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

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.

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An Insight into Oligopeptide Transporter 3 (OPT3) family proteins

Protein and Peptide Letters ◽

10.2174/0929866527666200625202028 ◽

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.

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

European Radiology ◽

10.1007/s00330-020-07598-8 ◽

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.

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PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response

BMC Genomics ◽

10.1186/s12864-021-07366-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Xiaojie Liu ◽

Xiaoshuang Li ◽

Xuejing Wen ◽

Yan Zhang ◽

Yu Ding ◽

...

Keyword(s):

Dynamic Response ◽

Early Response ◽

Full Length ◽

Differentially Expressed ◽

Late Response ◽

Response Mechanism ◽

Necrotrophic Pathogen ◽

Canker Disease ◽

Malus Sieversii ◽

Highly Correlated

Abstract Background Valsa canker is a serious disease in the stem of Malus sieversii, caused by Valsa mali. However, little is known about the global response mechanism in M. sieversii to V. mali infection. Results Phytohormone jasmonic acid (JA) and salicylic acid (SA) profiles and transcriptome analysis were used to elaborate on the dynamic response mechanism. We determined that the JA was initially produced to respond to the necrotrophic pathogen V. mali infection at the early response stage, then get synergistically transduced with SA to respond at the late response stage. Furthermore, we adopted Pacific Biosciences (PacBio) full-length sequencing to identify differentially expressed transcripts (DETs) during the canker response stage. We obtained 52,538 full-length transcripts, of which 8139 were DETs. Total 1336 lncRNAs, 23,737 alternative polyadenylation (APA) sites and 3780 putative transcription factors (TFs) were identified. Additionally, functional annotation analysis of DETs indicated that the wild apple response to the infection of V. mali involves plant-pathogen interaction, plant hormone signal transduction, flavonoid biosynthesis, and phenylpropanoid biosynthesis. The co-expression network of the differentially expressed TFs revealed 264 candidate TF transcripts. Among these candidates, the WRKY family was the most abundant. The MsWRKY7 and MsWRKY33 were highly correlated at the early response stage, and MsWRKY6, MsWRKY7, MsWRKY19, MsWRKY33, MsWRKY40, MsWRKY45, MsWRKY51, MsWRKY61, MsWRKY75 were highly correlated at the late stage. Conclusions The full-length transcriptomic analysis revealed a series of immune responsive events in M. sieversii in response to V. mali infection. The phytohormone signal pathway regulatory played an important role in the response stage. Additionally, the enriched disease resistance pathways and differentially expressed TFs dynamics collectively contributed to the immune response. This study provides valuable insights into a dynamic response in M. sieversii upon the necrotrophic pathogen V. mali infection, facilitates understanding of response mechanisms to canker disease for apple, and provides supports in the identification of potential resistance genes in M. sieversii.

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

Chemosensors ◽

10.3390/chemosensors8030068 ◽

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.

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Desiccation-tolerance specific gene expression in leaf tissue of the resurrection plant Sporobolus stapfianus

Functional Plant Biology ◽

10.1071/fp06231 ◽

2007 ◽

Vol 34 (7) ◽

pp. 589 ◽

Cited By ~ 20

Author(s):

Tuan Ngoc Le ◽

Cecilia K. Blomstedt ◽

Jianbo Kuang ◽

Jennifer Tenlen ◽

Donald F. Gaff ◽

...

Keyword(s):

Drought Stress ◽

Desiccation Tolerance ◽

Molecular Mechanisms ◽

Leaf Tissue ◽

Resurrection Plant ◽

Specific Gene ◽

Irreversible Damage ◽

Cellular Processes ◽

Sporobolus Stapfianus ◽

Normal Metabolism

The desiccation tolerant grass Sporobolus stapfianus Gandoger can modulate cellular processes to prevent the imposition of irreversible damage to cellular components by water deficit. The cellular processes conferring this ability are rapidly attenuated by increased water availability. This resurrection plant can quickly restore normal metabolism. Even after loss of more than 95% of its total water content, full rehydration and growth resumption can occur within 24 h. To study the molecular mechanisms of desiccation tolerance in S. stapfianus, a cDNA library constructed from dehydration-stressed leaf tissue, was differentially screened in a manner designed to identify genes with an adaptive role in desiccation tolerance. Further characterisation of four of the genes isolated revealed they are strongly up-regulated by severe dehydration stress and only in desiccation-tolerant tissue, with three of these genes not being expressed at detectable levels in hydrated or dehydrating desiccation-sensitive tissue. The nature of the putative proteins encoded by these genes are suggestive of molecular processes associated with protecting the plant against damage caused by desiccation and include a novel LEA-like protein, and a pore-like protein that may play an important role in peroxisome function during drought stress. A third gene product has similarity to a nuclear-localised protein implicated in chromatin remodelling. In addition, a UDPglucose glucosyltransferase gene has been identified that may play a role in controlling the bioactivity of plant hormones or secondary metabolites during drought stress.

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

Proceedings of the Institution of Mechanical Engineers Part C Journal of Mechanical Engineering Science ◽

10.1177/0954406211417753 ◽

2011 ◽

Vol 225 (11) ◽

pp. 2759-2764 ◽

Cited By ~ 8

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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Design and topological optimization of rear pressure bulkhead for a typical aircraft

Aircraft Engineering and Aerospace Technology ◽

10.1108/aeat-05-2020-0097 ◽

2021 ◽

Vol ahead-of-print (ahead-of-print) ◽

Author(s):

Marshal Thakran ◽

Meenakshi ◽

Jitender Sharma ◽

Charles Gilbert Martin

Keyword(s):

Numerical Analysis ◽

Significant Influence ◽

Design Methodology ◽

Structural Integrity ◽

Topological Optimization ◽

Content Type ◽

Iterative Design ◽

Practical Implications ◽

Insight Into ◽

Selection Of

Purpose The purpose of this paper is to evaluate the model of a rear pressure bulkhead with different design optimizations to meet the pressurized cabin requirements of an aircraft. Design/methodology/approach This paper presents the results of the static analysis of a dome-shaped rear pressure bulkhead model designed in Catia-v5. Numerical analysis of model meshed in hyper-mesh and solved using Opti-Struct for iterative design optimizations. Findings All the iterative models are analyzed at 9 Psi. Rear pressure bulkhead designed with L-section stringer shows better results than the model optimized with T-section stringer for the same thickness. The model optimized with L-shaped stinger also reduces the weight of the bulkhead without affecting the structural integrity. Practical implications It has been concluded in this paper that the selection of specific shapes of the stringers shows a significant influence on weight reduction. Originality/value This paper provides a topical, technical insight into the design and development of a rear pressure bulkhead. It also outlines the future development of dome-shaped rear pressure bulkhead.

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Paradata in Documentation Standards and Recommendations for Digital Archaeological Visualisations

Digital Culture & Society ◽

10.14361/dcs-2020-0210 ◽

2020 ◽

Vol 6 (2) ◽

pp. 191-220

Author(s):

Lisa Börjesson ◽

Olle Sköld ◽

Isto Huvila

Keyword(s):

Research Data ◽

Data Reuse ◽

Lack Of Information ◽

National Heritage ◽

Processing History ◽

International Harmonisation ◽

Insight Into ◽

Current Standards ◽

Selection Of ◽

As If

Abstract Digitalisation of research data and massive efforts to make it findable, accessible, interoperable, and reusable has revealed that in addition to an eventual lack of description of the data itself (metadata), data reuse is often obstructed by the lack of information about the datamaking and interpretation (i.e. paradata). In search of the extent and composition of categories for describing processes, this article reviews a selection of standards and recommendations frequently referred to as useful for documenting archaeological visualisations. It provides insight into 1) how current standards can be employed to document provenance and processing history (i.e. paradata), and 2) what aspects of the processing history can be made transparent using current standards and which aspects are pushed back or hidden. The findings show that processes are often either completely absent or only partially addressed in the standards. However, instead of criticising standards for bias and omissions as if a perfect description of everything would be attainable, the findings point to the need for a comprehensive consideration of the space a standard is operating in (e.g. national heritage administration or international harmonisation of data). When a standard is used in a specific space it makes particular processes, methods, or tools transparent. Given these premises, if the standard helps to document what needs to be documented (e.g. paradata), and if it provides a type of transparency required in a certain space, it is reasonable to deem the standard good enough for that purpose.

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