Hyperforin Accumulates in the Translucent Glands of Hypericum perforatum

Annals of Botany 99: 1097–1100, 2007 Unfortunately in Fig. 1D     

Total and Component Carbon Fluxes of a Scots Pine Ecosystem from Chamber Measurements and Eddy Covariance

Annals of Botany 99: 345–353, 2007 The authors regret that the     

Self-assembling Plants and Integration across Ecological Scales

Annals of Botany 99: 1023–1034, 2007 There were errors in the colour reproduction of Figs 7     

Gut evacuation rates and ingestion rates of Eudiaptomus graciloides measured by means of the gut fluorescence method

Journal of Plankton Research, 8, 973–983, 1986 FIg. 2. Time-dependent changes in the gut content (percentageof initial ng pigment) of E. gro.ciloides at different temperaturesunder simultaneous feeding. Fig. 4. The relationship between instantaneous evacuation rateand temperature of E. graciloides. The regresston equation forfeeding animals: y = 0.0044 e(0.141 ) (r² = 0.90). For comparisonthe results of non-feeding animals are indicated with open circles.     

Contribution of Crenarchaeota and Euryarchaeota to the prokaryotic plankton in the coastal northwestern Black Sea

Journal of Plankton Research, 29,     

UMBONIUM VESTIARIUM (L.) (GASTROPODA, TROCHACEA) AS THE FOOD SOURCE FOR NATICID GASTROPODS AND A STARFISH ON A MALAYSIAN SANDY SHORE

Umbonium vestiarium (L.) forms virtually the entire diet of3 (possibly 4) species of naticid snails and the starfish Astropectenvappa Mueller annd Troschel on some north Penang sandy shores.Umbonium comprises about 99% of numbers and tissue of macrofauna.Predation totalled some 1.75 Umbonium (ca. 33 mg dry tissue).m^-2.day^-1 across much of the downshore sand flats rising to 2.3Umbonium (ca. 45 mg). m^-2. day^-1 near MLWS. Natica maculosaLamarck comprised > 80% of the predators and took 77–94%of the Umbonium eaten. Natica antonii Phillippi alone addedto this toll on the upper reaches of the zone while Polinicesspp and Astropecten appear to have taken 12–14% of thetotal toll of Umbonium near MLWS. Total predation is indicatedat 237–327 kJ.m^-2. year^-1 across the shore and this representsalmost the total flow of energy from primary consumers to intertidalbenthic predators on such shores and accounts for some 15.6%(lower shore)—20.5% (upper shore) of total Umbonium production. (Received 10 September 1982;     

贵州白山羊Bmp15和Gdf9基因多态性及其编码蛋白的进化分析(英文)

BMP15和GDF9是转化生长因子β（TGFβ）超家族的成员,对绵羊的繁殖性状有直接的调节作用,从中发现的多个高产突变位点直接提高了排卵数和产羔数。在之前的研究中,作者从贵州白山羊中找到了一个高产突变位点。为了进一步揭示Bmp15和Gdf9基因突变与繁殖性状之间的关系,对贵州白山羊Bmp15和Gdf9基因编码区进行了克隆,以人BMP7的晶体结构为模板构建了贵州白山羊BMP15和GDF9成熟肽的三维模型。贵州白山羊Bmp15和Gdf9基因分别编码394和453个氨基酸的蛋白前体。对BMP15和GDF9成熟肽序列进行分析发现,除了之前确认的BMP15中的FecX^B 突变（S99I）和GDF9中的V79I突变之外,还从贵州白山羊的BMP15和GDF9成熟肽分别发现7个和3个位点突变。其中,BMP15成熟肽的S32G、N66H、S99I/P99I和G107R突变可能影响二聚体与受体的结合;GDF9成熟肽的P78Q和V79I影响二聚体与I型受体的亲和力,将值得进一步深入研究。对Bmp15和Gdf9基因编码的蛋白前体序列进行聚类分析,结果显示在鱼类到哺乳类的进化过程中,BMP15出现长度逐渐增加的现象,以BMP15成熟肽N端长度增加为主。这种演变可能使BMP15对低排卵哺乳动物繁殖力的控制更为灵敏。该文的研究结果为贵州白山羊Bmp15和Gdf9基因变异与繁殖力的关系提出了合理的解释,并支持这两个因子是贵州白山羊高产性状重要调节因子的观点。     

Influence of the 3'-UTR-length of mKIAA cDNAs and their Sequence Features to the mRNA Expression Level in the Brain

We have previously described the sequence features of 1500 mouseKIAA (mKIAA) genes in comparison with those of human KIAA genes(Okazaki, N., Kikuno, R., Inamoto, S., Hara, Y., Nagase, T.,Ohara, O., and Koga, H. 2002, DNA Res., 9, 179–188; Okazaki,N., Kikuno, R., Ohara, R., Inamoto, S., Aizawa, H., Yuasa, S.,Nakajima, D., Nagase, T., Ohara, O., and Koga, H. 2003, DNARes., 10, 35–48; Okazaki, N., Kikuno, R., Ohara, R., Inamoto,S., Koseki, H., Hiraoka, S., Saga, Y., Nagase, T., Ohara, O.,and Koga, H. 2003, DNA Res., 10, 167–180; and Okazaki,N., F-Kikuno, R., Ohara, R., Inamoto, S., Koseki, H., Hiraoka,S., Saga, Y., Seino, S., Nishimura, M., Kaisho, T., Hoshino,K., Kitamura, H., Nagase, T., Ohara, O., and Koga, H. 2004,DNA Res., 11, 205–218). To validate the orthologous relationshipbetween mKIAA and KIAA genes in detail, we examined their chromosomalpositions and evolutionary rate of synonymous substitutionsand confirmed that >93% of the mKIAA/KIAA gene pairs areorthologous. During the sequence analysis of mKIAA genes, wefound that 3'-untranslated region (3'-UTR) lengths of mKIAAand KIAA genes are extremely long. In the meanwhile, we havealso examined the tissue-specific expression of 1700 mKIAA genesusing cDNA microarray and verified predominantly their expressionin adult brain (Koga, H., Yuasa, S., Nagase, T., Shimada, K.,Nagano, M., Imai, K., Ohara, R., Nakajima, D., Murakami, M.,Kawai, M., Miki, F., Magae, J., Inamoto, S., Okazaki, N., Ohara,O. 2004, DNA Res., 11, 293–304). To connect these twoevidences, we statistically analysed the relationship betweenthem by using the mKIAA genes. Consequently, a positive correlationwas observed between the 3'-UTR lengths and the relative expressionintensities in adult brain. Furthermore, we searched sequenceelements in the 3'-UTR possibly related with their expressionand found some candidates regarding the brain-specific expression.     

ELECTROPHORETIC AND MORPHOMETRIC CHARACTERS IN POPULATION DIFERENTIATION OF THE PEARL OYSTER, PINCTADA RADIATA (LEACH), FROM AROUND BAHRAIN

Variation at the leucine aminopeptidase (Lap), glucose phosphateisomerase (Gpi) and tetrazolium oxidase (To) loci was investigatedin samples of three populations, Al-Mayana (MAY), Shigita (SH)and Mina Salman (MS), of Pinctada radiata from pearl oysterbeds around Bahrain. The To locus was monomor-phic. SignificantLap and Gpi heterozygote deficiencies were evident and it issuggested that these were generated by selection. The MS population,to the East of Bahrain, differed significantly in Gpi allelefrequencies from both Northern populations (MAY, SH) and Nei'sgenetic identity indicates a close relationship between theNorthern populations. Measurements of shell morphometrics were used both as ratiosof one dimension to another, and as regressions of one dimensionon another to examine relatedness between populations. Boththese mor-phometric approaches gave different results from eachother and also differed from the electrophoretic data. It isconcluded that estimates of relatedness in pearl oysters basedon electrophoretic data will be more reliable than those basedon shell shape. (Received 20 November 1990; accepted 12 April 1991)     

Analysis of Concentration-response Relationship for Enhanced Sugar Responses of the Chorda Tympani Nerve in the Diabetic db/db Mouse

Chorda tympani responses to sugars were greater in diabetic(db/db) than in non-diabetic control mice. A kinetic analysissuggested that the greater sugar responses in db/db mice wereunlikely due to the increased number of sugar receptors. Chem.Senses 21: 59–63, 1996.     

Model-based deconvolution of genome-wide DNA binding

Motivation: Chromatin immunoprecipitation followed by hybridizationto a genomic tiling microarray (ChIP-chip) is a routinely usedprotocol for localizing the genomic targets of DNA-binding proteins.The resolution to which binding sites in this assay can be identifiedis commonly considered to be limited by two factors: (1) theresolution at which the genomic targets are tiled in the microarrayand (2) the large and variable lengths of the immunoprecipitatedDNA fragments. Results: We have developed a generative model of binding sitesin ChIP-chip data and an approach, MeDiChI, for efficientlyand robustly learning that model from diverse data sets. Wehave evaluated MeDiChI's performance using simulated data, aswell as on several diverse ChIP-chip data sets collected onwidely different tiling array platforms for two different organisms(Saccharomyces cerevisiae and Halobacterium salinarium NRC-1).We find that MeDiChI accurately predicts binding locations toa resolution greater than that of the probe spacing, even foroverlapping peaks, and can increase the effective resolutionof tiling array data by a factor of 5x or better. Moreover,the method's performance on simulated data provides insightsinto effectively optimizing the experimental design for increasedbinding site localization accuracy and efficacy. Availability: MeDiChI is available as an open-source R package,including all data, from http://baliga.systemsbiology.net/medichi. Contact: dreiss{at}systemsbiology.org Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Martin Bishop     

A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case

Motivation: The genomic methylation analysis is useful to typebacteria that have a high number of expressed type II methyltransferases.Methyltransferases are usually committed to Restriction andModification (R-M) systems, in which the restriction endonucleaseimposes high pressure on the expression of the cognate methyltransferasethat hinder R-M system loss. Conventional cluster methods donot reflect this tendency. An algorithm was developed for dendrogramconstruction reflecting the propensity for conservation of R-MType II systems. Results: The new algorithm was applied to 52 Helicobacter pyloristrains from different geographical regions and compared withconventional clustering methods. The algorithm works by firstgrouping strains that share a common minimum set of R-M systemsand gradually adds strains according to the number of the R-Msystems acquired. Dendrograms revealed a cluster of Africanstrains, which suggest that R-M systems are present in H.pylorigenome since its human host migrates from Africa. Availability: The software files are available at http://www.ff.ul.pt/paginas/jvitor/Bioinformatics/MCRM_algorithm.zip Contact: filipavale{at}fe.ucp.pt Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Martin Bishop     

Effect of Irradiance on Chlorophyll Estimation with the Minolta SPAD-502 Leaf Chlorophyll Meter

Leaf chlorophyll content may be used as an indirect indicatorof crop nitrogen status. Chlorophyll meter values (SPAD values)taken with the Minolta SPAD-502 chlorophyll meter in the shadeplantOxalis acetosellaL. and in winter wheat (Triticum aestivumL.)varied by 15 and 8%, respectively, with variation in irradiance.The lowest SPAD-values were measured at high irradiance. Duringa natural night-day-night cycle SPAD values for winter wheatwere lowest in the middle of the day, highest at low irradianceat dusk and dawn and intermediate in darkness before dawn andafter dusk. The results indicate that irradiance during measurementshould be considered when using the Minolta SPAD-502 chlorophyllmeter for the estimation of crop N-status.Copyright 1998 Annalsof Botany Company Chlorophyll meter, nitrogen, irradiance,Oxalis acetosellaL.,Triticum aestivumL., winter wheat.     

Interaction Between Cryopreservation, Rewarming Rate and Seed Humidification on the Germination of Two Spanish Endemic Species

The effects of humidification, storage in liquid nitrogen (1or 30 d) and rewarming rate on seed germination were studiedin two Spanish endemics. Humidification resulted in higher germinationpercentages only in the species with hard covers, especiallyin slowly rewarmed seeds. In an experiment lasting 21 weeks,seeds stored in liquid nitrogen were removed for 10 min eachweek to mimic the withdrawal of samples from a seed bank; thishad no effect on germination.Copyright 1998 Annals of BotanyCompany Centaurea hyssopifolia,Limonium dichotomum, cryopreservation, cypsela, endemics, germination, humidification, seeds.     

Unequal group variances in microarray data analyses

Motivation: In searching for differentially expressed (DE) genesin microarray data, we often observe a fraction of the genesto have unequal variability between groups. This is not an issuein large samples, where a valid test exists that uses individualvariances separately. The problem arises in the small-samplesetting, where the approximately valid Welch test lacks sensitivity,while the more sensitive moderated t-test assumes equal variance. Methods: We introduce a moderated Welch test (MWT) that allowsunequal variance between groups. It is based on (i) weightingof pooled and unpooled standard errors and (ii) improved estimationof the gene-level variance that exploits the information fromacross the genes. Results: When a non-trivial proportion of genes has unequalvariability, false discovery rate (FDR) estimates based on thestandard t and moderated t-tests are often too optimistic, whilethe standard Welch test has low sensitivity. The MWT is shownto (i) perform better than the standard t, the standard Welchand the moderated t-tests when the variances are unequal betweengroups and (ii) perform similarly to the moderated t, and betterthan the standard t and Welch tests when the group variancesare equal. These results mean that MWT is more reliable thanother existing tests over wider range of data conditions. Availability: R package to perform MWT is available at http://www.meb.ki.se/~yudpaw Contact: yudi.pawitan{at}ki.se Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Martin Bishop     

Estimation of thickness of airwaysurface liquid in ferret trachea in vitro

Duneclift, S., U. Wells, and J. Widdicombe. Estimationof thickness of airway surface liquid in ferret trachea in vitro. J. Appl. Physiol. 83(3): 761-767, 1997.The tracheae of ferrets and rabbits were mounted in vitro inorgan baths. While the tracheae were liquid filled, the permeabilitycoefficient ( P) was determined, and then while thetracheae were air filled, the percent clearance for^99mTc-labeleddiethylenetriaminepentaacetic acid (DTPA) was determined. The thicknessof airway surface liquid (ASL) was estimated by three methods.1) The initial concentration of^99mTc-DTPA and the total amount of^99mTc-DTPA (the sum of thatentering the outside medium, that draining from the trachea, and thatwashed out at the end of 40 min) gave the initial volume of ASL andthus its thickness. Mean values were 45.7 µm for the ferret and 41.9 µm for the rabbit. 2) Estimates ofASL thickness at the end of the 40-min period, based on the final^99mTc-DTPA concentration and theamount in the washout, were 42.9 µm for ferret and 45.4 µm forrabbit. 3) The ratio of Pto percent clearance gave mean ASL thickness values of 49.2 µm forthe ferret and 40.3 µm for the rabbit. Thus three separate methodsfor determining ASL thickness give very similar results, with means inthe range 40-49 µm. Administration of methacholine or atropineto ferret tracheae did not significantly change ASL thickness.

     

3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm

Motivation: Reliable structural modelling of protein–proteincomplexes has widespread application, from drug design to advancingour knowledge of protein interactions and function. This workaddresses three important issues in protein–protein docking:implementing backbone flexibility, incorporating prior indicationsfrom experiment and bioinformatics, and providing public accessvia a server. 3D-Garden (Global And Restrained Docking ExplorationNexus), our benchmarked and server-ready flexible docking system,allows sophisticated programming of surface patches by the uservia a facet representation of the interactors’ molecularsurfaces (generated with the marching cubes algorithm). Flexibilityis implemented as a weighted exhaustive conformer search foreach clashing pair of molecular branches in a set of 5000 modelsfiltered from around 340 000 initially. Results: In a non-global assessment, carried out strictly accordingto the protocols for number of models considered and model qualityof the Critical Assessment of Protein Interactions (CAPRI) experiment,over the widely-used Benchmark 2.0 of 84 complexes, 3D-Gardenidentifies a set of ten models containing an acceptable or bettermodel in 29/45 test cases, including one with large conformationalchange. In 19/45 cases an acceptable or better model is rankedfirst or second out of 340 000 candidates. Availability: http://www.sbg.bio.ic.ac.uk/3dgarden (server) Contact: v.lesk{at}ic.ac.uk Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Burkhard Rost