Regulatory mechanisms of plant rhizobacteria on plants to the adaptation of adverse agroclimatic variables.

The mutualistic plant rhizobacteria which improve plant development and productivity are known as plant growth-promoting rhizobacteria (PGPR). It is more significant due to their ability to help the plants in different ways. The main physiological responses, such as malondialdehyde, membrane stability index, relative leaf water content, photosynthetic leaf gas exchange, chlorophyll fluorescence efficiency of photosystem-II, and photosynthetic pigments are observed in plants during unfavorable environmental conditions. Plant rhizobacteria are one of the more crucial chemical messengers that mediate plant development in response to stressed conditions. The interaction of plant rhizobacteria with essential plant nutrition can enhance the agricultural sustainability of various plant genotypes or cultivars. Rhizobacterial inoculated plants induce biochemical variations resulting in increased stress resistance efficiency, defined as induced systemic resistance. Omic strategies revealed plant rhizobacteria inoculation caused the upregulation of stress-responsive genes-numerous recent approaches have been developed to protect plants from unfavorable environmental threats. The plant microbes and compounds they secrete constitute valuable biostimulants and play significant roles in regulating plant stress mechanisms. The present review summarized the recent developments in the functional characteristics and action mechanisms of plant rhizobacteria in sustaining the development and production of plants under unfavorable environmental conditions, with special attention on plant rhizobacteria-mediated physiological and molecular responses associated with stress-induced responses.

Dynamic Reconfiguration of Brain Functional Network in Stroke.

The brain continually reorganizes its functional network to adapt to post-stroke functional impairments. Previous studies using static modularity analysis have presented global-level behavior patterns of this network reorganization. However, it is far from understood how the brain reconfigures its functional network dynamically following a stroke. This study collected resting-state functional MRI data from 15 stroke patients, with mild (n = 6) and severe (n = 9) two subgroups based on their clinical symptoms. Additionally, 15 age-matched healthy subjects were considered as controls. By applying a multilayer temporal network method, a dynamic modular structure was recognized based on a time-resolved function network. The dynamic network measurements (recruitment, integration, and flexibility) were calculated to characterize the dynamic reconfiguration of post-stroke brain functional networks, hence, revealing the neural functional rebuilding process. It was found from this investigation that severe patients tended to have reduced recruitment and increased between-network integration, while mild patients exhibited low network flexibility and less network integration. It's also noted that previous studies using static methods could not reveal this severity-dependent alteration in network interaction. Clinically, the obtained knowledge of the diverse patterns of dynamic adjustment in brain functional networks observed from the brain neuronal images could help understand the underlying mechanism of the motor, speech, and cognitive functional impairments caused by stroke attacks. The present method not only could be used to evaluate patients' current brain status but also has the potential to provide insights into prognosis analysis and prediction.

Evaluation of Module Dynamics in Functional Brain Networks After Stroke.

The brain's functional network can be analyzed as a set of distributed functional modules. Previous studies using the static method suggested the modularity of the brain function network decreased due to stroke; however, how the modular network changes after stroke, particularly over time, is far from understood. This study collected resting-state functional MRI data from 15 stroke patients and 15 age-matched healthy controls. The patients exhibit distinct clinical symptoms, presenting in mild (n = 6) and severe (n = 9) subgroups. By using a multilayer network model, a dynamic modular structure was detected and corresponding interaction measurements were calculated. The results demonstrated that the module structure and interaction had changed following the stroke. Importantly, the significant differences in dynamic interaction measures demonstrated that the module interaction alterations were not independent of the initial degree of clinical severity. Mild patients were observed to have a significantly lower between-module interaction than severe patients as well as healthy controls. In contrast, severe patients showed remarkably lower within-module interaction and had a reduced overall interaction compared to healthy controls. These findings contributed to the development of post-stroke dynamics analysis and shed new light on brain network interaction for stroke patients.Clinical relevance- Dynamic module interaction analysis underpins the post-stroke functional plasticity and reorganization, and may enable new insight into rehabilitation strategies to promote recovery of function.

Tracking functional network connectivity dynamics in the elderly.

Introduction: Functional magnetic resonance imaging (fMRI) has shown that aging disturbs healthy brain organization and functional connectivity. However, how this age-induced alteration impacts dynamic brain function interaction has not yet been fully investigated. Dynamic function network connectivity (DFNC) analysis can produce a brain representation based on the time-varying network connectivity changes, which can be further used to study the brain aging mechanism for people at different age stages. Method: This presented investigation examined the dynamic functional connectivity representation and its relationship with brain age for people at an elderly stage as well as in early adulthood. Specifically, the resting-state fMRI data from the University of North Carolina cohort of 34 young adults and 28 elderly participants were fed into a DFNC analysis pipeline. This DFNC pipeline forms an integrated dynamic functional connectivity (FC) analysis framework, which consists of brain functional network parcellation, dynamic FC feature extraction, and FC dynamics examination. Results: The statistical analysis demonstrates that extensive dynamic connection changes in the elderly concerning the transient brain state and the method of functional interaction in the brain. In addition, various machine learning algorithms have been developed to verify the ability of dynamic FC features to distinguish the age stage. The fraction time of DFNC states has the highest performance, which can achieve a classification accuracy of over 88% by a decision tree. Discussion: The results proved there are dynamic FC alterations in the elderly, and the alteration was found to be correlated with mnemonic discrimination ability and could have an impact on the balance of functional integration and segregation.

Transcriptomic responses of Saccharum spontaneum roots in response to polyethylene glycol - 6000 stimulated drought stress.

Drought is the abiotic factor that adversely affects plant growth, development survival, and crop productivity, posing a substantial threat to sustainable agriculture worldwide, especially in warm and dry areas. However, the extent of damage depends upon the crop growth stage, severity and frequency of the stress. In general, the reproductive growth phase is more sensitive to stresses causing a substantial loss in crop productivity. Saccharum spontaneum (L.) is the most variable wild relative of sugarcane with potential for use in sugarcane crop improvement programs. In the present study addresses the transcriptomic analysis of drought stress imposed by polyethylene glycol-6000 (PED-6000; w/v- 25%) on the root tip tissues of S. spontaneum GX83-10. The analysis of microarrays of drought-stressed roots was performed at 0 (CK), 2 (T2), 4 (T4), 8 (T8) and 24 h (T24). The analyzed data were compared with the gene function annotations of four major databases, such as Nr, KOG/COG, Swiss-Prot, and KEGG, and a total of 62,988 single-gene information was obtained. The differently expressed genes of 56237 (T4), 59319 (T8), and 58583 (T24), among which CK obtained the most significant number of expressed genes (35920) as compared to T24, with a total of 53683 trend genes. Gene ontology (GO) and KEGG analysis were performed on the 6 important trends, and a total of 598 significant GO IDs and 42 significantly enriched metabolic pathways. Furthermore, these findings also aid in the selection of novel genes and promoters that can be used to potentially produce crop plants with enhanced stress resistance efficiency for sustainable agriculture.

Transcriptome Analysis Reveals a Gene Expression Pattern That Contributes to Sugarcane Bud Propagation Induced by Indole-3-Butyric Acid.

Sugarcane is a cash crop that plays an integral part in the sugar industry. The Sustainable Sugarcane Initiative (SSI) has been adopted globally, ensuring enough and aiming for more yield, helping increase disease-free sugarcane cultivation. Single-bud seeds could be the best approach for sugarcane cultivation. Indole-3-butyric acid (IBA) is a rooting agent utilized significantly in seedling propagation. Greenhouse experiment results discovered the significant growth promotion in sugarcane seedlings and accumulation of plant hormones at 100 ppm IBA. Next, we performed transcriptomic analysis of sugarcane buds using RNA sequencing and compared their gene expression during root development due to affect of IBA (100 ppm). A total of 113,475 unigenes were annotated with an average length of 836 bp (N50 = 1,536). The comparative RNA-seq study between the control (CK) and IBA-treated (T) buds showed significant differentially expressed unigenes (494 upregulated and 2086 downregulated). The IBA influenced major biological processes including metabolic process, the cellular process, and single-organism process. For cellular component category, cell, cell part, organelle, membrane, and organelle part were mainly affected. In addition, catalytic activity and binding were primarily affected in the molecular function categories. Furthermore, the expression of genes related to plant hormones and signaling pathways was analyzed by qRT-PCR, which was consistent with the RNA-seq expression profile. This study provides new insights into the IBA response to the bud sprouting in sugarcane based on RNA sequencing, and generated information could help further research on breeding improvement of sugarcane.

Nanosilicon: An approach for abiotic stress mitigation and sustainable agriculture.

Abiotic stresses causing extensive yield loss in various crops globally. Over the past few decades, the application of silicon nanoparticles (nSi) has emerged as one of the abiotic stress mitigators. The initial responses of plants are shown by the biogenesis of reactive oxygen species (ROS) to sustain cellular/organellar integrity to ensure in vivo operation of metabolic functions by regulating physiological and biochemical pathways during stress conditions. Plants have evolved various antioxidative systems to balance/maintain the process of homeostasis via enzymatic and non-enzymatic activities to repair the losses. In the adverse environment, supplementation of Si mitigates the stress condition and improved the growth and development of plants. Its ameliorative effects were correlated with the enhanced antioxidant enzymes activities to maintain the equilibrium between the ROS generation and reduction. However, there are limited studies covered the role of nSi in the abiotic stress condition. This review addresses the accumulation and/or uptake of nSi in several crops and its mode of action linked with improved plants' growth and tolerance capabilities to confer sustainable agriculture.

Weakly-supervised lesion analysis with a CNN-based framework for COVID-19.

Objective.Lesions of COVID-19 can be clearly visualized using chest CT images, and hence provide valuable evidence for clinicians when making a diagnosis. However, due to the variety of COVID-19 lesions and the complexity of the manual delineation procedure, automatic analysis of lesions with unknown and diverse types from a CT image remains a challenging task. In this paper we propose a weakly-supervised framework for this task requiring only a series of normal and abnormal CT images without the need for annotations of the specific locations and types of lesions.Approach.A deep learning-based diagnosis branch is employed for classification of the CT image and then a lesion identification branch is leveraged to capture multiple types of lesions.Main Results.Our framework is verified on publicly available datasets and CT data collected from 13 patients of the First Affiliated Hospital of Shantou University Medical College, China. The results show that the proposed framework can achieve state-of-the-art diagnosis prediction, and the extracted lesion features are capable of distinguishing between lesions showing ground glass opacity and consolidation.Significance.The proposed approach integrates COVID-19 positive diagnosis and lesion analysis into a unified framework without extra pixel-wise supervision. Further exploration also demonstrates that this framework has the potential to discover lesion types that have not been reported and can potentially be generalized to lesion detection of other chest-based diseases.

Functional relationship between photosynthetic leaf gas exchange in response to silicon application and water stress mitigation in sugarcane.

BACKGROUND: Water stress is one of the serious abiotic stresses that negatively influences the growth, development and production of sugarcane in arid and semi-arid regions. However, silicon (Si) has been applied as an alleviation strategy subjected to environmental stresses. METHODS: In this experiment, Si was applied as soil irrigation in sugarcane plants to understand the mitigation effect of Si against harmful impact of water stress on photosynthetic leaf gas exchange. RESULTS: In the present study we primarily revealed the consequences of low soil moisture content, which affect overall plant performance of sugarcane significantly. Silicon application reduced the adverse effects of water stress by improving the net photosynthetic assimilation rate (Anet) 1.35-18.75%, stomatal conductance to water vapour (gs) 3.26-21.57% and rate of transpiration (E) 1.16-17.83%. The mathematical models developed from the proposed hypothesis explained the functional relationships between photosynthetic responses of Si application and water stress mitigation. CONCLUSIONS: Silicon application showed high ameliorative effects on photosynthetic responses of sugarcane to water stress and could be used for mitigating environmental stresses in other crops, too, in future.

Functional relationship between photosynthetic leaf gas exchange in response to silicon application and water stress mitigation in sugarcane

BACKGROUND: Water stress is one of the serious abiotic stresses that negatively influences the growth, development and production of sugarcane in arid and semi-arid regions. However, silicon (Si) has been applied as an alleviation strategy subjected to environmental stresses. METHODS: In this experiment, Si was applied as soil irrigation in sugarcane plants to understand the mitigation effect of Si against harmful impact of water stress on photosynthetic leaf gas exchange. RESULTS: In the present study we primarily revealed the consequences of low soil moisture content, which affect overall plant performance of sugarcane significantly. Silicon application reduced the adverse effects of water stress by improving the net photosynthetic assimilation rate (Anet) 1.35-18.75%, stomatal conductance to water vapour (gs) 3.26-21.57% and rate of transpiration (E) 1.16-17.83%. The mathematical models developed from the proposed hypothesis explained the functional relationships between photosynthetic responses of Si application and water stress mitigation. CONCLUSIONS: Silicon application showed high ameliorative effects on photosynthetic responses of sugarcane to water stress and could be used for mitigating environmental stresses in other crops, too, in future.

Developing mathematical model for diurnal dynamics of photosynthesis in Saccharum officinarum responsive to different irrigation and silicon application.

In the dynamic era of climate change, agricultural farming systems are facing various unprecedented problems worldwide. Drought stress is one of the serious abiotic stresses that hinder the growth potential and crop productivity. Silicon (Si) can improve crop yield by enhancing the efficiency of inputs and reducing relevant losses. As a quasi-essential element and the 2nd most abundant element in the Earth's crust, Si is utilized by plants and applied exogenously to combat drought stress and improve plant performance by increasing physiological, cellular and molecular responses. However, the physiological mechanisms that respond to water stress are still not well defined in Saccharum officinarum plants. To the best of our knowledge, the dynamics of photosynthesis responsive to different exogenous Si levels in Saccharum officinarum has not been reported to date. The current experiment was carried out to assess the protective role of Si in plant growth and photosynthetic responses in Saccharum officinarum under water stress conditions. Saccharum officinarum cv. 'GT 42' plants were subjected to drought stress conditions (80-75%, 55-50% and 35-30% of soil moisture) after ten weeks of normal growth, followed by the soil irrigation of Si (0, 100, 300 and 500 mg L-1) for 8 weeks. The results indicated that Si addition mitigated the inhibition in Saccharum officinarum growth and photosynthesis, and improved biomass accumulation during water stress. The photosynthetic responses (photosynthesis, transpiration and stomatal conductance) were found down-regulated under water stress, and it was significantly enhanced by Si application. No phytotoxic effects were monitored even at excess (500 mg L-1). Soil irrigation of 300 mg L-1 of Si was more effective as 100 and 500 mg L-1 under water stress condition. It is concluded that the stress in Saccharum officinarum plants applied with Si was alleviated by improving plant fitness, photosynthetic capacity and biomass accumulation as compared with the control. Thus, this study offers new information towards the assessment of growth, biomass accumulation and physiological changes related to water stress with Si application in plants.

Genome-wide identification of leaf abscission associated microRNAs in sugarcane (Saccharum officinarum L.).

BACKGROUND: Sugarcane (Saccharum officinarum L.) is an economically important crop, mainly due to the production of sugar and biofuel (Azevedo RA, Carvalho RF, Cia MC, & Gratão PL, Trop Plant Biol 4:42-51, 2011). Grown mainly in tropical and subtropical countries, sugarcane is a highly polyploid plant with up to ten copies of each chromosome, which increases the difficulties of genome assembly and genetic, physiologic and biochemical analyses. The increasing demands of sugar and the increasing cost of sugarcane harvest require sugarcane varieties which can shed their leaves during the maturity time, so it is important to study the mechanism of leaf abscission in sugarcane. RESULTS: To improve the understanding of miRNA roles in sugarcane leaf abscission, we reported the genome-wide characterization of miRNAs and their putative targets in sugarcane using deep sequencing for six small RNA libraries. In total, 93 conserved miRNAs and 454 novel miRNAs were identified in sugarcane using previously reported transcriptome as reference. Among them, 25 up-regulated and 13 down-regulated miRNAs were identified in leaf abscission sugarcane plants (LASP) compared to leaf packaging sugarcane plants (LPSP). Target prediction revealed several miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC3 might be involved in the sugarcane leaf abscission. KEGG pathway enrichment analysis showed differentially expressed miRNAs may regulate pathways like "plant hormone signal transduction" and "plant-pathogen interaction", which is consistent with previous transcriptome study. In addition, we identified 96 variant miRNAs with 135 single nucleotide polymorphisms (SNPs). The expression of sugarcane miRNAs and variant miRNAs were confirmed by qRT-PCR. We identified a possible poaceae specific miRNA called miR5384 for the first time in sugarcane. CONCLUSIONS: We not only reported miR5384, a possible poaceae specific miRNA, for the first time in sugarcane but also presented some miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC in sugarcane. These modules might be involved in the regulation of sugarcane leaf abscission during the maturity time. All of these findings may lay ground work for future application of sugarcane breeding program and benefit research studies of sugarcane miRNAs.

Molecular Characterization of LRB7 Gene and a Water Channel Protein TIP2 in Chorispora bungeana.

Background. Water channel proteins, also called aquaporins, are integral membrane proteins from major intrinsic protein (MIP) family and involved in several pathways including not only water transport but also cell signaling, reproduction, and photosynthesis. The full cDNA and protein sequences of aquaporin in Chorispora bungeana Fisch. & C.A. Mey (C. bungeana) are still unknown. Results. In this study, PCR and rapid amplification of cDNA ends approaches were used to clone the full cDNA of LRB7 (GenBank accession number: EU636988) of C. bungeana. Sequence analysis indicated that it was 1235 bp, which had two introns and encoded a protein of 250 amino acids. Structure analysis revealed that the protein had two conserved NPA motifs, one of which is MIP signature sequence (SGxHxNPAVT), six membrane helix regions, and additional membrane-embedded domains. Phylogenetic analysis suggested that the protein was from TIP2 subgroup. Surprisingly, semiquantitative RT-PCR experiment and western blot analysis showed that LRB7 and TIP2 were only detectable in roots, unlike Arabidopsis and Raphanus. Connecting with our previous studies, LRB7 was supported to associate with chilling-tolerance in C. bungeana. Conclusion. This is the first time to characterize the full sequences of LRB7 gene and water channel protein in C. bungeana. Our findings contribute to understanding the water transports in plants under low temperatures.

De novo analysis of transcriptome reveals genes associated with leaf abscission in sugarcane (Saccharum officinarum L.).

BACKGROUND: Sugarcane (Saccharum officinarum L.) is an important sugar crop which belongs to the grass family and can be used for fuel ethanol production. The growing demands for sugar and biofuel is asking for breeding a sugarcane variety that can shed their leaves during the maturity time due to the increasing cost on sugarcane harvest. RESULTS: To determine leaf abscission related genes in sugarcane, we generated 524,328,950 paired reads with RNA-Seq and profiled the transcriptome of new born leaves of leaf abscission sugarcane varieties (Q1 and T) and leaf packaging sugarcane varieties (Q2 and B). Initially, 275,018 transcripts were assembled with N50 of 1,177 bp. Next, the transcriptome was annotated by mapping them to NR, UniProtKB/Swiss-Prot, Gene Ontology and KEGG pathway databases. Further, we used TransDecoder and Trinotate to obtain the likely proteins and annotate them in terms of known proteins, protein domains, signal peptides, transmembrane regions and rRNA transcripts. Different expression analysis showed 1,202 transcripts were up regulated in leaf abscission sugarcane varieties, relatively to the leaf packaging sugarcane varieties. Functional analysis told us 62, 38 and 10 upregulated transcripts were involved in plant-pathogen interaction, response to stress and abscisic acid associated pathways, respectively. The upregulation of transcripts encoding 4 disease resistance proteins (RPM1, RPP13, RGA2, and RGA4), 6 ABC transporter G family members and 16 transcription factors including WRK33 and heat stress transcription factors indicate they may be used as candidate genes for sugarcane breeding. The expression levels of transcripts were validated by qRT-PCR. In addition, we characterized 3,722 SNPs between leaf abscission and leaf packaging sugarcane plants. CONCLUSION: Our results showed leaf abscission associated genes in sugarcane during the maturity period. The output of this study provides a valuable resource for future genetic and genomic studies in sugarcane.