A family of parallel Runge-Kutta pairs

AbstractIncreasing availability of parallel computers has recently spurred a substantial amount of research concerned with designing explicit Runge-Kutta methods to be implemented on such computers. Here, we discuss a family of methods that require fewer processors than methods presently available do, still achieving a similar speed-up. In particular, (5,6) and (6,7) pairs are derived, that require a minimum number of function evaluations on two and three processors, respectively

An efficient Runge-Kutta (4,5) pair

AbstractA pair of explicit Runge-Kutta formulas of orders 4 and 5 is derived. It is significantly more efficient than the Fehlberg and Dormand-Prince pairs, and by standard measures it is of at least as high quality. There are two independent estimates of the local error. The local error of the interpolant is, to leading order, a problem-independent function of the local error at the end of the step

An Efficient Runge-Kutta (4,5) pair

A pair of explicit Runge-Kutta formulas of orders 4 and 5 is derived. It is significantly more efficient than the Fehlberg and Dormand-Prince pairs, and by standard measures it is of at least as high quality. There are two independent estimates of the local error. The local error of the interpolant is, to leading order, a problem-independent function of the local error at the end of the step

Effect of Nedocromil Sodium on Aspecific Bronchial Hyper-Reactivity in Asthmatic Children

The purpose of this study was to evaluate whether nedocromil sodium benefits urban asthmatic children showing seasonal bronchial hyper-reactivity to ultrasonic nebulization of distilled water (UNDW). A prospective, randomized, placebo-controlled, parallel-group, double-blind study was carried out at the outpatient pulmonology service at a tertiary-care teaching hospital. Twelve children living in Milan, who were 7–17 years of age, who were SPT and RAST-negative to perennial allergens, who were suffering from episodic asthma, and showing seasonal bronchial hyper-reactivity to UNDW during winter, participated in this study. All the children received either placebo or nedocromil sodium, 4 mg every 6 h for 6 weeks. Spirometry and UNDW challenge were done at the following times: day−7; day 0; day 1; day 7; day 14; day 28; day 42. No differences were found in the basal spirometric parameters, which were normal in both nedocromil and placebo groups. Bronchial reactivity to UNDW was found to be significantly decreased in the group treated with nedocromtl starting from day 7. It is therefore concluded that nedocromil sodium can reverse bronchial hyper-reactivity caused by seasonal factors such as cold, viral infections and atmospheric pollutants in children suffering from asthma

Genetic analysis of tolerance to Boron toxicity in the legume Medicago truncatula

Background: Medicago truncatula Gaertn. (barrel medic) is cultivated as a pasture legume for its high protein content and ability to improve soils through nitrogen fixation. Toxic concentrations of the micronutrient Boron (B) in agricultural soils hamper the production of cereal and leguminous crops. In cereals, the genetic analysis of B tolerance has led to the development of molecular selection tools to introgress and maintain the B tolerance trait in breeding lines. There is a comparable need for selection tools in legumes that grow on these toxic soils, often in rotation with cereals. Results: Genetic variation for B tolerance in Medicago truncatula was utilised to generate two F2 populations from crosses between tolerant and intolerant parents. Phenotyping under B stress revealed a close correlation between B tolerance and biomass production and a segregation ratio explained by a single dominant locus. M. truncatula homologues of the Arabidopsis major intrinsic protein (MIP) gene AtNIP5;1 and the efflux-type transporter gene AtBOR1, both known for B transport, were identified and nearby molecular markers screened across F2 lines to verify linkage with the B-tolerant phenotype. Most (95%) of the phenotypic variation could be explained by the SSR markers h2_6e22a and h2_21b19a, which flank a cluster of five predicted MIP genes on chromosome 4. Three CAPS markers (MtBtol-1,-2,-3) were developed to dissect the region further. Expression analysis of the five predicted MIPs indicated that only MtNIP3 was expressed when leaf tissue and roots were assessed. MtNIP3 showed low and equal expression in the roots of tolerant and intolerant lines but a 4-fold higher expression level in the leaves of B-tolerant cultivars. The expression profile correlates closely with the B concentration measured in the leaves and roots of tolerant and intolerant plants. Whereas no significant difference in B concentration exists between roots of tolerant and intolerant plants, the B concentration in the leaves of tolerant plants is less than half that of intolerant plants, which further supports MtNIP3 as the best candidate for the tolerance trait-defining gene in Medicago truncatula. Conclusion: The close linkage of the MtNIP3 locus to B toxicity tolerance provides a source of molecular selection tools to pasture breeding programs. The economical importance of the locus warrants further investigation of the individual members of the MIP gene cluster in other pasture and in grain legumes.Paul Bogacki, David M Peck, Ramakrishnan M Nair, Jake Howie and Klaus H Oldac

Genetic analysis of tolerance to the root lesion nematode Pratylenchus neglectus in the legume Medicago littoralis

BACKGROUND: The nematode Pratylenchus neglectus has a wide host range and is able to feed on the root systems of cereals, oilseeds, grain and pasture legumes. Under the Mediterranean low rainfall environments of Australia, annual Medicago pasture legumes are used in rotation with cereals to fix atmospheric nitrogen and improve soil parameters. Considerable efforts are being made in breeding programs to improve resistance and tolerance to Pratylenchus neglectus in the major crops wheat and barley, which makes it vital to develop appropriate selection tools in medics. RESULTS: A strong source of tolerance to root damage by the root lesion nematode (RLN) Pratylenchus neglectus had previously been identified in line RH-1 (strand medic, M. littoralis). Using RH-1, we have developed a single seed descent (SSD) population of 138 lines by crossing it to the intolerant cultivar Herald. After inoculation, RLN-associated root damage clearly segregated in the population. Genetic analysis was performed by constructing a genetic map using simple sequence repeat (SSR) and gene-based SNP markers. A highly significant quantitative trait locus (QTL), QPnTolMl.1, was identified explaining 49% of the phenotypic variation in the SSD population. All SSRs and gene-based markers in the QTL region were derived from chromosome 1 of the sequenced genome of the closely related species M. truncatula. Gene-based markers were validated in advanced breeding lines derived from the RH-1 parent and also a second RLN tolerance source, RH-2 (M. truncatula ssp. tricycla). Comparative analysis to sequenced legume genomes showed that the physical QTL interval exists as a synteny block in Lotus japonicus, common bean, soybean and chickpea. Furthermore, using the sequenced genome information of M. truncatula, the QTL interval contains 55 genes out of which five are discussed as potential candidate genes responsible for the mapped tolerance. CONCLUSION: The closely linked set of SNP-based PCR markers is directly applicable to select for two different sources of RLN tolerance in breeding programs. Moreover, genome sequence information has allowed proposing candidate genes for further functional analysis and nominates QPnTolMl.1 as a target locus for RLN tolerance in economically important grain legumes, e.g. chickpea.Klaus H Oldach, David M Peck, Ramakrishnan M Nair, Maria Sokolova, John Harris, Paul Bogacki, and Ross Ballar

Rhizoctonia solani AG8: New breakthroughs in control and management

The next generation of control options for Rhizoctonia solani (AG8), the causal agent of Rhizoctonia root rot, is in-furrow liquid injection. The efficacy of banding two new fungicides, Uniform® and EverGol® Prime, was evaluated as an alternative to seed treatments across three years of trials conducted in Western Australia (WA) by DAFWA and in South Australia (SA) by SARDI

Construction and Modelling of an Inducible Positive Feedback Loop Stably Integrated in a Mammalian Cell-Line

Understanding the relationship between topology and dynamics of transcriptional regulatory networks in mammalian cells is essential to elucidate the biology of complex regulatory and signaling pathways. Here, we characterised, via a synthetic biology approach, a transcriptional positive feedback loop (PFL) by generating a clonal population of mammalian cells (CHO) carrying a stable integration of the construct. The PFL network consists of the Tetracycline-controlled transactivator (tTA), whose expression is regulated by a tTA responsive promoter (CMV-TET), thus giving rise to a positive feedback. The same CMV-TET promoter drives also the expression of a destabilised yellow fluorescent protein (d2EYFP), thus the dynamic behaviour can be followed by time-lapse microscopy. The PFL network was compared to an engineered version of the network lacking the positive feedback loop (NOPFL), by expressing the tTA mRNA from a constitutive promoter. Doxycycline was used to repress tTA activation (switch off), and the resulting changes in fluorescence intensity for both the PFL and NOPFL networks were followed for up to 43 h. We observed a striking difference in the dynamics of the PFL and NOPFL networks. Using non-linear dynamical models, able to recapitulate experimental observations, we demonstrated a link between network topology and network dynamics. Namely, transcriptional positive autoregulation can significantly slow down the “switch off” times, as comparared to the nonautoregulatated system. Doxycycline concentration can modulate the response times of the PFL, whereas the NOPFL always switches off with the same dynamics. Moreover, the PFL can exhibit bistability for a range of Doxycycline concentrations. Since the PFL motif is often found in naturally occurring transcriptional and signaling pathways, we believe our work can be instrumental to characterise their behaviour