bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of hydrogen bonding environment in a-Si:H films for c-Si surface passivation
Authors: Burrows M. Z. , Das U. K. , Opila R. L. , De Wolf S. , Birkmire R. W.
Published: September 2008

The search for an ideal surface passivation layer of crystalline silicon (c-Si) to be employed in a silicon heterojunction photovoltaic device has garnered much attention. The leading candidate is a few nanometers of intrinsic amorphous silicon ((i)a-Si:H) film. Reported dependencies of film surface passivation quality on substrate preparation, orientation, and deposition temperature have been extended in this work to include H2 to SiH4 dilution ratio and postdeposition annealing. Simple avoidance of the deposition regimes that lead to epitaxial growth of Si on the c-Si substrate produces decent lifetimes on the order of 500μs. Subsequent low temperature annealings cause an important restructuring of Si–H bonding at the a-Si:H∕c-Si interface increasing the amount of monohydride at the c-Si surface. This restructuring would reduce the c-Si surface defect density and cause an improvement of surface passivation as confirmed by effective lifetime measurements. Final effective carrier lifetimes up to 2550μs are achieved postannealing. Initial results indicate the improvement depends on surplus SiH2 from the interface region.
Ferroelectric properties of Pb(Mn1/3Nb2/3)O3−Pb(Zr,Ti)O3 thin films epitaxially grown on (001)MgO substrates
Authors: Zhang Tao , Wasa Kiyotaka , Kanno Isaku , Zhang Shu-Yi
Published: September 2008

Ferroelectric ternary perovskite thin films of 0.06Pb(Mn1/3,Nb2/3)O3 (PMnN)−0.42PbZrO3 (PZ)−0.52PbTiO3 (PT) [0.06PMnN–0.94PZT(45/55)] have been grown on the (001)MgO substrates by radio frequency-magnetron sputtering with quenching processing. The deposition conditions, microstructures, piezoelectric, and ferroelectric properties of the ternary perovskite thin films are described in comparison with the binary compounds of PZ–PT (PZT). The out-plane x-ray diffraction (XRD) measurements for the ternary PMnN–PZT perovskite thin films of 1 to 1−3 μm in film thickness show strong single (001) orientation. The in-plane Φ-scan XRD curve verified the ternary thin films are single crystals of perovskite structure. Their lattice parameters are almost the same as bulk values and the ternary thin films are almost stress free. The PMnN–PZT thin films show high density without columnar structure. The PZT-based ternary perovskite thin films with the small addition of PMnN, i.e., 6 mole % PMnN, exhibit a strong hard ferroelectric response, i.e., Ps=60 μC/cm2 and 2Ec=230 kV/cm. Their effective piezoelectric constants are typically e31,eff=−7.7 C/m2. These values are slightly higher than those of binary perovskite PZT thin films.
Bulk ratio method for determining surface enhancement using Auger analysis
Authors: Geller J. D.
Published: September 2008

The surface analysis techniques of Auger electron spectroscopy (AES) and x-ray photoelectron spectroscopy (XPS) are often used to characterize the near surface composition of stainless steel. AES is most often used to determine the oxide thickness and the maximum chromium to iron ratio as this information is used to determine if the material is properly electropolished. XPS is primarily used to determine the near surface chemistry as well as the chromium to iron ratio. Instrument calibration is critical to reliable composition determination. For AES, the use of elemental sensitivity factors is found to be a significant source of error. Proposed is a new method for the determination of Cr∕Fe ratios using AES. The resulting depth profiles show the proper stainless steel composition under the surface enhanced layer.
Photo-induced surface functionalization of carbon surfaces: The role of photoelectron ejection
Authors: Colavita Paula E. , Sun Bin , Tse Kiu-Yuen , Hamers Robert J.
Published: September 2008

Carbon-based materials are attractive for a wide range of applications, from biomaterials to fuel cells; however, their effective use often requires controlling the surface chemistry to incorporate recognition moieties or reactive centers. The high stability of carbon also makes it a challenging material to functionalize; recently, the use of ultraviolet light (254nm) to initiate functionalization of carbon surfaces has emerged as a way to obtain carbon/organic interfaces with tailored properties. The authors have investigated the mechanism of covalent grafting of amorphous carbon surfaces with functional organic molecules using the photochemical reaction of terminal alkenes. Measurements comparing the reactivity of different n-alkenes bearing different terminal groups at the terminus opposite the olefin showed pronounced differences in reactivity. They characterized the rate and final coverage of the resulting organic layers using x-ray photoelectron spectroscopy and infrared reflection-absorption spectroscopy. Ultraviolet photoelectron spectroscopy and photocurrent measurements suggested that the reaction involves photoelectron emission from the carbon surface into the liquid phase. Density functional calculations show a strong correlation between the electron affinity of the alkenes and the observed reactivity. The specific terminal group opposite to the olefin was found to play an important role in the stabilization of excess negative charges on the molecule, thus explaining the strong dependence of reactivity on the particular terminal group. These findings suggest that the reaction involves injection of photoelectrons into the alkene acceptor levels, leading to the formation of radical anions in the liquid phase. Finally, the authors demonstrate that the grafting of marginally reactive alkenes can be enhanced by seeding the surface with a small amount of good electron accepting groups. These results provide fundamental new insights into the role of electronic excitations in controlling rates and mechanisms of olefin reactions at surfaces. While demonstrated here for amorphous carbon, these results may also be significant for the UV initiated grafting of olefins on other semiconductors.
Characterization of plasma etching induced interface states at Ti∕p-SiGe Schottky contacts
Authors: Mamor M. , Sellai A.
Published: September 2008

The authors have used current-voltage (I-V) data measured over a wide temperature range (100–300K) complemented by deep level transient spectroscopy (DLTS) for the assessment of the defects introduced in Si0.95Ge0.05 by argon plasma sputter etching. From DLTS, defect concentration depth profiling was extracted and revealed that the main defect introduced during argon plasma sputtering is located very close to the surface. I-V-T analysis shows that the electrical characteristics deviated from the ideal case and indicate the presence of interface states, resulting from the plasma etching induced surface states at Ti∕Si0.95Ge0.05 interface. The interface state density as well as its temperature dependence were obtained from forward bias I-V-T measurements by considering the bias dependence of effective barrier height Φe. It is found that interface states density is temperature dependent although weakly.
Photoconductive analysis of ion implantation damage and annealing in silicon wafers
Authors: Ahrenkiel R. K.
Published: September 2008

This work describes the use of a new method of detecting residual damage centers, which are produced in ion-implanted silicon. Contactless resonant-coupled photoconductive decay (RCPCD) measures the minority-carrier lifetime in the unimplanted region of the wafer. The analysis and data show that the lifetime is dominated by recombination in the implanted volume. By varying the wavelength of the RCPCD excitation, one can determine that the dominant recombination occurs in the implanted region. The data show that the carrier lifetime increases by orders of magnitude as the recombination mechanism changes from defect to Auger recombination. The latter arises from high-density, electrically activated acceptors in p-type silicon after thermal annealing.
Development of a cosputter-evaporation chamber for Fe–Ga films
Authors: Morley N. A. , Yeh S.-L. , Rigby S. , Javed A. , Gibbs M. R. J.
Published: September 2008

A new deposition technique involving the dc magnetron sputtering of Fe simultaneously with Ga evaporation has been developed to fabricate thin Fe(1−x)Gax (0<x<0.4) films. Simultaneous sputtering and evaporation has been developed as an alternative to the sputtering of alloy targets, where the need for compositional variation can be hard to address. The new technique allows the freedom of composition that cosputtering would offer, but mitigates the issue of being unable to sputter Ga. The need for the preparation of alloy targets is also avoided. To control the concentration of the Ga in the films, the evaporation rate, the dc magnetron power, and the chamber pressure were varied. The films fabricated were studied to determine their magnetic and microstructural properties. The Fe–Ga films fabricated had magnetostriction constants which had increased by a factor of 5 compared to the same thickness of Fe film.
Growth of InN on Si (111) by atmospheric-pressure metal-organic chemical vapor deposition using InN∕AlN double-buffer layers
Authors: Li Zhen-Yu , Lan Shan-Ming , Uen Wu-Yih , Chen Ying-Ru , Chen Meng-Chu , Huang Yu-Hsiang , Ku Chien-Te , Liao Sen-Mao , Yang Tsun-Neng , Wang Shing-Chung , Chi Gou-Chung
Published: September 2008

Indium nitride (InN) epilayers have been successfully grown on Si (111) substrates with low-temperature (450°C) grown InN and high-temperature (1050°C) grown AlN (InN∕AlN) double-buffer layers by atmospheric-pressure metal-organic chemical vapor deposition (AP-MOCVD). X-ray diffraction characterizations indicated that highly (0001)-oriented hexagonal InN was grown on Si (111) substrate. Photoluminescence (PL) analyses performed at room temperature showed a strong emission at 0.72eV with a full width at half maximum of 121meV. Excitation intensity dependent measurements demonstrated the PL mechanism to be the band-to-band transition. Time-resolved PL could be fitted by a single exponential exhibiting an ordered film and a recombination lifetime of around 0.85ns. In particular, transmission electron microscopy characterizations indicated that the use of AlN first buffer is very important to achieve a structurally uniform (0001)-oriented InN epilayer on Si (111) by AP-MOCVD.
Classical size effect in oxide-encapsulated Cu thin films: Impact of grain boundaries versus surfaces on resistivity
Authors: Sun Tik , Yao Bo , Warren Andrew P. , Kumar Vineet , Roberts Scott , Barmak Katayun , Coffey Kevin R.
Published: September 2008

A methodology is developed to independently evaluate surface and grain boundary scattering in silicon dioxide-encapsulated, polycrystalline Cu thin films. The room-temperature film resistivity for samples with film thicknesses in the range of 27 to 1 65 nm and different grain sizes (determined from approximately 400 to 1500 grains per sample) is compared to existing and empirical models of surface and grain boundary scattering. For the combined effects of surface and grain boundary scattering, the surface specularity parameter p is 0.6±0.2 and the grain boundary reflectivity coefficient R is 0.45±0.03. It is thereby shown that the resistivity contribution from grain boundary scattering is significantly greater than that of surface scattering for Cu thin films having Cu∕SiO2 surfaces and grain sizes similar to film thickness.
Optical radiation selective photodetectors based on III nitrides
Authors: Pillai R. , Starikov D. , Boney C. , Bensaoula A.
Published: September 2008

Wide direct band gap III nitride materials have opened up many new optoelectronic applications because they allow access to a very wide spectral range, from 200nmto1.77μm, from a single material system. Both light emission sources and photodetectors with advanced properties can be achieved through tailoring layered III nitride structures with various layer orders, chemical compositions, conductivities, and thicknesses. In addition, substrate selection plays an important role in the fabrication of these devices as well as in achieving desired device properties. Along with the efficiency of detection, in most cases it is important to provide selectivity of the optical radiation sensed by the optical device. Such selectivity can be achieved by using spectral properties of optical radiation. In this article the authors present results on the modeling of dual-band photodiode structures based on III nitrides, grown on silicon substrates. UV/IR visible- and solar-blind UV/IR photodetectors have been demonstrated. The peak responsivities of the dual-band photodetectors are 3.8 and 55mA∕W at wavelengths of 349 and 1000nm, respectively. Results on the modeling of the dual-band photodiodes in order to optimize the IR response and realize the solar-blind capability are presented.
Single-chamber plasma enhanced chemical vapor deposition of transparent organic/inorganic multilayer barrier coating at low temperature
Authors: Park S. M. , Kim D. J. , Kim S. I. , Lee N.-E.
Published: September 2008

Deposition of organic/inorganic multilayers is usually carried out by two different process steps by two different deposition methods. A single-chamber process for the deposition of multilayer stacks can make the process and deposition system simpler. In this work, SiOCH and plasma-polymerized methylcyclohexane (pp-MCH) films and their multilayer stacks for application to transparent diffusion barrier coatings were deposited in a single low-temperature plasma enhanced chemical vapor deposition reactor using hexamethyldisilazane/N2O∕O2∕Ar and methylcyclohexane/Ar mixtures for SiOCH and pp-MCH layers, respectively. The deposition rates of the SiOCH and pp-MCH layers were increased with increasing the N2O:O2 gas flow ratio and rf plasma power, respectively. Oxygen concentration in the SiOCH films was decreased and carbon and hydrogen incorporation was increased when increasing the N2O:O2 gas flow ratio from 0:1 to 3:1. In this work, the water vapor transmission rate of polyester sulfone substrate could be reduced from a level of 50 (bare substrate) to 0.8g∕m2day after deposition of a pp-MCH/SiOCH/pp-MCH multilayer coating.
Comment on "Age and Evolution of the Grand Canyon Revealed by U-Pb Dating of Water Table–Type Speleothems"
Authors: Pearthree Philip A. , Spencer Jon E. , Faulds James E. , House P. Kyle
Published: September 2008

Polyak
et al
. (Reports, 7 March 2008, p. 1377) reported that development of the western Grand Canyon began about 17 million years ago. However, their conclusion is based on an inappropriate conflation of Plio-Quaternary incision rates and longer-term rates derived from sites outside the Grand Canyon. Water-table declines at these sites were more likely related to local base-level changes and Miocene regional extensional tectonics.
4D Electron Diffraction Reveals Correlated Unidirectional Behavior in Zinc Oxide Nanowires
Authors: Yang Ding-Shyue , Lao Changshi , Zewail Ahmed H.
Published: September 2008

The confined electronic structure of nanoscale materials has increasingly been shown to induce behavior quite distinct from that of bulk analogs. Direct atomic-scale visualization of nanowires of zinc oxide was achieved through their unique pancake-type diffraction by using four-dimensional (4D) ultrafast electron crystallography. After electronic excitation of this wide-gap photonic material, the wires were found to exhibit colossal expansions, two orders of magnitude higher than that expected at thermal equilibrium; the expansion is highly anisotropic, a quasi–one-dimensional behavior, and is facilitated by the induced antibonding character. By reducing the density of nanowires, the expansions reach even larger values and occur at shorter times, suggesting a decrease of the structural constraint in transient atomic motions. This unanticipated ultrafast carrier-driven expansion highlights the optoelectronic consequences of nanoscale morphologies.
Master of the Universe
Authors: Coles Peter
Published: September 2008

Cosmology
.
By Steven Weinberg
. Oxford University Press, Oxford, 2008. 611 pp. $90, £45. ISBN 9780198526827.

In this technically challenging text, the Nobel Prize-winning author offers a thorough, authoritative account of cosmology that will reward students and established researchers alike.
Subfunctionality of Hydride Transferases of the Old Yellow Enzyme Family of Flavoproteins of
Pseudomonas putida
Authors: van Dillewijn Pieter , Wittich Rolf-Michael , Caballero Antonio , Ramos Juan-Luis
Published: September 2008

To investigate potential complementary activities of multiple enzymes belonging to the same family within a single microorganism, we chose a set of Old Yellow Enzyme (OYE) homologs of
Pseudomonas putida
. The physiological function of these enzymes is not well established; however, an activity associated with OYE family members from different microorganisms is their ability to reduce nitroaromatic compounds. Using an in silico approach, we identified six OYE homologs in
P. putida
KT2440. Each gene was subcloned into an expression vector, and each corresponding gene product was purified to homogeneity prior to in vitro analysis for its catalytic activity against 2,4,6-trinitrotoluene (TNT). One of the enzymes, called XenD, lacked in vitro activity, whereas the other five enzymes demonstrated type I hydride transferase activity and reduced the nitro groups of TNT to hydroxylaminodinitrotoluene derivatives. XenB has the additional ability to reduce the aromatic ring of TNT to produce Meisenheimer complexes, defined as type II hydride transferase activity. The condensations of the primary products of type I and type II hydride transferases react with each other to yield diarylamines and nitrite; the latter can be further reduced to ammonium and serves as a nitrogen source for microorganisms in vivo.
Type II Hydride Transferases from Different Microorganisms Yield Nitrite and Diarylamines from Polynitroaromatic Compounds
Authors: van Dillewijn Pieter , Wittich Rolf-Michael , Caballero Antonio , Ramos Juan-Luis
Published: September 2008

Homogenous preparations of XenB of
Pseudomonas putida
, pentaerythritol tetranitrate reductase of
Enterobacter cloacae
, and
N
-ethylmaleimide reductase of
Escherichia coli
, all type II hydride transferases of the Old Yellow Enzyme family of flavoproteins, are shown to reduce the polynitroaromatic compound 2,4,6-trinitrotoluene (TNT). The reduction of this compound yields hydroxylaminodinitrotoluenes and Meisenheimer dihydride complexes, which, upon condensation, yield stoichiometric amounts of nitrite and diarylamines, implying that type II hydride transferases are responsible for TNT denitration, a process with important environmental implications for TNT remediation.
Darkling Beetles (
Alphitobius diaperinus
) and Their Larvae as Potential Vectors for the Transfer of
Campylobacter jejuni
and
Salmonella enterica
Serovar Paratyphi B Variant Java between Successive Broiler Flocks
Authors: Hazeleger Wilma C. , Bolder Nico M. , Beumer Rijkelt R. , Jacobs-Reitsma Wilma F.
Published: September 2008

Broiler flocks often become infected with
Campylobacter
and
Salmonella
, and the exact contamination routes are still not fully understood. Insects like darkling beetles and their larvae may play a role in transfer of the pathogens between consecutive cycles. In this study, several groups of beetles and their larvae were artificially contaminated with a mixture of
Salmonella enterica
serovar Paratyphi B Variant Java and three
C. jejuni
strains and kept for different time intervals before they were fed to individually housed chicks. Most inoculated insects were positive for
Salmonella
and
Campylobacter
just before they were fed to the chicks. However,
Campylobacter
could not be isolated from insects that were kept for 1 week before they were used to mimic an empty week between rearing cycles. All broilers fed insects that were inoculated with pathogens on the day of feeding showed colonization with
Campylobacter
and
Salmonella
at levels of 50 to 100%. Transfer of both pathogens by groups of insects that were kept for 1 week before feeding to the chicks was also observed, but at lower levels. Naturally contaminated insects that were collected at a commercial broiler farm colonized broilers at low levels as well. In conclusion, the fact that
Salmonella
and
Campylobacter
can be transmitted via beetles and their larvae to flocks in successive rearing cycles indicates that there should be intensive control programs for exclusion of these insects from broiler houses.
Joint Immobilization of Plant Growth-Promoting Bacteria and Green Microalgae in Alginate Beads as an Experimental Model for Studying Plant-Bacterium Interactions
Authors: de-Bashan Luz E. , Bashan Yoav
Published: September 2008

A simple, quantitative experimental model, offering a convenient and basic approach to studies of plant-bacterium interactions, is proposed. This involves immobilizing a unicellular, freshwater microalga, a
Chlorella
species, serving as the plant, with a plant growth-promoting bacterium, an
Azospirillum
species, in small alginate beads to allow close interaction and to avoid external interference from bacterial contaminants.
Gene Transcription in
Lactarius quietus
-
Quercus petraea
Ectomycorrhizas from a Forest Soil
Authors: Courty P. E. , Poletto M. , Duchaussoy F. , Buée M. , Garbaye J. , Martin F.
Published: September 2008

Extracting fungal mRNA from ectomycorrhizas (ECMs) and forest soil samples for monitoring in situ metabolic activities is a significant challenge when studying the role of ECMs in biogeochemical cycles. A robust, simple, rapid, and effective method was developed for extracting RNA from rhizospheric soil and ECMs by adapting previous grinding and lysis methods. The quality and yield of the extracted RNA were sufficient to be used for reverse transcription. RNA extracted from ECMs of
Lactarius quietus
in a 100-year-old oak stand was used to construct a cDNA library and sequence expressed sequence tags. The transcripts of many genes involved in primary metabolism and in the degradation of organic matter were found. The transcription levels of four targeted fungal genes (glutamine synthase, a general amino acid transporter, a tyrosinase, and
N
-acetylhexosaminidase) were measured by quantitative reverse transcription-PCR in ECMs and in the ectomycorrhizospheric soil (the soil surrounding the ECMs containing the extraradical mycelium) in forest samples. On average, levels of gene expression for the
L. quietus
ECM root tips were similar to those for the extraradical mycelium, although gene expression varied up to 10-fold among the samples. This study demonstrates that gene expression from ECMs and soil can be analyzed. These results provide new perspectives for investigating the role of ectomycorrhizal fungi in the functioning of forest ecosystems.
Unique Substrate Spectrum and PCR Application of
Nanoarchaeum equitans
Family B DNA Polymerase
Authors: Choi Jeong Jin , Song Jae-Geun , Nam Ki Hoon , Lee Jong Il , Bae Heejin , Kim Gun A. , Sun Younguk , Kwon Suk-Tae
Published: September 2008

The known archaeal family B DNA polymerases are unable to participate in the PCR in the presence of uracil. Here, we report on a novel archaeal family B DNA polymerase from
Nanoarchaeum equitans
that can successfully utilize deaminated bases such as uracil and hypoxanthine and on its application to PCR.
N. equitans
family B DNA polymerase (
Neq
DNA polymerase) produced λ DNA fragments up to 10 kb with an approximately 2.2-fold-lower error rate (5.53 × 10
−6
) than
Taq
DNA polymerase (11.98 × 10
−6
). Uniquely,
Neq
DNA polymerase also amplified λ DNA fragments using dUTP (in place of dTTP) or dITP (partially replaced with dGTP). To increase PCR efficiency,
Taq
and
Neq
DNA polymerases were mixed in different ratios; a ratio of 10:1 efficiently facilitated long PCR (20 kb). In the presence of dUTP, the PCR efficiency of the enzyme mixture was two- to threefold higher than that of either
Taq
and
Neq
DNA polymerase alone. These results suggest that
Neq
DNA polymerase and
Neq
plus DNA polymerase (a mixture of
Taq
and
Neq
DNA polymerases) are useful in DNA amplification and PCR-based applications, particularly in clinical diagnoses using uracil-DNA glycosylase.
Reconstitution of Iron Oxidase from Sulfur-Grown
Acidithiobacillus ferrooxidans
Authors: Taha Taher M. , Kanao Tadayoshi , Takeuchi Fumiaki , Sugio Tsuyoshi
Published: September 2008

The iron oxidation system from sulfur-grown
Acidithiobacillus ferrooxidans
ATCC 23270 cells was reconstituted in vitro. Purified rusticyanin, cytochrome
c
, and
aa
3
-type cytochrome oxidase were essential for reconstitution. The iron-oxidizing activity of the reconstituted system was 3.3-fold higher than that of the cell extract from which these components were purified.
Soil Formate Regulates the Fungal Nitrous Oxide Emission Pathway
Authors: Ma W. K. , Farrell R. E. , Siciliano S. D.
Published: September 2008

Fungal activity is a major driver in the global nitrogen cycle, and mounting evidence suggests that fungal denitrification activity contributes significantly to soil emissions of the greenhouse gas nitrous oxide (N
2
O). The metabolic pathway and oxygen requirement for fungal denitrification are different from those for bacterial denitrification. We hypothesized that the soil N
2
O emission from fungi is formate and O
2
dependent and that land use and landforms could influence the proportion of N
2
O coming from fungi. Using substrate-induced respiration inhibition under anaerobic and aerobic conditions in combination with
15
N gas analysis, we found that formate and hypoxia (versus anaerobiosis) were essential for the fungal reduction of
15
N-labeled nitrate to
15
N
2
O. As much as 65% of soil-emitted N
2
O was attributable to fungi; however, this was found only in soils from water-accumulating landforms. From these results, we hypothesize that plant root exudates could affect N
2
O production from fungi via the proposed formate-dependent pathway.
Metagenomic Screening for Bleomycin Resistance Genes
Authors: Mori Toshio , Mizuta Shiori , Suenaga Hikaru , Miyazaki Kentaro
Published: September 2008

A metagenomic library of activated sludge was screened for bleomycin resistance genes. Two genes were identified that differed greatly from each other, from the genes of bleomycin-producing actinomycetes, and from those of clinical isolates. Therefore, the nonclinical environment is a rich reservoir of new resistance elements, and metagenomics can be used to sample the resistome rapidly.
Multilocus Sequence Analysis for Assessment of the Biogeography and Evolutionary Genetics of FourBradyrhizobiumSpecies That Nodulate Soybeans on the Asiatic Continent
Authors: Vinuesa Pablo , Rojas-Jiménez Keilor , Contreras-Moreira Bruno , Mahna Suresh K. , Prasad Braj Nandan , Moe Hla , Selvaraju Suresh Babu , Thierfelder Heidemarie , Werner Dietrich
Published: September 2008

A highly supported maximum-likelihood species phylogeny for the genusBradyrhizobiumwas inferred from a supermatrix obtained from the concatenation of partialatpD,recA,glnII, andrpoBsequences corresponding to 33 reference strains and 76 bradyrhizobia isolated from the nodules ofGlycine max(soybean) trap plants inoculated with soil samples from Myanmar, India, Nepal, and Vietnam. The power of the multigene approach using multiple strains per species was evaluated in terms of overall tree resolution and phylogenetic congruence, representing a practical and portable option for bacterial molecular systematics. Potential pitfalls of the approach are highlighted. Seventy-five of the isolates could be classified asB. japonicumtype Ia (USDA110/USDA122-like),B. liaoningense,B. yuanmingense, orB. elkanii, whereas one represented a novelBradyrhizobiumlineage. Most NepaleseB. japonicumIa isolates belong to a highly epidemic clone closely related to strain USDA110. Significant phylogenetic evidence against the monophyly of the ofB. japonicumI and Ia lineages was found. Analysis of their DNA polymorphisms revealed high population distances, significant genetic differentiation, and contrasting population genetic structures, suggesting that the strains in the Ia lineage are misclassified asB. japonicum. The DNA polymorphism patterns of all species conformed to the expectations of the neutral mutation and population equilibrium models and, excluding theB. japonicumIa lineage, were consistent with intermediate recombination levels. All species displayed epidemic clones and had broad geographic and environmental distribution ranges, as revealed by mapping climate types and geographic origins of the isolates on the species tree.
Rapid Determination ofEscherichia coliO157:H7 Lineage Types and Molecular Subtypes by Using Comparative Genomic Fingerprinting
Authors: Laing Chad , Pegg Crystal , Yawney Davis , Ziebell Kim , Steele Marina , Johnson Roger , Thomas James E. , Taboada Eduardo N. , Zhang Yongxiang , Gannon Victor P. J.
Published: September 2008

In this study, variably absent or present (VAP) regions discovered through comparative genomics experiments were targeted for the development of a rapid, PCR-based method to subtype and fingerprintEscherichia coliO157:H7. Forty-four VAP loci were analyzed for discriminatory power among 79E. coliO157:H7 strains of 13 phage types (PT). Twenty-three loci were found to maximize resolution among strains, generating 54 separate fingerprints, each of which contained strains of unique PT. Strains from the three previously identified majorE. coliO157:H7 lineages, LSPA6-LI, LSPA6-LI/II, and LSPA6-LII, formed distinct branches on a dendrogram obtained by hierarchical clustering of comparative genomic fingerprinting (CGF) data. By contrast, pulsed-field gel electrophoresis (PFGE) typing generated 52 XbaI digestion profiles that were not unique to PT and did not cluster according to O157:H7 lineage. Our analysis identified a subpopulation comprised of 25 strains from a closed herd of cattle, all of which were of PT87 and formed a cluster distinct from all otherE. coliO157:H7 strains examined. CGF found five related but unique fingerprints among the highly clonal herd strains, with two dominant subtypes characterized by a shift from the presence of locus fprn33 to its absence. CGF had equal resolution to PFGE typing but with greater specificity, generating fingerprints that were unique among phenotypically relatedE. coliO157:H7 lineages and PT. As a comparative genomics typing method that is amenable for use in high-throughput platforms, CGF may be a valuable tool in outbreak investigations and strain characterization.
inlAPremature Stop Codons Are Common amongListeria monocytogenesIsolates from Foods and Yield Virulence-Attenuated Strains That Confer Protection against Fully Virulent Strains
Authors: Nightingale K. K. , Ivy R. A. , Ho A. J. , Fortes E. D. , Njaa B. L. , Peters R. M. , Wiedmann M.
Published: September 2008

Previous studies showed that a considerable proportion ofListeria monocytogenesisolates obtained from foods carry a premature stop codon (PMSC) mutation ininlAthat leads to production of a truncated and secreted InlA. To further elucidate the role these mutations play in virulence ofL. monocytogenes, we created isogenic mutants, including (i) natural isolates where aninlAPMSC was reverted to a wild-typeinlAallele (without a PMSC) and (ii) natural isolates where a PMSC mutation was introduced into a wild-typeinlAallele; isogenic mutant sets were constructed to represent two distinctinlAPMSC mutations. Phenotypical and transcriptional analysis data showed thatinlAPMSC mutations do not have a polar effect on the downstreaminlB. Isogenic and natural strains carrying aninlAPMSC showed significantly reduced invasion efficiencies in Caco-2 and HepG2 cell lines as well as reduced virulence in oral guinea pig infections. Guinea pigs were also orally infected with a natural strain carrying the most commoninlAPMSC mutation (vaccinated group), followed by challenge with a fully virulentL. monocytogenesstrain 15 days postvaccination to probe potentially immunizing effects of exposure toL. monocytogeneswithinlAPMSC mutations. Vaccinated guinea pigs showed reduced bacterial loads in internal organs and improved weight gain postchallenge, indicating reduced severity of infections in guinea pigs exposed to natural strains withinlAPMSC mutations. Our data support that (i)inlAPMSC mutations are causally associated with attenuated virulence in mammalian hosts and (ii) naturally occurring virulence-attenuatedL. monocytogenesstrains commonly found in food confer protective immunity.
Dynamic Localization of MreB in
Vibrio parahaemolyticus
and in the Ectopic Host Bacterium
Escherichia coli
Authors: Chiu Shen-Wen , Chen Shau-Yan , Wong Hin-chung
Published: September 2008

MreB, a homolog of eukaryotic actin, participates in morphogenesis, cell division, cell polarity, and chromosome segregation in prokaryotes. In this study, a yellow fluorescent protein conjugate (YFP-MreB
Vp
) was generated to investigate the behavior of MreB in merodiploid strain SC9 of the enteropathogen
Vibrio parahaemolyticus
. Under normal growth conditions, YFP-MreB
Vp
formed helical filaments with a pitch of 0.64 ± 0.09 μm in about 85% of exponential-phase cells, and different clusters, relaxed coils, and ring configurations were observed in a small proportion of the cells. Overexpression of YFP-MreB
Vp
substantially altered the structure of the MreB cytoskeleton and resulted in swollen and pleomorphic cells. Disturbing the activities of penicillin-binding proteins or adding magnesium suppressed the morphological distortions. These results indicate that mislocalization of cell wall-synthesizing machinery was responsible for morphological abnormality. By expressing YFP-MreB
Vp
in the ectopic host bacterium
Escherichia coli
, shrinkage, fragmentation, and annealing of MreB
Vp
filaments were directly observed. This work revealed the dynamic pattern of the localization of YFP-MreB
Vp
in
V. parahaemolyticus
and its relationship to cell morphogenesis, and the YFP-MreB
Vp
-
E. coli
system may be used to investigate the dynamic spatial structures of the MreB cytoskeleton in vivo.
Simple and Safe Method for Simultaneous Isolation of Microbial RNA and DNA from Problematic Populations
Authors: McIlroy Simon , Porter Kate , Seviour Robert J. , Tillett Daniel
Published: September 2008

We describe a novel, rapid, and safe method for extracting RNA and DNA from refractory microbes, which avoids the use of phenol or chloroform. It has been used successfully to isolate high-quality nucleic acids from pure cultures and environmental populations known to resist widely used extraction protocols.
Mutational Analysis of the Class IIa Bacteriocin Curvacin A and Its Orientation in Target Cell Membranes
Authors: Haugen Helén Sophie , Kristiansen Per Eugen , Fimland Gunnar , Nissen-Meyer Jon
Published: September 2008

To analyze the orientation in target cell membranes of the pediocin-like bacteriocin (antimicrobial peptide) curvacin A, 55 variants were generated by site-directed mutagenesis and their potencies against four different target cells determined. The result suggest that the somewhat hydrophilic short central helix (residues 19 to 24), along with the N-terminal β-sheet-like structure (residues 1 to 16), inserts in the interface region of the target cell membrane, with Ala22 close to the hydrophobic core of the membrane. The following hinge region, with Gly28 as an important residue, may then form a turn wherein Gly28 becomes positioned near the border between the interface and the hydrophobic regions, thus permitting the longer and more-hydrophobic C-terminal helix (residues 29 to 41) to insert into the hydrophobic core of the membrane. This helix contains three glycine residues (G33, G37, and G40) that form a putative helix-helix-interacting GxxxGxxG motif. The replacement of any of these glycines with a larger residue was very detrimental, suggesting their possible involvement in helix-helix interactions with a membrane-embedded receptor protein.
Evaluating the Insecticidal Genes and Their Expressed Products in
Bacillus thuringiensis
Strains by Combining PCR with Mass Spectrometry
Authors: Sun Yunjun , Fu Zujiao , Ding Xuezhi , Xia Liqiu
Published: September 2008

By a combination of PCR and mass spectrometry, a total of five
cry
genes (
cry1Aa, cry1Ac, cry2Aa, cry2Ab
, and
cry1Ia
) were detected in genomic DNA from the wild-type
Bacillus thuringiensis
strain 4.0718, and three protoxins (Cry1Aa, Cry1Ac, and Cry2Aa) were identified in the strain's parasporal crystals. These results indicated that this complementary method may be useful in evaluating
B. thuringiensis
strains at both the gene and protein levels.
Role of DNA Protection and Repair in Resistance of
Bacillus subtilis
Spores to Ultrahigh Shock Pressures Simulating Hypervelocity Impacts
Authors: Moeller Ralf , Horneck Gerda , Rabbow Elke , Reitz Günther , Meyer Cornelia , Hornemann Ulrich , Stöffler Dieter
Published: September 2008

Impact-induced ejections of rocks from planetary surfaces are frequent events in the early history of the terrestrial planets and have been considered as a possible first step in the potential interplanetary transfer of microorganisms. Spores of
Bacillus subtilis
were used as a model system to study the effects of a simulated impact-caused ejection on rock-colonizing microorganisms using a high-explosive plane wave setup. Embedded in different types of rock material, spores were subjected to extremely high shock pressures (5 to 50 GPa) lasting for fractions of microseconds to seconds. Nearly exponential pressure response curves were obtained for spore survival and linear dependency for the induction of sporulation-defective mutants. Spores of strains defective in major small, acid-soluble spore proteins (SASP) (α/β-type SASP) that largely protect the spore DNA and spores of strains deficient in nonhomologous-end-joining DNA repair were significantly more sensitive to the applied shock pressure than were wild-type spores. These results indicate that DNA may be the sensitive target of spores exposed to ultrahigh shock pressures. To assess the nature of the critical physical parameter responsible for spore inactivation by ultrahigh shock pressures, the resulting peak temperature was varied by lowering the preshock temperature, changing the rock composition and porosity, or increasing the water content of the samples. Increased peak temperatures led to increased spore inactivation and reduced mutation rates. The data suggested that besides the potential mechanical stress exerted by the shock pressure, the accompanying high peak temperatures were a critical stress parameter that spores had to cope with.
Distribution of Different Species of the
Bacteroides fragilis
Group in Individuals with Japanese Cedar Pollinosis
Authors: Odamaki Toshitaka , Xiao Jin-Zhong , Sakamoto Mitsuo , Kondo Shizuki , Yaeshima Tomoko , Iwatsuki Keiji , Togashi Hideo , Enomoto Tadao , Benno Yoshimi
Published: September 2008

We investigated associations of species of the
Bacteroides fragilis
group with Japanese cedar pollinosis (JCPsis). Cell numbers of
Bacteroides fragilis
and
Bacteroides intestinalis
were significantly higher in JCPsis subjects than in non-JCPsis subjects before the pollen season. They correlated positively with both symptom scores and JCPsis-specific immunoglobulin E levels.
Molecular Characterization of a Variant of
Bacillus anthracis
-Specific Phage AP50 with Improved Bacteriolytic Activity
Authors: Sozhamannan Shanmuga , McKinstry Michael , Lentz Shannon M. , Jalasvuori Matti , McAfee Farrell , Smith Angela , Dabbs Jason , Ackermann Hans-W. , Bamford Jaana K. H. , Mateczun Alfred , Read Timothy D.
Published: September 2008

The genome sequence of a
Bacillus anthracis
-specific clear plaque mutant phage, AP50c, contains 31 open reading frames spanning 14,398 bp, has two mutations compared to wild-type AP50t, and has a colinear genome architecture highly similar to that of gram-positive
Tectiviridae
phages. Spontaneous AP50c-resistant
B. anthracis
mutants exhibit a mucoid colony phenotype.
Broiler
Campylobacter
Contamination and Human Campylobacteriosis in Iceland
Authors: Callicott Kenneth A. , Harðardóttir Hjördís , Georgsson Franklín , Reiersen Jarle , Friðriksdóttir Vala , Gunnarsson Eggert , Michel Pascal , Bisaillon Jean-Robert , Kristinsson Karl G. , Briem Haraldur , Hiett Kelli L. , Needleman David S. , Stern Norman J.
Published: September 2008

To examine whether there is a relationship between the degree of
Campylobacter
contamination observed in product lots of retail Icelandic broiler chicken carcasses and the incidence of human disease, 1,617 isolates from 327 individual product lots were genetically matched (using the
flaA
short variable region [SVR[) to 289 isolates from cases of human campylobacteriosis whose onset was within approximately 2 weeks from the date of processing. When there was genetic identity between broiler isolates and human isolates within the appropriate time frame, a retail product lot was classified as implicated in human disease. According to the results of this analysis, there were multiple clusters of human disease linked to the same process lot or lots. Implicated and nonimplicated retail product lots were compared for four lot descriptors: lot size, prevalence, mean contamination, and maximum contamination (as characterized by direct rinse plating). For retail product distributed fresh, Mann-Whitney U tests showed that implicated product lots had significantly (
P
= 0.0055) higher mean contamination than nonimplicated lots. The corresponding median values were 3.56 log CFU/carcass for implicated lots and 2.72 log CFU/carcass for nonimplicated lots. For frozen retail product, implicated lots were significantly (
P
= 0.0281) larger than nonimplicated lots. When the time frame was removed, retail product lots containing
Campylobacter flaA
SVR genotypes also seen in human disease had significantly higher mean and maximum contamination numbers than lots containing no genotypes seen in human disease for both fresh and frozen product. Our results suggest that cases of broiler-borne campylobacteriosis may occur in clusters and that the differences in mean contamination levels may provide a basis for regulatory action that is more specific than a presence-absence standard.
Transcriptional Regulation of
xyr1
, Encoding the Main Regulator of the Xylanolytic and Cellulolytic Enzyme System in
Hypocrea jecorina
Authors: Mach-Aigner Astrid R. , Pucher Marion E. , Steiger Matthias G. , Bauer Gudrun E. , Preis Sonja J. , Mach Robert L.
Published: September 2008

In
Hypocrea jecorina
, Xyr1 (xylanase regulator 1) is the main transcription activator of hydrolase-encoding genes, such as
xyn1
,
xyn2
,
bxl1
,
cbh1
,
cbh2
,
egl1
, and
bgl1
. Even though Xyr1 mediates the induction signal for all these genes derived from various inducing carbon sources and compounds,
xyr1
transcription itself is not inducible by any of these substances. However, cultivation on glucose as the carbon source provokes carbon catabolite repression of
xyr1
transcription mediated by Cre1. In addition,
xyr1
transcription is repressed by the specific transcription factor Ace1. Moreover, Xyr1 is permanently available in the cell, and no de novo synthesis of this factor is needed for a first induction of
xyn1
transcription. The constitutive expression of
xyr1
leads to a significant elevation/deregulation of the
xyn1
,
xyn2
, and
bxl1
transcription compared to what is seen for the parental strain. Overall, the corresponding xylanolytic enzyme activities are clearly elevated in a constitutively
xyr1
-expressing strain, emphasizing this factor as an auspicious target for genetically engineered strain improvement.
Involvement of a Novel Enzyme, MdpA, in Methyl
tert
-Butyl Ether Degradation in
Methylibium petroleiphilum
PM1
Authors: Schmidt Radomir , Battaglia Vince , Scow Kate , Kane Staci , Hristova Krassimira R.
Published: September 2008

Methylibium petroleiphilum
PM1 is a well-characterized environmental strain capable of complete metabolism of the fuel oxygenate methyl
tert
-butyl ether (MTBE). Using a molecular genetic system which we established to study MTBE metabolism by PM1, we demonstrated that the enzyme MdpA is involved in MTBE removal, based on insertional inactivation and complementation studies. MdpA is constitutively expressed at low levels but is strongly induced by MTBE. MdpA is also involved in the regulation of
tert
-butyl alcohol (TBA) removal under certain conditions but is not directly responsible for TBA degradation. Phylogenetic comparison of MdpA to related enzymes indicates close homology to the short-chain hydrolyzing alkane hydroxylases (AH1), a group that appears to be a distinct subfamily of the AHs. The unique, substrate-size-determining residue Thr
59
distinguishes MdpA from the AH1 subfamily as well as from AlkB enzymes linked to MTBE degradation in
Mycobacterium austroafricanum
.
Time-Lapse Microscopy of
Streptomyces coelicolor
Growth and Sporulation
Authors: Jyothikumar Vinod , Tilley Emma J. , Wali Rashmi , Herron Paul R.
Published: September 2008

Bacteria from the genus
Streptomyces
are among the most complex of all prokaryotes; not only do they grow as a complex mycelium, they also differentiate to form aerial hyphae before developing further to form spore chains. This developmental heterogeneity of streptomycete microcolonies makes studying the dynamic processes that contribute to growth and development a challenging procedure. As a result, in order to study the mechanisms that underpin streptomycete growth, we have developed a system for studying hyphal extension, protein trafficking, and sporulation by time-lapse microscopy. Through the use of time-lapse microscopy we have demonstrated that
Streptomyces coelicolor
germ tubes undergo a temporary arrest in their growth when in close proximity to sibling extension sites. Following germination, in this system, hyphae extended at a rate of ∼20 μm h
−1
, which was not significantly different from the rate at which the apical ring of the cytokinetic protein FtsZ progressed along extending hyphae through a spiraling movement. Although we were able to generate movies for streptomycete sporulation, we were unable to do so for either the erection of aerial hyphae or the early stages of sporulation. Despite this, it was possible to demonstrate an arrest of aerial hyphal development that we suggest is through the depolymerization of FtsZ-enhanced green fluorescent protein (GFP). Consequently, the imaging system reported here provides a system that allows the dynamic movement of GFP-tagged proteins involved in growth and development of
S. coelicolor
to be tracked and their role in cytokinesis to be characterized during the streptomycete life cycle.