bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relation between weight matrix and substitution matrix: motif search by similarity
Authors: Zheng Wei-Mou 
Published: October 2004

AbstractMotivation: 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

AbstractSummary: 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

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

Abstract
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

AbstractMotivation: 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/distributedContact: 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

AbstractSummary: 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

Abstract
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

ABSTRACTNitrate‐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

ABSTRACTEpiphyte 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

ABSTRACTThe 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

ABSTRACTIn 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

ABSTRACTEach 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

ABSTRACTWe 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

ABSTRACTExcised 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

ABSTRACTA 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

ABSTRACTCirri 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

ABSTRACTCircadian 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

ABSTRACTSmall 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.