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.     

Chromosome-level genome assembly and characterization of Sophora Japonica

Sophora japonica is a medium-size deciduous tree belonging to Leguminosae family and famous for its high ecological, economic and medicinal value. Here, we reveal a draft genome of S. japonica, which was ∼511.49 Mb long (contig N50 size of 17.34 Mb) based on Illumina, Nanopore and Hi-C data. We reliably assembled 110 contigs into 14 chromosomes, representing 91.62% of the total genome, with an improved N50 size of 31.32 Mb based on Hi-C data. Further investigation identified 271.76 Mb (53.13%) of repetitive sequences and 31,000 protein-coding genes, of which 30,721 (99.1%) were functionally annotated. Phylogenetic analysis indicates that S. japonica separated from Arabidopsis thaliana and Glycine max ∼107.53 and 61.24 million years ago, respectively. We detected evidence of species-specific and common-legume whole-genome duplication events in S. japonica. We further found that multiple TF families (e.g. BBX and PAL) have expanded in S. japonica, which might have led to its enhanced tolerance to abiotic stress. In addition, S. japonica harbours more genes involved in the lignin and cellulose biosynthesis pathways than the other two species. Finally, population genomic analyses revealed no obvious differentiation among geographical groups and the effective population size continuously declined since 2 Ma. Our genomic data provide a powerful comparative framework to study the adaptation, evolution and active ingredients biosynthesis in S. japonica. More importantly, our high-quality S. japonica genome is important for elucidating the biosynthesis of its main bioactive components, and improving its production and/or processing.