bluuebunny/crossref_metadata_2025_split huggingface dataset:
Directional analysis of digitized three‐dimensional images by configuration counts
Authors: GUTKOWSKI P. , JENSEN E. B. V. , KIDERLEN & M. 
Published: October 2004

SummaryA method for estimating the orientated rose of normal directions of a three‐dimensional (3D) set Z from a digitization of Z, i.e. a voxel image, is presented. It is based on counts of informative configurations in n×n×n voxel cubes. An algorithm for finding all informative configurations is proposed and an estimation procedure is described in detail for the case n= 2. The presented method is a 3D version of a method of estimating the orientated rose of binary planar images using n×n configurations. A new feature is the design‐based approach, being more appropriate for biomedical image analysis than the formerly applied model‐based approach.
A convenient and rapid sample repositioning approach for atomic force microscopy
Authors: SU M. , PAN Z. , DRAVID V. P. 
Published: October 2004

SummaryA novel repositioning approach is described for repeated observations of a specimen at a close proximal location in the atomic force microscope. The approach is similar to keystone architecture, whereby the repositioning is achieved by forming a male structured base for the specimen, and a corresponding female counterpart as the frame. For the combination of an acrylic acid frame and a metal base, 90% translation shifts are less than 10 µm, and almost all angular disorientations are within +3° to −3°. Nanometre‐scale surface features can be relocated easily and reliably even after 40 imaging–removal–imaging cycles, dipping the specimen in solutions or heating up to 500 °C.
Signal analysis of total internal reflection fluorescent speckle microscopy (TIR‐FSM) and wide‐field epi‐fluorescence FSM of the actin cytoskeleton and focal adhesions in living cells
Authors: ADAMS M. C. , MATOV A. , YARAR D. , GUPTON S. L. , DANUSER G. , WATERMAN‐STORER C. M. 
Published: October 2004

SummaryFluorescent speckle microscopy (FSM) uses low levels of fluorescent proteins to create fluorescent speckles on cytoskeletal polymers in high‐resolution fluorescence images of living cells. The dynamics of speckles over time encode subunit turnover and motion of the cytoskeletal polymers. We sought to improve on current FSM technology by first expanding it to study the dynamics of a non‐polymeric macromolecular assembly, using focal adhesions as a test case, and second, to exploit for FSM the high contrast afforded by total internal reflection fluorescence microscopy (TIR‐FM). Here, we first demonstrate that low levels of expression of a green fluorescent protein (GFP) conjugate of the focal adhesion protein, vinculin, results in clusters of fluorescent vinculin speckles on the ventral cell surface, which by immunofluorescence labelling of total vinculin correspond to sparse labelling of dense focal adhesion structures. This demonstrates that the FSM principle can be applied to study focal adhesions. We then use both GFP‐vinculin expression and microinjected fluorescently labelled purified actin to compare quantitatively the speckle signal in FSM images of focal adhesions and the actin cytoskeleton in living cells by TIR‐FM and wide‐field epifluorescence microscopy. We use quantitative FSM image analysis software to define two new parameters for analysing FSM signal features that we can extract automatically: speckle modulation and speckle detectability. Our analysis shows that TIR‐FSM affords major improvements in these parameters compared with wide‐field epifluorescence FSM. Finally, we find that use of a crippled eukaryotic expression promoter for driving low‐level GFP‐fusion protein expression is a useful tool for FSM imaging. When used in time‐lapse mode, TIR‐FSM of actin and GFP‐conjugated focal adhesion proteins will allow quantification of molecular dynamics within interesting macromolecular assemblies at the ventral surface of living cells.
Structured illumination microscopy: artefact analysis and reduction utilizing a parameter optimization approach
Authors: SCHAEFER L. H. , SCHUSTER D. , SCHAFFER J. 
Published: October 2004

SummaryPractical applications of structured illumination microscopy (SIM) often suffer from various artefacts that result from imprecise instrumental hardware and certain bleaching properties of the sample. These artefacts can be observed as residual stripe patterns originating from the illumination grating. We investigated some significant causes of these artefacts and developed a correction approach that can be applied to images after acquisition. Most of the artefacts can be attributed to changes in illumination and detection intensities during acquisition. The proposed correction algorithm has been shown to be functional on noisy image data, and produces exceptional, artefact‐free results in everyday laboratory work.
FIELD AND CULTURE STUDIES OF A POPULATION OF ENDARACHNE BINGHAMIAE (PHAEOPHYTA) FROM SOUTHERN CALIFORNIA1
Authors: Brophy Thomas C. , Murray Steven N. 
Published: October 2004

ABSTRACTAbundances of the erect, blade phase of Endarachne binghamiae J. Ag. (Scytosiphonales, Phaeophyta) varied seasonally at a southern California rocky intertidal site. Blade cover and density were much greater in the fall through early spring; blades were mostly absent from quadrats during the summer. Blade abundances were negatively correlated with both seasonal variations in seawater temperature and photoperiod. Laboratory culture studies failed to provide evidence for sexual reproduction. The life history appears to be of the “direct” type with plurangia‐produced zooids germinating into crustose disks. Most disks developed erect blade clusters under spring/fall (17° C) and winter (13° C) temperatures over the range of natural photoperiods employed (14:10, 12:12, 10:14 h LD). In contrast, cultures held under the summer temperature (21° C) produced almost entirely crustose growths regardless of photoperiod. Similar results were obtained for cultures grown at 100 and 200 μE · m−2· s−1. E. binghamiae blades were fertile throughout the year and produced viable zooids indicating that reproductive seasonality did not influence the seasonal pattern of blade abundance. Culture and field studies suggest that the initiation of new erect blade clusters from crustose disks is confined to the cooler months of the year (winter and spring). The summer reduction or absence of E. binghamiae blades appears to be due to increased mortality rates and temperature constraints on the development of new erect bladed thalli. Hypothetical causes of mortality are desiccation stress, sand burial, increased grazing activity and a genetically‐based short life span.
REVERSIBLE KINETIC MODEL FOR THE SHORT‐TERM REGULATION OF METHYLAMMONIUM UPTAKE IN TWO PHYTOPLANKTON SPECIES, DUNALIELLA TERTIOLECTA (CHLOROPHYCEAE) AND PHAEODACTYLUM TRICORNUTUM (BACILLARIOPHYCEAE)1
Authors: Roche Julie La , Harrison W. Glen 
Published: October 2004

ABSTRACTMethylammonium, an ammonium analog, was used to study the short‐term kinetics of ammonium uptake in a diatom, Phaeodactylum tricornutum Bohlin, and a green alga, Dunaliella tertiolecta Butcher. Time courses of methylammonium disappearance were measured over a wide range of initial substrate concentrations for the two species. It was shown that feedback inhibition, described mathematically by a reversible enzyme kinetic model, can be used to explain the data. For the two species, there was good agreement between the kinetic parameters obtained from the analysis of the uptake versus substrate curve and those from the fit of the reversible kinetic model to the time‐course data. All time courses of CH3NH3+ disappearance could be described by constants Vm and ks. Ammonium time‐course data show some similarities to its analog, methylammonium. Our study suggests that the apparent change in Vm and ks with time measured after the addition of saturating ammonium concentrations reflects an uncoupling between transport and assimilation of the substrate rather than a real change in the kinetic parameters of the transport mechanism.
EVIDENCE OF DARK AVOIDANCE BY PHOTOTROPHIC PERIPHYTIC DIATOMS IN LOTIC SYSTEMS1
Authors: Bothwell Max L. , Suzuki Kelly E. , Bolin Mary K. , Hardy F. Joan 
Published: October 2004

ABSTRACTShort‐term (24–48 h) colonization dynamics of periphytic diatoms on artificial (styrofoam) substrata were examined using fast‐flushing, continuous‐flow troughs located on the North Thompson River, British Columbia. Two parallel troughs, one exposed to natural light and the other completely darkened, showed significant differences in periphyton biomass, chlorophyll a, and algal taxonomic composition with 24 h. Experiments which commenced at the onset of natural darkness demonstrated that rates of algal immigration during the night were the same in both troughs. Within 2–3 h of sunrise, however, certain diatom species (most notably Hannaea arcus (Ehr.) Pair, and Diatoma tenue Ag.) selectively emigrated from the artificially darkened trough but remained in the trough exposed to natural light. More closely adhering species such as Achnanthes minutissima Kütz, also showed significant emigration from the darkened trough after light deprivation for two photoperiods. Data from adhesion, emigration, and sinking rate experiments indicate that differential egress of cells from the darkened versus the lighted environments is the result of cellular regulation of buoyancy or form resistance.
ULTRASTRUCTURAL ASPECTS OF SEXUAL REPRODUCTION IN THE RED TIDE DINOFLAGELLATEGONYAULAX TAMARENSIS1
Authors: Fritz Lawrence , Anderson Donald M. , Triemer Richard E. 
Published: October 2004

ABSTRACTThe marine dinoflagellateGonyaulax tamarensisLebour is best known for its propensity to form blooms known as red tides in coastal waters worldwide. This paper examines the sexual cycle of this organism using light and electron microscopy. Sexual reproduction begins with contact between thecate gametes which subsequently shed their thecae to fuse along their pellicular layers. Nuclear fusion occurs well after cytoplasmic fusion and is characterized by several distinctive features: a highly vesiculate nucleoplasm without microtubules; nucleoli and V‐shaped chromosomes abut the nuclear envelope distal to the region of nuclear contact; and each chromosome possesses a longitudinal line, the central chromosomal axis. Fusion results in a planozygote with numerous cytoplasmic storage products and a slightly thickened layer beneath the pellicle. Subsequent loss of thecal plates and a thickening of the sub‐pellicular layer results in a non‐motile hypnozygote. A newly‐formed hypnozygote possesses numerous minute papillae along its outer surface, formed by the up‐folding of the accumulating wall layer. Maturation of the hypnozygote wall results in a smooth three‐layered wall, the outermost layer of which is the pellicular layer. Hypnozygote germination produces a large quadriflagellate plan‐omeiocyte with a single nucleus and thecal plates identical to vegetative cells. Two subsequent divisions, presumably meiotic, result in Jour cells morphologically identical to vegetative cells.
AN HERBICIDE (SULFOMETURON METHYL) RESISTANT MUTANT IN PORPHYRIDIUM (RHODOPHYTA)1
Authors: Van‐Moppes Dorit , Barak Ze'ev , Chipman David M. , Gollop Natan , Arad Shoshana (Malis) 
Published: October 2004

ABSTRACTThe unicellular red alga Porphyridium sp. is, like many bacteria, fungi and higher plants, sensitive to the sulfonylurea herbicide sulfometuron methyl (SMM). However, the minimal inhibitory concentration for SMM in Porphyridium (55 μM) is higher than in green plants. We isolated a spontaneous SMM‐resistant mutant SMR1 of Porphyridium sp. by use of a double‐layered agar technique. The mutation frequency and the similarity of the mutant's morphology and growth patterns to the parent strain strongly suggest that SMR1 is a single gene mutation. The activity of the enzyme acetohydroxy acid synthase (AHAS) in crude extracts of the mutant SMR1 is at least two orders of magnitude less sensitive to SMM than that of the parent strain, which indicates that AHAS is the target of SMM (as has been shown in a variety of organisms). We propose that such a mutation, the first isolated in a unicellular rhodophyte, would be a useful marker for genetic studies of Porphyridium. It may also be useful for maintaining unialgal cultures in large scale open ponds.
PURIFICATION OF SPECIES SPECIFIC ANTIBODIES TO CARBOHYDRATE COMPONENTS OF MACROCYSTIS PYRIFERA (PHAEOPHYTA)1
Authors: Hempel William M. , Sutton Celia W. , Kaska Deborah , Ord David C. , Reed Daniel C. , Laur David R. , Ebeling Alfred W. , Eardley Diane D. 
Published: October 2004

ABSTRACTPolyclonal rabbit antibodies to cell wall components were produced against gametophytes of the giant kelp Macrocystis pyrifera (Linnaeus) C. Agardh. These antibodies were found to react with carbohydrates extracted from M. pyrifera and Pterygophora californica Ruprecht by carbohydrate based enzyme immunoassay (EIA). The antibodies reacted with carbohydrates from both species. After affinity purification on a column with M. pyrifera carbohydrate coupled to AH‐Sepharose, the eluted antibody was specific for M. pyrifera carbohydrate with little cross reactivity to P. californica carbohydrate in the EIA test. In experiments carried out to characterize the antigenic specificity of unfractionated antibody using commercially prepared carbohydrates in the EIA, the antibodies were shown to react primarily with fucoidan and to a lesser degree, alginate. The unfractionated antibody was also shown to bind to proteins from both M. pyrifera and P. californica. These results indicate that species specific carbohydrate determinants may be present in the kelp cell wall.
FUNCTIONAL VALVE MORPHOLOGY IN SOME SURIRELLA SPECIES (BACILLARIOPHYCEAE) AND A COMPARISON WITH THE NAVICULACEAE1
Authors: Krammer Kurt 
Published: October 2004

ABSTRACTOn the basis of results of stratigraphic and comparative morphological studies on the diatom frustule, the Surirellaceae is generally assumed to be the endpoint of the evolution of the Pennales. The present study shows that a line of development, based on frustule construction and which parallels the search for optimum design of comparable elements in engineering, can be traced from the Naviculaceae to the Surirellaceae. In both cases lightweight construction is achieved through economy of material and energy expenditure. This leads to structural stability and in the case of the diatom valve, a larger area for metabolic exchange.From the functional‐morphological point of view, three construction principles can be distinguished in the genus Surirella: 1. valves with pennate costal framework, raphe keels and fibulae (Surirella gemma group); 2. frustules where all supporting elements are in the form of corrugations, with raphe keel and fibulae (Pinnatae, Fastuosae, Surirella striatula group); and 3. as in 2, but with true alae with alar canals (Robustae) instead of keels with fibulae.
AMMONIUM, NITRATE, PHOSPHATE, AND INORGANIC CARBON UPTAKE IN AN OLIGOTROPHIC LAKE: SEASONAL VARIATIONS AMONG LIGHT RESPONSE VARIABLES1
Authors: Dodds Walter K. , Priscu John C. 
Published: October 2004

ABSTRACTThe dependence of substrate saturated uptake of 15NH4+, 15NO3−, 32PO43−, and 14CO2 on photosynthetic photon flux density (PPFD or photsynthetically active radiation, 400–700 nm) was characterized seasonally in oligotrophic Flathead Lake, Montana. PO43− uptake was not dependent upon PPFD at any time of the year, whereas NH4+, NO3−, and CO2 uptake were consistently dependent on PPFD over all seasons. Maximal rates of NH4+, NO3− and CO2 uptake usually occurred near 40% of surface PPFD, which corresponded to about 5 m in the lake; inhibition was evident at PPFD levels greater than 40%. NH4+, NO3− and PO43− were incorporated in the dark at measurable rates most of the year, whereas dark CO2 uptake was always near 0 relative to light uptake. CO2 and NO3− uptake were more strongly influenced by PPFD than was NH43− uptake. The PPFD dependence of PO43−, NH4+, NO3− and CO2 uptake may affect algal growth and nutrient status by influencing the balance in diel and seasonal C:N:P uptake ratios.
A CIRCADIAN RHYTHM IN THE LONG‐DAY PHOTOPERIODIC INDUCTION OF ERECT AXIS DEVELOPMENT IN THE MARINE RED ALGA NEMALION HELMINTHOIDES1,2
Authors: Cunningham Eamon M. , Guiry Michael D. 
Published: October 2004

ABSTRACTTwo isolates of Nemalion helminthoides from the west coast of Ireland showed a heteromorphic life history in which tetraspores formed under short‐day conditions on uniaxial, prostrate tetrasporophytes gave rise to uniaxial, prostrate growths similar in morphology to the tetrasporophytes. The induction of multiaxial, erect axes on tetraspore‐derived plants was a long‐day photoperiodic response. At 11°C, 16:8 h LD, nitrate concentration in the enriched seawater medium had little effect on the numbers of erect exes formed. Induction of erect axes occurred only in daylengths ≥ 12 h, mainly between 7–13° C, and the critical daylength, which generally lies between 14 and 16 h, changed with temperature. Night‐breaks (NB) of 1 h light in the middle of 16 h night were ineffective in the promotion of erect axis formation, and day‐breaks (DB) of 1 h darkness in the middle of a 16 h day did not inhibit axis formation. Neither continuous light nor NB of 1–1.5 h given at various times during the dark period of an 8:16 h LD cycle promoted the formation of erect axes. At 9° C, equivalent photon exposures (0.69 and 0.34 mol·m−2) at two different instantaneous photon flux densities resulted in erect axis formation only in the 14 h, 16 h and DB regimes. Photoregimes of 16 h light in combination with dark cycles of various lengths resulted in the maximal promotion of the formation of erect axes in diurnal (22–24 h) and bi‐diurnal (44–48 h) cycles, a diminishing response in non‐diurnal cycles greater than 24 and 48 h, and a minimal response at 32 h. These data show that the formation of erect axes is a long‐day photoperiodic response and provide further evidence for a connection between endogenous circadian rhythms and long‐day photoperiodic responses.
NEW GENERA AND SPECIES OF CERAMIACEAE (RHODOPHYTA) FROM THE SOUTHEASTERN UNITED STATES1
Authors: Searles Richard B. , Schneider Craig W. 
Published: October 2004

ABSTRACTFive Ceramiaceae (Rhodophyta) are reported from the offshore waters of the southeastern, warm temperate coast of the United States. These include two new monotypic genera,Calliclavula trifurcateSchneider in the Griffithsieae andNwynea grandisporaSearles in the Sphondylothamnieae, and three new species,Callithamniella silvaeSearles,Ptilothamnion occidentaleSearles, andLejolisia expositaSchneider et Searles.
CYTOCHEMICAL STUDIES ON PROCHLOROPHYTES: LOCALIZATION OF DNA AND RIBULOSE 1,5‐BISPHOSPHATE CARBOXYLASE‐OXYGENASE1
Authors: Swift Hewson , Leser George P. 
Published: October 2004

ABSTRACTWe studied the distribution of the DNA‐containing region and the ribulose 1,5‐bisphosphate carboxylase‐oxygenase (RuBisCo) content of polyhedral bodies in three different prochlorophyte cell types in a search for broad evolutionary affinities of these chlorophyll b‐containing prokaryotes. DNA was localized by DAPI staining and electron microscopy utilizing monoclonal anti‐DNA antibody 2C‐10 plus a secondary antibody labeled with colloidal gold. Antibodies against the large RuBisCo subunit from a higher plant raised in rabbits were used to localize RuBisCo in polyhedral bodies. We studied Prochloron Lewin cells from two different didemnid ascidian hosts (Lissoclinum patella and Didemnum molle) collected in Palau, West Caroline Islands, and cells of Prochlorothrix hollandica Burger‐Wiersma, Stal, and Mur grown in laboratory culture. Cells of the blue‐green alga Anabaena 7120 were studied for comparison. The DNA distribution was markedly different in the two Prochloron cell types. The thylakoids in cells from L. patella were concentrically arranged around a large central vacuole; the DNA‐containing stromal areas appeared in thin sections as a concentric arcs between the thylakoid stacks. The central vacuole was lacking in cells from D. molle, and the thylakoid stacks and strands of DNA‐containing stroma showed a more haphazard arrangement. In the filamentous Prochlorothrix the DNA‐containing stroma was largely limited to a central nucleoid structure running the length of the cell. Although the DNA arrangements in Prochloron might be considered “chloroplast‐like” since DNA‐containing stroma is distributed, as in chloroplasts, in scattered sites among photosynthetic membranes, this is not so in Prochlorothrix, where there is an axial nucleoid, as in many filamentous cyanobacteria. Our anti‐RuBisCo antibodies were selectively bound to the polyhedral bodies of all three cell types, indicating that Prochloron and Prochlorothrix, like many other autotrophic prokaryotes, possess typical carboxysomes.
TEMPERATURE EFFECTS ON SILICON‐ AND PHOSPHORUS‐LIMITED GROWTH AND COMPETITIVE INTERACTIONS AMONG THREE DIATOMS1
Authors: van Donk Ellen , Kilham Susan Soltau 
Published: October 2004

ABSTRACTThree diatom species, Stephanodiscus hantzschii (Ehr.) Grun., Asterionella formosa Hass. and Fragilaria crotonensis Kitt. Hass. were isolated from Lake Maarsseveen where they are dominant and show a successional sequence. The physiological responses of each species to temperature and limitation by silicon and phosphorus were determined over the temperature range of 5° to 20° C using short‐term batch culture methods. Stephanodiscus hantzschii had higher maximum growth rates than the other two species at all temperatures, and the maximum growth rates of all species increased with increasing temperature. Temperature affected not only maximum growth rates but also half‐saturation constants (Ks) and the minimum cell quotas. S. hantzschii had low silicon requirements for growth under Si‐limiting conditions, and A. formosa and F. crotonensis had higher and nearly identical silicon requirements. The Ks values for silicon for S. hantzschii were essentially constant from 5° to 20° C but varied greatly for the other two species. A. formosa had the lowest requirements for growth under phosphorus limitation, F. crotonensis was intermediate and S. hantzschii had the highest growth requirements for phosphorus. The K1 values for phosphorus were constant over the temperature range for both A. formosa and F. crotonensis and were much higher and variable for S. hantzschii.Nutrient competition experiments were performed in continuous cultures at four temperatures and various Si:P ratios. The results generally, but not always, confirmed the predictions based on the Monod relationships for each species. Results not in agreement with predictions were usually because of similar physiological properties of A. formosa and F. crotonensis or because of decreased loss rates for F. crotonensis due to wall growth. In cultures with all three species phosphorus‐limited (Si:P > 75), A. formosa often dominated as predicted, although F. crotonensis was sometimes the most abundant species. As predicted, S. hantzschii never dominated at high Si:P ratios. At intermediate Si:P ratios when A. formosa and F. crotonensis were both Si‐limited and S. hantzschii P‐limited, all three species coexisted because A. formosa and F. crotonensis have almost identical silicon requirements, although sometimes F. crotonensis was more abundant than predicted. At 10°C the results agreed best with the predictions; A. formosa dominated at high Si:P ratios and S. hantzschii dominated as predicted at low Si:P ratios when all three species were Si‐limited.