bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling complex vapor-transport systems using Monte-Carlo techniques: Radioactive ion beam applications
Authors: Zhang Y. , Alton G. D.
Published: November 2005

A Monte-Carlo code has been developed that can be used to optimally design vapor transport systems for isotope-separator-on-line-based radioactive ion beam facilities in lieu of costly iterative trial and error design methods. The code provides a powerful means for delineating diffusion-release and effusive-flow (molecular-flow) processes, in combination, the delay times of which are principal intensity limiters of short-lived radioactive species at such facilities. The code provides time dependent particle evacuation, average distance traveled per particle, and particle/wall interaction information during particle transit through a given vapor-transport system under molecular-flow conditions, independent of the chemistry between particles of interest and the materials of which the transport system are constructed. In addition, the code provides powerful graphical insight via particle trajectories that serve as strong assets in arriving at a final design by identifying regions within the transport system where hold-up times are problematical. In this article, we compare simulation and experimental measurement results for transport of noble gases through selected vapor-transport systems using both cosine and isotropic particle re-emission distributions about the normal to the surface following adsorption (isotropic re-emission distributions are found to be in close agreement with experimental measurements) and describe a concept vapor-transport system that reduces transport times over those of conventional systems by >two orders of magnitude.
Indium growth on Si(100)-2×1 by femtosecond pulsed laser deposition
Authors: Hafez M. A. , Hegazy M. S. , Elsayed-Ali H. E.
Published: November 2005

Indium was grown on Si(100)-2×1 at room temperature by femtosecond pulsed laser deposition. Reflection high-energy electron diffraction (RHEED) was performed in situ to study film morphology and in-plane lattice spacing. Indium was found to grow on Si(100)-2×1 by the Stranski–Krastanov mode. The initial two-dimensional In layer formed in the In-2×1 structure with a lattice constant of 3.65Å. The full-width at half-maximum (FWHM) of the specular peak decreased during the growth, indicating an increase of the In islands size. Further In growth on the initial In-2×1 layer showed the formation of hexagonal, elongated, and hemispherical islands when examined ex situ by atomic force microscopy. The hexagonal islands were faceted and varied in size from ∼170to∼400nm, with an average height of 5nm. The elongated islands showed preferential growth orientation and had a length and height of ∼200 and ∼60nm, respectively.
Direct imprinting using soft mold and gas pressure for large area and curved surfaces
Authors: Chang Jer-Haur , Cheng Fang-Sung , Chao Chi-Chung , Weng Yung-Chun , Yang Sen-Yeu , Wang Lon A.
Published: November 2005

In this paper we report a simple and effective method that renders direct imprinting of sub-micron structures onto PMMA resist coated on large area and curved substrates using the PDMS mold on a closed chamber. Nitrogen gas was employed to generate a uniform pressure. The patterns of the soft mold could be replicated with high quality over an entire 12in. resist-coated area. The process was further successfully applied to the imprinting of a curved substrate.
Etching characteristics of high-k dielectric HfO2 thin films in inductively coupled fluorocarbon plasmas
Authors: Takahashi Kazuo , Ono Kouichi , Setsuhara Yuichi
Published: November 2005

Inductively coupled fluorocarbon (CF4∕Ar and C4F8∕Ar) plasmas were used to etch HfO2, which is a promising high-dielectric-constant material for the gate of complementary metal-oxide-semiconductor devices. The etch rates of HfO2 in CF4∕Ar plasmas exceeded those in C4F8∕Ar plasmas. The tendency for etch rates to become higher in fluorine-rich (high F∕C ratio) conditions indicates that HfO2 can be chemically etched by fluorine-containing species. In C4F8∕Ar plasmas with a high Ar dilution ratio, the etch rate of HfO2 increased with increasing bias power. The etch rate of Si, however, decreasd with bias power, suggesting that the deposition of carbon-containing species increased with increasing the power and inhibited the etching of Si. The HfO2∕Si selectivity monotonically increased with increasing power, then became more than 5 at the highest tested bias power. The carbon-containing species to inhibit etching of Si play an important role in enhancing the HfO2∕Si selectivity in C4F8∕Ar plasmas.
In situ photovoltage measurements using femtosecond pump-probe photoelectron spectroscopy and its application to metal–HfO2–Si structures
Authors: Lim Daeyoung , Haight Richard
Published: November 2005

We report in situ photovoltage measurements of metal-oxide-semiconductor (MOS) structures using femtosecond pump-probe photoelectron spectroscopy. This technique, which employs a single femtosecond laser, is a noncontact noninvasive measurement method for extracting the magnitude and direction of the band bending in Si substrates covered with high-k dielectric stacks and thin metal layers. We studied MOS structures consisting of thin metal layers of both high and low work functions deposited atop HfO2 grown on Si (100) substrates during various phases of processing. Excitation of the sample by a pulse of laser light flattens the bands of the Si substrate, which can be monitored as a rigid shift in the observed photoelectron spectrum. Particular attention is given to the potential effects of electron-hole recombination and metallic screening on the magnitude of the shift in the photoelectron spectra. We find that while as-deposited metals follow the metal-induced gap state model, thermal annealing of these structures drives the interface silicon Fermi energy to midgap. Charged oxygen-vacancy related defects at or near the HfO2/metal interface contribute significantly to the Fermi energy shift.
Low-temperature synthesis of gallium nitride thin films using electron cyclotron resonance plasma assisted pulsed laser deposition from a GaAs target
Authors: Sun J. , Wu A. M. , Xu N. , Ying Z. F. , Shen X. K. , Dong Z. B. , Wu J. D. , Shi L. Q.
Published: November 2005

Using reactive pulsed laser deposition assisted by electron cyclotron resonance (ECR) plasma, we have synthesized GaN thin films from a polycrystalline GaAs target at low temperatures. This was achieved by ablating the GaAs target in the reactive environment of a nitrogen plasma generated from ECR microwave discharge in pure nitrogen gas and depositing the films with concurrent bombardment by the low-energy nitrogen plasma stream. High-energy ion backscattering spectroscopy analysis shows that the synthesized films are gallium rich. Characterizations by x-ray photoelectron spectroscopy and Fourier transform infrared spectroscopy confirm the presence of GaN bonds in the films. The recorded absorption spectrum also reveals GaN stretching mode characteristic of the hexagonal GaN phase. The synthesized GaN films are transparent in the visible region and have a band gap of 3.38eV. Optical emission from the plume during film deposition reveals that the plume created by pulsed laser ablation of the GaAs target consists mainly of monoatomic atoms and ions of gallium and arsenic. Mechanisms responsible for the formation of GaN molecules and the growth of GaN films are also discussed.
Diamond microstructures fabricated using silicon molds
Authors: Salvadori M. C. , Martins D. R. , Mansano R. D. , Verdonck P. , Brown I. G.
Published: November 2005

We have fabricated diamond microstructures using silicon molds into which microcrystalline diamond was deposited by plasma assisted chemical vapor deposition. Prior to diamond deposition the silicon molds were seeded with the diamond powder of two different grain sizes, 14 and 1μm. Scanning electron microscopy and atomic force microscopy were used to view and characterize the resultant diamond microstructures. Analysis of the diamond replicas indicates better reproduction fidelity for the 14μm diamond powder, and a surface roughness of 20 nm.
Experimental and numerical study of the optimal operation pressure within Crookes radiometer
Authors: Lu Zhangde
Published: November 2005

The optimal operation pressure within Crookes radiometer is studied using experimental and direct simulation Monte Carlo (DSMC) method. The rotational rates of the rotor in the Crookes radiometer versus pressure are measured using a freely rotating rotor with two different dimensions, one is called a 20mm rotor, which the side length of rotor blade is 20mm, and the other is called a 10mm one. The experiment results indicate that the optimal operation pressure varies with the side length of rotor blade and appears at 0.1Pa and 3Pa in the cases of 20mm and 10mm rotors, respectively. The pressure difference distributions of gas on the back and front surfaces of the rotor blades are simulated by DSMC method. It is indicated that the maximum pressure differences appear at 0.1–0.5Pa in the case of the 20mm rotor, and at 2–5Pa in the case of the 10mm rotor, respectively. The results are consistent with the experiment results. The velocity vector fields of gas within Crookes radiometer with the 20mm rotor under four different pressures are also presented.
Quest for high brightness, monochromatic noble gas ion sources
Authors: Tondare V. N.
Published: November 2005

Focused ion beam (FIB) machines are key tools for state-of-the art sample preparation in electron microscopy, for characterization and repair in material sciences, for the semiconductor industry and for nanotechnology in general. Liquid-metal ion sources (LMIS) are widely used in FIB machines because they meet the minimum ion source requirements such as source brightness and reliability. However, in FIB machines, noble gas ion sources are favorable for sputtering, beam-induced etching and deposition, because the implanted ions do not change the electrical behavior of the substrate significantly. There are several efforts by various researchers to develop noble gas ion sources that can be used in FIB machines instead of LMIS. The gas ion sources could not meet the minimum ion source requirements. Therefore, LMIS are still a popular choice among FIB machine users. This review article takes a critical look at the reported efforts in the literature to develop noble gas ion sources for FIB machines.
Technique for the production, preservation, and transportation of H atoms in metal chambers for processings
Authors: Ansari S. G. , Umemoto Hironobu , Morimoto Takashi , Yoneyama Koji , Masuda Atsushi , Matsumura Hideki , Ikemoto Manabu , Ishibashi Keiji
Published: November 2005

Three different coating materials for lowering the H-atom recombination probability on stainless-steel chamber walls were investigated and the results were compared. SiO2 films prepared by natural oxidation of perhydropolysilazane, polytetrafluoroethene (Teflon) films, and H3PO4 coated SiO2 films were used as coating materials. Among them, the SiO2 film was found to be the most useful for this purpose. The densities of H atoms produced by catalytic decomposition of H2 on heated tungsten surfaces were measured by a vacuum-ultraviolet laser absorption technique under various conditions. The H-atom density increased by one order of magnitude with SiO2 and Teflon coating, the former of which is easier to use and more economical. No further increase in H-atom density was observed when the chamber was coated with H3PO4. SiO2 films prepared from perhydropolysilazane were not etched by H atoms. Quadrupole mass spectrometric analysis showed that the production of either SiH4 or H2O is extremely minor. No surface etching was confirmed by x-ray photoelectron spectroscopy (XPS), either. Scanning electron microscopic (SEM) observations showed that the SiO2 films are not porous even after H-atom exposure. It is also suggested that cooling of the chamber walls is important to preserve the H-atom density.
Morphology evolution on diamond surfaces during ion sputtering
Authors: Mayer T. M. , Adams D. P. , Vasile M. J. , Archuleta K. M.
Published: November 2005

We have conducted an extensive study of the evolution of surface morphology of single crystal diamond surfaces during sputtering by 20keV Ga+ and Ga++H2O. We observe the formation of well-ordered ripples on the surface for angles of incidence between 40 and 70°. We have also measured sputter yields as a function of angle of incidence, and ripple wavelength and amplitude dependence on angle of incidence and ion fluence. Smooth surface morphology is observed for <40°, and a transition to a step-and-terrace structure is observed for >70°. The formation and evolution of well-ordered surface ripples is well characterized by the model of Bradley and Harper, where sputter-induced roughening is balanced by surface transport smoothing. Smoothing is consistent with an ion-induced viscous relaxation mechanism. Ripple amplitude saturates at high ion fluence, confirming the effect of nonlinear processes. Differences between Ga+ and Ga++H2O in ripple wavelength, amplitude, and time to saturation of amplitude are consistent with the increased sputter yield observed for Ga++H2O. For angle of incidence <40°, an ion bombardment-induced “atomic drift” mechanism for surface smoothing may be responsible for suppression of ripple formation. For Ga++H2O, we observe anomalous formation of very large amplitude and wavelength, poorly ordered surface ridges for angle of incidence near 40°. Finally, we observe that ripple initiation on smooth surfaces can take place by initial stochastic roughening followed by evolution of increasingly well-ordered ripples.
Thermal reaction of polycrystalline AlN with XeF2
Authors: Watanabe Morimichi , Mori Yukimasa , Ishikawa Takahiro , Sakai Hiroaki , Iida Takashi , Akiyama Keijiro , Narita Shogo , Sawabe Kyoichi , Shobatake Kosuke
Published: November 2005

Detailed studies on the thermal reaction behavior of polycrystalline aluminum nitride (AlN) with effusive xenon difluoride (XeF2) have been carried out over the sample temperature (Ts) range from 300to920K using molecular beam mass spectrometry combined with a time-of-flight technique and ex situ surface analyses, i.e., X-ray photoelectron spectroscopy, Auger electron spectroscopy, and scanning electron microscopy (SEM). The species desorbed from the AlN∕XeF2 system were monitored using molecular beam mass spectrometry, as a function of sample temperature. Above Ts=800K, the desorbed reaction products were identified as N2 and AlF3, and their flux intensities increase monotonically as the sample temperature is increased. The flux intensity of XeF2 desorbed after physisorption to the AlN surface is found to decrease as Ts is raised above Ts=800K, and approximately one half of the incoming XeF2 is consumed by the thermal reaction at 920K. The results of surface analyses show that the thermal reaction of AlN with XeF2 starts at approximately Ts=700K, forming a reaction layer composed of AlF3. The AlF3 layer becomes thick as Ts is increased from Ts=700–800K. Above Ts=800K, however, as a result of fast desorption of AlF3 and F atoms from the AlF3 layer, only partially fluorinated AlFx (x=1 and/or 2) layers are formed and the bulk AlN is revealed again. The SEM photographs indicate that the surfaces exposed above Ts=850K are strongly etched but a slight change is observed at Ts⩽800K. On the basis of these results, three reaction stages are proposed for the AlN∕XeF2 reaction depending on the sample temperature range: Stage 1 (300⩽Ts<700K); no reaction, stage 2 (700⩽Ts<800K); surface fluorination, and stage 3 (800⩽Ts); etching. At stage 3, AlF3 formed on the surface starts to evaporate and fast etching proceeds, since the vapor pressure of AlF3 is high enough in this temperature range.
Language Acquisition and Brain Development
Authors: Sakai Kuniyoshi L.
Published: November 2005

Language acquisition is one of the most fundamental human traits, and it is obviously the brain that undergoes the developmental changes. During the years of language acquisition, the brain not only stores linguistic information but also adapts to the grammatical regularities of language. Recent advances in functional neuroimaging have substantially contributed to systems-level analyses of brain development. In this Viewpoint, I review the current understanding of how the “final state” of language acquisition is represented in the mature brain and summarize new findings on cortical plasticity for second language acquisition, focusing particularly on the function of the grammar center.
Structures of the Bacterial Ribosome at 3.5 Å Resolution
Authors: Schuwirth Barbara S. , Borovinskaya Maria A. , Hau Cathy W. , Zhang Wen , Vila-Sanjurjo Antón , Holton James M. , Cate Jamie H. Doudna
Published: November 2005

We describe two structures of the intact bacterial ribosome from
Escherichia coli
determined to a resolution of 3.5 angstroms by x-ray crystallography. These structures provide a detailed view of the interface between the small and large ribosomal subunits and the conformation of the peptidyl transferase center in the context of the intact ribosome. Differences between the two ribosomes reveal a high degree of flexibility between the head and the rest of the small subunit. Swiveling of the head of the small subunit observed in the present structures, coupled to the ratchet-like motion of the two subunits observed previously, suggests a mechanism for the final movements of messenger RNA (mRNA) and transfer RNAs (tRNAs) during translocation.
A Direct Role for Dual Oxidase in
Drosophila
Gut Immunity
Authors: Ha Eun-Mi , Oh Chun-Taek , Bae Yun Soo , Lee Won-Jae
Published: November 2005

Because the mucosal epithelia are in constant contact with large numbers of microorganisms, these surfaces must be armed with efficient microbial control systems. Here, we show that the
Drosophila
nicotinamide adenine dinucleotide phosphate (NADPH) oxidase enzyme, dual oxidase (dDuox), is indispensable for gut antimicrobial activities. Adult flies in which
dDuox
expression is silenced showed a marked increase in mortality rate even after a minor infection through ingestion of microbe-contaminated food. This could be restored by the specific reintroduction of dDuox, demonstrating that this oxidase generates a unique epithelial oxidative burst that limits microbial proliferation in the gut. Thus, oxidant-mediated antimicrobial responses are not restricted to the phagocytes, but rather are used more broadly, including in mucosal barrier epithelia.
Retrograde Signaling by Syt 4 Induces Presynaptic Release and Synapse-Specific Growth
Authors: Yoshihara Motojiro , Adolfsen Bill , Galle Kathleen T. , Littleton J. Troy
Published: November 2005

The molecular pathways involved in retrograde signal transduction at synapses and the function of retrograde communication are poorly understood. Here, we demonstrate that postsynaptic calcium 2
+
ion (Ca
2+
) influx through glutamate receptors and subsequent postsynaptic vesicle fusion trigger a robust induction of presynaptic miniature release after high-frequency stimulation at
Drosophila
neuromuscular junctions. An isoform of the synaptotagmin family, synaptotagmin 4 (Syt 4), serves as a postsynaptic Ca
2+
sensor to release retrograde signals that stimulate enhanced presynaptic function through activation of the cyclic adenosine monophosphate (cAMP)–cAMP-dependent protein kinase pathway. Postsynaptic Ca
2+
influx also stimulates local synaptic differentiation and growth through Syt 4–mediated retrograde signals in a synapse-specific manner.
Treatment of Autoimmune Neuroinflammation with a Synthetic Tryptophan Metabolite
Authors: Platten Michael , Ho Peggy P. , Youssef Sawsan , Fontoura Paulo , Garren Hideki , Hur Eun Mi , Gupta Rohit , Lee Lowen Y. , Kidd Brian A. , Robinson William H. , Sobel Raymond A. , Selley Michael L. , Steinman Lawrence
Published: November 2005

Local catabolism of the amino acid tryptophan (Trp) by indoleamine 2,3-dioxygenase (IDO) is considered an important mechanism of regulating T cell immunity. We show that IDO transcription was increased when myelin-specific T cells were stimulated with tolerogenic altered self-peptides. Catabolites of Trp suppressed proliferation of myelin-specific T cells and inhibited production of proinflammatory T helper–1 (T
H
1) cytokines.
N
-(3,4,-Dimethoxycinnamoyl) anthranilic acid (3,4-DAA), an orally active synthetic derivative of the Trp metabolite anthranilic acid, reversed paralysis in mice with experimental autoimmune encephalomyelitis, a model of multiple sclerosis (MS). Trp catabolites and their derivatives offer a new strategy for treating T
H
1-mediated autoimmune diseases such as MS.
Tissue-Specific TAFs Counteract Polycomb to Turn on Terminal Differentiation
Authors: Chen Xin , Hiller Mark , Sancak Yasemin , Fuller Margaret T.
Published: November 2005

Polycomb transcriptional silencing machinery is implicated in the maintenance of precursor fates, but how this repression is reversed to allow cell differentiation is unknown. Here we show that testis-specific TAF (TBP-associated factor) homologs required for terminal differentiation of male germ cells may activate target gene expression in part by counteracting repression by
Polycomb
. Chromatin immunoprecipitation revealed that testis TAFs bind to target promoters, reduce Polycomb binding, and promote local accumulation of H3K4me3, a mark of Trithorax action. Testis TAFs also promoted relocalization of Polycomb Repression Complex 1 components to the nucleolus in spermatocytes, implicating subnuclear architecture in the regulation of terminal differentiation.
Improvement of Galactose Uptake in
Saccharomyces cerevisiae
through Overexpression of Phosphoglucomutase: Example of Transcript Analysis as a Tool in Inverse Metabolic Engineering
Authors: Bro Christoffer , Knudsen Steen , Regenberg Birgitte , Olsson Lisbeth , Nielsen Jens
Published: November 2005

Through genome-wide transcript analysis of a reference strain and two recombinant
Saccharomyces cerevisiae
strains with different rates of galactose uptake, we obtained information about the global transcriptional response to metabolic engineering of the
GAL
gene regulatory network. One of the recombinant strains overexpressed the gene encoding the transcriptional activator Gal4, and in the other strain the genes encoding Gal80, Gal6, and Mig1, which are negative regulators of the
GAL
system, were deleted. Even though the galactose uptake rates were significantly different in the three strains, we surprisingly did not find any significant changes in the expression of the genes encoding the enzymes catalyzing the first steps of the pathway (i.e., the genes encoding Gal2, Gal1, Gal7, and Gal10). We did, however, find that
PGM2
, encoding the major isoenzyme of phosphoglucomutase, was slightly up-regulated in the two recombinant strains with higher galactose uptake rates. This indicated that
PGM2
is a target for overexpression in terms of increasing the flux through the Leloir pathway, and through overexpression of
PGM2
the galactose uptake rate could be increased by 70% compared to that of the reference strain. Based on our findings, we concluded that phosphoglucomutase plays a key role in controlling the flux through the Leloir pathway, probably due to increased conversion of glucose-1-phosphate to glucose-6-phosphate. This conclusion was supported by measurements of sugar phosphates, which showed that there were increased concentrations of glucose-6-phosphate, galactose-6-phosphate, and fructose-6-phosphate in the strain construct overexpressing
PGM2
.
Diversity of “
Candidatus
Liberibacter asiaticus,” Based on the
omp
Gene Sequence
Authors: Bastianel C. , Garnier-Semancik M. , Renaudin J. , Bové J. M. , Eveillard S.
Published: November 2005

Huanglongbing (yellow dragon disease) is a destructive disease of citrus. The etiological agent is a noncultured, phloem-restricted alpha-proteobacterium, “
Candidatus
Liberibacter africanus” in Africa and “
Candidatus
Liberibacter asiaticus” in Asia. In this study, we used an
omp
-based PCR-restriction fragment length polymorphism (RFLP) approach to analyze the genetic variability of “
Ca
. Liberibacter asiaticus” isolates. By using five different enzymes, each the 10 isolates tested could be associated with a specific combination of restriction profiles. The results indicate that the species “
Ca
. Liberibacter asiaticus,” even within a given region, may comprise several different variants. Thus,
omp
-based PCR-RFLP analysis is a simple method for detecting and differentiating “
Ca
. Liberibacter asiaticus” isolates.
Isolation and Partial Characterization of Antagonistic Peptides Produced by
Paenibacillus
sp. Strain B2 Isolated from the Sorghum Mycorrhizosphere
Authors: Selim S. , Negrel J. , Govaerts C. , Gianinazzi S. , van Tuinen D.
Published: November 2005

Paenibacillus
sp. strain B2, isolated from the mycorrhizosphere of sorghum colonized by
Glomus mosseae
, produces an antagonistic factor. This factor has a broad spectrum of activity against gram-positive and gram-negative bacteria and also against fungi. The antagonistic factor was isolated from the bacterial culture medium and purified by cation-exchange, reverse-phase, and size exclusion chromatography. The purified factor could be separated into three active compounds following characterization by amino acid analysis and by combined reverse-phase chromatography and mass spectrometry (liquid chromatography-mass spectrometry and mass spectrometry-mass spectrometry). The first compound had the same retention time as polymyxin B
1
, whereas the two other compounds were more hydrophobic. The molecular masses of the latter compounds are 1,184.7 and 1,202.7 Da, respectively, and their structure is similar to that of polymyxin B
1
, with a cyclic heptapeptide moiety attached to a tripeptide side chain and a fatty acyl residue. They both contain threonine, phenylalanine, leucine, and 2,4-diaminobutyric acid residues. The peptide with a molecular mass of 1,184.7 contains a 2,3-didehydrobutyrine residue with a molecular mass of 101 Da replacing a threonine at the A2 position of the polymyxin side chain. This modification could explain the broader range of antagonistic activity of this peptide compared to that of polymyxin B.
A Bile Salt-Resistant Derivative of
Bifidobacterium animalis
Has an Altered Fermentation Pattern When Grown on Glucose and Maltose
Authors: Ruas-Madiedo Patricia , Hernández-Barranco Ana , Margolles Abelardo , de los Reyes-Gavilán Clara G.
Published: November 2005

The growth of
Bifidobacterium animalis
subsp.
lactis
IPLA 4549 and its derivative with acquired resistance to bile,
B. animalis
subsp.
lactis
4549dOx, was evaluated in batch cultures with glucose or the glucose disaccharide maltose as the main carbon source. The acquisition of bile salt resistance caused a change in growth pattern for both sugars, which mainly resulted in a preferential use of maltose compared to glucose, whereas the mother strain used both carbohydrates in a similar way. High-performance liquid chromatography and gas chromatography-mass spectrometry analyses were performed to determine the amounts of glucose consumption and organic acid and ethanol formation from glucose by buffered resting cells taken at different points during growth. Resting cells of the bile-adapted strain generally consumed less glucose than those of the nonadapted one but showed an enhanced production of ethanol and higher acetic acid-to-lactic acid as well as formic acid-to-lactic acid ratios. These findings suggest a shift in the catabolism of carbohydrates promoted by the acquisition of bile resistance that may cause changes in the redox potential and improvements in the cellular ATP yield.
The Halophilic Fungus
Hortaea werneckii
and the Halotolerant Fungus
Aureobasidium pullulans
Maintain Low Intracellular Cation Concentrations in Hypersaline Environments
Authors: Kogej Tina , Ramos José , Plemenitaš Ana , Gunde-Cimerman Nina
Published: November 2005

Hortaea werneckii
and
Aureobasidium pullulans
, black yeast-like fungi isolated from hypersaline waters of salterns as their natural ecological niche, have been previously defined as halophilic and halotolerant microorganisms, respectively. In the present study we assessed their growth and determined the intracellular cation concentrations of salt-adapted and non-salt-adapted cells of both species at a wide range of salinities (0 to 25% NaCl and 0 to 20% NaCl, respectively). Although 5% NaCl improved the growth of
H. werneckii
, even the minimal addition of NaCl to the growth medium slowed down the growth rate of
A. pullulans
, confirming their halophilic and halotolerant nature. Salt-adapted cells of
H. werneckii
and
A. pullulans
kept very low amounts of internal Na
+
even when grown at high NaCl concentrations and can be thus considered Na
+
excluders, suggesting the existence of efficient mechanisms for the regulation of ion fluxes. Based on our results, we can conclude that these organisms do not use K
+
or Na
+
for osmoregulation. Comparison of cation fluctuations after a hyperosmotic shock, to which nonadapted cells of both species were exposed, demonstrated better ionic homeostasis regulation of
H. werneckii
compared to
A. pullulans
. We observed small fluctuations of cation concentrations after a hyperosmotic shock in nonadapted
A. pullulans
similar to those in salt-adapted
H.werneckii
, which additionally confirmed better regulation of ionic homeostasis in the latter. These features can be expected from organisms adapted to survival within a wide range of salinities and to occasional exposure to extremely high NaCl concentrations, both characteristic for their natural environment.
Suitability of RecombinantEscherichia coliandPseudomonas putidaStrains for Selective Biotransformation ofm-Nitrotoluene by Xylene Monooxygenase
Authors: Meyer Daniel , Witholt Bernard , Schmid Andreas
Published: November 2005

Escherichia coliJM101(pSPZ3), containing xylene monooxygenase (XMO) fromPseudomonas putidamt-2, catalyzes specific oxidations and reductions ofm-nitrotoluene and derivatives thereof. In addition to reactions catalyzed by XMO, we focused on biotransformations by native enzymes of theE. colihost and their effect on overall biocatalyst performance. Whilem-nitrotoluene was consecutively oxygenated tom-nitrobenzyl alcohol,m-nitrobenzaldehyde, andm-nitrobenzoic acid by XMO, the oxidation was counteracted by an alcohol dehydrogenase(s) from theE. colihost, which reducedm-nitrobenzaldehyde tom-nitrobenzyl alcohol. Furthermore, the enzymatic background of the host reduced the nitro groups of the reactants resulting in the formation of aromatic amines, which were shown to effectively inhibit XMO in a reversible fashion. Host-intrinsic oxidoreductases and their reaction products had a major effect on the activity of XMO during biocatalysis ofm-nitrotoluene.P. putidaDOT-T1E andP. putidaPpS81 were compared toE. coliJM101 as alternative hosts for XMO. These promising strains contained an additional dehydrogenase that oxidizedm-nitrobenzaldehyde to the corresponding acid but catalyzed the formation of XMO-inhibiting aromatic amines at a significantly lower level thanE. coliJM101.
Detection, Characterization, and In Vitro and In Vivo Expression of Genes Encoding S-Proteins in
Lactobacillus gallinarum
Strains Isolated from Chicken Crops
Authors: Hagen Karen E. , Guan Le Luo , Tannock Gerald W. , Korver Doug R. , Allison Gwen E.
Published: November 2005

Thirty-eight isolates of
Lactobacillus gallinarum
cultured from the crops of broiler chickens were screened for the presence of genes encoding S-layer proteins. All of the isolates had two S-protein genes, which were designated
Lactobacillus gallinarum
S-protein (
lgs
) genes. One gene in each isolate was either
lgsA
or
lgsB
. The
Lactobacillus
isolates were further characterized by pulsed-field gel electrophoresis of DNA digests, which grouped the isolates into 17 genotypes (strains). The second gene in each of eight representative strains was sequenced and shown to differ among strains (
lgsC
,
lgsD
,
lgsE
,
lgsF
,
lgsG
,
lgsH
, and
lgsI
). The genome of each strain thus encoded a common S-protein (encoded by either
lgsA
or
lgsB
) and a strain-specific S-protein. The extraction of cell surface proteins from cultures of the eight strains showed that each strain produced a single S-protein that was always encoded by the strain-specific
lgs
gene. Two of the strains were used to inoculate chickens maintained in a protected environment which were
Lactobacillus
-free prior to inoculation. DNAs and RNAs extracted from the digesta of the chickens were used for PCR and reverse transcription-PCR, respectively, to demonstrate the presence and transcription of
lgs
genes in vivo. In both cases, only the strain-specific gene was transcribed. Both of the strains adhered to the crop epithelium, consistent with published data predicting that S-proteins of lactobacilli are adhesins. The results of this study provide a basis for the investigation of gene duplication and sequence variation as mechanisms by which bacterial strains of the same species can share the same habitat.
Viral Production, Decay Rates, and Life Strategies along a Trophic Gradient in the North Adriatic Sea
Authors: Bongiorni Lucia , Magagnini Mirko , Armeni Monica , Noble Rachel , Danovaro Roberto
Published: November 2005

Although the relationships between trophic conditions and viral dynamics have been widely explored in different pelagic environments, there have been few attempts at independent estimates of both viral production and decay. In this study, we investigated factors controlling the balance between viral production and decay along a trophic gradient in the north Adriatic basin, providing independent estimates of these variables and determining the relative importance of nanoflagellate grazing and viral life strategies. Increasing trophic conditions induced an increase of bacterioplankton growth rates and of the burst sizes. As a result, eutrophic waters displayed highest rates of viral production, which considerably exceeded observed rates of viral decay (up to 2.9 × 10
9
VLP liter
−1
h
−1
). Viral decay was also higher in eutrophic waters, where it accounted for ca. 40% of viral production, and dropped significantly to 1.3 to 10.7% in oligotrophic waters. These results suggest that viral production and decay rates may not necessarily be balanced in the short term, resulting in a net increase of viruses in the system. In eutrophic waters nanoflagellate grazing, dissolved-colloidal substances, and lysogenic infection were responsible together for the removal of ca. 66% of viral production versus 17% in oligotrophic waters. Our results suggest that different causative agents are primarily responsible for the removal of viruses from the water column in different trophic conditions. Factors other than those considered in the past might shed light on processes responsible for the removal and/or decay of viral particles from the water column.
Ability of Shiga Toxin-Producing
Escherichia coli
and
Salmonella
spp. To Survive in a Desiccation Model System and in Dry Foods
Authors: Hiramatsu Reiji , Matsumoto Masakado , Sakae Kenji , Miyazaki Yutaka
Published: November 2005

In order to determine desiccation tolerances of bacterial strains, the survival of 58 diarrheagenic strains (18 salmonellae, 35 Shiga toxin-producing
Escherichia coli
[STEC], and 5 shigellae) and of 15 nonpathogenic
E. coli
strains was determined after drying at 35°C for 24 h in paper disks. At an inoculum level of 10
7
CFU/disk, most of the salmonellae (14/18) and the STEC strains (31/35) survived with a population of 10
3
to 10
4
CFU/disk, whereas all of the shigellae (5/5) and the majority of the nonpathogenic
E. coli
strains (9/15) did not survive (the population was decreased to less than the detection limit of 10
2
CFU/disk). After 22 to 24 months of subsequent storage at 4°C, all of the selected salmonellae (4/4) and most of the selected STEC strains (12/15) survived, keeping the original populations (10
3
to 10
4
CFU/disk). In contrast to the case for storage at 4°C, all of 15 selected strains (5 strains each of
Salmonella
spp., STEC O157, and STEC O26) died after 35 to 70 days of storage at 25°C and 35°C. The survival rates of all of these 15 strains in paper disks after the 24 h of drying were substantially increased (10 to 79 times) by the presence of sucrose (12% to 36%). All of these 15 desiccated strains in paper disks survived after exposure to 70°C for 5 h. The populations of these 15 strains inoculated in dried foods containing sucrose and/or fat (e.g., chocolate) were 100 times higher than those in the dried paper disks after drying for 24 h at 25°C.
Intervening Sequence Acquired by Lateral Gene Transfer in
Tropheryma whipplei
Results in 23S rRNA Fragmentation
Authors: Crapoulet Nicolas , Robineau Sylvianne , Raoult Didier , Renesto Patricia
Published: November 2005

Completion of
Tropheryma whipplei
genome sequencing may provide insights into the evolution of the molecular mechanisms underlying the pathogenicity of this microorganism. The first postgenomic application was the successful design of a comprehensive culture medium that allows axenic growth of this bacterium, which is particularly recalcitrant to cultivation. This achievement in turn permitted analysis of
T. whipplei
RNA without contaminating eukaryotic nucleic acids. To obtain high-quality RNA, several extraction methods were compared, but under all conditions tested an atypical profile was observed. By using a Northern blot assay we demonstrated that an insertion sequence previously described in
T. whipplei
23S rRNA is in fact an intervening sequence excised during maturation. This cleavage could involve an RNase III identified in the genome of this microorganism. Among the bacteria with a 23S rRNA insertion sequence,
T. whipplei
is the only gram-positive microorganism. We present phylogenetic evidence that this mobile genetic element was acquired by lateral gene transfer from another enteric bacterium.
Enhanced Hydrogen Production from Formic Acid by Formate Hydrogen Lyase-Overexpressing
Escherichia coli
Strains
Authors: Yoshida Akihito , Nishimura Taku , Kawaguchi Hideo , Inui Masayuki , Yukawa Hideaki
Published: November 2005

Genetic recombination of
Escherichia coli
in conjunction with process manipulation was employed to elevate the efficiency of hydrogen production in the resultant strain SR13 2 orders of magnitude above that of conventional methods. The formate hydrogen lyase (FHL)-overexpressing strain SR13 was constructed by combining FHL repressor (
hycA
) inactivation with FHL activator (
fhlA
) overexpression. Transcription of large-subunit formate dehydrogenase,
fdhF
, and large-subunit hydrogenase,
hycE
, in strain SR13 increased 6.5- and 7.0-fold, respectively, compared to the wild-type strain. On its own, this genetic modification effectively resulted in a 2.8-fold increase in hydrogen productivity of SR13 compared to the wild-type strain. Further enhancement of productivity was attained by using a novel method involving the induction of the FHL complex with high-cell-density filling of a reactor under anaerobic conditions. Continuous hydrogen production was achieved by maintaining the reactor concentration of the substrate (free formic acid) under 25 mM. An initial productivity of 23.6 g hydrogen h
−1
liter
−1
(300 liters h
−1
liter
−1
at 37°C) was achieved using strain SR13 at a cell density of 93 g (dry weight) cells/liter. The hydrogen productivity reported in this work has great potential for practical application.
Expression of Rumen Microbial Fibrolytic Enzyme Genes in Probiotic
Lactobacillus reuteri
Authors: Liu Je-Ruei , Yu Bi , Liu Fu-Hwa , Cheng Kuo-Joan , Zhao Xin
Published: November 2005

This study was aimed at evaluating the cloning and expression of three rumen microbial fibrolytic enzyme genes in a strain of
Lactobacillus reuteri
and investigating the probiotic characteristics of these genetically modified lactobacilli. The
Neocallimastix patriciarum
xylanase gene
xynCDBFV
, the
Fibrobacter succinogenes
β-glucanase (1,3-1,4-β-
d
-glucan 4-glucanohydrolase [EC 3.2.1.73]) gene, and the
Piromyces rhizinflata
cellulase gene
eglA
were cloned in a strain of
L. reuteri
isolated from the gastrointestinal tract of broilers. The enzymes were expressed and secreted under the control of the
Lactococcus lactis lacA
promoter and its secretion signal. The
L. reuteri
transformed strains not only acquired the capacity to break down soluble carboxymethyl cellulose, β-glucan, or xylan but also showed high adhesion efficiency to mucin and mucus and resistance to bile salt and acid.
Links between Plant and Rhizoplane Bacterial Communities in Grassland Soils, Characterized Using Molecular Techniques
Authors: Nunan Naoise , Daniell Timothy J. , Singh Brajesh K. , Papert Artemis , McNicol James W. , Prosser James I.
Published: November 2005

Molecular analysis of grassland rhizosphere soil has demonstrated complex and diverse bacterial communities, with resultant difficulties in detecting links between plant and bacterial communities. These studies have, however, analyzed “bulk” rhizosphere soil, rather than rhizoplane communities, which interact most closely with plants through utilization of root exudates. The aim of this study was to test the hypothesis that plant species was a major driver for bacterial rhizoplane community composition on individual plant roots. DNA extracted from individual roots was used to determine plant identity, by analysis of the plastid tRNA leucine (trnL) UAA gene intron, and plant-related bacterial communities. Bacterial communities were characterized by analysis of PCR-amplified 16S rRNA genes using two fingerprinting methods: terminal restriction fragment length polymorphisms (T-RFLP) and denaturing gradient gel electrophoresis (DGGE). Links between plant and bacterial rhizoplane communities could not be detected by visual examination of T-RFLP patterns or DGGE banding profiles. Statistical analysis of fingerprint patterns did not reveal a relationship between bacterial community composition and plant species but did demonstrate an influence of plant community composition. The data also indicated that topography and other, uncharacterized, environmental factors are important in driving bacterial community composition in grassland soils. T-RFLP had greater potential resolving power than DGGE, but findings from the two methods were not significantly different.
Polyphenol Oxidase Activity Expression in
Ralstonia solanacearum
Authors: Hernández-Romero Diana , Solano Francisco , Sanchez-Amat Antonio
Published: November 2005

Sequencing of the genome of
Ralstonia solanacearum
revealed several genes that putatively code for polyphenol oxidases (PPOs). To study the actual expression of these genes, we looked for and detected all kinds of PPO activities, including laccase, cresolase, and catechol oxidase activities, in cellular extracts of this microorganism. The conditions for the PPO assays were optimized for the phenolic substrate, pH, and sodium dodecyl sulfate concentration used. It was demonstrated that three different PPOs are expressed. The genes coding for the enzymes were unambiguously correlated with the enzymatic activities detected by generation of null mutations in the genes by using insertional mutagenesis with a suicide plasmid and estimating the changes in the levels of enzymatic activities compared to the levels in the wild-type strain. The protein encoded by the RSp1530 locus is a multicopper protein with laccase activity. Two other genes, RSc0337 and RSc1501, code for nonblue copper proteins exhibiting homology to tyrosinases. The product of RSc0337 has strong tyrosine hydroxylase activity, and it has been shown that this enzyme is involved in melanin synthesis by
R. solanacearum
. The product of the RSc1501 gene is an enzyme that shows a clear preference for oxidation of
o
-diphenols. Preliminary characterization of the mutants obtained indicated that PPOs expressed by
R. solanacearum
may participate in resistance to phenolic compounds since the mutants exhibited higher sensitivity to
l
-tyrosine than the wild-type strain. These results suggest a possible role in the pathogenic process to avoid plant resistance mechanisms involving the participation of phenolic compounds.
Escherichia coli
O157:H7 in Environments of Culture-Positive Cattle
Authors: Davis Margaret A. , Cloud-Hansen Karen A. , Carpenter John , Hovde Carolyn J.
Published: November 2005

Outbreaks of
Escherichia coli
O157:H7 disease associated with animal exhibits have been reported with increasing frequency. Transmission can occur through contact with contaminated haircoats, bedding, farm structures, or water. We investigated the distribution and survival of
E. coli
O157:H7 in the immediate environments of individually housed, experimentally inoculated cattle by systematically culturing feed, bedding, water, haircoat, and feed bunk walls for
E. coli
O157:H7 for 3 months. Cedar chip bedding was the most frequently culture-positive environmental sample tested (27/96 or 28.15%). Among these, 12 (44.0%) of positive bedding samples were collected when the penned animal was fecal culture negative. Survival of
E. coli
O157:H7 in experimentally inoculated cedar chip bedding and in grass hay feed was determined at different temperatures. Survival was longest in feed at room temperature (60 days), but bacterial counts decreased over time. The possibility that urine plays a role in the environmental survival of
E. coli
O157:H7 was investigated. Cedar chip bedding moistened with sterile water or bovine urine was inoculated with
E. coli
O157:H7. Bedding moistened with urine supported growth of
E. coli
O157:H7, whereas inoculated bedding moistened with only water yielded decreasing numbers of bacteria over time. The findings that environmental samples were frequently positive for
E. coli
O157:H7 at times when animals were culture negative and that urine provided a substrate for
E. coli
O157:H7 growth have implications for understanding the on-farm ecology of this pathogen and for the safety of ruminant animal exhibits, particularly petting zoos and farms where children may enter animal pens.
Monitoring Stress-Related Genes during the Process of Biomass Propagation of
Saccharomyces cerevisiae
Strains Used for Wine Making
Authors: Pérez-Torrado Roberto , Bruno-Bárcena Jose M. , Matallana Emilia
Published: November 2005

Physiological capabilities and fermentation performance of
Saccharomyces cerevisiae
strains to be employed during industrial wine fermentations are critical for the quality of the final product. During the process of biomass propagation, yeast cells are dynamically exposed to a mixed and interrelated group of known stresses such as osmotic, oxidative, thermic, and/or starvation. These stressing conditions can dramatically affect the parameters of the fermentation process and the technological abilities of the yeast, e.g., the biomass yield and its fermentative capacity. Although a good knowledge exists of the behavior of
S. cerevisiae
under laboratory conditions, insufficient knowledge is available about yeast stress responses under the specific media and growth conditions during industrial processes. We performed growth experiments using bench-top fermentors and employed a molecular marker approach (changes in expression levels of five stress-related genes) to investigate how the cells respond to environmental changes during the process of yeast biomass production. The data show that in addition to the general stress response pathway, using the
HSP12
gene as a marker, other specific stress response pathways were induced, as indicated by the changes detected in the mRNA levels of two stress-related genes,
GPD1
and
TRX2
. These results suggest that the cells were affected by osmotic and oxidative stresses, demonstrating that these are the major causes of the stress response throughout the process of wine yeast biomass production.