MAGI: Methylation analysis using genome information

By incorporating annotation information into the analysis of next-generation sequencing DNA methylation data, we provide an improvement in performance over current testing procedures. Methylation analysis using genome information (MAGI) is applicable for both unreplicated and replicated data, and provides an effective analysis for studies with low sequencing depth. When compared with current tests, the annotation-informed tests provide an increase in statistical power and offer a significance-based interpretation of differential methylation.     

Origin and evolution of the endemic Macaronesian Inuleae (Asteraceae): evidence from the internal transcribed spacers of nuclear ribosomal DNA

The tribe Inuleae (Asteraceae) has 10 species endemic to the Macaronesian islands, including the three endemic genera Allagopappus, Schizogyne, and Vierea. Phylogenetic analyses of DNA sequence data from the internal transcribed spacers (ITS) of the nuclear ribosomal DNA of 47 taxa were performed using all Macaronesian endemics and representative species from 21 of the 36 genera of the Inuleae. The resulting ITS phylogeny reveals that Allagopappus is sister to a large clade that contains all genera with a predominantly Mediterranean distribution. This finding suggests that Allagopappus may represent an ancient lineage that found refuge in the Canary Islands following the major climatic and/or geologic changes in the Mediterranean basin after the Tertiary. The Macaronesian endemic genus Schizogyne is sister to Limbarda from the Mediterranean. The third Macaronesian endemic genus, Vierea, is sister to Perralderia, which is restricted to Morocco and Algeria. Pulicaria canariensis is sister to P. mauritanica, a species endemic to Morocco and Algeria. In contrast, P. diffusa from the Cape Verde Islands is sister to a broadly distributed species, P. crispa, that occurs from North Africa to the Arabian peninsula. Based on the ITS data, the genera Blumea, Inula, and Pulicaria are not monophyletic. The ITS trees suggested that Blumea mollis belongs to the tribe Plucheeae, a finding that is congruent with recent morphological evidence. A possible southern African origin for the core of the Laurasian taxa of the Inuleae is also suggested.     

Autotropism in Fungal Spores

Autotropism was examined in germinating spore pairs of Rhizopusstolonifer, Mucor plumbeus, Trichoderma viride, and Botrytiscinerea. When germinated on agar surfaces the first three speciesexhibited negative autotropism, B. cinerea being neutral inits autotropic behaviour. More pronounced negative autotropismwas shown by the first three species when germinated on a filmof Cellophane applied to an agar surface. Under these conditionsB. cinerea displayed positive autotropism. Spore pairs of R. stolonifer germinated on agar containing cellulosepowder or charcoal showed less negative autotropism than onagar alone. Touching spore pairs of each species showed a markedtendency towards cis-ness, i.e. germ-tubes beginning on thesame side of a line joining the two spore centres, under theculture conditions described, the one exception being the reductionin cis-ness recorded when R. stolonifer was germinated on agarcontaining charcoal. Time courses of germination were determined for single sporesand touching spore pairs of R. stolonifer and M. plumbeus anda significant promotion was obtained in the spore pairs as comparedwith the single spores. Although both these species exhibitmarked negative autotropism there was a strong tendency forthe positive germ-tube, i.e. one beginning more nearly towardsits neighbour, to emerge before the negative germ-tube in thosespore pairs having one germtube positive and the other negativein orientation. Also, in R. stolonifer, the replacement of germination-promotersby germination-inhibitors in filtrates from spore suspensionsas they age is correlated with a change from positive to negativeautotropism in germinating members of (+ –) spore pairs. Possible mechanisms are discussed to account for the observedeffects.     

Carbohydrate Partitioning and Compartmental Analysis for a Highly Productive CAM Plant, Opuntia ficus-indica

Carbon partitioning patterns of Opuntia ficus-indica, a widelycultivated crassulacean acid metabolism species, were analysedto estimate carbon fluxes. After labelling a cladode with ¹⁴CO₂,activities of ¹⁴C in various organs were measured for 6 weeks;the observed ¹⁴C time-courses for ¹⁴C in the labelled cladodeand for transfer into other organs were simulated with a compartmentmodel. Within the first week, half of the newly synthesizedcarbohydrate in the labelled cladode was either converted intostructural material in that cladode, lost by respiration ofthat cladode, or moved to other organs. In the non-labelledcladode and the roots, such newly synthesized carbohydrate initiallyincreased, reached maxima, and then declined. The basal cladodeand the daughter cladode used 65 and 96%, respectively, of theirown assimilate. Roots imported 12 and 2 % of carbohydrate fromthe basal cladode and the daughter cladode, respectively. Whenthe whole plant was shaded, the daughter cladode incorporatednearly threefold more carbohydrate from the basal cladode intostructural material compared with the control. When plants weredroughted, roots incorporated 23 % more and the daughter cladodeincorporated 68 % less carbohydrate from the basal cladode intotheir structural material than for the control. The basal cladodesof the 18-month-old plants exported 60% more carbon than thoseof the 6-month-old plants. Carbon flux rates derived from compartmentalanalysis can be used as parameter values in plant productionmodels. Carbon partitioning, compartment model, drought, plant age, shading     

INFLUENCE OF OXIDATION-REDUCTION REDUCTANTS ON SALMONELLA TYPHIMURIUM GROWTH RATES AFTER INITIAL pH ADJUSTMENT AND ZINC COMPOUND ADDITION

The objective of this study was to examine the separate influence of acidic pH, reductants (cysteine and sulfide) and zinc compounds (Zn acetate and Zn sulfate) during anaerobic growth of a S. typhimurium poultry isolate in rich or minimal media. The anaerobic growth of a S. typhimurium poultry isolate in TSB medium was significantly inhibited by either acidic initial pH or higher concentrations of Zn acetate. S. typhimurium anaerobic growth in M9 minimal medium was significantly inhibited by either acidic pH or higher concentrations of Zn acetate or Zn sulfate. Most anaerobic growth rates of the S. typhimurium poultry isolate in acidic media and with higher concentrations of Zn acetate or Zn sulfate were less than 0.10 h^-1. The overall anaerobic growth rates of S. typhimurium were inhibited more in the presence (0.089 h^-1) of reductants than in the absence (0.102 h^-1) of reductants in M9 medium. Results in this study suggest that either increasing Zn concentration or decreasing initial pH can reduce growth rate of foodborne Salmonella under anaerobic growth conditions.     

APPLICATION OF A TRANSPOSON FOOTPRINTING TECHNIQUE FOR RAPID IDENTIFICATION OF SALMONELLA TYPHIMURIUM TN5 MUTANTS REQUIRED FOR SURVIVAL UNDER DESICCATION STRESS CONDITIONS

Salmonella spp. are one of the foodborne pathogens that can be isolated in the environments of poultry houses and desiccation is a potential stress condition that can influence the survival of Salmonella spp. in this environment. In order to investigate the desiccation survival mechanism of Salmonella spp. the genome of S. typhimurium ATCC 14028 was screened for the genes potentially required for survival during desiccation using a novel method based on Tn5 mutagenesis previously developed in our laboratory. This method, termed transposon footprinting, simultaneously amplifies the Tn5-flanking sequences in a complex pool of the Tn5 mutants. As the length of the amplified DNA fragment should be unique for each distinct Tn5 mutant, the polymerase chain reaction (PCR) products separated on an agarose gel generate transposon footprints with each band in the footprint representing the corresponding Tn5 mutant. By comparing the transposon footprints from the pools of S. typhimurium Tn5 mutants before and after exposure to desiccation, Tn5 mutants that were not recovered after the selection were rapidly identified that would be easily isolated for further genetic analysis.