Simulation methods with extended stability for stiff biochemical Kinetics

Background  

With increasing computer power, simulating the dynamics of complex systems in chemistry and biology is becoming increasingly routine. The modelling of individual reactions in (bio)chemical systems involves a large number of random events that can be simulated by the stochastic simulation algorithm (SSA). The key quantity is the step size, or waiting time, τ, whose value inversely depends on the size of the propensities of the different channel reactions and which needs to be re-evaluated after every firing event. Such a discrete event simulation may be extremely expensive, in particular for stiff systems where τ can be very short due to the fast kinetics of some of the channel reactions. Several alternative methods have been put forward to increase the integration step size. The so-called τ-leap approach takes a larger step size by allowing all the reactions to fire, from a Poisson or Binomial distribution, within that step. Although the expected value for the different species in the reactive system is maintained with respect to more precise methods, the variance at steady state can suffer from large errors as τ grows.     

Typing of Genetic Markers Involved in Stress Response by Fluorescent cDNA-Amplified Fragment Length Polymorphism Technique

Identification of genetic markers involved in stress response to physical factors or chemical substances in organisms is a challenging task. Typing of upregulated gene expression due to selective antibacterial pressure is a promising approach in the search of molecular mechanisms responsible for development of resistance. cDNA-Fluorescent Amplified Fragment Length Polymorphism (cDNA-FAFLP) strategy was developed and applied in the search of antimycotic drug resistance marker(s) in medically important fungi as an alternative method to microarray analysis. We compared differential gene expression of two sensitive Candida albicans reference strains (ATCC 10231 and ATCC 60133) and two of their paired resistant to fluconazole and itraconazole mutants. Resistant mutants Candida albicans FLC-R, resistant to fluconazole (MIC > 128 μg/ml) and Candida albicans ICZ-R, resistant to itraconazole (MIC > 4 μg/ml) were obtained in subcultures with gradual increase of the antifungal in the culture medium. cDNA-AFLP profile in both itraconazole resistant mutants showed specific spectrophotometric peaks with 5–6-fold RNA overexpression product of 500 bp length compared to the sensitive strains. Fluconazole mutants do not reveal RNA level changes under tested by us typing conditions. These results indicate that the cDNA-FAFLP strategy is a relatively rapid, simple, and reliable method for simultaneous typing of both constitutive and induced differences in expression of host genes providing insight into the biological processes involved in response to drugs in bacteria and fungi. Moreover, this methodology could be tested for typing of the genome response of any organism to physical or chemical stress factors.     

Predicted impact of exotic vines on an endangered ecological community under future climate change

Potential interactions between climate change and exotic plant invasions may affect areas of high conservation value, such as land set aside for the protection of endangered species or ecological communities. We investigated this issue in eastern Australia using species distribution models for five exotic vines under climate regimes for 2020 and 2050. We examined how projected changes in the distribution of climatically suitable habitat may coincide with the remaining remnants of an endangered ecological community—littoral rainforests—in this region. The number of known infestations of each weed in tropical, subtropical and temperate areas was used to assess the likelihood of further expansion into areas projected to provide suitable habitat under future conditions. Littoral rainforest reserves were consistently predicted to provide bioclimatically suitable habitat for the five vines examined under both current and future climate scenarios. We explore the consequences and potential strategies for managing exotic plant invasions in these protected areas in the coming decades.     

Temporal and spatial differences in the emission of calls by pipistrelle bats<Emphasis Type="Italic">Pipistrellus pipistrellus</Emphasis> and<Emphasis Type="Italic">P. pygmaeus</Emphasis>

The number of orientation, feeding and social calls emitted by pipistrelle batsPipistrellus pipistrellus Schreber, 1774 andP. pygmaeus Leach, 1825 was recorded throughout the night at eight different sites. Social calls were unaffected by weather variables, whereas orientation calls and feeding buzzes were both significantly affected by cloud and temperature conditions. The number of emissions of each call type was significantly different between sites, indicating that the bats used different sites for different activities. Significant positive correlations between all three combinations of call types occurred only during the middle of the night, corresponding with the nadir of flying insects. This suggests that bats were engaged in activities other than feeding at this time, such as territory protection or mate attraction.     

FURTHER OBSERVATIONS ON JUVENILE AND ADULT HEDERA

Robbins , William J. (The New York Botanical Garden, New York, N. Y.) Further observations on juvenile and adult Hedera. Amer. Jour. Bot. 47(6) : 485–491. Illus. 1960.—Plants of arborescent Hedera helix sprayed with gibberellic acid produced juvenile shoots. Juvenile characters appeared in December to March from applications of gibberellic acid made from May to July. Gibberellic acid modified inflorescences toward a vegetative condition. Previous reports that seeds of arborescent Hedera helix produce juvenile plants were confirmed. Seedlings of a variant, Hedera helix ‘238th Street,‘ which has adult-shaped leaves on a vine type of growth produced vines with lobed leaves. Heavy pruning of arborescent Hedera helix caused the production of juvenile shoots.     

EFFECTS OF X IRRADIATION ON LEMNA PERPUSILLA

Posner , Herbert B., and William S. Hillman . (Yale U., New Haven, Conn.) Effects of x irradiation on Lemna perpusilla. Amer. Jour. Bot. 47(6): 506–511. Illus. 1960.—The effects of x rays on the multiplication rates (MR), percent flowering (Fl%) and gross morphology of aseptically grown cultures of Lemna perpusilla, strain 6746, were studied. MR values are unaffected by doses of less than 300 r but are progressively depressed as the dose increases. The effect of a given dose on short-term MR values is the same at the 2 dosage intensities used, 500 and 2000 r/min. The inhibitory effect of intermediate doses on long-term growth is delayed; high doses have an “immediate” effect. Bleaching of fronds and cessation of growth occur in all cultures given 5,000 r or higher. Radiosensitivity is not altered by addition of yeast extract and casein hydrolysate to the medium. Depressed Fl% and seed production appear to be consequences of lowered MR. Morphological aberrations such as small size, epinasty and wrinkling are temporary. Frond-sequence may be altered by x rays but this aberration is permanent. Various aspects of the results are discussed.