scholarly journals Transcriptome Analysis Identified Core Genes Involved in Maize Resistance to Rhizoctonia Solani

2021 ◽  
Author(s):  
Hongxiang Cao ◽  
Zhangshuai Yang ◽  
Shu Song ◽  
Jiazong Liu ◽  
Ning Li
Keyword(s):  
Rhizoctonia Solani ◽  
Defense Mechanisms ◽  
Process Analysis ◽  
Interaction Mechanism ◽  
The Core ◽  
Core Set ◽  
Maize Response ◽  
Go Terms ◽  
Insight Into ◽  
Core Genes

Abstract BackgroundBanded leaf and sheath blight (BLSB) caused by the necrotrophic fungus Rhizoctonia solani is a devasting disease on maize worldwide, especially in China and Southeast Asia. It is important to understand the interaction mechanism between maize and R. solani for control of invasion and expansion.ResultsIn this study, the expression profile of maize infected by low virulence strain (LVS) and high virulence strain (HVS) of R. solani for 3 and 5 d was analyzed by RNA-sequencing. A total of 3015 and 1628 differentially expressed genes (DEGs) were identified under LVS and HVS infection, respectively. Meanwhile, these DEGs were classified by Gene Ontology (GO) for biological process analysis. Only defense-related GO terms were commonly enriched in LVS- and HVS-regulated genes. Furthermore, a core set of 388 up-regulated genes that are involved in maize response to R. solani infection were identified. Additionally, among the core genes, overexpressing ZmNAC41 and ZmBAK1 enhanced rice resistance to R. solani.ConclusionThe results in this study provide additional insight into maize defense mechanisms against R. solani, and the core genes identified in this study will be important resources for improving BLSB resistance in the future.

scholarly journals Transcriptome analysis identified core genes involved in maize resistance to Rhizoctonia solani

2021 ◽  
Author(s):  
Hongxiang Cao ◽  
Zhangshuai Yang ◽  
Shu Song ◽  
Jiazong Liu ◽  
Ning Li
Keyword(s):  
Rhizoctonia Solani ◽  
Defense Mechanisms ◽  
Process Analysis ◽  
The Core ◽  
Core Set ◽  
Maize Resistance ◽  
Maize Response ◽  
Go Terms ◽  
Insight Into ◽  
Core Genes

Abstract Banded leaf and sheath blight (BLSB) caused by the necrotrophic fungus Rhizoctonia solani is a devasting disease on maize worldwide, especially in China and Southeast Asia. To explore the maize defense mechanisms against R. solani expansion, the expression profile of maize infected by low virulence strain (LVS) and high virulence strain (HVS) of R. solani for 3 and 5 d was analyzed by RNA-sequencing. A total of 3015 and 1628 differentially expressed genes (DEGs) were identified under LVS and HVS infection, respectively. Meanwhile, these DEGs were classified by Gene Ontology (GO) for biological process analysis. Only defense-related GO terms were commonly enriched in LVS- and HVS-regulated genes. Furthermore, a core set of 388 up-regulated genes that are involved in maize response to R. solani infection were identified. Additionally, among the core genes, overexpressing ZmNAC41 and ZmBAK1 enhanced rice resistance to R. solani. Taken together, our study provides additional insight into maize defense mechanisms against R. solani, and the core genes identified in this study will be important resources for improving BLSB resistance in the future.

Will Love Tear Us Apart: Adapting the Lyrical to the Ludic

CounterText ◽  
2016 ◽  
Vol 2 (2) ◽  
pp. 217-235
Author(s):  
Gordon Calleja
Keyword(s):  
Design Process ◽  
Game Design ◽  
Digital Games ◽  
Design Decisions ◽  
The Core ◽  
Lyrical Poetry ◽  
Insight Into ◽  
Made In

This paper gives an insight into the design process of a game adaptation of Joy Division's Love Will Tear Us Apart (1980). It outlines the challenges faced in attempting to reconcile the diverging qualities of lyrical poetry and digital games. In so doing, the paper examines the design decisions made in every segment of the game with a particular focus on the tension between the core concerns of the lyrical work being adapted and established tenets of game design.

Force in Nature

2020 ◽  
pp. 146-160
Author(s):  
David Carus
Keyword(s):  
Natural Science ◽  
The Body ◽  
The Core ◽  
Thing In Itself ◽  
The Will ◽  
Insight Into

This chapter explores Schopenhauer’s concept of force, which lies at the root of his philosophy. It is force in nature and thus in natural science that is inexplicable and grabs Schopenhauer’s attention. To answer the question of what this inexplicable term is at the root of all causation, Schopenhauer looks to the will within us. Through will, he maintains that we gain immediate insight into forces in nature and hence into the thing in itself at the core of everything and all things. Will is thus Schopenhauer’s attempt to answer the question of the essence of appearance. Yet will, as it turns out, cannot be known immediately as it is subject to time, and the acts of will, which we experience within us, do not correlate immediately with the actions of the body (as Schopenhauer had originally postulated). Hence, the acts of will do not lead to an explanation of force, which is at the root of causation in nature. Schopenhauer sets out to explain what is at the root of all appearances, derived from the question of an original cause, or as Schopenhauer states “the cause of causation,” but cannot determine this essence other than by stating that it is will; a will, however, that cannot be immediately known.

scholarly journals Comparative Genomics: Insights on the Pathogenicity and Lifestyle of Rhizoctonia solani

2021 ◽  
Vol 22 (4) ◽  
pp. 2183
Author(s):  
Nurhani Mat Razali ◽  
Siti Norvahida Hisham ◽  
Ilakiya Sharanee Kumar ◽  
Rohit Nandan Shukla ◽  
Melvin Lee ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Rhizoctonia Solani ◽  
Abiotic Factors ◽  
Biotic Factor ◽  
Protein Coding ◽  
Sustainable Food ◽  
Repeat Elements ◽  
Gene Sets ◽  
Core Genes

Proper management of agricultural disease is important to ensure sustainable food security. Staple food crops like rice, wheat, cereals, and other cash crops hold great export value for countries. Ensuring proper supply is critical; hence any biotic or abiotic factors contributing to the shortfall in yield of these crops should be alleviated. Rhizoctonia solani is a major biotic factor that results in yield losses in many agriculturally important crops. This paper focuses on genome informatics of our Malaysian Draft R. solani AG1-IA, and the comparative genomics (inter- and intra- AG) with four AGs including China AG1-IA (AG1-IA_KB317705.1), AG1-IB, AG3, and AG8. The genomic content of repeat elements, transposable elements (TEs), syntenic genomic blocks, functions of protein-coding genes as well as core orthologous genic information that underlies R. solani’s pathogenicity strategy were investigated. Our analyses show that all studied AGs have low content and varying profiles of TEs. All AGs were dominant for Class I TE, much like other basidiomycete pathogens. All AGs demonstrate dominance in Glycoside Hydrolase protein-coding gene assignments suggesting its importance in infiltration and infection of host. Our profiling also provides a basis for further investigation on lack of correlation observed between number of pathogenicity and enzyme-related genes with host range. Despite being grouped within the same AG with China AG1-IA, our Draft AG1-IA exhibits differences in terms of protein-coding gene proportions and classifications. This implies that strains from similar AG do not necessarily have to retain similar proportions and classification of TE but must have the necessary arsenal to enable successful infiltration and colonization of host. In a larger perspective, all the studied AGs essentially share core genes that are generally involved in adhesion, penetration, and host colonization. However, the different infiltration strategies will depend on the level of host resilience where this is clearly exhibited by the gene sets encoded for the process of infiltration, infection, and protection from host.

scholarly journals Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Seth Commichaux ◽  
Kiran Javkar ◽  
Padmini Ramachandran ◽  
Niranjan Nagarajan ◽  
Denis Bertrand ◽  
...  
Keyword(s):  
Public Health ◽  
Public Health Response ◽  
High Quality ◽  
Short Read ◽  
Short Reads ◽  
The Core ◽  
Long Reads ◽  
Health Response ◽  
Long Read ◽  
Core Genes

Abstract Background Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks. Quasimetagenomics can substantially reduce the amount of culturing needed before a high quality genome can be recovered. Highly accurate short read data is analyzed for single nucleotide polymorphisms and multi-locus sequence types to differentiate strains but cannot span many genomic repeats, resulting in highly fragmented assemblies. Long reads can span repeats, resulting in much more contiguous assemblies, but have lower accuracy than short reads. Results We evaluated the accuracy of Listeria monocytogenes assemblies from enrichments (quasimetagenomes) of naturally-contaminated ice cream using long read (Oxford Nanopore) and short read (Illumina) sequencing data. Accuracy of ten assembly approaches, over a range of sequencing depths, was evaluated by comparing sequence similarity of genes in assemblies to a complete reference genome. Long read assemblies reconstructed a circularized genome as well as a 71 kbp plasmid after 24 h of enrichment; however, high error rates prevented high fidelity gene assembly, even at 150X depth of coverage. Short read assemblies accurately reconstructed the core genes after 28 h of enrichment but produced highly fragmented genomes. Hybrid approaches demonstrated promising results but had biases based upon the initial assembly strategy. Short read assemblies scaffolded with long reads accurately assembled the core genes after just 24 h of enrichment, but were highly fragmented. Long read assemblies polished with short reads reconstructed a circularized genome and plasmid and assembled all the genes after 24 h enrichment but with less fidelity for the core genes than the short read assemblies. Conclusion The integration of long and short read sequencing of quasimetagenomes expedited the reconstruction of a high quality pathogen genome compared to either platform alone. A new and more complete level of information about genome structure, gene order and mobile elements can be added to the public health response by incorporating long read analyses with the standard short read WGS outbreak response.

scholarly journals Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Mehrshad Golesorkhi ◽  
Javier Gomez-Pilar ◽  
Shankar Tumati ◽  
Maia Fraser ◽  
Georg Northoff
Keyword(s):  
Time Window ◽  
Human Cortex ◽  
The Core ◽  
Novel Variant ◽  
Open Issue ◽  
Task Differences ◽  
Spatial Hierarchy ◽  
Fundamental Insight ◽  
Insight Into ◽  
And Task

AbstractThe human cortex exhibits intrinsic neural timescales that shape a temporal hierarchy. Whether this temporal hierarchy follows the spatial hierarchy of its topography, namely the core-periphery organization, remains an open issue. Using magnetoencephalography data, we investigate intrinsic neural timescales during rest and task states; we measure the autocorrelation window in short (ACW-50) and, introducing a novel variant, long (ACW-0) windows. We demonstrate longer ACW-50 and ACW-0 in networks located at the core compared to those at the periphery with rest and task states showing a high ACW correlation. Calculating rest-task differences, i.e., subtracting the shared core-periphery organization, reveals task-specific ACW changes in distinct networks. Finally, employing kernel density estimation, machine learning, and simulation, we demonstrate that ACW-0 exhibits better prediction in classifying a region’s time window as core or periphery. Overall, our findings provide fundamental insight into how the human cortex’s temporal hierarchy converges with its spatial core-periphery hierarchy.

scholarly journals A Fast and Exact Greedy Algorithm for the Core–Periphery Problem

Symmetry ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 94 ◽  
Author(s):  
Dario Fasino ◽  
Franca Rinaldi
Keyword(s):  
Structural Analysis ◽  
Optimization Problem ◽  
Polynomial Time Algorithm ◽  
Time Algorithm ◽  
Combinatorial Optimization Problem ◽  
Connected Subgraph ◽  
Optimal Solutions ◽  
The Core ◽  
Core Set ◽  
Key Concepts

The core–periphery structure is one of the key concepts in the structural analysis of complex networks. It consists of a partitioning of the node set of a given graph or network into two groups, called core and periphery, where the core nodes induce a well-connected subgraph and share connections with peripheral nodes, while the peripheral nodes are loosely connected to the core nodes and other peripheral nodes. We propose a polynomial-time algorithm to detect core–periphery structures in networks having a symmetric adjacency matrix. The core set is defined as the solution of a combinatorial optimization problem, which has a pleasant symmetry with respect to graph complementation. We provide a complete description of the optimal solutions to that problem and an exact and efficient algorithm to compute them. The proposed approach is extended to networks with loops and oriented edges. Numerical simulations are carried out on both synthetic and real-world networks to demonstrate the effectiveness and practicability of the proposed algorithm.

scholarly journals Developing a Delphi-Based Comprehensive Core Set from the International Classification of Functioning, Disability, and Health Framework for the Rehabilitation of Patients with Burn Injuries

2021 ◽  
Vol 18 (8) ◽  
pp. 3970
Author(s):  
Yu-Ru Lin ◽  
Jr-Yi Wang ◽  
Shun-Cheng Chang ◽  
Kwang-Hwa Chang ◽  
Hung-Chou Chen ◽  
...  
Keyword(s):  
Burn Injury ◽  
Functional Limitations ◽  
Rehabilitation Program ◽  
International Classification ◽  
Burn Injuries ◽  
International Classification Of Functioning ◽  
Disability And Health ◽  
The Core ◽  
Core Set

Burn injuries cause disability and functional limitations in daily living. In a 2015 fire explosion in Taiwan, 499 young people sustained burn injuries. The construction of an effective and comprehensive rehabilitation program that enables patients to regain their previous function is imperative. The International Classification of Functioning, Disability, and Health (ICF) includes multiple dimensions that can contribute to meeting this goal. An ICF core set was developed in this study for Taiwanese patients with burns. A consensus process using three rounds of the Delphi technique was employed. A multidisciplinary team of 30 experts from various institutions was formed. The questionnaire used in this study comprised 162 ICF second-level categories relevant to burn injuries. A 5-point Likert scale was used, and participants assigned a weight to the effect of each category on daily activities after burns. The consensus among ratings was assessed using Spearman’s ρ and semi-interquartile range indices. The core set for post-acute SCI was developed from categories that attained a mean score of ≥4.0 in the third round of the Delphi exercise. The core ICF set contained 68 categories. Of these, 19 comprised the component of body functions, 5 comprised body structures, 37 comprised activities and participation, and 7 comprised environmental factors. This preliminary core set offers a comprehensive system for disability assessment and verification following burn injury. The core set provides information for effective rehabilitation strategy setting for patients with burns. Further feasibility and validation studies are required in the future.

Identification of CCNB2 expression in triple-negative breast cancer based on bioinformatics results

2021 ◽  
Author(s):  
jintao cao ◽  
SHUAI SUN ◽  
RAN LI ◽  
RUI MIN ◽  
XINGYU FAN ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Triple Negative Breast Cancer ◽  
Protein Complex ◽  
Triple Negative ◽  
Expression Profiles ◽  
Pathway Enrichment Analysis ◽  
Analysis Tool ◽  
The Core ◽  
Core Genes

Abstract Background The current epidemiology shows that the incidence of breast cancer is increasing year by year and tends to be younger. Triple-negative breast cancer is the most malignant of breast cancer subtypes. The application of bioinformatics in tumor research is becoming more and more extensive. This study provided research ideas and basis for exploring the potential targets of gene therapy for triple-negative breast cancer (TNBC). Methods We analyzed three gene expression profiles (GSE64790、GSE62931、GSE38959) selected from the Gene Expression Omnibus (GEO) database. The GEO2R online analysis tool was used to screen for differentially expressed genes (DEGs) between TNBC and normal tissues. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were applied to identify the pathways and functional annotation of DEGs. Protein–protein interaction network of these DEGs were visualized by the Metascape gene-list analysis tool so that we could find the protein complex containing the core genes. Subsequently, we investigated the transcriptional data of the core genes in patients with breast cancer from the Oncomine database. Moreover, the online Kaplan–Meier plotter survival analysis tool was used to evaluate the prognostic value of core genes expression in TNBC patients. Finally, immunohistochemistry (IHC) was used to evaluated the expression level and subcellular localization of CCNB2 on TNBC tissues. Results A total of 66 DEGs were identified, including 33 up-regulated genes and 33 down-regulated genes. Among them, a potential protein complex containing five core genes was screened out. The high expression of these core genes was correlated to the poor prognosis of patients suffering breast cancer, especially the overexpression of CCNB2. CCNB2 protein positively expressed in the cytoplasm, and its expression in triple-negative breast cancer tissues was significantly higher than that in adjacent tissues. Conclusions CCNB2 may play a crucial role in the development of TNBC and has the potential as a prognostic biomarker of TNBC.

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