Modelling effects of prolonged conditioning on dormancy and germination of Striga hermonthica

The impact of environment on the germination biology of the parasite was studied in the laboratory with seeds conditioned at various water potentials, urea concentrations and at 17.5 to 37.5°C for up to 133 days. Maximum germination was observed at 20 to 25°C. Water stress and urea suppressed maximum germination. The final percentage germination response to period of conditioning showed a non-linear relationship and suggests the release of seeds from dormancy during the initial period and later on dormancy induction. Germination percentage increased with increase in conditioning period to a threshold and remained stable for variable periods followed by a decline with further extension of conditioning time. The decline in germination finally terminated in zero germination in most treatments before the end of experimentation. The investigated factors of temperature, water potential and urea showed clear effects on the expression of dormancy pattern of the parasite. The effects of water potential and urea were viewed as modifying a primary response of seeds to temperature during conditioning. The changes in germinability potential during conditioning were consistent with the hypothesis that dormancy periods are normally distributed within seed populations and that loss of primary dormancy precedes induction of secondary dormancy. Hence an additive mathematical model of loss of primary dormancy and induction of secondary as affected by environment was developed as: G = {[Φ-1 (Kp+ (po+pnN+pwW) (T-Tb) t)]-[Φ-1 (Ks+ ((swW+sa)+sorT)t)]}[Φ-1(aT2+bT+c+cwW)].

Immersive Projection for biochemical pattern matching

In all biological processes, protein molecules and other small molecules interact to function and form transient macromolecular complexes. This interaction of two or more molecules can be described by a docking event. Docking is an important phase for structure-based drug design strategies, as it can be used as a method to simulate protein-ligand interactions. Various docking programs exist that allow automated docking, but most of them have limited visualization and user interaction. It would be advantageous if scientists could visualize the molecules participating in the docking process, manipulate their structures and manually dock them before submitting the new conformations to an automated docking process in an immersive environment, which can help stimulate the design/docking process. This also could greatly reduce docking time and resources. To achieve this, we propose a new virtual modelling/docking program, whereby the advantages of virtual modelling programs and the efficiency of the algorithms in existing docking programs will be merged.

Influence of sodium chloride on seed germination and seedling root growth of cotton (Gossypium hirsutum L.)

Response of cotton (Gossypium hirsutum L. cv. NIAB-78) to salinity, in terms of seed germination, seedling root growth and root Na+ and K+ content was determined in a laboratory experiment. Cotton seeds were exposed to increasing salinity levels using germination water with Sodium chloride concentrations of 0, 50, 100, 150 and 200 mM, to provide different degrees of salt stress. Germinated seeds were counted and roots were harvested at 24, 48, 72 and 96 h after the start of the experiment. It appeared that seed germination was only slightly affected by an increase in salinity (in most cases the differences between treatment were non-significant), whereas root length, root growth rate, root fresh and dry weights were severely affected, generally highly significant differences in these variables were found for comparisons involving most combinations of salinity levels, in particular with increased incubation period. K+ contents decreased with increasing salinity levels, although differences in K+ content were only significant when comparing the control and the 4 salinity levels. Na+ content of the roots increased with increasing levels of NaCl in the germination water, suggesting an exchange of K+ for Na+. The ratio K+/Na+ strongly decreased with rising levels of salinity from around 4.5 for the control to similar to 1 at 200 mM NaCl.

Illustration of micro-scale advection using grid-pattern mini-lysimeters

Twenty-five small soil-filled perspex boxes arranged in a square, with dwarf sunflowers growing in them, were used to study micro-scale advection. Hydrological heterogeneity was introduced by applying two different amounts of irrigation water (low-irrigation, L, versus high-irrigation, H). The nine central boxes (4 H, 4 L and I bare box) were precision weighing lysimeters, yielding diurnal measurements of evaporation. After the onset of soil water stress, a large difference in latent heat flux (up to 4-fold) was observed between the lysimeters of the H and L treatments, mainly caused by large differences between H and L stomatal conductance values. This resulted in micro-advection, causing H soil-sunflower systems to evaporate well above equilibrium latent heat flux. The occurrence of micro-advective enhancement was reflected in large values of the Priestley-Taylor constant (often larger than 2.0) and generally negative values of sensible heat flux for the H treatment. (c) 2005 Elsevier B.V. All rights reserved.

Amygdala and ventromedial prefrontal cortex are inversely coupled during regulation of negative affect and predict the diurnal pattern of cortisol secretion among older adults

Among younger adults, the ability to willfully regulate negative affect, enabling effective responses to stressful experiences, engages regions of prefrontal cortex (PFC) and the amygdala. Because regions of PFC and the amygdala are known to influence the hypothalamic-pituitary-adrenal axis, here we test whether PFC and amygdala responses during emotion regulation predict the diurnal pattern of salivary cortisol secretion. We also test whether PFC and amygdala regions are engaged during emotion regulation in older (62- to 64-year-old) rather than younger individuals. We measured brain activity using functional magnetic resonance imaging as participants regulated (increased or decreased) their affective responses or attended to negative picture stimuli. We also collected saliva samples for 1 week at home for cortisol assay. Consistent with previous work in younger samples, increasing negative affect resulted in ventral lateral, dorsolateral, and dorsomedial regions of PFC and amygdala activation. In contrast to previous work, decreasing negative affect did not produce the predicted robust pattern of higher PFC and lower amygdala activation. Individuals demonstrating the predicted effect (decrease s attend in the amygdala), however, exhibited higher signal in ventromedial prefrontal cortex (VMPFC) for the same contrast. Furthermore, participants displaying higher VMPFC and lower amygdala signal when decreasing compared with the attention control condition evidenced steeper, more normative declines in cortisol over the course of the day. Individual differences yielded the predicted link between brain function while reducing negative affect in the laboratory and diurnal regulation of endocrine activity in the home environment.

A pattern language for goals

Previous work has established the value of goal-oriented approaches to requirements engineering. Achieving clarity and agreement about stakeholders’ goals and assumptions is critical for building successful software systems and managing their subsequent evolution. In general, this decision-making process requires stakeholders to understand the implications of decisions outside the domains of their own expertise. Hence it is important to support goal negotiation and decision making with description languages that are both precise and expressive, yet easy to grasp. This paper presents work in progress to develop a pattern language for describing goal refinement graphs. The language has a simple graphical notation, which is supported by a prototype editor tool, and a symbolic notation based on modal logic.

Discriminative pattern mining in software fault detection

We present a method to enhance fault localization for software systems based on a frequent pattern mining algorithm. Our method is based on a large set of test cases for a given set of programs in which faults can be detected. The test executions are recorded as function call trees. Based on test oracles the tests can be classified into successful and failing tests. A frequent pattern mining algorithm is used to identify frequent subtrees in successful and failing test executions. This information is used to rank functions according to their likelihood of containing a fault. The ranking suggests an order in which to examine the functions during fault analysis. We validate our approach experimentally using a subset of Siemens benchmark programs.

Syk-Dependent Cytokine Induction by Dectin-1 Reveals a Novel Pattern Recognition Pathway for C Type Lectins

Pattern-recognition receptors (PRRs) detect molecular signatures of microbes and initiate immune responses to infection. Prototypical PRRs such as Toll-like receptors (TLRs) signal via a conserved pathway to induce innate response genes. In contrast, the signaling pathways engaged by other classes of putative PRRs remain ill defined. Here, we demonstrate that the β-glucan receptor Dectin-1, a yeast binding C type lectin known to synergize with TLR2 to induce TNFα and IL-12, can also promote synthesis of IL-2 and IL-10 through phosphorylation of the membrane proximal tyrosine in the cytoplasmic domain and recruitment of Syk kinase. syk−/− dendritic cells (DCs) do not make IL-10 or IL-2 upon yeast stimulation but produce IL-12, indicating that the Dectin-1/Syk and Dectin-1/TLR2 pathways can operate independently. These results identify a novel signaling pathway involved in pattern recognition by C type lectins and suggest a potential role for Syk kinase in regulation of innate immunity.

Effects of prolonged conditioning on dormancy and germination of Striga hermonthica

The impact of environment on the germination biology of Striga hermonthica was studied in the laboratory by conditioning seeds at various water potentials and urea concentrations at 17.5 to 37.5°C for up to 133 days. The experimental results presented in this research are related to the effects of temperature, water potential and urea nitrogen concentration during conditioning on subsequent germination percentage of S. hermonthica. Maximum germination in S. hermonthica seeds was observed at conditioning temperatures of 20 to 25°C within the range investigated of 17.5 to 37.5°C. Water stress and also urea during conditioning suppressed maximum germination. However, the conditioning temperature ranges at which maximum germination percentages occur vary with water stress and also urea concentration. In the presence of a high concentration of urea (3.16 mM), temperatures required for maximum germination narrowed to between 17.5 to 20°C. The optimum period of conditioning decreased with increase in water stress and also urea concentration similar to previous reports. The implications of these findings on Striga hermonthica field infestations have been investigated and being reported in another paper. Germination was greatly suppressed by conditioning environments including 3.16 mM urea and at 37.5°C. At the high concentration of 3.16 mM, temperatures required for maximum germination narrowed to between 17.5 and 20°C. Optimum conditioning period decreased with water stress and with increase in urea concentration.

Seed dormancy and germination of Ficus lundellii and tropical forest restoration

We investigated seed dormancy and germination in Ficus lundellii Standl. (Moraceae), a native species of Mexico's Los Tuxtlas tropical rain forest. In an 8-h photoperiod at an alternating diurnal (16/8 h) temperature of 20/30 degrees C, germination was essentially complete (96%) within 28 days, whereas in darkness, all seeds remained dormant. Neither potassium nitrate (0.05-0.2%) applied continuously nor gibberellic acid applied either continuously (10-200 ppm) or as a 24 hour pretreatment (2000 ppm) induced germination in the dark. Germination in the light was not reduced by a 24-h hydrochloric acid (0.1-1%) pretreatment, but it was reduced both by a 24-h pretreatment with either H2O2 (0. 1-5 M) or 5% HCl, or by more than 5 days of storage at 40 degrees C (4.5% seed water content). In a study with a 2-dimensional temperature gradient plate, seeds germinated fully and rapidly in the light at a constant temperature of 30 degrees C, and fully but less rapidly in the light at alternating temperatures with low amplitudes (< 12 degrees C) about the optimal constant temperature. The base, optimal and ceiling temperatures for rate of germination were estimated as 13.8, 30.1 and 41.1 degrees C, respectively. In all temperature regimes, light was essential for the germination of F lundellii seeds.

Effects of desiccation on seed germination, cracking, fungal infection and survival in storage of Sterculia foetida L

Seeds of Sterculia foetida were tested for germination following desiccation and subsequent hermetic storage. Whereas seeds at 10.3% moisture content were intact and provided 98% germination, further desiccation reduced germination substantially. The majority of seed coats had cracked after desiccation to 5.1% moisture content. Ability to germinate was not reduced after 12 months' hermetic storage at 10.3% and 7.3% moisture content at 15 degrees C or -18 degrees C, but was reduced considerably at 5.1%. Fungal infection was detected consistently for cracked seeds in germination tests and they did not germinate. However, almost all embryos extracted from cracked seeds germinated if first disinfected with sodium hypochlorite (1%, 5 minutes). In addition. 80 -100% of disinfected extracted embryos from cracked seeds stored hermetically for 28 d at -18 degrees C or -82 degrees C with 3.3% to 6.0% moisture content, and excised embryos stored in this way, were able to germinate. Hence. failure of the very dry seeds of Sterculia foetida to germinate was not due to embryo death from desiccation but to cracking increasing susceptibility to fungal infection upon rehydration. Cracking was associated negatively and strongly with relative humidity and appears to be a mechanical consequence of substantial differences between the isotherms of whole seeds compared with cotyledons and axes.