GlycoBase and autoGU: tools for HPLC-based glycan analysis

Summary: The development of robust high-performance liquid chromatography(HPLC) technologies continues to improve the detailed analysisand sequencing of glycan structures released from glycoproteins.Here, we present a database (GlycoBase) and analytical tool(autoGU) to assist the interpretation and assignment of HPLC-glycanprofiles. GlycoBase is a relational database which containsthe HPLC elution positions for over 350 2-AB labelled N-glycanstructures together with predicted products of exoglycosidasedigestions. AutoGU assigns provisional structures to each integratedHPLC peak and, when used in combination with exoglycosidasedigestions, progressively assigns each structure automaticallybased on the footprint data. These tools are potentially verypromising and facilitate basic research as well as the quantitativehigh-throughput analysis of low concentrations of glycans releasedfrom glycoproteins. Availability: http://glycobase.ucd.ie Contact: matthew.campbell{at}nibrt.ie Associate Editor: Limsoon Wong Present address: Dublin-Oxford Glycobiology Laboratory, NationalInstitute for Bioprocessing Research and Training, Conway Institute,University College Dublin, Dublin, Ireland. Present address: Ludger Ltd, Culham Science Centre, Abingdon,Oxfordshire OX14 3EB., UK.     

BicOverlapper: a tool for bicluster visualization

Summary: BicOverlapper is a tool to visualize biclusters fromgene-expression matrices in a way that helps to compare biclusteringmethods, to unravel trends and to highlight relevant genes andconditions. A visual approach can complement biological andstatistical analysis and reduce the time spent by specialistsinterpreting the results of biclustering algorithms. The techniqueis based on a force-directed graph where biclusters are representedas flexible overlapped groups of genes and conditions. Availability: The BicOverlapper software and supplementary materialare available at http://vis.usal.es/bicoverlapper Contact: rodri{at}usal.es Associate Editor: John Quackenbush The first two authors should be reported as joint first authors.     

LibSBML: an API library for SBML

Summary: LibSBML is an application programming interface libraryfor reading, writing, manipulating and validating content expressedin the Systems Biology Markup Language (SBML) format. It iswritten in ISO C and C++, provides language bindings for CommonLisp, Java, Python, Perl, MATLAB and Octave, and includes manyfeatures that facilitate adoption and use of both SBML and thelibrary. Developers can embed libSBML in their applications,saving themselves the work of implementing their own SBML parsing,manipulation and validation software. Availability: LibSBML 3 was released in August 2007. Sourcecode, binaries and documentation are freely available underLGPL open-source terms from http://sbml.org/software/libsbml. Contact: sbml-team{at}caltech.edu Associate Editor: Olga Troyanskaya The first two authors should be regarded as First Author.     

Regulation of sexual agglutinability in Saccharomyces cerevisiae of {alpha} and {alpha} types by sex-specific factors produced by their respective opposite mating types

The sexual agglutinability of haploid cells of heterothallicSaccharomyces cerevisiae was repressed when they were culturedin the absence of easily fermentable sugars, such as glucoseand mannose. The repression was reversed by the action of hormone-likesubstances of the opposite mating types. The substance producedby mating type cells was identical to subtsance-I which isknown to induce sexual agglutinability of inducible matingtype cells. The mating type cells produce a new hormone-likesubstance which induces or enhances sexual agglutinability of mating type cells. A crude fraction of the mating type-specific substance ( substance-I)was obtained by passing the culture filtrate of mating typecells through Amberlite CG-50 (H⁺ form), followed by elutionwith 1.5 M ammonia. ² On leave from Osaka City University. (Received December 25, 1975; )     

A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments

Motivation: The proliferation of public data repositories createsa need for meta-analysis methods to efficiently evaluate, integrateand validate related datasets produced by independent groups.A t-based approach has been proposed to integrate effect sizefrom multiple studies by modeling both intra- and between-studyvariation. Recently, a non-parametric ‘rank product’method, which is derived based on biological reasoning of fold-changecriteria, has been applied to directly combine multiple datasetsinto one meta study. Fisher's Inverse ² method, which only dependson P-values from individual analyses of each dataset, has beenused in a couple of medical studies. While these methods addressthe question from different angles, it is not clear how theycompare with each other. Results: We comparatively evaluate the three methods; t-basedhierarchical modeling, rank products and Fisher's Inverse ²test with P-values from either the t-based or the rank productmethod. A simulation study shows that the rank product method,in general, has higher sensitivity and selectivity than thet-based method in both individual and meta-analysis, especiallyin the setting of small sample size and/or large between-studyvariation. Not surprisingly, Fisher's ² method highly dependson the method used in the individual analysis. Application toreal datasets demonstrates that meta-analysis achieves morereliable identification than an individual analysis, and rankproducts are more robust in gene ranking, which leads to a muchhigher reproducibility among independent studies. Though t-basedmeta-analysis greatly improves over the individual analysis,it suffers from a potentially large amount of false positiveswhen P-values serve as threshold. We conclude that careful meta-analysisis a powerful tool for integrating multiple array studies. Contact: fxhong{at}jimmy.harvard.edu Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: David Rocke Present address: Department of Biostatistics and ComputationalBiology, Dana-Farber Cancer Institute, Harvard School of PublicHealth, 44 Binney Street, Boston, MA 02115, USA.     

Isolation of Subunits of Coupling Factor 1 from Maize and Spinach Chloroplasts and Properties of Combinations of Subunits with ATPase Activity

Subunits (, ß, ) and mixtures of subunits ( ß, , ß , ß ) were isolated without denaturationfrom a chloroform extract of chloroplast coupling factor 1 (CF₁)from maize (Zea mays var. Ushiku 5-4) and from spinach by fastprotein liquid chromatography (FPLC), on an anion-exchange columnof Mono-Q in the presence of n-octylglucoside (OG) and on achromatofocusing column of Mono-P. The ß -subunitcomplex (CF¹ ß ) was the minimum unit required forATPase activity, as was confirmed by the reconstituted complexof ß and subunits. An subunit isolated from maizeinhibited the ATPase activity of CF₁ ß from bothmaize and spinach. CF₁ ß was found to contain anOG-dependent Mg²⁺-ATPase. The ATPase activity of CF₁ ß required divalent cations, such as Mg²⁺ or Mn²⁺, for its expressionin the presence of OG; its optimum pH was 8.0 and it was markedlyinhibited by NaN₃. The enzyme hydrolyzed ATP in prefernece toGTP but not CTP, UTP, ADP, AMP or pNPP. Lineweaver-Burk plotsof its activity were curvilinear in the range of 0.6–0.7mM ATP.Mg²⁺. ¹Present address: Department of Biology, School of Education,Waseda University, Shinjuku-ku, Tokyo, 160 Japan. (Received February 15, 1989; Accepted April 20, 1989)     

Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays

Motivation: High-density DNA microarrays provide us with usefultools for analyzing DNA and RNA comprehensively. However, thebackground signal caused by the non-specific binding (NSB) betweenprobe and target makes it difficult to obtain accurate measurements.To remove the background signal, there is a set of backgroundprobes on Affymetrix Exon arrays to represent the amount ofnon-specific signals, and an accurate estimation of non-specificsignals using these background probes is desirable for improvementof microarray analyses. Results: We developed a thermodynamic model of NSB on shortnucleotide microarrays in which the NSBs are modeled by duplexformation of probes and multiple hypothetical targets. We fittedthe observed signal intensities of the background probes withthose expected by the model to obtain the model parameters.As a result, we found that the presented model can improve theaccuracy of prediction of non-specific signals in comparisonwith previously proposed methods. This result will provide auseful method to correct for the background signal in oligonucleotidemicroarray analysis. Availability: The software is implemented in the R languageand can be downloaded from our website (http://www-shimizu.ist.osaka-u.ac.jp/shimizu_lab/MSNS/). Contact: furusawa{at}ist.osaka-u.ac.jp Supplementary information: Supplementary data are availableat Bioinformatics online. The authors wish it to be known that, in their opinion, thefirst two authors should be regarded as joint First Authors. Associate Editor: Trey Ideker     

Integrated likelihood functions for non-Bayesian inference

Consider a model with parameter = (, ), where is the parameterof interest, and let L(, ) denote the likelihood function. Oneapproach to likelihood inference for is to use an integratedlikelihood function, in which is eliminated from L(, ) by integratingwith respect to a density function (|). The goal of this paperis to consider the problem of selecting (|) so that the resultingintegrated likelihood function is useful for non-Bayesian likelihoodinference. The desirable properties of an integrated likelihoodfunction are analyzed and these suggest that (|) should be chosenby finding a nuisance parameter that is unrelated to and thentaking the prior density for to be independent of . Such anunrelated parameter is constructed and the resulting integratedlikelihood is shown to be closely related to the modified profilelikelihood.     

Natural Abundance of {delta}15N Confirms Insectivorous Habit ofRoridula gorgonias, Despite it Having No Proteolytic Enzymes

Natural abundance values of plant ¹⁵N give an indication asto the source of nitrogen. In particular, carnivorous plantsare expected to be relatively enriched due to trophic enrichmentof their prey. Values of ¹⁵N for adultRoridula gorgonias(mean+3.02)are 4–9 greater than co-occurring non-carnivorous plantspecies and 5.24 greater than juvenileR. gorgoniasplants. Theyare also 3.5–4.26 greater than co-occurringDroseraspecieswhich, being sundews, are considered to be carnivorous. Thesehigh levels of ¹⁵N in adult plants are best explained as beingdue to access to trophically enriched N from insects. As isthe case for other carnivorous plants, leaves and stems ofR.gorgoniasare highly ultraviolet reflective and are thereforeprobably attractive to potential insect prey. This is furthersupport for this plant species being insectivorous.Copyright1998 Annals of Botany Company Nitrogen isotopes, carnivorous plants, insectivorous plant, ultraviolet,Roridula gorgoniasL.     

Thermodynamic Roles of Solubility in Taste Responses of Amino Acids

Bitter, sour and sweet responses of amino acids were relatedto their solubilities S_w, which are virtually equal to the reciprocalsof activity coefficients at infinite dilution in water _w, andalso related to their excess partial molar entropies of transferTS_t^E. Chem. Senses 21: 405–409, 1996. Present address: 5-32-12 Tamanawa, Kamakura-shi, 247 Japan     

The Meaning of Matric Potential

The commonly used equation, = P - + , which describes thepartitioning of plant water potential, , into components ofhydrostatic pressure, P, osmotic pressure, , and matric potential,, is misleading. The term , which is supposed to show the influenceof a solid phase on , is zero if a consistent definition ofpressure is used in the standard thermodynamic derivation. However,it can be usefully defined by = + _D, where _D is the osmoticpressure of the equilibrium dialysate of the system. The practicaland theoretical significance of this definition is discussed.     

An Error in the Calibration of Xylem-water Potential against Leaf-water Potential

An error occurs in the calibration of xylem pressure potential() against leaf-water potential () when the calibration is madeusing plant material in which the water stress has been inducedartificially after excision. The impostion of water stress afterexcision affects the determination more than it affects , consequentlythe relationship between these two indices of water stress isaltered. Care should be exercised to ensure that identical proceduresare adopted during . calibrations and during susbsequent fieldmeasurements of with the pressure-chamber apparatus.     

Discovery of Natural Photosynthesis using Zn-Containing Bacteriochlorophyll in an Aerobic Bacterium Acidiphilium rubrum

We discovered natural photosynthesis using Zn-containing bacteriochlorophyll in an acidophilic bacterium Acidiphilium rubrum. Chemical analysisof the cell extracts gave a 13 : 2 :1 molar ratio of Zn-bacteriochlorophyll : Mg-bacteriochlorophyll : bacteriopheophytin . Most of thepigments are associated with fully active reaction center andlight-harvesting complexes analogous to those in purple photosyntheticbacteria. The finding indicates an unexpectedly wide variabilityof photosynthesis. ⁷Present address: Department of Ecological Engineering, ToyohashiUniversity of Technology, Tenpaku-cho, Toyohashi, 441 Japan     

Genotypic Differences in Leaf Water Relations between Brassica juncea and B. napus

Various kinds of measurement of tissue water status were madeseveral times during water stress and recovery in Brassica juncea(cv Canadian Black) and B napus (cv Drakkar) Unstressed plantsof the two species had similar leaf water potentials (_w), solute(_s) and turgor potentials (_p) Values of relative water content(RWC) and the slope of the linear relationship between _p andRWC (_p/RWC) were greater in B napus than in B juncea Statistical correlations of pooled data for the watered andstressed treatments differentiated the relationships among RWC,_w and its components in the two species The major statisticaldifference was that _p/RWC was related to RWC in B napus andto _w and _s in B juncea A decline in _p/RWC with decreasing _sin B juncea may be a mechanism for maintaining _p at low soilwater potentials through maintenance of more elastic cell walls. Brassica juncea, Brassica napus, osmotic adjustment, tissue elasticity, water relations     

Pumpkin (Cucurbita sp.) seed globulin III. Comparison of subunit structures among seed globulins of various Cucurbita species and characterization of peptide components

Various Cucurbita seed globulins showed patterns similar toone another on SDS-gel electrophoresis, and ß bandsfor unreduced globulins and , ', and ' bands for reduced ones.On gel electrophoresis in 6 M urea, reduced globulin gave twoacidic and two basic bands. These corresponded to and ' chainsand ₁ and ₂ chains, respectively, identified by two-dimensionalurea-SDS gel electrophoresis. The compositions of the and ßsubunits were proposed. (Received September 8, 1977; )     

Taste of methyl-{alpha}-D-mannopyranoside: Effects of cross adaptation and Gymnema sylvestre

Methyl--D-mannopyranoside is a glycoside with a bitter-sweettaste. Adaptation to sucrose reduces the sweetness and adaptationto quinine sulphate reduces the bitterness of methyl--Dmannopyranoside.Application of Gymnema sylvestre reduces the sweetness of methyl--D-mannopyranosidewithout reducing its bitterness. These results, predicted byprevious studies, contradict a recent hypothesis and reportby Birch and Mylvaganam. ¹Supported by NIH Grant 2-RO1-NS07873-9     

Physiological detection of a binding substance for the agglutinability-inducing pheromone, {alpha} substance-I in Saccharomyces cerevisiae

We found a substance which binds to substance-I to inactivatethe biological activity of the pheromone to induce sexual agglutinabilityof a mating type cells. Both living and boiled cells of thea mating type had the substance-I-absorbing action. The absorbingaction of living cells was detected almost equally at both 0and 28?C. Cell extract of the a mating type showed the substance-I-inactivatingaction. The biological activity of substance-I inactivatedby shaking with cell-free culture medium of the a mating typewas recovered by heating at 100?C, which destroyed the inactivatingaction of the culture medium with little effect on the substance-Iactivity, indicating that a substance in the culture mediuminactivated substance-I by binding to it. This is supportedby the fact that the inactivating action completely stoppedin 30 min, leaving a considerable amount of active substance-I,when the concentration of the inactivating substance was lowcompared with that of substance-I. The ability to produce thebinding substance as specific to the a mating type. The bindingsubstance was different from the a agglutination substance responsiblefor sexual agglutination. ² On leave from Osaka City University. (Received April 6, 1977; )     

Sialylation of n-alkyllactosides, galactosides and glucosides by sialyltransferases from rat liver Golgi vesicles

nAlkyl - and -lactosides, galactosides and glucosides with differentalkyl chain lengths (C₂, C₈, C₁₄, and C₂₀) were synthesizedand used as acceptors for sialyltransferases from rat liverGolgi vesicles. The -galactosides, -glucosides, and both - and-lactosides, were sialylated. Keeping the acceptor concentrationconstant, sialylation rates reached a maximum for the n-octyl- and -lactosides, n-Octyl -galactoside and noctyl -glucoside,respectively. noctyl -glucoside, respectivwly. n-Octyl -galactosideand n-octyl -glucoside were not sialylated. The reaction productswere characterized by TLC. With n-octyl lactoside and galactosideas acceptors, two major sialylation products were formed. Thjeycould be separated by preparative TLC, and their structureswere identified as 2–3 and 2–6 sialylated acceptors,respectively, by a combination of periodated oxidation, NaBD₄reduction,permethylation and subsequent analysis by fast atombombardment mass spectrometry (FAB-MS). The structure of thesingle product obtained from n-ictyl -glucoside was determinedto be the 2–6 sialylated glucoside. Competition experimentswith n-octyl lactoside and lactosylceramide and gangliosideGal1-3GalNAc1-4(NeuAc2–3)Gal1–4Glcbeeta1–1Cer(GM1) as acceptors for sialyltransferases suggested that SAT-I[NeuAc2–3Gal1–4Glc1-1Cer (GM3) synthase] was atleast in least in part responsible for the 2–3 sialylationof n-octyl lactoside. alkylgalactosides alkylglucosides alkyllactosides neoglycolipids sialytransferases