bluuebunny/crossref_metadata_2025_split huggingface dataset:
All‐digital image capture and whole‐field analysis of ciliary beat frequency
Authors: Sisson J. H. , Stoner J. A. , Ammons B. A. , Wyatt T. A. 
Published: July 2003

SummaryWe hypothesized that a high‐speed all‐digital video imaging system, with computerized analysis, would precisely capture and measure ciliary beat frequency (CBF) and would shorten the time from data capture to data analysis. We compared a conventional analog video system with a new high‐speed digital system we developed for CBF analysis. Using ciliated primary bovine bronchial epithelial cells we made simultaneous analog and digital CBF measurements of the same region of interest (ROI) while temperature was varied. This yielded nearly identical data over a wide range of frequencies (7–15 Hz) using either system. Unlike the digital system however, the analog system did not accurately detect CBF above 15 Hz (temperatures higher than 30 °C). We also compared ROI analysis with a new analysis algorithm we have named whole‐field analysis (WFA). WFA measurement of CBF agreed with ROI and reduced operator time required to analyse data by more than 90% compared with the analog system. We conclude that all‐digital computerized CBF analysis correlates closely with standard video methods, markedly speeds up data analysis and provides new ways, including WFA, to analyse entire fields of motile cilia simultaneously. We have termed this system ‘Sisson–Ammons Video Analysis’ (SAVA).
Statistical analysis of intramembranous particles using freeze fracture specimens
Authors: Schladitz Katja , Särkkä Aila , Pavenstädt Iris , Haferkamp Otto , Mattfeldt Torsten 
Published: July 2003

SummaryWe studied the point processes of intramembranous particles of mitochondrial membranes from HeLa cells using the freeze fracture technique. Three groups – under normal conditions, after exposition with rotenone, and after exposition with sodium acid – were compared. First, we used several summary statistics in order to study the two‐dimensional point patterns of intramembranous particles within each group. Then, we compared the patterns in different groups by bootstrap tests using the K‐function and the nearest neighbour distance function G(r). Estimation of the G‐function provided significant results but no significant differences between groups were found using the classical K‐function; estimation of G(r) should therefore not be omitted when studying observed planar point patterns.
Wavelet‐based image restoration for compact X‐ray microscopy
Authors: Stollberg H. , Boutet De Monvel J. , Holmberg A. , Hertz H. M. 
Published: July 2003

SummaryCompact water‐window X‐ray microscopy with short exposure times will always be limited on photons owing to sources of limited power in combination with low‐efficency X‐ray optics. Thus, it is important to investigate methods for improving the signal‐to‐noise ratio in the images. We show that a wavelet‐based denoising procedure significantly improves the quality and contrast in compact X‐ray microscopy images. A non‐decimated, discrete wavelet transform (DWT) is applied to original, noisy images. After applying a thresholding procedure to the finest scales of the DWT, by setting to zero all wavelet coefficients of magnitude below a prescribed value, the inverse DWT to the thresholded DWT produces denoised images. It is concluded that the denoising procedure has potential to reduce the exposure time by a factor of 2 without loss of relevant image information.
Preparation of site‐specific cross‐sections of heterogeneous catalysts prepared by focused ion beam milling
Authors: Haswell R. , McComb D. W. , Smith W. 
Published: July 2003

SummaryFocused ion beam (FIB) milling offers a novel approach to preparation of site‐specific cross‐sections of heterogeneous catalysts for examination in the transmission electron microscope (TEM). Electron‐transparent sections can be obtained without the need to embed or grind the original sample. Because the specimen can be imaged in the FIB with submicrometre resolution before, during and after milling it is possible to select precisely the region from which the section is removed and to control the thickness of the section to within tens of nanometres. The ability to produce sections in this way opens the possibility of studying a range of catalyst systems that have previously been impossible to examine with the TEM.
Four‐dimensional imaging and computer‐assisted track analysis of nuclear migration in root hairs of Arabidopsis thaliana
Authors: Van Bruaene N. , Joss G. , Thas O. , Van Oostveldt P. 
Published: July 2003

SummaryNuclear migration is a fundamental mechanism necessary for the proper growth and development of many eukaryotic organisms. In this study root hairs of Arabidopsis thaliana were used as a research model to gain insight into the dynamics of nuclear migration. Root hairs are long tubular outgrowths of epidermal cells and are responsible for the uptake of water and nutrients. During the development of root hairs, the nucleus migrates into the hair after the bulge is formed. The position of the nucleus relative to the tip plays an essential role in the growth process. However, what is happening to the nucleus in full‐grown root hairs is still unclear. To study nuclear dynamics in living root hair cells, stably transformed plants with the fusion proteins Histone2B‐YFP and NLS‐GFP‐GUS were used. Four‐dimensional confocal laser scanning microscopy made it possible to monitor the exact position of the nucleus in different root hairs. To analyse the sequential positions of the nuclei in the root hairs, a new computer‐assisted method was developed. After track analysis a number of parameters could be extracted from the movies, such as the average speed, the amplitude, direction factor and the range of movement in the root hairs. Our results show that nuclei do not reach a final position in full‐grown root hairs and this sustained movement seems to be more similar in root hairs lying close to each other. Moreover, with this methodology it could be quantitatively demonstrated that the integrity of actin is necessary for nuclear movement.
A strand‐specific model for chromosome segregation in bacteria
Authors: Rocha Eduardo P. C. , Fralick Joe , Vediyappan Govindsamy , Danchin Antoine , Norris Vic 
Published: July 2003

SummaryChromosome separation and segregation must be executed within a bacterial cell in which the membrane and cytoplasm are highly structured. Here, we develop a strand‐specific model based on each of the future daughter chromosomes being associated with a different set of structures or hyperstructures in an asymmetric cell. The essence of the segregation mechanism is that the genes on the same strand in the parental cell that are expressed together in a hyperstructure continue to be expressed together and segregate together in the daughter cell. The model therefore requires an asymmetric distribution of classes of genes and of binding sites and other structures on the strands of the parental chromosome. We show that the model is consistent with the asymmetric distribution of highly expressed genes and of stress response genes in Escherichia coli and Bacillus subtilis. The model offers a framework for interpreting data from genomics.
Prion protein gene polymorphisms in Saccharomyces cerevisiae
Authors: Resende Catarina G. , Outeiro Tiago F. , Sands Laina , Lindquist Susan , Tuite Mick F. 
Published: July 2003

SummaryThe yeast Saccharomyces cerevisiae genome encodes several proteins that, in laboratory strains, can take up a stable, transmissible prion form. In each case, this requires the Asn/Gln‐rich prion‐forming domain (PrD) of the protein to be intact. In order to further understand the evolutionary significance of this unusual property, we have examined four different prion genes and their corresponding PrDs, from a number of naturally occurring strains of S. cerevisiae. In 4 of the 16 strains studied we identified a new allele of the SUP35 gene (SUP35Δ19) that contains a 19‐amino‐acid deletion within the N‐terminal PrD, a deletion that eliminates the prion property of Sup35p. In these strains a second prion gene, RNQ1, was found to be highly polymorphic, with eight different RNQ1 alleles detected in the six diploid strains studied. In contrast, for one other prion gene (URE2) and the sequence of the NEW1 gene encoding a PrD, no significant degree of DNA polymorphism was detected. Analysis of the naturally occurring alleles of RNQ1 and SUP35 indicated that the various polymorphisms identified were associated with DNA tandem repeats (6, 12, 33, 42 or 57 bp) within the coding sequences. The expansion and contraction of DNA repeats within the RNQ1 gene may provide an evolutionary mechanism that can ensure rapid change between the [PRION+] and [prion–] states.
Co‐operative interactions control conjugative transfer of broad host‐range plasmid RK2: full effect of minor changes in TrbA operator depends on KorB
Authors: Bingle Lewis E.H. , Zatyka Malgorzata , Manzoor Susan E. , Thomas Christopher M. 
Published: July 2003

SummaryA network of circuits, with KorB and TrbA as key regulators, controls genes for conjugative transfer of broad host range plasmid RK2. To assess the importance of the TrbA regulon, mutational analysis was applied to the TrbA operator at the trbB promoter and then to other TrbA‐regulated promoters in the tra region. All identified TrbA operators are submaximal; in the case of trbBp, a G to A transition that made the operator core a perfect palindrome increased repression by about 50% compared to the wild type. When this change was introduced into the RK2 genome, decreases in transfer frequency of up to three orders of magnitude were observed, with bigger effects when Escherichia coli was the donor compared to Pseudomonas putida. Western blotting showed a significant decrease in Trb protein levels. These effects were much greater than the effect of the mutation on repression by TrbA alone. When KorB was introduced into the reporter system, the effects were closer to those observed in the whole RK2 context. These results indicate that co‐operativity, previously observed between TrbA and KorB, allows big changes in transfer gene expression to result from small changes in individual regulator activities.
Tree root and soil heterotrophic respiration as revealed by girdling of boreal Scots pine forest: extending observations beyond the first year
Authors:   BHUPINDERPAL‐SINGH, NORDGREN A. , OTTOSSON LÖFVENIUS M. , HÖGBERG M. N. , MELLANDER P. ‐E. , HÖGBERG P. 
Published: July 2003

ABSTRACTLimitations in available techniques to separate autotrophic (root) and soil heterotrophic respiration have hampered the understanding of forest C cycling. The former is here defined as respiration by roots, their associated mycorrhizal fungi and other micro‐organisms in the rhizosphere directly dependent on labile C compounds leaked from roots. In order to separate the autotrophic and heterotrophic components of soil respiration, all Scots pine trees in 900 m2 plots were girdled to instantaneously terminate the supply of current photosynthates from the tree canopy to roots. Högberg et al. (Nature 411, 789–792, 2001) reported that autotrophic activity contributed up to 56% of total soil respiration during the first summer of this experiment. They also found that mobilization of stored starch (and likely also sugars) in roots after girdling caused an increased apparent heterotrophic respiration on girdled plots. Herein a transient increase in the δ13C of soil CO2 efflux after girdling, thought to be due to decomposition of 13C‐enriched ectomycorrhizal mycelium and root starch and sugar reserves, is reported. In the second year after girdling, when starch reserves of girdled tree roots were exhausted, calculated root respiration increased up to 65% of total soil CO2 efflux. It is suggested that this estimate of its contribution to soil respiration is more precise than the previous based on one year of observation. Heterotrophic respiration declined in response to a 20‐day‐long 6 °C decline in soil temperature during the second summer, whereas root respiration did not decline. This did not support the idea that root respiration should be more sensitive to variations in soil temperature. It is suggested that above‐ground photosynthetic activity and allocation patterns of recent photosynthates to roots should be considered in models of responses of forest C balances to global climate change.
Leaf, floret and seed infection of wheat by Pyrenophora semeniperda
Authors: Campbell M. A. , Medd R. W. 
Published: July 2003

Infection processes of Pyrenophora semeniperda on seedling and adult wheat leaves and wheat ears were investigated. Almost 100% germination of conidia occurred on seedling leaves, compared with 20–30% on adult leaves. Appressoria formed over the anticlinal epidermal cell walls and haloes always accompanied infection. Sometimes papillae formed within the leaves as a resistance mechanism. Infection hyphae ramified through the intercellular spaces of the mesophyll resulting in cellular disruption. The infection processes on floral tissues were similar to those observed on leaves; however, no infection occurred on anther, stigmatic or stylar tissues. Infection of ovarian tissue occurred both with and without appressoria formation. Hyphae grew mainly in the epidermal layers and appeared unable to breach the integumental layer as no growth was observed in endosperm or embryo tissues. The optimum dew period temperature for conidial germination was 23·6°C, compared with 19·9°C for lesion development, 20·4°C for the production of infection structures on seedling leaves and 23·7°C for floret infection. Leaf disease development occurred in a logistic manner in response to dew period, with maximum infection observed after 21 h compared with > 48 h in seeds. An initial dark phase during the dew period was necessary for infection and temperature after the dew period had an effect, with significantly more numerous and larger lesions being formed at 15°C compared with 30°C. Seedling leaves were found to be more susceptible than older leaves, under both field and controlled environment conditions. Infection of wheat seeds following inoculation of ears, or after harvest burial of inoculated disease‐free seeds, was demonstrated. In the latter, 3‐week‐old seedlings were slightly stunted, whereas older plants were unaffected. The apparent unimportance of this plant pathogen as a cause of leaf disease in relation to its poor adaptation to dew periods and dew period temperature is discussed, along with the importance of its seed borne characteristics.
An optimized screening method for identifying levels of resistance to Crinipellis perniciosa in cocoa (Theobroma cacao)
Authors: Surujdeo‐Maharaj S. , Umaharan P. , Butler D. R. , Sreenivasan T. N. 
Published: July 2003

The effects of host age, leaf number, host type (clone or seedling), pathogen spore concentration and incubation time on inoculation with Crinipellis perniciosa (witches’ broom disease of cocoa) were studied in greenhouse experiments using susceptible cocoa genotypes. Three methods of inoculation (agar‐drop, water‐drop and spray) were also tested. An optimized inoculation method was selected and tested for its repeatability as well as its ability to discriminate between various levels of resistance to C. perniciosa in cocoa. The optimized method (350 000 viable basidiospores per mL, 60 h incubation, agar‐drop technique) produced 100% infection repeatedly, on both clonal and seedling plants of a susceptible genotype. Seedling age (2–12 months) and leaf number did not significantly affect the percentage of plants with symptoms or broom characteristics. This method discriminated effectively between the various levels of resistance in 14 cocoa genotypes and is recommended as an inoculation method to identify levels of resistance in germplasm collections. Symptom severity was shown to be a better measure of resistance than infection success.
Sedimentary architecture and genesis of Holocene shallow‐water mud‐mounds, northern Belize
Authors: Mazzullo S. J. , Teal Chellie S. , Bischoff William D. , Dimmick‐Wells Kimberly , Wilhite Brian W. 
Published: July 2003

Abstract Cangrejo and Bulkhead Shoals are areally extensive, Holocene biodetrital mud‐mounds in northern Belize. They encompass areas of 20 km2 and 35 km2 in distal and proximal positions, respectively, on a wide and shallow‐water, microtidal carbonate shelf where storms are the major process affecting sediment dynamics. Sediments at each mound are primarily biodetrital and comprise part of a eustatically forced, dominantly subtidal cycle with a recognizable deepening‐upward transgressive systems tract, condensed section and shallowing‐upward highstand systems tract. Antecedent topographic relief on Pleistocene limestone bedrock also provided marine accommodation space for deposition of sediments that are a maximum of 7·6 m thick at Cangrejo and 4·5 m thick at Bulkhead. Despite differences in energy levels and location, facies and internal sedimentological architectures of the mud‐mounds are similar. On top of Pleistocene limestone or buried soil developed on it are mangrove peat and overlying to laterally correlative shelly gravels. Deposition of these basal transgressive, premound facies tracked the rapid rate of sea‐level rise from about 6400–6500 years BP to 4500 years BP, and the thin basal sedimentation unit of the overlying mound‐core appears to be a condensed section. Following this, the thick and complex facies mosaic comprising mound‐cores represents highstand systems tract sediments deposited in the last≈ 4500 years during slow and decelerating sea‐level rise. Within these sections, there is an early phase of progradationally offlapping catch‐up deposition and a later (and current) phase of aggradational keep‐up deposition. The mound‐cores comprise stacked storm‐deposited autogenic sedimentation units, the upper bounding surfaces of which are mostly eroded former sediment–water interfaces below which depositional textures have largely been overprinted by biogenic processes associated with Thalassia‐colonized surfaces. Vertical stacking of these units imparts a quasi‐cyclic architecture to the section that superficially mimics metre‐scale parasequences in ancient rocks. The locations of the mud‐mounds and the tidal channels transecting them have apparently been stable over the last 50 years. Characteristics that might distinguish these mud‐mounds and those mudbanks deposited in more restricted settings such as Florida Bay are their broad areal extent, high proportion of sand‐size sediment fractions and relatively abundant biotic particles derived from adjoining open shelf areas.
The effect of surface moisture on the entrainment of dune sand by wind: an evaluation of selected models
Authors: Cornelis W. M. , Gabriels D. 
Published: July 2003

Abstract Reliable predictions of wind erosion depend on the accuracy of determining whether erosion occurs or not. Among the several factors that govern the initiation of soil movement by wind, surface moisture is one of the most significant. Some widely used models that predict the threshold shear velocity for particle detachment of wet soils by wind were critically reviewed and evaluated. Wind‐tunnel experiments were conducted on pre‐wetted dune sand with moisture contents ranging from 0·00 to 0·04 kg kg−1. Sand samples were exposed to different wind speeds for 2 min. Moisture content was determined gravimetrically before and after each experiment, and the saltation of sand particles was recorded electronically with a saltiphone. Shear velocities were deduced from the wind speed profiles. For each moisture content, the experiments were repeated at different shear velocities, with the threshold shear velocity being determined by least‐squares analysis of the relationships between particle number rates and shear velocity.Within the 2‐min test runs, temporal changes in particle number rates and moisture contents were detected. A steep increase in the threshold shear velocity with moisture content was observed. When comparing the models, large differences between the predicted results became apparent. At a moisture content of 0·007 kg kg−1, which is half the moisture content retained to the soil matrix at a water tension (or matric potential) of −1·5 MPa, the increase in ‘wet’ threshold shear velocity predicted with the different models relative to the dry threshold shear velocity ranged from 117% to 171%. The highest care should therefore be taken when using current models to predict the threshold shear velocity of wet sediment. Nevertheless, the models of Chepil (1956; Proc. Soil Sci. Soc. Am., 20, 288–292) and Saleh & Fryrear (1995; Soil Sci., 160, 304–309) are the best alternatives available.
A method for profiling classes of plant hormones and their metabolites using liquid chromatography‐electrospray ionization tandem mass spectrometry: an analysis of hormone regulation of thermodormancy of lettuce (Lactuca sativa L.) seeds
Authors: Chiwocha Sheila D. S. , Abrams Suzanne R. , Ambrose Stephen J. , Cutler Adrian J. , Loewen Mary , Ross Andrew R. S. , Kermode Allison R. 
Published: July 2003

SummaryA highly selective and sensitive method for the simultaneous analysis of several plant hormones and their metabolites is described. The method combines high‐performance liquid chromatography (HPLC) with positive and negative electrospray ionization‐tandem mass spectrometry (ESI–MS/MS) to quantify a broad range of chemically and structurally diverse compounds. The addition of deuterium‐labeled analogs for these compounds prior to sample extraction permits accurate quantification by multiple reaction monitoring (MRM). Endogenous levels of abscisic acid (ABA), abscisic acid glucose ester (ABA‐GE), 7′‐hydroxy‐abscisic acid (7′‐OH‐ABA), phaseic acid (PA), dihydrophaseic acid (DPA), indole‐3‐acetic acid (IAA), indole‐3‐aspartate (IAAsp), zeatin (Z), zeatin riboside (ZR), isopentenyladenine (2iP), isopentenyladenosine (IPA), and gibberellins (GA)1, GA3, GA4, and GA7 were determined simultaneously in a single run. Detection limits ranged from 0.682 fmol for Z to 1.53 pmol for ABA. The method was applied to the analysis of plant hormones and hormonal metabolites associated with seed dormancy and germination in lettuce (Lactuca sativa L. cv. Grand Rapids), using extracts from only 50 to 100 mg DW of seed. Thermodormancy was induced by incubating seeds at 33°C instead of 23°C. Germinating seeds transiently accumulated high levels of ABA‐GE. In contrast, thermodormant seeds transiently accumulated high levels of DPA after 7 days at 33°C. GA1 and GA3 were detected during germination, and levels of GA1 increased during early post‐germinative growth. After several days of incubation, thermodormant seeds exhibited a striking transient accumulation of IAA, which did not occur in seeds germinating at 23°C. We conclude that hormone metabolism in thermodormant seeds is surprisingly active and is significantly different from that of germinating seeds.