An Insight into Oligopeptide Transporter 3 (OPT3) family proteins

2020 ◽  
Vol 27 ◽  
Author(s):  
Fırat Kurt
Keyword(s):  
Stress Responses ◽  
Chelating Agent ◽  
Biological Processes ◽  
Biotic And Abiotic Stress ◽  
Oligopeptide Transporter ◽  
Binding Residues ◽  
Fe Homeostasis ◽  
Proteins Interactions ◽  
Insight Into ◽  
Selection Of

: Oligopeptide transporter 3 (OPT3) proteins are one of the subsets of OPT clade, yet little is known about these transporters. Therefore, homolog OPT3 proteins in several plant species were investigated and characterized using bioinformatical tools. Motif and co-expression analyses showed that OPT3 proteins may be involved in both biotic and abiotic stress responses as well as growth and developmental processes. AtOPT3 usually seemed to take part in Fe homeostasis whereas ZmOPT3 putatively interacted with proteins involved in various biological processes from plant defense system to stress responses. Glutathione (GSH), as a putative alternative chelating agent, was used in the AtOPT3 and ZmOPT3 docking analyses to identify their putative binding residues. The information given in this study will contribute to the understanding of OPT3 proteins’ interactions in various pathways and to the selection of potential ligands for OPT3s.

scholarly journals A Label-Free Proteomic and Complementary Metabolomic Analysis of Leaves of the Resurrection Plant Xerophyta schlechteri during Dehydration

Life ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1242
Author(s):  
Hawwa Gabier ◽  
David L. Tabb ◽  
Jill M. Farrant ◽  
Mohamed Suhail Rafudeen
Keyword(s):  
Desiccation Tolerance ◽  
Early Response ◽  
Resurrection Plant ◽  
Late Response ◽  
Biological Processes ◽  
Label Free ◽  
Relative Water ◽  
Leaf Tissues ◽  
Insight Into ◽  
Selection Of

Vegetative desiccation tolerance, or the ability to survive the loss of ~95% relative water content (RWC), is rare in angiosperms, with these being commonly called resurrection plants. It is a complex multigenic and multi-factorial trait, with its understanding requiring a comprehensive systems biology approach. The aim of the current study was to conduct a label-free proteomic analysis of leaves of the resurrection plant Xerophyta schlechteri in response to desiccation. A targeted metabolomics approach was validated and correlated to the proteomics, contributing the missing link in studies on this species. Three physiological stages were identified: an early response to drying, during which the leaf tissues declined from full turgor to a RWC of ~70–80%, a mid-response in which the RWC declined to 40% and a late response where the tissues declined to 10% RWC. We identified 517 distinct proteins that were differentially expressed, of which 253 proteins were upregulated and 264 were downregulated in response to the three drying stages. Metabolomics analyses, which included monitoring the levels of a selection of phytohormones, amino acids, sugars, sugar alcohols, fatty acids and organic acids in response to dehydration, correlated with some of the proteomic differences, giving insight into the biological processes apparently involved in desiccation tolerance in this species.

Exonic circular RNAs are involved in Arabidopsis immune response against bacterial and fungal pathogens by function synergistically with corresponding linear RNAs

2021 ◽  
Author(s):  
LIN WANG ◽  
Jiao Li ◽  
Baohuan Guo ◽  
Le Xu ◽  
Leyao Li ◽  
...  
Keyword(s):  
Immune Response ◽  
Pseudomonas Syringae ◽  
Stress Responses ◽  
Fungal Pathogens ◽  
Biological Function ◽  
Expression Profiles ◽  
Circular Rnas ◽  
Biological Processes ◽  
Biotic And Abiotic Stress ◽  
The Relationship

Circular RNAs (circRNAs) are a group of covalently closed RNAs, and their biological function is largely unknown. In this study, we focused on circRNAs that are generated from exon back-splicing (exonic circRNAs). The linear RNA counterparts encode functional proteins, that we can compare and investigate the relationship between circular and linear RNAs. We compared circRNA expression profiles between untreated and Pseudomonas syringae-infected Arabidopsis, and identified and experimentally validated differentially expressed exonic circRNAs by multiple approaches. We found that exonic circRNAs are preferentially enriched in biological processes that associate with biotic and abiotic stress responses. We discovered that circR194 and circR4022 are involved in plant response against P. syringae infection, while circR11208 is involved in response against Botrytis cinerea infection. Intriguingly, our results indicate that these exonic circRNAs function synergistically with their corresponding linear RNAs. Furthermore, circR4022 and circR11208 also play substantial roles in Arabidopsis tolerance to salt stress. This study extends our understanding of the molecular functions of plant circRNAs.

scholarly journals Mechanisms and Functions of Long Non-Coding RNAs at Multiple Regulatory Levels

2019 ◽  
Vol 20 (22) ◽  
pp. 5573 ◽  
Author(s):  
Xiaopei Zhang ◽  
Wei Wang ◽  
Weidong Zhu ◽  
Jie Dong ◽  
Yingying Cheng ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Stress Responses ◽  
Transcriptional Activation ◽  
Rna Processing ◽  
Mrna Translation ◽  
Biological Processes ◽  
Biotic And Abiotic Stress ◽  
Plant Growth And Development ◽  
Regulate Gene Expression ◽  
Non Coding Rnas

Long non-coding (lnc) RNAs are non-coding RNAs longer than 200 nt. lncRNAs primarily interact with mRNA, DNA, protein, and miRNA and consequently regulate gene expression at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels in a variety of ways. They play important roles in biological processes such as chromatin remodeling, transcriptional activation, transcriptional interference, RNA processing, and mRNA translation. lncRNAs have important functions in plant growth and development; biotic and abiotic stress responses; and in regulation of cell differentiation, the cell cycle, and the occurrence of many diseases in humans and animals. In this review, we summarize the functions and mechanisms of lncRNAs in plants, humans, and animals at different regulatory levels.

scholarly journals Genome-Wide Identification of WRKY Genes and Their Response to Cold Stress in Coffea canephora

Forests ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 335 ◽  
Author(s):  
Xiangshu Dong ◽  
Yanan Yang ◽  
Ziying Zhang ◽  
Ziwei Xiao ◽  
Xuehui Bai ◽  
...  
Keyword(s):  
Cold Stress ◽  
Stress Responses ◽  
Gene Expression Analysis ◽  
Target Genes ◽  
Coffea Canephora ◽  
Biological Processes ◽  
Genome Wide ◽  
A Genome ◽  
Cold Responses ◽  
Insight Into

WRKY transcription factors are known to play roles in diverse stress responses in plants. Low temperatures limit the geographic distribution of Coffea canephora Pierre ex A.Froehner. The WRKYs of C. canephora are still not well characterized, and the response of C. canephora WRKYs (CcWRKYs) under cold stress is still largely unknown. We identified 49 CcWRKYs from the C. canephora genome to gain insight into these mechanisms. These CcWRKYs were divided into three groups that were based on the conserved WRKY domains and zinc-finger structure. Gene expression analysis demonstrated that 14 CcWRKYs were induced during the cold acclimation stage, 17 CcWRKYs were preferentially upregulated by 4 °C treatment, and 12 CcWRKYs were downregulated by cold stress. Subsequently, we carried out a genome-wide analysis to predict 14,513 potential CcWRKY target genes in C. canephora. These isolated genes were involved in multiple biological processes, and most of them could be grouped by the response to stimulus. Among the putative CcWRKY target genes, 235 genes were categorized into response to the cold process, including carbohydrate metabolic, lipid metabolic, and photosynthesis process-related genes. Furthermore, the qRT-PCR and correlation analysis indicated that CcWRKY might control their putative targets that respond to cold stress. These results provide a basis for understanding the molecular mechanism for CcWRKY-mediated cold responses.

scholarly journals Incorporating radiomics into clinical trials: expert consensus on considerations for data-driven compared to biologically driven quantitative biomarkers

2021 ◽  
Author(s):  
Laure Fournier ◽  
Lena Costaridou ◽  
Luc Bidaut ◽  
Nicolas Michoux ◽  
Frederic E. Lecouvet ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Quantitative Imaging ◽  
A Priori ◽  
External Validation ◽  
Data Driven ◽  
Imaging Biomarkers ◽  
Clinical Validation ◽  
Biological Processes ◽  
Imaging Data ◽  
Selection Of

Abstract Existing quantitative imaging biomarkers (QIBs) are associated with known biological tissue characteristics and follow a well-understood path of technical, biological and clinical validation before incorporation into clinical trials. In radiomics, novel data-driven processes extract numerous visually imperceptible statistical features from the imaging data with no a priori assumptions on their correlation with biological processes. The selection of relevant features (radiomic signature) and incorporation into clinical trials therefore requires additional considerations to ensure meaningful imaging endpoints. Also, the number of radiomic features tested means that power calculations would result in sample sizes impossible to achieve within clinical trials. This article examines how the process of standardising and validating data-driven imaging biomarkers differs from those based on biological associations. Radiomic signatures are best developed initially on datasets that represent diversity of acquisition protocols as well as diversity of disease and of normal findings, rather than within clinical trials with standardised and optimised protocols as this would risk the selection of radiomic features being linked to the imaging process rather than the pathology. Normalisation through discretisation and feature harmonisation are essential pre-processing steps. Biological correlation may be performed after the technical and clinical validity of a radiomic signature is established, but is not mandatory. Feature selection may be part of discovery within a radiomics-specific trial or represent exploratory endpoints within an established trial; a previously validated radiomic signature may even be used as a primary/secondary endpoint, particularly if associations are demonstrated with specific biological processes and pathways being targeted within clinical trials. Key Points • Data-driven processes like radiomics risk false discoveries due to high-dimensionality of the dataset compared to sample size, making adequate diversity of the data, cross-validation and external validation essential to mitigate the risks of spurious associations and overfitting. • Use of radiomic signatures within clinical trials requires multistep standardisation of image acquisition, image analysis and data mining processes. • Biological correlation may be established after clinical validation but is not mandatory.

scholarly journals The Craterostigma plantagineum protein kinase CpWAK1 interacts with pectin and integrates different environmental signals in the cell wall

Planta ◽  
2021 ◽  
Vol 253 (5) ◽  
Author(s):  
Peilei Chen ◽  
Valentino Giarola ◽  
Dorothea Bartels
Keyword(s):  
Cell Wall ◽  
Stress Responses ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Cell Wall Protein ◽  
Biological Processes ◽  
Environmental Signals ◽  
High Affinity ◽  
Craterostigma Plantagineum ◽  
Receptor Kinases

Abstract Main conclusion The cell wall protein CpWAK1 interacts with pectin, participates in decoding cell wall signals, and induces different downstream responses. Abstract Cell wall-associated protein kinases (WAKs) are transmembrane receptor kinases. In the desiccation-tolerant resurrection plant Craterostigma plantagineum, CpWAK1 has been shown to be involved in stress responses and cell expansion by forming a complex with the C. plantagineum glycine-rich protein1 (CpGRP1). This prompted us to extend the studies of WAK genes in C. plantagineum. The phylogenetic analyses of WAKs from C. plantagineum and from other species suggest that these genes have been duplicated after species divergence. Expression profiles indicate that CpWAKs are involved in various biological processes, including dehydration-induced responses and SA- and JA-related reactions to pathogens and wounding. CpWAK1 shows a high affinity for “egg-box” pectin structures. ELISA assays revealed that the binding of CpWAKs to pectins is modulated by CpGRP1 and it depends on the apoplastic pH. The formation of CpWAK multimers is the prerequisite for the CpWAK–pectin binding. Different pectin extracts lead to opposite trends of CpWAK–pectin binding in the presence of Ca2+ at pH 8. These observations demonstrate that CpWAKs can potentially discriminate and integrate cell wall signals generated by diverse stimuli, in concert with other elements, such as CpGRP1, pHapo, Ca2+[apo], and via the formation of CpWAK multimers.

scholarly journals Methane and Inflammation - A Review (Fight Fire with Fire)

2019 ◽  
Vol 7 (1) ◽  
Author(s):  
Marietta Zita Poles ◽  
László Juhász ◽  
Mihály Boros
Keyword(s):  
Stress Responses ◽  
Nitrosative Stress ◽  
Ischemia Reperfusion ◽  
Signalling Pathways ◽  
Experimental Conditions ◽  
Neuroprotective Effects ◽  
Oxidative And Nitrosative Stress ◽  
Carbohydrate Fermentation ◽  
Insight Into

AbstractMammalian methanogenesis is regarded as an indicator of carbohydrate fermentation by anaerobic gastrointestinal flora. Once generated by microbes or released by a non-bacterial process, methane is generally considered to be biologically inactive. However, recent studies have provided evidence for methane bioactivity in various in vivo settings. The administration of methane either in gas form or solutions has been shown to have anti-inflammatory and neuroprotective effects in an array of experimental conditions, such as ischemia/reperfusion, endotoxemia and sepsis. It has also been demonstrated that exogenous methane influences the key regulatory mechanisms and cellular signalling pathways involved in oxidative and nitrosative stress responses. This review offers an insight into the latest findings on the multi-faceted organ protective activity of exogenous methane treatments with special emphasis on its versatile effects demonstrated in sepsis models.

scholarly journals Genome-wide analysis and expression profile of the bZIP gene family in poplar

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kai Zhao ◽  
Song Chen ◽  
Wenjing Yao ◽  
Zihan Cheng ◽  
Boru Zhou ◽  
...  
Keyword(s):  
Salt Stress ◽  
Systems Biology ◽  
Gene Family ◽  
Stress Responses ◽  
Metal Ion ◽  
Gene Networks ◽  
Expression Patterns ◽  
Gene Set Enrichment Analysis ◽  
Specific Gene ◽  
Biological Processes

Abstract Background The bZIP gene family, which is widely present in plants, participates in varied biological processes including growth and development and stress responses. How do the genes regulate such biological processes? Systems biology is powerful for mechanistic understanding of gene functions. However, such studies have not yet been reported in poplar. Results In this study, we identified 86 poplar bZIP transcription factors and described their conserved domains. According to the results of phylogenetic tree, we divided these members into 12 groups with specific gene structures and motif compositions. The corresponding genes that harbor a large number of segmental duplication events are unevenly distributed on the 17 poplar chromosomes. In addition, we further examined collinearity between these genes and the related genes from six other species. Evidence from transcriptomic data indicated that the bZIP genes in poplar displayed different expression patterns in roots, stems, and leaves. Furthermore, we identified 45 bZIP genes that respond to salt stress in the three tissues. We performed co-expression analysis on the representative genes, followed by gene set enrichment analysis. The results demonstrated that tissue differentially expressed genes, especially the co-expressing genes, are mainly involved in secondary metabolic and secondary metabolite biosynthetic processes. However, salt stress responsive genes and their co-expressing genes mainly participate in the regulation of metal ion transport, and methionine biosynthetic. Conclusions Using comparative genomics and systems biology approaches, we, for the first time, systematically explore the structures and functions of the bZIP gene family in poplar. It appears that the bZIP gene family plays significant roles in regulation of poplar development and growth and salt stress responses through differential gene networks or biological processes. These findings provide the foundation for genetic breeding by engineering target regulators and corresponding gene networks into poplar lines.

scholarly journals Nanometre-Scale Visualization of Chemical Parameter Changes by T1-Weighted ODMR Imaging Using a Fluorescent Nanodiamond

Chemosensors ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 68
Author(s):  
Takahiro Fujisaku ◽  
Ryuji Igarashi ◽  
Masahiro Shirakawa
Keyword(s):  
Magnetic Resonance ◽  
Laser Pulse ◽  
Real Time ◽  
Physical Parameters ◽  
Biological Processes ◽  
Chemical Parameter ◽  
Ph Conditions ◽  
Optically Detected ◽  
Life Phenomena ◽  
Selection Of

The dynamics of physical parameters in cells is strongly related to life phenomena; thus, a method to monitor and visualize them on a single-organelle scale would be useful to reveal unknown biological processes. We demonstrate real-time nanometre-scale T1-weighted imaging using a fluorescent nanodiamond. We explored optically detected magnetic resonance (ODMR) contrast at various values of interval laser pulse (τ), showing that sufficient contrast is obtained by appropriate selection of τ. By this method, we visualized nanometre-scale pH changes using a functionalized nanodiamond whose T1 has a dependence on pH conditions.

Exact analysis of the bending of wide beams by a modified elastica approach

2011 ◽  
Vol 225 (11) ◽  
pp. 2759-2764 ◽  
Author(s):  
L F Campanile ◽  
R Jähne ◽  
A Hasse
Keyword(s):  
Finite Element ◽  
Substantial Reduction ◽  
Short Review ◽  
Computational Effort ◽  
Two Dimensional ◽  
Finite Element Calculations ◽  
Dimensional Finite Element ◽  
Wide Beams ◽  
Insight Into ◽  
Selection Of

Classical beam models do not account for partial restraint of anticlastic bending and are therefore inherently inaccurate. This article proposes a modification of the exact Bernoulli–Euler equation which allows for an exact prediction of the beam's deflection without the need of two-dimensional finite element calculations. This approach offers a substantial reduction in the computational effort, especially when coupled with a fast-solving schema like the circle-arc method. Besides the description of the new method and its validation, this article offers an insight into the somewhat disregarded topic of anticlastic bending by a short review of the published theories and a selection of representative numerical results.

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