bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytoskeleton and surface structures of cells directly attached to the tooth in the rat junctional epithelium
Authors: Ishikawa Hiroki , Hashimoto Sadamitsu , Tanno Michie , Ishikawa Tatsuya , Tanaka Teruo , Shimono Masaki 
Published: June 2005

Objective:  It is still an open question whether cells directly attached to the tooth (DAT) cells are migratory or non‐migratory cells. The purpose of this study was to examine cytoskeletal and surface structures of DAT cells that might be involved in migration.Methods:  We investigated the distribution of stress fibers composed of actin filaments in DAT cells using phallacidin fluorescent dye methods in a confocal laser scanning microscope. To observe the three‐dimensional structure of the DAT cell surface, the osmium maceration scanning electron microscope (SEM) method, which removes various soluble materials between DAT cells and the enamel, was employed.Results:  Stress fibers were found in the most apically located DAT cells, and were arranged in parallel to the presumable cervical‐line, whereas some of the fibers ran parallel to the tooth axis in the more coronally located DAT cells. The parallel arrangement to the tooth axis of the fibers may be involved with migration for turnover, and the parallel accumulation to the presumable cervical‐line may be concerned with the cervical contraction of DAT cells. Osmium maceration SEM images at high magnification revealed the existence of microvilli‐like structures on the enamel surfaces (facing to the tooth surface) of DAT cells after removal of the soluble matrices. The thicknesses of the microvilli‐like structures on the enamel surfaces and cell processes of intercellular bridges were significantly different.Conclusion:  DAT cells possess stress fibers arranged in parallel to the tooth axis and to the presumable cervical‐line in the cytoplasm, and microvilli‐like structures on their enamel surfaces. These results suggest that these structures contribute to DAT cell migration.
Rhyme and Ritual: a new approach to teaching children to read and write
Authors: Merttens Ruth , Robertson Catherine 
Published: June 2005

AbstractThis paper concerns an approach to raising literacy standards which is rather different from the prevailing orthodoxy – the Rhyme and Ritual project. The project is run by the Hamilton Reading Project, which comprises a series of initiatives funded by the Hamilton Trust, an educational charity, and implemented in fifteen primary schools in a large and socio‐economically deprived city area in southern England. It incorporates both a supposedly ‘old‐fashioned’ traditional notion – that children can be supported in learning to read through approaching a text known off by heart (the phrase is important, since the text must not only be familiar but also pleasurable to the individual child) – and also the currently valued approach of expanding and extending children's appropriation and use of elaborated language, particularly in relation to imaginative, descriptive and expressive writing. It is the former aspect of the Rhyme and Ritual project, namely the provision of short texts to be memorised by young children and then read from ‘text only’ books (with decoration but no illustrations) that we believe is uncommon as the basis of an educational initiative with the overt aim of raising literacy standards. The article gives a detailed outline of this initiative, with its two‐pronged and ‘pincer’ approach, and also some indication of how it is succeeding.
Synergistic Regulation of Competence Development inBacillus subtilisby Two Rap-Phr Systems
Authors: Bongiorni Cristina , Ishikawa Shu , Stephenson Sophie , Ogasawara Naotake , Perego Marta 
Published: June 2005

ABSTRACTThe 11 Rap proteins ofBacillus subtiliscomprise a conserved family of tetratricopeptide (TPR)-containing regulatory proteins. Their activity is inhibited by specific Phr pentapeptides produced from the product ofphrgenes through an export-import maturation process. We found that one of the proteins, namely RapF, is involved in the regulation of competence to DNA transformation. The ComA response regulator and transcription factor for initiation of competence development is the target of RapF. Specific binding of RapF to the carboxy-terminal DNA-binding domain of ComA inhibits the response regulator's ability to bind its target DNA promoters. The PhrF C-terminal pentapeptide, QRGMI, inhibits RapF activity. The activity of RapF and PhrF in regulating competence development is analogous to the previously described activity of RapC and PhrC (L. J. Core and M. Perego, Mol. Microbiol.49:1509-1522, 2003). In fact, the RapF and PhrF pair of proteins acts synergistically with RapC and PhrC in the overall regulation of the ComA transcription factor. Since the transcription of the RapC- and RapF-encoding genes is positively regulated by their own target ComA, an autoregulatory circuit must exist for the competence transcription factor in order to modulate its activity.
pyd
Genes of
Rhizobium
sp. Strain TAL1145 Are Required for Degradation of 3-Hydroxy-4-Pyridone, an Aromatic Intermediate in Mimosine Metabolism
Authors: Awaya Jonathan D. , Fox Paul M. , Borthakur Dulal 
Published: June 2005

ABSTRACT

Rhizobium
sp. strain TAL1145 degrades the
Leucaena
toxin mimosine and its degradation product 3-hydroxy-4-pyridone (HP). The aim of this investigation is to characterize the
Rhizobium
genes for HP degradation and transport. These genes were localized by subcloning and mutagenesis on a previously isolated cosmid, pUHR263, containing
mid
genes of TAL1145 required for mimosine degradation. Two structural genes,
pydA
and
pydB
, encoding a metacleavage dioxygenase and a hydrolase, respectively, are required for degradation of HP, and three genes,
pydC
,
pydD
, and
pydE
, encoding proteins of an ABC transporter, are involved in the uptake of HP by TAL1145. These genes are induced by HP, although both
pydA
and
pydB
show low levels of expression without HP.
pydA
and
pydB
are cotranscribed, while
pydC
,
pydD
, and
pydE
are each transcribed from separate promoters. PydA and PydB show no homology with other dioxygenases and hydrolases in
Sinorhizobium meliloti
,
Mesorhizobium loti
, and
Bradyrhizobium japonicum
. Among various root nodule bacteria, the ability to degrade mimosine or HP is unique to some
Leucaena
-nodulating
Rhizobium
strains.
Host- and Tissue-Specific Pathogenic Traits of
Staphylococcus aureus
Authors: van Leeuwen Willem B. , Melles Damian C. , Alaidan Alwaleed , Al-Ahdal Mohammed , Boelens Hélène A. M. , Snijders Susan V. , Wertheim Heiman , van Duijkeren Engeline , Peeters Justine K. , van der Spek Peter J. , Gorkink Roy , Simons Guus , Verbrugh Henri A. , van Belkum Alex 
Published: June 2005

ABSTRACT

Comparative genomics were used to assess genetic differences between
Staphylococcus aureus
strains derived from infected animals versus colonized or infected humans. A total of 77 veterinary isolates were genetically characterized by high-throughput amplified fragment length polymorphism (AFLP). Bacterial genotypes were introduced in a large AFLP database containing similar information for 1,056 human
S. aureus
strains. All
S. aureus
strains isolated from animals in close contact with humans (e.g., pet animals) were predominantly classified in one of the five main clusters of the AFLP database (cluster I). In essence, mastitis-associated strains from animals were categorized separately (cluster IVa) and cosegregated with bacteremia-associated strains from humans. Distribution of only 2 out of 10 different virulence genes differed across the clusters. The gene encoding the toxic shock syndrome protein (
tst
) was more often encountered among veterinary strains (
P
< 0.0001) and even more in the mastitis-related strains (
P<
0.0001) compared to human isolate results. The gene encoding the collagen binding protein (
cna
) was rarely detected among invasive human strains. The virulence potential, as indicated by the number of virulence genes per strain, did not differ significantly between the human- and animal-related strains. Our data show that invasive infections in pets and humans are usually due to
S. aureus
strains with the same genetic background. Mastitis-associated
S. aureus
isolated in diverse farm animal species form a distinct genetic cluster, characterized by an overrepresentation of the toxic shock syndrome toxin superantigen-encoding gene.
Sialylation of Group B Streptococcal Capsular Polysaccharide Is Mediated bycpsKand Is Required for Optimal Capsule Polymerization and Expression
Authors: Chaffin D. O. , Mentele L. M. , Rubens C. E. 
Published: June 2005

ABSTRACTSeveral bacterial pathogens have evolved the means to escape immune detection by mimicking host cell surface carbohydrates that are crucial for self/non-self recognition. Sialic acid, a terminal residue on these carbohydrates, inhibits activation of the alternate pathway of complement by recruiting the immune modulating molecule factors H, I, and iC3b. Sialylation of capsular polysaccharide (CPS) is important for virulence of group B streptococci (GBS), a significant human pathogen. We previously reported thatcpsK, a gene within thecpslocus of type III GBS, could complement a sialyltransferase deficientlstmutant ofHaemophilus ducreyi, implicating its role in sialylation of the GBS capsule. To explore the function ofcpsKin GBS capsule production, we created a mutant incpsK. Immunoblot analysis and enzyme-linked immunosorbent assay using anti-type III CPS antisera demonstrated that the mutant CPS did not contain sialic acid. This was confirmed by high-performance liquid chromatography after mild acid hydrolysis of the CPS. Although increased CPS chain length was seen for this strain, CPS production was <20% of the parental isolate. An episomalcpsKcopy restored synthesis of sialo-CPS to wild-type levels. These data support our hypothesis thatcpsKencodes the GBS CPS sialyltransferase and provide further evidence that lack of CPS oligosaccharide sialylation reduces the amount of CPS expressed on the cell surface. These observations also imply that one or more of the components involved in synthesis or transport of oligosaccharide repeating units requires a sialo-oligosaccharide for complete activity.
Activities of the
Serratia marcescens
Heme Receptor HasR and Isolated Plug and β-Barrel Domains: the β-Barrel Forms a Heme-Specific Channel
Authors: Létoffé Sylvie , Wecker Karine , Delepierre Muriel , Delepelaire Philippe , Wandersman Cécile 
Published: June 2005

ABSTRACT

The
Serratia marcescens
hemophore-specific outer membrane receptor HasR is a member of the TonB-dependent family of autoregulated receptors. It can transport either heme itself or heme bound to the hemophore HasA. On the basis of sequence and functional similarities with other TonB-dependent outer membrane receptors whose three-dimensional structures have been determined, a HasR structure model was proposed. The mature HasR protein comprises a 99-residue amino-terminal extension necessary for
hasR
transcription, followed by a plug domain of 139 amino acids and a β-barrel domain inserted in the outer membrane, the lumen of which is closed by the plug. This model was used to generate
hasR
deletions encoding HasR proteins with the native signal peptides but lacking either the N-terminal regulatory extension or encoding the plug or the β-barrel alone. The protein lacking the N-terminal extension, HasR Δ11-91, was incorporated in the outer membrane and was fully functional for active uptake of free and hemophore-bound heme. The HasR β-barrel, Δ11-192, was also incorporated in the outer membrane and bound the hemophore but expressed no active heme transport properties. The HasR plug remained in the periplasm. Coexpression of the plug and the β-barrel allowed partial plug insertion in the outer membrane, demonstrating that these two HasR domains interact in vivo. The β-barrel and the plug also interact in vitro. Nevertheless, the two domains did not complement each other to reconstitute an active TonB-dependent receptor for free or hemophore-bound heme uptake. Production of the β-barrel alone selectively increased passive diffusion of heme but not of other exogenous compounds. A mutation at histidine 603, which is required for heme uptake through the wild-type receptor, abolished heme diffusion, showing that HasR Δ11-192 forms a specific heme channel.
Methylocella
Species Are Facultatively Methanotrophic
Authors: Dedysh Svetlana N. , Knief Claudia , Dunfield Peter F. 
Published: June 2005

ABSTRACT

All aerobic methanotrophic bacteria described to date are unable to grow on substrates containing carbon-carbon bonds. Here we demonstrate that members of the recently discovered genus
Methylocella
are an exception to this. These bacteria are able to use as their sole energy source the one-carbon compounds methane and methanol, as well as the multicarbon compounds acetate, pyruvate, succinate, malate, and ethanol. To conclusively verify facultative growth, acetate and methane were used as model substrates in growth experiments with the type strain
Methylocella silvestris
BL2. Quantitative real-time PCR targeting the
mmoX
gene, which encodes a subunit of soluble methane monooxygenase, showed that copies of this gene increased in parallel with cell counts during growth on either acetate or methane as the sole substrate. This verified that cells possessing the genetic basis of methane oxidation grew on acetate as well as methane. Cloning of 16S rRNA genes and fluorescence in situ hybridization with strain-specific and genus-specific oligonucleotide probes detected no contaminants in cultures. The growth rate and carbon conversion efficiency were higher on acetate than on methane, and when both substrates were provided in excess, acetate was preferably used and methane oxidation was shut down. Our data demonstrate that not all methanotrophic bacteria are limited to growing on one-carbon compounds. This could have major implications for understanding the factors controlling methane fluxes in the environment.
Distribution of mtDNA haplotypes (cyt b) of Emys orbicularis in France and implications for postglacial recolonization
Authors: Fritz Uwe , Cadi Antoine , Cheylan Marc , Coïc Christophe , Détaint Mathieu , Olivier Anthony , Rosecchi Elisabeth , Guicking Daniela , Lenk Peter , Joger Ulrich , Wink Michael 
Published: June 2005

Abstract
The European pond turtle, Emys orbicularis, is a wide ranging species,
distributed from Northwest Africa over a large part of Europe and Asia Minor
to the Caspian and Aral Seas. For 106 pond turtles from France mtDNA
sequence variation has been assessed, using a 1031 bp portion of the
mitochondrial cytochrome b gene. Three of nine haploclades currently known
from the entire species' range were found in France. One clade (II) is
represented with four very similar haplotypes, differing by one mutation,
and the two other clades (V, VI) are represented with one haplotype each. A
syntopic occurrence of clades II and V is reported for the first time for
the Camargue. Besides, clade II occurs in the French regions Aquitaine,
Centre-Val de Loire, and Rhône-Alpes. Outside of France, it is found mainly
in the catchment areas of the Danube and Oder rivers and in the Balkans.
Haploclade V, which is also known from the Apennine peninsula, Sardinia, and
the northern Mediterranean coast of Spain, is restricted in France to
Corsica and the Provence-Alpes-Côte d'Azur region. A single individual
bearing a haplotype of an Iberian and North African clade (VI) was found in
Aquitaine near Pau. This could indicate gene flow between the Iberian
peninsula and West France, if the specimen is native. The distribution of
the distinct haploclades in France probably reflects Holocene range
expansions, especially of haploclade II turtles. In the postglacial,
haploclade II terrapins arrived from the east and spread over the Rhône
corridor to the Mediterranean coast. In the southern Rhône area they met and
hybridized with haploclade V turtles. Further research is needed to clarify
whether this hybridization is a locally restricted phenomenon.
Physics and Dynamics of Density-Compensated Temperature and Salinity Anomalies. Part I: Theory
Authors: Tailleux Rémi , Lazar Alban , Reason C. J. C. 
Published: June 2005

AbstractSubducted temperature anomalies have been invoked as a possible way for midlatitudes to alter the climate variability of equatorial regions through the so-called thermocline bridge, both in the Pacific and Atlantic Oceans. To have a significant impact on the equatorial heat balance, however, temperature anomalies must reach the equatorial regions sufficiently undamped. In the oceans, the amplitude of propagating temperature (and salinity) anomalies can be altered both by diabatic (nonconservative) and adiabatic (conservative) effects. The importance of adiabatic alterations depends on whether the anomalies are controlled by wave dynamics or by passive advection associated with density compensation. Waves being relatively well understood, this paper seeks to understand the amplitude variations of density-compensated temperature and salinity anomalies caused by adiabatic effects, for which no general methodology is available. The main assumption is that these can be computed independent of amplitude variations caused by diabatic effects. Because density compensation requires the equality T′/S′ = βS/α to hold along mean trajectories, the ratio T′/S′ may potentially undergo large amplitude variations if the ratio βS/α does, where α and βS are the thermal expansion and haline contraction coefficients, respectively. In the oceans, the ratio βS/α may decrease by an order-1 factor between the extratropical and tropical latitudes, but such large variations are in general associated with diapycnal rather than isopycnal motion and hence are likely to be superimposed in practice with diabatically induced variations. To understand the individual variations of T′ and S′ along the mean streamlines, two distinct theories are constructed that respectively use density/salinity and density/spiciness as prognostic variables. If the coupling between the prognostic variables is neglected, as is usually done, both theories predict at leading order that temperature (salinity) anomalies should be systematically and significantly attenuated (conserved or amplified), on average, when propagating from extratropical to tropical latitudes. Along particular trajectories following isopycnals, however, both attenuation and amplification appear to be locally possible. Assuming that the density/spiciness formulation is the most accurate, which is supported by a theoretical assessment of higher-order effects, the present results provide an amplification mechanism for subducted salinity anomalies propagating equatorward, by which the latter could potentially affect decadal equatorial climate variability through their slow modulation of the equatorial mixed layer, perhaps more easily than their attenuated temperature counterparts. This could be by affecting, for instance, barrier layers by which salinity is known to strongly affect local heat fluxes and heat content.
Intensification of the Atlantic Deep Circulation by the Canadian Archipelago Throughflow
Authors: Komuro Yoshiki , Hasumi Hiroyasu 
Published: June 2005

Abstract
Low-salinity water export through the Canadian Archipelago is one of the main components of the freshwater budget in the Arctic Ocean. Nevertheless, the Canadian Archipelago is closed in most global ocean models. How it is that deep-water formation at high latitudes of the Northern Hemisphere depends on the opening and closing of the Canadian Archipelago is investigated. An ice–ocean coupled model, whose horizontal resolution is 1°, is used without restoring surface salinity to observed data. When the Canadian Archipelago is open, the Atlantic deep circulation strengthens by 21%. This enhancement is caused by intensification of deep-water formation in the northern North Atlantic Ocean. Surface salinity in these regions is affected by the East Greenland Current, which flows from the Fram Strait and increases its salinity when the Canadian Archipelago is opened. The low-salinity flow through the Canadian Archipelago affects surface salinity only in the western part of the Labrador Sea. A cyclonic circulation in the Labrador Sea plays an important role in limiting the direct impact of the Canadian Archipelago throughflow. Consequently, the deep-water formation there is intensified and the Atlantic deep circulation is strengthened. Thus, it is suggested that the Canadian Archipelago throughflow does not weaken the Atlantic deep circulation by the freshening of the Labrador Sea but strengthens it by the salinity increase in the Fram Strait.
The Response of an Idealized Ocean Basin to Variable Buoyancy Forcing
Authors: Lucas M. A. , Hirschi J. J. , Stark J. D. , Marotzke J. 
Published: June 2005

Abstract
The response of an idealized ocean basin to variable buoyancy forcing is examined. A general circulation model that employs a Gent–McWilliams mixing parameterization is forced by a zonally constant restoring surface temperature profile, which varies with latitude and time over a period P. In each experiment, 17 different values of P are studied, ranging from 6 months to 32 000 yr. The model's meridional overturning circulation (MOC) exhibits a very strong response on all time scales greater than 15 yr, up to and including the longest forcing time scales examined. The peak-to-peak values of the MOC oscillations reach up to 125% of the steady-state maximum MOC and exhibit resonance-like behavior, with a maximum at centennial to millennial forcing periods (depending on the vertical diffusivity). This resonance-like behavior stems from the existence of two adjustment time scales, one of which is set by the vertical diffusion and the other of which is set by the basin width. Furthermore, the linearity of the response as well as its lag with the forcing varies with the forcing period. The considerable deviation from the quasi-equilibrium response at all time scales above 15 yr is surprising and suggests a potentially important role of the ocean circulation for climate, even at Milankovich time scales.