High performance hybrid functional Petri net simulations of biological pathway models on CUDA

Hybrid functional Petri nets are a wide-spread tool for representing and simulating biological models. Due to their potential of providing virtual drug testing environments, biological simulations have a growing impact on pharmaceutical research. Continuous research advancements in biology and medicine lead to exponentially increasing simulation times, thus raising the demand for performance accelerations by efficient and inexpensive parallel computation solutions. Recent developments in the field of general-purpose computation on graphics processing units (GPGPU) enabled the scientific community to port a variety of compute intensive algorithms onto the graphics processing unit (GPU). This work presents the first scheme for mapping biological hybrid functional Petri net models, which can handle both discrete and continuous entities, onto compute unified device architecture (CUDA) enabled GPUs. GPU accelerated simulations are observed to run up to 18 times faster than sequential implementations. Simulating the cell boundary formation by Delta-Notch signaling on a CUDA enabled GPU results in a speedup of approximately 7x for a model containing 1,600 cells.     

Metal Sorption to Pseudomonas fluorescens: Influence of pH,Ionic Strength and Metal Concentrations

Migration behavior of radionuclides should be understood in order to estimate the impact of high-level radioactive waste (HLW) disposal on the environment. Bacteria, one of the major organic sorbents in solid and aquatic environments, can affect the fate of actinides and lanthanides by sorption onto their cell surfaces. In this study, the sorption of the radionuclide Americium (Am(III)) and several metal ions (Eu(III), Cu(II) and Ca(II)) to Pseudomonas fluorescens were measured under various conditions. It was revealed that as pH decreased, the sorption of Eu(III) and Am(III) increased when the metals were at relatively low concentrations but decreased at higher metal concentrations. On the other hand, sorption of Cu(II) followed the opposite trend. In the case of calcium, an increase in calcium ions was observed due to release from the cells. These findings suggest that the sorption mechanisms for low levels of Eu(III) and Am(III) on the cells of Pseudomonas fluorescens are different from those of Cu(II), Ca(II), and high concentrations of Eu(III) (> 10 ^{? 5} M).     

Enhancement of Coenzyme Q10 Accumulation by Mutation and Effects of Medium Components on the Formation of Coenzyme Q Homologs by Pseudomonas N842 and Mutants

Mutation of Pseudomonas N842 was carried out to increase CoQ₁₀ production. The productivity of CoQ₁₀ was improved considerably by repeated mutation, and the content of CoQ₁₀ per unit cell of the fifth generation mutant was approximately 6 times that of the wild strain, Pseudomonas N842. CoQ₁₁, which was hardly detectable in the wild strain, increased significantly by mutation, and the ratio of CoQ₁₁ to total CoQ exceeded 20% in the fourth generation mutant. Intermittent feeding of glucose to the culture medium during cultivation increased cell yield and CoQ production. When total glucose added was 5 times that of basal medium, cell yield and CoQ formation respectively increased about 3 and 4 times.     

Floral development of petaloid Alismatales as an insight into the origin of the trimerous Bauplan in monocot flowers

Monocots are remarkably homogeneous in sharing a common trimerous pentacyclic floral Bauplan. A major factor affecting monocot evolution is the unique origin of the clade from basal angiosperms. The origin of the floral Bauplan of monocots remains controversial, as no immediate sister groups with similar structure can be identified among basal angiosperms, and there are several possibilities for an ancestral floral structure, including more complex flowers with higher stamen and carpel numbers, or strongly reduced flowers. Additionally, a stable Bauplan is only established beyond the divergence of Alismatales. Here, we observed the floral development of five members of the three ‘petaloid’ Alismatales families Butomaceae, Hydrocharitaceae, and Alismataceae. Outer stamen pairs can be recognized in mature flowers of Alismataceae and Butomaceae. Paired stamens always arise independently, and are either shifted opposite the sepals or close to the petals. The position of stamen pairs is related to the early development of the petals. In Butomaceae, the perianth is not differentiated and the development of the inner tepals is not delayed; the larger inner tepals (petals) only permit the initiation of stamens in antesepalous pairs. Alismataceae has delayed petals and the stamens are shifted close to the petals, leading to an association of stamen pairs with petals in so-called stamen–petal complexes. In the studied Hydrocharitaceae species, which have the monocot floral Bauplan, paired stamens are replaced by larger single stamens and the petals are not delayed. These results indicate that the origin of the floral Bauplan, at least in petaloid Alismatales, is closely linked to the position of stamen pairs and the rate of petal development. Although the petaloid Alismatales are not immediately at the base of monocot divergence, the floral evolution inferred from the results should be a key to elucidate the origin of the floral Bauplan of monocots.     

Postnatal Development of Noradrenaline and 3-Methoxy-4-Hydroxyphenylethyleneglycol Sulphate Levels in Rat Brain Regions

Abstract: Developmental changes in brain levels of noradrenaline (NA) and 3-methoxy-4-hydroxyphenylethyleneglycolsulphate (MHPG-SO₄) were studied in rats. In most brain regions, MHPG-SO₄ level rapidly increased to approach or exceed adult levels at the time of weaning, while NA levels increased more gradually and reached adult levels following weaning, Pharmacological studies showed that the MHPG-SO₄ level in the neonatal brain reflects the degradation of released NA. The developmental characteristics of noradrenergic neurons in eight discrete brain regions are discussed.     

Morphological and functional changes in the tight junctions of the bile canaliculi induced by bile duct ligation

Summary Thin sections after bile duct ligation showed that the depth of tight junctions appeared to increase and that the distance between individual punctate contacts appeared to become irregular and wider than in controls. The freeze fracture replicas clearly demonstrated these changes in the tight junction morphology. Changes were noted most conspicuously in the tight junction three weeks after ligation. Measurements of the junctional morphology in control and ligated specimens showed that the junctional depth had increased two fold in the latter, whereas the number of strands had scarcely changed. Lanthanum tracer experiments showed that the tight junctions did not permit the passage of the tracer in normal nor ligated rats. It was concluded that the mechanism of obstructive jaundice could not be related to changes in junctional morphology causing increased junctional permeability.Tight junction depth in this paper is synonymously used with Tight junction width or Tight junction thickness     

Physiological and biochemical markers of alveolar epithelial barrier dysfunction in perfused human lungs

To study air space fluid clearance (AFC) under conditions that resemble the clinical setting of pulmonary edema in patients, we developed a new perfused human lung preparation. We measured AFC in 20 human lungs rejected for transplantation and determined the contribution of AFC to lung fluid balance. AFC was then compared with air space and perfusate levels of a biological marker of epithelial injury. The majority of human lungs rejected for transplant had intact basal (75%) and beta(2)-adrenergic agonist-stimulated (70%) AFC. For lungs with both basal and stimulated AFC, the basal AFC rate was 19 +/- 10%/h, and the beta(2)-adrenergic-stimulated AFC rate was 43 +/- 13%/h. Higher rates of AFC were associated with less lung weight gain (Pearson coefficient -0.90, P < 0.0001). Air space and perfusate levels of the type I pneumocyte marker receptor for advanced glycation end products (RAGE) were threefold and sixfold higher, respectively, in lungs without basal AFC compared with lungs with AFC (P < 0.05). These data show that preserved AFC is a critical determinant of favorable lung fluid balance in the perfused human lung, raising the possibility that beta(2)-agonist therapy to increase edema fluid clearance may be of value for patients with acute lung injury and pulmonary edema. Also, although additional studies are needed, a biological marker of alveolar epithelial injury may be useful clinically in predicting preserved AFC.     

What affects the desiccation tolerance threshold of Brazilian Eugenia (Myrtaceae) seeds?

Desiccation sensitive (DS) seeds are shed at high water contents (WC) and metabolically active, but WC thresholds vary broadly among species even in the same genus. Eugenia is an important ecological genus that has high occurrence in several Brazilian morphoclimatic domains. In this study, we assessed seed desiccation tolerance of five Eugenia species collected in specific meteorological conditions. We reported the species geographical ranges and verified the rainfall and temperature of species sites in the year prior to seed collection. We also assessed initial WC, seed germination and vigor and seedling growth upon desiccation. Eugenia uniflora was the widest spread among the five species, while E. astringens was the most restricted. In this specific study, widespread species showed a higher WC threshold than restricted species. In the same way, the WC of fresh seeds was not correlated to the desiccation tolerance threshold. Seed desiccation tolerance was species dependent and correlated with the environmental status of seed collection sites. Wetter and warmer conditions were correlated to the E. uniflora higher DS threshold. Low rainfall and temperature corresponded to a lower desiccation sensitivity of E. astringens seeds. Seeds of the five species lost half viability between 0.44 and 0.25 g H₂O g DW^??1 and after 65–270 h of desiccation. Our results indicate that abiotic factors impact plant populations during the seed production season and can drive seed desiccation tolerance threshold and physiological behavior. These results should be taken into account in ex-situ plant conservation programs and tropical species management.