bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental evidence of correctness of improved model of ferroelectric planar capacitor
Authors: Vendik O. G. , Razumov S. V. , Tumarkin A. V. , Nikol’skii M. A. , Gaidukov M. M. , Gagarin A. G.
Published: January 2005

Planar capacitors, consisting of a thin (≈1μm) ferroelectric film and a dielectric substrate, widely used at microwaves, are normally designed on the basis of the conformal mapping technique and the use of the traditional formula for electric field in the capacitor gap: E=U∕s. U is applied voltage and s is the width of the gap. The important characteristic of the planar capacitor is its tunability defined as n=C(0)∕C(U). The dependence of the tunability on the ferroelectric film thickness (hf) has been experimentally investigated. The saturation or feebly marked maximum on the dependence of n on hf was observed. The appearance of the maximum can be explained using the corrected formula for the field in the gap: E≅U∕(s+hf). The formula was earlier theoretically developed on the basis of minimization of the free energy accumulated in the planar capacitor and using the Ginzburg–Devonshire equation for the nonlinear polarization of the ferroelectric film. The result should be considered as a correction of the model of a planar capacitor based on the conformal mapping technique.
Coherent array of white-light continuum filaments produced by diffractive microlenses
Authors: Cook K. , McGeorge R. , Kar A. K. , Taghizadeh M. R. , Lamb R. A.
Published: January 2005

The generation of a regular arrangement of stable, coherent white-light continuum filaments in B270 crown glass is observed by using an array of diffractive microlenses. Each lens allows the formation of between one and four filaments originating from aberrations induced by the focusing geometry. These filament groups generate very stable interference fringes in the far field.
Vortex avalanche phenomena in MgB2 superconducting film studied by current noise measurements
Authors: Eggenhöffner R. , Celasco E. , Ferrando V. , Celasco M.
Published: January 2005

Vortex avalanche phenomenon enhanced by thermomagnetic instabilities suppresses critical current in MgB2 films. This effect is investigated at 4.2K by spectral noise power measurements up to 1kHz with a dc superconducting quantum interference device apparatus. 1∕fγ behavior is shown at low frequencies in magnetic fields and feeding currents below jc. γ increases from 1 to 2 at increasing magnetic field, typical of fluxon avalanche processes. A peak in the power spectrum frequency behavior, observed only in magnetic field, is attributed to vortex–antivortex annihilations. Thermal instabilities disappear when an efficient thermal link to the He bath is attained and no vortex avalanche extra-noise is observed.
Carrier transport and light-spot movement in carbon-nanotube infrared emitters
Authors: Guo Jing , Alam Muhammad A.
Published: January 2005

Infrared emission from a carbon-nanotube (CNT) field-effect transistor, with the position of the light spot controlled by applied bias, was recently reported. In this letter, a self-consistent simulation, which couples a quantum treatment of the metal–CNT contacts to a semiclassical treatment of the channel, is performed to understand carrier transport and light emission in a CNT infrared emitter. The results show that when the channel is long, light emission significantly affects carrier transport, and reduces the source–drain current by a factor of 2 in ambipolar transport regime. The experimentally observed light-spot movement along the channel can be mostly understood and explained by a simple, semiclassical picture.
Near-field optical microscopy with a scanning tunneling microscope
Authors: Barbara A. , López-Ríos T. , Quémerais P.
Published: January 2005

A homemade apertureless near-field optical microscope using a scanning tunneling microscope (STM) is described. The experimental set-up simultaneously provides optical and topographic images of the sample. Technical details and features of the set-up are presented, together with results demonstrating the sub-wavelength resolution achieved as well as its sensitivity to dielectric contrasts. We show that the use of a STM permits to precisely control very small distances between the tip and the sample which is a great advantage to excite localized optical resonances between the tip and the surface.
Electrically commanded surfaces for nematic liquid crystal displays
Authors: Komitov Lachezar , Helgee Bertil , Felix Johan , Matharu Avtar
Published: January 2005

Electrically commanded surfaces (ECS) is a liquid crystal display concept whereby the switching of the alignment layer, which is driven by an electric field applied across the layer, is further transferred to the bulk liquid crystal material via elastic forces. This work presents the electro-optic response of a sandwich cell with alignment layer made of siloxane-based ferroelectric liquid crystal polymer, representing the ECS. The bulk liquid crystal material of choice was an in-house nematic mixture comprising fluorinated liquid crystalline compounds with negative dielectric anisotropy (Δε<0). We report a distinct linear electro-optic response, arising from the field-induced in-plane switching of the nematic which in turn is mediated by the ECS.
AlGaInP laser diodes incorporating a 3λ∕4 multiple quantum barrier
Authors: Sobiesierski A. , Sandall I. C. , Smowton P. M. , Blood P. , Krysa A. B. , Brown M. R. , Teng K. S. , Wilks S. P.
Published: January 2005

Using segmented contact measurements to determine gain versus quasi-Fermi level separation and nonradiative recombination we demonstrate that placing a multiquantum barrier (MQB) within the p-type cladding of 670 nm AlGaInP laser diodes reduces electron leakage current as a function of quasi-Fermi level separation compared to otherwise identical reference devices. At 300 K, where thermally activated leakage is absent, devices with and without a MQB have the same threshold current density whereas at 375 K the threshold current density of a 320 μm laser is reduced by 1735±113Acm−2 for the device containing the MQB.
Large electrostriction near the solubility limit in BaTiO3–CaTiO3 ceramics
Authors: Wang Xusheng , Yamada Hiroshi , Xu Chao-Nan
Published: January 2005

This study prepared (1−x)BaTiO3–xCaTiO3 (x=0.20–1.0) ceramics. Their structural and electric properties were analyzed. High electrostrictive strain of 0.22%, higher by 157% as compared to BaTiO3 ceramic, was obtained near the solubility limit in the side of composite (x=0.23), which is a diphasic ceramic composed of a ferroelectric tetragonal Ba0.8Ca0.2TiO3 solid solution and a normal dielectric orthorhombic Ba0.07Ca0.93TiO3 solid solution. This enhanced electrostriction resulted from the coupling of the large ionic polarization in Ba0.07Ca0.93TiO3 with the non-180° domains in Ba0.8Ca0.2TiO3 during the external electric field exertion.
Formation of binary phase gratings in photopolymer-liquid crystal composites by a surface-controlled anisotropic phase separation
Authors: Park Jae-Hong , Khoo Iam Choon , Yu Chang-Jae , Jung Min-Sik , Lee Sin-Doo
Published: January 2005

We report on formation of binary phase gratings in photopolymer-liquid crystal (PLC) composites using a surface-controlled phase separation method. The binary nature of the PLC phase gratings is produced by employing a single step photo-ablation through an amplitude photomask which precisely controls the interfacial interactions between the LC and the photopolymer on the alignment layer. A subsequent illumination of the ultraviolet light onto the whole PLC promotes an anisotropic phase separation resulting in the formation of distinct binary patterns for the PLC structure. The electrically tunable diffraction properties of the binary phase gratings are presented.
Observation of trapping defects in 4H–silicon carbide metal-oxide-semiconductor field-effect transistors by spin-dependent recombination
Authors: Meyer David J. , Lenahan Patrick M. , Lelis Aivars J.
Published: January 2005

We utilize a highly sensitive electron spin resonance technique called spin-dependent recombination to observe deep level dangling bond centers at and very near the SiC∕SiO2 interface in fully processed n-channel 4H–SiC lateral metal-oxide-semiconductor field-effect transistors. The axially symmetric g tensor of the largest signal strongly suggests that the responsible defect is a dangling bond center with the dangling bond orbital pointing along the crystalline c axis.
Direct observation of self-heating in intrinsic Josephson junction array with a nanoelectrode in the middle
Authors: Wang H. B. , Hatano T. , Yamashita T. , Wu P. H. , Müller P.
Published: January 2005

Modifying the double-sided fabrication method we invented a few years ago, a new type of Bi2Sr2CaCu2O8 intrinsic Josephson junction (IJJs) array is explored in which, in addition to the indispensable top and bottom electrodes, there is an electrode only 100 nm thick fabricated in the middle of the array. This electrode provides easy access to the inside of the IJJs, enabling us to understand the device physics better than was possible before. As the first application of such a new device, we have clearly shown how “hot” a junction stack can be under various bias conditions.
Toward ultracompact pseudospark switches
Authors: Jiang Chunqi , Kuthi Andras , Gundersen Martin A.
Published: January 2005

This letter reports studies of small pseudospark switches wherein the volume is reduced by one order of magnitude relative to the smallest previously reported versions operating with a peak current >1kA. In preliminary testing, the switch holds off >20kV with a peak current >4kA and a pulse duration of 150 ns. The switch was operated in an optically triggered mode (backlighted thyratron) with helium fill for >106 discharges at 13.5 kV and 3.3 kA, with 0.5 mC transfer per pulse, at a repetition rate of 10 Hz without significant decay of switch performance. Preliminary observations indicate that the device operates in a superemissive cathode mode, demonstrating a pathway towards ultracompact superemissive cathode switches for repetitive pulsed power applications.
Near-field enhanced imaging by a magnetized ferrite slab
Authors: Marqués R. , Mesa F. , Medina F.
Published: January 2005

This letter demonstrates the near-field imaging enhancement at microwave frequencies of two-dimensional sources by a ferrite slab magnetized to saturation. It is shown that this effect is based on the nonreciprocal amplification of magnetostatic surface waves (MSSW) across the ferrite slab. The inclusion of losses in our analysis has also made it possible to prove this effect for realistic yttrium iron garnet ferrite samples. For ferrite slabs of width d, the resolution at the image plane (at a distance 2d from the source) is better than the resolution in air at a distance d of the source, which leads to an equivalent air length of the ferrite slab less than zero. Since the constitutive parameters of saturated ferrites depend on the external magnetizing field, the operation frequency of the proposed imaging devices can be tuned by varying this biasing field.
Reversion by ozone treatment of acute nephrotoxicity induced by cisplatin in rats
Authors: González Ricardo , Borrego Aluet , Zamora Zullyt , Romay Cheyla , Hernández Frank , Menéndez Silvia , Montero Teresita , Rojas Enis
Published: January 2005

BACKGROUND: Ozone therapy has become a useful treatment for pathological processes, in which the damage mediated by reactive oxygen species is involved. Several lines of evidence suggest that cisplatin‐induced acute nephrotoxicity is partially mediated by reactive oxygen species.

Aims: To analyze the effect of ozone administration after cisplatin‐induced acute nephrotoxicity.

Methods: Male Sprague‐Dawley rats were treated with five intra‐rectal applications of ozone/oxygen mixture at 0.36, 1.1 and 1.8 mg/kg after cisplatin intraperitoneal injection (6 mg/kg). Serum and kidneys were taken off 5 days after cisplatin treatment. Creatinine was measured in the serum and the activities of antioxidant enzymes and thiobarbituric acid reactive substances and glutathione content were analyzed in renal homogenate.

Results: Ozone treatment diminished the increase in serum creatinine levels, the glutathione depletion and also reversed the inhibition of superoxide dismutase, catalase and glutathione peroxidase activities induced by cisplatin in the rat kidney. Also, the renal content of thiobarbituric reactive substances was decreased by ozone/oxygen mixture applied after cisplatin.

Conclusion: Intrarectal applications of ozone reversed the renal pro‐oxidant unbalance induced by cisplatin treatment by the way of stimulation to some constituents of antioxidant system in the kidney, and thereby it decreased the renal damage.
Physical landscapes in biological membranes: physico–chemical terrains for spatio–temporal control of biomolecular interactions and behaviour
Authors: O'Shea Paul
Published: January 2005

The evolving complexities of biological membranes are discussed from the point of view of potential roles of the physical constitution of the membrane. These include features of the surface and dipole potentials and membrane ‘rafts’. These properties are outlined; they emphasize that protein–lipid and specific lipid environments are influential parameters in how biomolecular interactions may take place with and within membranes. Several fluorescence detection technologies directed towards measurement of these properties are also outlined that permit high–resolution experimental determination of intermolecular interactions with membranes by measuring small changes of these potentials. These point to the possibility that the membrane dipole potential in particular is enormously influential in determining the behaviour of receptor and signalling systems within membrane rafts, and offers the means of a novel mechanism for biological control.
Dynamics of actomyosin interactions in relation to the cross-bridge cycle
Authors: Holmes K. C. , Trentham D. R. , Simmons R. , Zeng Wei , Conibear Paul B. , Dickens Jane L. , Cowie Ruth A. , Wakelin Stuart , Málnási–Csizmadia András , Bagshaw Clive R.
Published: January 2005

Transient kinetic measurements of the actomyosin ATPase provided the basis of the Lymn–Taylor model for the cross–bridge cycle, which underpins current models of contraction. Following the determination of the structure of the myosin motor domain, it has been possible to introduce probes at defined sites and resolve the steps in more detail. Probes have been introduced in the
Dicytostelium
myosin II motor domain via three routes: (i) single tryptophan residues at strategic locations throughout the motor domain; (ii) green fluorescent protein fusions at the N and C termini; and (iii) labelled cysteine residues engineered across the actin–binding cleft. These studies are interpreted with reference to motor domain crystal structures and suggest that the tryptophan (W501) in the relay loop senses the lever arm position, which is controlled by the switch 2 open–to–closed transition at the active site. Actin has little effect on this process
per se
. A mechanism of product release is proposed in which actin has an indirect effect on the switch 2 and lever arm position to achieve mechanochemical coupling. Switch 1 closing appears to be a key step in the nucleotide–induced actin dissociation, while its opening is required for the subsequent activation of product release. This process has been probed with F239W and F242W substitutions in the switch 1 loop. The E706K mutation in skeletal myosin IIa is associated with a human myopathy. To simulate this disease we investigated the homologous mutation, E683K, in the
Dictyostelium
myosin motor domain.
Mice exclusively expressing the short isoform of Smad2 develop normally and are viable and fertile
Authors: Dunn N. Ray , Koonce Chad H. , Anderson Dorian C. , Islam Ayesha , Bikoff Elizabeth K. , Robertson Elizabeth J.
Published: January 2005

Smad2 and Smad3 are closely related effectors of TGFβ/Nodal/Activin-related signaling. Smad3 mutant mice develop normally, whereas Smad2 plays an essential role in patterning the embryonic axis and specification of definitive endoderm. Alternative splicing of Smad2 exon 3 gives rise to two distinct protein isoforms. The short Smad2(Δexon3) isoform, unlike full-length Smad2, Smad2(FL), retains DNA-binding activity. Here, we show that Smad2(FL) and Smad2(Δexon3) are coexpressed throughout mouse development. Directed expression of either Smad2(Δexon3) or Smad3, but not Smad2(FL), restores the ability of Smad2-deficient embryonic stem (ES) cells to contribute descendants to the definitive endoderm in wild-type host embryos. Mice engineered to exclusively express Smad2(Δexon3) correctly specify the anterior–posterior axis and definitive endoderm, and are viable and fertile. Moreover, introducing a human Smad3 cDNA into the mouse Smad2 locus similarly rescues anterior–posterior patterning and definitive endoderm formation and results in adult viability. Collectively, these results demonstrate that the short Smad2(Δexon3) isoform or Smad3, but not full-length Smad2, activates all essential target genes downstream of TGFβ-related ligands, including those regulated by Nodal.
FAST TRACK: Legacy lost: genetic variability and population size of extirpated US grey wolves (Canis lupus)
Authors: LEONARD JENNIFER A. , VILÀ CARLES , WAYNE ROBERT K.
Published: January 2005

By the mid 20th century, the grey wolf (Canis lupus) was exterminated from most of the conterminous United States (cUS) and Mexico. However, because wolves disperse over long distances, extant populations in Canada and Alaska might have retained a substantial proportion of the genetic diversity once found in the cUS. We analysed mitochondrial DNA sequences of 34 pre‐extermination wolves and found that they had more than twice the diversity of their modern conspecifics, implying a historic population size of several hundred thousand wolves in the western cUS and Mexico. Further, two‐thirds of the haplotypes found in the historic sample are unique. Sequences from Mexican grey wolves (C. l. baileyi) and some historic grey wolves defined a unique southern clade supporting a much wider geographical mandate for the reintroduction of Mexican wolves than currently planned. Our results highlight the genetic consequences of population extinction within Ice Age refugia and imply that restoration goals for grey wolves in the western cUS include far less area and target vastly lower population sizes than existed historically.
The molecular population genetics of the Tomato spotted wilt virus (TSWV) genome
Authors: TSOMPANA M. , ABAD J. , PURUGGANAN M. , MOYER J. W.
Published: January 2005

RNA viruses are characterized by high genetic variability resulting in rapid adaptation to new or resistant hosts. Research for plant RNA virus genetic structure and its variability has been relatively scarce compared to abundant research done for human and animal RNA viruses. Here, we utilized a molecular population genetic framework to characterize the evolution of a highly pathogenic plant RNA virus [Tomato spotted wilt virus (TSWV), Tospovirus, Bunyaviridae]. Data from genes encoding five viral proteins were used for phylogenetic analysis, and for estimation of population parameters, subpopulation differentiation, recombination, divergence between Tospovirus species, and selective constraints on the TSWV genome. Our analysis has defined the geographical structure of TSWV, attributed possibly to founder effects. Also, we identify positive selection favouring divergence between Tospovirus species. At the species level, purifying selection has acted to preserve protein function, although certain amino acids appear to be under positive selection. This analysis provides demonstration of population structuring and species‐wide population expansions in a multisegmented plant RNA virus, using sequence‐based molecular population genetic analyses. It also identifies specific amino acid sites subject to selection within Bunyaviridae and estimates the level of genetic heterogeneity of a highly pathogenic plant RNA virus. The study of the variability of TSWV populations lays the foundation in the development of strategies for the control of other viral diseases in floral crops.
Environmental and population dependency of genetic variability‐fitness correlations inRana temporaria
Authors: LESBARRÈRES DAVID , PRIMMER CRAIG R. , LAURILA ANSSI , MERILÄ JUHA
Published: January 2005

Considerable effort has been invested in studying the relationship between fitness and genetic variability. While evidence exists both for and against positive genetic variability–fitness correlations (GFC), the possible environment and population‐dependency of GFCs has seldom been tested. We investigated GFCs in common frog (Rana temporaria) tadpoles reared under different temperatures and feeding regimes in four replicate populations. Genetic variability in eight microsatellite loci in 238 parents was used to estimate heterozygosity (H) and mean expectedd2in 158‐sibships (4515 offspring). Generalized linear mixed model analyses of offspring fitness traits (survival to metamorphosis, developmental and growth rate) revealed that offspring survival probability was positively correlated withH, and that relationships were similar in all four populations tested. However, significant interaction between other genetic variability measures (d2, relatedness) and treatment conditions indicated that GFCs were detectable in some, but not in all environments. Interestingly, GFCs between survival and both heterozygosity and relatedness were most pronounced in stressful environments (i.e. limited food). Developmental and growth rates were significantly associated withd2but less withHand relatedness. Furthermore, many of these GFCs were population‐specific. These results suggest — in line with the contention that expression of inbreeding depression can be environment dependent — that GFCs can also be highly sensitive to the environmental conditions under which they are measured. The results further suggest that the observed positive correlation betweenHand survival probability is likely to be explainable by the ‘general’, rather than by the ‘local’ or ‘direct’ effect hypotheses.
Mating system of the Eurasian badger,Meles meles, in a high density population
Authors: CARPENTER PETRA J. , POPE LISA C. , GREIG CAROLYN , DAWSON DEBORAH A. , ROGERS LUCY M. , ERVEN KRISTIEN , WILSON GAVIN J. , DELAHAY RICHARD J. , CHEESEMAN CHRIS L. , BURKE TERRY
Published: January 2005

Badgers are facultatively social, forming large groups at high density. Group‐living appears to have high reproductive costs for females, and may lead to increased levels of inbreeding. The extent of female competition for reproduction has been estimated from field data, but knowledge of male reproductive success and the extent of extra‐group paternity remains limited. Combining field data with genetic data (16 microsatellite loci), we studied the mating system of 10 badger social groups across 14 years in a high‐density population. From 923 badgers, including 425 cubs, we were able to assign maternity to 307 cubs, with both parents assigned to 199 cubs (47%) with 80% confidence, and 14% with 95% confidence. Age had a significant effect on the probability of reproduction, seemingly as a result of a deficit of individuals aged two years and greater than eight years attaining parentage. We estimate that approximately 30% of the female population successfully reproduced in any given year, with a similar proportion of the male population gaining paternity across the same area. While it was known there was a cost to female reproduction in high density populations, it appears that males suffer similar, but not greater, costs. Roughly half of assigned paternity was attributed to extra‐group males, the majority of which were from neighbouring social groups. Few successful matings occurred between individuals born in the same social group (22%). The high rate of extra‐group mating, previously unquantified, may help reduce inbreeding, potentially making philopatry a less costly strategy.
Evidence for male dispersal along the coasts but no migration in pelagic waters in dusky dolphins (Lagenorhynchus obscurus)
Authors: CASSENS INSA , VAN WAEREBEEK KOEN , BEST PETER B. , TZIKA ATHANASIA , VAN HELDEN ANTON L. , CRESPO ENRIQUE A. , MILINKOVITCH MICHEL C.
Published: January 2005

Using nine nuclear species‐specific microsatellite loci and two mitochondrial gene fragments (cytochrome b and control region), we investigated the processes that have shaped the geographical distribution of genetic diversity exhibited by contemporary dusky dolphin (Lagenorhynchus obscurus) populations. A total of 221 individuals from four locations (Peru, Argentina, southern Africa, and New Zealand) were assayed, covering most of the species’ distribution range. Although our analyses identify a general demographic decline in the Peruvian dusky dolphin stock (recently affected by high natural and human‐induced mortality levels), comparison between the different molecular markers hint at an ancient bottleneck that predates recent El Niño oscillations and human exploitation. Moreover, we find evidence of a difference in dispersal behaviour of dusky dolphins along the South American coast and across the Atlantic. While data in Peruvian and Argentine waters are best explained by male‐specific gene flow between these two populations, our analyses suggest that dusky dolphins from Argentina and southern Africa recently separated from an ancestral Atlantic population and, since then, diverged without considerable gene flow. The inclusion of a few New Zealand samples further confirms the low levels of genetic differentiation among most dusky dolphin populations. Only the Peruvian dusky dolphin stock is highly differentiated, especially at mitochondrial loci, suggesting that major fluctuations in its population size have led to an increased rate of genetic drift.
Spatially‐focussed melt formation in aluminous metapelites from Broken Hill, Australia
Authors: WHITE R. W. , POWELL R. , HALPIN J. A.
Published: January 2005

Large garnet poikiloblasts hosted by leucosome in metapelitic gneiss from Broken Hill reflect complex mineral–melt relationships. The spatial relationship between the leucosomes and the garnet poikiloblasts implies that the growth of garnet was strongly linked to the production of melt. The apparent difficulty of garnet to nucleate a large number of grains during the prograde breakdown of coexisting biotite and sillimanite led to the spatial focussing of melting reactions around the few garnet nuclei that formed. Continued reaction of biotite and sillimanite required diffusion of elements from where minerals were reacting to sites of garnet growth. This diffusion was driven by chemical potential gradients between garnet‐bearing and garnet‐absent parts of the rock. As a consequence, melt and peritectic K‐feldspar also preferentially formed around the garnet. The diffusion of elements led to the chemical partitioning of the rock within an overall context in which equilibrium may have been approached. Thus, the garnet‐bearing leucosomes record in situ melt formation around garnet porphyroblasts rather than centimetre‐scale physical melt migration and segregation. The near complete preservation of the high‐grade assemblages in the mesosome and leucosome is consistent with substantial melt loss. Interconnected networks between garnet‐rich leucosomes provide the most likely pathway for melt migration. Decimetre‐scale, coarse‐grained, garnet‐poor leucosomes may represent areas of melt flux through a large‐scale melt transfer network.
KNOX homeobox genes potentially have similar function in both diploid unicellular and multicellular meristems, but not in haploid meristems
Authors: Sano Ryosuke , Juárez Cristina M. , Hass Barbara , Sakakibara Keiko , Ito Motomi , Banks Jo Ann , Hasebe Mitsuyasu
Published: January 2005

Summary
Members of the class 1 knotted‐like homeobox (KNOX) gene family are important regulators of shoot apical meristem development in angiosperms. To determine whether they function similarly in seedless plants, three KNOX genes (two class 1 genes and one class 2 gene) from the fern Ceratopteris richardii were characterized. Expression of both class 1 genes was detected in the shoot apical cell, leaf primordia, marginal part of the leaves, and vascular bundles by in situ hybridization, a pattern that closely resembles that of class 1 KNOX genes in angiosperms with compound leaves. The fern class 2 gene was expressed in all sporophyte tissues examined, which is characteristic of class 2 gene expression in angiosperms. All three CRKNOX genes were not detected in gametophyte tissues by RNA gel blot analysis. Arabidopsis plants overexpressing the fern class 1 genes resembled plants that overexpress seed plant class 1 KNOX genes in leaf morphology. Ectopic expression of the class 2 gene in Arabidopsis did not result in any unusual phenotypes. Taken together with phylogenetic analysis, our results suggest that (a) the class 1 and 2 KNOX genes diverged prior to the divergence of fern and seed plant lineages, (b) the class 1 KNOX genes function similarly in seed plant and fern sporophyte meristem development despite their differences in structure, (c) KNOX gene expression is not required for the development of the fern gametophyte, and (d) the sporophyte and gametophyte meristems of ferns are not regulated by the same developmental mechanisms at the molecular level.
Genome Sequence of the PCE-Dechlorinating BacteriumDehalococcoides ethenogenes
Authors: Seshadri Rekha , Adrian Lorenz , Fouts Derrick E. , Eisen Jonathan A. , Phillippy Adam M. , Methe Barbara A. , Ward Naomi L. , Nelson William C. , Deboy Robert T. , Khouri Hoda M. , Kolonay James F. , Dodson Robert J. , Daugherty Sean C. , Brinkac Lauren M. , Sullivan Steven A. , Madupu Ramana , Nelson Karen E. , Kang Katherine H. , Impraim Marjorie , Tran Kevin , Robinson Jeffrey M. , Forberger Heather A. , Fraser Claire M. , Zinder Stephen H. , Heidelberg John F.
Published: January 2005

Dehalococcoides ethenogenesis the only bacterium known to reductively dechlorinate the groundwater pollutants, tetrachloroethene (PCE) and trichloroethene, to ethene. Its 1,469,720âbase pair chromosome contains large dynamic duplicated regions and integrated elements. Genes encoding 17 putative reductive dehalogenases, nearly all of which were adjacent to genes for transcription regulators, and five hydrogenase complexes were identified. These findings, plus a limited repertoire of other metabolic modes, indicate thatD. ethenogenesis highly evolved to utilize halogenated organic compounds and H2. Diversification of reductive dehalogenase functions appears to have been mediated by recent genetic exchange and amplification. Genome analysis provides insights into the organism's complex nutrient requirements and suggests that an ancestor was a nitrogen-fixing autotroph.
Grain Boundary Decohesion by Impurity Segregation in a Nickel-Sulfur System
Authors: Yamaguchi Masatake , Shiga Motoyuki , Kaburaki Hideo
Published: January 2005

The sulfur-induced embrittlement of nickel has long been wrapped in mystery as to why and how sulfur weakens the grain boundaries of nickel and why a critical intergranular sulfur concentration is required. From first-principles calculations, we found that a large grain-boundary expansion is caused by a short-range overlap repulsion among densely segregated and neighboring sulfur atoms. This expansion results in a drastic grain-boundary decohesion that reduces the grain-boundary tensile strength by one order of magnitude. This decohesion may directly cause the embrittlement, because the critical sulfur concentration of this decohesion agrees well with experimental data on the embrittlement.
Biofilm Formation by
Escherichia coli
O157:H7 on Stainless Steel: Effect of Exopolysaccharide and Curli Production on Its Resistance to Chlorine
Authors: Ryu Jee-Hoon , Beuchat Larry R.
Published: January 2005

The resistance of
Escherichia coli
O157:H7 strains ATCC 43895-, 43895-EPS (an exopolysaccharide [EPS]-overproducing mutant), and ATCC 43895+ (a curli-producing mutant) to chlorine, a sanitizer commonly used in the food industry, was studied. Planktonic cells of strains 43895-EPS and/or ATCC 43895+ grown under conditions supporting EPS and curli production, respectively, showed the highest resistance to chlorine, indicating that EPS and curli afford protection. Planktonic cells (ca. 9 log
10
CFU/ml) of all strains, however, were killed within 10 min by treatment with 50 μg of chlorine/ml. Significantly lower numbers of strain 43895-EPS, compared to those of strain ATCC 43895-, attached to stainless steel coupons, but the growth rate of strain 43895-EPS on coupons was not significantly different from that of strain ATCC 43895-, indicating that EPS production did not affect cell growth during biofilm formation. Curli production did not affect the initial attachment of cells to coupons but did enhance biofilm production. The resistance of
E. coli
O157:H7 to chlorine increased significantly as cells formed biofilm on coupons; strain ATCC 43895+ was the most resistant. Population sizes of strains ATCC 43895+ and ATCC 43895- in biofilm formed at 12°C were not significantly different, but cells of strain ATCC 43895+ showed significantly higher resistance than did cells of strain ATCC 43895-. These observations support the hypothesis that the production of EPS and curli increase the resistance of
E. coli
O157:H7 to chlorine.
Microbial Desulfurization of Gasoline in a
Mycobacterium goodii
X7B Immobilized-Cell System
Authors: Li Fuli , Xu Ping , Feng Jinhui , Meng Ling , Zheng Yuan , Luo Lailong , Ma Cuiqing
Published: January 2005

Mycobacterium goodii
X7B, which had been primarily isolated as a bacterial strain capable of desulfurizing dibenzothiophene to produce 2-hydroxybiphenyl via the 4S pathway, was also found to desulfurize benzothiophene. The desulfurization product was identified as
o
-hydroxystyrene by gas chromatography (GC)-mass spectrometry analysis. This strain appeared to have the ability to remove organic sulfur from a broad range of sulfur species in gasoline. When Dushanzi straight-run gasoline (DSRG227) containing various organic sulfur compounds was treated with immobilized cells of strain X7B for 24 h, the total sulfur content significantly decreased, from 227 to 71 ppm at 40°C. GC flame ionization detection and GC atomic emission detection analysis were used to qualitatively evaluate the effects of
M. goodii
X7B treatment on the contents of gasoline. In addition, when immobilized cells were incubated at 40°C with DSRG275, the sulfur content decreased from 275 to 54 ppm in two consecutive reactions. With this excellent efficiency, strain X7B is considered a good potential candidate for industrial applications for the biodesulfurization of gasoline.
Starch-Binding Domain Affects Catalysis in Two
Lactobacillus
α-Amylases
Authors: Rodríguez-Sanoja R. , Ruiz B. , Guyot J. P. , Sanchez S.
Published: January 2005

A new starch-binding domain (SBD) was recently described in α-amylases from three lactobacilli (
Lactobacillus amylovorus
,
Lactobacillus plantarum
, and
Lactobacillus manihotivorans
). Usually, the SBD is formed by 100 amino acids, but the SBD sequences of the mentioned lactobacillus α-amylases consist of almost 500 amino acids that are organized in tandem repeats. The three lactobacillus amylase genes share more than 98% sequence identity. In spite of this identity, the SBD structures seem to be quite different. To investigate whether the observed differences in the SBDs have an effect on the hydrolytic capability of the enzymes, a kinetic study of
L. amylovorus
and
L. plantarum
amylases was developed, with both enzymes acting on several starch sources in granular and gelatinized forms. Results showed that the amylolytic capacities of these enzymes are quite different; the
L. amylovorus
α-amylase is, on average, 10 times more efficient than the
L. plantarum
enzyme in hydrolyzing all the tested polymeric starches, with only a minor difference in the adsorption capacities.
Intracellular Butyryl Phosphate and Acetyl Phosphate Concentrations in
Clostridium acetobutylicum
and Their Implications for Solvent Formation
Authors: Zhao Yinsuo , Tomas Christopher A. , Rudolph Fredrick B. , Papoutsakis Eleftherios T. , Bennett George N.
Published: January 2005

It has been suggested (L. H. Harris, R. P. Desai, N. E. Welker, and E. T. Papoutsakis, Biotechnol. Bioeng.
67:
1-11, 2000) that butyryl phosphate (BuP) is a regulator of solventogenesis in
Clostridium acetobutylicum
. Here, we determined BuP and acetyl phosphate (AcP) levels in fermentations of
C. acetobutylicum
wild type (WT), degenerate strain M5, a butyrate kinase (
buk
) mutant, and a phosphotransacetylase (
pta
) mutant. A sensitive method was developed to measure BuP and AcP in the same sample. Compared to the WT, the
buk
mutant had higher levels of BuP and AcP; the BuP levels were high during the early exponential phase, and there was a peak corresponding to solvent production. Consistent with this, solvent formation was initiated significantly earlier and was much stronger in the
buk
mutant than in all other strains. For all strains, initiation of butanol formation corresponded to a BuP peak concentration that was more than 60 to 70 pmol/g (dry weight), and higher and sustained levels corresponded to higher butanol formation fluxes. The BuP levels never exceeded 40 to 50 pmol/g (dry weight) in strain M5, which produces no solvents. The BuP profiles were bimodal, and there was a second peak midway through solventogenesis that corresponded to carboxylic acid reutilization. AcP showed a delayed single peak during late solventogenesis corresponding to acetate reutilization. As expected, in the
pta
mutant the AcP levels were very low, yet this strain exhibited strong butanol production. These data suggest that BuP is a regulatory molecule that may act as a phosphodonor of transcriptional factors. DNA array-based transcriptional analysis of the
buk
and M5 mutants demonstrated that high BuP levels corresponded to downregulation of flagellar genes and upregulation of solvent formation and stress genes.
Starvation for Different Nutrients in
Escherichia coli
Results in Differential Modulation of RpoS Levels and Stability
Authors: Mandel Mark J. , Silhavy Thomas J.
Published: January 2005

Levels of RpoS increase upon glucose starvation in
Escherichia coli
, which leads to the transcription of genes whose products combat a variety of stresses. RpoS stability is a key level of control in this process, as SprE (RssB)-mediated degradation is inhibited under glucose starvation. Starvation for ammonia or phosphate also results in increased stress resistance and induction of RpoS-dependent genes. However, we demonstrate that RpoS levels following ammonia starvation are only slightly increased compared to growing cells and are 10-fold below the levels observed under glucose or phosphate limitation. This difference is largely due to regulated proteolysis of RpoS, as its stability in ammonia-starved cells is intermediate between that in logarithmic-phase cells and glucose-starved cells. Use of an
rpoS
construct that is devoid of the gene's native transcriptional and translational control regions reveals that stability differences are sufficient to explain the different levels of RpoS observed in logarithmic phase, ammonia starvation, and glucose starvation. Under phosphate starvation, however,
rpoS
translation is increased. The cellular response to nutrient limitation is much more complex than previously appreciated, as there is not simply one response that is activated by starvation for any essential nutrient. Our data support the hypothesis that SprE activity is the key level at which ammonia and glucose starvation signals are transmitted to RpoS, and they suggest that carbon source and/or energy limitation are necessary for full inactivation of the SprE pathway.
Interaction between Components of the Type III Secretion System ofChlamydiaceae
Authors: Slepenkin Anatoly , de la Maza Luis M. , Peterson Ellena M.
Published: January 2005

Members of the familyChlamydiaceaepossess at least 13 genes, distributed throughout the chromosome, that are homologous with genes of known type III secretion systems (TTS). The aim of this study was to use putative TTS proteins ofChlamydophila pneumoniae, whose equivalents in other bacterial TTS function as chaperones, to identify interactions between chlamydial proteins. Using the BacterioMatch Two-Hybrid Vector system (Stratagene, La Jolla, Calif.),lcrH-2andsycE, positions 1021 and 0325, respectively, fromC. pneumoniaeCM-1 were used as “bait” to identify target genes (positions 0324, 0705, 0708, 0808 to 0810, 1016 to 1020, and 1022) in close proximity on the chromosome. Interaction between the products of thelcrH-2(1021) andlcrE(copN) (0324) genes was detected and confirmed by pull-down experiments and enzyme immunoassays using recombinant LcrH-2 and LcrE. As further confirmation of this interaction, the homologous genes fromChlamydia trachomatis, serovar E, andChlamydophila psittaci, Texas turkey, were also cloned in the two-hybrid system to determine if LcrH-2 and LcrE would interact with their orthologs in other species. Consistent with their genetic relatedness, LcrH-2 fromC. pneumoniaeinteracted with LcrE produced from the three species ofChlamydiaceae; LcrH-2 fromC. psittacireacted with LcrE fromC. pneumoniaebut not fromC. trachomatis; andC. trachomatisLcrH-2 did not react with LcrE from the other two species. Deletions from the N and C termini of LcrE fromC. pneumoniaeidentified the 50 C-terminal amino acids as essential for the interaction with LcrH-2. Thus, it appears that in theChlamydiaceaeTTS, LcrH-2 interacts with LcrE, and therefore it may serve as a chaperone for this protein.
Nature of the Promoter Activated by C.PvuII, an Unusual Regulatory Protein Conserved among Restriction-Modification Systems
Authors: Knowle Dieter , Lintner Robert E. , Touma Yara M. , Blumenthal Robert M.
Published: January 2005

A widely distributed family of small regulators, called C proteins, controls a subset of restriction-modification systems. The C proteins studied to date activate transcription of their own genes and that of downstream endonuclease genes; this arrangement appears to delay endonuclease expression relative to that of the protective methyltransferase when the genes enter a new cell. C proteins bind to conserved sequences called C boxes. In the PvuII system, the C boxes have been reported to extend from −23 to +3 relative to the transcription start for the gene for the C protein, an unexpected starting position relative to a bound activator. This study suggests that transcript initiation within the C boxes represents initial, C-independent transcription ofpvuIICR. The major C protein-dependent transcript appears to be a leaderless mRNA starting farther downstream, at the initiation codon for thepvuIICgene. This conclusion is based on nuclease S1 transcript mapping and the effects of a series of nested deletions in the promoter region. Furthermore, replacing the region upstream of thepvuIICinitiation codon with a library of random oligonucleotides, followed by selection for C-dependent transcription, yielded clones having sequences that resemble −10 promoter hexamers. The −35 hexamer of this promoter would lie within the C boxes. However, the spacing between C boxes/−35 and the apparent −10 hexamer can be varied by ±4 bp with little effect. This suggests that, like some other activator-dependent promoters, PpvuIICRmay not require a −35 hexamer. Features of this transcription activation system suggest explanations for its broad host range.
The
N
5
-Glutamine
S
-Adenosyl-
l
-Methionine-Dependent Methyltransferase PrmC/HemK in
Chlamydia trachomatis
Methylates Class 1 Release Factors
Authors: Pannekoek Yvonne , Heurgué-Hamard Valérie , Langerak Ankie A. J. , Speijer Dave , Buckingham Richard H. , van der Ende Arie
Published: January 2005

The gene
prmC
, encoding the putative
S
-adenosyl-
l
-methionine (AdoMet)-dependent methyltransferase (MTase) of release factors (RFs) of the obligate intracellular pathogen
Chlamydia trachomatis
, was functionally analyzed. Chlamydial PrmC expression suppresses the growth defect of a
prmC
knockout strain of
Escherichia coli
K-12, suggesting an interaction of chlamydial PrmC with
E. coli
RFs in vivo. In vivo methylation assays carried out with recombinant PrmC and RFs of chlamydial origin demonstrated that PrmC methylates RFs within the tryptic fragment containing the universally conserved sequence motif Gly-Gly-Gln. This is consistent with the enzymatic properties of PrmC of
E. coli
origin. We conclude that
C. trachomatis
PrmC functions as an
N
5
-glutamine AdoMet-dependent MTase, involved in methylation of RFs.
Comparative Genomics of
Staphylococcus aureus
Musculoskeletal Isolates
Authors: Cassat James E. , Dunman Paul M. , McAleese Fionnuala , Murphy Ellen , Projan Steven J. , Smeltzer Mark S.
Published: January 2005

Much of the research aimed at defining the pathogenesis of
Staphylococcus aureus
has been done with a limited number of strains, most notably the 8325-4 derivative RN6390. Several lines of evidence indicate that this strain is unique by comparison to clinical isolates of
S. aureus
. Based on this, we have focused our efforts on two clinical isolates (UAMS-1 and UAMS-601), both of which are hypervirulent in our animal models of musculoskeletal infection. In this study, we used comparative genomic hybridization to assess the genome content of these two isolates relative to RN6390 and each of seven sequenced
S. aureus
isolates. Our comparisons were done by using an amplicon-based microarray from the Pathogen Functional Genomics Resource Center and an Affymetrix GeneChip that collectively represent the genomes of all seven sequenced strains. Our results confirmed that UAMS-1 and UAMS-601 share specific attributes that distinguish them from RN6390. Potentially important differences included the presence of
cna
and the absence of
isaB, sarT, sarU
, and
sasG
in the UAMS isolates. Among the sequenced strains, the UAMS isolates were most closely related to the dominant European clone EMRSA-16. In contrast, RN6390, NCTC 8325, and COL formed a distinct cluster that, by comparison to the other four sequenced strains (Mu50, N315, MW2, and SANGER-476), was the most distantly related to the UAMS isolates and EMRSA-16.
Functional Dissection of a Conserved Motif within the Pilus Retraction Protein PilT
Authors: Aukema Kelly G. , Kron Erin M. , Herdendorf Timothy J. , Forest Katrina T.
Published: January 2005

PilT is a hexameric ATPase required for type IV pilus retraction in gram-negative bacteria. Retraction of type IV pili mediates intimate attachment to and signaling in host cells, surface motility, biofilm formation, natural transformation, and phage sensitivity. We investigated the in vivo and in vitro roles of each amino acid of the distinct, highly conserved C-terminal AIRNLIRE motif in PilT. Substitution of amino acids A288, I289, L292, and I293 as well as a double substitution of R290 and R294 abolished
Pseudomonas
aeruginosa
PilT function in vivo, as measured by a loss of surface motility and phage sensitivity. When introduced into purified
Aquifex
aeolicus
PilT, substitutions in the AIRNLIRE motif did not disrupt ATPase activity or oligomerization. In contrast, a K136Q substitution in the broadly conserved nucleotide binding motif prevented PilT function in vivo as well as in vitro. We propose that the AIRNLIRE motif forms an amphipathic α helix which transmits signals between a surface-exposed protein interaction site and the ATPase core of PilT, and we recognize a potential functional homology in other type II secretion ATPases.