Space as the final frontier in stochastic simulations of biological systems

Recent technological and theoretical advances are only now allowing the simulation of detailed kinetic models of biological systems that reflect the stochastic movement and reactivity of individual molecules within cellular compartments. The behavior of many systems could not be properly understood without this level of resolution, opening up new perspectives of using computer simulations to accelerate biological research. We review the modeling methodology applied to stochastic spatial models, also to the attention of non-expert potential users. Modeling choices, current limitations and perspectives of improvement of current general-purpose modeling/simulation platforms for biological systems are discussed.     

Rule-based modeling and simulations of the inner kinetochore structure

Background

Combinatorial complexity is a central problem when modeling biochemical reaction networks, since the association of a few components can give rise to a large variation of protein complexes. Available classical modeling approaches are often insufficient for the analysis of very large and complex networks in detail. Recently, we developed a new rule-based modeling approach that facilitates the analysis of spatial and combinatorially complex problems. Here, we explore for the first time how this approach can be applied to a specific biological system, the human kinetochore, which is a multi-protein complex involving over 100 proteins.

Results

Applying our freely available SRSim software to a large data set on kinetochore proteins in human cells, we construct a spatial rule-based simulation model of the human inner kinetochore. The model generates an estimation of the probability distribution of the inner kinetochore 3D architecture and we show how to analyze this distribution using information theory. In our model, the formation of a bridge between CenpA and an H3 containing nucleosome only occurs efficiently for higher protein concentration realized during S-phase but may be not in G1. Above a certain nucleosome distance the protein bridge barely formed pointing towards the importance of chromatin structure for kinetochore complex formation. We define a metric for the distance between structures that allow us to identify structural clusters. Using this modeling technique, we explore different hypothetical chromatin layouts.

Conclusions

Applying a rule-based network analysis to the spatial kinetochore complex geometry allowed us to integrate experimental data on kinetochore proteins, suggesting a 3D model of the human inner kinetochore architecture that is governed by a combinatorial algebraic reaction network. This reaction network can serve as bridge between multiple scales of modeling. Our approach can be applied to other systems beyond kinetochores.     

马铃薯生育期和干物质积累的动态模拟研究

根据三年的田间试验数据和有关气象资料,提出了马铃薯生育期和干物质积累的模拟模型、用高斯方程计算每天的温度条件对马铃薯生育期和干物质积累的生理效应,改进了前人的生育期模型和温度条件对干物质积累影响系数的计算方法．以每天的单位叶面积变化、群体上方的有效辐射和温度变化模拟群体的干物质积累、结果表明,本研究的模型有明确的机理性和较高的精度．用Visual Basic 6．0界面表达每日生态条件变化对群体光合生产和干物质积累的影响,模拟结果具有直观的机理性,从而克服了同类研究中的缺陷。     

Disease-associated variants of microsomal retinol dehydrogenase 12 (RDH12) are degraded at mutant-specific rates

Mutations in retinol dehydrogenase 12 (RDH12) cause severe retinal degeneration. However, some of the disease-associated RDH12 mutants retain significant catalytic activity, indicating the existence of additional pathophysiological mechanisms. This study demonstrates that the catalytically active T49M and I51N mutants undergo accelerated degradation, which results in their reduced cellular levels. Inhibition of proteasome leads to significant accumulation of ubiquitylated T49M and I51N. Furthermore, the degree of ubiquitylation strongly correlates with the half-lives of the proteins. These results suggest that the accelerated degradation of RDH12 mutants by the ubiquitin-proteasome system contributes to the pathophysiology and phenotypic variability associated with mutations in the RDH12 gene.

Structured summary

MINT-7383581, MINT-7383598: RDH12 (uniprotkb:Q96NR8) physically interacts (MI:0915) with ubiquitin (uniprotkb:P62988) by anti tag coimmunoprecipitation (MI:0007)     

A novel gene expression index (GEI) with software support for comparing microarray gene signatures

This study was aimed to examine the validity of commonly used statistical tests for comparison of expression data from simulated and real gene signatures as well as pathway-characterized gene sets. A novel algorithm based on 10 sub-gradations (5 for up- and 5 for down-regulation) of fold-changes has been designed and testified using an Excel add-in software support. Our findings showed the limitations of conventional statistics for comparing the microarray gene expression data. However, the newly introduced Gene Expression Index (GEI) appeared to be more robust and straightforward for two-group comparison of normalized data. The software automation simplifies the task and the results are displayed in a comprehensive format including a color-coded bar showing the intensity of cumulative gene expression.     

Identification and characterization of retinoid-active short-chain dehydrogenases/reductases in Drosophila melanogaster

Background

In chordates, retinoid metabolism is an important target of short-chain dehydrogenases/reductases (SDRs). It is not known whether SDRs play a role in retinoid metabolism of protostomes, such as Drosophila melanogaster.

Methods

Drosophila genome was searched for genes encoding proteins with ∼ 50% identity to human retinol dehydrogenase 12 (RDH12). The corresponding proteins were expressed in Sf9 cells and biochemically characterized. Their phylogenetic relationships were analyzed using PHYLIP software.

Results

A total of six Drosophila SDR genes were identified. Five of these genes are clustered on chromosome 2 and one is located on chromosome X. The deduced proteins are 300 to 406 amino acids long and are associated with microsomal membranes. They recognize all-trans-retinaldehyde and all-trans-3-hydroxyretinaldehyde as substrates and prefer NADPH as a cofactor. Phylogenetically, Drosophila SDRs belong to the same branch of the SDR superfamily as human RDH12, indicating a common ancestry early in bilaterian evolution, before a protostome–deuterostome split.

Conclusions

Similarities in the substrate and cofactor specificities of Drosophila versus human SDRs suggest conservation of their function in retinoid metabolism throughout protostome and deuterostome phyla.

General significance

The discovery of Drosophila retinaldehyde reductases sheds new light on the conversion of β-carotene and zeaxantine to visual pigment and provides a better understanding of the evolutionary roots of retinoid-active SDRs.     

Glucose conversion by multiple pathways in brain extract: theoretical and experimental analysis

Experimental and model studies were performed to characterize the flux of glucose metabolism and the sharing of glucose-6-phosphate (Glu6P) by the upper parts of glycolytic and pentosephosphate pathways in the brain extract. A mathematical model based upon the kinetic equations of the individual enzymes was evaluated to fit the experimental data. Glucose is converted to glucose-6-phosphate by hexokinase that controls almost exclusively the glucose metabolism. Experiments showed that this crossroad-metabolite was shared between glycolysis and pentosephosphate pathway in the brain extract in a ratio of 1.5:1. This ratio was favorable to the pentosephosphate pathway by the addition of high excess of exogenous glucose-6-phosphate dehydrogenase, standardly used for the activity assay of hexokinase, but still a significant part (17+/-3%) of the common intermediate was converted into the direction of glycolysis. Stimulation of glucose-6-phosphate formation via moderate (30-50%) increase of hexokinase activity by adding exogenous hexokinase or tubulin resulted in the slight increase of the relative flux into direction of glycolysis. The model correctly described all of these observations. However, when the activity of hexokinase was doubled with exogenous enzyme, significantly less glucose-6-phosphate was converted into direction of glycolysis than predicted. This discrepancy shows that the system did not behave in this case as an ideal one, which could be due to the formation of distinct pools for the intermediate.     

An empirical approach to characterizing trunk muscle coactivation using simulation input modeling techniques

Accurately describing trunk muscle coactivation is fundamental to quantifying the spine reaction forces that occur during lifting tasks and has been the focus of a great deal of research in the spine biomechanics literature. One limitation of previous approaches has been a lack of consideration given to the variability in these coactivation strategies. The research presented in this paper is an empirical approach to quantifying and modeling trunk muscle coactivation using simulation input modeling techniques. Electromyographic (EMG) data were collected from 28 human subjects as they performed controlled trunk extension exertions. These exertions included isokinetic (10 and 45°/s) and constant acceleration (50°/s/s) trunk extensions in symmetric and asymmetric (30°) postures at two levels of trunk extension moment (30 and 80 Nm). The EMG data were collected from the right and left pairs of the erector spinae, latissimus dorsi, rectus abdominis, external obliques and internal obliques. Each subject performed nine repetitions of each combination of independent variables. The data collected during these trials were used to develop marginal distributions of trunk muscle activity as well as a 10×10 correlation matrix that described how the muscles cooperated to produce these extension torques. These elements were then combined to generate multivariate distributions describing the coactivation of the trunk musculature. An analysis of these distributions revealed that increases in extension moment, extension velocity and sagittal flexion angle created increases in both the mean and the variance of the distributions of the muscular response, while increases in the rate of trunk extension acceleration decreased both the mean and variance of the distributions of activity across all muscles considered. Increases in trunk asymmetry created a decrease in mean of the ipsi–lateral erector spinae and an increase in the mean of all other muscles considered, but there was little change in the variance of these distributions as a function of asymmetry.     

Analysis of DNA distributions from flow cytometry

A recently proposed automatic procedure for analyzing DNA distribution from flow cytometric data is extensively tested against simulated data. After a discussion of the procedure itself and of the simulation program, the results obtained are reported. They are evidence of the reliability of the procedure in extracting the proper underlying DNA distribution from sets of data obtained under various simulated instances. The different sources of error are then analyzed, along with their quantitative effects on the fit of the fluorescence histogram.     

Structure of the class IV adenylyl cyclase reveals a novel fold

The crystal structure of the class IV adenylyl cyclase (AC) from Yersinia pestis (Yp) is reported at 1.9 A resolution. The class IV AC fold is distinct from the previously described folds for class II and class III ACs. The dimeric AC-IV folds into an antiparallel eight-stranded barrel whose connectivity has been seen in only three previous structures: yeast RNA triphosphatase and two proteins of unknown function from Pyrococcus furiosus and Vibrio parahaemolyticus. Eight highly conserved ionic residues E10, E12, K14, R63, K76, K111, D126, and E136 lie in the barrel core and form the likely binding sites for substrate and divalent cations. A phosphate ion is observed bound to R63, K76, K111, and R113 near the center of the conserved cluster. Unlike the AC-II and AC-III active sites that utilize two-Asp motifs for cation binding, the AC-IV active site is relatively enriched in glutamate and features an ExE motif as its most conserved element. Homologs of Y. pestis AC-IV, including human thiamine triphosphatase, span the three kingdoms of life and delineate an ancient family of phosphonucleotide processing enzymes.     

Computer modeling and nanosecond simulation of the enzyme–substrate complex of the common lymphoblastic leukemia antigen (neprilysin) indicates shared residues at the primary specificity pocket (S1') with matrix metalloproteases

The common acute lymphoblastic leukemia antigen (neprilysin, CD10, neutral endopeptidase 24.11) is a member of the neprilysin family, and projects functions in signaling pathways in pathophysiological processes such as cancer, Alzheimer's disease and hypertension. Given its pathophysiological importance, an investigation of the natural substrate specificity of this metalloprotease is presented here through the application of enzyme-substrate modeling and molecular dynamics simulations. The results show that the substrate modeled, LATAC downward arrow FG, satisfies a complementary backbone H-bonding with Ala543-Tyr545, thereby suggested to be the putative substrate-binding beta-sheet, analogously to matrix metalloproteases. The modeling further suggests that phenylalanine at the P1' position (substrate) is directed in the same fashion as the synthetic inhibitor of the reference crystal structure and that this enzyme does not bind the P3'/P4' positions of a substrate, as other metalloproteases do. After a specific comparison with one member of the matrix metalloproteases, MMP-3, a common conserved valine residue at the primary S1' subsite was found to be shared between these two otherwise different proteases. These results may prove useful for selective drug design for neprilysin, and lay a foundation for future subsite analysis for other members of the neprilysin family.     

Electrophoretically mediated microscale reaction of glycosidases: kinetic analysis of some glycosidases at the nanoliter scale

Capillary electrophoresis (CE) is one of the extremely important analytical techniques known for its high sensitivity and resolution. We have investigated electrophoretically mediated microanalysis (EMMA) for the assay of some native glycosidases. Under optimized conditions, the enzymatic reactions of alpha-glucosidase, beta-galactosidase and beta-N-acetylglucosaminidase were carried out, and the Michaelis constants were obtained. The current method may have advantages over traditional assay methods, especially in terms of the amount of enzyme and substrate required for a reaction.     

茂原链霉菌谷氨酰胺转胺酶序列分析及三维结构建模

利用DNASTAR、VectorNTI9、SignalP等生物信息学平台对茂原链霉菌(Streptomyces mobaraensis)谷氨酰胺转胺酶(TGase)进行了序列分析和三维结构建模。结果表明:茂原链霉菌TGase同已报道其他微生物来源的TGase有较高的同源性,无信号肽,存在一个跨膜结构区,二级结构是由多个α螺旋、转角和少量β折叠构成。同时在一二级结构分析的基础上,利用同源建模的方法完成了三维结构的建模。     

Identification of differentially expressed genes using multi-resolution wavelet transformation analysis combined with SAM

Although many statistical methods have been proposed for identifying differentially expressed genes, the optimal approach has still not been resolved. Therefore, it is necessary to develop more efficient methods of finding differentially expressed genes while accounting for noise and false discovery rate (FDR). We propose a method based on multi-resolution wavelet transformation analysis combined with SAM for identifying differentially expressed genes by adjusting the Δ and computing the FDR. This method was applied to a microarray expression dataset from adenoma patients and normal subjects. The number of differentially expressed genes gradually reduced with an increasing Δ value, and the FDR was reduced after wavelet transformation. At a given Δ value, the FDR was also reduced before and after wavelet transformation. In conclusion, a greater number and quality of differentially expressed genes were detected using the method when compared to non-transformed data, and the FDRs were notably more controlled and reduced.     

构建和评估猪氨基酰化酶I的三维结构

运用同源模建的方法构建了pACY1三维结构模型,并在能量最小化后对模型进行分子动力学模拟和结构合理性评估。同源模建生成了50个原始模型,经过PROCHECK评测后,筛选出模型A、B进行能量最小化,并得到模型A1、B1。分子动力学模拟结果表明模型B1二聚体结构较稳定。PROCHECK、ProSa以及WHATIF检测结果验证了模型B1属于合理性结构。得到的猪氨基酰化酶Ⅰ(pACY1)的三维结构,为研究其结构与功能关系打下基础。     

Microbial and Carbohydrate Active Enzyme profile of buffalo rumen metagenome and their alteration in response to variation in the diet

Rumen microbiome represents rich source of enzymes degrading complex plant polysaccharides. We describe here analysis of Carbohydrate Active Enzymes (CAZymes) from 3.5 gigabase sequences of metagenomic data from rumen samples of Mehsani buffaloes fed on different proportions of green or dry roughages to concentrate ration. A total of 2597 contigs encoding putative CAZymes were identified by CAZyme Analysis Toolkit (CAT). The phylogenetic analysis of these contigs by MG-RAST revealed predominance of Bacteroidetes, followed by Firmicutes, Proteobacteria, and Actinobacteria phyla. Moreover, a higher abundance of oligosaccharide degrading and debranching enzymes in buffalo rumen metagenome and that of cellulases and hemicellulases in termite hindgut was observed when we compared glycoside hydrolase (GH) profile of buffalo rumen metagenome with cow rumen, termite hindgut and chicken caecum metagenome. Further, comparison of microbial profile of green or dry roughage fed animals showed significantly higher abundance (p-value < 0.05) of various polysaccharide degrading bacterial genera like Fibrobacter, Prevotella, Bacteroides, Clostridium and Ruminococcus in green roughage fed animals. In addition, we found a significantly higher abundance (p-value < 0.05) of enzymes associated with pectin digestion such as pectin lyase (PL) 1, PL10 and GH28 in green roughage fed animals. Our study outlines CAZyme profile of buffalo rumen metagenome and provides a scope to study the role of abundant enzyme families (oligosaccharide degrading and debranching enzymes) in digestion of coarse feed.     

Cornell Net Carbohydrate and Protein System: A model for precision feeding of dairy cattle

The Cornell Net Carbohydrate and Protein System (CNCPS) predicts cattle requirements and nutrient supply for site-specific situations. This paper describes the CNCPS version 6 (CNCPSv6), which represents a re-engineering and updating of CNCPS version 5 with the following objectives: (1) improve the organization of the model and user interface to improve speed and accuracy in formulating diets for a herd of dairy cattle, (2) expand the carbohydrate pools to include sugars, soluble fibers, and organic and volatile fatty acids, (3) integrate a fat model to account for ruminal lypolization and biohydrogenation, and absorption of fatty acids in the small intestine, and (4) update the computational sub-models with new information. The CNCPSv6 model was re-designed using object-oriented programming in which physiological functions (e.g. growth, lactation, pregnancy) and anatomical compartments (e.g. rumen, intestines) were programmed as objects. The interface uses farm, location, and group flow, which decreases the number of inputs required per cattle group and allows for more rapid evaluation of diets, feed requirements, and nutrient excretion by location, group, and herd. The revised implementation of the body reserves sub-model allows accounting for fluxes in energy reserves when formulating diets. Updated equations and coefficients include the prediction of rumen ammonia balance and feed passage rates, indigestible DM, MP lactation efficiency, and DMI. The CNCPSv6 was evaluated with data from individually fed lactating dairy cows from three independent studies. As implemented, CNCPSv6 accounted for a similar proportion of the variation (86%) in first limiting (ME or MP) milk production as CNCPSv5 but with a lower bias (1% versus 4%, respectively). We concluded the re-designing and updating of the CNCPS improved its ability to formulate and evaluate a feeding program for a herd of dairy cattle with greater accuracy and efficiency.