Quantitative Biology

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Pharmacodynamics simulation of HOEC by a computational model of arachidonic acid metabolic network
Wen Yang, Xia Wang, Kenan Li, Yuanru Liu, Ying Liu, Rui Wang, Honglin Li
Quant. Biol.    2019, 7 (1): 30-41.   https://doi.org/10.1007/s40484-018-0163-4
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Background: Arachidonic acid (AA) metabolic network is activated in the most inflammatory related diseases, and small-molecular drugs targeting AA network are increasingly available. However, side effects of above mentioned drugs have always been the biggest obstacle. (+)-2-(1-hydroxyl-4-oxocyclohexyl) ethyl caffeate (HOEC), a natural product acted as an inhibitor of 5-lipoxygenase (5-LOX) and 15-LOX in vitro, exhibited weaker therapeutic effect in high dose than that in low dose to collagen induced arthritis (CIA) rats. In this study, we tried to elucidate the potential regulatory mechanism by using quantitative pharmacology.

Methods: First, we generated an experimental data set by monitoring the dynamics of AA metabolites’ concentration in A23187 stimulated and different doses of HOEC co-incubated RAW264.7. Then we constructed a dynamic model of A23187-stimulated AA metabolic model to evaluate how a model-based simulation of AA metabolic data assists to find the most suitable treatment dose by predicting the pharmacodynamics of HOEC.

Results: Compared to the experimental data, the model could simulate the inhibitory effect of HOEC on 5-LOX and 15-LOX, and reproduced the increase of the metabolic flux in the cyclooxygenase (COX) pathway. However, a concomitant, early-stage of stimulation-related decrease of prostaglandins (PGs) production in HOEC incubated RAW264.7 cells was not simulated in the model.

Conclusion: Using the model, we predict that higher dose of HOEC disrupts the flux balance in COX and LOX of the AA network, and increased COX flux can interfere the curative effects of LOX inhibitor on resolution of inflammation which is crucial for the efficient and safe drug design.

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Insights into the antineoplastic mechanism of Chelidonium majus via systems pharmacology approach
Xinzhe Xiao, Zehui Chen, Zengrui Wu, Tianduanyi Wang, Weihua Li, Guixia Liu, Bo Zhang, Yun Tang
Quant. Biol.    2019, 7 (1): 42-53.   https://doi.org/10.1007/s40484-019-0165-x
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Background: The antineoplastic activity of Chelidonium majus has been reported, but its mechanism of action (MoA) is unsuspected. The emerging theory of systems pharmacology may be a useful approach to analyze the complicated MoA of this multi-ingredient traditional Chinese medicine (TCM).

Methods: We collected the ingredients and related compound-target interactions of C. majus from several databases. The bSDTNBI (balanced substructure-drug-target network-based inference) method was applied to predict each ingredient’s targets. Pathway enrichment analysis was subsequently conducted to illustrate the potential MoA, and prognostic genes were identified to predict the certain types of cancers that C. majus might be beneficial in treatment. Bioassays and literature survey were used to validate the in silico results.

Results: Systems pharmacology analysis demonstrated that C. majus exerted experimental or putative interactions with 18 cancer-associated pathways, and might specifically act on 13 types of cancers. Chelidonine, sanguinarine, chelerythrine, berberine, and coptisine, which are the predominant components of C. majus, may suppress the cancer genes by regulating cell cycle, inducing cell apoptosis and inhibiting proliferation.

Conclusions: The antineoplastic MoA of C. majus was investigated by systems pharmacology approach. C. majus exhibited promising pharmacological effect against cancer, and may consequently be useful material in further drug development. The alkaloids are the key components in C. majus that exhibit anticancer activity.

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Characterizing robustness and sensitivity of convolutional neural networks for quantitative analysis of mitochondrial morphology
Xiaoqi Chai, Qinle Ba, Ge Yang
Quant. Biol.    2018, 6 (4): 344-358.   https://doi.org/10.1007/s40484-018-0156-3
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Background: Quantitative analysis of mitochondrial morphology plays important roles in studies of mitochondrial biology. The analysis depends critically on segmentation of mitochondria, the image analysis process of extracting mitochondrial morphology from images. The main goal of this study is to characterize the performance of convolutional neural networks (CNNs) in segmentation of mitochondria from fluorescence microscopy images. Recently, CNNs have achieved remarkable success in challenging image segmentation tasks in several disciplines. So far, however, our knowledge of their performance in segmenting biological images remains limited. In particular, we know little about their robustness, which defines their capability of segmenting biological images of different conditions, and their sensitivity, which defines their capability of detecting subtle morphological changes of biological objects.

Methods: We have developed a method that uses realistic synthetic images of different conditions to characterize the robustness and sensitivity of CNNs in segmentation of mitochondria. Using this method, we compared performance of two widely adopted CNNs: the fully convolutional network (FCN) and the U-Net. We further compared the two networks against the adaptive active-mask (AAM) algorithm, a representative of high-performance conventional segmentation algorithms.

Results: The FCN and the U-Net consistently outperformed the AAM in accuracy, robustness, and sensitivity, often by a significant margin. The U-Net provided overall the best performance.

Conclusions: Our study demonstrates superior performance of the U-Net and the FCN in segmentation of mitochondria. It also provides quantitative measurements of the robustness and sensitivity of these networks that are essential to their applications in quantitative analysis of mitochondrial morphology.

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WaveNano: a signal-level nanopore base-caller via simultaneous prediction of nucleotide labels and move labels through bi-directional WaveNets
Sheng Wang, Zhen Li, Yizhou Yu, Xin Gao
Quant. Biol.    2018, 6 (4): 359-368.   https://doi.org/10.1007/s40484-018-0155-4
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Background: The Oxford MinION nanopore sequencer is the recently appealing third-generation genome sequencing device that is portable and no larger than a cellphone. Despite the benefits of MinION to sequence ultra-long reads in real-time, the high error rate of the existing base-calling methods, especially indels (insertions and deletions), prevents its use in a variety of applications.

Methods: In this paper, we show that such indel errors are largely due to the segmentation process on the input electrical current signal from MinION. All existing methods conduct segmentation and nucleotide label prediction in a sequential manner, in which the errors accumulated in the first step will irreversibly influence the final base-calling. We further show that the indel issue can be significantly reduced via accurate labeling of nucleotide and move labels directly from the raw signal, which can then be efficiently learned by a bi-directional WaveNet model simultaneously through feature sharing. Our bi-directional WaveNet model with residual blocks and skip connections is able to capture the extremely long dependency in the raw signal. Taking the predicted move as the segmentation guidance, we employ the Viterbi decoding to obtain the final base-calling results from the smoothed nucleotide probability matrix.

Results: Our proposed base-caller, WaveNano, achieves good performance on real MinION sequencing data from Lambda phage.

Conclusions: The signal-level nanopore base-caller WaveNano can obtain higher base-calling accuracy, and generate fewer insertions/deletions in the base-called sequences.

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ShapeShifter: a novel approach for identifying and quantifying stable lariat intronic species in RNAseq data
Allison J Taggart, William G Fairbrother
Quant. Biol.    2018, 6 (3): 267-274.   https://doi.org/10.1007/s40484-018-0141-x
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Background: Most intronic lariats are rapidly turned over after splicing. However, new research suggests that some introns may have additional post-splicing functions. Current bioinformatics methods used to identify lariats require a sequencing read that traverses the lariat branchpoint. This method provides precise branchpoint sequence and position information, but is limited in its ability to quantify abundance of stabilized lariat species in a given RNAseq sample. Bioinformatic tools are needed to better address these emerging biological questions.

Methods: We used an unsupervised machine learning approach on sequencing reads from publicly available ENCODE data to learn to identify and quantify lariats based on RNAseq read coverage shape.

Results: We developed ShapeShifter, a novel approach for identifying and quantifying stable lariat species in RNAseq datasets. We learned a characteristic “lariat” curve from ENCODE RNAseq data and were able to estimate abundances for introns based on read coverage. Using this method we discovered new stable introns in these samples that were not represented using the older, branchpoint-traversing read method.

Conclusions: ShapeShifter provides a robust approach towards detecting and quantifying stable lariat species.

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Developing a low-cost milliliter-scale chemostat array for precise control of cellular growth
David Skelding, Samuel F M Hart, Thejas Vidyasagar, Alexander E Pozhitkov, Wenying Shou
Quant. Biol.    2018, 6 (2): 129-141.   https://doi.org/10.1007/s40484-018-0143-8
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Background: Multiplexed milliliter-scale chemostats are useful for measuring cell physiology under various degrees of nutrient limitation and for carrying out evolution experiments. In each chemostat, fresh medium containing a growth rate-limiting metabolite is pumped into the culturing chamber at a constant rate, while culture effluent exits at an equal rate. Although such devices have been developed by various labs, key parameters — the accuracy, precision, and operational range of flow rate — are not explicitly characterized.

Methods: Here we re-purpose a published multiplexed culturing device to develop a multiplexed milliliter-scale chemostat. Flow rates for eight chambers can be independently controlled to a wide range, corresponding to population doubling times of 3~13 h, without the use of expensive feedback systems.

Results: Flow rates are precise, with the maximal coefficient of variation among eight chambers being less than 3%. Flow rates are accurate, with average flow rates being only slightly below targets, i.e., 3%–6% for 13-h and 0.6%–1.0% for 3-h doubling times. This deficit is largely due to evaporation and should be correctable. We experimentally demonstrate that our device allows accurate and precise quantification of population phenotypes.

Conclusions: We achieve precise control of cellular growth in a low-cost milliliter-scale chemostat array, and show that the achieved precision reduces the error when measuring biological processes.

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BMTK: a toolkit for determining modules in biological bipartite networks
Bei Wang, Jinyu Chen, Shihua Zhang
Quant. Biol.    2018, 6 (2): 186-192.   https://doi.org/10.1007/s40484-018-0132-y
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Background: Module detection is widely used to analyze and visualize biological networks. A number of methods and tools have been developed to achieve it. Meanwhile, bipartite module detection is also very useful for mining and analyzing bipartite biological networks and a few methods have been developed for it. However, there is few user-friendly toolkit for this task.

Methods: To this end, we develop an online web toolkit BMTK, which implements seven existing methods.

Results: BMTK provides a uniform operation platform and visualization function, standardizes input and output format, and improves algorithmic structure to enhance computing speed. We also apply this toolkit onto a drug-target bipartite network to demonstrate its effectiveness.

Conclusions: BMTK will be a powerful tool for detecting bipartite modules in diverse bipartite biological networks.

Availability: The web application is freely accessible at http://www.zhanglabtools.net/BMTK.

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MRHCA: a nonparametric statistics based method for hub and co-expression module identification in large gene co-expression network
Yu Zhang, Sha Cao, Jing Zhao, Burair Alsaihati, Qin Ma, Chi Zhang
Quant. Biol.    2018, 6 (1): 40-55.   https://doi.org/10.1007/s40484-018-0131-z
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Background: Gene co-expression and differential co-expression analysis has been increasingly used to study co-functional and co-regulatory biological mechanisms from large scale transcriptomics data sets.

Methods: In this study, we develop a nonparametric approach to identify hub genes and modules in a large co-expression network with low computational and memory cost, namely MRHCA.

Results: We have applied the method to simulated transcriptomics data sets and demonstrated MRHCA can accurately identify hub genes and estimate size of co-expression modules. With applying MRHCA and differential co-expression analysis to E. coli and TCGA cancer data, we have identified significant condition specific activated genes in E. coli and distinct gene expression regulatory mechanisms between the cancer types with high copy number variation and small somatic mutations.

Conclusion: Our analysis has demonstrated MRHCA can (i) deal with large association networks, (ii) rigorously assess statistical significance for hubs and module sizes, (iii) identify co-expression modules with low associations, (iv) detect small and significant modules, and (v) allow genes to be present in more than one modules, compared with existing methods.

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Deciphering the protein-DNA code of bacterial winged helix-turn-helix transcription factors
Adam P. Joyce, James J. Havranek
Quant. Biol.    2018, 6 (1): 68-84.   https://doi.org/10.1007/s40484-018-0130-0
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Background: Sequence-specific binding by transcription factors (TFs) plays a significant role in the selection and regulation of target genes. At the protein:DNA interface, amino acid side-chains construct a diverse physicochemical network of specific and non-specific interactions, and seemingly subtle changes in amino acid identity at certain positions may dramatically impact TF:DNA binding. Variation of these specificity-determining residues (SDRs) is a major mechanism of functional divergence between TFs with strong structural or sequence homology.

Methods: In this study, we employed a combination of high-throughput specificity profiling by SELEX and Spec-seq, structural modeling, and evolutionary analysis to probe the binding preferences of winged helix-turn-helix TFs belonging to the OmpR sub-family in Escherichia coli.

Results: We found that E. coli OmpR paralogs recognize tandem, variably spaced repeats composed of “GT-A” or “GCT”-containing half-sites. Some divergent sequence preferences observed within the “GT-A” mode correlate with amino acid similarity; conversely, “GCT”-based motifs were observed for a subset of paralogs with low sequence homology. Direct specificity profiling of a subset of OmpR homologues (CpxR, RstA, and OmpR) as well as predicted “SDR-swap” variants revealed that individual SDRs may impact sequence preferences locally through direct contact with DNA bases or distally via the DNA backbone.

Conclusions: Overall, our work provides evidence for a common structural “code” for sequence-specific wHTH-DNA interactions, and demonstrates that surprisingly modest residue changes can enable recognition of highly divergent sequence motifs. Further examination of SDR predictions will likely reveal additional mechanisms controlling the evolutionary divergence of this important class of transcriptional regulators.

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Variable importance-weighted Random Forests
Yiyi Liu, Hongyu Zhao
Quant. Biol.    2017, 5 (4): 338-351.   https://doi.org/10.1007/s40484-017-0121-6
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Background: Random Forests is a popular classification and regression method that has proven powerful for various prediction problems in biological studies. However, its performance often deteriorates when the number of features increases. To address this limitation, feature elimination Random Forests was proposed that only uses features with the largest variable importance scores. Yet the performance of this method is not satisfying, possibly due to its rigid feature selection, and increased correlations between trees of forest.

Methods: We propose variable importance-weighted Random Forests, which instead of sampling features with equal probability at each node to build up trees, samples features according to their variable importance scores, and then select the best split from the randomly selected features.

Results: We evaluate the performance of our method through comprehensive simulation and real data analyses, for both regression and classification. Compared to the standard Random Forests and the feature elimination Random Forests methods, our proposed method has improved performance in most cases.

Conclusions: By incorporating the variable importance scores into the random feature selection step, our method can better utilize more informative features without completely ignoring less informative ones, hence has improved prediction accuracy in the presence of weak signals and large noises. We have implemented an R package “viRandomForests” based on the original R package “randomForest” and it can be freely downloaded from http://zhaocenter.org/software.

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