scholarly journals Dual RNA-Sequencing Analysis of Resistant (Pinus pinea) and Susceptible (Pinus radiata) Hosts during Fusarium circinatum Challenge

2021 ◽  
Vol 22 (10) ◽  
pp. 5231
Author(s):  
Cristina Zamora-Ballesteros ◽  
Gloria Pinto ◽  
Joana Amaral ◽  
Luis Valledor ◽  
Artur Alves ◽  
...  
Keyword(s):  
Pinus Radiata ◽  
Early Stage ◽  
Integrated Approach ◽  
Effective Field ◽  
Pinus Pinea ◽  
Sequencing Analysis ◽  
Fusarium Circinatum ◽  
Pr Genes ◽  
Pathogen Infection ◽  
Pine Species

Fusarium circinatum causes one of the most important diseases of conifers worldwide, the pine pitch canker (PPC). However, no effective field intervention measures aiming to control or eradicate PPC are available. Due to the variation in host genetic resistance, the development of resistant varieties is postulated as a viable and promising strategy. By using an integrated approach, this study aimed to identify differences in the molecular responses and physiological traits of the highly susceptible Pinus radiata and the highly resistant Pinus pinea to F. circinatum at an early stage of infection. Dual RNA-Seq analysis also allowed to evaluate pathogen behavior when infecting each pine species. No significant changes in the physiological analysis were found upon pathogen infection, although transcriptional reprogramming was observed mainly in the resistant species. The transcriptome profiling of P. pinea revealed an early perception of the pathogen infection together with a strong and coordinated defense activation through the reinforcement and lignification of the cell wall, the antioxidant activity, the induction of PR genes, and the biosynthesis of defense hormones. On the contrary, P. radiata had a weaker response, possibly due to impaired perception of the fungal infection that led to a reduced downstream defense signaling. Fusarium circinatum showed a different transcriptomic profile depending on the pine species being infected. While in P. pinea, the pathogen focused on the degradation of plant cell walls, active uptake of the plant nutrients was showed in P. radiata. These findings present useful knowledge for the development of breeding programs to manage PPC.

scholarly journals Genome-Wide Identification and Characterization of Fusarium circinatum-Responsive lncRNAs in Pinus radiata

2021 ◽  
Author(s):  
Cristina Zamora-Ballesteros ◽  
Jorge Martin-Garcia ◽  
Aroa Suarez-Vega ◽  
Julio Diez
Keyword(s):  
Cell Wall ◽  
Pinus Radiata ◽  
Target Genes ◽  
Early Stage ◽  
Gc Content ◽  
Fusarium Circinatum ◽  
Protein Coding ◽  
Biotic Stresses ◽  
Non Coding Rnas

One of the most promising strategies of Pine Pitch Canker (PPC) management is the use of reproductive plant material resistant to the disease. Understanding the complexity of plant transcriptome that underlies the defence to the causal agent Fusarium circinatum, would greatly facilitate the development of an accurate breeding program. Long non-coding RNAs (lncRNAs) are emerging as important transcriptional regulators under biotic stresses in plants. However, to date, characterization of lncRNAs in conifer trees has not been reported. In this study, transcriptomic identification of lncRNAs was carried out using strand-specific paired-end RNA sequencing, from Pinus radiata samples inoculated with F. circinatum at an early stage of infection. Overall, 13,312 lncRNAs were predicted through a bioinformatics approach, including long intergenic non-coding RNAs (92.3%), antisense lncRNAs (3.3%) and intronic lncRNAs (2.9%). Compared with protein-coding RNAs, pine lncRNAs are shorter, have lower expression, lower GC content and harbour fewer and shorter exons. A total of 164 differentially expressed (DE) lncRNAs were identified in response to F. circinatum infection in the inoculated versus mock-inoculated P. radiata seedlings. The predicted cis-regulated target genes of these pathogen-responsive lncRNAs were related to defence mechanisms such as kinase activity, phytohormone regulation, and cell wall reinforcement. Co-expression network analysis of DE lncRNAs, DE protein-coding RNAs and lncRNA target genes also indicated a potential network regulating pectinesterase activity and cell wall remodelling. This study presents the first analysis of conifer lncRNAs involved in the regulation of defence network and provides the basis for future functional characterizations of lncRNAs in relation to pine defence responses against F. circinatum.

scholarly journals Transcriptome Analysis Reveals the Genes Involved in Bifidobacterium Longum FGSZY16M3 Biofilm Formation

2021 ◽  
Vol 9 (2) ◽  
pp. 385 ◽  
Author(s):  
Zongmin Liu ◽  
Lingzhi Li ◽  
Qianwen Wang ◽  
Faizan Ahmed Sadiq ◽  
Yuankun Lee ◽  
...  
Keyword(s):  
Network Analysis ◽  
Biofilm Formation ◽  
Extracellular Polymeric Substances ◽  
Molecular Mechanisms ◽  
Early Stage ◽  
Bifidobacterium Longum ◽  
Regulation Of Gene Expression ◽  
Interaction Network ◽  
Structural Development ◽  
Sequencing Analysis

Biofilm formation has evolved as an adaptive strategy for bacteria to cope with harsh environmental conditions. Currently, little is known about the molecular mechanisms of biofilm formation in bifidobacteria. A time series transcriptome sequencing analysis of both biofilm and planktonic cells of Bifidobacterium longum FGSZY16M3 was performed to identify candidate genes involved in biofilm formation. Protein–protein interaction network analysis of 1296 differentially expressed genes during biofilm formation yielded 15 clusters of highly interconnected nodes, indicating that genes related to the SOS response (dnaK, groS, guaB, ruvA, recA, radA, recN, recF, pstA, and sufD) associated with the early stage of biofilm formation. Genes involved in extracellular polymeric substances were upregulated (epsH, epsK, efp, frr, pheT, rfbA, rfbJ, rfbP, rpmF, secY and yidC) in the stage of biofilm maturation. To further investigate the genes related to biofilm formation, weighted gene co-expression network analysis (WGCNA) was performed with 2032 transcript genes, leading to the identification of nine WGCNA modules and 133 genes associated with response to stress, regulation of gene expression, quorum sensing, and two-component system. These results indicate that biofilm formation in B. longum is a multifactorial process, involving stress response, structural development, and regulatory processes.

Use of an Integrated Approach for Analysis and Design of Turbocharged Internal Combustion Engine

2021 ◽  
Author(s):  
Thiago Ebel ◽  
Mark Anderson ◽  
Parth Pandya ◽  
Mat Perchanok ◽  
Nick Tiney ◽  
...  
Keyword(s):  
Internal Combustion Engine ◽  
Combustion Engine ◽  
Early Stage ◽  
Pressure Ratio ◽  
Integrated Approach ◽  
Internal Combustion ◽  
Operating Conditions ◽  
Dynamics Simulation ◽  
Analysis And Design ◽  
Performance Requirements

Abstract When developing a turbocharged internal combustion engine, the choice of turbocharger is usually based on designer experience and existing hardware. However, proper turbocharger design relies on matching the compressor and turbine performance to the engine requirements so that parameters such as boost and back pressure, compressor pressure ratio, and turbine inlet temperatures meet the needs of the engine without exceeding its allowable operating envelope. Therefore, the ultimate measure of a successful turbocharger design is how well it is matched to an engine across various operating conditions. This, in turn, determines whether a new turbocharger is required, or an existing solution can be used. When existing turbocharger solutions are not viable, the engine designer is at a loss on how to define a new turbocharger that meets the desired performance requirements. A common approach in industry has been to scale the performance of an existing turbocharger (compressor and turbine maps) and take these requirements for Original Equipment Manufacturers to possibly match it with a real machine. However, the assumptions made in a basic scaling process are quite simplistic and generally not satisfactory in this situation. A better approach would be to use a validated meanline model for a compressor and turbine instead, allowing to perform an actual preliminary design of such components. Such approach allows to link the engine performance requirements in a very early stage of te component design project and it guides the designer for the design decisions, such as rotor size, variable geometry nozzles, diameter, or shroud trims and others. Therefore, a feasible solution is more likely with design less iterations. This paper describes a methodology for an integrated approach to design and analyze a turbocharged internal combustion engine using commercially available state-of-the-art 1D gas dynamics simulation tool linked to two powerful turbomachinery meanline programs. The outputs of this analysis are detailed performance data of the engine and turbocharger at different engine operating conditions. Two case studies are then presented for a 10-liter diesel truck engine. The first study demonstrates how the programs are used to evaluate an existing engine and reverse engineer an existing turbocharger based only on the available performance maps. Then a second study is done using a similar approach but redesigning a new turbocharger (based on the reverse engineered one) for an increased torque output of the same engine.

scholarly journals Changes in Photosynthesis Could Provide Important Insight into the Interaction between Wheat and Fungal Pathogens

2021 ◽  
Vol 22 (16) ◽  
pp. 8865
Author(s):  
Huai Yang ◽  
Peigao Luo
Keyword(s):  
Fungal Pathogens ◽  
Puccinia Striiformis ◽  
Early Stage ◽  
Acquired Resistance ◽  
Immune Defense ◽  
Pathogen Infection ◽  
Resistance Level ◽  
Growth Environment ◽  
Expression Of Genes ◽  
Host Materials

Photosynthesis is a universal process for plant survival, and immune defense is also a key process in adapting to the growth environment. Various studies have indicated that these two processes are interconnected in a complex network. Photosynthesis can influence signaling pathways and provide both materials and energy for immune defense, while the immune defense process can also have feedback effects on photosynthesis. Pathogen infection inevitably leads to changes in photosynthesis parameters, including Pn, Gs, and Ci; biochemical materials such as SOD and CAT; signaling molecules such as H2O2 and hormones; and the expression of genes involved in photosynthesis. Some researchers have found that changes in photosynthesis activity are related to the resistance level of the host, the duration after infection, and the infection position (photosynthetic source or sink). Interactions between wheat and the main fungal pathogens, such as Puccinia striiformis, Blumeria graminis, and Fusarium graminearum, constitute an ideal study system to elucidate the relationship between changes in host photosynthesis and resistance levels, based on the accessibility of methods for artificially controlling infection and detecting changes in photosynthesis, the presence of multiple pathogens infecting different positions, and the abundance of host materials with various resistance levels. This review is written only from the perspective of plant pathologists, and after providing an overview of the available data, we generally found that changes in photosynthesis in the early stage of pathogen infection could be a causal factor influencing acquired resistance, while those in the late stage could be the result of resistance formation.

scholarly journals NPR1 and Redox Rhythmx: Connections, between Circadian Clock and Plant Immunity

2019 ◽  
Vol 20 (5) ◽  
pp. 1211 ◽  
Author(s):  
Jingjing Zhang ◽  
Ziyu Ren ◽  
Yuqing Zhou ◽  
Zheng Ma ◽  
Yanqin Ma ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Systemic Acquired Resistance ◽  
Nuclear Translocation ◽  
Plant Immunity ◽  
Acquired Resistance ◽  
Defense Responses ◽  
Diurnal Changes ◽  
Pr Genes ◽  
Pathogen Infection ◽  
Physiological Reactions

The circadian clock in plants synchronizes biological processes that display cyclic 24-h oscillation based on metabolic and physiological reactions. This clock is a precise timekeeping system, that helps anticipate diurnal changes; e.g., expression levels of clock-related genes move in synchrony with changes in pathogen infection and help prepare appropriate defense responses in advance. Salicylic acid (SA) is a plant hormone and immune signal involved in systemic acquired resistance (SAR)-mediated defense responses. SA signaling induces cellular redox changes, and degradation and rhythmic nuclear translocation of the non-expresser of PR genes 1 (NPR1) protein. Recent studies demonstrate the ability of the circadian clock to predict various potential attackers, and of redox signaling to determine appropriate defense against pathogen infection. Interaction of the circadian clock with redox rhythm promotes the balance between immunity and growth. We review here a variety of recent evidence for the intricate relationship between circadian clock and plant immune response, with a focus on the roles of redox rhythm and NPR1 in the circadian clock and plant immunity.

scholarly journals A plea against over specialisation in forensic psychiatry

1992 ◽  
Vol 16 (7) ◽  
pp. 439-442 ◽  
Author(s):  
Eric F. Mendelson
Keyword(s):  
Forensic Psychiatry ◽  
Psychiatric Care ◽  
Early Stage ◽  
Integrated Approach ◽  
Integrated System ◽  
Forensic Patients ◽  
Secure Care ◽  
Regional Service ◽  
Forensic Psychiatric ◽  
Special Responsibility

The optimal system for delivering forensic psychiatric care has yet to be established. At an early stage, Gunn (1977) drew attention to the differing models of a ‘parallel’ service and an ‘integrated’ approach. Only with the integrated system do forensic patients pass to ordinary NHS facilities when they no longer require security or other specialist expertise. The debate can be extended into whether forensic services should be provided by regional units, by district services, or by a mixture of both. Indeed, the Royal College of Psychiatrists (1988) recognised that in addition to a regional service led by a fully trained forensic psychiatrist, secure care can be provided at a district level by consultants who have sufficient training to hold posts with a special responsibility. Furthermore, managers are understandably keen for as much as possible to be provided by their own district services.

scholarly journals Dual RNA-Seq Analysis of the Pine-Fusarium circinatum Interaction in Resistant (Pinus tecunumanii) and Susceptible (Pinus patula) Hosts

2019 ◽  
Vol 7 (9) ◽  
pp. 315 ◽  
Author(s):  
Erik A. Visser ◽  
Jill L. Wegrzyn ◽  
Emma T. Steenkamp ◽  
Alexander A. Myburg ◽  
Sanushka Naidoo
Keyword(s):  
Ergosterol Biosynthesis ◽  
Pinus Patula ◽  
Delayed Response ◽  
Fusarium Circinatum ◽  
Rna Seq ◽  
Susceptible Host ◽  
Pinus Tecunumanii ◽  
Host Pathogen ◽  
Phytohormone Signaling ◽  
Pine Species

Fusarium circinatum poses a serious threat to many pine species in both commercial and natural pine forests. Knowledge regarding the molecular basis of pine-F. circinatum host-pathogen interactions could assist efforts to produce more resistant planting stock. This study aimed to identify molecular responses underlying resistance against F. circinatum. A dual RNA-seq approach was used to investigate host and pathogen expression in F. circinatum challenged Pinus tecunumanii (resistant) and Pinus patula (susceptible), at three- and seven-days post inoculation. RNA-seq reads were mapped to combined host-pathogen references for both pine species to identify differentially expressed genes (DEGs). F. circinatum genes expressed during infection showed decreased ergosterol biosynthesis in P. tecunumanii relative to P. patula. For P. tecunumanii, enriched gene ontologies and DEGs indicated roles for auxin-, ethylene-, jasmonate- and salicylate-mediated phytohormone signalling. Correspondingly, key phytohormone signaling components were down-regulated in P. patula. Key F. circinatum ergosterol biosynthesis genes were expressed at lower levels during infection of the resistant relative to the susceptible host. This study further suggests that coordination of phytohormone signaling is required for F. circinatum resistance in P. tecunumanii, while a comparatively delayed response and impaired phytohormone signaling contributes to susceptibility in P. patula.

scholarly journals Herbaceous plants in the understory of a pitch canker-affected Pinus radiata plantation are endophytically infected with Fusarium circinatum

2018 ◽  
Vol 32 ◽  
pp. 65-71 ◽  
Author(s):  
L. Hernandez-Escribano ◽  
E. Iturritxa ◽  
M. Elvira-Recuenco ◽  
M. Berbegal ◽  
J.A. Campos ◽  
...  
Keyword(s):  
Pinus Radiata ◽  
Herbaceous Plants ◽  
Pitch Canker ◽  
Fusarium Circinatum
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