bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards clean and atomically flat ZnO (000&1macr;) surfaces
Authors: Seldrum T. , Couet S. , Brison J. , Moisson C. , Turover D. , Sporken R. , Dumont J. 
Published: March 2006

AbstractWe established a cleaning procedure to obtain atomically flat $000 \bar {1}$ surfaces from pressurized melt grown ZnO using ex‐situ and in‐situ processing. The ex‐situ chemical cleaning consisted in removing the surface fluid layer and contaminants from the surface. The physical in‐situ procedure used sputtering‐annealing cycles to clean and reconstruct the surface. 3 key parameters were in‐situ investigated: the annealing time, the annealing temperature and the sputtering energy. Investigations were carried out by means of Low Energy Electron Diffraction (LEED), Auger Electron Spectroscopy (AES), X‐ray Photoemission Spectroscopy (XPS), Time of Flight of Secondary Ion Mass Spectrometry (ToF‐SIMS), Atomic Force Microscopy and Spectroscopy (AFM and AFS) and Scanning Tunnelling Microscopy (STM). (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Microwave‐Assisted Dimroth Rearrangement of Thiazines to Dihydropyrimidinethiones: Synthetic and Mechanistic Aspects
Authors: Glasnov Toma N. , Vugts Danielle J. , Koningstein Manoe M. , Desai Bimbisar , Fabian Walter M. F. , Orru Romano V. A. , Kappe C. Oliver 
Published: March 2006

AbstractThe Dimroth rearrangement of a set of substituted 2‐amino‐6H‐1,3‐thiazines into 3,4‐dihydropyrimidine‐2‐thiones was investigated. The rearrangements were carried out under microwave irradiation conditions in batch or continuous flow format, employing either toluene or 1‐methyl‐2‐pyrrolidone as solvent. Thiazines bearing an ester group at the C5 position rearranged at a considerably higher temperature than derivatives without substituents at this position into the corresponding pyrimidinethiones. This strictly thermal rearrangement was studied in detail using differential scanning calorimetry and density functional theory computational methods. The reaction pathway involves a zwitterionic intermediate.
New tools for phenotypic analysis in Candida albicans: the WAR1 gene confers resistance to sorbate
Authors: Lebel Karine , MacPherson Sarah , Turcotte Bernard 
Published: March 2006

AbstractAvailability of the complete sequence of the Candida albicans genome allows for global gene analysis. We designed a gene deletion method to facilitate such studies. First, we constructed C. albicans strains that are both Δura3 and Δtrp1. Second, we designed a system that relies on in vitro recombination, using the Gateway® technology, for efficient generation of deletion cassettes. They are generated in two steps: (a) upstream and downstream DNA fragments of the chromosomal region to be deleted are amplified by PCR and introduced into two separate entry vectors; (b) the second step involves a quadruple recombination event including the two entry vectors, a plasmid bearing a marker of interest and a destination vector, in order to generate a plasmid containing the deletion cassette. The deletion plasmid contains very rare restriction sites for convenient excision of the knockout cassette. Selection in C. albicans can be performed with one of the following markers: the C. albicans URA3 gene, a modified S. cerevisiae TRP1 gene or the mycophenolic acid resistance (MPAR) gene. Upon integration into the genome, these markers can be removed by the use of 5‐fluoroorotic acid (URA3), 5‐fluoroanthranilic acid (TRP1) or the FLP recombinase (MPAR). Using this approach, we show that removal of the C. albicans orf19.1035 gene results in sensitivity to the weak acid sorbate, while its overexpression increases resistance to this compound. We named it WAR1, in analogy to its S. cerevisiae orthologue. Copyright © 2006 John Wiley & Sons, Ltd.
The relative merits of the tetO2 and tetO7 promoter systems for the functional analysis of heterologous genes in yeast and a compilation of essential yeast genes with tetO2 promoter substitutions
Authors: Wishart Jill A. , Osborn Michael , Gent Manda E. , Yen Kuangyu , Vujovic Zorana , Gitsham Paul , Zhang Nianshu , Ross Miller J. , Oliver Stephen G. 
Published: March 2006

AbstractWe have generated a collection of yeast strains, each of which has an essential yeast gene under the control of the tetracycline‐responsive, tetO, promoter. Screens using first‐generation promoter‐swap strains uncovered the non‐specific responsiveness of the tetO7 promoter to a known human transcription factor (hIRF‐1). Non‐specific regulation was not observed with the tetO2 promoter. Reporter assays have been used to demonstrate this phenomenon. Subsequent efforts to generate a collection of tetracycline‐regulatable strains have focused on the tetO2 promoter. These strains are available to the yeast community and can be used for functional genomics studies. Copyright © 2006 John Wiley & Sons, Ltd.
The more the merrier: comparative analysis of microarray studies on cell cycle‐regulated genes in fission yeast
Authors: Marguerat Samuel , Jensen Thomas S. , de Lichtenberg Ulrik , Wilhelm Brian T. , Jensen Lars J. , Bähler Jürg 
Published: March 2006

AbstractThe last two years have seen the publication of three genome‐wide gene expression studies of the fission yeast cell cycle. While these microarray papers largely agree on the main patterns of cell cycle‐regulated transcription and its control, there are discrepancies with regard to the identity and numbers of periodically expressed genes. We present benchmark and reproducibility analyses showing that the main discrepancies do not reflect differences in the data themselves (microarray or synchronization methods seem to lead only to minor biases) but rather in the interpretation of the data. Our reanalysis of the three datasets reveals that combining all independent information leads to an improved identification of periodically expressed genes. These evaluations suggest that the available microarray data do not allow reliable identification of more than about 500 cell cycle‐regulated genes. The temporal expression pattern of the top 500 periodically expressed genes is generally consistent across experiments and the three studies, together with our integrated analysis, provide a coherent and rich source of information on cell cycle‐regulated gene expression in Schizosaccharomyces pombe. The reanalysed datasets and other supplementary information are available from an accompanying website: http://www.cbs.dtu.dk/cellcycle/. We hope that this paper will resolve the apparent discrepancies between the previous studies and be useful both for wet‐lab biologists and for theoretical scientists who wish to take advantage of the data for follow‐up work. Copyright © 2006 John Wiley & Sons, Ltd.
Isolation and bioenergetic characterization of mitochondria from Pichia pastoris
Authors: Mar González‐Barroso M. , Ledesma Amalia , Lepper Simone , Pérez‐Magán Elisa , Zaragoza Pilar , Rial Eduardo 
Published: March 2006

AbstractPichia pastoris is a methylotrophic yeast of high biotechnological interest. The bioenergetic properties of mitochondria from Pichia pastoris have not yet been determined. We report on a protocol for the isolation of the mitochondria in a state that shows good energy coupling. Analysis of Pichia pastoris growth and bioenergetic properties of the isolated mitochondria reveals that glycerol is the carbon source that yields the best results. Under our growth conditions, mitochondria oxidize external NADH but do not possess an alternative oxidase. Finally, Pichia pastoris mitochondria also lack the nucleotide‐stimulated uncoupling pathway previously identified in Saccharomyces cerevisiae. Copyright © 2006 John Wiley & Sons, Ltd.
Food habits of Sika deer on Mt. Goyo, northern Honshu
Authors: Takatsuki Seiki 
Published: March 2006

AbstractThe food habits of Sika deer (Cervus nippon) on Mt. Goyo, northern Honshu (the main island of Japan), were studied. Among 88 plant species found in surveys, 36 species (40.9%) were eaten by the deer. The percentage frequency of feeding (F) was highest for graminoids (59.6%), followed by browses (16.6%) and ferns (7.7%) and lowest for forbs (5.4%). Though various kinds of plants were eaten, only limited species formed the bulk of the deer dietary composition. Sasa nipponica, in particular, was the most important constituent, ranking highest in F value (80.3%) and being the dominant component of feces. Fecal analyses revealed that, 1) in areas lower than 900 m in altitude, Sasa nipponica accounted for between 20 and 60% of the content and that pasture grasses were also important, and 2)S. nipponica occupied more than 50% in montane areas higher than 900 m, and even more than 80% in winter. The utilization of S. nipponica as a forage for Sika deer was discussed. This plant can be a key forage species because it meets all the necessary conditions: abundance and stability of supply, palatability, nutritive quality and tolerance to grazing.
Comparative ecophysiology of two representative Quercus species appearing in different stages of succession
Authors: Takenaka Akio 
Published: March 2006

AbstractEcophysiological comparisons were made of the growth and photosynthetic characteristics between seedlings of deciduous Quercus serrata and evergreen Quercus myrsinaefolia. Q. myrsinaefolia seedlings naturally occurring in secondary coppice forests showed exponential‐like growth in height with age, while sympatric Q. serrata seedlings were considerably smaller in height, their growth being limited by shortage of light. The photosynthetic characteristics measured under laboratory conditions showed no bases for the differences in growth between the two species on the forest floor: Light compensation points of the seedlings raised under 5% daylight were almost identical for the two species, being about 6.0 μE·m−2·s−1. Growth analysis of seedlings planted in a coppice forest showed that both Q. serrata and Q. myrsinaefolia could hardly grow during the summer under the shrub layer, when relative photon flux density (RPFD) was 0.9±0.5%. In the winter, when RPFD under the leafless canopy increased to 29.3±2.7%, the dry matter production of the evergreen seedlings of Q. myrsinaefolia was much improved. Current‐year seedlings of the species showed NAR of 0.102±0.021 g·dm−2·mo−1 during the winter. Temperature dependency of photosynthesis and increment of leaf temperature by direct solar beam also indicated active photosynthesis of Q. myrsinaefolia on the forest floor during the winter.
The seasonal abundance and vertical distribution of the <3‐μm phytoplakton in the north basin of Lake Biwa
Authors: Nagata Toshi 
Published: March 2006

AbstractThe seasonal changes in the size‐fractionated chlorophyll a concentrations (<3 μm, 3 to 25 μm, and >25 μm) were investigated at a pelagic site of the north basin of Lake Biwa during June to December 1985. Autofluorescing plankton cells in the <3‐μm fractions were also examined using the fluorescein isothiocyanate staining epifluorescence microscopic technique. The <3‐μm phytoplankton (usually dominated by chroococcoid cyanobacteria except for a few cases dominated by small eukaryotes) showed a clearly different pattern of seasonal change compared with the larger fractions. That is, from August to early September, chlorophyll a of the larger fractions declined considerably, while the <3‐μm chlorophyll a did not decrease significantly. Moreover, cyanobacterial cell density in the <3‐μm fraction showed a maximum value (2–3.5×105 cells·ml−1) during this period. The relative contribution of the <3‐μm chlorophyll a to the total chlorophyll a increased from <5% to 45% during the course of this change. No clear vertical trend in the distribution and composition of the <3‐μm phytoplankton was found, except that relatively large cyanobacteria (>4 μm3) appeared at a depth of 15m but not at 0,5 and 10 m from late July to August. These large cells were also found in November and December. The drastic seasonal change of phytoplankton size structure occurring in this basin was discussed in relation to grazing, nutrient depletion and sinking.
The spatial pattern and canopy‐understory association of trees in a cool temperate, mixed forest in western Japan
Authors: Akashi Nobuhiro 
Published: March 2006

AbstractThe spatial distribution pattern of trees and the association between canopy and understory individuals were examined with reference to the distribution of tree crowns in a cool temperate, mixed forest in Ohdaigahara, western Japan. Line transect and contact sampling methods were used to examine the pattern over various spatial scales. These methods are useful to detect patterns over a large study area. The dominance of Chamaecyparis obtusa on steep slopes forming large patches suggested that the distribution of this species is a consequence of landslides. Understory Fagus crenata showed a clumped distribution, and the relative coverage of this species was larger in canopy gaps than under a closed canopy. Understory individuals of Abies homolepis showed a positive association with canopy trees of F. crenata but a negative association with conspecific canopy individuals. These patterns suggested that F. crenata regenerates in canopy gaps and is replaced by A. homolepis. The dynamics of these two species are consistent with the process of gap dynamics. The effects of both small‐ and large‐scale disturbance must be evaluated to understand the mechanisms of patch formation and the coexistence of forest tree species.
Vegetation structure in relation to micro‐landform in an evergreen broad‐leaved forest on Amami Ohshima Island, south‐west Japan
Authors: Hara Masatoshi , Hirata Kazuhiro , Fujihara Michiro , Oono Keiichi 
Published: March 2006

AbstractThe relationship between micro‐landform and vegetation structure was studied in a plot that was established on a slope from the ridge to the valley bottom in an evergreen broad‐leaved forest on Amami Ohshima Island, south‐west Japan. Five micro‐landform units recognized in the plot were grouped into the upper and lower slopes by their location in relation to the erosion front, and plant distributions and vegetation structure were compared between them. Although small trees with d.b.h. less than 10 cm occurred almost all over the plot, the occurrence of larger trees was limited mostly to the upper slope. Based on the spatial distribution pattern in the plot, woody species are classified into three groups: group A mostly or strictly confined to the upper slope; group B confined to the lower slope; and group C associated statistically with neither slope. A well‐developed forest stand, whose dominant species were Castanopsis sieboldii ssp. lutchuensis and Schima wallichii, was seen on the upper slope, whereas only a poorly developed stand was seen on the lower slope. The difference in stability of the land surface is likely to be the major cause of the observed differences in stand structure between the upper and lower slopes. It is suggested that the erosion front is important as a line demarcating different habitats within a slope from the ridge to the valley bottom.
Differentiation and maintenance of topo‐community patterns with reference to regeneration dynamics in mixed cool temperate forests in the Chichibu Mountains, central Japan
Authors: Yoshida Naoya , Ohsawa Masahiko 
Published: March 2006

AbstractTopo‐community structure and dynamics were studied in mixed cool temperate forests, using the regeneration dynamics, to clarify the maintenance mechanisms of community patterns along a microtopographic gradient. The 76 stands studied were classified into two groups (i.e. convex slope and concave slope stands). The soil surface was more eroded on the concave slope than on the convex slope, while water potential was not significantly different between topographies. On the convex slope, even‐aged patches alternated between young phase patches dominated by shade intolerant species, such as Acer rufinerve and Betula grossa, and mature phase patches, with Tsuga sieboldii and Fagus crenata. A slower lateral growth rate of Tsuga canopy trees and the absence of suppressed saplings in the mature phase may prolong the gap phase, which provides a favorable situation to shade‐intolerant species. On the concave slope, patch structure was less clear, and process of replacement of canopy species by previously suppressed individuals of the same species was seen in the mature phase, which was mainly composed of F. crenata, Fagus japonica, Acer sieboldianum and Stewartia pseudo‐camellia. Gaps on the concave slope were formed frequently but were generally closed within 10 years by lateral growth of deciduous canopy trees and by upgrowth of suppressed trees, and thus some individuals underwent recurrent periods of suppression until they reached the canopy. We concluded that soil surface stability and gap encroachment pattern are critical to the maintenance of the community pattern along a microtopographic gradient.
Structure and regeneration of Fraxinus spaethiana‐Pterocarya rhoifolia forests in unstable valleys in the Chichibu Mountains, central Japan
Authors: Ann Seoung Won , Oshima Yasuyuki 
Published: March 2006

AbstractThe structure of temperate deciduous forests dominated by Fraxinus spaethiana and Pterocarya rhoifolia in V‐shaped valleys in the Chichibu Mountains, central Japan was studied to clarify their dynamics, with special reference to disturbance. Forest structure and annual ring analysis revealed that the forests have been subjected to mass movement (mud flow) in the past. The size and age structure, and diameter growth curves, indicated that F. spaethiana is relatively shade tolerant, long living and slow‐growing, while P. rhoifolia is less shade tolerant, short living, but fast growing. Pterocarya rhoifolia appears to depend on large‐scale but rare disturbances. Fraxinus spaethiana establishes its seedlings on relatively unstable substrate in V‐shaped valleys, but once established, they survive a long time with high shade tolerance. The dominance and coexistence of the two species may primarily depend on the intensity and frequency of geomorphological processes.
Vertical variation in fecundity of the intertidal gastropod Monodonta labio caused by different growth rates between tidal zones
Authors: Takada Yoshitake 
Published: March 2006

AbstractMonodonta labio (Gastropoda: Trochidae) occurs in a wide tidal zone on a boulder‐covered shore in Amakusa, Japan. To investigate sources of variation in reproductive output within a population, the fecundity of M. labio was estimated. Regressions of gonad egg counts on shell width were calculated from samples collected bi‐weekly at three tidal zones: high, mid and low intertidal. Seasonal fluctuations in the regression revealed that individual females spawn at least three times a year. Variation in fecundity between the three tidal zones was not detected at any time in standard 12 mm snails. Due to the high growth rate in the low zone during the reproductive season, annual fecundity in the low zone was larger than that in the high and mid zones. Thus, tidal zone variation in fecundity of M. labio was a result of growth variation between tidal zones.
Nutritional diversity of symbiotic ascidians in a Fijian seagrass meadow
Authors: Koike Isao , Suzuki Takao 
Published: March 2006

AbstractIn a coastal lagoon of Dravuni Island, Fiji, at least six species of compound ascidians, some of them harboring Prochloron as symbiotic algae, were found in a Syringodium‐dominated seagrass meadow. Based on their heterotrophic (filrer feeding rates) and autotrophic (photosynthetic) activities, carbon gain of the ascidians was categorized into two groups: (i) supported by heterotrophic metabolism; and (ii) supported by both heterotrophic and autotrophic metabolisms. Didemnum molle, Lissoclinum bistratum and Lissolinum voeltzkowi belong to the latter group, and the relative contribution of the autotrophic process was a significant portion of their carbon gain (52–74%). These symbiotic ascidians were found in light microhabitats, while the heterotrophic species occupied shady environments rich in suspended organic materials, such as the sheath surface of the seagrass.
Successional change of forest pattern along topographical gradients in warm‐temperate mixed forests in Mt Kiyosumi, central Japan
Authors: Ozaki Kemurio , Ohsawa Masahiko 
Published: March 2006

AbstractForest patterns along topographical gradients were compared between second‐ and old‐growth forested watersheds in a warm‐temperate zone of Mt Kiyosumi, central Japan. Three community types were distinguished depending on the topographical habitat type in each watershed, for example, conifer forest was dominated by Abies firma and Tsuga sieboldii on ridge sites, evergreen broad‐leaved forest was dominated by Quercus acuta, Q. salicina and Castanopsis cuspidata var. sieboldii on slope sites, and deciduous forest was dominated by Euptelea polyandra and Cornus controversa in valley sites. Beta diversity and distinctiveness of each topographical community type increased with progression of secondary succession. Conifers and evergreen broad‐leaved trees, which were intermingled with each other on ridges and slopes of the second‐growth watershed, were in turn restricted to the ridge and slope habitat type, respectively, in the old‐growth watershed. The process of this differentiation can be explained by the continuous regeneration of conifers on ridge sites, and its absence on slope sites due to different light conditions caused by progressive canopy closure of evergreen trees on the slope sites toward the old‐growth watershed. In the valley type habitat, frequent soil disturbance, such as landslides and soil creep, hinder the continuous growth of late successional evergreen trees, and thus seral or pioneer deciduous trees can persist in the habitat.
Seedling establishment of Castanopsis cuspidata var. sieboldii and Persea thunbergii on lava and scoria of the 1962 eruption on Miyake‐jima Island, the Izu Islands
Authors: Kamijo Takashi , Okutomi Kiyoshi 
Published: March 2006

AbstractSeedling establishment of Castanopsis cuspidata var. sieboldii Nakai and Persea thunbergii Kosterm. (Machilus thunbergii Sieb. et Zucc.) in early succession was studied on the lava and the scoria of the 1962 eruption on Miyake‐jima Island of the Izu Islands. While tall individuals (> 1 m) of P. thunbergii were found on both the lava and the scoria, those of C. cuspidata (> 1 m) were found only on the lava. The height growth rate of C. cuspidata was very low on the scoria, and there was no individual of C. cuspidata taller than 0.4 m on the scoria. The proportion of yellow leaved individuals was much higher (37.1%) in C. cuspidata than in P. thunbergii (4.0%) on the scoria, while it was similar between the two species on the lava. Persea thunbergii seemed to be able to establish on both the lava and the scoria, but C. cuspidata established only on the lava. The differences in growth rate and vigor between the two species on the lava and the scoria in early succession may influence later stages of succession.