Adaptable gene‐specific dye bias correction for two‐channel DNA microarrays

DNA microarray technology is a powerful tool for monitoring gene expression or for finding the location of DNA‐bound proteins. DNA microarrays can suffer from gene‐specific dye bias (GSDB), causing some probes to be affected more by the dye than by the sample. This results in large measurement errors, which vary considerably for different probes and also across different hybridizations. GSDB is not corrected by conventional normalization and has been difficult to address systematically because of its variance. We show that GSDB is influenced by label incorporation efficiency, explaining the variation of GSDB across different hybridizations. A correction method (Gene‐ And Slide‐Specific Correction, GASSCO) is presented, whereby sequence‐specific corrections are modulated by the overall bias of individual hybridizations. GASSCO outperforms earlier methods and works well on a variety of publically available datasets covering a range of platforms, organisms and applications, including ChIP on chip. A sequence‐based model is also presented, which predicts which probes will suffer most from GSDB, useful for microarray probe design and correction of individual hybridizations. Software implementing the method is publicly available.     

The Effect of NAA (1-Naphthaleneacetic Acid) and Morphactin (Methyl 2-Chloro-9-hydroxyfluorene-9-carboxylate) on RNA and Protein Synthesis in Senescing Bean Endocarp

The effect of NAA (1-naphthaleneacetic acid) and morphactin (methyl 2-chloro-9-hydroxyfluorene-9-carboxylate) on the uptake and incorporation of uridine-5-³H and l -leucineU-¹⁴C was studied in senescing bean endocarp (Phaseolus vulgaris L. cv. Kentucky wonder pole beans) sections. Both growth regulators inhibited uptake of these precursors and appeared to affect different components of the uptake mechanism. A possible synergistic inhibition was seen in case of leucine, but in case of uridine, the effect was less than additive. A strong synergistic increase in the incorporation of l -leucine into protein was seen. Thus, morphactin interacted with an exogenously applied auxin at the level of the protein synthesizing apparatus.     

Effect of Iron on Conversion of Acetic Acid to Methane During Methanogenic Fermentations

A semi-automatic method for the detection of salmonellas in food products is described. This method involves measurement of the fluorescence intensity of preparations stained with fluorescent antibody. An overall agreement of 89·6% was obtained when the method was compared with a standard cultural technique for the detection of salmonellas in foods, feeds and environmental samples, although false negatives were a problem with raw meat products. A saving in time of at least 18 h was achieved.     

The effects of ammonium sulphate deposition and root sinks on soil solution chemistry in coniferous forest soils

The effects of enhanced (NH_{4 2}SO₄deposition on soil solution cation and anion concentrations and annualionic fluxes were followed using a standardised experimental protocolin six European coniferous forests with contrasting soil types, pollutioninputs and climate. Native soil cores containing a ceramic suction cupwere installed in the field, roofed and watered every two weeks withlocal throughfall or local throughfall with added(NH₄)₂SO₄ at 75 kgNH₄ ⁺-N ha^-1 a^-1. Livingroot systems were established in half of the lysimeters.Untreated throughfall NH₄ ⁺-N deposition at thesites ranged from 3.7 to 29 kg ha^-1 a^-1Soil leachates were collected at two weekly intervalsover 12 months and analysed for volume, andconcentrations of major anions and cations. Increasesin soil solution NO₃ ^- concentrations inresponse to N additions were observed after 4–9months at three sites, whilst one sandy soil with highC:N ratio failed to nitrify under any of thetreatments. Changes in NO₃ ^- concentrationsin soil solution controlled soil solution cationconcentrations in the five nitrifying soils, withAl³⁺ being the dominant cation in the more acidsoils with low base saturation. The acidification responses ofthe soils to the (NH_{4 2}SO₄additions were primarily related to the ability of thesoils to nitrify the added NH₄ ⁺. pH and soiltexture seemed important in controllingNH₄ ⁺ leaching in response to the treatments,with two less acidic, clay/clay loam sites showingalmost total retention of added NH₄ ⁺, whilstnearly 75% of the added N was leached asNH₄ ⁺ at the acid sandy soils. The presenceof living roots significantly reduced soil solutionNO₃ ^- and associated cation concentrations attwo of the six sites. The very different responses of the sixsoils to increased (NH₄)₂SO₄deposition emphasise that the establishment of N critical loadsfor forest soils need to allow for differences in N storagecapacity and nitrification potential.     

Factors affecting nest-site choice and reproductive success of Curlews Numenius arquata on farmland

Nest-site choice and reproductive success of Curlews Numenius arquata in different habitats were studied at a mixed farmland site (grasslands and flooded tilled fields relatively common) and at an arable farmland site (dry tilled fields more dominant than at the mixed site) in central Sweden. At both sites Curlews preferred to nest on grassland and fallow fields, where hatching success was higher than on tillage fields. Nests were also situated further away from forest edges than random sites, but hatching success did not vary with distance to the forest edge. Only 35.6% of the pairs were estimated to hatch young. The main cause of nest loss was predation and the second most important factor was destruction by farming practices, which was an important factor in tillage early in season. Surprisingly, nest survival was higher at the arable than at the mixed farmland site, probably being an effect of the increased proportion of fallowing during recent years. Mortality of chicks was 79.7% before fledgling age (both sites combined) and, surprisingly, chick survival was lower on meadows than on arable fields and leys. The mean production of young was only 0.25 fledglings per pair, which is lower than in areas less affected by farming practice. The low production of young is probably an important factor in the decline of Curlew populations on Swedish farmland. On bogs 1.4 fledglings per pair were produced, indicating that reproductive success of Curlews is higher in more natural habitats.     

One-Leaf Cuttings as a Model to Study Second Growth in the Potato (Solanum tuberosum) Plant

Second growth is an important physiological disorder of thepotato (Solanum tuberosum L.) plant. A model system to studysecond growth was developed using one-leaf cuttings. Photoperiod,temperature, decapitation and leaf removal treatments were carriedout on the plants from which the cuttings were taken and onthe cuttings themselves. Tuberized, one-leaf cuttings takenfrom moderately-induced plants and exposed to 35 °C afterleaf removal showed 95% second growth within 10 d after treatmentinitiation. Conditions that promoted second growth also reducedstarch and dry-matter content, even in tubers that did not developsecond growth. Cuttings, second growth, potato, Solanum tuberosum L, cv, Bintje, Solanum tuberosum L. cv., Désirée, Solanum tuberosum L. cv., Russet Burbank, tuberization, starch content, dry-matter, heat, photoperiod, decapitation, leaf removal     

Sex roles, parental effort and offspring desertion in the monogamous Eurasian Curlew Numenius arquata

The reasons for female desertion of offspring and the evolution of predominantly male care among monogamous bird species are not clearly understood. We studied parental effort during the incubation and chick rearing periods in the Eurasian Curlew Numenius arquata in western Finland, and compared timing of brood desertion with other populations in Europe. Males and females contributed equally to incubation and showed no differences in the intensity of mobbing behaviour towards a potential nest predator (stuffed crow) shortly after hatching. However, females deserted their offspring approximately halfway through the brooding period ( c. 16 d after hatching), while males remained with chicks until independence ( c. 35 d). Females with late-laid clutches deserted their offspring sooner after hatching than those with clutches produced earlier in the season. Curlew females deserted younger chicks in northeast Europe, where laying dates were later, breeding seasons shorter and migration distances were longer, than in western and central Europe. We suggest that the most likely reasons for offspring desertion by females may be associated with increased female survivorship and maintenance of pairbond between years.     

Molecular evolution of a repetitive region within the per gene of Drosophila

The clock gene period (per) controls a number of biological rhythms in Drosophila. In D. melanogaster, per has a repetitive region that encodes a number of alternating threonine-glycine residues. We sequenced and compared this region from several different Drosophila species belonging to various groups within the Drosophila and Sophophora subgenera. This part of per shows a great variability in both DNA sequence and length. Furthermore, analysis of the data suggests that changes in the length of this variable region might be associated with amino acid replacements in the more conserved flanking sequences.