bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced Survival of
Salmonella enterica
in Vesicles Released by a Soilborne
Tetrahymena
Species
Authors: Brandl M. T. , Rosenthal B. M. , Haxo A. F. , Berk S. G. 
Published: March 2005

ABSTRACT

Nondestructive ingestion by soilborne protozoa may enhance the environmental resiliency of important bacterial pathogens and may model how such bacteria evade destruction in human macrophages. Here, the interaction of
Salmonella enterica
serovar Thompson with a soilborne
Tetrahymena
sp. isolate was examined using serovar Thompson cells labeled with the green fluorescent protein. The bacteria were mixed in solution with cells of
Tetrahymena
at several ratios. During incubation with serovar Thompson,
Tetrahymena
cells released a large number of vesicles containing green fluorescent serovar Thompson cells. In comparison, grazing on
Listeria monocytogenes
cells resulted in their digestion and thus the infrequent release of this pathogen in vesicles. The number of serovar Thompson cells per vesicle increased significantly as the initial ratio of serovar Thompson to
Tetrahymena
cells increased from 500:1 to 5,000:1. The density of serovar Thompson was as high as 50 cells per vesicle. Staining with propidium iodide revealed that a significantly higher proportion of serovar Thompson cells remained viable when enclosed in vesicles than when free in solution. Enhanced survival rates were observed in vesicles that were secreted by both starved (
F
= 28.3,
P
< 0.001) and unstarved (
F
= 14.09,
P
< 0.005)
Tetrahymena
cells. Sequestration in vesicles also provided greater protection from low concentrations of calcium hypochlorite. Thus, the release of this human pathogen from
Tetrahymena
cells in high-density clusters enclosed in a membrane may have important implications for public health.
Subtle Difference between Benzene and Toluene Dioxygenases of
Pseudomonas putida
Authors: Bagnéris Claire , Cammack Richard , Mason Jeremy R. 
Published: March 2005

ABSTRACT

Benzene dioxygenase and toluene dioxygenase from
Pseudomonas putida
have similar catalytic properties, structures, and gene organizations, but they differ in substrate specificity, with toluene dioxygenase having higher activity toward alkylbenzenes. The catalytic iron-sulfur proteins of these enzymes consist of two dissimilar subunits, α and β; the α subunit contains a [2Fe-2S] cluster involved in electron transfer, the catalytic nonheme iron center, and is also responsible for substrate specificity. The amino acid sequences of the α subunits of benzene and toluene dioxygenases differ at only 33 of 450 amino acids. Chimeric proteins and mutants of the benzene dioxygenase α subunit were constructed to determine which of these residues were primarily responsible for the change in specificity. The protein containing toluene dioxygenase C-terminal region residues 281 to 363 showed greater substrate preference for alkyl benzenes. In addition, we identified four amino acid substitutions in this region, I301V, T305S, I307L, and L309V, that particularly enhanced the preference for ethylbenzene. The positions of these amino acids in the α subunit structure were modeled by comparison with the crystal structure of naphthalene dioxygenase. They were not in the substrate-binding pocket but were adjacent to residues that lined the channel through which substrates were predicted to enter the active site. However, the quadruple mutant also showed a high uncoupled rate of electron transfer without product formation. Finally, the modified proteins showed altered patterns of products formed from toluene and ethylbenzene, including monohydroxylated side chains. We propose that these properties can be explained by a more facile diffusion of the substrate in and out of the substrate cavity.
Signal Transduction by Tga3, a Novel G Protein α Subunit of
Trichoderma atroviride
Authors: Zeilinger Susanne , Reithner Barbara , Scala Valeria , Peissl Isabel , Lorito Matteo , Mach Robert L. 
Published: March 2005

ABSTRACT

Trichoderma
species are used commercially as biocontrol agents against a number of phytopathogenic fungi due to their mycoparasitic characterisitics. The mycoparasitic response is induced when
Trichoderma
specifically recognizes the presence of the host fungus and transduces the host-derived signals to their respective regulatory targets. We made deletion mutants of the
tga3
gene of
Trichoderma atroviride
, which encodes a novel G protein α subunit that belongs to subgroup III of fungal Gα proteins. Δ
tga3
mutants had changes in vegetative growth, conidiation, and conidial germination and reduced intracellular cyclic AMP levels. These mutants were avirulent in direct confrontation assays with
Rhizoctonia solani
or
Botrytis cinerea
, and mycoparasitism-related infection structures were not formed. When induced with colloidal chitin or
N
-acetylglucosamine in liquid culture, the mutants had reduced extracellular chitinase activity even though the chitinase-encoding genes
ech42
and
nag1
were transcribed at a significantly higher rate than they were in the wild type. Addition of exogenous cyclic AMP did not suppress the altered phenotype or restore mycoparasitic overgrowth, although it did restore the ability to produce the infection structures. Thus,
T. atroviride
Tga3 has a general role in vegetative growth and can alter mycoparasitism-related characteristics, such as infection structure formation and chitinase gene expression.
Genomic Analysis of Bacteriophage ΦJL001: Insights into Its Interaction with a Sponge-Associated Alpha-Proteobacterium
Authors: Lohr Jayme E. , Chen Feng , Hill Russell T. 
Published: March 2005

ABSTRACT

Bacteriophage ΦJL001 infects a novel marine bacterium in the α subclass of the
Proteobacteria
isolated from the marine sponge
Ircinia strobilina
. ΦJL001 is a siphovirus and forms turbid plaques on its host. The genome sequence of ΦJL001 was determined in order to better understand the interaction between the marine phage and its sponge-associated host bacterium. The complete genome sequence of ΦJL001 comprised 63,469 bp with an overall G+C content of 62%. The genome has 91 predicted open reading frames (ORFs), and 17 ORFs have been assigned putative functions. ΦJL001 appears to be a temperate phage, and the integrase gene was identified in the genome. DNA hybridization analysis showed that the ΦJL001 genome does not integrate into the host chromosome under the conditions tested. DNA hybridization experiments therefore suggested that ΦJL001 has some pseudolysogenic characteristics. The genome of ΦJL001 contains many putative genes involved in phage DNA replication (e.g., helicase, DNA polymerase, and thymidylate synthase genes) and also contains a putative integrase gene associated with the lysogenic cycle. Phylogeny based on DNA polymerase gene sequences indicates that ΦJL001 is related to a group of siphoviruses that infect mycobacteria. Designation of ΦJL001 as a siphovirus is consistent with the morphology of the phage visualized by transmission electron microscopy. The unique marine phage-host system described here provides a model system for studying the role of phages in sponge microbial communities.
The relationships among lemons, limes and citron: a chromosomal comparison
Authors: Carvalho R. , Soares Filho W.S. , Brasileiro-Vidal A.C. , Guerra M. 
Published: March 2005

Lemons, limes and citron constitute a group of closely related <i>Citrus</i> species, whose species delimitations and taxonomic relationships are unclear. In order to identify karyotypic similarities and species relationships within this group, the CMA<sup>+</sup>/DAPI<sup>–</sup> banding pattern and the distribution of the 5S and 45S rDNA sites of 10 accessions of lime, lemon, and citron were investigated. The four cultivars of <i>C. limon</i> analyzed showed the same pattern of CMA<sup>+</sup> bands and rDNA sites, suggesting that they originated from a single germplasm, later differentiated by distinct somatic mutations. The lemons <i>C. jambhiri, C. limonia</i> and <i>C. volkameriana</i> displayed karyotypes very similar to each other, but they differed from <i>C. limon</i> by the absence of a single chromosome with one band in each telomere. The limes, <i>C. aurantifolia</i> and <i>C. limettioides</i>, seemed less related to each other and exhibited different heteromorphic chromosome pairs. In <i>C. aurantifolia</i>, the presence of a chromosome type unknown in all other <i>Citrus</i> species cytologically known so far supports the assumption that this accession may be derived from a hybrid with a species from the subgenus <i>Papeda</i> or from another genus. <i>Citrus medica</i> was the only homozygous accession of this group and all of its chromosome types were clearly represented in limes and lemons, some of them forming heteromorphic pairs. The analysis of the distribution of rDNA sites allowed a further refinement of the comparison among accessions. The lemons and limes were heterozygous for all rDNA sites, whereas <i>C. medica</i> was entirely homozygous. These data support the hypothesis that <i>C. medica</i> is a true species while the other nine accessions are hybrids.
Identification of individual chromosomes and parental genomes in <i>Brassica juncea</i> using GISH and FISH
Authors: Maluszynska J. , Hasterok R. 
Published: March 2005

The three diploid <i>(B. nigra, B. oleracea, B. campestris)</i> and three allotetraploid <i>(B. carinata, B. juncea, B. napus)</i> species of <i>Brassica</i>, known as the “U-triangle” are one of the best model systems for the study of polyploidy. Numerous molecular investigations have provided a wealth of new insights into the polyploid origin and changes during the evolution of <i>Brassica,</i> but there are still many controversial aspects of their relationship and evolution. Interpretation of genome changes during evolution requires individual chromosome identification within the genome and clear distinction of genomes within the allotetraploid. The aim of this study was to identify individual chromosomes of <i>B. juncea</i> (genome AABB; 2n = 4x = 36) and to determine their genomic origin. Fluorescence in situ hybridization with 5S and 45S rDNA probes enabled discrimination of a substantial number of chromosomes, providing chromosomal landmarks for 20 out of 36 chromosomes of <i>B. juncea</i>. Additionally, along with double target genomic in situ hybridization, it allowed assignment of all chromosomes to either the A or B genomes.
The Special Court for Sierra Leone: Challenging the Tradition of Impunity for Gender-based Crimes?
Authors: Damgaard Ciara 
Published: March 2005

AbstractThe focus of this article is the Special Court for Sierra Leone and the extent to which it can be said that the Special Court has already challenged, or will, in the future, challenge the tradition of impunity for gender-based crimes. In this regard, an analysis is undertaken of the Special Court's Statute, Rules of Procedure and Evidence and practice to date, in order to determine its treatment of gender-based crimes and whether it can be said that the Special Court for Sierra Leone challenges the tradition of impunity for gender-based crimes.
Effects of Moist Froude Number and CAPE on a Conditionally Unstable Flow over a Mesoscale Mountain Ridge
Authors: Chen Shu-Hua , Lin Yuh-Lang 
Published: March 2005

AbstractIn this study, idealized simulations are performed for a conditionally unstable flow over a two-dimensional mountain ridge in order to investigate the propagation and types of cloud precipitation systems controlled by the unsaturated moist Froude number (Fw) and the convective available potential energy (CAPE). A two-dimensional moist flow regime diagram, based on Fw and CAPE, is proposed for a conditionally unstable flow passing over a two-dimensional mesoscale mountain ridge. The characteristics of these flow regimes are 1) regime I: flow with an upstream-propagating convective system and an early, slowly moving convective system over the mountain; 2) regime II: flow with a long-lasting orographic convective system over the mountain peak, upslope, or lee slope; 3) regime III: flow with an orographic convective or mixed convective and stratiform precipitation system over the mountain and a downstream-propagating convective system; and 4) regime IV: flow with an orographic stratiform precipitation system over the mountain and possibly a downstream-propagating cloud system. Note that the fourth regime was not included in the flow regimes proposed by Chu and Lin and Chen and Lin. The propagation of the convective systems is explained by the orographic blocking and density current forcing associated with the cold-air outflow produced by evaporative cooling acting against the basic flow, which then determines the propagation and cloud types of the simulated precipitation systems.
EPIC 95°W Observations of the Eastern Pacific Atmospheric Boundary Layer from the Cold Tongue to the ITCZ
Authors: de Szoeke Simon P. , Bretherton Christopher S. , Bond Nicholas A. , Cronin Meghan F. , Morley Bruce M. 
Published: March 2005

Abstract
The atmospheric boundary layer (ABL) along 95°W in the eastern equatorial Pacific during boreal autumn is described using data from the East Pacific Investigation of Climate (EPIC) 2001, with an emphasis on the evolution of the thermodynamic ABL properties from the cold tongue to the cold-advection region north of the sea surface temperature (SST) front. Surface sensible and latent heat fluxes and wind stresses between 1°S and 12°N are calculated from data from eight NCAR C-130 research aircraft flights and from Tropical Atmosphere Ocean (TAO) buoys. Reduced surface wind speed and a 10 m s−1 jet at a height of 500 m are found over the equatorial cold tongue, demonstrating the dependence of the surface wind speed on surface stability.
The ABL exhibits a maximum in cloud cover on the north (downwind) side of the warm SST front, at 1°–3°N. Turbulent mixing driven by both surface buoyancy flux and radiative cooling at the cloud tops plays a significant role in maintaining the depth and structure of the ABL. The ABL heat budget between the equator and 3°N is balanced by comparable contributions from advective cooling, radiative cooling, surface warming, and entrainment warming. Entrainment drying is a weak contributor to the moisture budget, relative to dry advection and surface evaporation. Both the heat and moisture budgets are consistent with a rapid entrainment rate, 12 ± 2 mm s−1, deduced from the observed rise of the inversion with latitude between 0° and 4°N.
UARS/MLS Cloud Ice Measurements: Implications for H2O Transport near the Tropopause
Authors: Wu D. L. , Read W. G. , Dessler A. E. , Sherwood S. C. , Jiang J. H. 
Published: March 2005

Abstract
A technique for detecting large hydrometeors at high altitudes is described here and applied to the Upper Atmosphere Research Satellite/Microwave Limb Sounder (UARS/MLS) 203-GHz radiance measurements at tangent pressures between 200 and 46 hPa. At these tangent pressures the radiances remain optically thin and cloudy-sky radiances are brighter than normal clear-sky cases. Unlike infrared/visible cloud observations, the 203-GHz radiances can penetrate most ice clouds and are sensitive to ice crystals of convective origin. Rough ice water content (IWC) retrievals are made near the tropopause using estimated size distributions from in situ convective studies. The seasonal mean IWC observed at 100 hPa reaches vapor-equivalent 20 ppmv or more over convective centers, dominating the total water content. Convectively lofted ice, therefore, appears to be hydrologically significant at the tropical cold point. IWC is well correlated spatially with relative humidity with respect to ice (RHi) at 100 hPa during both the dry (January–March) and moist (July–September) periods.
A Radiation Algorithm with Correlated-k Distribution. Part I: Local Thermal Equilibrium
Authors: Li J. , Barker H. W. 
Published: March 2005

AbstractA new radiation scheme is proposed that uses the correlated-k distribution (CKD) method. The definition of the k-distribution function, the transformation between frequency space and k space, and the upper limit of the absorption coefficient in cumulative probability space (CPS) are discussed. The corresponding relation between each interval in CPS and the heating rate profile provides a method for determining the width of intervals in CPS. Three schemes are discussed for handling the spectral overlap of gases. Method 1 rearranges the appropriate combination of gaseous absorption coefficients when the spectral overlap of two gases is extensive. Method 2 applies to most overlapping gases and addresses the most important aspects of each gas’s spectrum in each interval of CPS. Method 3 applies to weak gases only and seeks to adjust the main absorption coefficients in order that radiative forcing at the surface and the top of the atmosphere is correct. This model is quite efficient because 1) relatively few intervals in CPS are used (up to 1 mb, only 35 intervals for solar radiation, and 46 for infrared); 2) for some intervals with very large absorption coefficients, the radiative transfer process is simplified by ignoring scattering; 3) the water vapor continuum is dealt with efficiently by neglecting its effect in some nonimportant intervals in CPS and at high altitudes; and 4) gaseous overlap methods are simple and effective. Moreover, this model contains a proper treatment of spectral overlap between solar and infrared radiation. For both solar and infrared radiation, heating rate errors are generally less than 0.2 K day−1, and errors in flux at the surface and the top of the atmosphere are generally less than 1 W m−2.
Methodological bias in cluster randomised trials
Authors: Hahn Seokyung , Puffer Suezann , Torgerson David J , Watson Judith 
Published: March 2005

Abstract
Background
Cluster randomised trials can be susceptible to a range of methodological problems. These problems are not commonly recognised by many researchers. In this paper we discuss the issues that can lead to bias in cluster trials.

Methods
We used a sample of cluster randomised trials from a recent review and from a systematic review of hip protectors. We compared the mean age of participants between intervention groups in a sample of 'good' cluster trials with a sample of potentially biased trials. We also compared the effect sizes, in a funnel plot, between hip protector trials that used individual randomisation compared with those that used cluster randomisation.

Results
There is a tendency for cluster trials, with evidence methodological biases, to also show an age imbalance between treatment groups. In a funnel plot we show that all cluster trials show a large positive effect of hip protectors whilst individually randomised trials show a range of positive and negative effects, suggesting that cluster trials may be producing a biased estimate of effect.

Conclusion
Methodological biases in the design and execution of cluster randomised trials is frequent. Some of these biases associated with the use of cluster designs can be avoided through careful attention to the design of cluster trials. Firstly, if possible, individual allocation should be used. Secondly, if cluster allocation is required, then ideally participants should be identified before random allocation of the clusters. Third, if prior identification is not possible, then an independent recruiter should be used to recruit participants.
Prevalence, types and demographic features of child labour among school children in Nigeria
Authors: Fetuga Bolanle M , Njokama Fidelis O , Olowu Adebiyi O 
Published: March 2005

Abstract
Background
To determine the prevalence, types and demographic features of child labour among school children in Nigeria.

Methods
A cross-sectional interview study of 1675 randomly selected public primary and secondary school pupils aged 5 to less than 18 years was conducted in the Sagamu Local Government Area of Ogun State, Nigeria from October 1998 to September 1999.

Results
The overall prevalence of child labour was 64.5%: 68.6% among primary and 50.3% among secondary school pupils. Major economic activities included street trading (43.6%), selling in kiosks and shops (25.4%) and farming (23.6%). No child was involved in bonded labour or prostitution. Girls were more often involved in labour activities than boys (66.8% versus 62.1%, p = 0.048): this difference was most obvious with street trading (p = 0.0004). Most of the children (82.2%) involved in labour activities did so on the instruction of one or both parents in order to contribute to family income. Children of parents with low socio-economic status or of poorly educated parents were significantly involved in labour activities (p = 0.01 and p = 0.001 respectively). Child labour was also significantly associated with increasing number of children in the family size (p = 0.002). A higher prevalence rate of child labour was observed among children living with parents and relations than among those living with unrelated guardians.

Conclusion
It is concluded that smaller family size, parental education and family economic enhancement would reduce the pressure on parents to engage their children in labour activities.
Discovery of adult T-cell leukemia
Authors: Takatsuki Kiyoshi 
Published: March 2005

Abstract
Adult T-cell leukemia (ATL) was first reported as a distinct clinical entity in 1977 in Japan. The predominant physical findings are skin lesions, lymphadenopathy and hepatosplenomegaly. The ATL cells are of mature T-helper phenotype and have a characteristic appearance with indented nuclei. There is striking frequent hypercalcemia with increased numbers of osteoclasts. Central to the identification of the disease is a striking geographic clustering in southwestern Japan and the isolation of human T-cell lymphotropic virus type-1 (HTLV-1) from the cell lines of patients. Worldwide epidemiological studies have been made through international collaborations. Several diseases were found to be related to HTLV-1 infection. Moreover, it was noted that an immunodeficiency state may be induced by HTLV-1 infection. In Japan, HTLV-1 carriers have been estimated to be 1.2 million, and more than 700 cases of ATL have been diagnosed each year.
The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum
Authors: Martin Rowena E , Henry Roselani I , Abbey Janice L , Clements John D , Kirk Kiaran 
Published: March 2005

Abstract
Background
The uptake of nutrients, expulsion of metabolic wastes and maintenance of ion homeostasis by the intraerythrocytic malaria parasite is mediated by membrane transport proteins. Proteins of this type are also implicated in the phenomenon of antimalarial drug resistance. However, the initial annotation of the genome of the human malaria parasite Plasmodium falciparum identified only a limited number of transporters, and no channels. In this study we have used a combination of bioinformatic approaches to identify and attribute putative functions to transporters and channels encoded by the malaria parasite, as well as comparing expression patterns for a subset of these.

Results
A computer program that searches a genome database on the basis of the hydropathy plots of the corresponding proteins was used to identify more than 100 transport proteins encoded by P. falciparum. These include all the transporters previously annotated as such, as well as a similar number of candidate transport proteins that had escaped detection. Detailed sequence analysis enabled the assignment of putative substrate specificities and/or transport mechanisms to all those putative transport proteins previously without. The newly-identified transport proteins include candidate transporters for a range of organic and inorganic nutrients (including sugars, amino acids, nucleosides and vitamins), and several putative ion channels. The stage-dependent expression of RNAs for 34 candidate transport proteins of particular interest are compared.

Conclusion
The malaria parasite possesses substantially more membrane transport proteins than was originally thought, and the analyses presented here provide a range of novel insights into the physiology of this important human pathogen.