bluuebunny/crossref_metadata_2025_split huggingface dataset:
Initial Steps of Colicin E1 Import across the Outer Membrane of
Escherichia coli
Authors: Masi Muriel , Vuong Phu , Humbard Matthew , Malone Karen , Misra Rajeev 
Published: February 2007

ABSTRACT

Data suggest a two-receptor model for colicin E1 (ColE1) translocation across the outer membrane of
Escherichia coli
. ColE1 initially binds to the vitamin B
12
receptor BtuB and then translocates through the TolC channel-tunnel, presumably in a mostly unfolded state. Here, we studied the early events in the import of ColE1. Using in vivo approaches, we show that ColE1 is cleaved when added to whole cells. This cleavage requires the presence of the receptor BtuB and the protease OmpT, but not that of TolC. Strains expressing OmpT cleaved ColE1 at K84 and K95 in the N-terminal translocation domain, leading to the removal of the TolQA box, which is essential for ColE1's cytotoxicity. Supported by additional in vivo data, this suggests that a function of OmpT is to degrade colicin at the cell surface and thus protect sensitive
E. coli
cells from infection by E colicins. A genetic strategy for isolating
tolC
mutations that confer resistance to ColE1, without affecting other TolC functions, is also described. We provide further in vivo evidence of the multistep interaction between TolC and ColE1 by using cross-linking followed by copurification via histidine-tagged TolC. First, secondary binding of ColE1 to TolC is dependent on primary binding to BtuB. Second, alterations to a residue in the TolC channel interfere with the translocation of ColE1 across the TolC pore rather than with the binding of ColE1 to TolC. In contrast, a substitution at a residue exposed on the cell surface abolishes both binding and translocation of ColE1.
Expression of the
bviIR
and
cepIR
Quorum-Sensing Systems of
Burkholderia vietnamiensis
Authors: Malott Rebecca J. , Sokol Pamela A. 
Published: February 2007

ABSTRACT

Burkholderia vietnamiensis
has both the
cepIR
quorum-sensing system that is widely distributed among the
Burkholderia cepacia
complex (BCC) and the
bviIR
system. Comparison of the expression of
cepI
,
cepR
,
bviI
, and
bviR-luxCDABE
fusions in
B. vietnamiensis
G4 and the G4
cepR
and
bviR
mutants determined that the expression of
bviI
requires both a functional cognate regulator, BviR, and functional CepR. The
cepIR
system, however, is not regulated by BviR. Unlike the
cepIR
genes in other BCC species, the
cepIR
genes are not autoregulated in G4.
N-
Acyl-homoserine lactone (AHL) production profiles in G4
cepI
,
cepR
,
bviI
, and
bviR
mutants confirmed the regulatory organization of the G4 quorum-sensing systems. The regulatory network in strain PC259 is similar to that in G4, except that CepR positively regulates
cepI
and negatively regulates
cepR
. AHL production and the
bviI
expression levels in seven
B. vietnamiensis
isolates were compared. All strains produced
N-
octanoyl-homoserine lactone and
N-
hexanoyl-homoserine lactone; however, only one of four clinical strains but all three environmental strains produced the BviI synthase product,
N-
decanoyl-homoserine lactone (DHL). The three strains that did not produce DHL expressed
bviR
but not
bviI
. Heterologous expression of
bviR
restored DHL production in these strains. The
bviIR
loci of the non-DHL-producing strains were sequenced to confirm that
bviR
encodes a functional transcriptional regulator. Lack of expression of G4
bviI
in these three strains indicated that an additional regulatory element may be involved in the regulation of
bviIR
expression in certain strains of
B. vietnamiensis
.
Essentiality of Ribosomal and Transcription Antitermination Proteins Analyzed by Systematic Gene Replacement in
Escherichia coli
Authors: Bubunenko Mikhail , Baker Teresa , Court Donald L. 
Published: February 2007

ABSTRACT

We describe here details of the method we used to identify and distinguish essential from nonessential genes on the bacterial
Escherichia coli
chromosome. Three key features characterize our method: high-efficiency recombination, precise replacement of just the open reading frame of a chromosomal gene, and the presence of naturally occurring duplications within the bacterial genome. We targeted genes encoding functions critical for processes of transcription and translation. Proteins from three complexes were evaluated to determine if they were essential to the cell by deleting their individual genes. The transcription elongation Nus proteins and termination factor Rho, which are involved in rRNA antitermination, the ribosomal proteins of the small 30S ribosome subunit, and minor ribosome-associated proteins were analyzed. It was concluded that four of the five bacterial transcription antitermination proteins are essential, while all four of the minor ribosome-associated proteins examined (RMF, SRA, YfiA, and YhbH), unlike most ribosomal proteins, are dispensable. Interestingly, although most 30S ribosomal proteins were essential, the knockouts of six ribosomal protein genes,
rpsF
(S6),
rpsI
(S9),
rpsM
(S13),
rpsO
(S15),
rpsQ
(S17), and
rpsT
(S20), were viable.
IntDOT Interactions with Core- and Arm-Type Sites of the Conjugative Transposon CTnDOT
Authors: DiChiara Jeanne M. , Mattis Aras N. , Gardner Jeffrey F. 
Published: February 2007

ABSTRACT

CTnDOT is a
Bacteroides
conjugative transposon (CTn) that has facilitated the spread of antibiotic resistances among bacteria in the human gut in recent years. Although the integrase encoded by CTnDOT (IntDOT) carries the C-terminal set of conserved amino acids that is characteristic of the tyrosine family of recombinases, the reaction it catalyzes involves a novel step that creates a short region of heterology at the joined ends of the element during recombination. Also, in contrast to tyrosine recombinases, IntDOT catalyzes a reaction that is not site specific. To determine what types of contacts IntDOT makes with the DNA during excision and integration, we first developed an agarose gel-based assay for CTnDOT recombination, which facilitated the purification of the native IntDOT protein. The partially purified IntDOT was then used for DNase I footprinting analysis of the integration site
attDOT
and the excision sites
attL
and
attR
. Our results indicate that CTnDOT has five or six arm sites that are likely to be involved in forming higher-order nucleoprotein complexes necessary for synapsis. In addition, there are four core sites that flank the sites of strand exchange during recombination. Thus, despite the fact that the reaction catalyzed by IntDOT appears to be different from that typically catalyzed by tyrosine recombinases, the protein-DNA interactions required for higher-order structures and recombination appear to be similar.
Microarray Analysis of Transposon Insertion Mutations inBacillus anthracis: Global Identification of Genes Required for Sporulation and Germination
Authors: Day William A. , Rasmussen Suzanne L. , Carpenter Beth M. , Peterson Scott N. , Friedlander Arthur M. 
Published: February 2007

ABSTRACTA transposon site hybridization (TraSH) assay was developed for functional analysis of theBacillus anthracisgenome using a mini-Tn10transposon which permitted analysis of 82% of this pathogen's genes. The system, used to identify genes required for generation of infectious anthrax spores, spore germination, and optimal growth on rich medium, was predictive of the contributions of two conserved hypothetical genes for the phenotypes examined.
Diagnosis of Human Metapneumovirus Infection in Immunosuppressed Lung Transplant Recipients and Children Evaluated for Pertussis
Authors: Dare Ryan , Sanghavi Sonali , Bullotta Arlene , Keightley Maria-Cristina , St. George Kirsten , Wadowsky Robert M. , Paterson David L. , McCurry Kenneth R. , Reinhart Todd A. , Husain Shahid , Rinaldo Charles R. 
Published: February 2007

ABSTRACT
Human metapneumovirus (hMPV) is a recently discovered paramyxovirus that is known to cause respiratory tract infections in children and immunocompromised individuals. Given the difficulties of identifying hMPV by conventional culture, molecular techniques could improve the detection of this virus in clinical specimens. In this study, we developed a real-time reverse transcription-PCR (RT-PCR) assay designed to detect the four genetic lineages of hMPV. This assay and a commercial real-time nucleic acid sequence-based amplification (NASBA) assay (bioMérieux, Durham, NC) were used to determine the prevalence of hMPV in 114 immunosuppressed asymptomatic and symptomatic lung transplant recipients and 232 pediatric patients who were being evaluated for pertussis. hMPV was detected in 4.3% of the immunosuppressed lung transplant recipients and in 9.9% of children evaluated for pertussis. Both RT-PCR and NASBA assays were efficient in detection of hMPV infection in respiratory specimens. Even though hMPV was detected in a small number of the lung transplant recipients, it was still the most prevalent etiologic agent detected in patients with respiratory symptoms. In both of these diverse patient populations, hMPV infection was the most frequent viral respiratory tract infection identified. Given our findings, infection with hMPV infection should be determined as part of the differential diagnosis of respiratory illnesses.
Breeding traits of Hermann's tortoise Testudo hermanni hermanni in two western populations
Authors: Bertolero Albert , Nougarède Jean Pierre , Cheylan Marc , Marín Aurelio 
Published: February 2007

Abstract
Over a period of two years we used radiology to investigate breeding traits
in females of two western populations of the threatened Hermann's tortoise
Testudo hermanni hermanni. The main purpose of the study was to see if
reproductive traits – clutch size, clutch frequency, annual egg production
and egg width – varied between populations in Corsica (France) and the Ebro
Delta (Spain), and if these traits were affected by female body size and
amounts of spring rainfall. All the breeding traits analysed were greater in
the Corsican population than in the Ebro Delta population. These differences
were also significant when we used female body size as a covariable. In both
populations the amount of spring rainfall affected breeding traits but not
clutch size. Nevertheless, only in the Corsican population did clutch
frequency, annual egg production and egg width increase significantly in the
year with a wet spring. Contrary to the predictions of Optimal Propagule
Size theory, we found that egg size and clutch size increased with female
size, and that both variables were independent. On the other hand, clutch
frequency was not related to female body size. Thus, in the Hermann's
tortoise, as clutch size did not change between years and clutch frequency
was independent of female size, all females are able to increase their
reproductive output in years with favourable conditions by increasing their
clutch frequency. Nevertheless, other factors besides female size and
rainfall may influence in a highly complex way variability in breeding
traits among populations.
The impacts of selective logging on three sympatric species of Leptodactylus in a Central Guyana rainforest
Authors: Ernst Raffael , Konrad Tillmann , Linsenmair K. Eduard , Rödel Mark-Oliver 
Published: February 2007

Abstract
Selective logging has the potential to significantly alter environmental
conditions experienced by both larval and adult amphibians and, therefore,
may affect the population viability of particular species. In this study we
evaluated the impacts of selective logging on the occurrence, larval
development, and survival of three sympatric foam nest-constructing
Leptodactylus species in a central Guyanan rainforest. The occurrence and
abundance of adults differed among species and between habitat complexes.
Species-habitat associations appeared to be linked to species-specific
reproductive habitat requirements. The response of tadpoles to
logging-related habitat alterations varied among species. Experiments on one
of the focal species showed that tadpole development and growth depend on
larval residence time within foam nests, and on environmental factors
related to solar exposure and temperature of aquatic habitats. Tadpoles that
were reared in foam nests over extended periods of time showed significant
decrease in body mass. Tadpoles reared under exposed conditions developed
more slowly than those reared under shaded conditions. Likewise, larval
growth decelerated in the former. Larval survival differed among species and
between habitats. Species-specific responses to disturbance-related
environmental changes indicate that simplified generalizations that do not
take into account species-specific variation are problematic. We, therefore,
argue that sound conservation strategies for this group of amphibians would
benefit by moving from generalizations to species specific
recommendations.
Bergmann's rule and the Italian Hermann's tortoises (Testudo hermanni): latitudinal variations of size and shape
Authors: Sacchi Roberto , Pupin Fabio , Rosa Daniele Pellitteri , Fasola Mauro 
Published: February 2007

Abstract
We used geometric morphometric analysis to investigate latitudinal variation
in size and shape of carapace and plastron of 111 Testudo hermanni hermanni
(60 males and 51 females) collected in 6 different Italian regions. Basing
on a sample of 14 landmarks for carapace and 18 landmarks for plastron, we
showed that the size and shape of both sexes changed according to a
North-South cline following the Bergmann's rule, tortoises of Northern Italy
being 1.1-1.2 larger than that of Southern Italy. Shape variation was higher
in carapace probably because sexual selection in this species acts stronger
on plastron than on carapace shape.
The nematode community in cyanobacterial biofilms in the river Llobregat, Spain
Authors: Muñoz Isabel , Gaudes Ainhoa , Sabater Sergi , Vilalta Elisabet 
Published: February 2007

AbstractThe aim of our study was to understand the role of the nematode community in a cyanobacterial-dominated biofilm located in the river Llobregat, NE Spain. This biofilm was mainly composed of oscillatorial species and diatoms. Fractions of these mats can become detached from the substrata and become free-floating, dispersing downstream and acquiring different structural and physiological properties. Both cyanobacterial biofilms, attached and free-floating, were compared with another benthic biofilm that occurred in the reach of the river that was studied. The nematode diversity was restricted, and was dominated by Chromadorita leuckarti, Diplogaster rivalis, Plectus parvus, Neotobrilus diversipapillatus, Monhystera spp., Dorylaimus sp. and Mononchus sp. Nematode density and biomass were significantly greater in the free-floating biofilm (maximum values of 752 ind/cm2 and 171.3 μgC/cm2). Different trophic and sexual strategies were observed. The free-floating biofilm showed higher abundances of juveniles and a high proportion of gravid females. A positive correlation was observed between cyanobacterial density and the abundance of juveniles or adults of the commonest nematode species, indicating their potential as food resources.
Field studies on the enhancement of nematicidal activity of ammonia-releasing fertilisers by alkaline amendments
Authors: Shuker Shimshon , Rosenberg Rivka , Oka Yuji , Tkachi Nadia , Suriano Shoshi , Roded Liat , Fine Pinchas 
Published: February 2007

AbstractNematicidal activities of ammonia-releasing organic and inorganic fertilisers, applied with alkaline amendments, were tested against Meloidogyne javanica and M. incognita under field conditions. In microplots infested with M. javanica, ammonium sulphate applied with alkaline-stabilised biosolid (ASB) significantly reduced the root-galling index of tomato plants compared with that of plants grown in soils treated with ammonium sulphate or ASB alone. Although ammonia concentrations in the soil treated with broiler litter plus cement kiln dust were high (ca 60-200 mg kg−1), this treatment was less effective. Ammonia volatilisation resulted in rather low concentrations of ammonium in the soils treated with alkaline amendments. The combination of ASB and ammonium sulphate reduced the tomato root-galling index and the number of M. javanica juveniles recovered from the soil in a field experiment. On an organic farm, application of slaked lime in combination with broiler litter significantly reduced the root-galling index of pepper plants infested with M. incognita. Calcification of excess hydroxyls in the ASB or lime lowered the soil pH to values normally found in these soils in the field experiments.
Volatile compounds in pine stands suffering from pine wilt disease: qualitative and quantitative evaluation
Authors: Futai Kazuyoshi , Kanzaki Natsumi , Takeuchi Yuko 
Published: February 2007

AbstractPine wilt disease causes ecological and economic damage in Japanese pine forests in spite of intensive effort to protect them from the pine wood nematode, Bursaphelenchus xylophilus. Pine trees infected with B. xylophilus emit a characteristic bouquet of volatile compounds bioactive to the vector beetle of the nematode, Monochamus alternatus, and potentially affecting symptom development inside the trees. To investigate the qualitative and quantitative properties of volatile compounds in the field, we profiled the volatile emissions in two Japanese black pine stands, one naturally suffering from pine wilt disease and the other artificially inoculated with B. xylophilus. In both pine stands, the emission of some terpenoids from the infected trees such as (−)-α-pinene, began to increase in summer, overlapping the oviposition season of the vector beetle, but peaked in the summer and autumn. These data suggest that the beetles may not necessarily depend on the tremendous quantity of volatiles alone when they search for suitable trees on which to oviposit.
Self-assembly of Nanorod-like Architecture of CdTe Nanocrystals in Langmuir Monolayer of Bolaamphiphiles
Authors: Liu Mingxian , Gan Lihua , Zeng Yaling , Wang Jinghong , Xu Zijie , Hao Zhixian , Liu Honglai , Chen Longwu 
Published: January 2007

Abstract
A novel fabrication of two-dimensional CdTe nanoarchitecture was developed through the interaction between bolaamphiphiles of 1,3-bis(hexadecyldimethylammonio)propane dibromide and the prepared negatively charged CdTe nanocrystals hydrosols by controlling the surface pressure of the monolayer. The formed amphiphiles/CdTe nanocrystals composite monolayer confirm that plenty of CdTe nanorod-like nanostructure with the lengths of roughly 100–300 nm and the widths of about 25-nm distribute in Langmuir layer by a self-assembly way at low surface pressure.
Low-temperature Hydrothermal Synthesis of Orthorhombic Vanadium Pentoxide Nanowires
Authors: Zhou Fu , Zhao Xuemei , Yuan Cunguang , Li Li , Xu Hai 
Published: January 2007

Abstract
Orthorhombic V2O5 single-crystalline nanowires with diameters of 30–50 nm, and lengths up to hundreds of micrometers, which was by far the longest 1-D nanostructure of vanadium oxide been fabricated, were synthesized on a large scale through a template-free mild and direct hydrothermal reaction between VOSO4·xH2O and KMnO4. The ability of the oxidizing agent was testified to be the decisive factor in the successful fabrication of as-obtained ultralong orthorhombic V2O5 single-crystalline nanowires, which might be a superior cathode material for the lithium ion batteries.
Direct Monitoring of Both Phosphorolysis and Elongation of Amylopectin Catalyzed by Phosphorylase on a 27-MHz Quartz-crystal Microbalance
Authors: Murakawa Akiko , Mori Toshiaki , Okahata Yoshio 
Published: January 2007

Abstract
All kinetic parameters such as the enzyme binding process and the catalytic processes (phosphorolysis and polymerization) by phosphorylase from Potato could be obtained using an amylopectin-immobilized 27-MHz quartz-crystal microbalance (QCM).
Carbenoid Addition to Phenols to Give Cycloheptatrienols. Stereochemical Regulation and Ligand-dependent Switching of Chemoselectivity
Authors: Im Chun Young , Okuyama Tadashi , Sugimura Takashi 
Published: January 2007

Abstract
Cycloheptatrienols were prepared stereoselectively by the intramolecular Büchner reaction of phenols using a 2,4-pentanediol tether of suitable stereochemistry, where the intrinsically favorable O–H insertion is effectively suppressed.
Syntheses and Properties of Novel Quarterphenylene-based Materials for Blue Organic Light-emitting Devices
Authors: Agata Yuya , Shimizu Hitoshi , Kido Junji 
Published: January 2007

Abstract
A series of quarterphenylene-based compounds were prepared and investigated as the hole-transport layer and the host materials in organic light-emitting devices (OLEDs). These compounds have wide HOMO–LUMO energy gaps (ca. 3.57 eV) due to the twisted backbone. A maximum external efficiency of 17% was achieved for blue organic light-emitting device using iridium(III)–bis[2-(4,6-difluorophenyl)pyridinate-N,C2′]picolinate (FIrpic) as an emitting material.
Multipole Resonance Modes in Localized Surface Plasmon of Single Hexagonal/Triangular Gold Nanoplates
Authors: Uwada Takayuki , Asahi Tsuyoshi , Masuhara Hiroshi , Ibano Daisuke , Fujishiro Manabu , Tominaga Toshihiro 
Published: January 2007

Abstract
We investigated the optical properties of the hexagonal/triangle gold nanoplates by single particle spectroscopy. By comparison with scanning electron microscope (SEM) observations, we successfully demonstrated that light scattering spectra of the hexagonal nanoplates with 360 ± 120-nm edge lengths and the triangular ones of 190 ± 60 nm exhibited two peaks in visible–near infrared region corresponding to quadrupole and higher multipole modes of localized surface plasmon resonance (LSPR).
Nanoparticle Formation by Irreversible In situ Aggregation of Rigid π-Stacked Segments of a Flexible–Rigid Block Copolymer
Authors: Nakano Tamaki , Yade Tohru , Fukuda Yasuyuki , Takewaki Kazuyuki 
Published: January 2007

Abstract
Block copolymers of dibenzofulvene and methyl methacrylate obtained by living anionic polymerization formed stable, soluble nanoparticles by in situ molecular aggregation of the poly(dibenzofulvene) segments having a rigid π-stacked conformation; the nanoparticles indicated red-shifted absorption bands and reduced oxidation potential relative to a single chain poly(dibenzofulvene).
Additional Alkylsilanization of Aminosilane-modified Glass Slide: Effect of Alkylsilane Structure for Enhancing Surface Amine Functionality
Authors: Kamisetty Nagendra K , Pack Seung Pil , Nonogawa Mitsuru , Devarayapalli Kamakshaiah C , Kodaki Tsutomu , Makino Keisuke 
Published: January 2007

Abstract
Efficient amine-functionalized glass slides were developed by capping with alkylsilanes, which might reduce nonspecific interactions of amino groups with the surface silanol. We explored the types of alkylsilanes (used as silanol capping reagents) for designing high amine functionality on the glass slide.
Preparation and Characterization of Polyaminophenylsilsesquioxane Particles by Two-step Acid–Base-catalyzed Sol–Gel Process
Authors: Takahashi Kenji , Tadanaga Kiyoharu , Hayashi Akitoshi , Tatsumisago Masahiro 
Published: January 2007

Abstract
Spherical polyaminophenylsilsesquioxane (H2NC6H4SiO3/2) particles were prepared by a two-step acid–base-catalyzed sol–gel process, and we found that the particles showed the glass transition behavior. Amino groups in the H2NC6H4SiO3/2 particles were partially changed to amido ones by acetylation using acetic anhydride.
Pyridine-3-carboxylic Anhydride (3-PCA): A Versatile, Practical, and Inexpensive Reagent for Condensation Reaction between Carboxylic Acids and Alcohols
Authors: Mukaiyama Teruaki , Funasaka Setsuo 
Published: January 2007

Abstract
A synthesis of carboxylic esters from various carboxylic acids and alcohols is successfully carried out by using a condensation reagent, pyridine-3-carboxylic anhydride (3-PCA). This reaction materialized synthesis of various carboxylic esters to be carried out under mild conditions by simple experimental procedure.