Comprehensive computational analysis reveals H5N1 influenza virus-encoded miRNAs and host-specific targets associated with antiviral immune responses and protein binding

H5N1 virus (H5N1V) is highly contagious among birds and it was first detected in humans in 1997 during a poultry outbreak in Hong Kong. As the mechanism of its pathogenesis inside the host is still lacking, in this in-silico study we hypothesized that H5N1V might create miRNAs, which could target the genes associated with host cellular regulatory pathways, thus provide persistent refuge to the virus. Using bioinformatics approaches, several H5N1V produced putative miRNAs as well as the host genes targeted by these miRNAs were found. Functional enrichment analysis of targeted genes revealed their involvement in many biological pathways that facilitate their host pathogenesis. Eventually, the microarray dataset (GSE28166) was analyzed to validate the altered expression level of target genes and found the genes involved in protein binding and adaptive immune responses. This study presents novel miRNAs and their targeted genes, which upon experimental validation could facilitate in developing new therapeutics against H5N1V infection.

Application of Cerium Dioxide Nanoparticles and Chromium-Resistant Bacteria Reduced Chromium Toxicity in Sunflower Plants

The continuous increase in the heavy metals concentration in the soil due to anthropogenic activities has become a global issue. The chromium, especially hexavalent chromium, is highly toxic for living organisms due to high mobility, solubility, and carcinogenic properties. Considering the beneficial role of nanoparticles and bacteria in alleviating the metal stress in plants, a study was carried out to evaluate the role of cerium dioxide (CeO₂) nanoparticles (NPs) and Staphylococcus aureus in alleviating the chromium toxicity in sunflower plants. Sunflower plants grown in chromium (Cr) contaminated soil (0, 25, and 50 mg kg^-1) were treated with CeO₂ nanoparticles (0, 25, and 50 mg L^-1) and S. aureus. The application of Cerium Dioxide Nanoparticles (CeO₂ NPs) significantly improved plant growth and biomass production, reduced oxidative stress, and enhanced the enzymatic activities in the sunflower plant grown under chromium stress. The application of S. aureus further enhanced the beneficial role of nanoparticles in alleviating metal-induced toxicity. The maximum improvement was noted in plants treated with both nanoparticles and S. aureus. The augmented application of CeO₂ NPs (50 mg l^-1) at Cr 50 mg kg^-1 increased the chl a contents from 1.2 to 2.0, chl b contents 0.5 to 0.8 and mg g^-1 FW, and decreased the leakage of the electrolyte from 121 to 104%. The findings proved that the application of CeO₂ nanoparticles and S. aureus could significantly ameliorate the metal-induced stress in sunflower plants. The findings from this study can provide new horizons for research in the application of nanoparticles in phytoremediation and bioremediation.

Variation in the Primary and Secondary Metabolites, Antioxidant and Antibacterial Potentials of Tomatoes, Grown in Soil Blended with Different Concentration of Fly Ash

The aim of the study was to investigate the variation in nutritional composition, antioxidant, and antibacterial activities of tomatoes grown in fly ash blended soils, i.e.,T1 (soil 100% + 0% fly ash), T2 (soil 75%+ 25% fly ash), and T3 (soil 50% + 50% fly ash) soils. The tomato samples were harvested and screened for their proximate analysis, mineral composition, vitamin C contents, phenolic profile, and antioxidant and antibacterial activities. Results showed that T3 soil crop has high proximate composition, vitamin C, and phenolic contents as compared with T2 and T1 soil crops. Furthermore, significant variation in the elements analysis was observed in the crops grown in T1, T2, and T3 soils. T3 soil crop exhibited better antioxidant activity in term of total phenolic contents (TPC), total flavonoids contents (TFC), DPPH radical scavenging capacity, and ferric reducing potential as compared with T2 and T1 soil crops. Similarly, maximum inhibition zones were observed for T3 soil crop when tested for Staphylococcus aureus isolate 1 and 3 and methicillin-resistant Staphylococcus aureus (MRSA). In conclusion, the crop grown in T3 blended soil had high antioxidant and antibacterial potentials and better nutritional composition.

Genetic architecture of salt tolerance in a Multi-Parent Advanced Generation Inter-Cross (MAGIC) cowpea population

Background

Previous reports have shown that soil salinity is a growing threat to cowpea production, and thus the need for breeding salt-tolerant cowpea cultivars. A total of 234 Multi-Parent Advanced Generation Inter-Cross (MAGIC) lines along with their 8 founders were evaluated for salt tolerance under greenhouse conditions. The objectives of this study were to evaluate salt tolerance in a multi-parent advanced generation inter-cross (MAGIC) cowpea population, to identify single nucleotide polymorphism (SNP) markers associated with salt tolerance, and to assess the accuracy of genomic selection (GS) in predicting salt tolerance, and to explore possible epistatic interactions affecting salt tolerance in cowpea. Phenotyping was validated through the use of salt-tolerant and salt-susceptible controls that were previously reported. Genome-wide association study (GWAS) was conducted using a total of 32,047 filtered SNPs. The epistatic interaction analysis was conducted using the PLINK platform.

Results

Results indicated that: (1) large variation in traits evaluated for salt tolerance was identified among the MAGIC lines, (2) a total of 7, 2, 18, 18, 3, 2, 5, 1, and 23 were associated with number of dead plants, salt injury score, leaf SPAD chlorophyll under salt treatment, relative tolerance index for leaf SPAD chlorophyll, fresh leaf biomass under salt treatment, relative tolerance index for fresh leaf biomass, relative tolerance index for fresh stem biomass, relative tolerance index for the total above-ground fresh biomass, and relative tolerance index for plant height, respectively, with overlapping SNP markers between traits, (3) candidate genes encoding for proteins involved in ion transport such as Na+/Ca2+ K+ independent exchanger and H+/oligopeptide symporter were identified, and (4) epistatic interactions were identified.

Conclusions

These results will have direct applications in breeding programs aiming at improving salt tolerance in cowpea through marker-assisted selection. To the best of our knowledge, this study was one of the earliest reports using a MAGIC population to investigate the genetic architecture of salt tolerance in cowpea.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08332-y.

Phytohormones Trigger Drought Tolerance in Crop Plants: Outlook and Future Perspectives

In the past and present, human activities have been involved in triggering global warming, causing drought stresses that affect animals and plants. Plants are more defenseless against drought stress; and therefore, plant development and productive output are decreased. To decrease the effect of drought stress on plants, it is crucial to establish a plant feedback mechanism of resistance to drought. The drought reflex mechanisms include the physical stature physiology and biochemical, cellular, and molecular-based processes. Briefly, improving the root system, leaf structure, osmotic-balance, comparative water contents and stomatal adjustment are considered as most prominent features against drought resistance in crop plants. In addition, the signal transduction pathway and reactive clearance of oxygen are crucial mechanisms for coping with drought stress via calcium and phytohormones such as abscisic acid, salicylic acid, jasmonic acid, auxin, gibberellin, ethylene, brassinosteroids and peptide molecules. Furthermore, microorganisms, such as fungal and bacterial organisms, play a vital role in increasing resistance against drought stress in plants. The number of characteristic loci, transgenic methods and the application of exogenous substances [nitric oxide, (C28H48O6) 24-epibrassinolide, proline, and glycine betaine] are also equally important for enhancing the drought resistance of plants. In a nutshell, the current review will mainly focus on the role of phytohormones and related mechanisms involved in drought tolerance in various crop plants.