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.     

Fast and easy detection of mouse sex chimeras using electrophoretic polymorphism of phosphoglycerate kinase-1, an X chromosome-linked enzyme

About half of the chimeras produced by aggregation of two mouse embryos are sex chimeras composed of both XX and XY cells. We developed a fast and easy method to identify sex chimeras by using electrophoretic bimorphism of an X-linked enzyme, phosphoglycerate kinase-1 (PGK-1), as a marker. When embryos resulting from the crossing of a Pgk-1b/Pgk-1b female and a Pgk-1a/Y male are aggregated, the genotype of sex chimeras is Pgk-1b/Pgk-1a----Pgk-1b/Y. Most of these were identifiable from the PGK-1 electrophoretic pattern of blood cells (i.e., AB type) and the appearance of genitalia (male type or apparently abnormal). Genotypes of functional sperm in the testes of the male-type sex chimeras were also identifiable from the PGK-1 electrophoretic pattern of progenies. Examination of gonads of the sex chimeras revealed that a considerable proportion was hermaphorditic. With this method, reasonable numbers of male-type sex chimeras and hermaphrodites may be selected and used as material for investigating sexual differentiation.     

猪-C反应蛋白的分离纯化及其性质的研究

以猪血清为材料,通过磷酸乙醇胺—琼脂糖亲和层析,Sepharose 4B柱层析和Sephacryl—S300凝胶过滤,获得了猪C—反应蛋白的结晶。猪C—反应蛋白可与肺炎球菌壁C多糖发生特异的沉淀反应,这种结合是依赖钙离子的。EDTA和一些磷脂代谢产物如磷酸胆碱,磷酸乙醇胺等,能抑制猪C—反应蛋白与C多糖的结合。在SDS—聚丙烯酰胺凝胶电泳及梯度聚丙烯酰胺凝胶电泳中,猪C—反应蛋白表现出与人C—反应蛋白相同的行为,亚基是一条分子量为23.5kD的肽链,全分子的表观分子量为150kD。猪C—反应蛋白与兔抗人C—反应的蛋白的抗血清能发生免疫交叉反应。     

Bacterioplankton interactions with Daphnia and algae in experimental enclosures

Development of bacterioplankton was studied by manipulation of planktivorous fish and/or nutrients in experimental enclosures in a fish pond. Grazing pressure exerted by large zooplankton (Daphnia galeata and Daphnia pulicaria) strongly influenced the counts and size distribution of bacterial populations. Morphometric analyses by scanning electron microscope revealed a shift in size distribution from larger mainly rod-type bacteria under low grazing pressure towards smaller mainly coccus-type under strong grazing pressure. The metabolic activity of bacteria measured as glucose uptake was higher under strong grazing pressure. After removal of large daphnids, the increase in bacterial density was probably the result of two additive factors: low grazing pressure and high level of dissolved organic matter (DOM) due to photosynthetic activity of more abundant algae. Composition of bacterial populations shifted toward larger, rod-type bacteria, and their metabolic efficiency measured by uptake, was lowered. The basic dimensionality of the system and interactions between variables was describe by R-mode factor analysis. The manipulated enclosures were relate with factor score.     

Conformation and structure of 2-amino-8-(β-d-ribofuranosyl)imidazo [1,2-a]-s-triazin-4-one (5-aza-7-deaza guanosine), a potent antiviral nucleoside

The crystal and molecular structure of one imidazo[1,2-a]-s-triazine nucleoside and its antiviral activity are described. The crystal structure of 2-amino-8-(β-d-ribofuranosyl)imidazo-[1,2-a]-s-triazin-4-one monohydrate (C₁₀H₁₃N₅O₅·H₂O) was solved by X-ray counter data. The compound crystallizes in the monoclinic space group P2₁ with cell dimensions a = 7.353 (1), b = 6.465 (1), c = 13.701 (1) Å, β = 104.64 (1)°. The structure was solved by direct methods and refined by full matrix least-squares technique to a final value of the conventional R-factor of 0.049 using 1998 observed intensities. The orientation of the base relative to the sugar ring defined in terms of rotation about the C(1′)-N(8) glycosyl bond is anti (47.8°). The ribose moiety exhibits C(2′)-endo, ²E conformation. The conformation around C(4′)-C(5′) is gauche^?. Molecular packing is dominated by hydrogen bonds. Base stacking occurs long the b axis. 5-Aza-7-deazaguanosine has shown a marked antiviral activity in vitro against herpes simplex virus despite the fact that N(3) is effective as the hydrogen acceptor only.     

N-Acetylcysteine ameliorates lipopolysaccharide-induced organ damage in conscious rats

Lipopolysaccharide is strongly associated with septic shock, leading to multiple organ failure. It can activate monocytes and macrophages to release proinflammatory mediators such as tumor necrosis factor- (TNF-), interleukin-1 (IL-1), and nitric oxide (NO). The present experiments were designed to induce endotoxin shock by an intravenous injection ofKlebsiella pneumoniae lipopolysaccharide (LPS, 10 mg/kg) in conscious rats. Arterial pressure and heart rate (HR) were continuously monitored for 48 h after LPS administration. N-Acetyl-cysteine was used to study its effects on organ damage. Biochemical substances were measured to reflect organ functions. Biochemical factors included blood urea nitrogen (BUN), creatinine (Cre), lactic dehydrogenase (LDH), creatine phosphokinase (CPK), aspartate transferase (GOT), alanine transferase (GPT), TNF-, IL-1, methyl guanidine (MG), and nitrites/nitrates. LPS caused significant increases in blood BUN, Cre, LDH, CPK, GOT, GPT, TNF-, IL-1, MG levels, and HR, as well as a decrease in mean arterial pressure and an elevation of nitrites/nitrates. N-Acetylcysteine suppressed the release of TNF-, IL-1, and MG, but enhanced NO production. These actions ameliorate LPS-induced organ damage in conscious rats. The beneficial effects may suggest a potential chemopreventive effect of this compound in sepsis prevention and treatment.     

新生大鼠辣椒素处理后脊髓内阿片受体的变化

本实验用受体放射自显影方法,研究了新生大鼠辣椒素皮下注射,成年后脊髓内３Ｈ－埃托菲（３Ｈ－ｅｔｏｒｐｈｉｎｅ）结合位点数的变化。发现新生鼠辣椒素处理可以引起脊髓后角浅层及中央管周围’Ｈ－ｅｔｏｒｐｈｉｎｅ结合位点明显减,其中Ⅰ、Ⅱ层自显影银粒数减少３６％左右。Ⅲ层减少２０％,中央管周围减少１１％。而前角及背外测束３Ｈ－ｅｔｏｒｐｈｉｎｅ结合位点数无显著性差异。结果表明脊髓内初级感觉传入细纤维上有阿片受体分布。本研究为探明阿片类物质在脊髓水平的痛觉调控机制提供一定的形态学依据。