Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins

Background  

Phylogenies capture the evolutionary ancestry linking extant species. Correlations and similarities among a set of species are mediated by and need to be understood in terms of the phylogenic tree. In a similar way it has been argued that biological networks also induce correlations among sets of interacting genes or their protein products.     

Isolation of polymorphic tetranucleotide microsatellite markers for the ornate nursery frog Cophixalus ornatus

We have isolated 18 polymorphic microsatellite loci for Cophixalus ornatus from genomic libraries enriched for (AAAG)_n, (AACC)_n and (AAGG)_n repetitive elements. The number of alleles ranges from five to 22 per locus with the observed heterozygosity ranging from 0.10 to 0.92. These markers will be useful for the analysis of population structure in C. ornatus and testing alternative models of speciation.     

Responses of Vegetable Seeds to Controlled Hydration

Leek, onion and carrot seeds were imbibed in water and in solutionsof polyethylene glycol (PEG) 6000 over the range –0.5to –4.0 MPa osmotic potential, for periods up to 28 dat 15 C. Seeds started to germinate after 7 and 14 d at –0.5MPa and –1.0 MPa PEG, respectively, but in the lattercase, germination did not exceed 5%. No germination occurredin solutions of lower (more negative) osmotic potential. Seedmoisture content increased with osmotic potential in all threespecies and the relationships were unaffected by the durationof imbibition in solutions of –1.0 to –4.0 MPa,though leek seeds had higher moisture contents than the otherspecies for any given osmotic potential. Linear relationships between response to priming (differencebetween mean germination times of primed and untreated seeds)and seed moisture content were obtained for each species, positiveresponses being obtained above 30–35% seed moisture contentwith optima at 46, 44.5 and 44% seed moisture contents in leek,onion and carrot, respectively. Priming had no effect on embryovolume or cell number per embryo in leek and onion. Carrot embryovolume increased by 43% and cell number per embryo doubled inprimed compared with untreated seeds, whereas seeds imbibedin water showed only a slight increase in cell number per embryoat the stage when radicles were beginning to penetrate the seedcoat. Allium cepa L. cv. Rijnsburger Robusta, onion, Allium porrum L. cv. Winterreuzen, leek, Daucus carota L. cv. Nantaise, carrot, germination, priming, polyethylene glycol, seed moisture, cell number, embryo volume     

The Effect of Inhibitors of Photosynthetic and Respiratory Electron Transport on Nitrate Reduction and Nitrite Accumulation in Excised Z. mays L. Leaves

The assimilation of nitrate and nitrite under dark and lightconditions in Zea mays L. leaves was investigated. Nitrate wasassimilated under dark-aerobic conditions. Anaerobiosis stimulatednitrate reduction and nitrite accumulation under dark conditions.Vacuum infiltration of inhibitors of respiratory electron transport,antimycin A and rotenone, stimulated nitrate reduction and nitriteaccumulation under dark-aerobic conditions. Vacuum infiltrationof low concentrations of PCP, DNP and mCCCP depressed nitratereduction and nitrite accumulation under dark-aerobic conditions,whereas, infiltration of higher concentrations stimulated nitratereduction and nitrite accumulation. The greatest level of nitrateand nitrite reduction occurred under light conditions. The inhibitorof photosynthetic electron transport, DCMU, stimulated the accumulationof nitrite in the light, but decreased nitrate reduction. Whenthe inhibitors of respiratory electron transport antimycin Aand rotenone, were supplied together with DCMU in the light,nitrite accumulation was enhanced. Low concentrations of mCCCPdecreased both nitrate reduction and nitrite accumulation underlight conditions when supplied with DCMU. Key words: Nitrate reduction, Nitrite accumulation, Leaves     

Ecology of nematophagous fungi: distribution and habitat

A survey of 161 samples of soil and plant material collected from sites throughout Ireland has shown that nematophagous fungi exist in a wide range of habitats. 205 isolations were made consisting of 11 endoparasitic and 20 predatory species. The commonest endoparasites and their frequency of occurrence were Myzocytium spp. (9·3%), Acrostalagmus obovatus (6·8%) and Harposporium anguillulae (6·2%). Predators were equally abundant, the commonest being Dactylella bembicodes (8·7%), D. mammillata (6·8%) and D. ellipsospora (6·2%). Arthrobotrys oligospora and A. musiformis both had a highly restricted distribution. Adhesive knobs and constricting rings were significantly more abundant than the other trapping mechanisms. All the samples were classified into one of 10 broad habitat types. Of these temporary agricultural pasture, coastal vegetation and coniferous leaf litter had the greatest percentage of sites from which nematophagous fungi were isolated. A number of species showed distinct habitat associations, in particular Arthrobotrys robusta, A. musiformis and Dactylella cionopaga.     

Homologies to the tomato endopolygalacturonase gene in the peach genome

Abstract. Peach endopolygalacturonase was isolated from the mesocarp tissue of soft ripe, freestone peach fruit, but was not detectable in mature pre-ripening fruit. It is a basic protein with a M_r of approximately 45000 Da, and cross-reacts with antibody to tomato endopolygalacturonase. Using a cDNA to the tomato enzyme as a probe, a fragment of peach genomic DNA was isolated which encoded about 50% of the peach enzyme. The nucleotide sequence of the fragment was determined and the amino acid sequence of part of the peach endopolygalacturonase peptide derived. Coding regions of the peach gene show extensive homology with related regions of the tomato gene. Introns are dissimilar. Endopolygalacturonase activity occurs in ripe 'freestone'peaches but not in the firmer 'clingstone'varieties. Hybridization studies identified a similar gene fragment in freestone, semi-freestone and clingstone peach varieties.     

The effects of ripening and drying of carrot seed (Daucus carota) crops on germination

Carrot seeds taken from the parent plant were capable of germinating before the stage when maximum seed dry weight was reached but even after this stage, when the seed moisture content had fallen below 20%, improvement in seed germination characteristics continued. In the latter stages of seed growth losses by shedding were 12–20 kg/ha/day. For low density crops (10 plants/m²) the yield of viable seed was at a maximum in crops whose seed was harvested with a moisture content of between 20 and 40% but no consistent relationship could be established for high density crops (80 plants/m²). There were no effects of umbel order or plant density on mean germination time or spread of germination. At any early harvest, percentage germination was highest for primary-umbel-seeds and seeds from low density crops but the differences between the seed origins diminished with later harvests. Drying the seeds on the umbels improved the percentage germination, reduced the mean germination time and the spread of germination particularly at the early harvests compared with seeds removed from the umbels and germinated immediately without drying.