3 function during each intermolt period result in defects at all subsequent molts. Assaying candidate gene expression in populations of animals treated with CHR3 (nhr-23) RNA-mediated interference has identifieddpy-7as a potential gene acting downstream of CHR3. These results define CHR3 as a critical regulator of allC. elegansmolts and begin to define the molecular pathway for its function.
Biosynthesis of terpenoids: 4-Diphosphocytidyl-2-
C
-methyl-
d
-erythritol kinase from tomato
Authors: Rohdich Felix , Wungsintaweekul Juraithip , Lüttgen Holger , Fischer Markus , Eisenreich Wolfgang , Schuhr Christoph A. , Fellermeier Monika , Schramek Nicholas , Zenk Meinhart H. , Bacher Adelbert
Published: July 2002

The putative catalytic domain (residues 81–401) of a predicted tomato protein with similarity to 4-diphosphocytidyl-2-
C
-methyl-
d
-erythritol kinase of
Escherichia coli
was expressed in a recombinant
E. coli
strain. The protein was purified to homogeneity and was shown to catalyze the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2-
C
-methyl-
d
-erythritol at a rate of 33 μmol⋅mg
−1
⋅min
−1
. The structure of the reaction product, 4-diphosphocytidyl-2-
C
-methyl-
d
-erythritol 2-phosphate, was established by NMR spectroscopy. Divalent metal ions, preferably Mg
2+
, are required for activity. Neither the tomato enzyme nor the
E. coli
ortholog catalyzes the phosphorylation of isopentenyl monophosphate.