bluuebunny/crossref_metadata_2025 huggingface dataset:
Aspects of isolation underpinning mitotic behaviour in lupin protoplasts
Authors: Sinha Anupam , Caligari Peter D. S.
Published: October 2004

This study reports on the influence of critical isolation factors on the subsequent culture of protoplasts of Lupinus albus L. Protoplasts were isolated from in vitro seedling cotyledons of five early maturing accessions in which protoplast yields and division frequencies appeared to be correlated as a high protoplast yield corresponded with a high division frequency. The overall difference among the accessions for mitosis was non-significant, although the highest yield and division frequency were observed in accession LA132, with Alban giving a significantly lower level. Accession Lucrop produced the lowest number of protoplasts, all of which collapsed during culture. Of the enzyme types used for tissue maceration, Pectolyase Y23, was significantly inferior to Macerase in terms of giving way to mitosis. The extent of division in Macerase-isolated protoplast population was 266% higher than that in the Pectolyase Y23-isolated one. The physiological maturity level of the explant, expressed in terms of developmental age, was optimal when 14–18-day-old seedling cotyledons were used for protoplast production and culture, rather than more mature ones, despite higher protoplast yields in the latter. On K8p medium, the protoplast division frequency was 129% greater when 18-day-old seedling cotyledons were used, than that with any other treatment. This work on protoplast culture of the potentially important lupin species, which is a pulse rich in dietary protein, oil and fibre, allows a further understanding of the biology, with an aim to advance lupin biotechnology.
Effects of soil disturbance, weed control and mulch treatments on establishment of Themeda triandra (Poaceae) in a degraded white box (Eucalyptus albens) woodland in central western New South Wales
Authors: Cole Ian , Lunt Ian D. , Koen Terry
Published: October 2004

Temperate grassy woodlands are endangered ecosystems in Australia, and many degraded remnants are in desperate need of understorey restoration. This experiment compared the effects of soil disturbance, weed control and mulch treatments on establishment of the original dominant grass, Themeda triandra Forssk., in a degraded white box (Eucalyptus albens Benth.) woodland at Cowra in central New South Wales (NSW). Awned Themeda seeds were surface-sown into replicated plots treated as follows: soil scalping, soil disturbance (by ripping), herbicide (simazine) application and retention of natural mulch.
Scalping combined with soil disturbance best promoted Themeda establishment (47.8% after 40 days and 28% after 518 days), and also reduced broadleaf-herb densities. By contrast, scalping without soil disturbance had the worst effect on Themeda establishment (5.2% after 40 days and 4.5% after 518 days). Disturbance significantly enhanced Themeda establishment and decreased the density of annual grasses and the basal cover of non-Themeda species. By contrast, the retention of 500–800 kg of natural surface mulch had no apparent effect on Themeda establishment. Contrary to expectations, simazine reduced the density and basal cover of all species, including Themeda, which is normally resistant to this herbicide. All combinations of the mulched, disturbed and herbicide treatments (i.e. all treatments except scalping) gave similar results, ranging from 10.7 to 22.0 Themeda plants m–2 after 518 days. These results suggest that Themeda stands can be established in degraded box woodlands by using awned seed materials, with minimal seedbed preparation and simple sowing techniques. Further studies are required to determine whether established swards can resist weed invasion in the absence of ongoing weed management, and whether establishment success varies with soil conditions and landscape position.
Computerized microfluidic cell culture using elastomeric channels and Braille displays
Authors: Gu Wei , Zhu Xiaoyue , Futai Nobuyuki , Cho Brenda S. , Takayama Shuichi
Published: October 2004

Computer-controlled microfluidics would advance many types of cellular assays and microscale tissue engineering studies wherever spatiotemporal changes in fluidics need to be defined. However, this goal has been elusive because of the limited availability of integrated, programmable pumps and valves. This paper demonstrates how a refreshable Braille display, with its grid of 320 vertically moving pins, can power integrated pumps and valves through localized deformations of channel networks within elastic silicone rubber. The resulting computerized fluidic control is able to switch among: (
i
) rapid and efficient mixing between streams, (
ii
) multiple laminar flows with minimal mixing between streams, and (
iii
) segmented plug-flow of immiscible fluids within the same channel architecture. The same control method is used to precisely seed cells, compartmentalize them into distinct subpopulations through channel reconfiguration, and culture each cell subpopulation for up to 3 weeks under perfusion. These reliable microscale cell cultures showed gradients of cellular behavior from C2C12 myoblasts along channel lengths, as well as differences in cell density of undifferentiated myoblasts and differentiation patterns, both programmable through different flow rates of serum-containing media. This technology will allow future microscale tissue or cell studies to be more accessible, especially for high-throughput, complex, and long-term experiments. The microfluidic actuation method described is versatile and computer programmable, yet simple, well packaged, and portable enough for personal use.
The stochastic piston problem
Authors: Lin G. , Su C. H. , Karniadakis G. E.
Published: October 2004

We obtain analytical solutions for the perturbed shock paths induced by time-varying random motions of a piston moving inside an adiabatic tube of constant area. The variance of the shock location grows quadratically with time for early times and switches to linear growth for longer times. The analytical results are confirmed by stochastic numerical simulations, and deviations for large random piston motions are established.
Evidence that the cysteine-rich domain of
Drosophila
Frizzled family receptors is dispensable for transducing Wingless
Authors: Chen Chiann-mun , Strapps Walter , Tomlinson Andrew , Struhl Gary
Published: October 2004

Members of the Frizzled family of serpentine transmembrane receptors are required to transduce Wingless/Int (Wnt) signals and contain in their N-terminal regions a conserved Wnt-binding cysteine-rich domain (CRD). Each CRD has specific affinities for particular Wnts, and it is generally believed that signal transduction depends on the strength of this interaction. Here, we report
in vivo
evidence that the CRD is dispensable for Frizzled family receptors to transduce Wingless (Wg), the primary Wnt signal in
Drosophila
. Thus, we infer that signal transduction does not require binding of Wg to the CRD, but instead depends on interactions between Wg and other portions of the receptor, or other proteins of the receptor complex.
Heterogeneity explains features of “anomalous” thermodynamics and statistics
Authors: Gheorghiu Stefan , Coppens Marc-Olivier
Published: October 2004

Phenomena characterized by power-law probability distributions abound in nature and the applied sciences. We show that many of these power laws are well described by the Student, ort, distribution, and we discuss the origin of this universality based on three examples (Brownian motion, Knudsen diffusion in rough pores, and bubbly multiphase flow). These case studies are representative for a large class of systems with heterogeneous features, examples of which can be found from Earth sciences to astrophysics, and even in the social sciences. We show that common forms of polydispersity, such as polydispersity arising naturally as a result of aggregation–fragmentation phenomena, typically lie at the basis of the observed scaling. We conclude that complicated arguments based on long-range correlations or nonergodicity are often incorrect or misleading in explaining many naturally observed power laws and, in particular, those described by the Student distribution.
Industrial Policy in Developing Economies: Developing Dynamic Comparative Advantage in the South African Automobile Sector
Authors: Barnes Justin , Kaplinsky Raphael , Morris Mike
Published: October 2004

Mainstream economics and the Washington Consensus caution against industrial policies that target sectors, firms and regions. At the most they favour cross***sectoral policies which address generalized market failures. This paper analyses the success of an industry-specific policy, South Africa's Motor Industry Development Programme. It documents significant learning processes and shows the impact of the sector's growth on macroeconomic performance. It also addresses the ‘costs' of industrial policy and shows how well-designed scale-enhancing selective policies can provide domestic consumers with global-quality products at global-price levels, without subsidy from the exchequer. The conclusion addresses the relevance of such selective policies to other developing economies, arguing the case for intelligent and appropriately crafted industrial policy.
Accountability in the East Asian Economic Miracle, Crisis and Recovery
Authors: Ritchie John
Published: October 2004

Despite claims that accountability enables ‘good governance’ proper, its specific origins, character and limitations are not yet fully clear. In order to explicate the nature of accountability better this paper will, therefore, formulate and apply its own comparative framework to the case of the East Asian economic miracle, crisis and recovery in particular. In so doing it finds that, even when accountability emerged as a mid-crisis issue that was dramatically reconfigured for any due recovery later, it was not itself then sufficiently explicated for all the implications and consequences to be realized fully. Once it is explicated more fully, however, the further implications and consequences of changing accountability for economic governance question precisely what is to be expected from accountability per se.
Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm
Authors: Kimura Shuhei , Ide Kaori , Kashihara Aiko , Kano Makoto , Hatakeyama Mariko , Masui Ryoji , Nakagawa Noriko , Yokoyama Shigeyuki , Kuramitsu Seiki , Konagaya Akihiko
Published: October 2004

Motivation: To resolve the high-dimensionality of the genetic network inference problem in the S-system model, a problem decomposition strategy has been proposed. While this strategy certainly shows promise, it cannot provide a model readily applicable to the computational simulation of the genetic network when the given time-series data contain measurement noise. This is a significant limitation of the problem decomposition, given that our analysis and understanding of the genetic network depend on the computational simulation.

Results: We propose a new method for inferring S-system models of large-scale genetic networks. The proposed method is based on the problem decomposition strategy and a cooperative coevolutionary algorithm. As the subproblems divided by the problem decomposition strategy are solved simultaneously using the cooperative coevolutionary algorithm, the proposed method can be used to infer any S-system model ready for computational simulation. To verify the effectiveness of the proposed method, we apply it to two artificial genetic network inference problems. Finally, the proposed method is used to analyze the actual DNA microarray data.

Contact:  skimura@gsc.riken.jp

Supplementary information: See Bioinformatics Online.
Superior feature-set ranking for small samples using bolstered error estimation
Authors: Sima Chao , Braga-Neto Ulisses , Dougherty Edward R.
Published: October 2004

Motivation: Ranking feature sets is a key issue for classification, for instance, phenotype classification based on gene expression. Since ranking is often based on error estimation, and error estimators suffer to differing degrees of imprecision in small-sample settings, it is important to choose a computationally feasible error estimator that yields good feature-set ranking.

Results: This paper examines the feature-ranking performance of several kinds of error estimators: resubstitution, cross-validation, bootstrap and bolstered error estimation. It does so for three classification rules: linear discriminant analysis, three-nearest-neighbor classification and classification trees. Two measures of performance are considered. One counts the number of the truly best feature sets appearing among the best feature sets discovered by the error estimator and the other computes the mean absolute error between the top ranks of the truly best feature sets and their ranks as given by the error estimator. Our results indicate that bolstering is superior to bootstrap, and bootstrap is better than cross-validation, for discovering top-performing feature sets for classification when using small samples. A key issue is that bolstered error estimation is tens of times faster than bootstrap, and faster than cross-validation, and is therefore feasible for feature-set ranking when the number of feature sets is extremely large.

Availability: We provide a companion website, which contains the complete set of tables and plots regarding the simulation study, and a compilation of references on feature-set ranking with applications in Genomics. The companion website can be accessed at the URL http://ee.tamu.edu/~edward/bolster_ranking

Contact:  edward@ee.tamu.edu
Relation between weight matrix and substitution matrix: motif search by similarity
Authors: Zheng Wei-Mou
Published: October 2004

Motivation: The discovery of patterns shared by several sequences that differ greatly is a basic task in sequence analysis, and still a challenge. Several methods have been developed for detecting patterns. Methods commonly used for motif search include the Gibbs sampler, Expectation-Maximization (EM) algorithm and some intuitive greedy approaches. One cannot guarantee the optimality of the result produced by the Gibbs sampler in a single run. The deterministic EM methods tend to get trapped by local optima. Solutions found by greedy approaches are rarely sufficiently good.

Results: A simple model describing a motif or a portion of local multiple sequence alignment is the weight matrix model, in which a motif is characterized with position-specific probabilities. Two substitution matrices are proposed to relate the sequence similarity with the weight matrix. Combining the substitution matrix and weight matrix, we examine three typical sets of protein sequences with increasing complexity. At a low score threshold for pair similarity, sliding windows are compared with a seed window to find the score sum, which provides a measure of statistical significance for multiple sequence comparison. Such a similarity analysis reveals many aspects of motifs. Blocks determined by similarity can be used to deduce a primary weight matrix or an improved substitution matrix. The algorithm successfully obtains the optimal solution for the test sets by just greedy iteration.

Availability: Softwares and sequence datasets are available on request from the author.

Contact:  zheng@itp.ac.cn
BACCardI—a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison
Authors: Bartels Daniela , Kespohl Sebastian , Albaum Stefan , Drüke Tanja , Goesmann Alexander , Herold Julia , Kaiser Olaf , Pühler Alfred , Pfeiffer Friedhelm , Raddatz Günter , Stoye Jens , Meyer Folker , Schuster Stephan C.
Published: October 2004

Summary: We provide the graphical tool BACCardI for the construction of virtual clone maps from standard assembler output files or BLAST based sequence comparisons. This new tool has been applied to numerous genome projects to solve various problems including (a) validation of whole genome shotgun assemblies, (b) support for contig ordering in the finishing phase of a genome project, and (c) intergenome comparison between related strains when only one of the strains has been sequenced and a large insert library is available for the other. The BACCardI software can seamlessly interact with various sequence assembly packages.

Motivation: Genomic assemblies generated from sequence information need to be validated by independent methods such as physical maps. The time-consuming task of building physical maps can be circumvented by virtual clone maps derived from read pair information of large insert libraries.

Availability: The BACCardI tool is freely available at http://www.cebitec.uni-bielefeld.de/groups/brf/software/baccardi/

Contact:  fm@Cebitec.Uni-Bielefeld.DE
Clustering of gene expression data using a local shape-based similarity measure
Authors: Balasubramaniyan Rajarajeswari , Hüllermeier Eyke , Weskamp Nils , Kämper Jörg
Published: October 2004

Motivation: Microarray technology enables the study of gene expression in large scale. The application of methods for data analysis then allows for grouping genes that show a similar expression profile and that are thus likely to be co-regulated. A relationship among genes at the biological level often presents itself by locally similar and potentially time-shifted patterns in their expression profiles.

Results: Here, we propose a new method (CLARITY; Clustering with Local shApe-based similaRITY) for the analysis of microarray time course experiments that uses a local shape-based similarity measure based on Spearman rank correlation. This measure does not require a normalization of the expression data and is comparably robust towards noise. It is also able to detect similar and even time-shifted sub-profiles. To this end, we implemented an approach motivated by the BLAST algorithm for sequence alignment.

We used CLARITY to cluster the times series of gene expression data during the mitotic cell cycle of the yeast Saccharomyces cerevisiae. The obtained clusters were related to the MIPS functional classification to assess their biological significance. We found that several clusters were significantly enriched with genes that share similar or related functions.

Contact:  kaemper@staff.uni-marburg.de; eyke@mathematik.uni-marburg.de

Availability: Upon request from the authors.
COBrA: a bio-ontology editor
Authors: Aitken Stuart , Korf Roman , Webber Bonnie , Bard Jonathan
Published: October 2004

COBrA is a Java-based ontology editor for bio-ontologies that distinguishes itself from other editors by supporting the linking of concepts between two ontologies, and providing sophisticated analysis and verification functions. In addition to the Gene Ontology and Open Biology Ontologies formats, COBrA can import and export ontologies in the Semantic Web formats RDF, RDFS and OWL.

Availability:  http://www.xspan.org

Contact:  stuart@aiai.ed.ac.uk
DPRml: distributed phylogeny reconstruction by maximum likelihood
Authors: Keane T. M. , Naughton T. J. , Travers S. A. A. , McInerney J. O. , McCormack G. P.
Published: October 2004

Motivation: In recent years there has been increased interest in producing large and accurate phylogenetic trees using statistical approaches. However for a large number of taxa, it is not feasible to construct large and accurate trees using only a single processor. A number of specialized parallel programs have been produced in an attempt to address the huge computational requirements of maximum likelihood. We express a number of concerns about the current set of parallel phylogenetic programs which are currently severely limiting the widespread availability and use of parallel computing in maximum likelihood-based phylogenetic analysis.

Results: We have identified the suitability of phylogenetic analysis to large-scale heterogeneous distributed computing. We have completed a distributed and fully cross-platform phylogenetic tree building program called distributed phylogeny reconstruction by maximum likelihood. It uses an already proven maximum likelihood-based tree building algorithm and a popular phylogenetic analysis library for all its likelihood calculations. It offers one of the most extensive sets of DNA substitution models currently available. We are the first, to our knowledge, to report the completion of a distributed phylogenetic tree building program that can achieve near-linear speedup while only using the idle clock cycles of machines. For those in an academic or corporate environment with hundreds of idle desktop machines, we have shown how distributed computing can deliver a ‘free’ ML supercomputer.

Availability: The software (and user manual) is publicly available under the terms of the GNU general public licence from the system webpage at http://www.cs.may.ie/distributed

Contact:  tom.naughton@may.ie
hp-DPI:Helicobacter pyloriDatabase of Protein Interactomes—embracing experimental and inferred interactions
Authors: Lin Chung-Yen , Chen Chia-Ling , Cho Chi-Shiang , Wang Li-Ming , Chang Chia-Ming , Chen Pao-Yang , Lo Chen-Zen , Hsiung Chao A.
Published: October 2004

Summary: We implemented a statistical model into our protein interaction database for validation of two-hybrid assays of Helicobacter pylori, and prediction of putative protein interactions not yet discovered experimentally. To present the enormous amount of experimental and inferred protein interaction networking maps, the H.pylori Database of Protein Interactomes (hp-DPI) is developed with a succinct yet comprehensive visualization tool integrated with annotation from Genbank, GO, and KEGG. hp-DPI is first built with, but not limited to, H.pylori protein interactions and is expected to naturally include other organisms’ protein interacting relationships in the future.

Availability:  hp-DPI can be accessed at http://www.dpi.nhri.org.tw/hp/

Contact:  cylin@nhri.org.tw
GOChase: correcting errors from Gene Ontology-based annotations for gene products
Authors: Park Yu Rang , Park Chan Hee , Kim Ju Han
Published: October 2004

Summary: The Gene Ontology (GO) is a controlled biological vocabulary that provides three structured networks of terms to describe biological processes, cellular components and molecular functions. Many databases of gene products are annotated using the GO vocabularies. We found that some GO-updating operations are not easily traceable by the current biological databases and GO browsers. Consequently, numerous annotation errors arise and are propagated throughout biological databases and GO-based high-level analyses. GOChase is a set of web-based utilities to detect and correct the errors in GO-based annotations.

Availability:  http://www.snubi.org/software/GOChase/

Contact:  juhan@snu.ac.kr
NITROGEN METABOLISM AND AMINO ACID NUTRITION IN THE SOIL ALGA STICHOCOCCUS BACILLARIS (CHLOROPHYCEAE)1
Authors: Hellebust Johan A. , Ahmad Iftikhar
Published: October 2004

Nitrate‐grown cells of Stichococcus bacillaris Naeg. (UTEX 314) contained much higher activities of glutamine synthetase (GS) and NADPH‐glutamate dehydrogenase (GDH) than ammonium‐grown cells. Methylamine, a non‐metabolizable ammonium analog, caused a decrease in GS activity in nitrate‐grown cells suggesting that GS is regulated by the size of the endogenous ammonium pool. The decrease in GS observed in methylammonium‐loaded nitrate‐grown cells was accompanied by an increase in NADPH‐GDH activity. Stichococcus bacillaris can be grown in the presence of methionine sulfoximine (MSX), a potent inhibitor of GS. However, only a fraction of a control cell population showed a requirement for glutamine or arginine for growth following MSX addition. Fully adapted MSX‐grown cells were indistinguishable from control cells in their ability to photosynthesize and utilize amino acids as nitrogen sources. Alanine, arginine, asparagine, glutamine, glycine and proline were good nitrogen sources, and maximum capacity for amino acid transport was developed in cells grown on these amino acids. Compared to nitrate‐grown cells the activity of GS in ammo acid‐grown cells was low, whereas NADPH‐GDH was very active. The activity of NADH‐GDH in amino acid‐grown cells was highest under heterotrophic conditions.
MICROBIAL COLONIZATION ON NATURAL AND ARTIFICIAL MACROPHYTES IN A PHOSPHORUS‐LIMITED, HARDWATER LAKE1
Authors: Burkholder JoAtnn M. , Wetzel Robert G.
Published: October 2004

Epiphyte communities in a phosphorus‐limited hard‐water lake were compared over a 14‐week period from Potamogeton illinoensis and structurally similar artificial plants of different leaf ages. Artificial plants were serially incubated in the lake to simulate the age of natural leaves. The physiognomy of loosely attached epiphytes appeared similar on the two substrata. Algal cell number and biovolume were 15‐fold and 17‐fold higher, respectively, on artificial leaves early in the growing season, but total algal density gradually became similar on natural and artificial plants. In contrast, the taxonomic composition of loosely attached algae became increasingly distinct, and mean cell biovolume on natural leaves was twice that on artificial leaves. Adnate epiphytes on both substrata developed from sparse populations of bacteria on new leaves to a community of diatoms, blue‐green algae and numerous bacteria on mature and senescent leaves. Adnate community succession on natural leaves in late senescence/death differed from that on artificial leaves colonized for comparable periods in having (1) a marked increase in filamentous blue‐green algae, (2) a subsequent decrease in all algae, and (3) a final fungi‐dominated stage. The trends in colonization indicate that macrophytes in this oligotrophic lake provided a distinct habitat from that of artificial substrata for epiphytes throughout the growing season.
THE ROLE OF UNICELLS IN THE POLYMORPHIC SCENEDESMUS ARMATUS (CHLOROPHYCEAE)1
Authors: Egan Patrick F. , Trainor Francis R.
Published: October 2004

The UTEX 2193 strain of Scenedesmus armatus (Chod.) Chod, when cultured in any of several media (whether natural or artificial, concentrated or dilute) produced a variety of colonial morphologies as well as a unicell population. Morphological expression was related to culture ape. When the initial cell density was just a feu1 hundred cells per mL. the culture first produced a unicell population, then spiny colonies, and as stationary phase was approached, spine‐less colonies.

Two classes of spiny colonies were detected. Type I colonies had elongate cells with the terminal cells shorter than median cells. Spines were longer than cell length. The wider, oval, grainy cells of Type II colonies were uniform m length. Spines were shorter and thicker than those on Type I colonies. Only Type I colonies produced unicells: the latter appeared as two morphs. The smaller unicell was obovoid with four delicate spines: the larger had ovate cells bearing four thicker spines.

Control of unicell development in all media was achieved by carefully monitoring colony type and cell number used for the inoculum. A unicellular population developed in batch culture in defined media, both concentrated and dilute, when the initial cell density (either Type I or Type II colonies) was low (below 1000 cells‐mL−1), as well as in synchronous cultures. With higher initial cell densities, e.g. 2 × 104 cells·mL−1, the inoculum had to contain Type I colonies to produce unicells. Unicells were also produced in water from Agronomy Pond, where the strain originated. We discuss the role of unicell populations in the distribution of Scenedesmus.
PHOTOADAPTATION AND THE “PACKAGE” EFFECT INDUNALIELLA TERTIOLECTA(CHLOROPHYCEAE)1
Authors: Berner Tamar , Dubinsky Zvy , Wyman Kevin , Falkowski Paul G.
Published: October 2004

In the marine unicellular chlorophyte,Dunaliella tertiolectaButcher, the spectrally averaged m vivo absorption cross section, normalized to chlorophyll a (so‐called a* values), vary two‐fold in response to changes in growth irradiance. We used a kinetic approach to examine the specific factors which account for these changes in optical properties as cells photoadapt. Using Triton X‐100 to solubilize membranes, we were able to differentiate between “package” effects and pigmentation effects. Our analyses suggest that 43–49% of the variability in a* is due to changes in pigmentation, whereas 51–57% is due to the “package” effect. Further analyses revealed that changes in cell sue did not significantly affect packaging, while thylakoid stacking and the transparency of thylakoid membranes were important factors. Our results suggest that thylakoid membrane protein/lipid ratios change during photoadaptation, and these changes influence the effective rate of light harvesting per unit chlorophylla.
MORPHOGENESIS OF THE LABIATE PROCESS IN THE ARAPHID PENNATE DIATOM DIATOM A VULGARE1
Authors: Pickett‐Heaps Jeremy
Published: October 2004

Each valve of the araphid pennate diatom Diatoma has a labiate process (LP) at one end; in a frustule, the LPs are at diagonally opposite ends. After mitosis is over, an elongated dense body detaches from the spindle pole and migrates to one end of the daughter cell, always diagonally opposite the LP of the parental valve. This dense body trails a cone‐shaped array of microtubules (MTs). Meanwhile, the new valve has begun to form within the Silica Deposition Vesicle (SDV). Having reached the end of the cell, this dense body moves back slightly and then settles onto the SDV, developing a layered substructure as it does so. Immediately beneath it, the LP of the new daughter valve differentiates. This dense object is clearly the homologue of the fibrous Labiate Process Apparatus (LPA) involved in the differentiation of the LP in several centric diatoms. In a few cases, these LPAs also hair been shown to originate from some component of the spindle pole. Thus, the homologue of the LPA of centric diatoms has now been found in an araphid pennate diatom; in each case, the LPA apparently comes from the pole of the spindle and presumably uses a cytoskeleton of MTs to locate the LP in its correct position. These observations support the possibility that the raphe evolved from the LP.
VARIATION IN BENTHIC DIATOM (BACILLARIOPHYCEAE) IMMIGRATION WITH HABITAT CHARACTERISTICS AND CELL MORPHOLOGY1
Authors: Stevenson R. Jan , Peterson Christopher G.
Published: October 2004

We studied the hypothesis that diatom immigration abilities are related to their fitness for colonizing stream substrates. Diatom abundances on artificial substrates exposed for 24 h (the measure of immigration rate) and abundances of stream plankton were determined in six habitats. Diatom immigration varied among habitats from 50–2500 cells·cm−2·d−1. Immigration rates decreased 10‐fold with increases in current from 10 to 30 cm·s−1 but changed little during a 40‐d summer period. Immigration abilities of diatom taxa were characterized as ratios of either their abundances or relative abundances in immigration assemblages versus in the plankton. Immigration abilities varied over 100‐fold among different species. Immigration of some species could be characterized as slower than others in different streams; however, variation in immigration abilities of other species among streams indicated that environment also affected immigration. Diurnal variation in abundance and species composition of the immigration pool (stream plankton) can be important in assessing immigration abilities. Immigration ability may affect benthic diatom fitness. Monoraphid diatoms had a lower probability of immigrating from the plankton than araphid diatoms.
TEMPERATURE, PHOTOPERIOD AND LIGHT INTERACTIONS ON GROWTH AND FERTILITY OF GLOSSOPHORA KUNTHII (PHAEOPHYTA, DICTYOTALES) FROM CENTRAL CHILE1
Authors: Hoffmann Alicia J. , Malbrán M. Elena
Published: October 2004

Excised ligulae of Glossophora kunthii from central Chile were cultured of temperatures of 5–25° C, photoperiods of 16:8 and 8:16 h LD cycles, with photon irradiances of 10 and 50 μmol · m−2· s−1. Growth of the ligulae, number of fertile ligulae and number of tetrasporangia forming on the ligulae were assessed. Ligulae tolerated temperatures between 10 and 23°C. Temperature interacted with daylength and photon dose, determining quantitative responses in the growth and fertility of ligulae. Growth was least at 8:16 h LD and was not affected significantly by temperature. It was greatest at 16:8 h LD, 50 μmol · m−2· s−1 and increased with temperature up to 20°C. Percentage of fertile ligulae and number of tetrasporangia increased with temperature at the 8:16 h LD cycle, reaching a maximum at 20°C. Fertility was low at 16:8 h LD, except at 20° C (and low photon dose) suggesting that reproduction at 20° C is independent of daylength in this species. Ligulae grew larger at the long‐day photoperiods and the proportions of fertile ligulae were higher at the short‐day photoperiods, irrespective of the total photon dose received. These results suggest that some aspects of growth and fertility are controlled by photoperiod.
EXAMINATION OF TWO DIMENSIONAL SPATIAL PATTERN OF PERIPHYTIC DIATOMS USING AN ADHESIVE SURFICIAL PEEL TECHNIQUE1
Authors: Goldsborough L. Gordon
Published: October 2004

A simple surficial peel technique using adhesive tape was developed for quantitative removal of haptobenthic diatom communities from topographically simple substrata. The method combines high removal efficiency with low peel distortion, permitting the use of spatial statistics to test whether populations are distributed in the peel randomly or form aggregated or uniform patterns. Using this technique, the microdistribution of Cocconeis placentula Ehr. on a smooth acrylic rod was examined. Using conventional nearest neighbor analyses, a clonal population of C. placentula. characterized by an indentation of the value margin, was significantly aggregated, whereas the overall C. placentula population was uniform or aggregated depending on whether the method of analysis allowed for cell size. Using refined nearest neighbor analysis, the indented population was aggregated, and the overall population was random at distances greater than cell size. The results suggest that the indented clone was weakly motile following cell division and that its directional bearing was random.
ZYGOTE APPENDAGES (CIRRI), A NEW STRUCTURAL FEATURE IN THE SPHAEROPLEACEAE(CHLOROPHYCEAE)1
Authors: Hoffman Larry R. , Buchheim Mark A.
Published: October 2004

Cirri are curled appendages borne on the surface of mature zygotes in some members of the green algal family Sphaeropleaceae. Structures equivalent to cirri have not been reported previously in any green algae. We found cirri in four taxa: Sphaeroplea fragilis Buchheim et Hoffman, Atractomorpha porcata Hoffman, and two new undescribed species of Atractomorpha from Africa. Zygotes of seven other sphaeropleacean taxa were examined, but they did not produce cirri. Cirri may be either simple or compound. Simple cirri are less than 0.5 μm in diameter and show no evidence of longitudinal striations or subunits. Compound cirri are more massive (commonly 2.0–3.5 μm, and up to 4 μm diameter in S. fragilis) and possess longitudinal striations suggesting that each is formed of longitudinally arranged subunits ca. 0.5 μm in diameter. Simple and compound cirri are formed by zygotes of all four taxa that produce cirri. Both types may occur on the same zygote. Nonetheless, the patterns of variation in length, shape, and distribution of the two types of cirri are sufficiently distinct to characterize each taxon. Energy dispersive X‐ray microanalysis (EDX) shows that cirri lack appreciable mineralization and are thus primarily organic in nature. The potential value of cirri as a taxonomic character in the Sphaeropleaceae is discussed.
A CIRCADIAN RHYTHM IN CELL DIVISION IN A PROKARYOTE, THE CYANOBACTERIUM SYNECHOCOCCUS WH78031
Authors: Sweeney Beatrice M. , Borgese M. Beatriz
Published: October 2004

Circadian rhythms are common in eukaryotes, but the several claimed cases in prokaryotes are all open to alternative interpretation. We report here a clearcut circadian rhythm in cell division in a marine Synechococcus sp. strain WH7803, under conditions where the generation time is longer than one day, that is entrained by a light–dark cycle, and that persists for at least four cycles in continuous light (2 μE·m−2·s−1) and constant temperature (22, 20 or 16°C) with a maximum in dividing cells at about 24 h intervals. Thus, the prokaryote, Synechococcus, satisfies the criteria for the possession of a true temperature‐compensated circadian clock. Were the existence of such a rhythm confirmed, current hypotheses that intracellular compartments are required for circadian timing may require modification.
MACROALGAE SURVIVE DIGESTION BY FISHES1
Authors: Paya Ignacio , Santelices Bernabe
Published: October 2004

Small individuals (<15 cm long) of the clingfish Sicyases sanguineus consume as many as 18 seaweed species in Central Chile. Enteromorpha sp. was the only species able to survive digestion by fish recently collected from the field. Enteromorpha compressa and Gelidium chilense also survived by tissue regeneration when offered as food in the laboratory, but only E. compressa showed stimulation of swarmer production. In general, our results on a vertebrate species reproduce previous findings on diverse invertebrate species. Since fish are highly motile, their capacity to disperse algal species by defecation might be of great ecological importance.
OCCURRENCE AND ABUNDANCE OF GREEN‐FLUORESCING DINOFLAGELLATES IN SURFACE WATERS OF THE NORTHWEST ATLANTIC AND NORTHEAST PACIFIC OCEANS1
Authors: Shapiro Lynda P. , Haugen Elin M. , Carpenter Edward J.
Published: October 2004

We have cultured green fluorescing heterotrophic dinoflagellates whose continuous green fluorescence is due to an unidentified compound, probably a flavin, that excites with blue (∼460 nm) light and emits green (∼535 nm) light. No evidence of bioluminescence was found, but we note that compounds with similar fluorescence characteristics have been associated with bioluminescence in other taxa. These cells, all naked gymnodinoids, are widespread and abundant in the Northwest Atlantic and Northeast Pacific Oceans (103–105 L−1). They comprise 4–100% of the total heterotrophic dinoflagellate component which, in turn, is usually equivalent magnitude to the phototrophic naked dinoflagellate component of the phytoplankton community.
STRIP‐LIKE COVERING REVEALED ON “WALL‐LESS”ASTEROMONAS (CHLOROPHYCEAE)1
Authors: Chappell Dorothy F. , Hoops Harold J. , Floyd Gary L.
Published: October 2004

Asteromonas Artari previously described as a wall‐less biflagellated unicell exhibits a strip‐like cell covering on some cells. Both tannic acid fixation and freeze‐etch reveal the covering of electron opaque strips outside the plasmalemma. Cross striations are apparent in the surface strips. Golgi vesicles contain material presumed to be precursor components of the covering strips. The crystalline pattern of the freeze‐etched material is similar to that reported for other, walled volvocalean algae.
GENITIC VARIABILITY IN TOXIN POTENCIES AMONG SEVENTEEN CLONES OF GAMBIERDISCUS TOXICUS (DINOPHYCEAE)1
Authors: Bomber Jeffrey W. , Tindall Donald R. , Miller Donald M.
Published: October 2004

Seventeen clones of the ciguatera‐causing dinoflagellate Gambierdiscus toxicus Adachi and Fukuyo were acclimated to the same environments over several months. Significant variance components were detected between non‐acclimated and acclimated cultures for cell potencies, yields and reproduction rates. The resultant variance in acclimated potencies among clones was statistically significant (P < 0.0001), indicating that potency can be used for genetic comparisons. However, cell potency differences for a clone of G. toxicus in the acclimated vs. non‐acclimated phases can exceed genetic differences between clones. This stresses the need for a rigorous acclimation process. Caribbean isolates of G. toxicus were inherently more toxic than isolates from other areas. One Caribbean clone yielded 55 × 10−4 mu (mouse units)·cell−1 whereas clones Bermuda, the Bahamas, and Florida ranged from only 1.8 × 10−4 mu·cell−1 to a maximum of 19.8 × 10−4 mu·cell−1. Toxicity decreased with increasing latitude (r =–0.819, P < 0.01), indicating that environmental differences probably influenced the potencies. A comparison of acclimated reproduction rates at four light intensities also indicated that genetic differences among clones existed. The resulting reproduction rate/light slopes overlapped, indicating that the clones may be adapted to specific light regimes.
AN EXPANDED SURVEY OF THE ULTRASTRUCTURE OF RED ALGAL PIT PLUGS1
Authors: Pueschel Curt M.
Published: October 2004

The fine structure of pit plugs in 90 species of red algae was examined, bringing the total number of species in the continuing survey to 153. The organization of plug caps was confirmed to be a stable, predictable trait within thalli, between generations in heteromorphic life histories, and within the presently recognized orders, with one exception—the Acrochaetiales. Two forms of the outer cap were found in this group, a thin plate, as in the Nemaliales and Palmariales, and a dome, as in Batrachospermales and Corallinales. Variation of pit plug structure indicates that the Acrochaetiales are a heterogeneous assemblage and that pit plugs will be useful in reappraising their systematics. The systematic affinities of several species of uncertain affinities are clarified.Schmitziella endophloeaBornet et Batters is excluded from both orders, Corallinales and Acrochaetiales, with which it previously was allied. Although other ordinal attributions are not precluded by pit plug structure alone, pit plug structure is consistent with placement ofApophlaea sinclairiiHarvey andHildenbrandia rivularis(Liebman) J. Agardh in the Hildenbrandiales,Plagiospora gracilisKuckuck,Schmitziella endophloea,andWurdemannia miniata(Duby) J. Feldmann et Hamel in the Gigartinales, andPseudorhododiscus nipponicusMasuda in the Palmariales.
EFFECTS OF NUTRIENT ENRICHMENT ON NATURAL POPULATIONS OF THE BROWN TIDE PHYTOPLANKTON AUREOCOCCUS ANOPHAGEFFERENS (CHRYSOPHYCEAE)1
Authors: Keller Aimee A. , Rice Robin L.
Published: October 2004

The brown tide picoalga Aureococcus anophagefferens Hargraves et Sieburth was present in approximately equal numbers in 12 large scale (13,000 L) mesocosms at the start of a nutrient addition experiment in June 1985. Increases in abundance in untreated systems mimicked the pattern of bloom development in Narragansett Bay, Rhode Island, the seawater source for the experiment. Aureococcus increased to maximal values of 2.6 × 109 cells. L−1 and persisted at high numbers (108 cells·L−1) for 7–8 weeks. In nutrient addition tanks, the picoalgae bloomed briefly (1–3 weeks) but rapidly declined to the usual level (∼107 cells·L−1) for eukaryotic algae in Narragansett Bay. The decline in picoalgae abundance was followed by an increase in total diatoms in all nutrient treated tanks. Mean picoalgae abundance in the mesocosms and the bay was significantly (P < 0.05) and inversely correlated (r =–0.93) with mean concentration of dissolved inorganic nitrogen. The persistence of the brown tide species in control mesocosms and Narragansett Bay appears related to its ability to grow at very low concentrations of dissolved inorganic nitrogen, levels previously shown to limit diatom growth.
LIPOPHILIC PIGMENTS FROM CYANOBACTERIAL (BLUE‐GREEN ALGAL) AND DIATOM MATS IN HAMELIN POOL, SHARK BAY, WESTERN AUSTRALIA1
Authors: Palmisano Anna C. , Summons Roger E. , Cronin Sonja E. , Des Marais David J.
Published: October 2004

Lipophilic pigments were examined in microbial mat communities dominated by cyanobacteria in the intertidal zone and by diatoms in the subtidal and sublittoral zones of Hamelin Pool, Shark Bay, Western Australia. These microbial mats have evolutionary significance because of their similarity to lithified stromatolites from the Proterozoic and Early Paleozoic eras. Fucoxanthin, diatoxanthin, diadinoxanthin, β‐carotene, and chlorophylls a and c characterized the diatom mats, whereas cyanobacterial mats contained myxoxanthophyll zeaxanthin, echinenone, β‐carotene, chlorophyll a and, in some cases, sheath pigment. The presence of bacteriochlorophyll a with in the mats suggest a close association of photosynthetic bacteria with diatoms and cyanobacteria. The high carotenoids: chlorophyll a ratios (0.84–2.44 wt/wt) in the diatom mats suggest that carotenoids served a photoprotective function in this high light environment. By contrast, cyanobacterial sheath pigment may have largely supplanted the photoprotective role of carotenoids in the intertidal mats.
ELECTRON MICROSCOPY OF A CONTRACTILE‐VACUOLE MUTANT OF CHLAMYDOMONAS MOEWUSII (CHLOROPHYTA) DEFECTIVE IN THE LATE STAGES OF DIASTOLE1
Authors: Denning Gerene M. , Fulton Alice B.
Published: October 2004

Electron microscopy of a “vacuole‐less” mutant of Chlamydomonas moewusii Gerloff revealed the presence of small anterior vacuoles. These vacuoles behaved like contractile vacuoles in wild‐type cells, but they were apparently unable to complete diastole and discharge their contents. When wild‐type and mutant cells were incubated in hypertonic medium, small coated vacuoles persisted in the region where contractile vacuoles form. When these cells were transferred to hypotonic medium, the vacuoles appeared to fill and fuse to form larger vacuoles Shortly after the appearance of full expanded contractile vacuoles, collapsed vacuoles were observed in wild‐type cells suggesting the completion of diastole and the onset of systole. In mutant cells, the initial steps of filling and fusion to form larger vacuoles apparent interactions of vacuoles with the plasma membrane were not observed. New contractile vacuoles accumulated around the nucleus. When fusion of the contractile vacuole with the plasma membrane was blocked by EGTA, a similar accumulation of large vacuoles occurred. Our observations suggest that the contractile‐vacuole mutant of C. Moewusii produces vacuoles which can accumulate excess water as part of the mechanism of osmoregulation but which cannot complete diastole.
SALINITY AND NUTRIENT LIMITATIONS ON GROWTH OF BENTHIC ALGAE FROM TWO ALKALINE SALT LAKES OF THE WESTERN GREAT BASIN (USA)1
Authors: Herbst David B. , Bradley Timothy J.
Published: October 2004

Enrichment cultures of littoral benthic algae from Mono Lake, California, and Abert Lake, Oregon, were grown under conditions of varied salinity and nutrient content. Field‐collected inocula were composed mainly of diatoms and filamentous blue‐green and green algae. The yield of long‐term cultures (30 days) showed tolerance over a broad salinity range (50–150 g·L−1) for Mono Lake‐derived algae. Algae from Abert Lake had a lower range of tolerance (25–100 g·L−1) Organic content and pigment concentrations of algae from both lakes were also reduced above the tolerated salinity level. Within the range of salinity tolerance for Mono Lake algae, initial growth rates and organic content were reduced by increased salinity. The effects of macro‐ and micronutrient enrichment on algal growth in Mono Lake water were also tested. Only nitrogen enrichment (either as ammonium or nitrate) stimulated algal growth. Although the benthic algae cultured here had wide optima for salinity tolerance, the rates of growth and storage were limited by increased salinity within the optimum range. Although the lakes compared had similar species composition, the range and limits of tolerance of the algae were related to salinity of the lake of origin.