An approach to multiscale modelling with graph grammars

Background and Aims

Functional–structural plant models (FSPMs) simulate biological processes at different spatial scales. Methods exist for multiscale data representation and modification, but the advantages of using multiple scales in the dynamic aspects of FSPMs remain unclear. Results from multiscale models in various other areas of science that share fundamental modelling issues with FSPMs suggest that potential advantages do exist, and this study therefore aims to introduce an approach to multiscale modelling in FSPMs.

Methods

A three-part graph data structure and grammar is revisited, and presented with a conceptual framework for multiscale modelling. The framework is used for identifying roles, categorizing and describing scale-to-scale interactions, thus allowing alternative approaches to model development as opposed to correlation-based modelling at a single scale. Reverse information flow (from macro- to micro-scale) is catered for in the framework. The methods are implemented within the programming language XL.

Key Results

Three example models are implemented using the proposed multiscale graph model and framework. The first illustrates the fundamental usage of the graph data structure and grammar, the second uses probabilistic modelling for organs at the fine scale in order to derive crown growth, and the third combines multiscale plant topology with ozone trends and metabolic network simulations in order to model juvenile beech stands under exposure to a toxic trace gas.

Conclusions

The graph data structure supports data representation and grammar operations at multiple scales. The results demonstrate that multiscale modelling is a viable method in FSPM and an alternative to correlation-based modelling. Advantages and disadvantages of multiscale modelling are illustrated by comparisons with single-scale implementations, leading to motivations for further research in sensitivity analysis and run-time efficiency for these models.     

Critical evaluation of random mutagenesis by error-prone polymerase chain reaction protocols, Escherichia coli mutator strain, and hydroxylamine treatment

Random mutagenesis methods constitute a valuable protein modification toolbox with applications ranging from protein engineering to directed protein evolution studies. Although a variety of techniques are currently available, the field is lacking studies that would directly compare the performance parameters and operational range of different methods. In this study, we have scrutinized several of the most commonly used random mutagenesis techniques by critically evaluating popular error-prone polymerase chain reaction (PCR) protocols as well as hydroxylamine and a mutator Escherichia coli strain mutagenesis methods. Relative mutation frequencies were analyzed using a reporter plasmid that allowed direct comparison of the methods. Error-prone PCR methods yielded the highest mutation rates and the widest operational ranges, whereas the chemical and biological methods generated a low level of mutations and exhibited a narrow range of operation. The repertoire of transitions versus transversions varied among the methods, suggesting the use of a combination of methods for high-diversity full-scale mutagenesis. Using the parameters defined in this study, the evaluated mutagenesis methods can be used for controlled mutagenesis, where the intended average frequency of induced mutations can be adjusted to a desirable level.     

Effect of double-strand break DNA sequence on the PARP-1 NHEJ pathway

Efficient repair of DNA double-strand breaks (DSBs) is critical for the maintenance of genomic integrity. In mammalian cells, DSBs are preferentially repaired by non-homologous end-joining (NHEJ). We have previously described a new DSBs microhomology end-joining pathway depending on PARP-1 and the XRCC1/DNA ligase III complex. In this study we analysed, with recombinant proteins and protein extracts, the effect of DSB end sequences: (i) on the DSB synapsis activity; (ii) on the end-joining activity. We report that PARP-1 DSB synapsis activity is independent of the DSB sequence and could be detected with non-complementary DSBs. We demonstrate also that the efficiency of DSBs repair by PARP-1 NHEJ is strongly dependent on the presence of G:C base pairs at microhomology termini. These results highlight a new role of the PARP-1 protein on the synapsis of DSBs and could explain why the PARP-1 NHEJ pathway is strongly dependent on the DSBs microhomology sequence.     

Interference of bovine herpesvirus 1 (BHV-1) in sorbitol-Induced apoptosis

In order to determine the ability of bovine herpesvirus type 1 (BHV-1) to suppress apoptosis, we examined the effects of BHV-1 infection on sorbitol-induced apoptosis on Madin-Darby bovine kidney (MDBK) cells. BHV-1 suppresses sorbitol-induced apoptosis in a manner similar to that of herpes simplex virus type 1 (HSV-1), indicating that BHV-1 has one or more anti-apoptotic genes. To elucidate the molecular mechanisms of apoptosis, expression of some genes encoding apoptosis-inhibiting and -promoting factors were analyzed on BHV-1 infected cells during the process of sorbitol-induced apoptosis. Our results revealed that the expression of bcl-2 and bcl-x(L) decreased after 5 and 3 h p.i., respectively; while bax and procaspase-3 expression increased with respect to control as a function of p.i. times and at 7 h p.i. they were not observed. We further show that the expression of p53 gene was also enhanced, suggesting that this apoptotic mechanism is p53 dependent. From these results, we propose that BHV-1 has one or more genes encoding apoptosis-inhibiting factors which interfere with the involvement of bcl-2 gene family members and apoptotic pathway, depending upon caspase-3, triggered by sorbitol.     

Whole-genome analysis of structural variations between Xiang pigs with larger litter sizes and those with smaller litter sizes

To gain a better knowledge of structural variations (SVs) in Xiang pig, we used next-generation sequencing to analyze the Xiang pigs with larger (XL) or smaller litter sizes (XS). Our analysis yielded 28,040 putative SVs in the Xiang pig. These SVs distributed throughout all of chromosomes. Some functional regions including exons and untranslated regions were less varied than introns and intergenic regions. We detected 4637 and 4119 specific SVs, which contained 1697 and 1582 genes in XL and XS group, respectively. These genes were mainly enriched in the well-known pathways involved in development and reproduction processes. Population validation was carried out on 50 SVs candidates using PCR method in 144 Xiang pig crowds. All of 50 SVs were confirmed by PCR method and 14 SVs were associated with the litter size of Xiang pigs. These results may be helpful for the elucidation of growth and reproduction regulation in Xiang pig.     

Plasmodium yoelii: influence of antimalarial treatment on acquisition of immunity in BALB/c and DBA/2 mice

The effect of antimalarial drugs on immune responses to the malaria infection is evaluated in vivo using two experimental self-cured rodent models. BALB/c and DBA/2 mice were infected by Plasmodium yoelii 17XNL and 17XL strains, respectively, and then treated with different doses of antimalarial drugs: chloroquine (228mg/kg or 114mg/kg of the body weight) or artesunate (78mg/kg or 39mg/kg). The effect of antimalarial drugs on host immune responses was evaluated by parasitemia, splenocyte IFN-gamma production level, and parasite-specific IgG level in the serum, however, no significant differences were observed between drug-treated and untreated groups. Moreover, most of the infected mice of all groups showed the ability to resist homologous reinfection (challenged on day 60 post-infection), only a few mice experienced transient, low parasitemia. The rechallenged mice were accompanied by high level of parasite-specific IgG. Therefore, this research implicated that, for BALB/c and DBA/2 mice, chloroquine or artesunate treatment of blood-stage P. yoelii infections does not compromise acquired immunity to malaria in either primary infection or upon rechallenge.     

miR-184通过抑制EPB41L5调控大鼠肾癌细胞增殖及迁移

为了探讨miR-184对肾癌细胞的影响及机制,本研究选取肾癌细胞株786-0细胞,随机分为对照组、空白转染组和miR-184转染组,其中miR-184转染组转染miR-184 mimic,空白转染组转染空白mimic,采用CCK-8细胞增殖实验检测各组细胞增殖,流式细胞仪检测各组细胞凋亡,划痕实验检测各组细胞迁移,Western blotting检测各组EPB41L5蛋白表达。研究结果表明miR-184转染组培养48 h和培养72 h时OD值分别为(0.964±0.103)和(1.011±0.121),明显低于对照组和空白转染组(p<0.05);miR-184转染组培养72 h后细胞凋亡率为(18.22±2.26)%,明显高于对照组和空白转染组(p<0.05);miR-184转染组培养24 h后细胞迁移数为(17.21±3.06)个,明显低于对照组和空白转染组(p<0.05);miR-184转染组细胞EPB41L5蛋白相对表达量为(0.241±0.061),明显低于对照组和空白转染组(p<0.05)。本研究初步表明:miR-184可抑制肾癌786-0细胞增殖和迁移,促进细胞凋亡,其可能与其抑制EPB41L5蛋白表达有关。     

Candidate tumour suppressor CCDC19 regulates miR‐184 direct targeting of C‐Myc thereby suppressing cell growth in non‐small cell lung cancers

We previously reported and revised the nasopharyngeal epithelium specific protein CCDC19 and identified it as a potential tumour suppressor in nasopharyngeal carcinoma. The purpose of this study was to investigate the involvement of CCDC19 in the pathogenesis of human non‐small cell lung cancers (NSCLC). Down‐regulated CCDC19 expression was observed in NSCLC tissues and cells compared to normal tissues. However, reduced protein expression did not correlate with the status of NSCLC progression. Instead, we observed that patients with lower CCDC19 expression had a shorter overall survival than did patients with higher CCDC19 expression. Lentiviral‐mediated CCDC19 overexpression significantly suppressed cell proliferation and cell cycle transition from G1 to S and G2 phases in NSCLC cells. Knocking down CCDC19 expression significantly restored the ability of cell growth in CCDC19 overexpressing NSCLC cells. Mechanistically CCDC19 functions as a potential tumour suppressor by stimulating miR‐184 suppression of C‐Myc thus blocking cell growth mediated by the PI3K/AKT/C‐Jun pathway. Our studies are the first to demonstrate that reduced expression of CCDC19 is an unfavourable factor in NSCLC.     

Ultrasonic measurements of two-component lipid bilayer suspensions

Two-component lipid bilayers of dipalmitoylphosphatidylcholine and dimyristoylphosphatidylcholine were studied by measuring, ultrasonic velocity and absorption at 3 MHz. The phase diagram of the two-component lipid bilayers is discussed based upon the transition anomalies of the ultrasonic velocity as well as absorption, and it is suggested that this binary system has two critical points. The bulk modulus of lipid bilayers was determined from the ultrasonic velocity to be (2.2–3.0) × 10¹⁰$\text{dyne}\text{cm}{}^2$, whereas the bulk viscosity calculated from the absorption was 10–20 P except for the transition regions.