Multi-epitopes vaccine design for surface glycoprotein against SARS-CoV-2 using immunoinformatic approach.

Background: The recent COVID vaccinations have successfully reduced death and severity but did not stop the transmission of viruses by the emerging SARS-CoV-2 strain. There is a need for better and long-lasting dynamic vaccines for numerous prevailing strains and the evolving SARS-CoV-2 virus, necessitating the development of broad-spectrum strains being used to stop infection by reducing the spread rate and re-infection. The spike (S) glycoprotein is one of the proteins expressed commonly in the early phases of SARS-CoV-2 infection. It has been identified as the most immunogenic protein of SARS-CoV-2. Methods: In this study, advanced bioinformatics techniques have been exploited to design the novel multi-epitope vaccine using conserved S protein portions from widespread strains of SARS-CoV-2 to predict B cell and T cell epitopes. These epitopes were selected based on toxicity, antigenicity score and immunogenicity. Epitope combinations were used to construct the maximum potent multi-epitope construct with potential immunogenic features. EAAAK, AAY, and GPGPG were used as linkers to construct epitopes. Results: The developed vaccine has shown positive results. After the chimeric vaccine construct was cloned into the PET28a (+) vector for expression screening in Escherichia coli, the potential expression of the construct was identified. Conclusion: The construct vaccine performed well in computer-based immune response simulation and covered a variety of allelic populations. These computational results are more helpful for further analysis of our contract vaccine, which can finally help control and prevent SARS-CoV-2 infections worldwide.

Morphological, physiological and molecular assessment of cotton for drought tolerance under field conditions.

Climate change could be an existential threat to many crops. Drought and heat stress are becoming harder for cultivated crops. Cotton in Pakistan is grown under natural high temperature and low moisture, could be used as a source of heat and drought tolerance. Therefore, the study was conducted to morphological, physiological and molecular characterization of cotton genotypes under field conditions. A total of 25 cotton genotypes were selected from the gene pool of Pakistan based on tolerance to heat and drought stress. In field trail, the stress related traits like boll retention percentage, plant height, number of nodes and inter-nodal distance were recorded. In physiological assessment, traits such as photosynthesis rate, stomatal conductance, transpiration rate, leaf temperature, relative water content and excised leaf water loss were observed. At molecular level, a set of 19 important transcription factors, controlling drought/heat stress tolerance (HSPCB, GHSP26, HSFA2, HSP101, HSP3, DREB1A, DREB2A, TPS, GhNAC2, GbMYB5, GhWRKY41, GhMKK3, GhMPK17, GhMKK1, GhMPK2, APX1, HSC70, ANNAT8, and GhPP2A1) were analyzed from all genotypes. Data analyses depicted that boll retention percentage, photosynthesis, stomatal conductance, relative water content under the stress conditions were associated with the presence of important drought & heat TF/genes which depicts high genetic potential of Pakistani cotton varieties against abiotic stress. The variety MNH-886 appeared in medium plant height, high boll retention percentage, high relative water content, photosynthesis rate, stomatal conductance, transpiration rate and with maximum number transcription factors under study. The variety may be used as source material for heat and drought tolerant cotton breeding. The results of this study may be useful for the cotton breeders to develop genotype adoptable to environmental stresses under climate change scenario.

Impact of heat stress responsive factors on growth and physiology of cotton (Gossypium hirsutum L.).

Pakistan ranked highest with reference to average temperatures in cotton growing areas of the world. The heat waves are becoming more intense and unpredictable due to climate change. Identification of heat tolerant genotypes requires comprehensive screening using molecular, physiological and morphological analysis. Heat shock proteins play an important role in tolerance against heat stress. In the current study, eight heat stress responsive factors, proteins and genes (HSFA2, GHSP26, GHPP2A, HSP101, HSC70-1, HSP3, APX1 and ANNAT8) were evaluated morphologically and physiologically for their role in heat stress tolerance. For this purpose, cotton crop was grown at two temperature conditions i.e. normal weather and heat stress at 45 °C. For molecular analysis, genotypes were screened for the presence or absence of heat shock protein genes. Physiological analysis of genotypes was conducted to assess net photosynthesis, stomatal conductance, transpiration rate, leaf-air temperature and cell membrane stability under control as well as high temperature. The traits photosynthesis, cell membrane stability, leaf-air temperature and number of heat stress responsive factors in each genotypes showed a strong correlation with boll retention percentage under heat stress. The genotypes with maximum heat shock protein genes such as Cyto-177, MNH-886, VH-305 and Cyto-515 showed increased photosynthesis, stomatal conductance, negative leaf-air temperature and high boll retention percentage under heat stress condition. These varieties may be used as heat tolerant breeding material.

The Critical Role of Small RNAs in Regulating Plant Innate Immunity.

Plants, due to their sessile nature, have an innate immune system that helps them to defend against different pathogen infections. The defense response of plants is composed of a highly regulated and complex molecular network, involving the extensive reprogramming of gene expression during the presence of pathogenic molecular signatures. Plants attain proper defense against pathogens through the transcriptional regulation of genes encoding defense regulatory proteins and hormone signaling pathways. Small RNAs are emerging as versatile regulators of plant development and act in different tiers of plant immunity, including pathogen-triggered immunity (PTI) and effector-triggered immunity (ETI). The versatile regulatory functions of small RNAs in plant growth and development and response to biotic and abiotic stresses have been widely studied in recent years. However, available information regarding the contribution of small RNAs in plant immunity against pathogens is more limited. This review article will focus on the role of small RNAs in innate immunity in plants.

Quantitative trait loci (QTL) mapping for physiological and biochemical attributes in a Pasban90/Frontana recombinant inbred lines (RILs) population of wheat (Triticum aestivum) under salt stress condition.

Salt stress causes nutritional imbalance and ion toxicity which affects wheat growth and production. A population of recombinant inbred lines (RILs) were developed by crossing Pasban90 (salt tolerant) and Frontana (salt suceptible) for identification of quantitative trait loci (QTLs) for physiological traits including relative water content, membrane stability index, water potential, osmotic potential, total chlorophyll content, chlorophyll a, chlorophyll b and biochemical traits including proline contents, superoxide dismutase, sodium content, potassium content, chloride content and sodium/potassium ratio by tagging 202 polymorphic simple sequence repeats (SSR) markers. Linkage map of RILs comprised of 21 linkage group covering A, B and D genome for tagging and maped a total of 60 QTLs with major and minor effect. B genome contributed to the highest number of QTLs under salt stress condition. Xgwm70 and Xbarc361 mapped on chromosome 6B was linked with Total chlorophyll, water potential and sodium content. The increasing allele for all these QTLs were advanced from parent Pasban90. Current study showed that Genome B and D had more potentially active genes conferring plant tolerance against salinity stress which may be exploited for marker assisted selection to breed salinity tolerant high yielding wheat varieties.