scholarly journals Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Li Guo ◽  
Mengjie Ji ◽  
Kai Ye
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sk Md Mosaddek Hossain ◽  
Aanzil Akram Halsana ◽  
Lutfunnesa Khatun ◽  
Sumanta Ray ◽  
Anirban Mukhopadhyay

AbstractPancreatic Ductal Adenocarcinoma (PDAC) is the most lethal type of pancreatic cancer, late detection leading to its therapeutic failure. This study aims to determine the key regulatory genes and their impacts on the disease’s progression, helping the disease’s etiology, which is still mostly unknown. We leverage the landmark advantages of time-series gene expression data of this disease and thereby identified the key regulators that capture the characteristics of gene activity patterns in the cancer progression. We have identified the key gene modules and predicted the functions of top genes from a reconstructed gene association network (GAN). A variation of the partial correlation method is utilized to analyze the GAN, followed by a gene function prediction task. Moreover, we have identified regulators for each target gene by gene regulatory network inference using the dynamical GENIE3 (dynGENIE3) algorithm. The Dirichlet process Gaussian process mixture model and cubic spline regression model (splineTimeR) are employed to identify the key gene modules and differentially expressed genes, respectively. Our analysis demonstrates a panel of key regulators and gene modules that are crucial for PDAC disease progression.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xinyu Li ◽  
Wei Zhang ◽  
Jianming Zhang ◽  
Guang Li

Abstract Background Given expression data, gene regulatory network(GRN) inference approaches try to determine regulatory relations. However, current inference methods ignore the inherent topological characters of GRN to some extent, leading to structures that lack clear biological explanation. To increase the biophysical meanings of inferred networks, this study performed data-driven module detection before network inference. Gene modules were identified by decomposition-based methods. Results ICA-decomposition based module detection methods have been used to detect functional modules directly from transcriptomic data. Experiments about time-series expression, curated and scRNA-seq datasets suggested that the advantages of the proposed ModularBoost method over established methods, especially in the efficiency and accuracy. For scRNA-seq datasets, the ModularBoost method outperformed other candidate inference algorithms. Conclusions As a complicated task, GRN inference can be decomposed into several tasks of reduced complexity. Using identified gene modules as topological constraints, the initial inference problem can be accomplished by inferring intra-modular and inter-modular interactions respectively. Experimental outcomes suggest that the proposed ModularBoost method can improve the accuracy and efficiency of inference algorithms by introducing topological constraints.


PLoS ONE ◽  
2013 ◽  
Vol 8 (6) ◽  
pp. e66980 ◽  
Author(s):  
Qian Zheng ◽  
Rui Hou ◽  
Juanyu ◽  
Zhang ◽  
Jiwen Ma ◽  
...  

2017 ◽  
Vol 64 (1) ◽  
pp. 285-301 ◽  
Author(s):  
Piao Yang ◽  
Yunyun Chen ◽  
Huiming Wu ◽  
Wenqin Fang ◽  
Qifu Liang ◽  
...  

2002 ◽  
Vol 15 (11) ◽  
pp. 1119-1127 ◽  
Author(s):  
Zhanming Hou ◽  
Chaoyang Xue ◽  
Youliang Peng ◽  
Talma Katan ◽  
H. Corby Kistler ◽  
...  

Fusarium graminearum is an important pathogen of small grains and maize in many areas of the world. Infected grains are often contaminated with mycotoxins harmful to humans and animals. During the past decade, F. graminearum has caused several severe epidemics of head scab in wheat and barley. In order to understand molecular mechanisms regulating fungal development and pathogenicity in this pathogen, we isolated and characterized a MAP kinase gene, MGV1, which is highly homologous to the MPS1 gene in Magnaporthe grisea. The MGV1 gene was dispensable for conidiation in F. graminearum but essential for female fertility during sexual reproduction. Vegetative growth of mgv1 deletion mutants was normal in liquid media but reduced on solid media. Mycelia of the mgv1 mutants had weak cell walls and were hypersensitive to cell wall degrading enzymes. Interestingly, the mgv1 mutants were self-incompatible when tested for heterokaryon formation, and their virulence was substantially reduced. The ability of the mutants to accumulate trichothecene mycotoxins on inoculated wheat was also greatly reduced. Our data suggest that MGV1 in F. graminearum is involved in multiple developmental processes related to sexual reproduction, plant infection, and cell wall integrity.


2018 ◽  
Author(s):  
Gregory R Smith ◽  
Deepraj Sarmah ◽  
Mehdi Bouhaddou ◽  
Alan D. Stern ◽  
James Erskine ◽  
...  

SummaryNetwork reconstruction is an important objective for understanding biological interactions and their role in disease mechanisms and treatment. Yet, even for small systems, contemporary reconstruction methods struggle with critical network properties: (i) edge causality, sign and directionality; (ii) cycles with feedback or feedforward loops including self-regulation; (iii) dynamic network behavior; and (iv) environment-specific effects. Moreover, experimental noise significantly impedes many methods. We report an approach that addresses the aforementioned challenges to robustly and uniquely infer edge weights from sparse perturbation time course data that formally requires only one perturbation per node. We apply this approach to randomized 2 and 3 node systems with varied and complex dynamics as well as to a family of 16 non-linear feedforward loop motif models. In each case, we find that it can robustly reconstruct the networks, even with highly noisy data in some cases. Surprisingly, the results suggest that incomplete perturbation (e.g. 50% knockdown vs. knockout) is often more informative than full perturbation, which may fundamentally change experimental strategies for network reconstruction. Systematic application of this method can enable unambiguous network reconstruction, and therefore better prediction of cellular responses to perturbations such as drugs. The method is general and can be applied to any network inference problem where perturbation time course experiments are possible.


Author(s):  
Yuanye Zhu ◽  
Yuanshuai Zhang ◽  
Yabing Duan ◽  
Dongya Shi ◽  
Yi ping Hou ◽  
...  

The plant pathogen Fusarium graminearum contains two α-tubulin (α 1 and α 2 ) isotypes and two β-tubulin isotypes (β 1 and β 2 ). The functional roles of these tubulins in microtubule assembly are not clear. Previous studies showed that α 1 - and β 2 -tubulin deletion mutants showed severe growth defects and hypersensitivity to carbendazim, which have not been well explained. Here, we investigated the interaction between α- and β-tubulin of F. graminearum . Co-localization experiments demonstrated that β 1 - and β 2 -tubulin are co-localized. Co-immunoprecipitation experiment suggested that β 1 -tubulin binds to both α 1 - and α 2 -tubulin and β 2 -tubulin can also bind to α 1 - or α 2 -tubulin. Interestingly, deletion of α 1 -tubulin increased the interaction between β 2 -tubulin and α 2 -tubulin. Microtubule observation assays showed that deletion of α 1 -tubulin completely disrupted β 1 -tubulin-containing microtubules and significantly decreased β 2 -tubulin-containing microtubules. Deletion of α 2 -, β 1 - or β 2 -tubulin respectively had no obvious effect on the microtubule cytoskeleton. However, microtubules in α 1 - and β 2 -tubulin deletion mutants were easily depolymerized in the presence of carbendazim. The sexual reproduction assay indicates that α 1 - and β 1 -tubulin deletion mutants could not produce asci and ascospores. These results implied that α 1 -tubulin may be essential for the microtubule cytoskeleton. However, our Δα 1 -2×α 2 mutant (α 1 -tubulin deletion mutant containing two copies of α 2 -tubulin) exhibited a normal microtubule network, growth and sexual reproduction. Interestingly, the Δα 1 -2×α 2 mutant was still hypersensitive to carbendazim. In addition, both β 1 -tubulin and β 2 -tubulin were found to bind the mitochondrial outer membrane voltage-dependent anion channel (VDAC), indicating they could regulate the function of VDAC. Importance: In this study, we found that F. graminearum contains four different α-/β-tubulin heterodimers (α 1 -β 1 , α 1 -β 2 , α 2 -β 1 and α 2 -β 2 ) and they assemble together into a single microtubule. Moreover, α 1 -, α 2 -tubulins are functionally interchangeable in microtubule assembly, vegetative growth and sexual reproduction. These results provide more insights into functional roles of different tubulins of F. graminearum which could be helpful for purification of tubulin heterodimers and developing new tubulin-binding agents.


Microbiology ◽  
2012 ◽  
Vol 158 (7) ◽  
pp. 1723-1733 ◽  
Author(s):  
Jungkwan Lee ◽  
Kilseon Myong ◽  
Jung-Eun Kim ◽  
Hee-Kyoung Kim ◽  
Sung-Hwan Yun ◽  
...  

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