Transcription Factors and MicroRNA Interplay: A New Strategy for Crop Improvement

MicroRNAs (miRNAs) and transcription factors are master regulators of the cellular system. Plant genomes contain thousands of protein-coding and non-coding RNA genes; which are differentially expressed in different tissues at different times during growth and development. Complex regulatory networks that are controlled by transcription factors and microRNAs, which coordinate gene expression. Transcription factors, the key regulators of plant growth and development, are the targets of the miRNAs families. The combinatorial regulation of transcription factors and miRNAs guides the appropriate implementation of biological events and developmental processes. The resources on the regulatory cascades of transcription factors and miRNAs are available in the context of human diseases, but these resources are meager in case of plant diseases. On the other hand, it is also important to understand the cellular and physiological events needed to operate the miRNAs networks. The relationship between transcription factors and miRNA in different plant species described in this chapter will be of great interest to plant scientists, providing better insights into the mechanism of action and interactions among transcription factors (TFs) and miRNA networks culminating in improving key agronomic traits for crop improvement to meet the future global food demands

Establishment of a primary cell culture of Thrips palmi (Thysanoptera: Thripidae)

Thrips palmi (Thysanoptera: Thripidae) is an important pest of vegetables, ornamental plants and fruit crops. In addition to the direct damage caused by feeding, it transmits several tospoviruses. The absence of an in vitro assay system is a major bottleneck in investigating thrips-tospovirus interactions. The present study reports the establishment of a primary cell culture of T. palmi, which was initiated using embryonic tissue as an explant in modified Kimura's medium. Fibroblast-like cells began to be produced 3 h after tissue implantation and were the dominant cell type. They grew in size and number and covered most of the surface. This primary cell culture survived for 37 days providing sufficient time for analytical molecular studies on the replication of tospovirus and interactions with the vector components

Nanotechnology based approaches for detection and delivery of microRNA in healthcare and crop protection

Abstract Nanobiotechnology has the potential to revolutionize diverse sectors including medicine, agriculture, food, textile and pharmaceuticals. Disease diagnostics, therapeutics and crop protection strategies are fast emerging using nanomaterials preferably nanobiomaterials. It has potential for development of novel nanobiomolecules which offer several advantages over conventional treatment methods. RNA nanoparticles with many unique features are promising candidates in disease treatment. The miRNAs are involved in many biochemical and developmental pathways and their regulation in plants and animals. These appear to be a powerful tool for controlling various pathological diseases in human, plants and animals, however there are challenges associated with miRNA based nanotechnology. Several advancements made in the field of miRNA therapeutics make it an attractive approach, but a lot more has to be explored in nanotechnology assisted miRNA therapy. The miRNA based technologies can be employed for detection and combating crop diseases as well. Despite these potential advantages, nanobiotechnology applications in the agricultural sector are still in its infancy and have not yet made its mark in comparison with healthcare sector. The review provides a platform to discuss nature, role and use of miRNAs in nanobiotechnology applications

A rapid field-based assay using recombinase polymerase amplification for identification of Thrips palmi, a vector of tospoviruses

Thrips palmi (Thysanoptera: Thripidae) is an important pest of vegetables, ornamentals, and legumes worldwide. Besides damage caused by feeding, it transmits several tospoviruses. Identification of T. palmi at an early stage is crucial in implementing appropriate pest management strategies. Morpho-taxonomic identification of T. palmi based on the adult stage is time-consuming and needs taxonomic expertise. Here, we report a rapid, on-site, field-based assay for identification of T. palmi based on recombinase polymerase amplification (RPA), its first application in insects. RPA primers designed based on 3′ polymorphisms of the Internal Transcribed Spacer 2 region efficiently discriminated T. palmi without any cross-reactivity to\ua0other predominant thrips species. RPA was performed with crude DNA, extracted from single T. palmi simply by crushing in sterile distilled water and could be completed within 20\ua0min by holding the reaction tubes in the hand. The assay was further simplified by using fluorescent as well as colorimetric dyes thus eliminating the gel-electrophoresis steps. The presence of T. palmi was visualized by a change in color from dark blue to sky blue. The assay was validated with known thrips specimens and found to be effective in diagnosing the presence of T. palmi in natural vegetation. This on-site, rapid assay for diagnosis of T. palmi can be used by non-expert personnel in the field of quarantine and pest management

Genetic linkage mapping and QTL identification for salinity tolerance in Indian mustard (Brassica juncea L. Czern and Coss.) using SSR markers

Soil salinity is one of the major environmental constraints that limits crop yield and nearly 7% of the total area worldwide is affected by salinity. Salinity-induced oxidative stress causes membrane damage during germination and seedling growth. Indian mustard is a major oilseed crop in India and its production and productivity are severely affected by salt stress. Breeding Brassica cultivars for salinity tolerance by conventional means is very difficult and time-consuming. Therefore, understanding the molecular components associated with salt tolerance is needed to facilitate breeding for salt tolerance in Brassica. In this investigation, quantitative trait loci (QTLs) associated with salt tolerance were identified using F2:3 mapping population developed from a cross between CS52 (salinity tolerant) and RH30 (salinity sensitive). Parents and F2:3 were evaluated under controlled and salinity stress conditions for 14 morpho-physiological traits for two consecutive generations (F2 and F2:3), explaining proportion of the phenotypic variance under control condition. Simple sequence repeat (SSR) markers were used for mapping studies. A genetic linkage map based on 42 simple sequence repeats (SSRs) markers was constructed covering 2298.5 ​cM (Haldane) to identify the loci associated with salt tolerance in Brassica juncea. Forty-one SSRs showing polymorphism in the parents (CS52 and RH30) were mapped on 8 linkage groups (C1–C8). One marker (nga 129) did not map to any of the linkage group and was excluded from mapping. Linkage group 5 (C5; 317.9 ​cM) was longest and linkage group 1 (C1, 255.0 ​cM) was shortest. Further, we identified 15 QTLs controlling 8 traits using F2:3 population. These QTLs explained 12.44–60.63% of the phenotypic variation with a LOD score range of 3.62–5.97. Out of these QTLs, QMI4.1 related to membrane injury showed 51.28% phenotypic variance with a LOD score of 3.34. QTL QBYP8.1 related to biological yield per plant showed 60.63% phenotypic variance at a LOD score of 3.62. The highest LOD score of 5.97 was recorded for QTL related to seed yield per plant (QSYP4.1). Major QTLs were QTL for biological yield per plant (QBYP8.1), QTL for siliquae per plant (QSP4.1), QTL for primary branches (QPB4.1), QTLs for seed per siliqua (QSS4.1, QSS4.2), QTL for seed yield per plant (QSYP4.1), and QTL for membrane injury (QMI8.1) which showed more than 50% phenotypic variance. These QTLs identified in our study need to be confirmed in other populations as well so that these can be used in marker-assisted selection and breeding to enhance salt tolerance in Brassica juncea

Assessment of Fine Particulate Matter for Port City of Eastern Peninsular India Using Gradient Boosting Machine Learning Model

An assessment and prediction of PM2.5 for a port city of eastern peninsular India is presented. Fifteen machine learning (ML) regression models were trained, tested and implemented to predict the PM2.5 concentration. The predicting ability of regression models was validated using air pollutants and meteorological parameters as input variables collected from sites located at Visakhapatnam, a port city on the eastern side of peninsular India, for the assessment period 2018–2019. Highly correlated air pollutants and meteorological parameters with PM2.5 concentration were evaluated and presented during the period under study. It was found that the CatBoost regression model outperformed all other employed regression models in predicting PM2.5 concentration with an R2 score (coefficient of determination) of 0.81, median absolute error (MedAE) of 6.95 µg/m3, mean absolute percentage error (MAPE) of 0.29, root mean square error (RMSE) of 11.42 µg/m3 and mean absolute error (MAE) of 9.07 µg/m3. High PM2.5 concentration prediction results in contrast to Indian standards were also presented. In depth seasonal assessments of PM2.5 concentration were presented, to show variance in PM2.5 concentration during dominant seasons

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Not AvailableThrips palmi (Thysanoptera: Thripidae) is the predominant tospovirus vector in Asia-Pacific region. It transmits economically damaging groundnut bud necrosis virus (GBNV, family Tospoviridae) in a persistent propagative manner. Thrips serve as the alternate host, and virus reservoirs making tospovirus management very challenging. Insecticides and host plant resistance remain ineffective in managing thrips–tospoviruses. Recent genomic approaches have led to understanding the molecular interactions of thrips–tospoviruses and identifying novel genetic targets. However, most of the studies are limited to Frankliniella species and tomato spotted wilt virus (TSWV). Amidst the limited information available on T. palmi–tospovirus relationships, the present study is the first report of the transcriptome-wide response of T. palmi associated with GBNV infection. The differential expression analyses of the triplicate transcriptome of viruliferous vs. nonviruliferous adult T. palmi identified a total of 2,363 (1,383 upregulated and 980 downregulated) significant transcripts. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses showed the abundance of differentially expressed genes (DEGs) involved in innate immune response, endocytosis, cuticle development, and receptor binding and signaling that mediate the virus invasion and multiplication in the vector system. Also, the gene regulatory network (GRN) of most significant DEGs showed the genes like ABC transporter, cytochrome P450, endocuticle structural glycoprotein, gamma-aminobutyric acid (GABA) receptor, heat shock protein 70, larval and pupal cuticle proteins, nephrin, proline-rich protein, sperm-associated antigen, UHRF1-binding protein, serpin, tyrosine–protein kinase receptor, etc., were enriched with higher degrees of interactions. Further, the expression of the candidate genes in response to GBNV infection was validated in reverse transcriptase-quantitative real-time PCR (RT-qPCR). This study leads to an understanding of molecular interactions between T. palmi and GBNV and suggests potential genetic targets for generic pest control.Not Availabl

TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation

The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently affecting millions of lives worldwide. Large retrospective studies indicate that an elevated level of inflammatory cytokines and pro-inflammatory factors are associated with both increased disease severity and mortality. Here, using multidimensional epigenetic, transcriptional, in vitro, and in vivo analyses, we report that topoisomerase 1 (TOP1) inhibition suppresses lethal inflammation induced by SARS-CoV-2. Therapeutic treatment with two doses of topotecan (TPT), an FDA-approved TOP1 inhibitor, suppresses infection-induced inflammation in hamsters. TPT treatment as late as 4 days post-infection reduces morbidity and rescues mortality in a transgenic mouse model. These results support the potential of TOP1 inhibition as an effective host-directed therapy against severe SARS-CoV-2 infection. TPT and its derivatives are inexpensive clinical-grade inhibitors available in most countries. Clinical trials are needed to evaluate the efficacy of repurposing TOP1 inhibitors for severe coronavirus disease 2019 (COVID-19) in humans