Tailoring crops with superior product quality through genome editing: an update.

MAIN CONCLUSION: In this review, using genome editing, the quality trait alterations in important crops have been discussed, along with the challenges encountered to maintain the crop products' quality. The delivery of economic produce with superior quality is as important as high yield since it dictates consumer's acceptance and end use. Improving product quality of various agricultural and horticultural crops is one of the important targets of plant breeders across the globe. Significant achievements have been made in various crops using conventional plant breeding approaches, albeit, at a slower rate. To keep pace with ever-changing consumer tastes and preferences and industry demands, such efforts must be supplemented with biotechnological tools. Fortunately, many of the quality attributes are resultant of well-understood biochemical pathways with characterized genes encoding enzymes at each step. Targeted mutagenesis and transgene transfer have been instrumental in bringing out desired qualitative changes in crops but have suffered from various pitfalls. Genome editing, a technique for methodical and site-specific modification of genes, has revolutionized trait manipulation. With the evolution of versatile and cost effective CRISPR/Cas9 system, genome editing has gained significant traction and is being applied in several crops. The availability of whole genome sequences with the advent of next generation sequencing (NGS) technologies further enhanced the precision of these techniques. CRISPR/Cas9 system has also been utilized for desirable modifications in quality attributes of various crops such as rice, wheat, maize, barley, potato, tomato, etc. The present review summarizes salient findings and achievements of application of genome editing for improving product quality in various crops coupled with pointers for future research endeavors.

miR-155 activates cytokine gene expression in Th17 cells by regulating the DNA-binding protein Jarid2 to relieve polycomb-mediated repression.

Specification of the T helper 17 (Th17) cell lineage requires a well-defined set of transcription factors, but how these integrate with posttranscriptional and epigenetic programs to regulate gene expression is poorly understood. Here we found defective Th17 cell cytokine expression in miR-155-deficient CD4+ T cells in vitro and in vivo. Mir155 was bound by Th17 cell transcription factors and was highly expressed during Th17 cell differentiation. miR-155-deficient Th17 and T regulatory (Treg) cells expressed increased amounts of Jarid2, a DNA-binding protein that recruits the Polycomb Repressive Complex 2 (PRC2) to chromatin. PRC2 binding to chromatin and H3K27 histone methylation was increased in miR-155-deficient cells, coinciding with failure to express Il22, Il10, Il9, and Atf3. Defects in Th17 cell cytokine expression and Treg cell homeostasis in the absence of Mir155 could be partially suppressed by Jarid2 deletion. Thus, miR-155 contributes to Th17 cell function by suppressing the inhibitory effects of Jarid2.

Salinity stress tolerance and omics approaches: revisiting the progress and achievements in major cereal crops.

Salinity stress adversely affects plant growth and causes considerable losses in cereal crops. Salinity stress tolerance is a complex phenomenon, imparted by the interaction of compounds involved in various biochemical and physiological processes. Conventional breeding for salt stress tolerance has had limited success. However, the availability of molecular marker-based high-density linkage maps in the last two decades boosted genomics-based quantitative trait loci (QTL) mapping and QTL-seq approaches for fine mapping important major QTL for salinity stress tolerance in rice, wheat, and maize. For example, in rice, 'Saltol' QTL was successfully introgressed for tolerance to salt stress, particularly at the seedling stage. Transcriptomics, proteomics and metabolomics also offer opportunities to decipher and understand the molecular basis of stress tolerance. The use of proteomics and metabolomics-based metabolite markers can serve as an efficient selection tool as a substitute for phenotype-based selection. This review covers the molecular mechanisms for salinity stress tolerance, recent progress in mapping and introgressing major gene/QTL (genomics), transcriptomics, proteomics, and metabolomics in major cereals, viz., rice, wheat and maize.

Genome-Wide Association Mapping Reveals Novel Putative Gene Candidates Governing Reproductive Stage Heat Stress Tolerance in Rice.

Temperature rise predicted for the future will severely affect rice productivity because the crop is highly sensitive to heat stress at the reproductive stage. Breeding tolerant varieties is an economically viable option to combat heat stress, for which the knowledge of target genomic regions associated with the reproductive stage heat stress tolerance (RSHT) is essential. A set of 192 rice genotypes of diverse origins were evaluated under natural field conditions through staggered sowings for RSHT using two surrogate traits, spikelet fertility and grain yield, which showed significant reduction under heat stress. These genotypes were genotyped using a 50 k SNP array, and the association analysis identified 10 quantitative trait nucleotides (QTNs) for grain yield, of which one QTN (qHTGY8.1) was consistent across the different models used. Only two out of 10 MTAs coincided with the previously reported QTLs, making the remaing eight novel. A total of 22 QTNs were observed for spikelet fertility, among which qHTSF5.1 was consistently found across three models. Of the QTNs identified, seven coincided with previous reports, while the remaining QTNs were new. The genes near the QTNs were found associated with the protein-protein interaction, protein ubiquitination, stress signal transduction, and so forth, qualifying them to be putative for RSHT. An in silico expression analysis revealed the predominant expression of genes identified for spikelet fertility in reproductive organs. Further validation of the biological relevance of QTNs in conferring heat stress tolerance will enable their utilization in improving the reproductive stage heat stress tolerance in rice.

Influence of host genotype in establishing root associated microbiome of indica rice cultivars for plant growth promotion.

Rice plants display a unique root ecosystem comprising oxic-anoxic zones, harboring a plethora of metabolic interactions mediated by its root microbiome. Since agricultural land is limited, an increase in rice production will rely on novel methods of yield enhancement. The nascent concept of tailoring plant phenotype through the intervention of synthetic microbial communities (SynComs) is inspired by the genetics and ecology of core rhizobiome. In this direction, we have studied structural and functional variations in the root microbiome of 10 indica rice varieties. The studies on α and ß-diversity indices of rhizospheric root microbiome with the host genotypes revealed variations in the structuring of root microbiome as well as a strong association with the host genotypes. Biomarker discovery, using machine learning, highlighted members of class Anaerolineae, α-Proteobacteria, and bacterial genera like Desulfobacteria, Ca. Entotheonella, Algoriphagus, etc. as the most important features of indica rice microbiota having a role in improving the plant's fitness. Metabolically, rice rhizobiomes showed an abundance of genes related to sulfur oxidation and reduction, biofilm production, nitrogen fixation, denitrification, and phosphorus metabolism. This comparative study of rhizobiomes has outlined the taxonomic composition and functional diversification of rice rhizobiome, laying the foundation for the development of next-generation microbiome-based technologies for yield enhancement in rice and other crops.

Identification of mega-environments and rice genotypes for general and specific adaptation to saline and alkaline stresses in India.

In the present study, a total of 53 promising salt-tolerant genotypes were tested across 18 salt-affected diverse locations for three years. An attempt was made to identify ideal test locations and mega-environments using GGE biplot analysis. The CSSRI sodic environment was the most discriminating location in individual years as well as over the years and could be used to screen out unstable and salt-sensitive genotypes. Genotypes CSR36, CSR-2K-219, and CSR-2K-262 were found ideal across years. Overall, Genotypes CSR-2K-219, CSR-2K-262, and CSR-2K-242 were found superior and stable among all genotypes with higher mean yields. Different sets of genotypes emerged as winners in saline soils but not in sodic soils; however, Genotype CSR-2K-262 was the only genotype that was best under both saline and alkaline environments over the years. The lack of repeatable associations among locations and repeatable mega-environment groupings indicated the complexity of soil salinity. Hence, a multi-location and multi-year evaluation is indispensable for evaluating the test sites as well as identifying genotypes with consistently specific and wider adaptation to particular agro-climatic zones. The genotypes identified in the present study could be used for commercial cultivation across edaphically challenged areas for sustainable production.

Minimal access surgery in children - 5 years institutional experience.

CONTEXT: Minimal access surgery (MAS) in children are common place and performed worldwide with gratifying results as the learning curve of the surgeon attains plateau. We share our experience of this technically evolving modality of surgery, performed at our setup over a period of 5 years. We also review and individually compare the data for commonly performed procedures with other available series. Author also briefly discuss potential advantages of MAS in certain debatable conditions performed quickly and with cosmesis as open procedure. MATERIALS AND METHODS: We performed 677 MAS in children aged between 7 days and 12 years. Five hundred and sixty-eight of these were Laparoscopic procedures and 109 were Video assisted thoracoscopic surgeries (VATS). In all laparoscopic procedures, the primary port placement was by the Hasson's open technique. We have used 5, 3 and 2 mm instruments. Our study include 259 inguinal hernia, 161 Appendectomies, 95 VATS for empyema, 51 orchiopexies, 49 diagnostic laparoscopy, 29 cholecystectomies, 22 adhesionlysis and other uncommonly performed procedures. RESULTS: The ultimate outcome of all the performed procedures showed gratifying trend, the data of which are discussed in detail in the article. CONCLUSION: As we gained experience the operating time showed a decreasing trend, the complication rates and conversion rate also reduced. The advantages we came across were better postoperative appearances, less pain and early return to unrestricted activities.

Silicon nanosensor for diagnosis of cardiovascular proteomic markers.

A silicon nanosensor technology based on electrical impedance measurements has been developed for the detection of proteins. The nanosensor miniaturizes the high-density, low-volume multiwell plate concept. The scientific core of this technology lies in integrating nanoporous membranes with microfabricated chip platforms. This results in the conversion of individual pores into nanowells of picoliter volume. Monoclonal antibodies were localized and isolated into individual wells. Detection of two cardiac proteomic biomarkers has been demonstrated with this technology. The two proteins, C-reactive protein and NT-pro-brain natriuretic peptide (BNP), are associated with adverse cardiac outcomes in clinical samples when detected in the pg/mL concentration. The formation of the antibody-antigen binding complex occurs in individual wells. The membrane allows for robust separation among individual wells. This technology has the capability to achieve near real-time detection with improved sensitivity at 1 ag/mL for BNP and 1 fg/mL for CRP from human serum.

Iridium oxide nanomonitors: clinical diagnostic devices for health monitoring systems.

The objective of this research is to demonstrate the potential of iridium oxide (IrOx) nanowires based device towards detection of proteins that are disease biomarkers. This device is based on electrical detection of protein biomarkers wherein an immunoassay is built onto the iridium oxide nanowires that in turn undergoes specific electrical parameter perturbations during each binding event associated with the immunoassay. Detection of two inflammatory proteins C-reactive protein (CRP) and Myeloperoxidase (MPO) that are biomarkers of cardiovascular diseases is demonstrated. The performance metrics of the device in response to the two biomarkers in pure form and in serum samples were evaluated and compared to standard ELISA assays. The methodology that has been adopted is based on measuring impedance and calibrating its change in magnitude with concentration of proteins. We demonstrate the following performance metrics: limits of detection up to 1 ng/ml for CRP and 500 pg/ml for MPO in pure and serum samples; linear dynamic range of detection from 10 ng/ml to 100 microg/ml for CRP and 1 ng/ml to 1 microg/ml for MPO and cross-reactivity contained at less than 10% of selective binding for both the inflammatory proteins. Iridium oxide has an ability to detect very small changes to the surface charge and this capability is utilized for achieving the performance metrics and forms the basis of the key innovations of this technology, which are, improving the selectivity and sensitivity of detection.