scholarly journals Genome-Scale Reconstruction of Microbial Dynamic Phenotype: Successes and Challenges

2021 ◽  
Vol 9 (11) ◽  
pp. 2352
Author(s):  
Nicolai Panikov
Keyword(s):  
Growth Rate ◽  
Secondary Metabolism ◽  
Stress Responses ◽  
Stress Resistance ◽  
Environmental Conditions ◽  
The Real ◽  
Cell Composition ◽  
Primary And Secondary Metabolism ◽  
Conditional Expression ◽  
Genome Scale

This review is a part of the SI ‘Genome-Scale Modeling of Microorganisms in the Real World’. The goal of GEM is the accurate prediction of the phenotype from its respective genotype under specified environmental conditions. This review focuses on the dynamic phenotype; prediction of the real-life behaviors of microorganisms, such as cell proliferation, dormancy, and mortality; balanced and unbalanced growth; steady-state and transient processes; primary and secondary metabolism; stress responses; etc. Constraint-based metabolic reconstructions were successfully started two decades ago as FBA, followed by more advanced models, but this review starts from the earlier nongenomic predecessors to show that some GEMs inherited the outdated biokinetic frameworks compromising their performances. The most essential deficiencies are: (i) an inadequate account of environmental conditions, such as various degrees of nutrients limitation and other factors shaping phenotypes; (ii) a failure to simulate the adaptive changes of MMCC (MacroMolecular Cell Composition) in response to the fluctuating environment; (iii) the misinterpretation of the SGR (Specific Growth Rate) as either a fixed constant parameter of the model or independent factor affecting the conditional expression of macromolecules; (iv) neglecting stress resistance as an important objective function; and (v) inefficient experimental verification of GEM against simple growth (constant MMCC and SGR) data. Finally, we propose several ways to improve GEMs, such as replacing the outdated Monod equation with the SCM (Synthetic Chemostat Model) that establishes the quantitative relationships between primary and secondary metabolism, growth rate and stress resistance, process kinetics, and cell composition.

scholarly journals Wheat transcriptome profiling reveals abscisic and gibberellic acid treatments regulate early-stage phytohormone defense signaling, cell wall fortification, and metabolic switches following Fusarium graminearum-challenge

2020 ◽  
Author(s):  
Leann M. Buhrow ◽  
Ziying Liu ◽  
Dustin Cram ◽  
Tanya Sharma ◽  
Nora A. Foroud ◽  
...  
Keyword(s):  
Cell Wall ◽  
Gibberellic Acid ◽  
Secondary Metabolism ◽  
Fusarium Graminearum ◽  
Stress Responses ◽  
Early Stage ◽  
Molecular Transport ◽  
Defense Responses ◽  
Head Blight ◽  
Primary And Secondary Metabolism

ABSTRACTBackgroundApplication of the wheat phytohormones abscisic acid (ABA) or gibberellic acid (GA) affect Fusarium head blight (FHB) disease severity; however, the molecular underpinnings of the elicited phenotypes remain unclear. Herein, the transcriptomic responses of an FHB-susceptible wheat cultivar ‘Fielder’ were characterized upon treatment with ABA, an ABA receptor antagonist (AS6), or GA in the presence or absence of Fusarium graminearum (Fg) challenge.ResultsA total of 30,876 differentially expressed genes (DEGs) where identified in ‘Fielder’ (26,004) and Fg (4,872). Fg challenge alone resulted in the most substantial wheat DEGs contributing to 57.2% of the total transcriptomic variation. Using a combination of topology overlap and correlation analyses, 9,689 Fg-related wheat DEGs were defined. Further enrichment analysis of the top 1% networked wheat DEGs identified critical expression changes within defense responses, cell structural metabolism, molecular transport, and membrane/lipid metabolism. Fg-challenged conditions also included the expression of a putative Fg ABA-biosynthetic cytochrome P450 and repression of wheat FUS3 for dysregulating ABA and GA crosstalk. ABA treatment alone elicited 4536 (32%) wheat DEGs common to those of the Fg-challenge, and Fg+ABA further enhanced 888 (12.5%) of them. These ABA elicited DEGs are involved in defense through both classical and non-classical phytohormone signaling and regulating cell wall structures including polyphenolic metabolism. Conversely, Fg+GA opposed 2239 (33%) Fg-elicited wheat DEGs, including modulating primary and secondary metabolism, defense responses, and flowering genes. ABA and jointly ABA⍰Fg⍰[Fg+ABA] treatments repressed, while Fg+GA induced an over-representation of wheat DEGs mapping to chromosome 6BL. Finally, compared to Fg+ABA, co-application of Fg+AS6 did not antagonize ABA biosynthesis or signal but rather elicited antagonistic Fg (557) and wheat (11) DEGs responses directly tied to stress responses, phytohormone transport, and FHB.ConclusionsComparative transcriptomics highlight the effects of wheat phytohormones on individual pathway and global metabolism simultaneously. Application of ABA may reduce FHB severity through misregulating defense mechanisms and cell wall fortification pathways. GA application may alter primary and secondary metabolism, creating a metabolic shift to ultimately reduce FHB severity. By comparing these findings to those previously reported for four additional plant genotypes, an additive model of the wheat-Fg interaction is proposed.

DERADICALISATION IDEAS IN SOCIAL MEDIA THROUGH THE RELIGIOUS-MULTICULTURAL THERAPY APPROACH TO THE DA'WAH CULTURE

2020 ◽  
Vol 24 (1) ◽  
pp. 58
Author(s):  
Anwar Hafidzi
Keyword(s):  
Social Media ◽  
Real World ◽  
Environmental Conditions ◽  
Islamic Law ◽  
Research Tool ◽  
Therapy Approach ◽  
The Real ◽  
Multicultural Therapy ◽  
Online Social Media ◽  
Library Research

This research begins with an understanding of the endemic radicalism of society, not only of the real world, but also of various online social media. This study showed that the avoidance of online radicalism can be stopped as soon as possible by accusing those influenced by the radical radicality of a secular religious approach. The methods used must be assisted in order to achieve balanced understanding (wasathiyah) under the different environmental conditions of the culture through recognizing the meaning of religion. The research tool used is primarily library work and the journal writings by Abu Rokhmad, a terrorist and radicalise specialist. The results of this study are that an approach that supports inclusive ism will avoid the awareness of radicalization through a heart-to-heart approach. This study also shows that radical actors will never cease to argue dramatically until they are able to grasp different views from Islamic law, culture, and families.Keywords: radicalism, deradicalization, multiculturalism, culture, religion, moderate.Penelitian ini berawal dari paham radikalisme yang telah mewabah di masyarakat, bukan hanya di dunia nyata, bahkan sudah menyusup di berbagai media sosial online. Penelitian ini menemukan bahwa cara menangkal radikalisme online dapat dilakukan pencegahan sedini mungkin melalui pendekatan konseling religius multikultural terhadap mereka yang terkena paham radikal radikal. Diantara teknik yang digunakan adalah melalui pemahaman tentang konsep agama juga perlu digalakkan agar memunculkan pemahaman yang moderat (wasathiyah) diberbagai keadaan lingkungan masyarakat. Metode yang digunakan untuk penelitian ini adalah library research dengan sumber utama adalah karya dan jurnal karya Abu Rokhmad seorang pakar dalam masalah terorisme dan radikalisme. Temuan penelitian ini adalah paham radikalisasi itu dapat dihentikan dengan pendekatan hati ke hati dengan mengedepankan budaya yang multikultural. Kajian ini juga membuktikan bahwa pelaku paham radikal tidak akan pernah berhenti memberikan argumen radikal kecuali mampu memahami perbedaan pendapat yang bersumber dari syariat Islam, lingkungan sosial, dan keluarga.Kata kunci: radikalisme, deradikalisasi, multikultural, budaya, agama, moderat.

scholarly journals Metabolite profiling during graft union formation reveals the reprogramming of primary metabolism and the induction of stilbene synthesis at the graft interface in grapevine

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Duyên Prodhomme ◽  
Josep Valls Fonayet ◽  
Cyril Hévin ◽  
Céline Franc ◽  
Ghislaine Hilbert ◽  
...  
Keyword(s):  
Amino Acids ◽  
Secondary Metabolism ◽  
Fruits And Vegetables ◽  
Cell Formation ◽  
Union Formation ◽  
Primary Metabolism ◽  
Graft Union ◽  
Primary And Secondary Metabolites ◽  
Primary And Secondary Metabolism ◽  
Graft Interface

Abstract Background Grafting with rootstocks is essential for the culture of many perennial fruit crops and is increasing being used in the production of annual fruits and vegetables. Our previous work based on microarrays showed that transcripts encoding enzymes of both primary and secondary metabolism were differentially expressed during graft union formation in both homo-grafts (a genotype grafted with itself) and hetero-grafts (two different genotypes grafted together). The aim of this study was to profile primary and secondary metabolites, and quantify the activity of phenylalanine ammonia lyase (PAL) and neutral invertase (NI) in the scion and rootstock tissues and the graft interface of homo and hetero-grafts of grapevine 1 month after grafting. Table-top grafting was done on over-wintering stems (canes) of grapevine and the graft interface tissues (containing some woody stem tissues and callus) were compared to the surrounding rootstock and scion tissues. The objective was to identify compounds involved in graft union formation and hetero-grafting responses. Results A total of 54 compounds from primary and secondary metabolism (19 amino acids, five primary and 30 secondary compounds metabolites) and the activity of two enzymes were measured. The graft interface was associated with an increase in the accumulation of the branched-chain amino acids, basic amino acids, certain stilbene compounds and higher PAL and NI activity in comparison to the surrounding woody stem tissues. Some amino acids and stilbenes were identified as being accumulated differently between the graft interfaces of the scion/rootstock combinations in a manner which was unrelated to their concentrations in the surrounding woody stem tissues. Conclusions This study revealed the modification of primary metabolism to support callus cell formation and the stimulation of stilbene synthesis at the graft interface, and how these processes are modified by hetero-grafting. Knowledge of the metabolites and/or enzymes required for successful graft union formation offer us the potential to identify markers that could be used by nurseries and researchers for selection and breeding purposes.

MixAR

2019 ◽  
Vol 12 (4) ◽  
pp. 1-33 ◽  
Author(s):  
Telmo Adão ◽  
Luís Pádua ◽  
David Narciso ◽  
Joaquim João Sousa ◽  
Luís Agrellos ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
Mixed Reality ◽  
The Real ◽  
Points Of Interest ◽  
Real Scene ◽  
The Future

MixAR, a full-stack system capable of providing visualization of virtual reconstructions seamlessly integrated in the real scene (e.g. upon ruins), with the possibility of being freely explored by visitors, in situ, is presented in this article. In addition to its ability to operate with several tracking approaches to be able to deal with a wide variety of environmental conditions, MixAR system also implements an extended environment feature that provides visitors with an insight on surrounding points-of-interest for visitation during mixed reality experiences (positional rough tracking). A procedural modelling tool mainstreams augmentation models production. Tests carried out with participants to ascertain comfort, satisfaction and presence/immersion based on an in-field MR experience and respective results are also presented. Ease to adapt to the experience, desire to see the system in museums and a raised curiosity and motivation contributed as positive points for evaluation. In what regards to sickness and comfort, the lowest number of complaints seems to be satisfactory. Models' illumination/re-lightning must be addressed in the future to improve the user's engagement with the experiences provided by the MixAR system.

scholarly journals Control of sulfur partitioning between primary and secondary metabolism in Arabidopsis

2012 ◽  
Vol 3 ◽  
Author(s):  
Stanislav Kopriva ◽  
Sarah G. Mugford ◽  
Patrycja Baraniecka ◽  
Bok-Rye Lee ◽  
Colette A. Matthewman ◽  
...  
Keyword(s):  
Secondary Metabolism ◽  
Primary And Secondary Metabolism

The Design of ZigBee Wireless Network for the Detection Platform of the Cylinders

2012 ◽  
Vol 241-244 ◽  
pp. 2504-2509
Author(s):  
Yan Li ◽  
Qiao Xiang Gu
Keyword(s):  
Real Time ◽  
Wireless Network ◽  
Environmental Conditions ◽  
Protocol Stack ◽  
The Real ◽  
The Core ◽  
Core Components ◽  
Real Time Detection ◽  
Cable Connection

The equipment, called detection platform of the cylinders, is used for detecting cylinders so that cylinders can be at ease use. In order to transmit the real-time detection data to PC for further processing, the platform should be connected with PC. Cable connection, in some production and environmental conditions, is limited. Under the circumstance, building wireless network is the better choice. Through comparative studying, ZigBee is chosen to be the technology for building wireless network. ZigBee chip and ZigBee2006 protocol stack are the core components in the ZigBee nodes.

scholarly journals Intertissue small RNA communication mediates the acquisition and inheritance of hormesis in Caenorhabditis elegans

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Emiko Okabe ◽  
Masaharu Uno ◽  
Saya Kishimoto ◽  
Eisuke Nishida
Keyword(s):  
Caenorhabditis Elegans ◽  
Small Rna ◽  
Stress Resistance ◽  
Environmental Conditions ◽  
Production System ◽  
Small Rnas ◽  
Communication Systems ◽  
Rna Transport ◽  
Phenotypic Changes ◽  
Induced Stress

AbstractEnvironmental conditions can cause phenotypic changes, part of which can be inherited by subsequent generations via soma-to-germline communication. However, the signaling molecules or pathways that mediate intertissue communication remain unclear. Here, we show that intertissue small RNA communication systems play a key role in the acquisition and inheritance of hormesis effects – stress-induced stress resistance – in Caenorhabditis elegans. The miRNA-processing enzyme DRSH-1 is involved in both the acquisition and the inheritance of hormesis, whereas worm-specific Argonaute (WAGO) proteins, which function with endo-siRNAs, are involved only in its inheritance. Further analyses demonstrate that the miRNA production system in the neuron and the small RNA transport machinery in the intestine are both essential for its acquisition and that both the transport of small RNAs in the germline and the germline Argonaute HRDE-1 complex are required for its inheritance. Our results thus demonstrate that overlapping and distinct roles of small RNA systems in the acquisition and inheritance of hormesis effects.

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